KEYS TO UNLOCKING THE BIOFILM PHENOTYPE
OF A VIRULENT ENVIRONMENTAL ISOLATE
OF SALMONELLA
by
Stewart James Clark
A dissertation submitted in partial fulfillment of the requirements for the degree
of
Doctor of Philosophy
in
Microbiology
MONTANA STATE UNIVERSITY Bozeman, Montana
August 2008
©COPYRIGHT
by
Stewart James Clark
2008
All Rights Reserved ii
APPROVAL
of a dissertation submitted by
Stewart James Clark
This dissertation has been read by each member of the dissertation committee and has been found to be satisfactory regarding content, English usage, format, citation, bibliographic style, and consistency, and is ready for submission to the Division of Graduate Education.
Dr. Anne K. Camper
Approved for the Department of Microbiology
Dr. Mike Franklin
Approved for the Division of Graduate Education
Dr. Carl A. Fox
iii
STATEMENT OF PERMISSION TO USE
In presenting this dissertation in partial fulfillment of the requirements for a doctoral degree at Montana State University, I agree that the Library shall make it available to borrowers under rules of the Library. I further agree that copying of this dissertation is allowable only for scholarly purposes, consistent with “fair use” as prescribed in the U.S. Copyright Law. Requests for extensive copying or reproduction of this dissertation should be referred to ProQuest Information and Learning, 300 North
Zeeb Road, Ann Arbor, Michigan 48106, to whom I have granted “the exclusive right to reproduce and distribute my dissertation in and from microform along with the non- exclusive right to reproduce and distribute my abstract in any format in whole or in part.”
Stewart James Clark
August 2008
iv
ACKNOWLEDGMENTS
The author of this dissertation would like to acknowledge those friends and family both in Bozeman and in South Africa who have played a particularly important support role over the tenure of this degree.The microarrays used in this research were obtained through NIAID’s Pathogen Functional Genomics Resource Center, managed and funded by Division of Microbiology and Infectious Diseases, NIAID, NIH, DHHS and operated by the J. Craig Venter Institute. This research has been supported by a grant (DAAD 19-
03-1-0198) from the Army Research Office. Any opinions, findings and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the Army Research Office. And finally, this work is for you, my King.
v
TABLE OF CONTENTS
1. INTRODUCTION ...... 1
2. LITERATURE REVIEW ...... 3
Salmonella Background ...... 3 Nomenclature ...... 3 History of Salmonella Missouri – an Epidemiology...... 6 Other Examples of Occurrence and Abundance in Water ...... 8 Survival in Water and Preferred Environments ...... 10 Susceptibility to Disinfection ...... 13 The Three C’s of Salmonella Biofilms: Curli, Cellulose and Cyclic-di-GMP...... 16 The Hfq Regulon...... 22 Iron Utilization Genes ...... 24 1,2-Propanediol Utilization ...... 26 Pathogenicity ...... 32 Type III Secretion Systems ...... 34 Salmonella Pathogenicity Island 1 ...... 35 Salmonella Pathogenicity Island 2 ...... 38
3. A TRANSCRIPTIONAL STUDY OF AN ENVIRONMENTAL SALMONELLA ENTERICA ISOLATE BIOFILM ...... 41
Introduction ...... 41 Materials and Methods ...... 44 Strains and Growth ...... 44 Biomass Harvesting ...... 46 RNA Purification ...... 47 DNA Microarray Transcriptional Profiling ...... 48 Data Analysis ...... 52 Results and Discussion ...... 55 Bacterial Characterization ...... 55 RNA Purification ...... 59 Data Analysis ...... 60 Conclusions ...... 71
4. A TRANSCRIPTIONAL COMPARISON OF SALMONELLA TYPHIMURIUM LT2 AND AN ENVIRONMENTAL ISOLATE OF SALMONELLA ENTERICA ...... 80
Introduction ...... 80 Materials and Methods ...... 81 Strains and Growth ...... 81 vi
TABLE OF CONTENTS - CONTINUED
Biomass Harvesting ...... 83 RNA Purification ...... 84 DNA Microarray Transcriptional Profiling ...... 85 Data Analysis ...... 89 Results and Discussion ...... 92 Conclusions ...... 99
5. CONCLUSIONS ...... 104
Future Work ...... 106
REFERENCES ...... 109
APPENDICES ...... 126
APPENDIX A: Significant Genes Data Set for Chapter 3 ...... 127 APPENDIX B: Dataset for Figure 12 ...... 136 APPENDIX C: Dataset for Figure 13 ...... 138 APPENDIX D: Dataset for Figure 15 ...... 140 APPENDIX E: Significant MO Genes Data for Chapter 4 ...... 142 APPENDIX F: Significant LT2 Genes Data for Chapter 4 ...... 150
vii
LIST OF TABLES
Table Page
1. Salmonella enterica subspecies and numerical designations ...... 4
2. Space flight stimulon genes in Salmonella belonging to the Hfq regulon or involved with iron utilization or biofilm formation ...... 23
3. Regions of 10 or more genes recently acquired by Salmonella enterica serotype Typhimurium LT2 ...... 34
4. Top six sequences producing significant alignments (NCBI-BLAST) to a 702 bp sequence obtained by PCR amplifying a portion of the 16S rDNA gene of Salmonella Missouri ...... 57
5. The Institute for Genomic Research functional categories for the entire annotated genome and uniquely expressed genes of the observed transcriptomes for the planktonic and biofilm phenotypes ...... 96
viii
LIST OF FIGURES
Figure Page
1. Schematic overview of the role of CsgD in biofilm formation ...... 18
2. Scheme illustrating the role of different genes in the pathways leading to the synthesis of polysaccharides involved in the biofilm phenotype ...... 19
3. Regulatory concept of cyclic-di-GMP metabolism and signaling on the population level ...... 21
4. The struggle for iron: bacteria vs. host ...... 25
5. Anaerobic rhamnose catabolism in Salmonella ...... 27
6. Model of cobalamin-dependent utilization of rhamnose by intracellularly replicating Salmonella to recruit additional carbon, nitrogen and energy sources ...... 29
7. Invasion of Salmonella into the host epithelium as the initial stage of establishing infection (BioCarta, CA)...... 36
8. NCBI-BLAST phylogenetic tree using the neighbor-joining algorithm indicating relatedness of Salmonella Missouri (indicated by query ID lcl|13935) to other prokaryotic organisms based on a 702 bp sequence obtained by PCR amplifying a portion of the 16S rDNA gene ...... 56
9. Growth curve of Salmonella Missouri ...... 58
10. Electropherogram of Salmonella RNA ...... 59
11. Distribution of significantly expressed genes assigned to functional categories of the observed Salmonella Missouri transcriptome ...... 62
12. Expression patterns of genes involved in polysaccharide and curli fimbriae synthesis ...... 66
13. Changes in levels of gene expression in four Salmonella Pathogenicity Islands (SPI) and the spv operon on the Salmonella Pathogenicity Plasmid (PSLT) ...... 67
14. Distribution of gene expression on the Salmonella Pathogenicity Plasmid (PSLT) ...... 68 ix
LIST OF FIGURES – CONTINUED
Figure Page
15. Gene expression patterns in the 1,2-propanediol utilization operon (pdu), cobalamin synthesis operon (cbi-cob) and tetrathionate reductase operon (ttr) ...... 70
16. Photographs of overnight planktonic cultures of Salmonella Missouri and Salmonella Typhimurium LT2 ...... 92
17. Growth curves of Salmonella Typhimurium LT2 and Salmonella Missouri ...... 93
18. Venn diagram showing significantly up-regulated genes in Salmonella Missouri during planktonic growth and biofilm growth and in Salmonella Typhimurium LT2 during planktonic growth and biofilm growth ...... 95
x
LIST OF ABBREVIATIONS
ATCC American Type Culture Collection
BLAST Basic Local Alignment Search Tool
CDC Centers for Disease Control and Preventtion cDNA Complementary DNA
CDSC Communicable Disease Surveillance Center
CFU Colony Forming Units
CMR Comprehensive Microbial Database
CT99 Contact x Time to reduce the microbial population by 99%
DNR Missouri Department of Natural Resources
DOH Missouri Department of Health
EASE Expression Analysis Systematic Explorer
ECA Enterobacterial Common Antigen
EPA Environmental Protection Agency
EPS Exopolysaccharide
F99 Fluence required to reduce the microbial population by 99%
FDR False Discovery Rate
FHL Fumarate hydrogenlyase
IVET In vivo Expression Technology
IVS Intervening Sequences
JCVI J. Craig Venter Institute
LPS Lipopolysaccahride
MIDAS TIGR Microarray Data Analysis System
MO Missouri xi
LIST OF ABBREVIATIONS - CONTINUED
MPN Most Probable Number
NCBI National Center for Biotechnology Information
NIAID National Institute of Allergies and Infectious Diseases
OLE Operon-Linked Expression
ORF Open Reading Frame
PFGRC Pathogen Functional Genomics Research Center
PGFE Pulse Field Gel Electrophoresis
PLG Phase Lock Gel
PSLT Salmonella Typhimurium LT2 Pathogenicity Plasmid
RIN RNA Integrity Number
SAM Significance Analysis of Microarrays
SCV Salmonella-Containing Vacuole
SOP Standard Operating Protocol
SPI Salmonella Pathogenicity Island
T90 Time taken to reduce the microbial population by 90%
TIGR The Institute for Genomic Research
TMEV TIGR Multiexperiment Viewer
TTSS Type III Secretion System
UASB Upflow Anaerobic Sludge Blanket
VBNC Viable But Non Culturable
WHO World Health Organization
WWTP Wastewater Treatment Plant
xii
ABSTRACT
The aim of this research was to elucidate the phenotypic adaptation of an environmental isolate of Salmonella enterica grown in a single species biofilm using transcriptomic analysis. This environmental isolate was obtained from an outbreak in Gideon, MO, and was classified as Salmonella enterica serotype Missouri. Gene expression profiles obtained from this environmental isolate were compared with profiles of the ATCC type strain Salmonella enterica serotype Typhimurium LT2 grown under the same conditions. It was shown that there were distinct transcriptional differences in both of the strains between the biofilm and planktonic phenotypes. Both strains exhibited the strong up-regulation of several gene pathways that were unique to the biofilm phenotype. These included genes responsible for the cobalamin-dependent anaerobic utilization of 1,2-propanediol (cob-cbi-pdu), type III secretion system apparatus and effector proteins located on Salmonella Pathogenicity Island 2 (SPI-2) and the well characterized csg operon largely responsible for biofilm formation in Salmonella. A significant proportion of the genes present on the virulence plasmid PSLT were shown to be exclusively up-regulated in the biofilm phenotype of Salmonella Typhimurium LT2, illustrating the tendency of this pathogen to exhibit a promiscuous lifestyle whilst in the non-host environment. It was further demonstrated that the environmental isolate exhibited a more tenacious biofilm-forming tendency and overall greater survivability than the type strain in a low nutrient, non-host environment. It appeared from the transcriptional profile of Salmonella Typhimurium LT2 during planktonic growth that the organism struggled to adapt and survive under low nutrient conditions as evidenced by the increased expression of ribosomal subunit operons rps and rpl and several stress- related genes including dnaK and htp. The conclusion may be drawn that Salmonella Missouri has developed several key systems differentiating the biofilm and planktonic phenotypes and affording it a competitive advantage. While some of these traits have previously been studied exclusively in the context of host pathogenicity, this research indicates that perhaps these so-called virulence strategies may afford the pathogen enhanced survival in non-host environments as well. Therefore, these findings suggest that the use of excessively sub-cultured laboratory strains may be inappropriate surrogates for studying the behavior of real-world pathogens. 1
CHAPTER 1
INTRODUCTION
Salmonella has been recognized as a global threat to human health and in the
United States alone is the cause of an estimated USD 3 billion in hospital costs and loss of revenue (World Health Organization, 2005). Several hundreds of serotypes of
Salmonella may be circulating within the human population at any given time and these display varying degrees of virulence from causing mild gastric irritation (salmonellosis) through to full-blown typhoid fever (Centers for Disease Control and Prevention, 2007).
Furthermore, this pathogen tends to cycle between the host and non-host environment and has been shown to be quite capable of adapting to stressful conditions within both these settings. In the non-host environment, Salmonella may survive for lengthy periods of time as part of a microbial consortia termed a biofilm (Armon et al., 1997; Costerton et al., 1999; Latasa et al., 2005; Leriche and Carpentier, 1995; September et al., 2007).
Chapter 2 of this dissertation summarizes the current state of the literature available in this field and describes the important advances in Salmonella biofilm and physiology research and identifies some open questions which were addressed in this present work.
The goals of this study were to investigate some of the key transcriptional pathways involved in the switch from the planktonic to the biofilm phenotype using
Salmonella whole-genome microarrays. This method of analysis was first applied to one serotype of Salmonella enterica, an environmental isolate from a water-related outbreak in Gideon, MO, and the results of this study are presented in Chapter 3. Subsequently to 2
this, further experiments included an ATCC type strain of Salmonella enterica serotype
Typhimurium LT2 in order to demonstrate the differences between a virulent isolate and a lesser virulent, frequently passaged strain. The results of this study are presented in
Chapter 4. Each of these two studies will be submitted for publication individually in
order to contribute to the current state of the field. The work demonstrated in Chapter 3
will be published the first submission (to the Society for Applied Microbiology journal
“Environmental Microbiology”) and will form the basis for the second publication (to
“FEMS Microbiology Letters”) covering the work presented in Chapter 4.
The final chapter of this thesis (Chapter 5) communicates the conclusions of this
study and suggests possible directions for future study.
3
CHAPTER 2
LITERATURE REVIEW
Salmonella Background
Salmonella is a gram negative, rod shaped enteric bacterium bearing remarkable similarity to the well-characterized Escherichia coli. This organism is usually motile by peritrichous flagella. It is facultatively anaerobic and chemoorganotrophic, exhibiting both a respiratory and fermentative type of metabolism, depending on environmental cues and conditions. As such, Salmonella have been isolated from diverse environments spanning soil, water, invertebrates, reptiles, fish and mammals.
Nomenclature
Salmonella nomenclature has been the source of much contention in the literature over the years and until January 2003, there were still differing opinions between the
Centers for Disease Control and Prevention and the widely accepted Kauffmann-White scheme maintained by the World Health Organization (WHO) Collaborating Center for
Reference and Research on Salmonella at the Pasteur Institute, Paris, France (WHO
Collaborating Center). Brenner et al. (2000) published a guest commentary in the Journal of Clinical Microbiology entitled “Salmonella Nomenclature” in which they discussed the many issues and points of contention surrounding the naming of this pathogen. At that time, 2463 serotypes or serovars of Salmonella were defined by the WHO
Collaborating Center. According to the latest published report (Grimont and Weill, 2007), there are 2579 serovars of Salmonella. Furthermore, it was only in 2005 (Truper, 2005) 4
that the Judicial Commission of the International Committee of Systematic Bacteriology
officially applied the status of Type Strain to Salmonella enterica, replacing the previous
Type Strain Salmonella choleraesius.
Molecular methods have shown that the genus Salmonella consists of only two
species, Salmonella enterica and Salmonella bongori. Of these two species, S. bongori
only contributes 22 serovars to the overall number mentioned previously. According to
the official Kauffmann-White Scheme (Grimont and Weill, 2007), Salmonella enterica is further divided into six subspecies (Table 1) that can be differentiated by biochemical and genetic tests. These subspecies are designated by names or Roman numerals, the latter being simpler and more commonly used.
Table 1. Salmonella enterica subspecies and numerical designations.
Salmonella enterica subspecies
I enterica
II salamae
IIIa arizonae
IIIb diarizonae
IV houtenae
VI indica Serotyping of Salmonella is based on the immunoreactivity of two surface structures, the O and H antigens. The O antigen is a carbohydrate that is the outermost component of lipopolysaccharide. It is a polymer of O subunits, each O subunit usually composed of four to six sugars, depending on the O antigen. Variations in the O antigen result from variation in the sugar components, the covalent bonds between the subunits 5
and the nature of the linkages between O subunits. O antigens are designated by Arabic
numerals and are divided into O serogroups (Centers for Disease Control and Prevention,
2007).
The H antigen is the filamentous portion of the bacterial flagella, an organelle
being made up of a complex basal body, a curved hook and a helical filament functioning
as a rotary motor, universal joint and propeller respectively. The filament is a self-
assembling polymer made up of thousands of molecules of a single protein termed
flagellin. The ends of flagellin are conserved and give the filament its characteristic
structure. The antigenic variability occurs in the middle region of the flagellin protein
which is surface-exposed. Salmonella is unique among the enteric bacteria in that it can
express two different H antigens which are specified by two genes, fliC and fljB. These two distinct flagellar antigens are referred to as Phase 1 and Phase 2 antigens respectively, and the expression of the two genes is coordinated such that only one flagellar antigen is expressed at a time in a single bacterial cell. Monophasic isolates are those that express only a single flagellin type. If antigens are composed of multiple factors, they are designated so and separated by commas (Centers for Disease Control and Prevention, 2007).
In this study, the serotyping convention of the Kauffmann-White Scheme described above is adopted. Although Salmonella serotypes can be designated more precisely by a formula they can also be designated by a name. The typical format for a serotype formula is: 6
Genus [space] Subspecies Roman numeral [space] O antigen [colon] Phase 1 H antigen
[colon] Phase 2 H antigen.
The two serotypes used over the course of this study can therefore be designated:
Salmonella I 4,5,12:i:1,2 or Salmonella enterica serotype Typhimurium or Salmonella
Typhimurium; and Salmonella I 11:g, s, t or Salmonella enterica serotype Missouri or
Salmonella Missouri.
History of Salmonella Missouri – an Epidemiology
In early December of 1993, a waterborne disease outbreak was identified in the town of Gideon, Missouri, USA. The initial report originated with seven culture- confirmed cases of Salmonella, all patients exhibiting severe diarrhea (Clark et al., 1996).
The patients included three high school students, one child from a day care, two nursing home residents and one visitor to the nursing home. The Missouri Department of Health
(DOH) conducted preliminary interviews and determined that there were no food exposures common to the majority of patients and suggested a link with municipal water.
The Missouri Department of Natural Resources (DNR) was subsequently informed and initiated a sampling of the water supply. Water samples collected by the DNR were positive for fecal coliforms and on December 18, 1993, the city of Gideon, as required by the DNR, issued a boil water order. The CDC joined the surveillance on December 22,
1993.
Prior to the outbreak, the Gideon municipal water system, which obtained water from two adjacent 396 m deep wells, had no form of disinfection in place. The distribution system consisted primarily of small diameter (5, 10 and 15 cm) unlined steel 7
and cast iron pipe. Tuberculation and corrosion were major problems. Raw water
temperatures were unusually high for a ground water supply (14°C) because the system
was overlying a geologically active fault. There were also regular pressure drops under
high flow or flushing conditions. The municipal system also had two elevated tanks (189
m3 and 378 m3) (Angulo et al., 1997).
On December 23, 1993, a chlorinator was placed on-line at the city well by the
DNR. Prior to switching on the chlorinator, none of the water samples collected
contained chlorine and one sample was positive for the same strain of dulcitol-negative
Salmonella as had been isolated from the initial patients.
A CDC survey indicated that ~44% of the 1104 residents, or almost 600 people, were affected with diarrhea between November 11 and December 27, 1993 in Gideon,
MO. Through January 8, 1994, the DOH had identified 31 cases with laboratory- confirmed salmonellosis associated with the Gideon outbreak. Fifteen of the 31 culture- confirmed patients were hospitalized and two of these 15 patients had positive blood cultures. Seven nursing home residents died, four of whom were culture-confirmed (the other three were not cultured) (Clark et al., 1996).
A tank inspector observed birds roosting on the largest city-owned water storage tank which had a broad, flat roof. Subsequent laboratory study of the persistence of this
Salmonella strain isolated from the Gideon water supply demonstrated that the pathogenic agent was only reduced in density by 30% during a 4 day period at 15°C
(Clark et al., 1996). The suggestion has therefore been made that, with repeated new input of Salmonella from infected pigeons, there could have been a continuing high level 8
of this pathogen present in the water storage tank and distribution lines. Since the infective dose varies from 101 to more than 105 cells of Salmonella depending on strain,
as well as the human condition (age, overall health, lifestyle), an Environmental
Protection Agency (EPA) study concluded that the Salmonella outbreak was largely due
to inadequate disinfection and aged equipment (Clark et al., 1996).
Other Examples of Occurrence and Abundance in Water
In the natural environment the concentration of Salmonella can be as low as 5
CFU/100 mL (Lemarchand et al., 2004) and as high 103 - 105 organisms/liter such as is
found in raw wastewater in the US (Bitton, 2005) and even higher in developing nations
(September et al., 2007). Removal of Salmonella throughout a typical sewage treatment
system in the US has been measured. Typically there may exist 5 x 103 – 8 x 104 CFU/L
in raw sewage, 102 – 3 x 103 CFU/L after primary treatment only (primary sedimentation
and disinfection), 3 – 103 CFU/L after secondary treatment (including trickling filter or
activated sludge) and 10-6 CFU/L after advanced secondary treatment (including
coagulation, filtration and disinfection) (Maier et al., 2000). These figures however are
merely representative and removal rates can vary greatly. In a study from Spain, raw
water samples showed a high content of Salmonella, with a mean MPN of 266.7/100 mL
while treated water (after decanting and activated sludge) contained a Salmonella MPN
of 45/100 mL, representing a reduction of only 83% (Howard et al., 2004).
In a study conducted in California, effluents from 11 of 12 sewage treatment
plants tested positive for Salmonella when samples were analyzed downstream of a
chlorination/dechlorination site, before effluents merged with the receiving stream 9
(outside the plant). Six hundred and eighty three Salmonella isolations were made from
26 of the 32 sampling sites. Multiple serotypes of Salmonella were represented in the
isolations. During the sampling period, people were observed swimming and fishing in
the sewage treatment plant effluent within 30.5 m (100 ft) of the outfall. Subsequent to
this study, an interesting theoretical exercise was carried out. The daily production of
waste water per capita is estimated to be 400 liters. A person with acute salmonellosis
excretes Salmonella in quantities of 108 - 1011 organisms per gram of feces. In a
community with a population of 100,000 the Salmonella concentration will be: 1011 / 105 x 400 liters = 2.5 x 103 Salmonella per liter of sewage (Kinde et al., 1997).
In 2004, an outbreak of gastroenteritis was investigated on South Bass Island,
OH, an island of 900 residents that is visited by > 500,000 persons each year. Between
May and September 2004, 1450 persons reported illness. Out of 70 stool specimens
tested for bacterial pathogens, Salmonella enterica serotype Typhimurium was identified
in only 1 person. The remaining cases were shown to be due to Campylobacter jejuni,
norovirus and Giardia intestinalis. The environmental assessment demonstrated that
contamination of the karst aquifer beneath the island had occurred from multiple land
uses such as onsite septic systems, land application of septage, infiltration of land run-off,
and, possibly, a direct hydraulic connection with Lake Erie (O'Reilly et al., 2007). While
this study did not show the dominance of Salmonella in the outbreak, it did serve to
illustrate two important points about the pathogen’s modus operandi: first, it is seldom
the only pathogen in a waterborne outbreak and second it is a pathogen capable of
maintaining itself as a virulent agent even at low numbers in the environment. 10
In a study out of Japan, higher incidence of Salmonella in river water than sea
water suggested that salinity is a crucial factor in governing its distribution, but the
occurrence of Salmonella in Fukuyama port marine samples may have arisen from an increased discharge of polluted waters from an adjacent land or coastal area
(Venkateswaran et al., 1989). In addition to simply the presence of the pathogen in water systems, regrowth and survival of attached Salmonella has been shown in rural communities’ storage containers (polyethylene and galvanized steel) at low levels (< 1-15
CFU/cm2) (Momba and Kaleni, 2002), in domestic toilet bowls for up to four weeks after
diarrhea had stopped (Barker and Bloomfield, 2000) and in upflow anaerobic sludge
blanket (UASB) reactors in a wastewater treatment plant (Keller et al., 2003).
Survival in Water and Preferred Environments
Salmonella discharged in the effluents from municipal wastewater treatment
plants (WWTPs) may be able to survive for an extended time. In an experiment using
non-sterile river water, Salmonella was shown to actually increase 3 logs in the first 21
days and decreased 2 logs in the subsequent 21 days (Armon et al., 1997). Domingo et al. (2000) showed that Salmonella was able to survive in filtered river water for 31 days, although the culturable counts only represented about 0.001% of the total counts obtained by microscopy. Further investigation using direct viable counts and resuscitation studies showed that this value may have been at least a 4 log underestimate of actual survival, suggesting the presence of a not immediately culturable state of Salmonella. Several
mechanisms of survival have been suggested, including the adoption of a viable-but-non
culturable (VBNC) state, the integration of the pathogen into an existing biofilm (Barker 11
and Bloomfield, 2000; Esteves et al., 2005; Jones and Bradshaw, 1996; Solano et al.,
2002; Stepanovic et al., 2003) and internalization of the pathogen into a variety of
protozoan hosts (Labrousse et al., 2000; Tezcan-Merdol et al., 2004; Winfield and
Groisman, 2003). Although survival depends on a variety of factors, Salmonella survival
in water and its susceptibility to disinfection have been shown to be similar to those of
coliform bacteria (Health Canada, 2006; McFeters et al., 1974; Mitchell and Starzyk,
1975). As both are of fecal origin, the absence of E .coli should thus adequately indicate
the absence of Salmonella although exceptions are known (Health Canada, 2006) and the reverse may not necessarily be true.
Several species of Salmonella, including Salmonella Typhimurium, have been
shown to enter the VBNC state after lengthy exposure to oligotrophic fresh and seawater under ambient temperature (Cho and Kim, 1999; Jimenez et al., 1989; Roszak and
Colwell, 1987). These and many other microbial pathogens for which the VBNC state has been reported have also been suggested to retain the capacity to cause disease and therefore still be considered a threat (McDougald et al., 1998). Evidence for a VBNC state of Salmonella can be found in the following cases:
• In a study on the survival of pathogens under various storage conditions in bottled
mineral water, Salmonella Typhimurium exhibited greatest survival rates in both
sterile and non-sterile mineral water and persisted up to 60 days in bottled mineral
water stored under dark conditions (Ramalho et al., 2001) Most notable in this
study however was the fact that Salmonella, as well as the other pathogens tested,
exhibited significantly better recovery on non-selective media than on their 12
respective selective media. This observation confirms the notion that injured
pathogens may become susceptible to selective agents and that the dogmatic use
of selective media in microbiological testing laboratories may overlook these
microbes. This is a disconcerting notion considering that some researchers have
shown the ability of injured pathogens to retain their ability to cause disease
(McFeters and LeChevallier, 2000).
• Santo Domingo et al. (2000) showed that, in 3 of 4 serotypes of Salmonella
enterica inoculated into river water, several resuscitation techniques could be
used to detect viable pathogens over lengthy periods of time. Although the
culturable counts of two bacterial strains in filtered water after 31 days
represented approximately only 0.001% of the total Salmonella counts, direct
viable counts (using a modification of the Kogure-CTC method (Kogure et al.,
1979)) and resuscitation studies (using dilution and enrichment) suggested that the
number of viable bacteria was at least four orders of magnitude higher.
Survival of Salmonella in protozoa has been demonstrated in the following cases:
• Salmonella Typhimurium in water and sediments was tested using artificially
contaminated aquaria. Water samples remained culture positive for Salmonella for
up to 54 days. Sediment samples were culture positive up to 119 days (Moore et
al., 2003). Larval chironomids (midges) raised in contaminated sediments became
culture positive and the bacteria were carried over to adults after emergence.
Uptake of Salmonella by chironomid larvae and adults suggests that they are
possible vectors in both aquatic and terrestrial environments. 13
• The ability of Salmonella to become internalized and to survive and replicate in
amoebae was evaluated by using three separate serotypes of Salmonella enterica
and five different isolates of axenic Acanthamoeba species (Tezcan-Merdol et al.,
2004). The survival of Salmonella Typhimurium within Acanthamoeba castellanii
during chlorination was also reported, suggesting a protective intracellular habitat
for the bacteria (King et al., 1988). Results showed that A. rhysodes was able to
ingest Salmonella and that subsequent events included intracellular bacterial
replication. The study also detected a bacterium-mediated cytotoxicity that
appeared to be dependent on documented virulence genes, implying that genetic
determinants of Salmonella used for invasion and intracellular proliferation in
mammals could also be operative in the environment.
Susceptibility to Disinfection
To learn whether cellulose, an important component of Salmonella biofilm exopolysaccharide (discussed later), might be responsible for chlorine resistance and therefore the survival of Salmonella within biofilms in water supplies and food- processing plants, Solano et al. (2002) carried out survival experiments of wild-type strains and cellulose-deficient mutants. They used a concentration of NaOCl (30 ppm) that is 100- to 200-fold higher than the free chlorine concentrations typically obtained in municipal water supplies, reaching into the concentration range used as a sanitizer for food processing plants. After a 20 minute exposure period, 75% of the wild-type cells survived NaOCl exposure. In contrast, only 0.3% of cellulose-deficient mutant cells survived under the same experimental conditions. 14
Oliver et al. (2005) showed that when asodium hypochlorite (free chlorine) solution was added to provide a final concentration of 1 mg/L of free chlorine in
wastewater, culturability of control Salmonella Typhimurium cells in the stationary phase remained at about 106 CFU/mL while log phase cells exposed to this chlorination
protocol typically declined to < 10 CFU/mL after 20 seconds exposure time. Total cell
counts revealed the continued presence of > 106 total cells in all cases. On average,
regardless of the physiological state of the cells, 0.39% of the treated cells responded to
the Kogure-CTC (Kogure et al., 1979) viability assay (as opposed to culturability) after
60 minutes of chlorination, indicating a small portion of the cells were able to resist this
treatment. While such a percentage appeared low, it equated to roughly 103–104 cells/mL.
An often overlooked aspect of the susceptibility of pathogens to disinfection is
their evolutionary ability to survive within the gut of various protozoan species. To show
this, King et al. (1988) performed disinfection experiments on some common waterborne
pathogens including Salmonella Typhimurium which were ingested by a variety of
protozoans. As a baseline, they showed that the CT99 values (i.e. the concentration x
contact time required to inactivate 99% of a population) required to inactivate Salmonella when free-living are 0.4, 0.5 and 0.5 minutes with free chlorine residuals of 1.0, 0.5 and
0.25 mg/L respectively. However, when ingested by the protozoan Tetrahymena pyriformis, Salmonella Typhimurium exhibited more than 50-fold greater resistance to free chlorine. The CT99 values required for inactivation under these protected conditions
were around 90, 90, 80 and 50 minutes at free chlorine residuals of 0.5, 1.0, 2.0 and 4.0
mg/L respectively. 15
Berney et al. (2006) examined the efficacy of sunlight irradiation on the
inactivation of some common waterborne pathogens including Salmonella Typhimurium.
Resistance to sunlight at 37°C based on F99 values (i.e. the strength of radiation or fluence required to inactivate 99% of a population) was in the following order:
Salmonella Typhimurium > Escherichia coli > Shigella flexneri > Vibrio cholerae. While
F90 values of Salmonella Typhimurium and E. coli were similar, F99 values differed by
60% due to different inactivation curve shapes. These authors also pointed out that T90 values (i.e. the time required to inactivate 90% of a population) are not appropriate for the determination of irradiation efficacy because they do not take into account different irradiation intensities. They bemoan the fact that the display of T90 values has become
very common in solar disinfection publications, making comparisons among different
studies very difficult. Keller et al. (2003) showed that viable Salmonella in treated
wastewater effluents could be considerably reduced after UV exposure, although the
degree of inactivation depended on the turbidity of the effluent, with more turbid samples
requiring greater doses. They demonstrated that 2 log reductions in non-filtered effluent
could be achieved at doses of about 30 mWsec/cm2 whereas only 20 mWsec/cm2 doses
were required to achieve the same levels of inactivation in filtered effluent. These
findings were corroborated in a study by Rodriguez-Romo and Yousef (2005) who
demonstrated a 2 log reduction in viable Salmonella on the surfaces of egg shells at doses
of about 24 mWsec/cm2.
The inactivation of Salmonella by ozone has been shown to be an effective means
of controlling surface contamination on food surfaces such as egg shells, fruits and 16
berries (Rodriguez-Romo and Yousef, 2005) and in liquids such as apple cider, orange
juice and water (Lezcano et al., 1999; Restaino et al., 1995; Williams et al., 2004).
According to Restaino et al. (1995) more than 5 log units of Salmonella Typhimurium cells per mL were killed instantaneously after exposure to ozonated water at a concentration of around 0.19 ppm. These authors pointed out however that the efficacy of ozonation was more dependent on the type of organic material present in the water rather than the amount of the organics as was previously thought. They also indicated that the
currently held hypothesis of determining ozone concentrations for an all-or-none
inactivation may be faulty, showing that death caused by ozone followed a biphasic
pattern. The result of this finding suggested that the high dose-short time, or low dose-
long time approach may need to be revisited. Lezcano et al. (1999) showed that an
environmental isolate of Salmonella was more resistant in water to ozone than both
ATCC strains and environmental isolates of E. coli and Shigella sonnei. They demonstrated T90 of 3.44, 3.59, 1.69 and 0.62 minutes and T100 (complete inactivation) of
13, 10, 5 and 3 minutes at 0.48, 0.58, 1.04 and 1.75 mg/L ozone respectively.
The Three C’s of Salmonella Biofilms: Curli, Cellulose and Cyclic-di-GMP
The natural behavior of bacteria is often multicellular (biofilm state) and yet a
highly regulated transition to the single cell (planktonic state) for spread and distribution
is a prerequisite for survival. The genetic requirements of Salmonella in biofilm
establishment are being currently determined in several laboratories. It would appear
from the current state of the literature available on the genetic analysis of Salmonella 17
biofilms that several pathways and cellular responses are crucial in making the switch
from planktonic to biofilm.
It has been shown that Salmonella harbors genetic information for multicellular
behavior characterized by the expression of cellulose and curli fimbriae (formerly
designated thin aggregative fimbriae (Tafi)). Cellulose and curli fimbriae form the self-
produced extracellular matrix which embeds the cells in a honeycomb-like structure that
enables biofilm formation through cell–cell interactions and adhesion to biotic and
abiotic surfaces. The matrix components also protect against disinfectants and play a role
in bacterial–host interactions (Gerstel and Romling, 2003; Solano et al., 2002; White et
al., 2006; Zogaj et al., 2001).
The csgD gene (curli subunit gene D, previously called agfD in Salmonella
Typhimurium) encodes for a transcriptional regulator of the LuxR superfamily and has been shown to positively control the extracellular matrix compounds cellulose and curli
(Fig. 1) (Gerstel and Romling, 2003). 18
Figure 1. Schematic overview of the role of CsgD in biofilm formation (Gerstel and Romling, 2003).
Curli fimbriae are proteinaceous, filamentous appendages with highly adhesive properties. CsgD enables the production of curli fimbriae by transcriptional activation of the divergent csgDEFG-csgBAC (formerly agfDEFG-agfBAC) operon that encodes the structural genes of curli fimbriae (Gerstel and Romling, 2003; Solano et al., 2002).
Cellulose biosynthesis is also positively regulated by CsgD whereby CsgD stimulates the transcription of AdrA (agfD-dependent regulator), a putative inner membrane protein that harbors a cytoplasmic GGDEF domain. AdrA activates cellulose production on the post-transcriptional level either by direct interaction with one or more 19
of the gene products of the bacterial cellulose synthesis operons bcsABZC and bcsEFG
(also sometimes designated yhjOMNL and yhjSTU respectively) (Zogaj et al., 2001) or by production of a cyclic nucleotide, cyclic-di-GMP, which acts as an activator of cellulose biosynthesis (Garcia et al., 2004; Romling and Amikam, 2006).
Although cellulose has been identified as the major component of a Salmonella biofilm exopolysaccharides (EPS) matrix under nutrient deficient conditions, several other polysaccharides including colanic acid, lipopolysaccharide (LPS) and the enterobacterial common antigen (ECA) (Solano et al., 2002) have been identified (Fig.
2).
Figure 2. Scheme illustrating the role of different genes in the pathways leading to the synthesis of polysaccharides involved in the biofilm phenotype. Gene symbols are shown in boldface italics (Solano et al., 2002). 20
The environment in which a bacterium finds itself undoubtedly influences many
aspects of physiological responses including the formation, maturation and detachment of biofilms. The majority of these responses occur at the gene level, with signal transduction systems linking the specific environmental cues to appropriate alterations in bacterial gene expression. In some of these signal transduction mechanisms, perception of a primary signal may alter the level of a secondary intracellular signal called a secondary messenger (Dow et al., 2007). Bis-(3’,5’)-cyclic dimeric guanosine monophosphate
(cyclic-di-GMP) is one such secondary messenger now shown to be involved in the regulation of a range of functions including developmental transitions, aggregation behavior, adhesion, biofilm formation and virulence in diverse bacteria. An emerging trend in current literature is that high cellular levels of cyclic-di-GMP promote biofilm formation and aggregative behavior while low cellular levels promote motility and virulence (Fig. 3) (Garcia et al., 2004; Romling and Amikam, 2006).
Research has shown that the expression of genes encoding proteins exhibiting a
GGDEF domain potentially increase the cellular levels of c-di-GMP in several bacteria.
Synthesis of cyclic-di-GMP from two molecules of GTP is catalyzed by the GGDEF domain and is predicted to occur in two steps, while the degradation of the molecule to
GMP also occurs via a two step reaction. Proteins with an EAL domain have been shown to catalyze only the first step whereas proteins with an HD-GYP domain have been shown to catalyze both steps (Dow et al., 2007). 21
Figure 3. Regulatory concept of cyclic-di-GMP metabolism and signaling on the population level. GGDEF domains with consensus residues synthesize c-di-GMP from two molecules of GTP. EAL domains with consensus residues cleave the c-di-GMP molecule into pGpG (while HD-GYP domains cleave this to two molecules of GMP). High c-di-GMP levels promote sessility aided by the production of adhesive extracellular matrix components such as polysaccharides (cellulose) and fimbriae (curli fimbriae). Environmental and host persistence is also predicted to be promoted by high c-di-GMP levels. Conversely, low c-di-GMP levels promote motility behavior (swimming, swarming and twitching motility) and virulence (Romling and Amikam, 2006).
In Salmonella, research has shown that CsgD expression is affected by the production of cyclic-di-GMP through several GGDEF and EAL proteins. STM2123 and
STM3388 are both di-guanylate cyclases involved in producing c-di-GMP and have both been shown to be involved in CsgD expression. CsgD subsequently regulates the expression of agfD-dependent regulator, AdrA. Transcription of this GGDEF domain protein promotes cellulose production during Salmonella biofilm formation (Gerstel and
Romling, 2003) and was also shown to be responsible for over 60% of the cellular c-di-
GMP production in a study by Kader et al. (2006). In a study by Garcia et al. (2004), researchers identified seven novel proteins all of which contained the consensus GGDEF motif and were designated Gcp (GGDEF domain containing proteins). Several of these 22
proteins were also identified as carrying an EAL domain. One of these, GcpE, a putative
phosphodiesterase, appeared to totally abolish biofilm formation and cellulose synthesis
by degrading cyclic-di-GMP. In another study by Hisert et al. (2005), an in vivo screen
for genes required for Salmonella Typhimurium to resist oxidative killing by phagocytes
recovered STM1344 (from ydiV), an EAL-domain protein, as the sole output. The
participation of STM1344 in resistance to phagocytic oxidase was confirmed by in vitro
susceptibility of a ydiV mutant to hydrogen peroxide. However, the ydiV mutant was
concomitantly shown to kill macrophages earlier and was more cytotoxic than the wild
type. It is clear that although there may be a trend indicating that the high cyclic-di-GMP
levels induce biofilm formation and persistence while low levels of cyclic-di-GMP
promote motility and virulence, there are exceptions to every rule and more study is
needed to further the understanding of the role of this molecule in the lifecycle of
Salmonella.
The Hfq Regulon
The bacterial protein, Hfq, has been increasingly recognized as a post-
transcriptional regulator of global gene expression in a variety of bacteria, primarily in
response to envelop stress (in conjunction with the specialized σ factor RpoE),
environmental stress (by means of alteration of RpoE) and changes in metabolite
concentrations such as iron levels (via the Fur pathway) (Sittka et al., 2007; Wilson et al.,
2007). Several studies have also revealed that Hfq may be involved in the pathogenic
response of some bacteria including Salmonella (Sittka et al., 2007). Wilson et al. (2007)
have recently demonstrated that Hfq has a role in determining the responses observed in 23
Salmonella during space flight. Furthermore, there are several studies showing that virulence and biofilm formation are altered under microgravity conditions (Leys et al.,
2004; Mclean et al., 2001) and that these changes may be connected with Hfq activity.
During their study, Wilson et al. (2007) identified a list of space flight-stimulated genes in Salmonella belonging to the Hfq regulon or involved with iron utilization or biofilm formation. Because this present study is involved in biofilm formation and persistence of Salmonella, this list proved helpful in interpreting some of the results of this study, and the pertinent gene expression patterns from their study are summarized below in Table 2.
Table 2. Space flight stimulon genes in Salmonella belonging to the Hfq regulon or involved with iron utilization or biofilm formation (modified from Wilson et al. (2007)).
Fold Fold Gene change Function Gene change Function direction direction Hfq regulon genes (up‐regulated) Iron utilization/storage genes Outer membrane proteins adhE ↑ Fe‐dependent dehydrogenase ompA ↑ Outer membrane porin entE ↑ 2,3‐dihydroxybenzoate‐AMP ligase ompC ↑ Outer membrane porin hydN ↑ Electron transport (FeS center) ompD ↑ Outer membrane porin dmsC ↓ Anaerobic DMSO reductase nifU ↓ Fe‐S cluster formation protein Plasmid transfer apparatus fnr ↓ Transcriptional regulator, Fe‐binding traB ↑ Conjugative transfer fdnH ↓ Fe‐S formate dehydrogenase‐N traN ↑ Conjugative transfer frdC ↓ Fumarate reductase, anaerobic trbA ↑ Conjugative transfer bfr ↓ Bacterioferrin, iron storage traK ↑ Conjugative transfer ompW ↓ Outer membrane proteinW traD ↑ Conjugative transfer dps ↓ Stress response protein and ferritin trbC ↑ Conjugative transfer traH ↑ Conjugative transfer Genes implicated in/associated with biofilm formation traX ↑ Conjugative transfer wza ↑ Polysaccharide export protein traT ↑ Conjugative transfer wcaI ↑ Putative glycosyl transferase trbB ↑ Conjugative transfer ompA ↑ Outer membrane protein traG ↑ Conjugative transfer wcaD ↑ Putative colanic acid polymerase traF ↑ Conjugative transfer wcaH ↑ GDP‐mannose mannosyl hydrolase traR ↑ Conjugative transfer manC ↑ Mannose guanylyltransferase wcaG ↑ Bifunctional GDP fucose synthetase Hfq regulon genes (down‐regulated) wcaB ↑ Putative acyl transferase Ribosomal proteins fimH ↑ Fimbrial subunit rpsL ↓ 30S ribosomal subunit protein S12 fliS ↓ Flagellar biosynthesis rpsS ↓ 30S ribosomal subunit protein S19 flgM ↓ Flagellar biosynthesis rplD ↓ 50S ribosomal subunit protein L4 flhD ↓ Flagellar biosynthesis rpsF ↓ 30S ribosomal subunit protein S6 fliE ↓ Flagellar biosynthesis rplP ↓ 50S ribosomal subunit protein L16 fliT ↓ Flagellar biosynthesis rplA ↓ 50S ribosomal subunit protein L1 cheY ↓ Chemotaxic response rpme2 ↓ 50S ribosomal protein L31 cheZ ↓ Chemotaxic response rplY ↓ 50S ribosomal subunit protein L25
Various cellular functions hfq ↓ Host factor for phage replication rpoE ↓ σE (σ24) factor 24
Iron Utilization Genes
Iron is essential for the multiplication of enterobacteria, since it is a component of enzymes (e.g., ribonucleotide reductase) which are required for the biosynthesis of macromolecules (e.g., DNA) and energy-generating electron transport processes.
However, enterobacteria such as Salmonella frequently encounter iron-restricted conditions both in the host and non-host environments. In order to obtain iron from insoluble Fe (III) complexes present under aerobic growth conditions, Salmonella may release low-molecular-weight compounds, designated siderophores, which bind this metal ion with high affinity(Baumler et al., 1998). The Fe (III)-siderophore complexes are then internalized by iron-regulated outer membrane receptor proteins which display substrate specificity. The primary siderophore produced by Salmonella is enterobactin
(enterochelin), a cyclic trimer of N-(2,3-dihydroxybenzoyl)- L-serine (DBS). These siderophores are usually sequestered back to the bacteria and are transported across the outer membrane, a process mediated by outer membrane receptor proteins (Fig. 4). 25
Figure 4. The struggle for iron: bacteria vs. host. Within the host environment, most of the available iron is bound to host proteins such as transferrin and lactoferrin. Bacterial pathogens acquire iron either by producing iron chelating agents such as siderophores (e.g. enterochelin) or by utilizing heme-binding proteins. Modified from Klemm et al. (2007).
In Salmonella, several such receptor proteins have been identified, including
FepA and IroN (Rabsch et al., 1999). However, Salmonella also possesses several other outer membrane receptors, FhuA, FhuE and FoxA, which are involved in utilization of siderophores that are not produced by this pathogen itself, but rather represent a type of piracy mechanism allowing Salmonella to acquire Fe (III)-siderophore complexes from other microbes (Cornelissen and Sparling, 1994). 26
Another type of system identified in Salmonella is encoded by the feoAB locus and mediates the transport of iron (II) through the inner membrane. This system does not require siderophores, as iron (II) is soluble and therefore readily enters the periplasmic space by diffusion through the porins. Salmonella strains carrying mutations in known iron uptake systems are either minimally affected in virulence or not affected at all (Hall and Foster, 1996). This is surprising, as Salmonella are predicted to encounter iron- restricted environments in the course of their pathogenic cycle. The lack of strong phenotypes associated with mutations in iron uptake systems is therefore most likely due to the existence of several redundant systems that can mediate the uptake of this critical nutrient. Evidence of such redundancy came when yet another putative iron transport system, sitBCD, was identified on the Salmonella Pathogenicity Island 1 (SPI-1). This system belongs to the ABC family of transporters, is able to restore growth ability to an enterobactin-deficient strain of E. coli under iron-limiting conditions and is repressed under iron-rich growth conditions in a fur-dependent manner (Zhou et al., 1999).
1,2-Propanediol Utilization
Salmonella can grow aerobically as well as anaerobically on L-rhamnose, a
common plant-associated sugar, as a sole carbon and energy source (Cocks et al., 1974).
The pathway is mediated by a permease, isomerase, kinase and aldolase, yielding
dihydroxyacetone phosphate and L-lactaldehyde. Aerobically, L-lactaldehyde is
converted to L-lactate by the NAD-dependent lactaldehyde dehydrogenase and pyruvate
via a second enzyme-catalyzed oxidation. Anaerobically, L-lactaldehyde is reduced to
1,2-propanediol by an oxidoreductase, thereby regenerating NAD and allowing the 27
fermentation of rhamnose to proceed. The 1,2-propanediol is then excreted from the
bacterial cell (Fig. 5).
Figure 5. Anaerobic rhamnose catabolism in Salmonella. Modified from Boronat et al. (1979).
Although the same rhamnose pathway exists in E. coli, the 1,2-propanediol is not
further metabolized under either aerobic or anaerobic conditions. Salmonella, however,
appears to have gained an ecological advantage in being further able to utilize the
excreted product under both conditions. Since it would probably encounter this product in
many of its environmental niches, this ability may be significant. The persistence of
Salmonella in a biofilm may further highlight the usefulness of this pathway. De Beer et 28
al. (1994) showed that within biofilms there exist microniches of aerobic and anaerobic
pockets. Other researchers have also commented on this concept of partitioning within
biofilms, suggesting that within a cluster of cells, several different microenvironments
may exist, each facilitating distinct physiological pathways (Costerton et al., 1994; De
Beer and Stoodley, 2006).
Aerobic metabolism of 1,2-propanediol appears to involve the oxidation to
lactaldehyde through the action of an oxidoreductase. Lactaldehyde is subsequently
metabolized to lactate and pyruvate (Baldoma et al., 1988; Cocks et al., 1974). In
contrast, anaerobic metabolism of 1,2-propanediol has been reported to be mediated by a coenzyme B12-dependent diol dehydratase (Fig. 6) that yields propionaldehyde which is
immediately metabolized by a dismutation to n-propanol and proprionate (Obradors et
al., 1988). This anaerobic respiration can be carried out by Salmonella using tetrathionate
as a terminal electron acceptor only, as opposed to the more common anaerobic electron
acceptors nitrate, fumarate, trimethylamine-N-oxide or dimethyl sulfoxide (Bobik et al.,
1999). The genes involved in using tetrathionate as a terminal respiratory electron
acceptor are encoded by the divergently described operons ttrSR and ttrBCA. It has been
demonstrated that during anaerobic growth on 1,2-propanediol, Salmonella reduces
tetrathionate to thiosulfate which is then subsequently reduced to hydrogen sulfide. 29
Figure 6. Model of cobalamin-dependent utilization of rhamnose by intracellularly replicating Salmonella to recruit additional carbon, nitrogen and energy sources modified from Klumpp and Fuchs (2007).
The pdu genes are contiguous and co-regulated with the cobalamin (cbi-cob)
(vitamin B12) biosynthetic genes, indicating that propanediol catabolism is the primary reason for de novo B12 synthesis in Salmonella (Ailion et al., 1993; Bobik et al., 1999).
Jeter (1990) showed that de novo synthesis of cobalamin occurs only under anaerobic conditions. If one includes the cob genes, Salmonella enterica maintains 40 to 50 genes primarily for the transformation of propanediol. In fact, more than 1% of the Salmonella enterica genome is devoted to the utilization of propanediol and cobalamin biosynthesis
(Walter et al., 1997). Moreover, nearly all natural isolates of Salmonella tested synthesized B12 de novo and degraded propanediol (Lawrence and Roth, 1996).
The genes required for 1,2-propanediol degradation cluster at the pdu locus on centisome 44 of the S. enterica chromosome (Jeter, 1990). This locus includes the 30
positive transcriptional regulator, pocR, and a diffusion facilitator of 1,2-propanediol,
pduF in addition to the genes of the adjacent and divergently transcribed pdu operon
(Bobik et al., 1999). The pdu operon is estimated to include 21 genes. Of these genes,
four have unknown functions (pduLMVX), eight are reported to encode a polyhedral body
(pduABJKNSTU), a distant relative of a carboxysome shell, five encode a diol dehydratase (pduCDEGH), 3 encode for dehydrogenases (pduOPQ) and one encodes for a propionate kinase (pduW).
The regulation of the pdu operon has also been investigated. It is co-induced with the adjacent cob operon in response to 1,2-propanediol and its induction is influenced by cyclic AMP levels, the redox state of the cell, iron, magnesium, pH, and perhaps the growth phase (Ailion et al., 1993; Bobik et al., 1999; Heithoff et al., 1999; Rondon and
Escalante-Semerena, 1997). It would appear that the Crp/cAMP complex is the primary global regulator of pocR (and thus the cob and pdu operons) under aerobic conditions, while maximal anaerobic induction requires the additive effects of both the Crp/cAMP complex and the ArcA/ArcB system.
The polyhedral bodies involved in 1,2-propanediol degradation are similar in structure to carboxysomes. It has been suggested that these structures may be involved in sequestering toxic aldehydes formed during 1,2-propanediol degradation and in channeling them to subsequent pathway enzymes (Sampson and Bobik, 2008). It has also been put forward that polyhedral bodies may protect diol dehydratase from oxygen to which it is sensitive (Bobik et al., 1999). Whatever the functional purpose of the polyhedral bodies, due to the number of genes and energy expended in their formation, it 31
is evident that they play an important role in Salmonella survival and niche establishment
among the competitive flora of natural and host environments.
In vivo expression technology (IVET) has indicated that 1,2-propanediol
utilization (pdu) genes may be important for growth in host tissues (Conner et al., 1998)
and competitive index studies with mice have shown that pdu mutations confer a
virulence defect (Heithoff et al., 1999). Bobik et al. (1992) demonstrated a ~10 fold
decrease of intracellular replication of a pocR mutant, affecting both the control of
vitamin B12 synthesis and propanediol degradation, indicating that the cob-cbi-pdu gene
cluster increases the intracellular fitness of Salmonella. More recently, Klumpp et al.
(2007) showed that deletions within this same cluster resulted in attenuated replication in macrophages. Furthermore, Adkins et al. (2006) found, in acidic minimal medium, a 5- fold abundance of Pdu proteins of an environmental isolate of Salmonella enterica in
comparison with the less virulent type strain Salmonella Typhimurium LT2.
Several biotechnologically relevant processes such as unsaturated polyester
resins, liquid laundry detergents, pharmaceuticals, cosmetics, and antifreeze and deicers
depend on the production of 1,2-propanediol via a synthetic process from propylene
oxide, a non-renewable petrochemical derivative(Altaras et al., 2001). Although 1,2-
propanediol is primarily the result of the breakdown of rhamnose, researchers have also
shown that organisms such as Thermoanaerobacterium thermosaccharolyticum HG-8
(ATCC 31960), a naturally occurring microorganism, is able to ferment common sugars
such as D-glucose and D-xylose to 1,2-propanediol (Cameron et al., 1998). Furthermore,
Salmonella enterica possesses a 1,2-propanediol oxidoreductase (Ros and Aguilar, 1985) 32
which may convert glucose to 1,2-propanediol, albeit at very low levels (Badia et al.,
1985) and which is extremely sensitive to the presence of oxygen.
Glucose may also be converted to acetate via the Embden-Meyerhoff-Parnas
(EMP) or glycolytic pathway in which fructose-l,6-bisphosphate aldolase, as a key enzyme, splits the glucose backbone symmetrically to ultimately produce two molecules of pyruvate which in turn may be broken down to acetate via followed methanogenic acetate cleavage. The EMP pathway is widely distributed among hexose-fermenting anaerobic bacteria including Salmonella. Once acetate is formed, Starai et al. (2005) have demonstrated that the eut operon is required for the cobalamin-dependant excretion of acetate from the cell. This operon has been demonstrated to also form a carboxysome-like structure thought to contain acetaldehyde for removal from the cell (Rondon and
Escalante-Semerena, 1997).
Pathogenicity
Well over 1000 of the 4330 annotated ORFs of the Salmonella Typhimurium LT2
genome, approximately 25% of all genes, have probably been gained via lateral gene
transfer after the divergence of the Salmonella from E. coli around 100 million years ago,
since close homologs cannot be found in the genomes of E. coli, Yersinia pestis or
Klebsiella pneumoniae (Porwollik and McClelland, 2003). Included in this group of
genes are the four Salmonella Typhimurium LT2 prophages and the Salmonella
Pathogenicity Islands 1–5. However, there are also an additional 24 regions (Table 3)
with 10 or more genes (as well as many smaller clusters) that are not shared with E. coli,
K. pneumoniae or Y. pestis (McClelland et al., 2001). It can be expected that some, if not 33
most, of these regions contain genes that play a role in environmental adaptation and survival, host infection and disease development.
The biggest cluster of these deviant genes is the cob-cbi-pdu locus, which encompasses 42 genes and as has been discussed, is involved in de novo biosynthesis of adenosyl–cobalamin under anaerobic conditions and propanediol utilization as a carbon
and energy source. This cluster is missing in S. bongori and S. enterica subspecies VII
and IV (Porwollik et al., 2002).
The four functional phage genomes present in the Salmonella Typhimurium LT2
chromosome are the P2–like Fels-2, and the lambda-like phages Fels-1, Gifsy-1 and
Gifsy-2 (Figueroa-Bossi et al., 2001). The Fels-1 phage is very restricted in its
distribution and has so far only been detected in Salmonella Typhimurium LT2. Phage
Fels-2 has an effect on the SOS response (an inducible DNA repair system that allows
bacteria to survive sudden increases in DNA damage) of the bacterium, since mutations
within its genome allowed for non-lethality of a lexA null mutation (Bunny et al., 2002).
The Gifsy-2 phage contributes profoundly to the ability of Salmonella Typhimurium to
cause systemic disease in mice. Curing strains of the Gifsy-2 phage has been shown to
render the bacteria over 100-fold attenuated in their ability to establish a systemic
infection in mice, whereas the effect of Gifsy-1 is less pronounced and can only be shown
in cells that lack Gifsy-2 but retain the sodCI gene (Figueroa-Bossi et al., 2001). Recently
it has been shown that the outer membrane porin OmpC is a necessary receptor for Gifsy
phage entry into the bacterial cell. The gene encoding this receptor is present in all salmonellae (Ho and Slauch, 2001). The lambdoid Gifsy-3 phage is present in Salmonella 34
Typhimurium 14028s and contains the gene sspH1, encoding a leucine-rich substrate of the type III secretion apparatus of the SPI-1 (Figueroa-Bossi et al., 2001). SspH1 is suspected to be involved in host adaptation in concert with two other gene products present in several S. enterica genomes: SlrP and SspH2 (Tsolis et al., 1999).
Table 3. Regions of 10 or more genes recently (ca. 100 million years) acquired by Salmonella enterica serotype Typhimurium LT2. Modified from Porwollik et al. (2003).
Region Number of Prominent genes/operons Function (Locus) start genes
STM0014 25a bcf Fimbriae STM0266 43 saf, sinR Fimbriae, transcriptional regulator, virulence proteins? STM0328 37a stb, mod, res Fimbriae, transport proteins? DNA restriction/modification, transcriptional regulators? STM0514 19b all, glx Allantoin metabolism, glycerate kinase STM0543 24a fim, rfbI Fimbriae, glucosyl transferases, transcriptional regulator? STM0715 13 Glucosyl transferases, cell wall biogenesis STM0893 40 sodCIII, nanH Prophage Fels-1: super oxide dismutase, neuraminidase STM1005 52 sodCI, grvA, gtgE Prophage Gifsy-2: superoxide dismutase, virulence genes STM1087 11a pip, sopB SPI-5: virulence genes, effector protein STM1239 30a pag, env, msgA Virulence genes, PhoP regulated genes, ABC transport system STM1350 13b ydi Energy metabolism STM1379 44a ttr, sse, ssa SPI-2: type III secretion system STM1528 35a pqa Hydrogenases, PhoPQ regulated gene, transporters, transcriptional regulator? STM1610 12 PTS system STM1629 10 ABC transport STM1664 11 Transcriptional regulators? STM1853 21 sopE2, pagK, mig-3, pagO Phage genes, effector proteins, PhoPQ regulated genes, virulence genes c STM2019 40 cbi-cob-pdu Vitamin B12 synthesis, 1,2-propanediol utilization STM2082 16 rfb LPS side chain biosynthesis STM2230 16 sspH2, oafA Phage genes, effector protein STM2584 54 gipA, gogB Prophage Gifsy-1 STM2689 100a iro, fljAB, hin, tct, virK, mig-14 Prophage Fels-2, PTS system, phase 2 flagellin, H inversion, virulence genes, transporters, siderophores? STM2865 43a hil, spa, inv, sip SPI-1: type III secretion system and effectors, transporter STM3025 12 std Fimbriae STM3117 18 Transcriptional regulators? STM3752 13a mgt, sugR SPI-3 (part): Mg transport STM3766 10 PTS system STM4195 25 Prophage STM4305 16 Phage genes, DMSO reductase complex STM4417 20 Sugar transport, kinases STM4440 11c PTS component? STM4488 23a DNA repair? a Polyphyletic origin likely. b Present in E. coli, absent in S. bongori and five S. enterica subspecies. c Present in K. pneumoniae.
Type III Secretion Systems
Type III secretion systems (TTSS) are specialized structures found in several
Gram-negative bacterial pathogens, including Salmonella, that deliver effector proteins to 35
host cell membranes and cytosol (Hueck, 1998). The TTSS apparatus is a needle-like
structure which spans the inner and outer membranes of the bacterial envelope and
secretes translocator and effector proteins. There are structural similarities between the
needle complex and flagellar basal body, and some of its proteins, including those which
form the core of the central channel. Translocon proteins allow access of effector proteins
to the eukaryotic cell, probably by forming pores in the host cell membrane. Since TTSS
are involved in direct cell-cell contact transfer and in some cases a connecting channel
between the bacterium and the eukaryotic membrane may even be formed (Frankel et al.,
1998). The effector proteins subvert different aspects of host cell physiology and immunity, thereby promoting bacterial virulence (Galan and Wolf-Watz, 2006).
Salmonella Pathogenicity Island 1
Salmonella encodes two distinct virulence-associated TTSS within SPI-1 and SPI-
2. Salmonella Pathogenicity Islands are characterized by their absence from the E. coli
genome, a G + C content which is different from the average of the Salmonella genome,
and the presence of distinct genes, the impact and effects of which have been shown in
different stages of the infection process (Porwollik and McClelland, 2003).
The former of these pathogenicity islands found in Salmonella spp. was first demonstrated to contain genes required for the invasion phenotype by Mills et al. (1995).
The ability of Salmonella to enter epithelial cells has been reported to depend on growth
phase, low oxygen tension, pH and high osmolarity (Bajaj et al., 1996). Thus these conditions may be important drivers in controlling gene expression of the SPI-1. 36
The SPI-1 TTSS of Salmonella Typhimurium delivers several effector proteins
(e.g. SipB, SptP and AvrA) through the host cell plasma membrane. Most of these
effector proteins are involved in actin cytoskeleton rearrangements, leading to membrane
ruffling and subsequent Salmonella invasion (Galan, 1999). SPI-1 effectors also induce
IL-8 and pathogen-elicited epithelial chemoattractant secretion in intestinal epithelial cells, resulting in transmigration of neutrophils (Lostroh and Lee, 2001). The invasion
mechanism displayed by Salmonella (Fig. 7) and a description of this SPI-1-mediated
invasion follows.
Figure 7. Invasion of Salmonella into the host epithelium as the initial stage of establishing infection (BioCarta, 2008). 37
Pathogenic Salmonella enter cells such as those of the intestinal epithelium by altering cellular cytoskeletal structure and inducing membrane ruffling of the infected cell. Salmonella is able to alter the cytoskeleton and membrane through the action of SPI-
1 TTSS-mediated bacterial Sip proteins, SopE, SopB, and SptP that are inserted into the cytosol of the infected cell. Although not all of these effector proteins are encoded on the
SPI-1, their secretion is mediated by SPI-1 TTSS (Wang et al., 2004). Sip proteins encoded by Salmonella are required for the action of SopE and for the invasion of epithelial cells. SipA stabilizes actin filaments, inducing membrane ruffling and perhaps focusing membrane changes where bacteria are localized to allow their entry. The SPI-1 translocon protein SipB binds to and activates caspase-1, leading to the induction of apoptosis in macrophages (Hersh et al., 1999). SipC produces a similar effect on actin filaments and cytoskeletal structure. SopE acts as an exchange factor on Rac1 and Cdc42, two GTPases in the Rho family that regulate actin cytoskeleton. The activation of Rac2 and Cdc42 by Salmonella SopE induces changes in cytoskeleton structure that allow bacterial entry into the cell. SopB is another Salmonella protein that acts as an inositol polyphosphate phosphatase and also stimulates Cdc42 and Rac1. One of the cellular targets of both Cdc42 and Rac1 that affects actin structure is the Arp2/3 complex. Cdc42 and Rac1 activate Wasp, which activates Arp2/3. Activated Arp2/3 induces the formation of actin Y branches, which in combination with changes in actin caused by SipA and
SipC help to form lamellipodia, and causes membrane ruffling, leading to entry of
Salmonella into the affected cell (Galan and Zhou, 2000). 38
After the initial infection, cells quickly return to their normal morphology, a process that depends on the action of the bacterial protein SptP. While SopE acts as an exchange factor, SptP acts as a GTPase activating protein to inactivate Rac1 and Cdc42 once again. This inactivation of the original entry mechanism provides an example of the delicate balance between infectious organisms and their host (Galan and Zhou, 2000).
Mutations which prevent secretion through the SPI-1 TTSS lead to a 10- to 100- fold increase in attenuation in the mouse model of systemic infection when the bacterial inoculum was administered orally (Baumler et al., 1997; Galan and Curtiss, 1989; Jones et al., 1994). Evidently the lack of complete attenuation of SPI-1 null mutants reflects the ability of Salmonella to disseminate to the liver and spleen from the intestinal tract via an alternative route: carriage within transmigrating, CD-18 expressing phagocytic cells
(Vazquez-Torres et al., 1999). After the bacteria reach the spleen and liver, they replicate within membrane-bound compartments, called Salmonella-containing vacuoles (SCVs), inside macrophages (Richter-Dahlfors et al., 1997; Salcedo et al., 2001).
Salmonella Pathogenicity Island 2
One main function of the SPI-1 is to aid bacterial translocation from the intestinal lumen to the basolateral side of the intestinal mucosal membrane. This process also involves yet another drastic change in the surrounding environment of the infecting bacteria, requiring the pathogen to withstand the host antibacterial responses such as
professional phagocytic cells aimed at ingesting and killing the bacteria. The SPI-2 TTSS
is a multifunctional virulence system that is activated following entry of bacteria into
eukaryotic cells and facilitates bacterial multiplication in all cell types that have been 39
tested (Beuzon et al., 2002; Cirillo et al., 1998; Hensel, 2000). SPI-2 gene products are
thought to be induced by Mg2+ deprivation, phosphate starvation, low pH and oxidative stress (Hensel, 2000) and in bacterial growth experiments, genes are not induced until cells enter stationary phase (Monack et al., 2001).
Related in behavior to the SPI-2 is the expression of the spv operon located on a
96kb virulence plasmid in Salmonella Typhimurium (Eriksson et al., 2003; Gulig et al.,
1993; Rhen et al., 1993). Because intracellular growth and bacterial proliferation in
cultured cells is correlated with systemic growth in the host (Salcedo et al., 2001), this
explains the profound attenuation of SPI-2 or spv null mutants in vivo (Hensel, 2000;
Shea et al., 1996).
Although SPI-2 is almost 40 kb in length, genes encoding the type III secretion system are localized to a region of approximately 26 kb beginning at the centisome 30 end of the island. Here, 31 genes are organized in four operons termed (1) regulatory, (2)
structural I, (3) structural II and (4) effector/chaperone (Cirillo et al., 1998; Hensel et al.,
1998). In addition to several genes encoding evolutionarily conserved structural
components of the secreton machinery (Aizawa, 2001) and the translocon proteins SseB,
SseC and SseD, there are a few genes that appear to be unique to SPI-2, such as sseE,
whose functions are unknown. SseB is similar to EspA of enteropathogenic E. coli, and
might therefore link the secretion needle to the translocon pore (Beuzon et al., 1999).
SseB, SseC and SseD are not required for secretion of effectors, but are necessary for
their translocation across the vacuolar membrane (Waterman and Holden, 2003). Hence,
these proteins can be operationally defined as translocon components, although their 40
presence in the vacuolar membrane has not been demonstrated directly. In addition to the components of the secreton and translocon, SPI-2 also encodes at least three chaperones:
SscA, SscB and SseA. The partners of SscA and SscB have not been defined, but SseA is a chaperone for SseB and SseD (Ruiz-Albert et al., 2003; Zurawski and Stein, 2003). The
SPI-2 also encodes a two-component regulatory system which is required for expression
of all SPI-2 TTSS genes (Cirillo et al., 1998) as well as several genes located outside SPI-
2 which encode effector proteins (Beuzon et al., 2000; Knodler et al., 2002; Worley et al.,
2000). In other TTSS’s, some translocon proteins have been shown to function as
effectors, but there is no evidence yet to indicate whether this might be the case for SseB,
SseC or SseD. SpiC, SseF and SseG are proposed to be effector proteins encoded within
SPI-2 (Freeman et al., 2002; Kuhle and Hensel, 2002).
41
CHAPTER 3
A TRANSCRIPTIONAL STUDY OF AN ENVIRONMENTAL SALMONELLA
ENTERICA ISOLATE BIOFILM
Introduction
Salmonella enterica, like Escherichia coli, is an enteric pathogen belonging to the
family Enterobacteriaceae and has been identified as the second most common cause of
gastroenteritis in children under five years of age in the United Kingdom (Crowley et al.,
1997). This organism is responsible for salmonellosis, the second most common cause of bacterial food poisoning reported to the Communicable Disease Surveillance Center
(CDSC) (Evans et al., 1998) and accounts for 60% of all bacterial disease outbreaks in the US. It is estimated that over 4 million cases of Salmonella infection and 1000 related deaths occur in the United States annually (Feng, 1992). Individuals infected with
Salmonella shed the organisms in their feces, which can enter domestic sewage and consequently may contaminate drinking water sources.
Although the primary cause of salmonellosis is consumption of Salmonella- contaminated foods, there is increasing evidence that this pathogen may be associated with biofilms on materials of different nature and under different growth conditions
(Solano et al., 2002; Stepanovic et al., 2003) and may be important in drinking water distribution systems (Jones and Bradshaw, 1996). Salmonella discharged in the effluents from municipal wastewater treatment plants have been reported to survive for an extended time in nutrient-rich river water (Winfield and Groisman, 2003). Several 42
mechanisms of survival have been suggested, including the adoption of a viable-but-non
culturable (VBNC) state (Roszak et al., 1984), the integration of the pathogen into an
existing biofilm (Barker and Bloomfield, 2000; Jones and Bradshaw, 1996; Solano et al.,
2002; Stepanovic et al., 2003), internalization of the pathogen into a variety of protozoan
hosts (King et al., 1988; Moore et al., 2003; Tezcan-Merdol et al., 2004) and adaptation
via lateral gene transfer (Porwollik et al., 2002) whereby the pathogen gains a strategic
advantage over other microbes in the biofilm community to exploit a particular
microniche.
Disease is caused by the penetration of the Salmonella bacteria into the epithelium
of the small intestine and subsequent enterotoxin production resulting in electrolytic
imbalance. It has been suggested that biofilm formation which may aid in survival of
bacteria under various conditions might be related to increased virulence (Wilson et al.,
2007). Indeed, the formation of Salmonella biofilm on epithelial cells and its ability to
outcompete E. coli in heterologous infections supports the notion that biofilm growth
may be related to increased virulence (Esteves et al., 2005). Transcriptional profiling in related infectious models and biofilm communities may provide some clues to these methods of survival. However, due to the spatial and physiological heterogeneity within microbial biofilms (Costerton, 2000; De Beer and Stoodley, 2006), it is often technically challenging to isolate and purify mRNA from discrete populations within a biofilm community. Advances in laser dissection microscopy and mRNA stabilization may in the future offer the means with which to investigate physiological behavior of single cells 43
within discrete microniches of a biofilm, but for this present study, the entire
monoculture biofilm was regarded as a single unit.
It is traditionally thought that Salmonella has acquired various virulence-
associated genes through lateral gene transfer to allow it to evade host defense
mechanisms and increase its survival and persistence within the host. Such genes include
those operons located on Salmonella Pathogenicity Islands (SPIs) 1 and 2 which are
usually associated with enterocyte invasion (Ellermeier and Slauch, 2007) and
intracellular replication (Hensel, 2000) respectively. An additional pathway apparently
gained via lateral gene transfer is the cob-cbi-pdu operon which allows Salmonella to
utilize 1,2-propanediol as a sole carbon and energy source under anaerobic conditions
(Klumpp and Fuchs, 2007) in a cobalamin-dependent fashion (Sampson and Bobik,
2008). Induction is mediated by a positive regulatory protein (PocR) encoded by a gene
(pocR) that maps between the cob and pdu operons (Bobik et al., 1992). The proximity of these operons and their coordinate control probably reflect the fact that vitamin B12 is an essential cofactor for propanediol dehydratase, the first enzyme of propanediol degradation (Jeter, 1990). The coregulation also supports the idea that the major function of de novo vitamin B12 synthesis in Salmonella is in propanediol degradation (Ailion et
al., 1993). However, this regulon appears to be a paradox since PocR has been
demonstrated to induce expression of the divergent pathways both aerobically and
anaerobically, but de novo synthesis of vitamin B12 (a necessary co-factor in the utilization of 1,2-propanediol) only occurs under anaerobic conditions (Bobik et al.,
1992). It is suggested that this apparently paradoxical pathway may represent a 44
significant advantage for Salmonella within a biofilm community where it may encounter
both aerobic and anaerobic microniches (Costerton et al., 1994; De Beer et al., 1994;
Price-Carter et al., 2001).
Winfield and Groisman (2003) suggest that Salmonella, unlike E. coli, has actually evolved to actively cycle through host and non-host environments. These authors suggest that E. coli does not persist in non-host environments and that its presence in such locations results from recent excretion of waste by animal hosts. They report that this is essentially the logic behind the use of E. coli as the indicator organism for environmental fecal contamination, that is, as an indicator species, E. coli is assumed not to be a permanent resident of soil and water environments. It is suggested here that
several systems generally only associated with the host environment and/or virulence are
indeed activated in the non-host biofilm environment. These findings suggest that
Salmonella may have alternative uses for the so-called virulence genes and may be
adapted to persisting as a biofilm in the external environment.
Materials and Methods
Strains and Growth
The strain of Salmonella used in this study was an environmental pathogen
isolated from an outbreak in Gideon, MO, USA in 1993 (Clark et al., 1996). This highly
virulent strain of Salmonella was typed by pulsed gel field electrophoresis (PGFE) at the
CDC in Atlanta, GA, USA and is designated Salmonella Missouri in this paper. Sequence
analysis of the 16S rDNA gene was also performed (Research Technology Support
Facility, Michigan State University using a Perkin Elmer/Applied Biosystems 3100 45
capillary sequencer) to confirm the identity of this organism. Primers used to amplify a
highly conserved region of the 16S rDNA gene covered an area of approximately 1500 base pairs. These primers have been used regularly in this lab and are designated 8F and
1492R (Burr et al., 2006).
Planktonic growth rates were determined in M9 Minimal Media (Becton-
Dickinson, MD) with the addition of 0.4% glucose (Fisher Scientific, NJ) as the carbon
source (Ren et al., 2005). This was the defined medium used in all subsequent
experiments unless otherwise indicated. All cultures, both planktonic and biofilm, were
grown at an ambient temperature of 23°C. For each new experiment, Salmonella
Missouri was freshly prepared from a cryostock which had been maintained at -80°C
with minimal passaging. The ATCC type strain No. 700720, Salmonella enterica
serotype Typhimurium LT2, was cultured as a reference strain to provide a comparison of
growth rate.
In order to determine growth rates, a starter culture of the organism was prepared
by inoculating an overnight colony grown on XLD agar (EMD, NJ) into 100 mL volumes
of M9 + glucose in 250 mL baffled flasks (Pyrex, USA) with orbital shaking of 180 rpm.
These starter cultures were allowed to grow up for 24 hours at which point 100 µL was
inoculated into 100 mL fresh media in a 250 mL Nephelo flask (Wheaton, USA) and
these flasks were returned to the orbital shaking platform at 180 rpm. Optical density was
determined every 4 hours using a Spectronic 20D+ spectrophotometer (Thermo Electron
Corporation, MA) reading at a wavelength of 600 nm. 46
Planktonic cultures were grown under the same conditions as used in determining
experimental growth rates. For microarray experiments, cultures were harvested at 12
hours (empirically determined to be mid- to late-logarithmic phase for both strains of
Salmonella).
Biofilms were grown using the CDC biofilm reactor (www.biofilms.biz) with
glass coupons serving as surfaces for attachment. CDC reactors were preconditioned with
sterile M9 + glucose for 24 hours in batch mode to ensure sterility of the media and
equipment. An inoculum of 1mL Salmonella grown up as described previously for the
preparation of a growth curve experiment was aseptically introduced through a rubber
injection septum and an 18 hour batch mode was allowed in order to facilitate
establishment of the culture in the reactor. This period of batch growth was followed by
switching on the pump and allowing fresh media to flow into the reactor with a hydraulic
retention time of 7.6 hours to ensure that planktonic bacteria were washed out and the biofilm bacteria predominated.
Biomass Harvesting
For planktonic samples, 50 mL of a 12 hour culture was centrifuged at 4°C for 10
minutes at 10,000 x g. The supernatant was removed and the pellet was resuspended on
ice in a 1:1 mixture of 400 µL RNA Buffer A (50 mM sodium acetate, pH 5.5; 10 mM
EDTA, pH 8.0; 1% SDS) and 400 µL acidic phenol:chloroform (pH 4.5) (Ambion, TX).
For biofilm samples, biofilm material was scraped off three coupon surfaces using
a cell scraper (Fisher Scientific, NJ) into equal volumes of RNA Buffer A and acidic
phenol:chloroform. 47
RNA Purification
Several methods of RNA purification were attempted, including TRIzol
(Invitrogen, CA), RNA Power Kit for Soils (MoBio, CA) and RNeasy (QIAGEN, MD), before settling on the following optimized technique.
The phenol mixtures were transferred to Lysing Matrix Tube E (MPBio, OH) and
treated in a FastPrep Bead Beater FP120 (Bio101 Savant, NY) for 30 seconds at 5.5 rpm.
Samples were centrifuged at 4°C for 30 minutes at 14,000 x g.
Phenol was removed using successive chloroform extractions in 2 mL Phase Lock
Gel (PLG) Heavy tubes (Eppendorf, NY). All steps were subsequently performed quickly
and at room temperature. Briefly, the aqueous (top) phase of each sample was transferred
into a prespun (13,000 x g for 2 minutes) PLG Heavy tube to which 200 µL acidic
phenol:chloroform and 200 µL chloroform:isoamyl alcohol (Amresco, OH) were added.
The tubes were inverted gently to mix and incubated on ice for 10 minutes. Tubes were
then centrifuged at 13,000 x g for 5 minutes. A further 400 µL chloroform:isoamyl
alcohol was added, the tube was inverted to mix and centrifuged at 13,000 x g for 5
minutes.
The aqueous phase was then transferred to a new RNase-free tube and finally
treated with TURBO DNase (Ambion, TX). Briefly, a 0.1 volume of 10x TURBO DNase
Buffer was added to the sample followed by the addition of 5 µL TURBO DNase.
Samples were mixed gently by flicking the tubes and incubated at 37°C for 20 minutes.
Activity of the enzyme was inhibited by the addition of 0.1 volumes of resuspended
DNase Inactivation Reagent (Ambion, TX). The sample was incubated at room 48
temperature for 2 minutes with regular, gentle mixing and finally centrifuged at 10,000 x
g for 1 ½ minutes to pellet out the DNase Inactivation Reagent. The supernatant was transferred to a fresh RNase-free tube.
Finally the sample was cleaned up using a modified protocol of an RNeasy Clean- up Reaction (QIAGEN, MD). Briefly, aliquots of 200 µL RNA were mixed with 700 µL
RLT Buffer (QIAGEN, MD) followed by the addition of 500 µL absolute ethanol.
Volumes of 750 µL were loaded onto an RNeasy Column (QIAGEN, MD) and centrifuged at room temperature for 15 seconds at 10,000 x g. The eluate was discarded and subsequent volumes of RNA were loaded onto the same column until all the sample had been run through. The columns were then washed twice with Buffer RPE (QIAGEN,
MD) and RNA was eluted in two successive 50 µL volumes of RNase-free water. Yield was determined by spectrometry on a Nanodrop 1000 (Nanodrop Technologies, DE) and quality assayed with a 2100 Bioanalyzer (Agilent, CA).
DNA Microarray Transcriptional Profiling
RNA was reverse transcribed into cDNA and indirectly labeled according to
SOP#: M007 released by Pathogen Functional Group Research Center (PFGRC), J. Craig
Venter Institute (JCVI) (http://pfgrc.jcvi.org/index.php/microarray/protocols.html).
Briefly, 5 µg RNA was reverse transcribed using SuperScript III (Invitrogen, CA) with a
0.5 mM 5-(3-aminoallyl)-dUTP:dTTP (Sigma, MO) for 18 hours. The optimal ratio of aa-dUTP to dTTP varies depending on the GC content of the organism in question.
Organisms with high GC content, such as Pseudomonas aeruginosa PAO1 which has a
GC content of 66%, generally require a lower aa-dUTP to dTTP ratio. Organisms with 49
low GC content, such as Streptococcus pyogenes M1 GAS and Bacillus anthracis strain
Sterne which have GC contents of 38% and 35% respectively, usually require a higher
aa-dUTP to dTTP ratio. Since Salmonella Typhimurium LT2 has a GC content of 52%
(compared with the E. coli K12 GC content of 50%), a 2:1 ratio of aa-dUTP:dTTP was decided on. This first strand cDNA synthesis reaction was stopped and remaining RNA degraded by alkaline hydrolysis with sodium hydroxide and neutralization with TRIS.
Removal of unincorporated aa-dUTP and free amines was achieved using a modified protocol from the QIAGEN MinElute PCR purification kit (QIAGEN, MD).
These modifications included the substitution of a 5 mM phosphate wash buffer pH
8.5/80% ethanol for the kit wash buffer and nuclease-free water for the elution buffer.
These substitutions were made to avoid contamination with free amines which compete with the aa-dUTP in the subsequent Cy-dye coupling reaction.
The clean-up step was followed by drying for 35 minutes at 60°C in a CentriVap
DNA Vacuum Concentrator (Labconco, MO). Dried probes were then indirectly labeled with Cy3 or Cy5 (Amersham, NJ). Briefly, aminoallyl-labeled cDNA was resuspended in
4.5 µL 0.1 M sodium carbonate buffer, pH 9.3. This was followed by the addition of the appropriate DMSO-resuspended Cy dye and an incubation of between 1 and 2 hours at room temperature in the dark. After coupling was complete, 20 µL 4.5 M sodium acetate pH 5.2 (Ambion, TX) was added. Two important aspects of this step to note include the thorough resuspension of the dried probe before the addition of the Cy dye as well as adhering to the prescribed pH 9.3 of the sodium carbonate buffer to ensure optimum coupling of the aminoallyl-labeled cDNA to the Cy dye ester. 50
Labeled cDNA was purified using the MinElute PCR Purification kit (QIAGEN,
MD) according to manufacturer’s instructions. Analysis was performed to ensure
optimum yield and labeling efficiency using the “Microarray” function of a Nanodrop
1000 (Nanodrop, DE). For each sample, the total picomoles of cDNA synthesized was
determined using the following formula:
μ 37 /μ 1000 / 324.5 /
For each sample the total picomoles of dye incorporation (Cy3 or Cy5) was
determined using the following formula:
μ 3 0.15
μ 5 0.25
And finally, the incorporation ratio of cDNA to dye was determined using the formula:
#
Theoretically required limits were set at > 800 pmol of dye incorporation per
sample and a dye incorporation ratio of < 20 in order to obtain optimal microarray
hybridizations. 51
Following analysis, the two differentially labeled cDNA’s (Cy3 and Cy5) were mixed and dried for 35 minutes at 60°C in a CentriVap DNA Vacuum Concentrator
(Labconco, MO). Dried probes were stored at -80°C.
Hybridization was performed according to SOP#: M008
(http://pfgrc.jcvi.org/index.php/microarray/protocols.html) using 70-mer spotted
Salmonella Typhimurium/Typhi Version 5 arrays from the PFGRC, JCVI. These
microarrays were designed on Salmonella enterica serotype Typhimurium LT2,
Salmonella enterica serotype Typhi CT18 and Ty2. Oligonucleotides (single stranded 70- mers) were designed based on open reading frame sequences across all three genomes of the microarray and did not necessarily represent a single oligo from a single strain. The oligonucleotides were designed to provide coverage across all the organisms used in the creation of the microarray. The number of open reading frames used in the design of the microarray were 4553, 4395 and 4323 and the number of oligonucleotide sequences designed were 4504, 926 and 32 for the LT2, CT18 and Ty2 respectively. This yielded a total number of oligonucleotide sequences of 5462. Each oligo was replicated four times
on the slides. Additionally, each slide contained 10 Arabidopsis thaliana amplicons and
500 A. thaliana 70-mers as controls. The total number of elements on the array (minus
empty spots) was 23888. The PFGRC Universal Microarray Standard Set was used as an
internal control. These standards consisted of a mix of 1000 Cy-dye end labeled 40-mer
probes (500 Cy3 and 500 Cy5) complementary to the 500 A. thaliana 70-mer control
spots. The control probe mix was routinely spiked into the experimental probe mix
immediately before hybridization to the microarray. Spots associated with the PFGRC 52
Universal Microarray Standard Set have the designation “Atg1” on the annotation sheets used during data analysis.
Hybridized slides were incubated at 42°C overnight, washed in increasing stringency buffers and finally scanned using a GenePix 4000B microarray scanner
(Molecular Devices, CA) to generate 2-color 16-bit TIFF images. If slides could not be scanned immediately, they were stored in the dark in the final high stringency wash buffer with 10 mM DTT (to act as an ozone scavenger), however it was observed that storage in this manner only yielded acceptable results for up to 3 hours before washout of the dye occurred. Five hybridizations were performed from each of three biological replicate planktonic/biofilm pairs with two of these hybridizations (technical replicates) being dye swaps (flip dyes), performed as part of overall quality assurance.
Data Analysis
Processing of the 16-bit TIFF images from hybridized arrays was performed with the TIGR TM4 package (Saeed et al., 2003). Intensity values for Cy3 and Cy5 channels were obtained using TIGR Spotfinder software. Normalization was performed with the
LOWESS algorithm available in TIGR MIDAS, using the global mode and a smoothing parameter of 0.33. All intensity values less than two times greater than background were removed from subsequent analysis, and quadruplicate in-slide replicate intensities on each slide (considered a further one technical replicate) were reduced to a single value by computing the geometric mean.
To determine genes whose expression was significantly different from zero, significance analysis of microarrays (SAM) software (incorporated within the TIGR TM4 53
package) was employed using the one-class response with 8 unique permutations. While
the three biological replicates were used for final analysis, two additional flip dye
technical replicates were also compared to observe any irregularities. None were
observed. Significant genes were determined by setting the number of median falsely
called genes to less than one. At these levels, the q-values (a measure of significance in
terms of the false discovery rate) for all biological replicates were less than 0.1%.
Significantly different genes were then sorted according to the observed score (d) which
represents the relative difference of a gene between the samples.
Each SAM plotsheet contains all the genes plotted by their observed scores and
expected scores. The observed score is the relative difference in gene expression. It is
calculated by dividing the difference between gene relative abundances in the biofilm and planktonic samples by the pooled standard error of repeated measurements of that gene in the two samples. The expected score is calculated using the large set of permutations of gene relative abundance data of the biological replicates from the biofilm and planktonic samples.
The observed score provides a control over random fluctuation, while the
expected score allows assignment of statistical significance. The correlation of these two
scores is used for identifying genes with potentially significant differential expression. If a gene has absolutely no differential expression, the observed relative difference would be the same as the random fluctuation that is represented by the expected score. The data point of such a gene in the SAM plotsheet would fall on the 45° line through the origin.
Data points representing differentially expressed genes will deviate from this 45° line. 54
The point displacement of a gene from the 45° line through the origin is quantitatively
measured by a delta (Δ) value in SAM. Genes with Δ values beyond a certain threshold
are called significant. The 45° upper and lower Δ lines indicate the boundary defined by a
selected Δ value.
A fold change limit of 1.5 was also applied to significant genes (subsequent to
SAM-applied Δ values) in order to further gauge the magnitude of change. However,
since fold change is somewhat arbitrary, especially when attempting to ascertain
significant biological roles, imposing a typical 2-fold criterion which removes from
consideration a gene with a 1.9 fold change that is really key to a biological mechanism,
could alter the interpretation of a study. Therefore thedata before fold change limits were
applied is the primary data presented.
Expression Analysis Systematic Explorer (EASE) (incorporated within the TIGR
TM4 package) was used on the subset of genes determined to have significant changes in
expression as identified by the SAM analysis. EASE uses a modified Fisher exact test
(EASE score) to estimate the significance of classes of biological function present in a
subset of significant genes relative to the total as represented on the array (Hosack et al.,
2003). TIGR role categories (http://cmr.jcvi.org) determined as part of the whole-genome
annotations of Salmonella enterica serotype Typhimurium LT2, Salmonella enterica
Typhi CT18 and Ty2 were used as the biological classes examined for over-
representation in the lists of significant genes and for all annotation referred to in this study. Only biological classes with EASE scores of ≤ 10-3 were determined to be
significant. 55
Results and Discussion
Bacterial Characterization
The environmental isolate of Salmonella used in this work had been isolated from
an outbreak in Gideon, Missouri, USA in 1993 and had originally been typed at the CDC,
Atlanta, Georgia, USA by PFGE. At that time, the CDC was still using non-standardized
nomenclature for Salmonella and they identified that organism as Salmonella serovar typhimurium. Subsequent phylogenetic analysis (Fig. 8) of PCR-amplification and sequencing of a portion of the 16S rDNA gene revealed that the strain bore a 99% homology with various subspecies of S. enterica including S. enterica serotype
Typhimurium, Typhi and Paratyphi as well as S. enterica subsp. arizonae (Table 4).
According to the NCBI Taxonomy Browser, although over 200 serotypes of S. enterica
subsp. enterica are listed, from Aberdeen to Zanzibar, the Missouri isolate has to date not
been deposited within this database.
Table 4. Top six sequences producing significant alignments (NCBI-BLAST) to a 702 bp sequence obtained by PCR amplifying a portion of the 16S rDNA gene of Salmonella Missouri (Zhang et al., 2000).
Total Query Accession # Description Max score E value Max ident score coverage Salmonella Typhimurium LT2, section 124 of AE008820.1 1280 1280 100% 0 99% 220 of the complete genome Salmonella enterica subsp. enterica 16S AF332600.1 1279 1279 99% 0 99% ribosomal RNA gene, partial sequence Salmonella Typhi strain T1 16S ribosomal EU118108.1 1275 1275 100% 0 99% RNA gene, partial sequence Salmonella enteritidis strain E2 16S EU118101.1 1275 1275 100% 0 99% ribosomal RNA gene, partial sequence Salmonella enterica subsp. enterica serovar EU118091.1 Paratyphi C strain C2 16S ribosomal RNA 1275 1275 100% 0 99% gene, partial sequence Salmonella enterica subsp. enterica serovar EU118085.1 Paratyphi B strain B4 16S ribosomal RNA 1275 1275 100% 0 99% gene, partial sequence 56
Figure 8. NCBI-BLAST phylogenetic tree using the neighbor-joining algorithm indicating relatedness of Salmonella Missouri (indicated by query ID lcl|13935) to other prokaryotic organisms based on a 702 bp sequence obtained by PCR amplifying a portion of the 16S rDNA gene (Zhang et al., 2000).
It is interesting to note that according to its relatedness based on 16S rDNA sequence data, the Salmonella Missouri strain bore similarity to the more virulent serotypes of Salmonella enterica, namely Typhi and Paratyphi. This is not surprising, 57
considering the virulence this pathogen demonstrated during the Gideon outbreak, which affected about 44% of the town, hospitalizing 15 patients and causing mortality in seven
nursing home residents (Clark et al., 1996).
Subsequent to initial typing by PFGE, the CDC agreed to conform to the
Kauffman-White nomenclature scheme for Salmonella phylogeny, and this isolate was re-categorized as Salmonella enterica serotype Missouri. It is noteworthy that even such a subtle change can highlight potential elevation in virulence of a pathogen, considering that most clinicians do not associate the Salmonella Typhimurium serotype with such virulent pathology.
In order to characterize the experimental strain further based on growth characteristics, a standard growth curve (Fig. 9) was performed in M9 minimal media with 0.4% glucose as a carbon source at ambient temperature (ca. 23°C). The growth rate was relatively rapid, considering the minimal conditions and low temperature. The majority of microbiology texts would list Salmonella as having an optimal growth temperature at 37°C based on the traditional notion that it is an enteric pathogen. 58
0.7
0.6
0.5
0.4
Absorbance 0.3
0.2
0.1
0 0 5 10 15 20 25 Time (hours)
OD600nm Salmonella Missouri OD600nm Salmonella Typhimurium LT2
Figure 9. Growth curve of Salmonella Missouri (blue) based on absorbance at an optical density of 600 nm. The growth curve of the ATCC type strain Salmonella enterica Typhimurium LT2 (red) is shown for comparison.
The doubling time (g) of the strain Salmonella Missouri was determined, using the specific growth rate from the slope of the exponential portion (µ = 0.0778) of the growth curve, to be 8.91 hours when grown at ambient temperature in M9 + 0.4% glucose with constant shaking. The equivalent doubling time for the ATCC type strain
Salmonella Typhimurium LT2 was determined to be 13.84 hours under the same growth conditions.
ln 2 59
RNA Purification
During attempts to isolate high quality RNA from the biofilm and planktonic cultures for the microarray experiments, a third, seemingly spurious, band appearing on agarose gels and in BioAnalyzer electropherograms of total RNA extractions (Fig. 10) was noticed. Initially it was thought that the purification procedure was causing degradation of the RNA. However, after multiple attempts at RNA purification via numerous different methods, as well as the observation that the additional band always seemed to appear at the same distance relative to the other two bands, older literature was discovered with a possible explanation.
Figure 10. Electropherogram of Salmonella RNA used to check the quality of purified nucleic acid. L = 6000 RNA Ladder (Ambion, TX); 7 = purified RNA from Pseudomonas aeruginosa PAO1; 8 = purified RNA from Salmonella Missouri.
Burgin et al.(1990) discovered novel, approximately 90 bp intervening sequences
(IVSs) within the 23S rRNA genes of Salmonella. These non-rRNA sequences appear to 60
be transcribed and then excised by RNase III during rRNA maturation. The rRNA
fragments that result from the excision of the extra sequences are functional but not
relegated (Mattatall and Sanderson, 1996). This results in fragmented 23S rRNAs. They
showed that the fragmentation patterns can be understood as the result of two breakage
points (at helix-25 and helix-45) in the 23S rRNA. One type of fragmented 23S rRNA
(normally approximately 2.9 kb total) would consist of 0.5 kb and 2.4 kb fragments,
another of 1.2 kb and 1.7 kb fragments (as was regularly observed in this study), and a
third of 0.5 kb, 0.7 kb and 1.7 kb fragments. For this reason, the RNA Integrity Number
(RIN) generated by the BioAnalyzer, usually used to indicate acceptable RNA purity
(DNA- and protein-free) and quality (free from RNase degradation), was inappropriate for use in this study and is not reported here.
Data Analysis
After normalization and statistical analysis, the total number of significantly expressed genes was determined to be 857. This equated to 410 up-regulated biofilm-
associated genes (11% of 3839 total genes analyzed) and 447 up-regulated planktonic-
associated genes (12% of 3839 total genes analyzed). These genes were determined to be
significant by applying a SAM delta (Δ) of 0.86190873, yielding the number of falsely
significant genes (median) as 0.73978, a false discovery rate (FDR) median of 0.08572%
and q-values ≤ 0.1%.
Since the ultimate goal of any molecular microbial ecologist carrying out
transcriptomic studies is to assign biological relevance to a set of gene expression data,
the first iteration of analyses was implanted to determine whether there were any 61
functional role categories into which a significant portion of the expressed genes fell, and
if they were primarily associated with the planktonic or biofilm phenotype. To this end,
the use of the EASE algorithm was implemented. Since the entire genomes of Salmonella
Typhimurium, Typhi CT18 and Typhi Ty2 have been sequenced and mostly annotated,
gene expression data was deciphered into the cellular role categories according to The
Institute of Genomic Research (now called JCVI) Comprehensive Microbial Database
(CMR). Several flaws were noticed in using this annotation scheme, but owing to the fact that it is the most complete database available, these values herein but are submitted with the following caveat: of the 3839 total genes available in the dataset, only 2701 have been annotated and classified (1138 genes have not even been classified into “Unclassified” or
“Unknown function” categories). Similarly, of the 447 significant genes associated with the planktonic phenotype, only 302 have been annotated and classified; and of the 410 significant genes associated with the biofilm phenotype, only 303 have been annotated and classified. It is largely for this reason that the EASE scores were uncharacteristically high for such a global gene expression study (one usually considers EASE scores ≤ 10-3
to be significant for global gene expression studies).
Based on the completely annotated dataset available, it is demonstrated that there are only minor differences between the functional category breakdowns of the planktonic and biofilm phenotypes (Fig. 11). Most noticeably, the categories “Energy Metabolism” and “Protein Fate” were determined to be significant (EASE scores ≤ 10-3) in the biofilm
phenotype while “Unclassified” genes were somewhat important but not significant
(EASE score 7.9 x 10-2). “Amino Acid Biosynthesis” and “Cell Envelope” associated 62 genes were determined to be noteworthy but not significant (EASE scores 1.2 x 10-3 and
3.2 x 10-2 respectively) in the planktonic phenotype.
Planktonic Biofilm
Figure 11. Distribution of significantly up-regulated genes assigned to functional categories of the observed Salmonella Missouri transcriptome. Functional categories are according to the JCVI Comprehensive Microbial Database (CMR) Annotation Scheme. Values indicated are percentages.
Three noticeable pathways making up the bulk of the genes in the “Energy
Metabolism” category were the 1,2-propanediol utilization operon (pdu), the H2-evolving hydrogenase 3 complex (hyc) and the NADH dehydrogenase I operon (nuo). Although genes categorized as “Unclassified” in the biofilm phenotype fell below the significance threshold set for EASE scores, they were almost entirely associated with the 63 aforementioned pathways falling in either the “Energy Metabolism” or “Protein Fate” categories above.
The most abundant genes in the “Energy Metabolism” category were those genes associated with the 1,2-propanediol utilization operon. Associated genes such as the tetrathionate reductase complex (ttr), shown to be the terminal electron acceptor in the anaerobic utilization of 1,2-propanediol, and further pdu and cbi genes were found in the
“Unclassified” category. Collectively these genes encode for a pathway which has afforded Salmonella tremendous ecological niche advantages over evolutionally-related
E. coli in that Salmonella is able to produce vitamin B12 de novo under anaerobic conditions and ferment 1,2-propanediol, a breakdown product of the common plant sugar, rhamnose.
The hyc/hyp operon of Salmonella encodes the H2-evolving hydrogenase 3 complex that, in conjunction with formate dehydrogenase H (fdh), constitutes a membrane-associated formate hydrogenlyase (FHL) catalyzing the disproportionation of formate to CO2 and H2 during fermentative growth at low pH. Categorization of this operon was scattered between the “Energy Metabolism”, “Protein Fate” and
“Unclassified” categories. Several hyc, hyp and fdh genes were found in these categories.
The formate hydrogenlyase reaction is thought to relieve the buildup of reducing equivalents and, in addition, to offset acidification of growth media during fermentative growth. Although other hydrogenase isoenzymes are known in Salmonella and are thought to be involved in the second mode of hydrogen metabolism, namely hydrogen uptake where hydrogen is oxidized and energy liberated to support anaerobic growth, no 64 evidence that these genes were up-regulated in the biofilm phenotype came from the
EASE analysis.
The membrane-bound NADH dehydrogenase in Salmonella, NADH:ubiquinone oxidoreductase, is encoded by multiple genes on the nuo operon. Dekkers et al. (1998) observed a competitive plant root colonization defective mutant of Pseudomonas fluorescens with a mutation in the nuoD gene homolog. They suggest that NADH dehydrogenase I plays a role in root colonization in this plant-associated pathogen. More than half the genes of this operon were significantly expressed in the biofilm phenotype and fell under the “Energy Metabolism” category identified by EASE analysis.
The “Protein Fate” category contained multiple genes associated with the SPI-2
TTSS, primarily the ssa, ssc and sse genes. Other genes in this category included the stress response protein chaperones dnaK and hscC.
For the two noteworthy functional categories in the planktonic phenotype, namely
“Amino Acid Biosynthesis” and “Cell Envelope”, the genes did not seem to be highly related to any one particular pathway. The only exceptions were the rfa and rfb genes known to be involved in lipopolysaccharide (LPS) O-antigen biosynthesis. LPS has been extensively studied as one of the main virulence factors of Gram-negative bacteria where it is a major component of the outer membrane. It consists of three parts: the lipid A, which is hydrophobic and forms the outer leaflet of the outer membrane bilayer; the core oligosaccharide; and the O side chain also called the O-antigen. The lipid A part is responsible for the endotoxin activity and is involved in the interaction of the cell with the host (Khan et al., 1998). The O-antigen has been shown to function as a barrier 65 against complement mediated lysis (Hackett et al., 1987) and also plays a role in resistance to killing by the microbiocidal intracellular granules of polymorphonuclear leukocytes (Stinavage et al., 1989). The lipid A and core are highly conserved structurally and genetically within a genus. The O-antigen comprises chains of repeat units of either the same or different sugars and varies considerably among bacterial species with respect to chemical composition, structure, and antigenicity. The genes directing O-antigen biosynthesis are clustered mainly in the rfa, rfb and rfc regions of the bacterial chromosome.
In an attempt to discern further metabolically-related differences, significantly expressed genes were sorted according to locus position and scanned for clustering patterns which potentially signified unified operon expression (Sabatti et al., 2002).
Although this technique was not strictly performed according to the Bayesian classification technique implemented by Sabatti et al. (2002), it did prove to be a useful analysis method and several additional pathways were identified which the EASE functional category analysis was unable to resolve.
The first pathway found to be significantly up-regulated in the Salmonella
Missouri biofilm phenotype was the well known central mechanism involved in biofilm formation through curli and cellulose synthesis via the regulation of CsgD (Fig. 12).
Using the operon-linked expression (OLE) technique, it was confirmed that the csg operon was highly up-regulated in the biofilm phenotype, including the gene coding the
GGDEF domain-containing protein AdrA. From here, the search parameters were 66
widened to detect operons associated with the synthesis of exopolysaccharides in
Salmonella (refer to Fig. 2).
Figure 12. Expression patterns of genes involved in polysaccharide and curli fimbriae synthesis. Also included is a gene thought to be associated with cyclic-di-GMP levels in the cell where this molecule has impact on CsgD regulation. Red bars indicate up- regulation during planktonic growth while green bars represent up-regulation during biofilm growth. The degree of differential expression is shown by the observed d-score as determined by SAM. The SAM Δ was 0.14365146, false significant genes (median) was 584.05314 and FDR (median) was 18.64198%. Black dividing lines separate genes occurring within distinct operons. A = succinate dehydrogenase (sdh); B = fructose bisphosphate aldolase (fba); C = glucose phosphate isomerase and mutase (pgi and pgm respectively); D = mannose dehydratase (gmd); E = colanic acid synthesis (wca); F = enterobacterial common antigen and lipopolysaccharide synthesis (wec and rff respectively); G = cellulose synthesis (yhj or bcs); H = curli subunit genes (csg); I = agfD-dependent regulator (adrA); J = glycine activity (gly). 67
In contrast to experiments mentioned previously in which Salmonella has been
studied in the biofilm mode of growth where cellulose appears to be the predominant
component of the EPS, it was found that succinate dehydrogenase genes (sdh) in the
tricarboxylic acid cycle and subsequent genes involved in the mannose degradation
pathway, gmd, and synthesis of colanic acid, wca operon, were more highly expressed in
the biofilm. Genes involved in cellulose biosynthesis (bcs or yhj) were primarily up- regulated in planktonic cells. These results also confirmed the EASE-identified results that genes involved in LPS (rfa, rfb and rff) and ECA (wec) were up-regulated in planktonic cells.
The next major operons examined were those known to be associated with virulence in Salmonella. It was observed that multiple operons previously shown to be involved in the initial stages of virulence in murine models, namely the SPI-1, were up- regulated in planktonic cells while the virulence genes on SPI-2, involved in systemic persistence, were up-regulated in the biofilm phenotype (Fig. 13). 68
Figure 13. Changes in levels of gene expression in four Salmonella Pathogenicity Islands (SPI) and the spv operon on the Salmonella Pathogenicity Plasmid (PSLT). Red bars indicate up-regulation during planktonic growth while green bars represent up-regulation during biofilm growth. The degree of differential expression is shown by the observed d- score calculated by SAM. The SAM Δ was 0.14365146, false significant genes (median) was 584.05314 and FDR (median) was 18.64198%. Black dividing lines separate genes occurring within distinct operons. A = spv; B = SPI-5; C = SPI-2; D = SPI-1; E = SPI-3.
The OLE search was broadened to include genes on the PSLT (Fig. 14). A striking predominance (52%) of highly up-regulated genes was observed under planktonic culture conditions while only 21% of genes on the PSLT were associated with the biofilm phenotype. Curiously, the spv operon, located on the PSLT and normally co- regulated with SPI-2, was up-regulated in the planktonic phenotype (Fig. 13). The majority of significantly expressed (FDR 0.08572%) genes within the PSLT up-regulated 69 under planktonic growth conditions were associated with DNA replication, plasmid partitioning and conjugative transfer.
Figure 14. Distribution of gene expression on the Salmonella Pathogenicity Plasmid (PSLT). Significance was determined by SAM observed d-scores with q-values of less than 5% (except 4 genes included in the biofilm count and 6 genes included in the planktonic count). The SAM Δ was 0.14365146, false significant genes (median) was 584.05314 and FDR (median) was 18.64198%. The total number of genes currently identified on the PSLT is 111. Of these 9 genes are not yet annotated but are included as insignificant for the sake of completeness.
Possibly the most interesting result discovered using the OLE technique was the significance of the cbi-cob-pdu operon (Fig. 15). Although it was found some of these genes using the EASE functional category analysis, most of the genes associated with this pathway were unaccounted for. Since more than 1% of the entire Salmonella genome is devoted to genes involved in this pathway, one would expect there to be great importance of these genes in the survival of this pathogen in the environment. Furthermore, since
Salmonella is likely to spend more of its time associated as a biofilm in the natural 70
environment, one would expect this pathway to be strongly up-regulated in the biofilm
phenotype, as identified here.
2.5
1.5
0.5 pta ttrS ttrC ttrB ttrA cbiJ fucI cbiP cbiF cbiL cbiT cbiE fucP cbiC cibB fucR pduJ cbiO cbiQ cbiN prpE cbiK cbiH cbiG cbiD cbiA cobS fucO fucA fucK fucU prpD cobT pduP pduS pduF cbiM pduT ackA pocR pduE pduL cobU pudB pduC pduN pduO pduQ pduA pduD pduG pduH pduK pduU pduV pduX pduM pduW Score ‐0.5 Observed
SAM ‐1.5
‐2.5
‐3.5
A B C D E F G ‐4.5 Figure 15. Gene expression patterns in the 1,2-propanediol utilization operon (pdu), cobalamin synthesis operon (cbi-cob) and tetrathionate reductase operon (ttr). The transcriptional regulator pocR and 1,2-propanediol diffusion facilitator pduF are also included although these genes were not significantly expressed in either the biofilm or planktonic cultures. Also included are two additional operons encoding enzymes (phosphotransacetylase propionate kinase and propionyl-CoA synthetase) involved in 1,2-propanediol degradation. Red bars indicate up-regulation during planktonic growth while green bars represent up-regulation during biofilm growth. The degree of differential expression is shown by the observed d-score calculated by SAM. The SAM Δ was 0.14365146, false significant genes (median) was 584.05314 and FDR (median) was 18.64198%. Black dividing lines separate genes occurring within distinct operons. A = propionyl-CoA synthetase (prp); B = tetrathionate reductase (ttr); C = cobalamin synthesis (cob-cbi); D = propanediol utilization transcriptional regulator (pocR) and propanediol diffusion facilitator (pduF); E = propanediol utilization and polyhedral body formation (pdu); F = housekeeping enzymes; G = L-1,2-propanediol oxidoreductase and fucose genes (fuc). 71
Using the OLE technique, it was demonstrated that all the genes involved in the
anaerobic utilization of 1,2-propanediol via the cobalamin-dependent reaction were
almost exclusively up-regulated in the biofilm phenotype. These included the pdu genes
with dehydratase activity as well as those involved in polyhedral body formation; the cbi-
cob vitamin B12 adenosyl cobalamide precursor biosynthetic genes; the prp putative
acetyl-CoA synthetase genes; the ttr tetrathionate reductase genes involved in making
tetrathionate available as an electron acceptor through the reduction to thiosulfate; and
housekeeping genes ackA and pta. It was not demonstrated that the transcriptional
regulators pocR and pduF were significantly expressed under either growth condition. In
addition, several of the key genes involved in the ethanolamine (eut) degradation
pathway were up-regulated (data not shown) as were genes in the fucose-related (fuc)
operon.
Conclusions
In the current study, a full genome transcriptional analysis of an environmental
isolate, Salmonella enterica serotype Missouri, was undertaken to determine whether
significant gene expression pattern differences could be identified between the biofilm and planktonic phenotypes. Previous studies have indicated that Salmonella is
successfully able to regulate its response to environmental fluxes by altering
transcriptional control of discreet biochemical and physiological pathways (Adkins et al.,
2006). In particular, the response to changing conditions during host infection has been
studied and several key pathways have been identified as being central to Salmonella’s
pathogenicity and ability to survive within the host and persist under adverse conditions 72
(Bajaj et al., 1996; Hautefort et al., 2008). However, the lifecycle of Salmonella is not
limited to host infections and this pathogen has demonstrated a ubiquitous nature within
the environment. And although Salmonella is classified within the Enterobacteriaceae,
this pathogen appears to spend a major portion of its existence in non-host environments
(Labrousse et al., 2000; Pagnier et al., 2008; Tezcan-Merdol et al., 2004) and has
developed several key traits which allow it to persist and grow under potentially stressful
conditions (Leriche and Carpentier, 1995; Reissbrodt et al., 2002; Smith and Oliver,
2006).
Salmonella Missouri was the pathogenic agent responsible for an outbreak of
waterborne salmonellosis in Gideon, MO during the Christmas of 1993 (Clark et al.,
1996). This pathogen demonstrated tenacious pathogenicity, causing illness in over 40%
of the population and mortality in 7 people. An epidemiological study determined that the
source of contamination was an uncovered water storage tank which had been
contaminated by pigeon stool. That this pathogen was able to survive in the drinking water distribution system and cause infection over several weeks is evidence of its
adaptation to survive in certain ecological niches.
It was observed that this strain of Salmonella exhibited a rapid growth rate under
minimal, suboptimal growth conditions and that it was able to establish an observable
biofilm in overnight cultures, a trait not usually observed in typically less virulent enteric
pathogens (Andersson et al., 2008; Mohamed et al., 2007). On subsequent transcriptional
analysis of this organism grown either as a planktonic or biofilm culture, distinct patterns 73
were observed which may explain the ability of this organism to survive in the non-host environment.
Initial analysis using EASE to distinguish biologically relevant pathways in the two phenotypes was not particularly useful owing to the apparent inability of the EASE
algorithm to resolve important functional categories in Salmonella. This may be due to
the large number of genes on the Salmonella genome which have yet to be assigned to descriptive functional categories. Although the microarray used in this study was based on the combined annotated genomes of Salmonella Typhimurium LT2 and Salmonella
Typi CT18 and Ty2, there is still 5.92%, 7.93% and 4.51% respectively of each of
the genomes which have not yet been assigned to functional categories (not even
“Unclassified” or “Unknown function”). Nevertheless, the observation that the genes
within the categories “Energy Metabolism”, “Protein Fate” and “Unclassified” were for a
large part interrelated, and this method served as a launchpad for analysis.
Most interesting was the observation that the 1,2-propanediol utilization pathway was strongly up-regulated in the biofilm phenotype. This pathway has been the subject of several studies (Bobik et al., 1999; Chen et al., 1994; Jeter, 1990; Obradors et al., 1988;
Roth et al., 1996) and has been suggested to confer strategic niche advantage to this pathogen in terms of outcompeting natural host intestinal flora and survival in the fermentative environment of the gut (Korbel et al., 2005; Scott et al., 2006). In addition, the ability of an organism to utilize this breakdown product of the ubiquitous plant sugar, rhamnose, as the sole carbon and energy source under anaerobic conditions may reflect an important survival strategy in the non-host environment. However, since the only 74
carbon source made available in these experiments was glucose, it is suggested that
Salmonella Missouri has the ability to convert glucose to 1,2-propanediol via glycolysis
(Altaras et al., 2001; Cameron et al., 1998; Ros and Aguilar, 1985) under the largely
anaerobic conditions of the biofilm (Costerton et al., 1994; De Beer and Stoodley, 2006).
Evidence for this glucose to 1,2-propanediol conversion may be demonstrated by the up-
regulation of the fuc operon which includes genes responsible for encoding a propanediol
oxidoreducatse and some of the eut operon, highly similar to the pdu operon in that it
encodes a carboxysome-like structure to protect the cell from acetaldehyde during the
fermentation of ethanolamine (Price-Carter et al., 2001; Starai et al., 2005).
Furthermore, the apparent co-evolution of the pdu and eut operons with the ability
of Salmonella to synthesize vitamin B12 de novo under anaerobic conditions may
represent a further important niche advantage (Roth et al., 1996; Sampson and Bobik,
2008). Biofilms also represent a competitive strategy by microbes in the environment
(Boe-Hansen et al., 2002; Esteves et al., 2005). Taken together with the observations that these operons were significantly up-regulated in the biofilm phenotype strongly suggests that Salmonella has developed the ability to form a biofilm in the environment and may outcompete other microbes including the closely-related E. coli by accessing specialized biochemical pathways for carbon utilization.
Although by no means involved in biofilm-exclusive physiology, that an almost complete complement of hydrogenase 3 (hyc/hyp) complex was expressed in the biofilm phenotype indicates the advantage of this energy-generating complex. In addition, since the buildup of reducing equivalents and acidification in microniches in the biofilm may 75
represent disastrous consequences for the microbe, the ability of hydrogenase to mitigate
this stress may be highly beneficial. Biocorrosion as a result of hydrogenase activity in
biofilm communities has been reported (Vignais and Colbeau, 2004). Since Salmonella
has been conclusively demonstrated to inhabit aquatic environments and be entrained in
biofilms in drinking water distribution systems (Camper et al., 1998) and wastewater
treatment plants (Berge et al., 2006), this biocorrosion aspect of its physiology may
represent another area of necessary investigation.
Similarly, the orchestrated expression of NADH dehydrogenase I (nuo) genes
may represent an important biofilm-associated feature of Salmonella physiology and
virulence. Since it has been demonstrated that nuo plays a critical role in biofilm
formation and virulence of the plant pathogen, Pseudomonas fluorescens (Carvajal et al.,
2002), it is suggest that Salmonella may also use this energy-generating oxidoreductase to promote its survival in the biofilm phenotype in the non-host environment.
Corroboratory data that may be viewed as confirmation of the effectiveness of this
microarray study to elucidate pathways within the biofilm and planktonic phenotypes
come from the observations of the up-regulation of the csgD gene and related pathways.
Far and away the bulk of genetic studies carried out on Salmonella biofilms have
centered around the activity of this gene and related operon (Brombacher et al., 2006; Da
Re and Ghigo, 2006; Gerstel and Romling, 2003; Gibson et al., 2006; Kader et al., 2006;
Latasa et al., 2005; Prigent-Combaret et al., 2001). That the up-regulation of this operon
during biofilm growth of Salmonella Missouri was observed confirms its almost global
relatedness to the biofilm phenotype. However, more interesting was the fact that the 76 expression of cellulose synthetic genes were not observed in the biofilm phenotype but rather in the planktonic cultures of Salmonella Missouri, indicating that perhaps in this strain of the pathogen, cellulose may not be the predominant component of EPS in the biofilm matrix. This was further demonstrated when the search for known EPS matrix components was broadened and the up-regulation of genes in the mannose and colanic acid operons was demonstrated. This may be understood in the context of a pH-related shift, colanic acid being more stable under conditions found in the gastrointestinal tract than cellulose (Mao et al., 2006).
Although no assays for cyclic-di-GMP levels in the cells growing in the two different phenotypes were performed, it is suggested that cyclic-di-GMP levels were elevated in the biofilm cells. This is based on current opinions in the biofilm literature
(Romling and Amikam, 2006; Tamayo et al., 2007) and the fact that the up-regulation of adrA which encodes a GGDEF domain protein was observed.
The significantly observed “Protein Fate” category in EASE analysis of the TIGR biological roles contained several proteins which are located on the SPI-2, namely those effector and structural proteins associated with the second TTSS in Salmonella. In vivo, this pathogenicity island has been demonstrated to enhance persistence of the pathogen and establish systemic infection. Mutational analysis has revealed that knockouts within this island attenuate virulence and the infection was cleared by the immune system more rapidly than in wild-type infections (Cirillo et al., 1998; Rytkonen et al., 2007).
Furthermore, several aspects of the establishment of a systemic infection reflect the biofilm lifestyle, including protection from oxidative stress, competition for limiting 77 nutrients such as iron and magnesium, and long-term survival. It is suggested that perhaps this horizontally-acquired pathogenicity island may confer more than simply a virulence ability upon Salmonella within the host. Considering the metabolic tax involved in expressing this pathway, and the space occupied on the genome by this suite of genes, it is unlikely that Salmonella has maintained functionality of this complex exclusively for its survival in the host environment. Rather it is conceivable that there is a multipurpose usefulness for this island. Tezcan-Merdol et al. (2004) showed that while hilA, a key regulator in SPI-1-mediated invasion, was not required to establish persistence of
Salmonella in Acanthamoeba rhysodes, they suggest that SPI-2 may play a role in survival in the amoeba. More directly, Labrousse et al. (2000) have demonstrated that
SPI-2 does plays a role in the ability of Salmonella to exist within the model host
Caenorhabditis elegans, where the pathogen forms a biofilm-like structure in the intestine and terminal bulb of the pharynx of the nematode. In addition, Chakravortty et al. (2002) demonstrated that SPI-2 played a direct role in protecting Salmonella from the deleterious effects of reactive nitrogen intermediates synthesized by inducible nitric oxide synthase and which are involved in the control of intracellular pathogens, including
Salmonella. Furthermore, localization of nitrotyrosine residues in the surroundings was observed for SPI-2 mutant strains but not wild-type Salmonella, indicating that peroxynitrite, a potent antimicrobial compound, is excluded from Salmonella-containing vacuoles (SCV) by action of SPI-2. Since Salmonella may encounter similar reactive nitrogen intermediates in the natural environment as well as in food processing plants where nitric oxide is gaining popularity as a preservative (Fan et al., 2008), and 78
considering that the results show SPI-2 up-regulated in the biofilm phenotype, an
intrinsically recalcitrant lifestyle for any pathogen, this may prove to be an interesting
niche adaptation worth future study.
Concomitantly with the expression of SPI-2 in the biofilm phenotype, expression
of other pathogenicity islands (SPI-1, -3 and -5) in the planktonic phenotype was observed. Since the primary function of SPI-1 during host infection is to attach to and invade epithelial cells lining the gut, intuition would suggest that this set of genes would
be more likely expressed in the biofilm phenotype. However, it may be that these genes
were switched on under the iron-limiting conditions of the M9 minimal media and are not
necessarily a true planktonic phenotype expression. An alternative explanation is that
SPI-1 effector proteins may play a tactic role in Salmonella, aiding in locating a suitable
attachment surface. Curiously, the spv operon which is usually concomitantly expressed
with SPI-2, was up-regulated in the planktonic phenotype, while the SPI-2 was down-
regulated. However, too little is still known about this operon to comment on its
biological significance (Tezcan-Merdol et al., 2007).
In conclusion, this transcriptional study of Salmonella Missouri in the biofilm and planktonic phenotypes may reveal an accurate representation of the behavior of a virulent isolate of Salmonella in the non-host environment. The identification of some of the key
biological pathways characterizing the biofilm phenotype of Salmonella may hold clues
to better understanding the ability of this pathogen to survive in the environment and
persist outside of the host for long periods of time, competing for nutrients, dealing with 79
oxidative stress and overcoming predation, all of which mirror similar traits demonstrated by this organism in establishing infection in the human host. 80
CHAPTER 4
A TRANSCRIPTIONAL COMPARISON OF SALMONELLA TYPHIMURIUM LT2
AND AN ENVIRONMENTAL ISOLATE OF SALMONELLA ENTERICA
Introduction
The recent surge of Salmonella outbreaks in the United States associated with
improperly handled foodstuffs has highlighted the need for more research into the environmental reservoirs, lifestyle and survival of this pathogen (Kaye, 2008;
McDonough et al., 1999). Several divisions within the National Institute of Allergy and
Infectious Diseases (NIAID) currently support programs under the banner “emerging infectious diseases” (EIDs). Emerging diseases include outbreaks of previously unknown diseases or known diseases whose incidence in humans has significantly increased in the
past two decades. Re-emerging diseases are known diseases that have reappeared after a
significant decline in incidence. Re-emergence may be due to several factors including
the development of multidrug resistance by the pathogen and human behavior in terms of
reckless regard for the environment (Vidaver, 1996). In the NIAID strategic plan (2008),
NIAID: Planning for the 21st Century, it was documented that NIAID had recently joined
with several other US Government agencies to support research on the relationship
between man-made environmental changes and transmission of infectious diseases. The
intent was that future NIAID-supported studies would focus on whole-genome
approaches to pathogen research, including large-scale sequencing, bioinformatics and
functional genomics. Such investigations would hopefully provide tools critical to the 81 study of microbial evolution, adaptation and pathogenicity. Salmonella is listed as one of these re-emerging infections
(http://www3.niaid.nih.gov/research/topics/emerging/list.htm) and the primary focus of most of this research is in keeping with the NIAID directive to understand the pathobiology of Salmonella within the context of the non-host environment.
Interest in comparing the well-studied and characterized ATCC type strain of
Salmonella enterica serotype Typhimurium LT2 with a closely related environmental isolate Salmonella enterica serotype Missouri arose from observations of the differences in growth behavior of the two organisms. In addition, current thinking suggests that frequently passaged laboratory reference strains might have lost important pathophysiological characteristics and therefore might be inadequate to document ‘real- world’ pathogenesis (Fux et al., 2005; Nilsson et al., 2004; Somerville et al., 2002).
Furthermore, the close link between horizontal gene transfer and biofilm formation is being increasingly recognized (Schwartz et al., 2003). These observations of impaired biofilm formation by laboratory reference strains compared with clinical strains might indicate further-reaching genetic alterations affecting bacterial virulence on a broader level.
Materials and Methods
Strains and Growth
The strains of Salmonella used in this study were the ATCC type strain No.
700720, Salmonella enterica serotype Typhimurium LT2 and an environmental isolate from an outbreak in Gideon, MO, USA in 1993 (Clark et al., 1996). The latter was a 82
highly virulent strain of Salmonella enterica, typed by PGFE at the CDC in Atlanta, GA,
USA and has been designated Salmonella Missouri in this paper. Sequence analysis of the 16S rDNA gene was also performed (Research Technology Support Facility,
Michigan State University using a Perkin Elmer/Applied Biosystems 3100 capillary sequencer) to confirm the identities of both these organisms. Primers used to amplify a highly conserved region of the 16S rDNA gene covered an area of approximately 1500 base pairs. These primers have been used regularly in this lab and are designated 8F and
1492R (Burr et al., 2006).
Planktonic growth rates were determined in M9 Minimal Media (Becton-
Dickinson, MD) with the addition of 0.4% glucose (Fisher Scientific, NJ) as the carbon
source (Ren et al., 2005). This was the defined medium used in all subsequent
experiments unless otherwise indicated. All cultures, both planktonic and biofilm, were
grown at an ambient temperature of 23°C. For each new experiment, the relevant strain of
Salmonella was freshly prepared from a cryostock which had been maintained at -80°C
with minimal passaging.
In order to determine growth rates, a starter culture of the organism was prepared
by inoculating an overnight colony grown on XLD agar (EMD, NJ) into 100 mL volumes
of M9 + glucose in 250 mL baffled flasks (Pyrex, USA) with orbital shaking of 180 rpm.
These starter cultures were allowed to grow up for 24 hours at which point 100 µL was
inoculated into 100 mL fresh media in a 250 mL Nephelo flask (Wheaton, USA) and
these flasks were returned to the orbital shaking platform at 180 rpm. Optical density was 83
determined every 4 hours using a Spectronic 20D+ spectrophotometer (Thermo Electron
Corporation, MA) reading at a wavelength of 600 nm.
Planktonic cultures were grown under the same conditions as used in determining
experimental growth rates. For microarray experiments, cultures were harvested at 12
hours (empirically determined to be mid- to late-logarithmic phase for both strains of
Salmonella).
Biofilm cultures of each of the strains of Salmonella were obtained using the
CDC biofilm reactor (www.biofilms.biz) with glass coupons serving as surfaces for attachment. CDC reactors were preconditioned with sterile M9 + glucose for 24 hours in batch mode to ensure sterility of the media and equipment. An inoculum of 1mL
Salmonella grown up as described previously for the preparation of a growth curve experiment was aseptically introduced through a rubber injection septum and an 18 hour
batch mode was allowed in order to facilitate establishment of the culture in the reactor.
This period of batch growth was followed by switching on the pump and allowing fresh
media to flow into the reactor with a hydraulic retention time of 7.6 hours to ensure that
planktonic bacteria were washed out and the biofilm bacteria predominated.
Biomass Harvesting
For planktonic samples, 50 mL of a 12 hour culture was centrifuged at 4°C for 10
minutes at 10,000 x g. The supernatant was removed and the pellet was resuspended on
ice in a 1:1 mixture of 400 µL RNA Buffer A (50 mM sodium acetate, pH 5.5; 10 mM
EDTA, pH 8.0; 1% SDS) and 400 µL acidic phenol:chloroform (pH 4.5) (Ambion, TX). 84
For biofilm samples, biofilm material was scraped off three coupon surfaces
using a cell scraper (Fisher Scientific, NJ) into equal volumes of RNA Buffer A and
acidic phenol:chloroform.
RNA Purification
Several methods of RNA purification were attempted, including TRIzol
(Invitrogen, CA), RNA Power Kit for Soils (MoBio, CA) and RNeasy (QIAGEN, MD), before settling on the following optimized technique.
The phenol mixtures were transferred to Lysing Matrix Tube E (MPBio, OH) and
treated in a FastPrep Bead Beater FP120 (Bio101 Savant, NY) for 30 seconds at 5.5 rpm.
Samples were centrifuged at 4°C for 30 minutes at 14,000 x g.
Phenol was removed using successive chloroform extractions in 2mL Phase Lock
Gel (PLG) Heavy tubes (Eppendorf, NY). All steps were subsequently performed quickly
and at room temperature. Briefly, the aqueous (top) phase of each sample was transferred
into a prespun (13,000 x g for 2 minutes) PLG Heavy tube to which 200 µL acidic
phenol:chloroform and 200 µL chloroform:isoamyl alcohol (Amresco, OH) was added.
The tubes were inverted gently to mix and incubated on ice for 10 minutes. Tubes were
then centrifuged at 13,000 x g for 5 minutes. A further 400 µL chloroform:isoamyl
alcohol was added, the tube was inverted to mix and centrifuged at 13,000 x g for 5
minutes.
The aqueous phase was then transferred to a new RNase-free tube and finally
treated with TURBO DNase (Ambion, TX). Briefly, a 0.1 volume of 10x TURBO DNase
Buffer was added to the sample followed by the addition of 5 µL TURBO DNase. 85
Samples were mixed gently by flicking the tubes and incubated at 37°C for 20 minutes.
Activity of the enzyme was inhibited by the addition of 0.1 volumes of resuspended
DNase Inactivation Reagent (Ambion, TX). The sample was incubated at room temperature for 2 minutes with regular, gentle mixing and finally centrifuged at 10,000 x g for 1 ½ minutes to pellet out the DNase Inactivation Reagent. The supernatant was transferred to a fresh RNase-free tube.
Finally the sample was cleaned up using a modified protocol of an RNeasy Clean- up Reaction (QIAGEN, MD). Briefly, aliquots of 200 µL RNA were mixed with 700 µL
RLT Buffer (QIAGEN, MD) followed by the addition of 500 µL absolute ethanol.
Volumes of 750 µL were loaded onto an RNeasy Column (QIAGEN, MD) and centrifuged at room temperature for 15 seconds at 10,000 x g. The eluate was discarded and subsequent volumes of RNA were loaded onto the same column until all the sample had been run through. The columns were then washed twice with Buffer RPE (QIAGEN,
MD) and RNA was eluted in two successive 50 µL volumes of RNase-free water. Yield was determined by spectrometry on a Nanodrop 1000 (Nanodrop Technologies, DE) and quality was assayed by a 2100 Bioanalyzer (Agilent, CA).
DNA Microarray Transcriptional Profiling
RNA was reverse transcribed into cDNA and indirectly labeled according to
SOP#: M007 released by PFGRC, JCVI
(http://pfgrc.jcvi.org/index.php/microarray/protocols.html). Briefly, 5 µg RNA was reverse transcribed using SuperScript III (Invitrogen, CA) with a 0.5 mM 5-(3- aminoallyl)-dUTP:dTTP (Sigma, MO) for 18 hours. The optimal ratio of aa-dUTP to 86 dTTP varies depending on the GC content of the organism in question. Organisms with high GC content, such as Pseudomonas aeruginosa PAO1 which has a GC content of
66%, generally require a lower aa-dUTP to dTTP ratio. Organisms with low GC content, such as Streptococcus pyogenes M1 GAS and Bacillus anthracis strain Sterne which have
GC contents of 38% and 35% respectively, usually require a higher aa-dUTP to dTTP ratio. Since Salmonella Typhimurium LT2 has a GC content of 52% (compared with the
E. coli K12 GC content of 50%), 2:1 ratio of aa-dUTP:dTTP was decided upon. This first strand cDNA synthesis reaction was stopped and remaining RNA degraded by alkaline hydrolysis with sodium hydroxide and neutralization with TRIS.
Removal of unincorporated aa-dUTP and free amines was achieved using a modified protocol from the QIAGEN MinElute PCR purification kit (QIAGEN, MD).
These modifications included the substitution of a 5 mM phosphate wash buffer pH
8.5/80% ethanol for the kit wash buffer and nuclease-free water for the elution buffer.
These substitutions were made to avoid contamination with free amines which compete with the aa-dUTP in the subsequent Cy-dye coupling reaction.
The clean-up step was followed by drying for 30 minutes at 60°C in a CentriVap
DNA Vacuum Concentrator (Labconco, MO). Dried probes were then indirectly labeled with Cy3 or Cy5 (Amersham, NJ). Briefly, aminoallyl-labeled cDNA was resuspended in
4.5 µL 0.1 M sodium carbonate buffer, pH 9.3. This was followed by the addition of the appropriate DMSO-resuspended Cy dye and an incubation of between 1 and 2 hours at room temperature in the dark. After coupling was complete, 20 µL 4.5 M sodium acetate pH 5.2 (Ambion, TX) was added. Two important aspects of this step to note include the 87
thorough resuspension of the dried probe before the addition of the Cy dye as well as
adhering to the prescribed pH 9.3 of the sodium carbonate buffer to ensure optimum
coupling of the aminoallyl-labeled cDNA to the Cy dye ester.
Labeled cDNA was purified using the MinElute PCR Purification kit (QIAGEN,
MD) according to manufacturer’s instructions. Analysis was performed to ensure
optimum yield and labeling efficiency using the “Microarray” function of a Nanodrop
1000 (Nanodrop, DE). For each sample, the total picomoles of cDNA synthesized was
determined using the following formula:
μ 37 /μ 1000 / 324.5 /
For each sample the total picomoles of dye incorporation (Cy3 or Cy5) was
determined using the following formula:
μ 3 0.15
μ 5 0.25
And finally, the incorporation ratio of cDNA to dye was determined using the formula:
#
88
Theoretically required limits were set at > 800 pmol of dye incorporation per
sample and a dye incorporation ratio of < 20 in order to obtain optimal microarray
hybridizations.
Following analysis, the two differentially labeled cDNA’s (Cy3 and Cy5) were
mixed and dried for 30 minutes at 60°C in a CentriVap DNA Vacuum Concentrator
(Labconco, MO). Dried probes were stored at -80°C.
Hybridization was performed according to SOP#: M008
(http://pfgrc.jcvi.org/index.php/microarray/protocols.html) using 70-mer spotted
Salmonella Typhimurium/Typhi Version 5 arrays from the PFGRC, JCVI. These
microarrays were designed on Salmonella enterica serotype Typhimurium LT2,
Salmonella enterica serotype Typhi CT18 and Ty2. Oligonucleotides (single stranded 70- mers) were designed based on open reading frame sequences across all three genomes of the microarray and did not necessarily represent a single oligo from one particular strain.
The oligonucleotides were designed to provide coverage across all the organisms used in the creation of the microarray. The number of open reading frames used in the design of the microarray were 4553, 4395 and 4323 and the number of oligonucleotide sequences designed were 4504, 926 and 32 for LT2, CT18 and Ty2 respectively. This yielded a total number of oligonucleotide sequences of 5462. Each oligo was replicated four times on the slides. Additionally, each slide contained 10 Arabidopsis thaliana amplicons and 500
A. thaliana 70-mers as controls. The total number of elements on the array (minus empty spots) was 23888. The PFGRC Universal Microarray Standard Set was used as an internal control. These standards consisted of a mix of 1000 Cy-dye end labeled 40-mer 89 probes (500 Cy3 and 500 Cy5) complementary to the 500 A. thaliana 70-mer control spots. The control probe mix was routinely spiked into the experimental probe mix immediately before hybridization to the microarray. Spots associated with the PFGRC
Universal Microarray Standard Set have the designation “Atg1” on the annotation sheets used during data analysis. Hybridized slides were incubated at 42°C overnight, washed in increasing stringency buffers and finally scanned using a GenePix 4000B microarray scanner (Molecular Devices, CA) to generate 2-color 16-bit TIFF images. If slides could not be scanned immediately, they were stored in the dark in the final high stringency wash buffer with 10 mM DTT (to act as an ozone scavenger), however it was observed that storage in this manner only yielded acceptable results for up to 3 hours before washout of the dye occurred. Five hybridizations were performed for each of the
Salmonella strains. Three hybridizations were biological replicate planktonic/biofilm pairs and two hybridizations (technical replicates) were dye swaps (flip dyes), performed as part of overall quality assurance.
Data Analysis
Processing of the 16-bit TIFF images from hybridized arrays was performed with the TIGR TM4 package (Saeed et al., 2003). Intensity values for Cy3 and Cy5 channels were obtained using TIGR Spotfinder software. Normalization was performed with the
LOWESS algorithm available in TIGR MIDAS, using the global mode and a smoothing parameter of 0.33. All intensity values less than two times greater than background were removed from subsequent analysis, and quadruplicate in-slide replicate intensities on 90
each slide (considered a further one technical replicate) were reduced to a single value by
computing the geometric mean.
To determine genes whose expression was significantly different from zero,
significance analysis of microarrays (SAM) software (incorporated within the TIGR TM4
package) was employed using the one-class response with 8 unique permutations. This
analysis was performed separately for each of the two individual strains. While the three biological replicates were used for final analysis, two additional flip dye technical
replicates were also compared to observe any irregularities. None were observed.
Significant genes were determined by setting the number of median falsely called genes
to less than one and choosing similar false discovery percentage medians for each
biological replicate. At these levels, the q-values (a measure of significance in terms of
the false discovery rate) for all biological replicates were less than 0.1%. In order to
determine subsets of shared or different genes between the two strains (Salmonella
Missouri and Salmonella Typhimurium LT2) and in the two conditions (biofilm and
planktonic), the intersection function was used on significantly expressed clusters in
TMEV (Saeed et al., 2003) and generated Venn Diagrams using Venny (Oliveros, 2007).
Each SAM plotsheet contains all the genes plotted by their observed scores and
expected scores. The observed score is the relative difference in gene expression. It is
calculated by dividing the difference between gene relative abundances in the biofilm and
planktonic samples by the pooled standard error of repeated measurements of that gene in
the two samples. The expected score is calculated using the large set of permutations of 91
gene relative abundance data of the biological replicates from the biofilm and planktonic
samples.
The observed score provides a control over random fluctuation, while the
expected score allows assignment of statistical significance. The correlation of these two
scores is used for identifying genes with potentially significant differential expression. If a gene has absolutely no differential expression, the observed relative difference would be the same as the random fluctuation that is represented by the expected score. The data point of such a gene in the SAM plotsheet would fall on the 45° line through the origin.
Data points representing differentially expressed genes will deviate from this 45° line.
The point displacement of a gene from the 45° line through the origin is quantitatively measured by a delta (Δ) value in SAM. Genes with Δ values beyond a certain threshold are called significant. The 45° upper and lower Δ lines indicate the boundary defined by a selected Δ value.
A fold change limit of 1.5 was also applied to significant genes (subsequent to
SAM-applied Δ values) in order to further gauge the magnitude of change. However, since fold change is somewhat arbitrary, especially when attempting to ascertain significant biological roles, imposing a typical 2-fold criterion which removes from consideration a gene with a 1.9 fold change that is really key to a biological mechanism, could alter the interpretation of a study. Therefore data before fold change limits were applied is primarily reported.
Expression Analysis Systematic Explorer (EASE) (incorporated within the TIGR
TM4 package) was used on subsets of genes determined to have significant changes in 92
expression as identified by the SAM analysis. EASE uses a modified Fisher exact test
(EASE score) to estimate the significance of classes of biological function present in a
subset of significant genes relative to the total as represented on the array. TIGR role categories (http://cmr.jcvi.org) determined as part of the whole-genome annotations of
Salmonella enterica serotype Typhimurium LT2, Salmonella enterica Typhi CT18 and
Ty2 were used as the biological classes examined for over-representation in the lists of
significant genes and for all annotation referred to in this study. Although only biological
classes with EASE scores of ≤ 10-3 are considered significant, all results are reported for
completeness.
Results and Discussion
The ATCC type strain Salmonella enterica serotype Typhimurium LT2 was first
isolated in Sweden by Lilleengen (1948). Since then, it has been kept in culture at the
American Type Culture Collection (VA, USA).
Figure 16. Photographs of overnight planktonic cultures of Salmonella Missouri (left) and Salmonella Typhimurium LT2 (right). Notice the flocculation ring in the flask with the Missouri isolate. 93
Soon after first receiving the Salmonella Missouri isolate and culturing it in the lab during various experiments, it was noticed that it behaved with a marked difference from the ATCC type strain, Salmonella Typhimurium LT2, that this lab and most other researchers use in their work. Primarily, an increased growth rate was noticed (Fig. 17) at various temperatures and on different media (data not shown), and the flocculation behavior of the bacteria in liquid culture. Routinely during overnight growth in broth, a distinct “scum” ring (Fig. 16) around the inside of the flask in which the bacteria were being cultured was observed. This phenomenon was never observed with Salmonella
Typhimurium LT2.
0.8
0.7
0.6
0.5
0.4 Absorbance
0.3
0.2
0.1
0 0 5 10 15 20 25 Time (hours)
OD600nm Salmonella Missouri OD600nm Salmonella Typhimurium LT2
Figure 17. Growth curves of Salmonella Typhimurium LT2 and Salmonella Missouri based on absorbance at an optical density of 600nm. 94
This flocculation effect was observed in liquid cultures grown in tryptic soy broth,
Luria broth, Rappaport Vassiliadis broth and M9 minimal media. Since this same effect
had been observed previously with dynamic biofilm-forming bacteria (such as
Pseudomonas aeruginosa PAO1 and Staphylococcus aureus), side by side comparisons of Salmonella Typhimurium LT2 and Salmonella Missouri in CDC biofilm reactors were
set up. The results, revealing a thick biofilm formed by the Missouri isolate versus only a thin film by the type strain, prompted the remainder of this study.
Despite the fact that the CDC had initially typed the Missouri isolate via PFGE as
Salmonella typhimurium, preliminary observations suggested distinct differences between
this isolate and the ATCC type strain Salmonella Typhimurium LT2 with which this lab
had worked previously. Subsequently, analysis of 16S rDNA sequence data from the two
strains suggested that the Missouri isolate was more closely related to Salmonella Typhi
and Paratyphi serotypes (Table 4). Through whole genome transcriptomics, it was shown
that in fact when the two organisms were cultured under the same conditions (either
biofilm or planktonic), there were distinct differences in gene regulation. In fact, fewer
than half the genes significantly up-regulated in either the biofilm (39% and 33%
respectively) or planktonic (42% and 29% respectively) phenotypes were shared between
Salmonella Missouri and Salmonella Typhimurium LT2 (Fig. 18).
Of the significantly up-regulated genes in each of the strains under each growth
condition, 55 were diametrically expressed in the planktonic Salmonella Typhimurium
LT2 and biofilm Salmonella Missouri cultures while 41 were diametrically expressed in
the juxtaposed position (Fig. 18). 95
Unique populations of up-regulated genes were also observed: 161 and 170 genes
in the planktonic and biofilm growth phenotypes respectively for Salmonella Missouri; and 307 and 249 genes in the planktonic and biofilm growth phenotypes respectively for
Salmonella Typhimurium LT2 (Fig. 18).
Figure 18. Venn diagram showing significantly up-regulated genes in Salmonella Missouri during planktonic growth (blue) and biofilm growth (green) and in Salmonella Typhimurium LT2 during planktonic growth (yellow) and biofilm growth (red). Total up- regulated Salmonella Missouri genes: Biofilm = 368, Planktonic = 347. Total Up- regulated Salmonella Typhimurium LT2 genes: Biofilm = 433, Planktonic = 507.
In order to ascertain whether there were any significantly different biological themes associated with the uniquely expressed genes for each of the strains in each 96 growth condition, the EASE algorithm was used (Table 5). “Mobile and chromosomal element functions” emerged as a significant role category for biofilm-oriented Salmonella
Typhimurium LT2 cells while “Protein synthesis” emerged as significant for the
planktonic equivalents. “Energy metabolism” was shown to be significant in the biofilm
phenotype of Salmonella Missouri while “Transport and binding proteins” were
significant for the planktonic equivalents.
Table 5. The Institute for Genomic Research functional categories for the entire annotated genome and uniquely expressed genes of the observed transcriptomes for the planktonic and biofilm phenotypes. Shaded cells represent the most significant functional category for each strain and under each growth condition. Since not all genes on the genome have been allocated a specific functional category (not even “Unclassified” or “Unknown function”), the Size columns may not match the values indicated in the Venn diagram in Fig. 17.
Annotated Unique LT2 Biofilm Unique MO Biofilm Unique LT2 Planktonic Unique MO Planktonic TIGR Cellular Main Role Population Population Genes on List Size EASE List Size EASE List Size EASE List Size EASE Category Hits Size a List Hits List Hits List Hits List Hits Genome b Score c Score d Score e Score
Amino acid biosynthesis 132 64 1503 3 156 9.9E-01 9 121 1.3E-01 5 238 9.9E-01 7 106 2.9E-01 Biosynthesis of cofactors, 165 76 1503 4 156 9.9E-01 5 121 8.7E-01 20 238 2.2E-02 6 106 6.3E-01 prosthetic groups, and carriers Cell envelope 489 136 1503 12 156 8.5E-01 11 121 6.6E-01 14 238 9.9E-01 18 106 1.0E-02
Cellular processes 293 100 1503 13 156 3.3E-01 6 121 9.2E-01 20 238 2.2E-01 6 106 8.4E-01
Central intermediary metabolism 169 60 1503 5 156 8.8E-01 8 121 2.0E-01 5 238 9.9E-01 4 106 8.0E-01
DNA metabolism 162 54 1503 7 156 4.9E-01 1 121 1.0E+00 4 238 9.9E-01 3 106 9.0E-01
Energy metabolism 558 184 1503 21 156 4.4E-01 26 121 3.7E-03 23 238 9.5E-01 7 106 9.9E-01 Fatty acid and phospholipid 75 20 1503 2 156 8.9E-01 1 121 1.0E+00 6 238 2.0E-01 0 106 1.0E+00 metabolism Hypothetical proteins 1209 28 1503 5 156 3.3E-01 2 121 9.0E-01 4 238 8.4E-01 2 106 8.7E-01 Mobile and extrachromosomal 243 45 1503 17 156 3.5E-06 3 121 8.9E-01 1 238 1.0E+00 0 106 1.0E+00 element functions Protein fate 192 69 1503 5 156 9.4E-01 2 121 1.0E+00 16 238 1.1E-01 3 106 9.6E-01
Protein synthesis 378 138 1503 6 156 1.0E+00 9 121 8.8E-01 43 238 3.8E-06 4 106 1.0E+00 Purines, pyrimidines, nucleosides, 81 42 1503 3 156 9.4E-01 3 121 8.6E-01 5 238 9.2E-01 3 106 8.1E-01 and nucleotides Regulatory functions 310 84 1503 11 156 3.6E-01 8 121 5.1E-01 13 238 7.0E-01 2 106 1.0E+00
Signal transduction 26 7 1503 1 156 1.0E+00 0 121 1.0E+00 0 238 1.0E+00 0 106 1.0E+00
Transcription 52 26 1503 3 156 7.7E-01 2 121 8.9E-01 10 238 1.4E-02 0 106 1.0E+00
Transport and binding proteins 527 177 1503 14 156 9.4E-01 14 121 6.8E-01 24 238 8.8E-01 23 106 3.7E-03
Unclassified 347 91 1503 13 156 2.2E-01 7 121 7.5E-01 14 238 7.0E-01 8 106 4.5E-01
Unknown function 682 213 1503 24 156 4.4E-01 15 121 8.3E-01 25 238 9.8E-01 14 106 7.5E-01 Viral functions 94 2 1503 1 156 1.0E+00 0 121 1.0E+00 0 238 1.0E+00 1 106 1.0E+00 a actual number of significantly expressed genes was 1655. b actual number of significantly expressed unique LT2 biofilm genes was 249. c actual number of significantly expressed unique MO biofilm genes was 170. d actual number of significantly expressed unique LT2 planktonic genes was 307. e actual number of significantly expressed unique MO planktonic genes was 161. 97
On closer inspection of the uniquely expressed genes within these functional categories, it was found that the majority of the “Transport and binding” category for the
Salmonella Missouri planktonic phenotype consisted of genes involved in a novel outer membrane siderophore receptor (iroN) and iron uptake (fhu). Genes included on the iro operon (STM2773 – 2777) have been demonstrated to mediate utilization of structurally related catecholate siderophores, including N-(2,3-dihydroxybenzoyl)-L-serine, myxochelin A, benzaldehyde-2,3-dihydroxybenzhydrazone, 2-N,6-N-bis(2,3- dihydroxybenzoyl)-L-lysine, 2-N,6-N-bis(2,3-dihydroxybenzoyl)-L-lysine amide, and enterochelin (Baumler et al., 1998). The fhu operon is thought to code for an ABC superfamily transporter involved in hydroxymate-dependent iron transport and uptake.
In the biofilm phenotype of Salmonella Missouri, the majority of uniquely expressed genes were associated with “Energy metabolism” and included hydrogenase 3
(hypc/hyc), NADH dehydrogenase (nuo), 1,2-propanediol utilization (pdu), a glycine cleavage complex (gcv) and maltodextrin-associated (mal) genes.
Genes that appeared to be unique to the Salmonella Typhimurium planktonic phenotype were primarily assigned to the functional category of “Protein synthesis” and
were almost exclusively rps and rpl genes known to be 30S and 50S ribosomal subunit proteins. The regulation of the biosynthesis of ribosomes, which constitute the catalytic organelles for the translation reaction, is central for the adaptation of bacteria to different growth conditions. The synthesis of the different ribosomal RNA and ribosomal protein components is controlled and coordinated by a complex network of regulatory mechanisms to adjust the translational capacity to the required cell demands (Wagner, 98
2001). Recently it has been shown that the global regulator Hfq is responsible for the expression of many ribosomal structural protein genes (refer to Table 2) and repression of this regulon down-regulates the rpl and rps genes (Wilson et al., 2007). It is shown here that hfq was positively expressed in the Salmonella Typhimurium LT2 planktonic phenotype.
An interesting observation was made with regards to the Salmonella
Typhimurium biofilm phenotype. The uniquely expressed genes fell into the “Mobile and chromosomal elements” functional category and were primarily the three lambda-like
Gifsy-1, Gifsy-2 and Fels-1 prophage genes (Figueroa-Bossi et al., 2001) and the F plasmid conjugative transfer (tra) genes located on the PSLT virulence plasmid. Once again, Hfq has been demonstrated to negatively regulate the tra operon (Wilson et al.,
2007) a down-regulation of hfq in the biofilm phenotype of this strain was observed.
Significantly expressed genes shared between the strains in the biofilm phenotype included the well-studied csg genes involved in the control of curli and cellulose synthesis and which have also been implicated in the indirect control of c-di-GMP levels in Salmonella through the expression of the GGDEF-domain-containing AdrA protein
(Da Re and Ghigo, 2006; Kader et al., 2006). Also in this shared group were ssa/sse genes located on SPI-2 involved in TTSS and fep genes associated with the assimilation of iron from enterochelin (Hall and Foster, 1996; Yancey et al., 1979). It appeared that although the type culture LT2 strain did express some of the cob-cbi-pdu genes in common with the environmental isolate, Salmonella Missouri expressed this operon more completely. This same observation was made with the hydrogenase 3 (hyp/hyc) genes in 99
the biofilm phenotype and the NADH dehydrogenase (nuo) genes shared between the
more strongly expressing Missouri biofilm phenotype and the LT2 planktonic phenotype.
Interestingly, overlapping genes between the Salmonella Missouri planktonic
phenotype and the Salmonella Typhimurium biofilm phenotype were primarily located on the PSLT virulence plasmid as conjugative transfer (tra) genes or on the SPI-1 as the putative iron transport operon sitBCD (Zhou et al., 1999).
Conclusions
Current literature suggests that there is distinct attenuation in virulence of
repeatedly passaged microorganisms in microbiology laboratories (Fux et al., 2005). In
addition, observations have revealed that frequently cultured organisms tend to alter
physiological behavior over time, losing the ability to form biofilms, becoming less
resistant to physical and biological stress, and requiring more strictly controlled nutrient
regimes (data not shown). A case in point is the Salmonella Typhimurium LT2 ATCC
type strain, a culture which has been maintained in aseptic conditions for over half a
century (Lilleengen, 1948). This organism has been the strain of choice for hundreds of in
vitro and even in vivo experiments to study the physiology of this important human
pathogen. However, previous observations and this current study suggest that there may
be diminshed similarity between this repeatedly passaged strain and a recent
environmental isolate responsible for serious community impact.
Strikingly, over 50% of the transcriptomes of each of the biofilm and planktonic
phenotypes for the two strains were different, indicating that substantial physiological
differences exist between these two strains. On closer inspection of the differences, it was 100
evident that there were certain pathways which had become preferred by each of the
strains under specific growth conditions. This is the rationale underlying the process of natural selection in the theory of evolution, that the exposure of highly related organisms to different environmental conditions and pressures results in the gain and loss of genes and the alteration of physiology to maintain optimum energy economy and ensured survival within the lifecycle of the organism.
It should be pointed out that even the choice of a nomenclature scheme can drastically affect the severity or importance with which an organism is regarded. Most clinicians would regard a patient diagnosed with Salmonella Typhi as a more serious case than a patient diagnosed with Salmonella Typhimurium. That the Missouri outbreak was initially described using their former, non-standardized nomenclature scheme as
Salmonella typhimurium when the results here show that the strain was more closely related to Salmonella Typhi or Paratyphi, illustrates the potential underestimation of the severity of an outbreak depending on nomenclature and typing techniques used. The corrected classification of the pathogen to Salmonella Missouri at least offers the clinician the choice of urgency with which to regard the situation.
But it is not only the clinician that may be influenced by nomenclature. State and federal health agencies may choose to down-grade their emergency response if the causative agent carries the stigma of being only mildly virulent. Therefore, basing clinical and physiology studies on an attenuated strain of a pathogen may not serve the public’s best interests. Ansong et al. (2008) carried out a proteomic study in which they compared
Salmonella Typhi with Salmonella Typhimurium in an infection model to gain insights 101
into the molecular determinants that contribute to the narrow host range and pathogenicity traits in the typhoid infection. Their results were striking in that they were
able to demonstrate a subset of proteins which were unique in the typhoid model, suggesting that this difference in the protein complement between two genetically related
organisms can significantly alter pathogenicity and environmental response.
These findings corroborated the Ansong et al. (2008) results in that it was
demonstrated that expression of SPI-2 virulence genes ssa/sse were shared between the two strains under biofilm growth conditions. It was also demonstrated that expression of the apparent “universal” biofilm-related genes in Salmonella, those in the csg operon, were also shared between the strains, indicating that perhaps genes in this operon might serve as qualitative targets for detecting Salmonella in the biofilm phenotype in industrial settings. Furthermore, it was also shown that expression of the iron-deficiency genes located in the fep operon were also shared and that this ferrienterochelin may be important in sequestering iron during limiting nutrient conditions in biofilms where competition for micronutrients may be fierce. This might also explain why it was found that several genes of the cob-cbi-pdu operon were expressed in both strains exhibiting the biofilm phenotype. That said however, it must also be pointed out that the environmental isolate appeared to exhibit greater coverage and expression of the cobalamin-dependent
1,2-propanediol utilization pathway and that this might be indicative of an environmental adaptation that Salmonella Missouri has grown to be reliant upon whereas Salmonella
Typhimurium LT2 has had less need to compete for this particular carbon source and therefore has an attenuated behavior in this regard. It was previously demonstrated 102
(Chapter 3) that hydrogenase 3 (hpc/hyc) and NADH dehydrogenase I (nuo) may also be
intimately (though not necessarily exclusively) involved in the biofilm phenotype, but
with the same attenuated differences as the cob-cbi-pdu operon in the two strains.
It was curious to that one of the major subsets of genes that appeared to be
uniquely up-regulated in the planktonic phenotype of Salmonella Typhimurium LT2
should be genes involved in the regulation of ribosomal biosynthesis (rps and rpl), a
central mechanism for the adaptation of bacteria to changing growth conditions. This can
possibly be explained by the infrequency with which this domesticated strain is faced
with stressful or challenging conditions and the subsequent need for the organism to
expend valuable energy in synthesizing these ribosomal protein components to elevate
the translational capacity of the cell.
The presence of multiple phage genes uniquely expressed in the Salmonella
Typhimurium LT2 phenotype may be explained by their volatile nature within the
pathogen’s genome. These genes were apparently obtained via horizontal gene transfer
(Porwollik and McClelland, 2003) and have a tendency to migrate within natural
populations, being promiscuous in nature. Since Salmonella Typhimurium LT2 has been
maintained in relative isolation concerning the availability of lateral gene transfer target
or donor groups, whereas Salmonella Missouri has presumably been in regular contact
with other microbial species harboring these phage traits, it may be that the phage genes
have been lost or significantly altered on the genome of the environmental isolate, rendering the microarray inefficient at detecting such genes. This is supportive of the rationale behind using the genetically stable 16S rDNA regions of the chromosome for 103
phylogenetic purposes, with the assumption that little to no change occurs within these ribosomal genes over time, making them suitable epoch markers in the prokaryotic community.
In conclusion, the marked differences observed between the Salmonella
Typhimurium LT2 and Salmonella Missouri biofilm and planktonic phenotype transcriptomes is further evidence of the importance in using environmentally relevant strains for experimental studies. The differences between the two strains overall is evidence that so-called laboratory strains may not be the most representative strains in elucidating real-world scenarios. However, despite the numerous transcriptional differences, the similarities exhibited by the two strains particularly in the biofilm phenotype confirms the notion that the environmentally relevant pathways are often conserved in pathogens.
104
CHAPTER 5
CONCLUSIONS
This dissertation highlighted some of the major differences between the planktonic and biofilm phenotypes of the ATCC type strain, Salmonella enterica serotype
Typhimurium LT2, and an environmental isolate, Salmonella enterica serotype Missouri.
The goal of the study was to elucidate important phenotypic differences between the planktonic and biofilm growth phases in the enteric pathogen Salmonella at the transcriptional level. This goal was addressed in two separate chapters by first examining the transcriptional behavior of the robust biofilm-forming Salmonella Missouri in the two modes of growth (Chapter 3) and subsequently studying the differences in expression patterns between a less virulent, repeatedly cultured ATCC type strain, Salmonella
Typhimurium LT2 and a more virulent recently isolated environmental strain, Salmonella
Missouri (Chapter 4). This final chapter summarizes the key findings of each of these chapters and discusses future directions for this work.
Salmonella Missouri had been isolated and identified as the causative agent involved in a waterborne outbreak of salmonellosis in Gideon, MO, USA during the
Christmas of 1993. This virulent enteric pathogen had been responsible for infecting over
40% of the community, hospitalizing over 15 patients and causing mortality in a further seven. After obtaining a culture of this organism, it was observed that it was a persistent biofilm former and was able to survive for lengthy periods under low nutrient, sub- optimal conditions. It was decided to undertake a transcriptional study of this organism in order to delineate the major pathways active in the biofilm and planktonic phenotypes. 105
In agreement with existing literature, it was demonstrated that the global control
unit, csgD, was centrally involved in establishing the biofilm phenotype by activating
curli biosynthesis and possibly contributing to elevated levels of cyclic-di-GMP within
the cell through the activity of the GGDEF domain protein AdrA. Furthermore, it was
demonstrated that the so-called virulence plasmid and pathogenicity islands may play a
more universal role in the lifecycle of Salmonella than simply during host infection.
Although these pathogenicity islands have been primarily studied in the clinical context of disease establishment and progression in the host, it was suggested that SPI-2 may be intimately linked with the biofilm phenotype and involved in establishing persistence in the non-host environment where Salmonella may spend significant time. It was further suggested that SPI-1 may contribute to the pathogen’s ability to locate a suitable contact surface and initial adhesion in the switch from the planktonic to biofilm phenotype.
It appears that Salmonella has acquired several major sets of genes through horizontal gene transfer through evolutionary processes, affording the pathogen the ability to outcompete closely related bacteria and persist in the environment as a biofilm.
One such set of gene encodes for the cobalamin-dependent 1,2-propanediol utilization pathway (cob-cbi-pdu). This operon was observed to be consistently up-regulated in the biofilm phenotype of both Salmonella Typhimurium LT2 and Salmonella Missouri. This lead to the conclusion that the ability to convert several sugar compounds (including glucose, fucose and rhamnose) to 1,2-propanediol, and subsequently utilize 1,2- propanediol in a cobalamin-dependent manner under anaerobic conditions as a sole 106
carbon and energy source, may be a further reason for Salmonella to persist and thrive in
the host and non-host environments.
It was also evident, not only from visual observations of the differences in
physiological behavior of the two strains but also from transcriptomic analysis, that
Salmonella Missouri exhibits a greater degree of adaptation to survival and persistence in the non-host environment. This result is not at all surprising, considering the length of
time for which the ATCC type strain has been maintained in culture and the repeated
passaging of this organism. The transcriptional profile of the biofilm phenotype of
Salmonella Missouri illustrated how this organism has developed strategic pathways to overcome the stressful living conditions in which it may find itself both as a human pathogen and as an environmental inhabitant.
Future Work
This present study represents the culmination of several years of gathering fundamental information on the behavior of Salmonella as a biofilm in low nutrient conditions and onto which can be built a more complete picture of how this enteric pathogen survives and persists in a variety of niches.
One of the initial motivating factors in this research was the potential of
Salmonella to become a biothreat to the health and safety of human populations through the drinking water distribution system. Since it has been demonstrated that Salmonella is capable of establishing itself in biofilms on distribution pipes, filter media and premise plumbing, it would be helpful to understand the environmental factors and physiological responses involved in the biofilm phenotype of this pathogen. This study made use of 107
artificial media and standardized biofilm reactors in which to culture the organism for
study. However, as demonstrated with the ATCC type strain, Salmonella Typhimurium
LT2, that the use of an attenuated, lesser virulent strain of a pathogen may not effectively
demonstrate the risks of a true version of the pathogen in lab studies, so the use of
artificial environments and nutrients limits the reality of a pathogen’s potential to cause disease. This has been the rationale behind using progressive models, from in vitro to in
vivo studies and finally to clinical trials to test the efficacy of pharmaceuticals. Therefore,
the next stage of this research may be to repeat the planktonic and biofilm experiments
using the environmental isolate, Salmonella Missouri, in small-scale, closed distribution
system studies in order to determine the effects of surface material, residence time and
shear on the survivability of the organism.
A current shortcoming of transcriptomic studies is an inherent limitation in the
technology to effectively separate out the starting mRNA from the organism of interest
from other organisms. While this may be possible in separating out mRNA from a
eukaryotic organism in a microbial community because of the presence of useful polyA
overhangs present on eukaryotic mRNA, currently there technology is not yet advanced
enough to separate out sufficient quantities of mRNA from bacteria in mixed
communities. A possible solution to this problem may be the combined use of
cryosectioning and laser dissection microscopy where it might be possible to selectively
obtain single cell isolates of bacteria from mixed communities. However, this technique
has several shortcomings in and of itself. First, the rapid half life of mRNA in bacterial
cells would require that the biofilm or other form of cell culture be harvested and fixed 108 rapidly so as to preserve the transcriptional expression pattern at a particular time point.
Second, the current requirement for mRNA starting material necessitates the harvesting of large quantities of cells in order to obtain sufficient template for the cDNA reverse transcription reaction. This may be addressed by using direct RNA hybridization to cDNA microarrays, but again, this technology is severe limited by the rapid degradation of mRNA. Should the technology become sufficiently advanced that it is possible to obtain sufficient mRNA from discrete cells in mixed cultures, this would significantly enhance understanding of the behavior of this and hundreds of other pathogens, the majority of which are seldom found in pure cultures in the natural environment.
Finally, recent studies undertaken at the Center for Biofilm Engineering focusing on the behavior of Staphylococcus aureus grown as a biofilm on mammalian cell cultures have demonstrated the potential of a novel system in which to observe pathogen interaction with host cells in vivo. Preliminary attempts to manipulate this system for use with Salmonella demonstrated that in its current form, which inherently separates the bacterial pathogen from the mammalian cell culture by a porous membrane, Salmonella does not appear to cause cell damage. This can be understood within the context of
Salmonella pathogenicity, which is known to require direct contact with epithelial cells in order for the TTSSs to inject effector proteins responsible for actin rearrangement and penetration of the pathogen into the host cells. However, it may be possible to substitute the nanopore membranes currently employed in this assay with larger pore membranes to allow for occasional direct pathogen-host contact.
109
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APPENDICES 127
APPENDIX A
SIGNIFICANT GENES DATA SET FOR CHAPTER 3 128 Significant Genes from Salmonella MO with q‐values < 0.1%, Number False Sig Genes (Median) = 0.73978 and FDR 0.08572% (410 Biofilm Genes, 447 Planktonic Genes) Gene Expected Observed Denominator Locus Gene Name Numerator(r) q‐value (%) 107808 107809 107810 Symbol score (dExp) score(d) (s+s0) PSLT006 DNA replication repA 0.104944296 1.9600818 0.50870204 0.25953102 0.03676819 0.5171119 0.62749356 0.3815007 PSLT014 putative outer membrane protein orf6 ‐0.2717591 1.9315368 0.380888 0.19719426 0.035703473 0.3638063 0.3857596 0.39309806 PSLT023 DNA replication repA2 0.02902207 2.0378094 0.4901857 0.24054542 0 0.59046596 0.46488547 0.41520572 PSLT024 hypothetical protein 0.015338479 2.1821437 0.45487335 0.20845252 0 0.4361952 0.49495822 0.43346664 PSLT036 putative transposase, IS200‐like 0.6619383 1.9249718 0.4800788 0.24939522 0.035160456 0.42819518 0.41039482 0.60164636 PSLT039 Salmonella plasmid virulence: hydrophilic protein spvB 0.3451125 3.730863 0.8478979 0.22726588 0 0.8129133 0.9255149 0.8052654 PSLT040 Salmonella plasmid virulence: outer membrane protein spvA 0.12597384 3.0069344 0.9168429 0.3049095 0 1.0600393 1.004456 0.68603337 PSLT041 Salmonella plasmid virulence: regulation of spv operon spvR 0.5280604 1.7494527 0.57788384 0.33032265 0.058067188 0.7151635 0.29407802 0.72441 PSLT042 putative integrase protein 1.0153017 2.4233482 0.50700295 0.2092159 0 0.5352007 0.51944155 0.46636653 PSLT043 putative phosphoribulokinase / uridine kinase family ‐0.076198705 2.6377935 0.5201619 0.19719584 0 0.52404296 0.5330904 0.5033524 PSLT044 putative integrase protein rlgA ‐0.35482937 3.0464878 0.63300794 0.20778286 0 0.6716581 0.61639065 0.610975 PSLT046 putative carbonic anhydrase 0.43125764 1.6800685 0.4287064 0.25517198 0.052916735 0.29661897 0.5118478 0.47765243 PSLT047 putative cytoplasmic protein ‐0.36528504 2.0366328 0.4778348 0.23462 0 0.39670837 0.48000222 0.5567938 PSLT052 plasmid partition protein A parA 0.22071066 1.5905259 0.41512597 0.2609992 0.04736082 0.37233824 0.5566913 0.31634837 PSLT053 plasmid partition protein B parB 0.9242672 2.0767963 0.42101747 0.20272449 0 0.44112355 0.42865178 0.39327705 PSLT060 putative cytoplasmic protein ‐0.503064 ‐1.5957878 ‐0.34180608 0.2141927 0.04670303 ‐0.39337102 ‐0.3175781 ‐0.31446916 PSLT072 putative transglycosylase finP 0.33128756 1.6001691 0.4574093 0.2858506 0.048099868 0.27459073 0.60735095 0.4902862 PSLT075 conjugative transfer: regulation traJ ‐0.75755405 1.575407 0.3857001 0.24482569 0.04670303 0.34387413 0.49739492 0.3158313 PSLT094 conjugative transfer: assembly trbC ‐0.74059606 2.1151586 0.45043716 0.21295668 0 0.46203178 0.40329906 0.4859806 PSLT095 conjugative transfer: aggregate stability traN 0.072409235 1.9366502 0.45661223 0.23577425 0.035703473 0.5083317 0.49951515 0.3619898 PSLT096 conjugative transfer trbE 0.011326586 1.6559206 0.3692458 0.22298521 0.052023627 0.30819207 0.4279481 0.3715972 PSLT103 conjugative transfer: surface exclusion traT ‐0.05340151 2.1905904 0.48780736 0.22268306 0 0.5539146 0.47054815 0.43895933 PSLT104 conjugative transfer: DNA transport traD 0.32163835 2.0872748 0.4257448 0.20397161 0 0.40272415 0.4190764 0.45543385 STM0003 homoserine kinase thrB 0.3731943 ‐2.865248 ‐0.97947013 0.3418448 0 ‐0.69281363 ‐1.2177294 ‐1.0278673 STM0004 threonine synthase thrC ‐0.23842911 ‐1.6807305 ‐0.3645335 0.21688993 0.052916735 ‐0.314873 ‐0.36514962 ‐0.41357788 STM0007 transaldolase B talB 0.022878118 3.1774638 0.7765127 0.24438128 0 0.7974293 0.86131924 0.67078954 STM0012 chaperone Hsp70 in DNA biosynthesis/cell division dnaK ‐0.24008778 ‐2.589143 ‐0.6160514 0.2379364 0 ‐0.5170135 ‐0.66296506 ‐0.6681755 STM0027 fimbrial chaparone bcfG 0.39438474 ‐2.4562256 ‐0.78674674 0.3203072 0 ‐0.5230399 ‐0.91175896 ‐0.9254414 STM0031 putative transcription regulator 0.25770834 1.6790329 0.36837336 0.21939616 0.052916735 0.4192517 0.31224498 0.37362337 STM0032 putative arylsulfatase ‐0.31135422 2.076453 0.60086226 0.28936955 0 0.39936844 0.71335566 0.6898628 STM0041 putative glycosyl hydrolase ‐0.29370916 1.5048043 0.29460108 0.19577369 0.08572143 0.2974965 0.3056859 0.28062084 STM0054 putative oxalacetate decarboxylase, subunit beta ‐0.12743631 ‐2.4273508 ‐0.62845695 0.2589065 0 ‐0.5026722 ‐0.746571 ‐0.63612765 STM0056 putative oxalacetate decarboxylase, subunit gamma 0.7631232 ‐2.139305 ‐0.45572165 0.21302322 0 ‐0.45647347 ‐0.41269276 ‐0.49799874 STM0064 dihydrodipicolinate reductase dapB ‐0.061718486 ‐6.913448 ‐1.5090705 0.21828045 0 ‐1.4498417 ‐1.5317243 ‐1.5456456 STM0066 carbamoyl‐phosphate synthetase, glutamine‐hydrolysing small subunit carA 0.45898014 ‐5.0335317 ‐1.1686505 0.23217307 0 ‐1.1434257 ‐1.2538745 ‐1.1086514 STM0067 carbamoyl‐phosphate synthase, large subunit carB 0.05301397 ‐4.6263185 ‐1.1902834 0.25728524 0 ‐1.053431 ‐1.2448778 ‐1.2725413 STM0073 putative acyl‐CoA dehydrogenase, carnitine metabolism caiA 0.08282884 1.8060813 0.37246543 0.2062285 0.061239734 0.4080665 0.35277745 0.3565523 STM0074 putative BCCT family, betaine/carnitine/choline transport protein caiT ‐0.31307504 1.5931356 0.3547541 0.22267665 0.048099868 0.42188185 0.33328038 0.30910006 STM0096 RNA polymerase associated protein, putative SNF2 family hepA ‐0.46144098 ‐1.824222 ‐0.44441262 0.24361762 0.061239734 ‐0.35401532 ‐0.5445657 ‐0.43465686 STM0106 putative ABC‐transport protein yabJ ‐0.4388538 ‐1.6991203 ‐0.47691223 0.28068185 0.055124886 ‐0.38421997 ‐0.6614861 ‐0.38503063 STM0110 3‐isopropylmalate isomerase (dehydratase), subunit with LeuC leuD 0.095710576 6.583725 1.6092142 0.24442306 0 1.5279573 1.7166674 1.583018 STM0111 3‐isopropylmalate isomerase (dehydratase), subunit with LeuD leuC 1.2813643 8.166836 1.9181032 0.23486492 0 1.8703383 2.0110316 1.8729396 STM0112 3‐isopropylmalate dehydrogenase leuB 0.9146848 8.07625 1.8719113 0.23177975 0 1.9474282 1.8711624 1.7971433 STM0113 2‐isopropylmalate synthase leuA 0.54918724 10.239214 2.1105087 0.2061202 0 2.0958962 2.0898426 2.145787 STM0150 APC family, aromatic amino acid transporter aroP ‐0.90354496 1.7143809 0.37897933 0.22105901 0.055790044 0.33038053 0.36546996 0.44108745 STM0154 lipoamide dehydrogenase (NADH) component of 2‐oxodehydrogenase and lpdA 0.17271183 2.2910266 0.5616982 0.24517314 0 0.640753 0.5927695 0.4515722 STM0157 putative outer membrane protein yacH 0.56994534 ‐2.0895703 ‐0.44268334 0.21185377 0 ‐0.40804002 ‐0.4874071 ‐0.43260288 STM0169 glucose dehydrogenase gcd ‐1.7519572 1.5694543 0.3682456 0.2346329 0.04670303 0.2772285 0.39958212 0.4279262 STM0170 hypoxanthine phosphoribosyltransferase hpt 0.31792352 1.8715332 0.49547055 0.26474047 0.0654669 0.4162164 0.6481248 0.4220704 STM0171 putative carbonic anhydrase yadF 0.28780282 4.9549255 1.2961013 0.26157838 0 1.1643332 1.417171 1.3067999 STM0172 putative ABC‐type multidrug transport system, ATPase component yadG 0.48575526 1.5527482 0.35061258 0.22580132 0.046063263 0.29700285 0.42260903 0.3322259 STM0181 pantothenate synthetase panC 0.26421428 ‐1.6072483 ‐0.36514792 0.22718824 0.04736082 ‐0.43498638 ‐0.3594995 ‐0.3009579 STM0183 7,8‐dihydro‐6‐hydroxymethylpterin‐pyrophosphokinase, PPPK folK 0.25296074 ‐1.9135267 ‐0.38334984 0.20033681 0.033565152 ‐0.39269713 ‐0.39771083 ‐0.35964152 STM0191 outer membrane protein receptor / transporter for fhuA ‐0.9581498 2.0976856 0.5305229 0.25290868 0 0.6176664 0.56935674 0.4045455 STM0192 ABC superfamily (atp_bind), hydroxymate‐dependent iron transport fhuC ‐0.21520603 1.6930404 0.43968567 0.25970182 0.05455575 0.4876314 0.5320316 0.29939404 STM0211 putative cytoplasmic protein yaeH 0.5736256 3.3923361 0.7839944 0.23110752 0 0.70088106 0.80845404 0.84264797 STM0216 30S ribosomal subunit protein S2 rpsB 0.10987641 ‐1.98902 ‐0.552573 0.2778117 0.03676819 ‐0.4021984 ‐0.54393405 ‐0.7115866 STM0219 ribosome releasing factor frr 0.4616791 1.5258104 0.4298571 0.2817238 0.066927865 0.2711675 0.42408898 0.5943148 STM0223 putative membrane‐associated Zn‐dependent protease yaeL 0.05938715 1.6136407 0.30970484 0.19192925 0.04958284 0.3049555 0.31661424 0.3075448 STM0224 putative outer membrane antigen yaeT ‐0.47657797 1.6624389 0.4184704 0.2517208 0.052023627 0.43271163 0.52033836 0.30236128 STM0225 histone‐like protein, located in outer membrane hlpA ‐1.0063118 3.0332167 0.6145841 0.20261793 0 0.5923797 0.6102872 0.6410853 STM0228 UDP‐N‐acetylglucosamine acetyltransferase lpxA ‐0.48575526 1.6226844 0.3795888 0.23392646 0.04958284 0.46926323 0.32102868 0.3484745 STM0234 lysine decarboxylase 2, constitutive ldcC ‐0.3799009 1.6932362 0.3664753 0.21643484 0.05455575 0.4041073 0.38366818 0.31165048 STM0245 putative outer membrane lipoprotein yaeC ‐0.11784761 3.122391 0.7852388 0.2514864 0 0.7503361 0.9077048 0.6976756 STM0248 putative dehydratase yaeD ‐0.18181716 2.56547 0.49893078 0.19447929 0 0.5059839 0.5039926 0.48681587 STM0259 putative methyltransferase in menaquinone/biotin biosynthesis yafE ‐0.32467642 2.5306163 0.52342516 0.20683703 0 0.5335188 0.54910225 0.48765448 STM0262 putative SAM‐dependent methyltransferase yafS ‐0.19503678 2.269245 0.6194391 0.27297148 0 0.49389648 0.7803889 0.584032 STM0263 RNase HI, degrades RNA of DNA‐RNA hybrids rnhA 0.45729053 1.5386066 0.35818568 0.23279874 0.068245016 0.31111524 0.3165024 0.4469394 STM0266 putative cytoplasmic protein 0.03633827 ‐2.347133 ‐0.55782306 0.23766147 0 ‐0.51841563 ‐0.49931577 ‐0.6557377 STM0267 putative cytoplasmic protein 0.55740213 ‐2.31671 ‐0.6252847 0.269902 0 ‐0.46269473 ‐0.69639415 ‐0.7167651 STM0268 putative cytoplasmic protein 0.24975686 ‐2.5039003 ‐0.5029192 0.20085432 0 ‐0.49753565 ‐0.4845398 ‐0.5266822 STM0311 putative glutamine amidotransferase yafJ ‐0.3123075 1.9502835 0.485739 0.2490607 0.036121875 0.57043815 0.36815205 0.51862675 STM0316 aminoacyl‐histidine dipeptidase (peptidase D) pepD 0.29522222 2.1541834 0.54524845 0.25311142 0 0.4249264 0.6467224 0.56409657 STM0319 transcriptional regulator of cryptic csgA gene for crl ‐0.23575908 1.9872247 0.43583065 0.21931624 0 0.38255042 0.48966178 0.43527973 STM0322 gamma‐glutamylphosphate reductase proA 0.1268639 ‐2.2395682 ‐0.45645252 0.20381273 0 ‐0.42575482 ‐0.47432962 ‐0.46927315 STM0324 putative inner membrane protein ‐0.45898014 ‐1.7054257 ‐0.33347082 0.19553523 0.055790044 ‐0.34722316 ‐0.32326004 ‐0.32992923 STM0343 putative Diguanylate cyclase/phosphodiesterase domain 1 ‐0.21675953 2.677911 0.78673744 0.29378775 0 0.65208244 0.9945076 0.7136222 STM0350 homology to outer membrane efflux protein 1.1832253 ‐1.5723702 ‐0.5248595 0.33380148 0.068245016 ‐0.234343 ‐0.68150187 ‐0.65873355 STM0351 putative cation efflux system protein ‐0.4337433 ‐1.801101 ‐0.49487287 0.27476132 0.06083684 ‐0.37917757 ‐0.66379964 ‐0.44164142 STM0352 putative cation efflux pump 1.214031 ‐2.7127073 ‐0.63740706 0.23497082 0 ‐0.5922731 ‐0.7305447 ‐0.58940333 STM0354 putative transcriptional regulator 0.19398473 ‐2.0123951 ‐0.597014 0.29666838 0 ‐0.4025938 ‐0.77680856 ‐0.6116396 STM0358 DNA restriction (DNA helicase res 0.28092447 1.6455429 0.3113941 0.18923487 0.050878678 0.310187 0.3130102 0.31098506 STM0363 putative transcription regulator, AraC family ‐0.4730723 1.917425 0.3840036 0.20027047 0.034698687 0.3706963 0.37361923 0.40769526 STM0366 putative periplasmic protein yahO ‐0.12833788 3.479826 1.082961 0.31121123 0 0.91624224 1.010098 1.3225427 STM0369 putative citrate synthase prpC 1.6554445 ‐2.6600907 ‐0.82515436 0.31019783 0 ‐0.60706687 ‐1.0282005 ‐0.84019566 STM0371 putative acetyl‐CoA synthetase, propionate catabolism operon prpE 0.54299587 ‐1.8005381 ‐0.5133654 0.28511778 0.06083684 ‐0.701977 ‐0.4562795 ‐0.38183957 STM0383 putative cytoplasmic protein yaiB ‐0.46944648 ‐3.9394166 ‐0.9674523 0.24558263 0 ‐1.0665052 ‐0.96745145 ‐0.86840016 STM0385 putative diguanylate cyclase/phosphodiesterase domain 1 yaiC 0.59701335 ‐4.324508 ‐1.1396213 0.2635262 0 ‐1.035921 ‐1.2856466 ‐1.0972964 STM0388 shikimate kinase II aroL ‐0.05993005 2.91053 0.6445213 0.22144464 0 0.6025709 0.70973486 0.6212581 STM0389 putative cytoplasmic protein yaiA ‐0.30700204 2.3532898 0.50275105 0.21363755 0 0.5258289 0.45232546 0.53009886 STM0396 ATP‐dependent dsDNA exonuclease sbcD 0.60831934 ‐1.8980027 ‐0.39250594 0.20679946 0.0654669 ‐0.38914096 ‐0.3624438 ‐0.42593306 STM0401 maltodextrin glucosidase malZ 0.237694 ‐1.9701208 ‐0.5027518 0.25518832 0.036121875 ‐0.3888723 ‐0.62017125 ‐0.49921197 STM0428 2‐aminoethylphosphonate transporter,ATPase component phnT ‐0.16867991 ‐1.8471417 ‐0.42524725 0.23021907 0.063013285 ‐0.3416402 ‐0.4693416 ‐0.46475998 STM0431 2‐aminoethylphosphonate transport phnW ‐0.06288169 ‐1.5379883 ‐0.33342257 0.21679136 0.08572143 ‐0.32715797 ‐0.28767043 ‐0.3854393 STM0432 2‐aminoethylphosphonate transport phnX 0.8484593 ‐2.229105 ‐0.6137898 0.27535257 0 ‐0.44300044 ‐0.7276151 ‐0.67075384 STM0435 putative cytoplasmic protein yajQ 0.18962856 1.6703997 0.37248254 0.22299007 0.052916735 0.33008066 0.44103426 0.34633273 STM0436A IS903 transposase 0.46944648 ‐1.6752232 ‐0.38447344 0.22950579 0.052916735 ‐0.37019327 ‐0.461738 ‐0.32148904 STM0446 morphogene putative regulator of murein genes (BolA bolA 0.15034653 2.329697 0.5824739 0.2500213 0 0.46069 0.62693226 0.6597993 STM0447 peptidyl‐prolyl cis/trans isomerase, trigger factor a molecular tig 0.620536 2.3983042 0.6421274 0.26774225 0 0.77709967 0.50235707 0.6469255 STM0452 peptidyl prolyl isomerase cypD ‐1.301176 1.7160473 0.4151523 0.24192359 0.055790044 0.5217175 0.37075484 0.35298458 STM0460 putative ABC superfamily (atp) transporter mdlA 1.2157859 ‐2.1817987 ‐0.52821445 0.24210045 0 ‐0.4450372 ‐0.51094645 ‐0.6286598 STM0461 putative ABC superfamily (atp&membrane) transporter mdlB ‐0.18625572 ‐2.4928818 ‐0.6117885 0.24541417 0 ‐0.4977934 ‐0.66604364 ‐0.67152846 STM0462 regulatory protein, P‐II 2, for nitrogen assimilation glnK ‐0.42231038 ‐10.616214 ‐2.2544765 0.21236163 0 ‐2.2110238 ‐2.2586772 ‐2.2937286 STM0463 putative Amt family, ammonium transport protein amtB 0.5317064 ‐11.134695 ‐2.5194488 0.22627012 0 ‐2.5150805 ‐2.587126 ‐2.4561398 STM0464 acyl‐CoA thioesterase II tesB ‐0.17169346 ‐2.3282132 ‐0.65982836 0.28340548 0 ‐0.69778085 ‐0.4796042 ‐0.8021 STM0469 putative 50S ribosomal protein L31 (second copy) rpmE2 ‐0.001346741 5.337574 1.5835129 0.2966728 0 1.3985962 1.5783657 1.7735767 STM0470 putative 50S ribosomal protein L36 (second copy) rpmJ2 ‐2.1953468 6.5218506 1.562265 0.23954321 0 1.5099168 1.5123256 1.6645528 STM0471 putative inner membrane protein ylaC 0.33938333 1.9444011 0.50941765 0.26199207 0.036121875 0.38107553 0.511171 0.63600636 STM0476 acridine efflux pump acrA 0.5709482 1.5192364 0.3550747 0.23371918 0.06573839 0.3923507 0.40799665 0.26487678 STM0485 putative cytoplasmic protein ybaB ‐0.596286 2.1674752 0.5880913 0.2713255 0 0.42250806 0.66256225 0.6792037 STM0488 adenylate kinase adk 0.18878233 ‐2.1039302 ‐0.5463128 0.259663 0 ‐0.55290645 ‐0.41970772 ‐0.6663243 129 STM0498 putative copper‐transporting ATPase copA 1.7955384 ‐3.210016 ‐0.6610619 0.20593725 0 ‐0.63727254 ‐0.6506231 ‐0.69528997 STM0499 putative heavy metal transcriptional repressor (MerR family) cueR 0.19276725 ‐1.7597262 ‐0.4299958 0.24435382 0.05861933 ‐0.5260582 ‐0.43169698 ‐0.33223227 STM0500 putative Membrane protein implicated in regulation of ybbJ 0.11949775 ‐1.8477458 ‐0.52701235 0.28521907 0.063013285 ‐0.33343032 ‐0.619396 ‐0.62821084 STM0510 putative ABC‐type transport system ATPase component/cell division sfbA 0.1668846 6.0525165 1.477358 0.24408987 0 1.4184393 1.588685 1.4249496 STM0511 putative ABC‐type transport system ATPase component/cell division sfbB ‐0.08784842 1.9568615 0.40788195 0.2084368 0.03676819 0.44251212 0.37308457 0.40804917 STM0529 putative acyl‐CoA synthetase, involved in protein transport fdrA 0.41612765 ‐1.719746 ‐0.35023797 0.2036568 0.056731287 ‐0.37706634 ‐0.3494326 ‐0.324215 STM0530 putative cytoplasmic protein ylbE ‐0.5576427 ‐2.1532056 ‐0.46535012 0.21611968 0 ‐0.42593813 ‐0.4512766 ‐0.51883566 STM0533 phosphoribosylaminoimidazole carboxylase purK ‐0.112411916 ‐1.6155987 ‐0.41601005 0.2574959 0.048099868 ‐0.30675235 ‐0.39734474 ‐0.54393303 STM0534 phosphoribosylaminoimidazole carboxylase purE 0.46376753 ‐2.1505558 ‐0.44838896 0.2084991 0 ‐0.47301143 ‐0.4085483 ‐0.46360716 STM0536 peptidyl‐prolyl cis‐trans isomerase B (rotamase B) ppiB ‐0.33535585 1.6453243 0.43101352 0.26196265 0.050878678 0.28459483 0.49165556 0.51679015 STM0562 putative transport protein ‐0.0918953 ‐1.8481066 ‐0.39792618 0.2153156 0.063013285 ‐0.42998475 ‐0.4193589 ‐0.3444349 STM0570 outer membrane N‐acetyl phenylalanine beta‐naphthyl ester‐cleaving esterase apeE 1.1376332 ‐1.9821059 ‐0.5462902 0.275611 0.03676819 ‐0.37236246 ‐0.644741 ‐0.6217672 STM0576 putative transport protein, PTS system 0.7095931 ‐1.7835367 ‐0.35082793 0.19670351 0.05994943 ‐0.3486708 ‐0.33763683 ‐0.36617616 STM0585 outer membrane porin, receptor for ferric enterobactin fepA ‐0.26110312 4.4908957 0.99126065 0.22072671 0 0.9580155 1.0559162 0.9598503 STM0587 putative cytoplasmic protein ybdZ 0.49835232 7.501955 1.6706742 0.22269851 0 1.6586463 1.7351841 1.6181923 STM0589 ferric enterobactin (enterochelin) transporter fepE 0.008713709 2.366718 0.57368934 0.24239868 0 0.6729647 0.4872057 0.56089765 STM0603 putative aminotransferase ybdL 0.20608158 1.6621474 0.46642593 0.28061646 0.052023627 0.42625427 0.64241004 0.33061343 STM0605 putative 3‐phosphoadenosine 5‐phosphosulfate sulfotransferase (PAPS reductase)/FAD synthybdN ‐0.560405 1.9868742 0.4318384 0.21734561 0 0.3849634 0.48471278 0.425839 STM0607 periplasmic disulfide isomerase, thiol‐disulphide oxidase dsbG ‐0.26241556 2.3344712 0.58452135 0.25038704 0 0.5100641 0.70760614 0.53589386 STM0608 alkyl hydroperoxide reductase, C22 subunit detoxification of ahpC ‐0.4185652 1.8831567 0.42993405 0.22830498 0.033565152 0.35502318 0.4435194 0.49125957 STM0621 bifunctional citrate lyase alpha chain/citrate‐ACP transferase citF 1.7519572 ‐2.16279 ‐0.6100003 0.28204325 0 ‐0.5026058 ‐0.79658854 ‐0.5308066 STM0629 RNA chaperone, negative regulator of cspA transcription cspE 0.08445541 ‐3.0244715 ‐0.77316743 0.2556372 0 ‐0.7889897 ‐0.880915 ‐0.6495976 STM0632 putative Sec‐independent protein secretion pathway component ybeC 0.67103475 ‐4.526405 ‐1.0366611 0.22902527 0 ‐1.1095876 ‐1.0312442 ‐0.96915185 STM0635 putative ligase in lipoate biosynthesis lipB 0.03481237 1.676569 0.47140098 0.28117004 0.052916735 0.3011361 0.6204024 0.49266446 STM0639 rod shape‐determining membrane protein cell elongation in mrdB ‐0.85597587 2.961502 0.65604544 0.22152455 0 0.6760607 0.5913357 0.7007399 STM0659 putative heatshock protein, homolog of hsp70 in hscC 0.4057137 ‐1.94025 ‐0.39612734 0.20416304 0.035160456 ‐0.42572558 ‐0.37190017 ‐0.3907563 STM0661 putative purine nucleoside hydrolase ybeK 0.696366 ‐2.7483447 ‐0.58041734 0.21118797 0 ‐0.5770081 ‐0.5427533 ‐0.62149066 STM0662 ABC superfamily (atp_bind), glutamate/aspartate transporter gltL 0.77890545 ‐2.9508567 ‐0.9205653 0.31196544 0 ‐0.673679 ‐1.0342818 ‐1.0537351 STM0663 ABC superfamily (membrane), glutamate/aspartate transporter gltK ‐0.53539973 ‐2.2514381 ‐0.59583706 0.2646473 0 ‐0.5092478 ‐0.53041124 ‐0.74785215 STM0664 ABC superfamily (membrane), glutamate/aspartate transporter gltJ ‐0.04397718 ‐2.770816 ‐0.5858979 0.2114532 0 ‐0.5555748 ‐0.5709684 ‐0.63115054 STM0665 ABC superfamily (bind_prot), glutamate/aspartate transporter gltI ‐0.32732183 ‐3.290779 ‐0.731802 0.22237955 0 ‐0.66387933 ‐0.76356953 ‐0.7679571 STM0669 putative phosphate starvation‐inducible protein, ATP‐binding phoL ‐0.60831934 1.7770917 0.43248376 0.24336603 0.05994943 0.50777453 0.32545507 0.46422166 STM0671 putative monooxygenase ubiF 0.8493065 ‐1.9149624 ‐0.53705525 0.2804521 0.03424889 ‐0.3663575 ‐0.6821574 ‐0.56265086 STM0680 asparagine synthetase B asnB 0.9266177 ‐7.1684628 ‐1.5837377 0.22093129 0 ‐1.5608506 ‐1.6479359 ‐1.5424268 STM0690 citrate utilization protein b citB 0.7244088 ‐1.6129488 ‐0.39187354 0.24295473 0.04736082 ‐0.2981579 ‐0.48714057 ‐0.39032212 STM0693 transcriptional repressor of iron‐responsive genes (Fur family) fur 0.3812666 2.7272217 0.7778041 0.28520015 0 0.58997774 0.91239756 0.831037 STM0703 sensory kinase in two‐component regulatory system wtih kdpD ‐0.27883244 ‐1.7146358 ‐0.42435774 0.24749146 0.055790044 ‐0.33127868 ‐0.40781376 ‐0.5339808 STM0705 P‐type ATPase, high‐affinity potassium transport system, B kdpB ‐0.34951028 ‐1.5678964 ‐0.34875596 0.2224356 0.066927865 ‐0.2829152 ‐0.39667997 ‐0.3666727 STM0720 putative glycosyl transferase ‐0.41182843 2.2202878 0.5481772 0.24689466 0 0.63560265 0.43712685 0.5718021 STM0722 putative ABC transporter permease protein 0.42316884 1.9776976 0.6089239 0.30789536 0 0.37024572 0.7390249 0.71750104 STM0730 citrate synthase gltA 0.70858985 2.6080453 0.7048525 0.27026084 0 0.6266423 0.619384 0.86853135 STM0740 cytochrome d terminal oxidase, polypeptide subunit I cydA ‐0.23059107 ‐1.851417 ‐0.5488461 0.29644653 0.063013285 ‐0.33580783 ‐0.62395424 ‐0.68677634 STM0741 cytochrome d terminal oxidase polypeptide subunit II cydB ‐1.3062085 ‐1.6244359 ‐0.3364993 0.2071484 0.048099868 ‐0.30366108 ‐0.33722287 ‐0.368614 STM0742 putative outer membrane lipoprotein ybgT ‐0.22767934 ‐2.6640706 ‐0.51926285 0.19491333 0 ‐0.51026976 ‐0.5155848 ‐0.53193396 STM0749 tol protein required for outer membrane integrity pal 0.27062392 1.8569702 0.52224356 0.2812342 0.06489263 0.4004878 0.70452666 0.46171623 STM0756 quinolinate synthetase, A protein nadA ‐0.23515905 ‐1.6049786 ‐0.32340333 0.20150009 0.04736082 ‐0.3240194 ‐0.34578836 ‐0.30040222 STM0759 putative homeobox protein ybgS ‐0.3967707 2.4259317 0.6378029 0.2629105 0 0.5829259 0.5452446 0.7852382 STM0760 3‐deoxy‐D‐arabinoheptulosonate‐7‐phosphate synthase (DAHP synthetase, phenylalanine re aroG ‐0.43927655 2.1301208 0.49966294 0.23457024 0 0.54628253 0.40731314 0.5453931 STM0762 fumarate hydratase, alpha subunit 0.60460293 1.8738213 0.4617117 0.24640115 0.0654669 0.36975694 0.44643137 0.56894684 STM0764 transcriptional regulator, lysR family 0.4040136 1.6474941 0.4500975 0.2732013 0.050878678 0.2849219 0.56606615 0.49930444 STM0766 Oxalacetate decarboxylase: gamma chain dcoC 0.15832898 ‐2.394381 ‐0.49949095 0.20860963 0 ‐0.50166947 ‐0.46343914 ‐0.53336424 STM0768 Oxalacetate decarboxylase: beta chain dcoB 0.37165958 ‐1.9073848 ‐0.7278099 0.38157478 0.033565152 ‐0.34293717 ‐0.890913 ‐0.94957954 STM0771 putative ABC‐type cobalamin/Fe3 ‐siderophores transport system, ATPase component 1.193833 1.5206591 0.36208725 0.23811205 0.06573839 0.4087879 0.26271224 0.4147616 STM0772 phosphoglyceromutase 1 gpmA ‐0.8419666 2.968651 0.6427208 0.21650265 0 0.6452878 0.5928036 0.6900711 STM0782 ABC superfamily (membrane), molybdate transporter modB 0.35583586 ‐1.8115685 ‐0.38428447 0.21212803 0.061239734 ‐0.4180693 ‐0.33851707 ‐0.39626706 STM0792 putative Phospholipid‐binding protein ybhB ‐0.44278896 2.1622388 0.51662874 0.23893233 0 0.49917254 0.43913832 0.6115754 STM0793 7,8‐diaminopelargonic acid synthetase bioA 0.27155972 3.8552244 0.89793646 0.2329142 0 0.80960715 0.9323839 0.95181835 STM0802 molybdopterin biosynthesis, protein A moaA ‐0.5271988 3.1834714 0.66588086 0.20916815 0 0.65986574 0.6332867 0.7044902 STM0803 molybdopterin biosynthesis, protein B moaB 0.44850615 1.597035 0.39585403 0.24786809 0.048099868 0.29125378 0.49719876 0.39910957 STM0826 putative SAM‐dependent methyltransferase ybiN 0.15711944 ‐2.2844927 ‐0.62163687 0.27211156 0 ‐0.4781753 ‐0.7681317 ‐0.6186037 STM0828 ABC superfamily (atp_bind), glutamine high‐affinity transporter glnQ 0.61755073 ‐2.3183796 ‐0.6608881 0.28506464 0 ‐0.8392573 ‐0.6363069 ‐0.50710005 STM0829 ABC superfamily (membrane), glutamine high‐affinity transporter glnP 0.04622489 ‐2.4646764 ‐0.518 0.21016958 0 ‐0.4746565 ‐0.53600425 ‐0.54333925 STM0830 ABC superfamily (bind_prot), glutamine high‐affinity transporter glnH ‐0.027825346 ‐7.2183504 ‐1.6085253 0.22283834 0 ‐1.635288 ‐1.5401719 ‐1.650116 STM0831 stress response DNA‐binding protein starvation induced resistance dps 0.38856125 3.2509615 0.7384427 0.22714594 0 0.66140884 0.76958877 0.7843305 STM0833 outer membrane protease, receptor for phage OX2 ompX ‐0.894851 1.5788158 0.40480867 0.2564002 0.04670303 0.4758158 0.26884237 0.46976787 STM0834 putative Integral membrane protein ybiP ‐0.5037716 2.4400842 0.69245136 0.28378174 0 0.6281674 0.8801465 0.5690402 STM0846 molybdopterin biosynthesis protein moeA 0.98027563 ‐1.9357418 ‐0.4597353 0.23749825 0.034698687 ‐0.4043882 ‐0.5576657 ‐0.41715202 STM0852 putative Fe‐S oxidoreductases family 1 yliG 0.79355973 ‐2.0096643 ‐0.5237102 0.26059586 0 ‐0.4049356 ‐0.65422064 ‐0.5119743 STM0853 putative cytoplasmic protein yliH 0.59155977 ‐5.9793787 ‐1.538247 0.25725865 0 ‐1.6434526 ‐1.5626221 ‐1.4086663 STM0863 D‐alanyl‐D‐alanine carboxypeptidase penicillin‐binding protein 6a dacC ‐1.7955384 1.6642708 0.45627418 0.27415863 0.052023627 0.31407633 0.4442995 0.6104467 STM0887 ABC superfamily (bind_prot), arginine 3rd transport system artJ ‐0.6243266 ‐5.0072575 ‐1.3314965 0.26591334 0 ‐1.4173365 ‐1.4003847 ‐1.1767683 STM0891 ABC superfamily (atp&memb), arginine transport system artP 0.35814568 ‐2.1235948 ‐0.56166404 0.2644874 0 ‐0.71155953 ‐0.5094942 ‐0.4639384 STM0933 putative nucleoside‐diphosphate‐sugar epimerase ybjT 0.28247392 ‐1.5760477 ‐0.44895193 0.28485936 0.068245016 ‐0.25646675 ‐0.53386205 ‐0.556527 STM0934 L‐allo‐threonine aldolase ltaA ‐0.4631164 ‐1.7137818 ‐0.4338928 0.25317854 0.055790044 ‐0.30666682 ‐0.5187434 ‐0.47626817 STM0947 putative integrase protein ‐0.5565279 1.5861906 0.3204029 0.20199521 0.04736082 0.3429845 0.3222452 0.29597893 STM0959 regulator for lrp regulon and high‐affinity branched‐chain lrp ‐0.09547095 ‐1.7718674 ‐0.3830747 0.2161983 0.05861933 ‐0.4318177 ‐0.33552516 ‐0.38188127 STM0965 anaerobic dimethyl sulfoxide reductase, subunit B dmsB 0.32926166 ‐2.2748322 ‐0.5344706 0.23494947 0 ‐0.44168755 ‐0.57411414 ‐0.5876101 STM0972 homologous to secreted protein sopD ‐0.036557928 ‐9.174371 ‐1.8337104 0.19987315 0 ‐1.8201692 ‐1.8244267 ‐1.8565356 STM0973 pyruvate formate lyase I, induced anaerobically pflB ‐1.2157859 ‐7.2015295 ‐1.4780028 0.20523457 0 ‐1.4719023 ‐1.5097382 ‐1.4523679 STM0974 putative FNT family, formate transporter (formate channel focA 0.07664908 ‐5.7152643 ‐1.2789366 0.22377558 0 ‐1.2823764 ‐1.2160076 ‐1.338426 STM0988 CTP:CMP‐3‐deoxy‐D‐manno‐octulosonate transferase kdsB 0.22008257 ‐1.7235955 ‐0.38696107 0.22450806 0.056731287 ‐0.45908305 ‐0.34753028 ‐0.3542699 STM0989 mukF protein (killing factor KicB) ‐0.19417097 ‐2.5064335 ‐0.7407295 0.29553127 0 ‐0.8264857 ‐0.52779496 ‐0.86790794 STM0999 outer membrane protein 1a (iab ompF ‐0.62731314 2.7414734 0.6724593 0.2452912 0 0.559427 0.7175984 0.7403526 STM1066 ribosome modulation factor (involved in dimerization of rmf 1.3327785 ‐2.848908 ‐0.9029276 0.31693813 0 ‐1.0369891 ‐1.025873 ‐0.6459207 STM1068 putative protease lonH ‐0.7728079 2.1189413 0.42138618 0.19886638 0 0.40872064 0.44216406 0.41327387 STM1070 putative hydrogenase, membrane component ompA ‐0.18909171 3.1507075 0.97630244 0.30986768 0 1.1558242 1.0283022 0.74478096 STM1076 methylglyoxal synthase mgsA 0.17430596 ‐2.1019766 ‐0.46763796 0.22247534 0 ‐0.40152797 ‐0.51506615 ‐0.48631975 STM1077 putative periplasmic protein yccT 0.6117423 ‐2.5462399 ‐0.5262113 0.20666212 0 ‐0.5581323 ‐0.5256422 ‐0.4948595 STM1079 putative inner membrane protein yccV ‐0.37682334 1.7550408 0.39683345 0.22611067 0.05861933 0.3499813 0.36906227 0.4714568 STM1091 Salmonella outer protein: homologous to ipgD of sopB ‐0.6070124 2.089835 0.5049752 0.24163401 0 0.41726974 0.60111666 0.49653918 STM1102 4‐hydroxyphenylacetate catabolism hpaE ‐0.41014105 ‐2.3558972 ‐0.56243765 0.23873608 0 ‐0.56380033 ‐0.6489423 ‐0.47457036 STM1106 4‐hydroxyphenylacetate catabolism hpaI ‐0.23352773 ‐2.476858 ‐0.6124471 0.24726775 0 ‐0.7096139 ‐0.5062695 ‐0.62145776 STM1112 curved DNA‐binding protein cbpA 0.8542845 ‐1.7353709 ‐0.44503054 0.25644693 0.056731287 ‐0.3099581 ‐0.5270556 ‐0.49807793 STM1113 Suppression of copper sensitivity: putative copper binding scsA 0.21702328 ‐2.967234 ‐0.76023734 0.25621077 0 ‐0.63344216 ‐0.86534023 ‐0.7819296 STM1121 putative cytoplasmic protein ymdF ‐0.6821211 ‐5.8344264 ‐1.5654155 0.26830667 0 ‐1.585897 ‐1.6924452 ‐1.4179043 STM1122 putative transcriptional repressor (TetR/AcrR family) ycdC 0.4337433 ‐2.2432156 ‐0.5075514 0.22626063 0 ‐0.52784157 ‐0.5605943 ‐0.43421817 STM1124 bifunctional in plasma membrane proline dehydrogenase and putA 0.34658915 ‐2.6396484 ‐0.6631503 0.25122675 0 ‐0.6051473 ‐0.7886939 ‐0.5956098 STM1128 putative sodium/glucose cotransporter 0.42190516 1.7923956 0.34941962 0.19494559 0.06083684 0.34719974 0.3617121 0.339347 STM1139 putative transcriptional regulator in curly assembly/transport, 2nd csgG 0.77964735 ‐3.1918595 ‐1.0043005 0.31464434 0 ‐0.7588283 ‐1.1782665 ‐1.0758065 STM1140 curli production assembly/transport component, 2nd curli operon csgF ‐0.75900143 ‐3.496217 ‐0.8307732 0.23762059 0 ‐0.9241674 ‐0.7570996 ‐0.8110525 STM1141 curli production assembly/transport component, 2nd curli operon csgE ‐0.86330074 ‐2.6320384 ‐0.8747101 0.3323318 0 ‐1.0519996 ‐0.9824834 ‐0.58964723 STM1142 putative transcriptional regulator (LuxR/UhpA family) csgD 0.098342165 ‐4.3753157 ‐1.3654959 0.31209084 0 ‐1.3281112 ‐1.1724006 ‐1.5959761 STM1145 putative curli production protein csgC 0.16054967 ‐7.121766 ‐1.4728444 0.20680887 0 ‐1.4600596 ‐1.4493257 ‐1.5091476 STM1146 putative periplasmic protein ymdA 0.40154338 ‐4.225173 ‐1.2272855 0.29046988 0 ‐1.4272671 ‐1.1628419 ‐1.0917475 STM1147 putative ACR related to the C‐terminal domain 0.39656392 ‐3.2161393 ‐0.88336945 0.27466765 0 ‐0.7126416 ‐0.9903692 ‐0.94709754 STM1150 periplasmic glucans biosynthesis protein mdoG ‐0.5807144 2.3874726 0.59783334 0.25040427 0 0.5415282 0.7216828 0.53028905 STM1152 putative outer membrane lipoprotein yceK 1.4436659 ‐1.9095751 ‐0.41174266 0.21562004 0.033565152 ‐0.36696 ‐0.46095848 ‐0.4073095 STM1177 flagellar biosynthesis, hook protein flgE 0.55069715 ‐1.7683151 ‐0.49171424 0.27806935 0.05861933 ‐0.31285694 ‐0.5696439 ‐0.59264183 STM1178 flagellar biosynthesis, cell‐proximal portion of basal‐body rod flgF ‐0.1828094 ‐2.5236685 ‐0.6080689 0.24094641 0 ‐0.5251709 ‐0.5935623 ‐0.70547336 STM1179 flagellar biosynthesis, cell‐distal portion of basal‐body rod flgG ‐0.047583573 ‐2.0759044 ‐0.42729485 0.20583552 0 ‐0.41774648 ‐0.40301433 ‐0.46112373 STM1204 outer membrane receptor for Fe(III)‐coprogen, Fe(III)‐ferrioxamine B fhuE ‐0.8087064 1.758844 0.4042112 0.22981639 0.05861933 0.32385328 0.46183276 0.42694753 STM1210 putative esterase ycfP 0.4722967 ‐1.6445006 ‐0.4648065 0.28264293 0.05046221 ‐0.3665278 ‐0.65324485 ‐0.37464687 STM1214 putative outer membrane protein ycfR 0.25943294 ‐1.8843414 ‐0.42561358 0.22586861 0.06489263 ‐0.47596112 ‐0.44852042 ‐0.3523592 STM1218 ABC transporter, ATP‐binding protein ycfV 0.024447255 ‐1.9173665 ‐0.4429794 0.23103532 0.03424889 ‐0.3584991 ‐0.49531895 ‐0.4751201 130 STM1224 lysosomal glycoprotein (lgp)‐containing structures replication in macrophages sifA ‐0.6748907 ‐2.6178644 ‐0.7439603 0.28418598 0 ‐0.9267093 ‐0.7023861 ‐0.60278565 STM1237 putative ribosomal large subunit pseudouridine synthase ymfC 0.67902565 ‐1.8545784 ‐0.35797212 0.19302075 0.06410537 ‐0.3603536 ‐0.3645241 ‐0.34903866 STM1238 isocitrate dehydrogenase in e14 prophage, specific for icdA 0.3889185 1.7481579 0.3568656 0.2041381 0.058067188 0.33846152 0.38819313 0.34394217 STM1255 putative ABC transporter periplasmic binding protein ‐0.85976905 1.6431319 0.34467316 0.20976597 0.050878678 0.37114596 0.3023748 0.3604987 STM1261 putative cytoplasmic protein 0.4246444 1.5545261 0.4261478 0.27413356 0.046063263 0.27194655 0.56820977 0.43828702 STM1263 putative periplasmic protein ‐0.3720983 11.453309 2.2708313 0.19826858 0 2.2810953 2.2803102 2.2510886 STM1264 Aminoglycoside adenyltransferase aadA ‐0.4489355 1.5995172 0.3191596 0.19953495 0.048099868 0.3403232 0.3025448 0.31461075 STM1267 putative cytoplasmic protein ‐1.6276593 ‐2.0003424 ‐0.5169653 0.25843844 0 ‐0.5855323 ‐0.5884757 ‐0.376888 STM1274 putative inner membrane protein yeaQ ‐0.5106567 2.818252 0.73309934 0.26012555 0 0.65378964 0.6692242 0.8762841 STM1279 putative regulator (AraC/XylS family) yeaM 0.596286 ‐1.8185207 ‐0.47315857 0.26018873 0.061239734 ‐0.32984093 ‐0.53718746 ‐0.5524473 STM1280 putative inner membrane protein yeaL 0.41556072 ‐1.8218545 ‐0.3674988 0.20171687 0.061239734 ‐0.3692966 ‐0.34357765 ‐0.38962212 STM1284 putative cytoplasmic protein yeaH ‐1.0195017 1.5069036 0.33913857 0.22505657 0.08572143 0.2744936 0.40142876 0.3414933 STM1285 putative Ser protein kinase yeaG 0.5807144 3.1448574 0.6973707 0.22174954 0 0.68933046 0.7587421 0.6440396 STM1291 putative domain frequently associated with peptide methionine yeaA 0.2485467 2.4102736 0.6207158 0.2575292 0 0.5449279 0.75876415 0.5584553 STM1295 protease IV, a signal peptide peptidase sppA 0.009176371 ‐1.6234945 ‐0.38114733 0.2347697 0.048099868 ‐0.2943676 ‐0.45289037 ‐0.39618397 STM1304 arginine succinyltransferase astA 0.17579252 ‐2.2579145 ‐0.5842572 0.25875965 0 ‐0.44366714 ‐0.64911693 ‐0.6599875 STM1310 NAD synthetase, prefers NH3 over glutamine nadE ‐0.043558788 1.6405406 0.35218927 0.2146788 0.050878678 0.29985374 0.38263682 0.37407726 STM1315 transcriptional repressor of cel operon (AraC/XylS family) celD ‐0.22973107 2.3955271 0.5065527 0.21145771 0 0.5395745 0.46215114 0.5179325 STM1335 50S ribosomal subunit protein L35 rpmI ‐0.3579326 ‐5.4844904 ‐1.617162 0.29486093 0 ‐1.4608428 ‐1.5701078 ‐1.8205353 STM1336 50S ribosomal subunit protein L20 rplT ‐5.18E‐04 ‐4.481987 ‐1.1953037 0.26669058 0 ‐1.0606834 ‐1.1933404 ‐1.3318871 STM1338 phenylalanine tRNA synthetase, beta‐subunit pheT 0.589356 1.7982643 0.36011034 0.20025441 0.06083684 0.3735125 0.37035775 0.3364608 STM1341 ABC superfamily (binding protein), vitamin B12 transport btuE ‐0.72050655 1.9587833 0.4892975 0.24979666 0.03676819 0.5887696 0.37719476 0.50192815 STM1345 putative cytoplasmic protein ydiU 0.54063034 4.359923 1.3019979 0.29862866 0 1.1109093 1.4927708 1.3023136 STM1367 putative cytoplasmic protein ydiH ‐0.77816063 ‐4.127592 ‐1.1103107 0.2689972 0 ‐1.1607132 ‐1.217718 ‐0.95250094 STM1370 putative ABC transporter sufB 0.5088498 8.448214 1.8081558 0.21402818 0 1.8288628 1.8384182 1.7571864 STM1372 required for stability of iron‐sulfur component of sufD 0.31884903 6.0610247 1.4977404 0.2471101 0 1.4969852 1.599814 1.3964219 STM1373 selenocysteine lyase sufS 1.4544895 3.9399076 0.92516994 0.23482022 0 1.0143319 0.8581476 0.9030303 STM1374 putative SufE protein probably involved in Fe‐S ynhA 0.09703424 3.3610842 0.77273583 0.22990672 0 0.6949266 0.8367215 0.78655946 STM1378 pyruvate kinase I (formerly F), fructose stimulated pykF ‐0.72706467 4.527835 1.0338037 0.22832187 0 1.0706054 1.076777 0.9540288 STM1384 Tetrathionate reductase complex, subunit C ttrC 0.3823088 ‐1.8441163 ‐0.48361963 0.26225007 0.063013285 ‐0.3832782 ‐0.43991503 ‐0.62766564 STM1393 Secretion system apparatus ssaB ‐3.5863433 ‐3.321381 ‐0.94357896 0.28409234 0 ‐1.0297388 ‐1.0485076 ‐0.7524905 STM1396 Secretion system effector ssaE 1.0441267 ‐3.704352 ‐0.78974617 0.21319415 0 ‐0.81178594 ‐0.8172066 ‐0.74024594 STM1397 Secretion system effector sseA 0.97233033 ‐4.8352513 ‐1.2037889 0.24896097 0 ‐1.091089 ‐1.2985953 ‐1.2216823 STM1398 Secretion system effector sseB 0.41536158 ‐6.4116616 ‐1.57193 0.24516734 0 ‐1.6741128 ‐1.4779617 ‐1.5637157 STM1399 Secretion system chaparone sscA ‐0.018371316 ‐5.2020483 ‐1.1248634 0.2162347 0 ‐1.1751125 ‐1.1205108 ‐1.0789667 STM1400 Secretion system effector sseC ‐0.92264754 ‐2.8720765 ‐0.8302631 0.28908113 0 ‐0.89993477 ‐0.95905095 ‐0.6318036 STM1401 Secretion system effector sseD ‐0.29012236 ‐2.187747 ‐0.48835576 0.22322313 0 ‐0.45797774 ‐0.44925886 ‐0.55783063 STM1402 Secretion system effector sseE 0.35549143 ‐2.1521764 ‐0.58988625 0.27408823 0 ‐0.7404304 ‐0.5855545 ‐0.44367382 STM1406 Secretion system apparatus ssaG ‐0.52065974 ‐5.901822 ‐1.5728054 0.2664949 0 ‐1.7223208 ‐1.4588965 ‐1.5371989 STM1407 Secretion system apparatus ssaH ‐0.39101136 ‐11.970955 ‐2.4865324 0.2077138 0 ‐2.5226486 ‐2.480366 ‐2.4565828 STM1408 Secretion system apparatus ssaI ‐0.24232072 ‐7.416066 ‐1.7376173 0.23430444 0 ‐1.7125388 ‐1.8266512 ‐1.6736618 STM1409 Secretion system apparatus: homology with the yscJ/mxiJ/prgK ssaJ 0.28364876 ‐5.6432705 ‐1.5680448 0.277861 0 ‐1.745902 ‐1.4621507 ‐1.4960818 STM1410 putative cytoplasmic protein ‐0.06895825 ‐5.8044457 ‐1.2747184 0.2196107 0 ‐1.2823895 ‐1.324541 ‐1.2172247 STM1411 Secretion system apparatus ssaK 0.21816084 ‐3.228976 ‐0.98158574 0.3039929 0 ‐1.212782 ‐0.865683 ‐0.86629224 STM1412 Secretion system apparatus ssaL 0.9547462 ‐4.32037 ‐1.4888674 0.3446157 0 ‐1.1971893 ‐1.7317013 ‐1.5377116 STM1413 Secretion system apparatus ssaM ‐0.716915 ‐3.9147432 ‐0.8005478 0.20449561 0 ‐0.77967024 ‐0.8322191 ‐0.78975403 STM1419 Secretion system apparatus: homology with YscR of ssaR ‐0.13103093 ‐7.5789514 ‐2.0216393 0.26674393 0 ‐2.10759 ‐2.092133 ‐1.865195 STM1420 Secretion system apparatus: homology with YscS of ssaS 0.01898982 ‐2.9427886 ‐0.67480695 0.22930868 0 ‐0.6231562 ‐0.64566845 ‐0.7555962 STM1427 cyclopropane fatty acyl phospholipid synthase cfa 0.4185652 2.7529767 0.55761516 0.2025499 0 0.53838634 0.5852242 0.549235 STM1431 superoxide dismutase, iron sodB 0.17044921 ‐4.0022006 ‐1.0226153 0.25551325 0 ‐1.1040957 ‐1.0742626 ‐0.8894877 STM1440 copper/zinc superoxide dismutase sodC 0.2806547 2.893049 0.6454468 0.22310261 0 0.63274634 0.5926958 0.7108983 STM1445 putative outer membrane lipoprotein slyB ‐0.338812 2.7311957 0.6346749 0.23237987 0 0.54758734 0.6674519 0.6889855 STM1451 glutathionine S‐transferase gst ‐0.5933706 2.0478852 0.46913302 0.2290817 0 0.41312236 0.4460167 0.54826 STM1478 putative periplasmic protein ydgH ‐1.193833 1.9415034 0.36741075 0.18924034 0.036121875 0.36855495 0.3679174 0.36575988 STM1489 putative dethiobiotin synthase ynfK ‐0.6498044 ‐4.431105 ‐1.0965344 0.24746296 0 ‐1.1623932 ‐1.1485412 ‐0.97866875 STM1496 putative dimethylsulfoxide reductase 0.6945419 ‐1.5442942 ‐0.33959153 0.2199008 0.06573839 ‐0.3685398 ‐0.37358811 ‐0.27664664 STM1497 putative dimethyl sulphoxide reductase 0.6914045 ‐1.8863444 ‐0.4750416 0.25183186 0.0654669 ‐0.3500527 ‐0.55640876 ‐0.51866335 STM1509 putative cytoplasmic protein ydfZ ‐3.926644 ‐3.2346575 ‐1.1263951 0.348227 0 ‐1.3511477 ‐1.210879 ‐0.81715876 STM1512 dipeptidyl carboxypeptidase II dcp 0.18678641 1.5201771 0.33116612 0.21784706 0.06573839 0.27252302 0.3652916 0.35568377 STM1513 putative cytoplasmic protein 0.10918752 ‐1.6188295 ‐0.6046071 0.3734841 0.048099868 ‐0.7871764 ‐0.79220533 ‐0.23443952 STM1525 putative glutaminase yneH 0.41990083 ‐1.6722969 ‐0.4214768 0.2520347 0.052916735 ‐0.31196776 ‐0.5324096 ‐0.4200531 STM1552 putative cytoplasmic protein ‐0.52230024 1.8279696 0.3799975 0.20787956 0.063013285 0.35886806 0.4189197 0.3622047 STM1554 putative coiled‐coil protein 0.07525889 2.1909156 0.45562753 0.20796216 0 0.43193775 0.44049537 0.4944495 STM1567 alcohol dehydrogenase, propanol preferring adhP ‐0.3468314 1.9271544 0.42115048 0.21853489 0.035160456 0.4718006 0.42413142 0.3675194 STM1586 putative periplasmic protein ‐0.915721 4.32344 1.1393574 0.26353028 0 1.0042905 1.1498488 1.263933 STM1591 putative inner membrane protein ydcZ 0.13037644 ‐2.0564837 ‐0.55696636 0.27083433 0 ‐0.41115236 ‐0.5632204 ‐0.69652635 STM1592 putative cytoplasmic protein ydcY 0.7944661 ‐1.793019 ‐0.46596527 0.25987747 0.060340617 ‐0.38371983 ‐0.6083607 ‐0.4058153 STM1593 ssrAB activated gene srfA 0.20990089 ‐1.6977005 ‐0.5505139 0.32427034 0.055124886 ‐0.6197868 ‐0.28830865 ‐0.74344635 STM1594 ssrAB activated gene srfB 0.59881985 ‐2.2193012 ‐0.5292037 0.2384551 0 ‐0.44180423 ‐0.5306051 ‐0.6152019 STM1595 ssrAB activated gene: predicted coiled‐coil structure srfC 0.36089244 ‐1.7212176 ‐0.46938416 0.27270472 0.056731287 ‐0.6356835 ‐0.41037938 ‐0.36208963 STM1601 putative membrane protein: homology with chitinase from ugtL ‐0.25149482 ‐4.7809167 ‐1.178434 0.24648704 0 ‐1.0815575 ‐1.1713259 ‐1.2824186 STM1612 putative cellulase protein 0.088906236 ‐2.5167675 ‐0.6693413 0.2659528 0 ‐0.52231705 ‐0.7856752 ‐0.7000317 STM1613 putative PTS system, enzymeIIB component ‐0.10828866 ‐1.85785 ‐0.37949064 0.20426334 0.06410537 ‐0.3519927 ‐0.3795157 ‐0.40696353 STM1614 putative PTS system enzyme IIC component 0.49615058 ‐1.7630444 ‐0.48960954 0.27770686 0.05861933 ‐0.33452767 ‐0.6439114 ‐0.49038953 STM1616 putative Sugar Specific PTS Enzyme II 0.047583573 ‐2.7225544 ‐0.6297695 0.23131567 0 ‐0.5471751 ‐0.6508115 ‐0.69132197 STM1623 putative carboxylesterase 0.17831652 ‐2.429326 ‐0.6851491 0.28203258 0 ‐0.6286272 ‐0.8680327 ‐0.5587874 STM1644 putative periplasmic protein ydbL 0.43623662 ‐1.7277565 ‐0.33559528 0.1942376 0.056731287 ‐0.33070552 ‐0.32884836 ‐0.34723192 STM1645 putative outer membrane lipoprotein ynbE 0.44094396 ‐1.9450592 ‐0.41516778 0.21344738 0.035160456 ‐0.4214404 ‐0.4550827 ‐0.3689802 STM1651 putative pyruvate‐flavodoxin oxidoreductase nifJ 0.6186724 ‐1.5383135 ‐0.41540343 0.27003822 0.08572143 ‐0.5660243 ‐0.39470112 ‐0.28548488 STM1660 transcriptional regulation of aerobic, anaerobic respiration, osmotic fnr ‐0.85749865 1.5622748 0.38641268 0.24733976 0.046063263 0.2812335 0.39288732 0.4851172 STM1661 putative universal stress protein ydaA ‐0.15250711 1.6208183 0.31413227 0.19381091 0.04958284 0.30495355 0.31373945 0.3237038 STM1662 putative inner membrane protein ynaJ ‐0.43658268 2.4383981 0.5442187 0.22318698 0 0.532323 0.49079153 0.6095416 STM1682 thiol peroxidase tpx 0.3756022 2.793964 0.6592289 0.23594755 0 0.6041635 0.75391585 0.6196073 STM1698 putative inner membrane protein 0.045942247 ‐2.3116808 ‐0.6160934 0.26651317 0 ‐0.7111045 ‐0.4611765 ‐0.67599916 STM1708 putative N‐acetylglucosaminyl transferase yciM ‐0.7503825 1.6700544 0.37725565 0.22589423 0.052916735 0.30234858 0.41149044 0.41792795 STM1713 transcriptional regulator for cysteine regulon (LysR familiy) cysB ‐0.12179912 1.7845266 0.4553582 0.25517032 0.060340617 0.3855786 0.58886385 0.3916322 STM1716 putative peptidase sohB ‐0.23099546 1.8918875 0.4465226 0.23601963 0.033565152 0.5411348 0.38968608 0.40874696 STM1724 anthranilate synthase, component II, bifunctional: glutamine amidotransferase trpD 0.27366877 3.805509 0.752909 0.19784711 0 0.7407707 0.77152985 0.74642646 STM1725 bifunctional: N‐(5‐phosphoribosyl)anthranilate isomerase indole‐3‐glycerolphosphate synthe trpC 0.34277532 3.0510228 0.6466134 0.21193333 0 0.68937397 0.60817844 0.64228785 STM1726 tryptophan synthase, beta protein trpB ‐0.79187536 2.9440353 0.7161858 0.24326672 0 0.6247902 0.7092721 0.81449515 STM1728 putative cytoplasmic protein yciG 0.36959308 ‐3.1783125 ‐0.9411072 0.2961028 0 ‐0.90716577 ‐1.1423037 ‐0.77385217 STM1732 outer membrane protein W colicin S4 receptor ompW ‐0.12717927 ‐1.6688439 ‐0.42574275 0.25511238 0.052023627 ‐0.3329894 ‐0.555194 ‐0.3890448 STM1749 iron‐dependent alcohol dehydrogenase of the multifunctional alcohol adhE 0.37748227 ‐4.5034084 ‐1.0059755 0.22338091 0 ‐0.94126964 ‐1.0152637 ‐1.0613933 STM1751 DNA‐binding protein HLP‐II (HU, BH2, HD, NS) hns ‐0.72885436 1.5504103 0.4070008 0.26251167 0.046063263 0.28761715 0.39059618 0.5427891 STM1753 Response regulator in protein turnover: mouse virulence hnr ‐0.35583586 1.5627533 0.33332562 0.21329382 0.046063263 0.30030814 0.38211897 0.3175498 STM1754 putative phosphoesterase ychK ‐0.009772128 1.736842 0.39835596 0.22935647 0.057885446 0.47854376 0.34373415 0.37279 STM1764 nitrate reductase 1, alpha subunit narG ‐0.16630559 ‐1.5444626 ‐0.3304342 0.2139477 0.06573839 ‐0.28035256 ‐0.3466574 ‐0.36429262 STM1770 cation transport regulator chaB 0.48628333 2.3577487 0.534197 0.22657079 0 0.564737 0.45832387 0.5795301 STM1774 Regulation of invasion genes sirC 0.33346766 ‐1.602213 ‐0.4214592 0.26304817 0.04736082 ‐0.47131088 ‐0.27464998 ‐0.5184167 STM1781 putative SulP family transport protein ychM 0.30978233 ‐1.6164109 ‐0.3744907 0.2316804 0.048099868 ‐0.43034276 ‐0.2892813 ‐0.40384802 STM1782 putative inner membrane protein ychH ‐0.006837662 ‐1.7690433 ‐0.37773493 0.21352497 0.05861933 ‐0.42107615 ‐0.33402443 ‐0.37810418 STM1786 hydrogenase‐1 small subunit 0.72050655 ‐1.8940483 ‐0.4484414 0.23676343 0.0654669 ‐0.35838655 ‐0.5240665 ‐0.46287107 STM1788 putative Ni/Fe‐hydrogenase 1 b‐type cytochrome subunit 0.42897072 ‐2.9473095 ‐0.6711616 0.2277201 0 ‐0.7412754 ‐0.6669674 ‐0.6052419 STM1790 putative thiol‐disulfide isomerase and thioredoxins ‐0.5935595 ‐1.6620376 ‐0.39791244 0.23941241 0.052023627 ‐0.31401733 ‐0.38956434 ‐0.49015567 STM1801 putative CPA1 family, Na:H transport protein ycgO ‐0.06272232 ‐1.5632942 ‐0.31932694 0.20426542 0.066927865 ‐0.30309612 ‐0.3038189 ‐0.3510658 STM1812 putative Fumarylacetoacetate (FAA) hydrolase family ycgM ‐0.8043529 1.9445734 0.5223995 0.26864478 0.036121875 0.6757513 0.4047032 0.48674396 STM1815 cell division inhibitor, a membrane ATPase, activates minD ‐0.31884903 2.2938716 0.550004 0.23977105 0 0.64360964 0.539904 0.46649835 STM1823 putative cytoplasmic protein yoaH 0.4166632 ‐2.046521 ‐0.42742923 0.20885651 0 ‐0.40831774 ‐0.405646 ‐0.46832395 STM1825 putative NTP pyrophosphohydrolase yeaB ‐0.2603662 ‐1.9616361 ‐0.4049636 0.20644176 0.035703473 ‐0.38418204 ‐0.38979676 ‐0.440912 STM1836 putative penicillin‐binding protein‐3 0.10412655 1.7451955 0.34207723 0.19601083 0.058067188 0.339694 0.35629803 0.33023962 STM1837 cold shock protein, multicopy suppresses mukB mutants cspC 0.338812 ‐2.1933084 ‐0.46800873 0.21338026 0 ‐0.41805288 ‐0.49406308 ‐0.49191025 STM1838 putative cytoplasmic protein yobF ‐0.4868646 ‐1.6014076 ‐0.36553746 0.2282601 0.04736082 ‐0.30826873 ‐0.44221333 ‐0.34613034 STM1839 putative periplasmic or exported protein 0.9481789 ‐3.0785325 ‐0.74039847 0.24050371 0 ‐0.64205503 ‐0.8194449 ‐0.7596955 STM1840 putative inner membrane protein yobG ‐0.22598222 ‐2.68555 ‐0.56033957 0.20864984 0 ‐0.582477 ‐0.57865244 ‐0.51988935 131 STM1854 putative inner membrane protein ‐0.14225803 ‐1.8908732 ‐0.57870054 0.30604938 0.0654669 ‐0.8055051 ‐0.5195907 ‐0.4110058 STM1867 PhoPQ‐activated gene pagK 0.23225684 ‐1.7750379 ‐0.546496 0.3078785 0.05861933 ‐0.72634923 ‐0.5928366 ‐0.32030204 STM1888 pyruvate kinase II, glucose stimulated pykA ‐0.8872296 ‐1.7508423 ‐0.46418396 0.26512036 0.058067188 ‐0.45786908 ‐0.6001217 ‐0.33456108 STM1890 putative Peptidase yebA 0.48606992 3.0416074 0.7799957 0.25644192 0 0.7314299 0.6941771 0.91438 STM1891 ABC superfamily (bind_prot) high affinity Zn transport znuA 0.27830613 6.4869614 1.3998303 0.21579137 0 1.3631965 1.3828597 1.453435 STM1902 putative isochorismatase yecD 0.65049744 ‐1.8461673 ‐0.38982597 0.2111542 0.063013285 ‐0.3656827 ‐0.36847875 ‐0.43531647 STM1907 copper homeostasis protein cutC 0.04163464 ‐2.8789215 ‐0.64926696 0.22552437 0 ‐0.6602084 ‐0.707405 ‐0.58018756 STM1915 chemotactic response CheY protein phophatase cheZ 0.46254298 ‐1.6862135 ‐0.34680057 0.20566824 0.05455575 ‐0.377238 ‐0.34573472 ‐0.31742895 STM1916 chemotaxis regulator, transmits chemoreceptor signals to flagelllar cheY 0.6972522 ‐1.9842178 ‐0.40368968 0.20345029 0.03676819 ‐0.38359508 ‐0.43315798 ‐0.39431602 STM1945 phosphatidylglycerophosphate synthetase (CDP‐1,2‐diacyl‐sn‐glycero‐3‐phosphate phosphat pgsA 0.17695531 1.5019146 0.40419325 0.26911867 0.08572143 0.55077624 0.2722999 0.3895036 STM1946 UvrC with UvrAB is a DNA excision uvrC ‐0.5243877 2.2524245 0.46098557 0.20466195 0 0.4476193 0.49335694 0.4419805 STM1947 putative response regulator (LuxR/UhpA familiy) uvrY 0.08631868 2.1065667 0.44886565 0.21307926 0 0.4637784 0.48216712 0.40065145 STM1959 flagellar biosynthesis flagellin, filament structural protein fliC ‐0.4239646 2.0544918 0.53775656 0.26174676 0 0.39477825 0.5807938 0.6376977 STM1972 flagellum‐specific ATP synthase fliI 0.5728258 ‐1.9406577 ‐0.3873637 0.19960433 0.035160456 ‐0.3656029 ‐0.39357242 ‐0.40291575 STM1978 flagellar biosynthesis fliO 0.10780544 ‐2.7776895 ‐0.6053593 0.21793628 0 ‐0.57403517 ‐0.664406 ‐0.5776367 STM1990 putative permease yedA ‐0.03008651 ‐1.617108 ‐0.42059827 0.26009288 0.048099868 ‐0.28627598 ‐0.53123426 ‐0.44428456 STM2017 cobalamin 5‐phosphate synthase cobS 0.012055409 ‐1.613745 ‐0.37900436 0.23486014 0.048099868 ‐0.35943896 ‐0.31011033 ‐0.46746382 STM2022 synthesis of vitamin B12 adenosyl cobalamide precursor cbiN 0.1329408 ‐2.8734584 ‐0.6194955 0.21559231 0 ‐0.5787262 ‐0.67106575 ‐0.6086947 STM2024 synthesis of vitamin B12 adenosyl cobalamide precursor cbiL 0.6821211 ‐1.9011219 ‐0.48326436 0.25419956 0.0654669 ‐0.36653033 ‐0.5942693 ‐0.48899347 STM2025 synthesis of vitamin B12 adenosyl cobalamide precursor cbiK ‐0.17740087 ‐1.9498528 ‐0.54513216 0.27957606 0.035160456 ‐0.5268891 ‐0.39711508 ‐0.7113924 STM2027 synthesis of vitamin B12 adenosyl cobalamide precursor cbiH ‐0.34015727 ‐1.622655 ‐0.32925114 0.20290889 0.048099868 ‐0.30465424 ‐0.35490012 ‐0.32819906 STM2028 synthesis of vitamin B12 adenosyl cobalamide precursor cbiG ‐1.1164812 ‐1.7631509 ‐0.41459784 0.23514597 0.05861933 ‐0.35900822 ‐0.5075034 ‐0.37728187 STM2029 synthesis of vitamin B12 adenosyl cobalamide precursor cbiF 0.18976788 ‐2.417208 ‐0.53393686 0.22088991 0 ‐0.57792366 ‐0.55337656 ‐0.47051033 STM2033 synthesis of vitamin B12 adenosyl cobalamide precursor cbiC ‐0.23452298 ‐1.536577 ‐0.4781363 0.31116977 0.08572143 ‐0.6331885 ‐0.23571536 ‐0.565505 STM2039 Propanediol utilization: polyhedral bodies pudB 0.2779956 ‐2.9346273 ‐0.6442693 0.21954042 0 ‐0.60162073 ‐0.6262743 ‐0.70491284 STM2041 Propanediol utilization: dehydratase, medium subunit pduD 0.49715197 ‐2.9236968 ‐0.66400766 0.22711235 0 ‐0.6417456 ‐0.6109087 ‐0.7393687 STM2043 Propanediol utilization: diol dehydratase reactivation pduG ‐0.25450563 ‐2.400453 ‐0.7069993 0.29452744 0 ‐0.83050066 ‐0.49573913 ‐0.79475814 STM2045 Propanediol utilization: polyhedral bodies pduJ 0.78167754 ‐3.0361834 ‐0.8561333 0.28197682 0 ‐0.6813047 ‐1.001419 ‐0.8856762 STM2046 Propanediol utilization: polyhedral bodies pduK 0.242989 ‐2.8958943 ‐0.7494269 0.25878945 0 ‐0.8887621 ‐0.6972395 ‐0.662279 STM2048 Propanediol utilization pduM 0.7955477 ‐2.5935204 ‐0.5469762 0.21090107 0 ‐0.5684741 ‐0.5704763 ‐0.50197816 STM2049 Propanediol utilization: polyhedral bodies pduN ‐0.6600288 ‐3.3329809 ‐0.7046891 0.21142909 0 ‐0.7128168 ‐0.73989624 ‐0.6613542 STM2050 Propanediol utilization: B12 related pduO 0.134613 ‐4.498622 ‐1.186744 0.26380166 0 ‐1.039871 ‐1.2898437 ‐1.2305173 STM2052 Propanediol utilization: propanol dehydrogenase pduQ 0.06272232 ‐2.2732737 ‐0.5017642 0.22072317 0 ‐0.44857442 ‐0.49652287 ‐0.5601952 STM2053 Propanediol utilization: polyhedral bodies pduS 0.55507284 ‐2.4895022 ‐0.59797454 0.24019843 0 ‐0.49494177 ‐0.6589297 ‐0.6400521 STM2054 Propanediol utilization: polyhedral bodies pduT ‐0.7478967 ‐1.7570235 ‐0.48667103 0.27698606 0.058067188 ‐0.43534124 ‐0.6592007 ‐0.3654711 STM2056 Propanediol utilization pduV 0.20473526 ‐2.086925 ‐0.44307682 0.21231085 0 ‐0.4730784 ‐0.3958133 ‐0.46033874 STM2058 Propanediol utilization pduX 0.70679843 2.0807743 0.42267004 0.20313112 0 0.39321396 0.43653312 0.43826306 STM2059 putative cytoplasmic protein yeeX 0.07272805 1.5468447 0.37417004 0.24189243 0.068245016 0.32313725 0.3182445 0.48112833 STM2071 ATP phosphoribosyltransferase hisG 0.010775363 4.8080096 1.3240678 0.27538794 0 1.4977757 1.2457414 1.2286866 STM2072 histidinal dehydrogenase (also histidinol dehydrogenase activity) hisD 0.7553158 2.816082 0.59487605 0.21124245 0 0.62781864 0.60583025 0.55097926 STM2073 histidinol phosphate aminotransferase hisC 0.124783926 1.7110859 0.4798721 0.28044885 0.055790044 0.6341258 0.4897871 0.31570336 STM2083 LPS side chain defect: phosphomannomutase rfbK ‐1.1639477 2.0992186 0.5090754 0.2425071 0 0.4056601 0.53315276 0.58841336 STM2087 LPS side chain defect: abequosyltransferase rfbV 0.5941703 4.508169 0.95922565 0.21277499 0 0.98017097 0.9868867 0.9106193 STM2088 LPS side chain defect: putative O‐antigen transferase rfbX ‐0.48211044 1.9578187 0.5429813 0.27733994 0.03676819 0.64507776 0.3657743 0.61809194 STM2089 LPS side chain defect: CDP‐abequose synthase rfbJ 0.2607379 2.8666573 0.6779768 0.2365043 0 0.5925547 0.6823352 0.7590404 STM2090 LPS side chain defect: CDP‐6deoxy‐D‐xylo‐4‐hexulose‐3‐dehydrase rfbH 3.926644 2.1308615 0.4609501 0.216321 0 0.51607764 0.44115597 0.42561674 STM2091 LPS side chain defect: CDP glucose 4,6‐dehydratase rfbG 0.3878993 1.5706683 0.30383807 0.19344509 0.04670303 0.29437086 0.305522 0.3116214 STM2105 mannose‐1‐phosphate in colanic acid gene cluster manC ‐0.43147963 ‐2.6516657 ‐0.66243654 0.24981903 0 ‐0.59368026 ‐0.7849811 ‐0.60864836 STM2106 putative glycosyl transferase in colanic acid biosynthesis wcaI ‐0.06639378 ‐1.5617541 ‐0.35225782 0.22555268 0.066927865 ‐0.42459244 ‐0.30132776 ‐0.33085325 STM2107 GDP‐mannose mannosyl hydrolase in colanic acid biosynthesis wcaH ‐0.08616231 ‐2.3840563 ‐0.5075489 0.21289301 0 ‐0.5529024 ‐0.4688157 ‐0.5009287 STM2108 bifunctional GDP fucose synthetase in colanic acid wcaG 0.3645222 ‐1.8586746 ‐0.46265164 0.24891481 0.06410537 ‐0.5649272 ‐0.4675751 ‐0.35545263 STM2115 putative glycosyl transferase in colanic acid biosynthesis wcaA 0.25384754 ‐1.6581541 ‐0.4503259 0.27158266 0.050878678 ‐0.61527276 ‐0.38669783 ‐0.34900713 STM2137 putative cytoplasmic protein 0.0023499 1.7516836 0.37919724 0.21647587 0.058067188 0.3653426 0.43325955 0.3389896 STM2138 putative cytoplasmic protein 0.74059606 ‐2.107548 ‐0.4649673 0.22062004 0 ‐0.5279302 ‐0.42156166 ‐0.4454101 STM2139 putative inner membrane protein 0.32774305 ‐6.303984 ‐1.4011434 0.22226316 0 ‐1.4245783 ‐1.4444654 ‐1.3343866 STM2141 3‐oxoacyl‐[acyl‐carrier‐protein] synthase I fbaB 0.29865554 5.2366257 1.0823237 0.20668341 0 1.0503691 1.0828861 1.1137159 STM2146 bifunctional enzyme: hydroxy‐phosphomethylpyrimidine kinase (HMP‐P kinase) hydroxy‐metthiD 0.08117722 4.1462216 0.8702698 0.20989466 0 0.8380818 0.9110559 0.86167157 STM2147 hydoxyethylthiazole kinase (THZ kinase) thiM ‐0.15110785 3.2664611 0.79367554 0.24297719 0 0.8900621 0.7898668 0.70109767 STM2148 putative periplasmic protein ‐0.95610934 2.5296724 0.63332325 0.2503578 0 0.7350009 0.5211285 0.64384043 STM2165 putative ABC superfamily (bind_prot) transport protein (possibly yehZ ‐0.13962671 1.7878022 0.36244223 0.20273061 0.060340617 0.33395103 0.37947157 0.37390408 STM2177 putative flutathione S‐transferase 0.5935595 ‐2.0857024 ‐0.56562793 0.27119303 0 ‐0.43391448 ‐0.7184064 ‐0.5445629 STM2182 putative transmembrane protein yohK 0.41579372 ‐1.7213658 ‐0.4044415 0.23495384 0.056731287 ‐0.49740475 ‐0.35330626 ‐0.3626135 STM2199 outer membrane porin, receptor for colicin I cirA ‐0.12922949 1.5710416 0.3538934 0.22526036 0.04670303 0.42267513 0.34250376 0.29650134 STM2215 putative membrane protein involved in resistance to rtn ‐0.29431117 1.6561495 0.42364764 0.25580278 0.052023627 0.38642746 0.55447435 0.3300411 STM2220 putative cytoplasmic protein yejG ‐0.19318686 2.620795 0.6993397 0.26684257 0 0.545852 0.8042508 0.7479163 STM2228 putative hydrolase of alkaline phosphatase superfamily yejM ‐0.14666101 1.6415534 0.3987934 0.2429366 0.050878678 0.30365953 0.49258414 0.4001365 STM2232 O‐antigen five: acetylation of the O‐antigen (LPS) oafA 0.32732183 1.6109928 0.43825793 0.27204216 0.04958284 0.3239555 0.38961717 0.6012011 STM2238 putative phage protein 0.36262566 1.6090502 0.465682 0.28941423 0.04958284 0.27185622 0.51321316 0.6119766 STM2263 putative ABC‐type multidrug/protein/lipid transport system, ATPase component yojI ‐0.96113396 2.2059066 0.562082 0.2548077 0 0.6755607 0.4455595 0.56512576 STM2267 outer membrane protein 1b (ibc), porin ompC ‐0.7809095 ‐1.9021436 ‐0.53480476 0.28115898 0.033565152 ‐0.3649795 ‐0.68441063 ‐0.5550241 STM2277 ribonucleoside diphosphate reductase 1, alpha subunit nrdA ‐0.48932013 2.1312099 0.5401507 0.25344792 0 0.64364344 0.4201201 0.5566886 STM2278 ribonucleoside‐diphosphate reductase 1, beta subunit nrdB ‐2.1630812 2.0535486 0.43424866 0.21146257 0 0.45811883 0.38812217 0.45650494 STM2281 putative transcriptional regulator, LysR family 0.17133029 1.546044 0.43788272 0.28322786 0.068245016 0.48504767 0.5733965 0.25520396 STM2284 sn‐glycerol‐3‐phosphate dehydrogenase (anaerobic), large subunit glpA 0.6802861 ‐1.773006 ‐0.39965507 0.22541101 0.05861933 ‐0.4733156 ‐0.35640326 ‐0.3692464 STM2285 sn‐glycerol‐3‐phosphate dehydrogenase (anaerobic), membrane anchor subunit glpB ‐0.2790565 ‐2.5175543 ‐0.5193986 0.2063108 0 ‐0.5205092 ‐0.48782656 ‐0.5498602 STM2287 putative cytoplasmic protein 0.23472808 ‐6.2657723 ‐1.7654071 0.2817541 0 ‐1.9183186 ‐1.596153 ‐1.7817496 STM2288 putative cytoplasmic protein 0.2042397 ‐2.2096314 ‐0.5073072 0.22958905 0 ‐0.515934 ‐0.43203512 ‐0.5739523 STM2302 putative inner membrane protein 0.68675524 ‐1.565997 ‐0.340133 0.21719901 0.066927865 ‐0.29371068 ‐0.39288747 ‐0.3338009 STM2303 putative inner membrane protein 0.3675542 ‐1.538488 ‐0.39424852 0.25625712 0.08572143 ‐0.27444246 ‐0.50938594 ‐0.39891717 STM2305 o‐succinylbenzoate‐CoA ligase menE 0.52284837 ‐1.6581715 ‐0.41073996 0.24770656 0.050878678 ‐0.40995222 ‐0.51386285 ‐0.3084048 STM2309 bifunctional: 2‐oxoglutarate decarboxylase SHCHC synthase menD ‐0.6644143 ‐2.62942 ‐0.56831187 0.21613583 0 ‐0.5449582 ‐0.62357396 ‐0.5364034 STM2316 NADH dehydrogenase I chain N nuoN ‐0.3913837 ‐1.978606 ‐0.5714599 0.28881946 0.036121875 ‐0.3797041 ‐0.71908444 ‐0.61559105 STM2317 NADH dehydrogenase I chain M nuoM ‐0.070373535 ‐2.3020332 ‐0.6920966 0.3006458 0 ‐0.46761006 ‐0.8066455 ‐0.8020342 STM2318 NADH dehydrogenase I chain L nuoL 0.5106567 ‐3.9200768 ‐0.94015235 0.23983008 0 ‐0.8575317 ‐0.92838544 ‐1.0345399 STM2319 NADH dehydrogenase I chain K nuoK 0.5521063 ‐3.036932 ‐0.7651977 0.25196406 0 ‐0.81707346 ‐0.83978295 ‐0.6387367 STM2320 NADH dehydrogenase I chain J nuoJ ‐0.13995406 ‐1.7319527 ‐0.5037587 0.29086173 0.056731287 ‐0.6258309 ‐0.58527905 ‐0.3001663 STM2321 NADH dehydrogenase I chain I nuoI ‐0.64088565 ‐2.0668354 ‐0.50264955 0.24319766 0 ‐0.39599353 ‐0.57785195 ‐0.5341032 STM2323 NADH dehydrogenase I chain G nuoG ‐0.7296543 ‐2.155235 ‐0.49767953 0.23091659 0 ‐0.55333656 ‐0.52553827 ‐0.41416374 STM2324 NADH dehydrogenase I chain F nuoF 0.3997259 ‐3.00943 ‐1.1499493 0.38211533 0 ‐0.76764554 ‐1.3955622 ‐1.2866403 STM2326 NADH dehydrogenase I chain C,D nuoC 0.61789894 ‐3.8015668 ‐0.8547408 0.22483908 0 ‐0.90607184 ‐0.87389094 ‐0.7842597 STM2327 NADH dehydrogenase I chain B nuoB ‐1.7359381 ‐1.9314836 ‐0.3917852 0.20284158 0.034698687 ‐0.40745583 ‐0.36292687 ‐0.40497294 STM2328 NADH dehydrogenase I chain A nuoA ‐0.4166632 ‐2.5627573 ‐0.5517462 0.21529397 0 ‐0.5014692 ‐0.5934646 ‐0.56030476 STM2336 putative cytoplasmic protein ‐0.66304207 ‐1.6542156 ‐0.3539837 0.21398886 0.050878678 ‐0.3434763 ‐0.31585088 ‐0.40262392 STM2337 acetate kinase A (propionate kinase 2) ackA 0.5191252 ‐2.05375 ‐0.45850068 0.22325048 0 ‐0.39079365 ‐0.47798032 ‐0.50672805 STM2338 phosphotransacetylase pta 0.75595593 ‐2.351337 ‐0.49103177 0.20883088 0 ‐0.4616236 ‐0.48115346 ‐0.5303182 STM2352 ABC superfamily (membrane),histidine and lysine/arginine/ornithine transport protein hisM ‐0.48606992 ‐1.5773194 ‐0.382113 0.24225469 0.068245016 ‐0.3382629 ‐0.48924717 ‐0.31882894 STM2354 ABC superfamily (bind_prot), histidine transport protein hisJ 1.7563617 ‐2.774061 ‐0.66503084 0.23973188 0 ‐0.5936473 ‐0.7646353 ‐0.63680995 STM2355 ABC superfamily (bind_prot), lysine/arginine/ornithine transport protein argT ‐0.63420165 ‐6.5478616 ‐1.3726482 0.20963305 0 ‐1.400604 ‐1.3309743 ‐1.3863664 STM2356 3‐octaprenyl‐4‐hydroxybenzoate carboxy‐lyase ubiX 0.7143338 ‐1.7028176 ‐0.4425513 0.25989357 0.055124886 ‐0.52964103 ‐0.49722984 ‐0.3007831 STM2361 putative regulatory protein 0.8369787 1.6060458 0.34779134 0.21655132 0.048099868 0.3028818 0.3408225 0.39966974 STM2362 amidophosphoribosyltransferase (PRPP amidotransferase) purF 0.16881002 2.1691628 0.62381923 0.28758526 0 0.54774284 0.8205257 0.5031891 STM2378 3‐oxoacyl‐[acyl‐carrier‐protein] synthase I fabB 0.2437359 ‐2.6296556 ‐0.63853145 0.24281941 0 ‐0.70569223 ‐0.5307672 ‐0.67913485 STM2379 putative peptidase ‐0.031086246 ‐2.1643114 ‐0.4638559 0.21432032 0 ‐0.41575897 ‐0.50468045 ‐0.47112826 STM2381 putative cytoplasmic protein yfcM 0.44535005 ‐1.8295588 ‐0.42270818 0.23104377 0.062375717 ‐0.33975238 ‐0.44699302 ‐0.48137915 STM2387 phosphohistidine phosphatase sixA ‐0.1834248 ‐2.1401942 ‐0.46132487 0.2155528 0 ‐0.4210802 ‐0.44985646 ‐0.513038 STM2389 paral putative acetyl‐CoA acetyltransferase yfcY 0.13399245 ‐2.0348394 ‐0.56511503 0.27771974 0 ‐0.43354943 ‐0.735563 ‐0.5262327 STM2390 putative cytoplasmic protein yfcZ ‐0.28506687 ‐4.8828397 ‐1.0083835 0.20651579 0 ‐1.0053508 ‐1.0411766 ‐0.97862315 STM2398 Phosphoglycerate transport: protein for signal transmission pgtC ‐0.15515926 1.5940671 0.34968966 0.21936947 0.048099868 0.32204297 0.41152418 0.31550187 STM2402 putative aminotransferase yfdZ ‐0.08337924 2.7230554 0.5595862 0.2054994 0 0.55602515 0.5908321 0.53190136 STM2405 putative thiamine pyrophosphate enzymes ‐0.5341613 ‐1.5316386 ‐0.33553457 0.21906902 0.08572143 ‐0.30937022 ‐0.3005613 ‐0.39667216 STM2408 Nramp family, manganese/divalent cation transport prortein mntH ‐0.57709175 2.3724792 0.52456117 0.22110254 0 0.5733523 0.53790146 0.46242976 STM2409 NUP family, nucleoside transport nupC ‐0.8325245 2.2364955 0.4327145 0.19347881 0 0.4415167 0.4327222 0.42390454 STM2430 subunit of cysteine synthase A and O‐acetylserine cysK ‐0.54243934 2.981871 0.6296421 0.21115674 0 0.6733387 0.6188528 0.59673494 STM2432 General PTS family (Enzyme I) PEP‐protein phosphotransferase ptsI 1.0520763 1.9883046 0.48012874 0.24147645 0 0.5854015 0.41560653 0.43937817 132 STM2433 PTS family, glucose‐specific IIA component crr ‐0.65337825 1.8192166 0.3542742 0.19473998 0.062375717 0.35445872 0.3651713 0.34319264 STM2434 putative cytoplasmic protein ‐0.38856125 1.6121976 0.33624816 0.2085651 0.04958284 0.2990498 0.34132865 0.36836603 STM2467 putative cobalamin adenosyltransferase, ethanolamine utilization eutT ‐0.013171276 ‐2.8735518 ‐0.625198 0.21756977 0 ‐0.5692435 ‐0.638844 ‐0.6675065 STM2473 transaldolase A talA ‐0.16054967 2.561785 0.59729755 0.23315679 0 0.5624847 0.68613225 0.54327565 STM2474 transketolase 2, isozyme tktB ‐0.5674203 4.666097 1.0819167 0.23186758 0 1.0057616 1.0836624 1.156326 STM2479 putative oxidoreductase aegA ‐0.30372322 ‐1.926026 ‐0.46602872 0.24196388 0.03424889 ‐0.3615075 ‐0.49790597 ‐0.5386727 STM2494 putative inner membrane or exported 0.26768297 ‐1.5628579 ‐0.38142538 0.24405634 0.066927865 ‐0.49168766 ‐0.31301418 ‐0.33957434 STM2498 uracil phosphoribosyltransferase upp 0.6009477 ‐1.7749461 ‐0.38160723 0.21499652 0.05861933 ‐0.34565735 ‐0.43354815 ‐0.36561623 STM2502 exopolyphosphatase ppx 0.43058366 3.177252 0.6388487 0.20106958 0 0.61512345 0.6584442 0.64297855 STM2511 IMP dehydrogenase guaB 0.33034065 1.684308 0.4266534 0.25331077 0.052916735 0.5478117 0.32566613 0.4064823 STM2517 Similar to E. coli intimin and Y. sinH 0.2865135 2.1056473 0.56546915 0.26854885 0 0.47166616 0.72495323 0.499788 STM2519 putative GTP‐binding protein engA ‐0.17327718 3.3033478 0.8809325 0.2666787 0 0.7479109 1.0189564 0.87593013 STM2522 histidine tRNA synthetase hisS 0.26110312 1.5559567 0.33507386 0.2153491 0.046063263 0.3655798 0.28132844 0.3583133 STM2542 NifU homologs involved in Fe‐S cluster formation nifU 0.08616231 2.1722233 0.45517138 0.20954171 0 0.49533635 0.44656402 0.42361376 STM2544 believed to be involved in assembly of yfhP ‐0.37775114 9.5240965 1.9619348 0.20599695 0 1.9767494 1.9268703 1.9821848 STM2549 anaerobic sulfide reductase asrB 0.15547217 ‐2.385942 ‐0.53982776 0.22625351 0 ‐0.46834084 ‐0.59718376 ‐0.55395865 STM2551 putative inner membrane protein 0.23599179 ‐2.5028055 ‐0.5609435 0.22412588 0 ‐0.50833637 ‐0.62913424 ‐0.54535985 STM2553 stationary phase inducible protein csiE 0.09262392 ‐2.0437748 ‐0.52561206 0.25717708 0 ‐0.40518212 ‐0.6434078 ‐0.52824616 STM2555 serine hydroxymethyltransferase glyA ‐0.7095931 2.7489436 0.59083503 0.21493167 0 0.64363766 0.55979085 0.5690766 STM2565 phosphoribosylformylglycinamidine synthetase purG ‐0.021467928 ‐1.5699105 ‐0.31634206 0.20150323 0.068245016 ‐0.34233952 ‐0.30040976 ‐0.30627686 STM2579 gap repair gene recO 0.17475298 ‐1.9708909 ‐0.48655787 0.24687205 0.036121875 ‐0.371346 ‐0.561585 ‐0.52674264 STM2589 Gifsy‐1 prophage: similar to host specificity protein‐J 0.64088565 ‐2.3857079 ‐0.57298076 0.24017222 0 ‐0.4698734 ‐0.6328658 ‐0.6162032 STM2590 Gifsy‐1 prophage: similar to tail assembly protein 0.38600674 ‐3.466351 ‐0.76763445 0.22145317 0 ‐0.7199838 ‐0.7517651 ‐0.8311544 STM2591 Gifsy‐1 prophage: similar to tail assembly protein ‐0.7314146 ‐1.6680993 ‐0.32971835 0.1976611 0.052023627 ‐0.33095503 ‐0.34511426 ‐0.31308576 STM2592 Gifsy‐1 prophage: similar to phage tail component ‐0.1254499 ‐1.8686115 ‐0.37236515 0.19927372 0.064440414 ‐0.393688 ‐0.36545414 ‐0.35795328 STM2595 Gifsy‐1 prophage: similar to minor tail protein 0.31760445 ‐1.7917174 ‐0.41204378 0.22997141 0.060340617 ‐0.4272208 ‐0.3336518 ‐0.47525877 STM2596 Gifsy‐1 prophage: similar to minor tail protein 0.05993005 ‐1.582121 ‐0.33095923 0.20918705 0.046063263 ‐0.30662757 ‐0.31391972 ‐0.37233043 STM2602 Gifsy‐1 prophage: similar to DNA packaging protein 0.9521248 ‐1.7196335 ‐0.48144004 0.27996665 0.056731287 ‐0.3195953 ‐0.6365987 ‐0.48812613 STM2604 Gifsy‐1 prophage: similar to head protein gpshp 0.32908002 ‐2.585872 ‐0.6103121 0.23601791 0 ‐0.51528144 ‐0.6633785 ‐0.65227646 STM2605 Gifsy‐1 prophage: similar to head‐tail preconnector gp5 0.95610934 ‐2.3411322 ‐0.61972415 0.26471132 0 ‐0.46762577 ‐0.6847157 ‐0.7068311 STM2606 Gifsy‐1 prophage: similar to head‐tail preconnector gp4 ‐0.007332975 ‐1.9253645 ‐0.4464568 0.2318817 0.03424889 ‐0.4409544 ‐0.37403706 ‐0.5243789 STM2607 Gifsy‐1 prophage: similar to head to tail ‐0.029520666 ‐1.7281822 ‐0.35720184 0.20669223 0.056731287 ‐0.3932887 ‐0.34442255 ‐0.33389425 STM2610 Gifsy‐1 prophage 0.21790259 3.8077862 1.1969088 0.31433195 0 0.95621353 1.3815212 1.2529918 STM2639 anti sigma E (sigma 24) factor, negative rseA ‐0.08816588 ‐3.3410387 ‐0.7606921 0.22768132 0 ‐0.72710884 ‐0.83900166 ‐0.7159658 STM2640 sigma E (sigma 24 ) factor of rpoE 0.23431368 ‐2.2173152 ‐0.46861127 0.21134175 0 ‐0.47248483 ‐0.4270707 ‐0.5062783 STM2646 putative formate acetyltransferase yfiD ‐0.18066832 ‐11.103164 ‐2.4723043 0.22266665 0 ‐2.409216 ‐2.5270565 ‐2.4806406 STM2663 putative lipoprotein yfiO ‐0.6043905 1.5775374 0.35398266 0.22438939 0.04670303 0.42493463 0.3290534 0.30795994 STM2667 bifuctional: chorismate mutase P prephenate dehydratase pheA 2.0980732 3.5734046 0.79526293 0.2225505 0 0.8552046 0.7936667 0.7369175 STM2668 putative cytoplasmic protein 0.5136386 2.3783302 0.6116032 0.25715655 0 0.6434514 0.7115405 0.47981763 STM2669 bifunctional: chorismate mutase T prephenate dehydrogenase tyrA 0.081469074 5.419729 1.3014176 0.24012594 0 1.3667911 1.3381793 1.1992822 STM2670 3‐deoxy‐D‐arabinoheptulosonate‐7‐phosphate synthase (DAHP synthetase), tyrosine repress aroF 0.11829828 5.744588 1.4662604 0.25524205 0 1.4136881 1.5990025 1.3860908 STM2671 putative periplasmic protein yfiR ‐0.4149684 1.6690217 0.40024126 0.23980589 0.052916735 0.489211 0.31111732 0.40039545 STM2674 tRNA (guanine‐7‐)‐methyltransferase trmD 0.16898407 1.8849525 0.46972016 0.24919468 0.033565152 0.4924994 0.561775 0.354886 STM2677 4.5S‐RNP protein, GTP binding export factor, part ffh 0.3341258 1.5047429 0.3685255 0.24490929 0.08572143 0.3377278 0.47810686 0.28974184 STM2679 putative membrane protein yfjD ‐0.28888452 1.8464377 0.3972695 0.21515456 0.064440414 0.41756362 0.34423426 0.43001056 STM2746 putative Excinuclease ATPase subunit 0.28186047 2.202804 0.6331306 0.2874203 0 0.59398854 0.48456725 0.820836 STM2749 putative cytoplasmic protein 0.47202364 ‐2.092767 ‐0.42148352 0.20140012 0 ‐0.4076845 ‐0.40928802 ‐0.44747806 STM2751 putative PTS enzyme III glucitol ‐0.67629176 ‐1.6093239 ‐0.46324494 0.28785068 0.04736082 ‐0.26452866 ‐0.57024425 ‐0.5549619 STM2771 Flagellar synthesis: phase 2 flagellin (filament structural fljB 0.40745282 2.5403817 0.69475317 0.27348378 0 0.59391034 0.86389077 0.62645835 STM2773 putative glycosyl transferase, related to UDP‐glucuronosyltransferase iroB ‐1.0346557 6.189298 1.4180722 0.22911681 0 1.4615705 1.4559537 1.3366925 STM2774 putative ATP binding cassette (ABC) transporter iroC ‐0.011871857 6.68708 1.4215128 0.21257602 0 1.4685358 1.3882108 1.4077921 STM2775 Similar to enterochelin esterase of E. coli iroD 0.7353798 4.474524 0.8989909 0.20091319 0 0.88882965 0.9238883 0.88425475 STM2776 putative hydrolase of the alpha/beta superfamily iroE ‐0.19924144 4.0543313 0.9122978 0.22501807 0 0.8541298 0.9028306 0.97993296 STM2777 TonB‐dependent siderophore receptor protein iroN ‐0.4069506 7.56298 2.0399888 0.26973346 0 1.9108407 2.1902285 2.018897 STM2779 putative inner membrane protein 0.47630718 ‐5.8051662 ‐1.5396948 0.26522836 0 ‐1.6570932 ‐1.5668646 ‐1.3951266 STM2780 Homolog of pipB, putative pentapeptide repeats (8 ‐0.46633133 ‐3.59977 ‐0.9542383 0.26508313 0 ‐1.0780922 ‐0.8139626 ‐0.97066003 STM2782 putative transcription activator mig14 ‐0.25296074 4.1857886 1.0240896 0.2446587 0 0.9791757 1.1358998 0.95719343 STM2787 tricarboxylic transport 0.57586616 ‐2.0372272 ‐0.44473085 0.21830204 0 ‐0.386124 ‐0.48439232 ‐0.46367618 STM2788 tricarboxylic transport 0.9376291 ‐1.5308144 ‐0.4246101 0.2773753 0.08572143 ‐0.24668622 ‐0.5167338 ‐0.51041025 STM2795 putative LysM domain ygaU ‐0.03481237 2.9865005 0.7203916 0.24121596 0 0.6232691 0.73295707 0.8049486 STM2799 DNA‐binding protein with chaperone activity stpA 0.49670693 2.5214539 0.6293155 0.24958438 0 0.51035285 0.7136659 0.6639277 STM2800 putative inner membrane protein 0.21383426 ‐4.598871 ‐1.012539 0.22017121 0 ‐1.0397096 ‐1.0487089 ‐0.9491986 STM2805 glutaredoxin‐like protein hydrogen donor nrdH ‐0.36406824 6.1426373 1.52848 0.24883124 0 1.4108615 1.5631614 1.6114173 STM2806 stimulates ribonucleotide reduction nrdI 0.47769812 6.8323383 1.6026502 0.23456833 0 1.5859082 1.6896712 1.5323713 STM2807 ribonucleoside diphosphate reductase 2, alpha subunit nrdE ‐0.39838722 4.6810384 1.2849627 0.27450377 0 1.3610189 1.1131215 1.3807477 STM2808 ribonucleoside‐diphosphate reductase 2, beta subunit nrdF ‐0.07272805 6.8673444 1.417359 0.20639114 0 1.3861983 1.4173386 1.44854 STM2814 multidrug resistance secretion protein emrA 0.18665256 ‐3.0507817 ‐0.6271336 0.20556489 0 ‐0.6603798 ‐0.61795837 ‐0.6030626 STM2829 DNA strand exchange and recombination protein with recA 0.29619932 1.87776 0.4893526 0.26060444 0.0654669 0.36601838 0.616091 0.48594844 STM2839 putative regulator (EBP family) ygaA 0.892488 ‐1.9058558 ‐0.4110887 0.2156977 0.033565152 ‐0.37556294 ‐0.3929376 ‐0.46476558 STM2842 hydrogenase maturation protein hypF 0.0680781 ‐3.583148 ‐0.99806815 0.27854505 0 ‐1.0317818 ‐0.8278202 ‐1.1346024 STM2843 electron transport protein (FeS senter) from formate hydN ‐0.09703424 ‐9.977834 ‐2.1389928 0.21437447 0 ‐2.111915 ‐2.1141264 ‐2.1909368 STM2844 putative periplasmic or exported protein ‐0.30537802 ‐6.415396 ‐1.2712086 0.19814967 0 ‐1.2787188 ‐1.2830478 ‐1.2518593 STM2845 protease involved in processing C‐terminal end of hycI ‐0.008713709 ‐8.437943 ‐1.9920542 0.23608291 0 ‐2.0330992 ‐1.896973 ‐2.0460904 STM2846 processing of HycE (part of the FHL hycH 1.952237 ‐8.423226 ‐2.118257 0.2514781 0 ‐1.9982865 ‐2.2120636 ‐2.144421 STM2847 hydrogenase activity hycG 0.43555936 ‐7.27101 ‐1.8727365 0.25756207 0 ‐1.9896524 ‐1.878313 ‐1.750244 STM2848 hydrogenase 3, putative quinone oxidoreductase hycF ‐0.32774305 ‐6.8854866 ‐1.366492 0.19845976 0 ‐1.3526257 ‐1.386063 ‐1.3607873 STM2849 hydrogenase 3, large subunit (part of FHL hycE ‐0.10447852 ‐7.199212 ‐1.6625693 0.23093767 0 ‐1.5778861 ‐1.6977483 ‐1.7120734 STM2850 hydrogenase 3, membrane subunit (part of FHL hycD 0.8157917 ‐7.5005045 ‐1.6631119 0.22173335 0 ‐1.721211 ‐1.6057289 ‐1.6623961 STM2851 hydrogenase 3, membrane subunit (part of FHL hycC ‐0.1668846 ‐7.3001404 ‐1.5842414 0.21701519 0 ‐1.5309073 ‐1.5929081 ‐1.6289089 STM2852 hydrogenase‐3, iron‐sulfur subunit (part of FHL complex) hycB ‐0.7970295 ‐5.7668977 ‐1.6479834 0.28576604 0 ‐1.7143096 ‐1.7733897 ‐1.4562511 STM2853 transcriptional repressor of hyc and hyp operons hycA ‐0.6972522 ‐11.173628 ‐2.2596273 0.20222862 0 ‐2.2677011 ‐2.278509 ‐2.2326722 STM2854 guanine‐nucleotide binding protein in formate‐hydrogenlyase system, functions hypA ‐0.527547 ‐5.8847423 ‐1.4088316 0.23940413 0 ‐1.380965 ‐1.3377738 ‐1.5077561 STM2855 hydrogenase‐3 accessory protein, assembly of metallocenter hypB ‐0.59802824 ‐6.240275 ‐1.6178005 0.25925148 0 ‐1.510201 ‐1.5917325 ‐1.7514678 STM2856 putative hydrogenase expression/formation protein hypC 0.29370916 ‐5.545602 ‐1.4704473 0.26515558 0 ‐1.6043607 ‐1.3384742 ‐1.4685069 STM2857 putative hydrogenase expression/formation protein hypD ‐0.43555936 ‐5.526359 ‐1.4411981 0.26078618 0 ‐1.3017131 ‐1.5445496 ‐1.4773316 STM2858 putative hydrogenase expression/formation protein hypE ‐0.064038225 ‐6.1224804 ‐1.2040635 0.1966627 0 ‐1.2006162 ‐1.1917812 ‐1.2197933 STM2860 putative cytoplasmic protein ygbA 0.040863574 2.5183148 0.5333035 0.21176998 0 0.48882106 0.54308647 0.56800294 STM2861 Salmonella iron transporter: fur regulated sitA 0.7550373 7.4020724 1.6802702 0.22699997 0 1.7026858 1.6050758 1.7330488 STM2862 Salmonella iron transporter: fur regulated sitB ‐0.33848143 9.684762 1.9805951 0.20450632 0 2.0106812 1.9755465 1.9555578 STM2863 Salmonella iron transporter: fur regulated sitC ‐0.5332558 5.7489934 1.4459906 0.25152066 0 1.479524 1.534634 1.3238136 STM2864 Salmonella iron transporter: fur regulated sitD ‐0.46562156 3.4989843 0.9153204 0.26159602 0 1.0156461 0.77281904 0.95749605 STM2865 putative inner membrane protein avrA ‐0.2670785 2.6908598 0.5966483 0.22173147 0 0.6580734 0.54348016 0.5883913 STM2866 transcriptional regulator sprB 0.308206 2.6650038 0.8635065 0.324017 0 0.59358567 0.9752863 1.0216476 STM2869 putative flagellar biosynthesis/type III secretory pathway protein orgA 2.3926606 1.6843232 0.3551381 0.21084914 0.052916735 0.36044982 0.31386286 0.39110157 STM2870 putative inner membrane protein ‐0.3761747 2.4290555 0.5277148 0.21725103 0 0.58417714 0.5098313 0.48913586 STM2874 cell invasion protein prgH ‐0.696366 2.0439458 0.49309307 0.24124567 0 0.42180738 0.46114555 0.5963263 STM2876 invasion genes transcription activator hilA ‐0.33177054 2.5835035 0.5453996 0.21110852 0 0.5715682 0.5001568 0.56447375 STM2884 cell invasion protein sipC 0.21098736 1.5504521 0.40571925 0.26167804 0.046063263 0.43151522 0.5177704 0.2678721 STM2886 surface presentation of antigens secretory proteins sicA ‐0.7702837 2.5279467 0.51347303 0.2031186 0 0.48522937 0.5348135 0.52037615 STM2901 putative cytoplasmic protein 0.49063027 1.685345 0.5332098 0.3163802 0.052916735 0.28170028 0.617756 0.7001731 STM2911 putative permease ‐0.18137346 ‐1.5582019 ‐0.35548824 0.22814004 0.066927865 ‐0.36350116 ‐0.28299135 ‐0.4199722 STM2912 putative transcriptional regulators, LysR family 0.045784447 ‐1.5383174 ‐0.3232793 0.21015123 0.08572143 ‐0.3450248 ‐0.27976608 ‐0.34504697 STM2913 putative permease ‐0.6802861 ‐1.6398499 ‐0.36311668 0.22143288 0.05046221 ‐0.41174516 ‐0.37754562 ‐0.3000593 STM2915 putative endonuclease ygbM 0.13783324 ‐1.5541407 ‐0.3682516 0.23694868 0.06573839 ‐0.3617602 ‐0.28758729 ‐0.4554073 STM2916 putative fuculose phosphate aldolase ygbL ‐0.049529877 ‐2.2552972 ‐0.62285304 0.27617338 0 ‐0.4605548 ‐0.64603853 ‐0.7619659 STM2917 paral putative tRNA synthase ygbK 0.52850026 ‐2.4557018 ‐0.6114726 0.24900116 0 ‐0.5294304 ‐0.7297677 ‐0.57521975 STM2924 sigma S (sigma 38) factor of RNA rpoS ‐0.48767444 2.25904 0.76321775 0.33785045 0 1.0578645 0.65946704 0.5723216 STM2935 ATP‐sulfurylase, subunit 1 (ATP:sulfate adenylyltransferase) cysD ‐0.03192459 1.6190747 0.33162707 0.20482506 0.04958284 0.3542767 0.29968372 0.3409208 STM2951 putative Organic radical activating enzymes ygcF ‐1.4100732 1.8315825 0.55930185 0.30536535 0.063013285 0.62965447 0.71734643 0.33090457 STM2953 CTP synthetase pyrG ‐0.42557448 2.2851748 0.54230773 0.23731564 0 0.46347573 0.63191265 0.53153473 STM2963 putative MFS superfamily, D‐glucarate permease 2.5459478 2.8567734 0.59356046 0.20777303 0 0.6211641 0.5561981 0.6033192 STM2971 L‐serine dehydratase (L‐threonine deaminase 2) sdaB ‐1.0841919 ‐1.5614433 ‐0.35461727 0.22710864 0.066927865 ‐0.32765755 ‐0.43095577 ‐0.30523852 STM2976 L‐fucose isomerase fucI 0.0894275 ‐2.0800235 ‐0.6155243 0.2959218 0 ‐0.40149662 ‐0.7043617 ‐0.7407146 STM2992 N‐alpha‐acetylglutamate synthase (amino‐acid acetyltransferase) argA ‐0.6009477 ‐7.1791983 ‐1.8984652 0.2644397 0 ‐1.8826816 ‐2.0373597 ‐1.7753541 133 STM3003 General PTS system, enzyme I, transcriptional regulator ptsP 0.6755954 2.1136682 0.45365244 0.21462803 0 0.45904133 0.49615526 0.4057607 STM3033 putative nucleic acid‐binding protein, contains PIN domain 0.23257047 1.6121213 0.3775923 0.23422077 0.04958284 0.2999577 0.45859674 0.37422243 STM3034 putative cytoplasmic protein ‐0.06721762 2.057447 0.49821556 0.24215232 0 0.39470655 0.5751511 0.52478904 STM3036 putative inner membrane protein ‐0.25521052 1.8093271 0.49499306 0.27357852 0.061239734 0.40918556 0.6653593 0.41043428 STM3038 putative metalloendopeptidase 0.043558788 1.503213 0.33276376 0.22136833 0.08572143 0.3941764 0.2812448 0.3228701 STM3039 isopentenyldiphosphate isomerase idi 0.4110363 1.9553742 0.5108181 0.26123804 0.03676819 0.3653111 0.58983773 0.5773056 STM3040 lysine tRNA synthetase, constitutive lysS 0.43422556 2.0721443 0.55931985 0.2699232 0 0.5489557 0.705428 0.4235758 STM3048 putative aminomethyltransferase ygfZ ‐0.666905 1.6791351 0.34947154 0.20812592 0.052916735 0.37370208 0.3103816 0.36433092 STM3053 glycine cleavage complex protein P, glycine decarboxylase gcvP ‐0.1678553 ‐1.548765 ‐0.30206802 0.195038 0.06573839 ‐0.28896147 ‐0.31050998 ‐0.30673265 STM3054 glycine cleavage complex protein H, carrier of gcvH ‐0.4529079 ‐1.9693778 ‐0.45057556 0.22879082 0.036121875 ‐0.44275403 ‐0.3848467 ‐0.52412593 STM3055 glycine cleavage complex protein T, aminomethyltransferase, tetrahydrofolate‐dependent gcvT 0.1369937 ‐1.8163794 ‐0.4176878 0.22995625 0.061239734 ‐0.4154128 ‐0.34686542 ‐0.4907852 STM3060 putative cytoplasmic protein ygfE 0.48813185 ‐4.994263 ‐1.1262976 0.22551827 0 ‐1.2001287 ‐1.0961808 ‐1.0825833 STM3062 D‐3‐phosphoglycerate dehydrogenase serA ‐0.31056175 2.8053248 0.724494 0.25825673 0 0.8323728 0.74745554 0.5936536 STM3063 ribosephosphate isomerase, constitutive rpiA ‐0.950021 2.1047325 0.47034854 0.22347188 0 0.5394156 0.44647112 0.42515892 STM3067 putative membrane protein, involved in stability of yggB ‐0.26195955 2.2456944 0.4502834 0.20050965 0 0.47451338 0.4381121 0.4382247 STM3068 fructose‐bisphosphate aldolase fba ‐0.34157068 1.7177707 0.3701238 0.21546753 0.055790044 0.3727042 0.415672 0.32199523 STM3073 putative ABC‐type cobalt transport system, permease component 0.008064115 ‐3.549998 ‐0.95269996 0.26836634 0 ‐0.7943754 ‐1.0122044 ‐1.05152 STM3074 putative ABC‐type cobalt transport system, ATPase component 0.5741068 ‐2.210317 ‐0.5113617 0.23135222 0 ‐0.493748 ‐0.44734427 ‐0.5929929 STM3075 putative ABC‐type cobalt transport system, ATPase component ‐0.8996354 ‐1.6162373 ‐0.4140885 0.25620526 0.048099868 ‐0.499996 ‐0.46201798 ‐0.28025147 STM3076 transketolase 1 isozyme tktA 0.11028937 ‐1.7007806 ‐0.53263664 0.31317186 0.055124886 ‐0.2935491 ‐0.7141154 ‐0.5902455 STM3084 putative regulatory protein, gntR family 0.70009315 2.792682 0.72715414 0.26037842 0 0.6612686 0.6492397 0.87095416 STM3086 arginine decarboxylase speA 0.20643686 1.5791565 0.4206928 0.2664035 0.04670303 0.53480905 0.4557718 0.27149752 STM3111 putative cytoplasmic protein yggX ‐0.098475926 1.5307235 0.3294322 0.21521339 0.066927865 0.28002083 0.33606505 0.37221068 STM3118 putative acetyl‐CoA hydrolase 0.14759047 2.4272947 0.64203227 0.26450527 0 0.69300693 0.49232864 0.74076116 STM3123 putative arylsulfatase regulator 0.4846312 2.399998 0.53296655 0.22206959 0 0.48359686 0.5973249 0.51797795 STM3134 putative permease ‐0.5832454 1.956313 0.39576995 0.202304 0.03676819 0.36976013 0.4173206 0.40022916 STM3141 molybdenum‐binding periplasmic protein ‐0.23403399 ‐2.2366416 ‐0.4870507 0.21775983 0 ‐0.45330793 ‐0.46229258 ‐0.5455516 STM3160 putative inner membrane protein 0.28888452 ‐2.4107106 ‐0.5822555 0.24152857 0 ‐0.68835145 ‐0.52397484 ‐0.5344401 STM3161 cystathionine beta‐lyase (beta‐cystathionase) metC ‐0.21098736 1.6816583 0.4773572 0.283861 0.052916735 0.65483147 0.44960093 0.32763925 STM3163 putative transcriptional regulator (AraC/XylS family) yqhC ‐0.29278332 1.6084288 0.3853789 0.2395996 0.04958284 0.29529727 0.47260767 0.38823175 STM3175 putative bacterial regulatory helix‐turn‐helix proteins, araC family ‐0.12315611 ‐1.6195523 ‐0.33203724 0.20501792 0.048099868 ‐0.31041464 ‐0.32097733 ‐0.36471972 STM3176 putative outer membrane protein ygiW 0.32277566 ‐1.8365009 ‐0.36205012 0.19714127 0.062375717 ‐0.36870337 ‐0.37273464 ‐0.34471235 STM3214 putative transporter yqjH 1.0479784 2.268089 0.4899775 0.21603099 0 0.53003407 0.43696576 0.50293267 STM3217 aerotaxis sensor receptor, senses cellular redox state aer ‐0.56348324 1.6768337 0.33439645 0.19942135 0.052916735 0.35210353 0.31415823 0.33692762 STM3218 putative acetylornithine aminotransferase oat 0.2318009 6.66837 1.8616135 0.27917072 0 1.691354 2.0013297 1.892157 STM3229 putative inner membrane protein yqjD ‐0.98730326 1.5292214 0.4232078 0.27674723 0.066927865 0.3128186 0.3589067 0.59789807 STM3230 putative inner membrane protein yqjE 0.5157611 2.1823924 0.43675342 0.20012599 0 0.4432915 0.4529989 0.4139699 STM3231 putative inner membrane protein yqjK ‐0.22929639 1.8793113 0.43695128 0.23250607 0.0654669 0.44499046 0.5090171 0.3568463 STM3233 putative glutathione S‐transferase yqjG ‐0.49204087 1.9746901 0.40787387 0.20655082 0 0.43303484 0.3726188 0.41796798 STM3234 putative inner membrane protein yhaH ‐0.31471863 1.9638025 0.3988789 0.2031156 0.03676819 0.37349963 0.42449296 0.39864415 STM3237 putative cytoplasmic protein yhaL 0.35671255 ‐2.331444 ‐0.46848142 0.20094046 0 ‐0.4875742 ‐0.44483563 ‐0.47303447 STM3253 putative fructose/tagatose biphosphate aldolase ‐0.44171777 1.6612177 0.37201008 0.2239382 0.052023627 0.37932602 0.30711573 0.42958847 STM3255 putative phosphotransferase system fructose‐specific component IIB ‐0.32163835 1.6488768 0.4417901 0.26793396 0.050878678 0.28756332 0.55266887 0.4851381 STM3269 putative intracellular proteinase yhbO ‐0.16838183 4.024114 0.8957086 0.22258529 0 0.86880946 0.85471255 0.9636039 STM3283 30S ribosomal subunit protein S15 rpsO 0.30372322 ‐1.9455602 ‐0.47298902 0.243112 0.035160456 ‐0.5601261 ‐0.48675564 ‐0.37208533 STM3287 transcription pausing L factor nusA ‐0.33590025 1.5562496 0.42970932 0.27611852 0.046063263 0.45427257 0.5678735 0.26698193 STM3290 argininosuccinate synthetase argG ‐0.65049744 ‐3.6524975 ‐0.80491114 0.22037281 0 ‐0.8604555 ‐0.8045967 ‐0.7496812 STM3298 putative RNA‐binding protein containing KH domain yhbY ‐0.63119006 1.6343018 0.39191687 0.23980692 0.05046221 0.2899381 0.43150806 0.45430443 STM3301 putative GTP‐binding protein yhbZ 0.46059808 1.8668038 0.40519696 0.21705386 0.06489263 0.45941237 0.36197802 0.39420047 STM3307 UDP‐N‐acetylglucosamine 1‐carboxyvinyltransferase murA ‐0.045942247 1.6632278 0.34663767 0.20841262 0.052023627 0.31915554 0.385592 0.33516544 STM3310 putative ABC superfamily (atp&memb), transport protein yrbC 0.20944834 1.8080856 0.49032056 0.27118218 0.061239734 0.45055595 0.6493985 0.37100726 STM3319 putative ABC superfamily (atp_bind) transport protein yhbG 0.14287926 1.5383027 0.4402938 0.28622052 0.068245016 0.55796766 0.51682436 0.24608935 STM3321 putative sigma N modulation factor yhbH 0.18611106 4.0351615 1.1183393 0.27714857 0 1.0253689 1.2957793 1.0338696 STM3322 sugar specific PTS family, enzyme IIA, also ptsN ‐0.2806547 1.6364739 0.37110034 0.22676826 0.050878678 0.35407287 0.44442272 0.31480545 STM3323 putative P‐loop‐containing kinase yhbJ ‐0.19040503 2.044123 0.45387977 0.22204132 0 0.4593303 0.5092408 0.3930682 STM3330 glutamate synthase, large subunit gltB ‐1.1462337 ‐4.5282335 ‐1.144475 0.25274205 0 ‐1.2374511 ‐1.1750478 ‐1.0209262 STM3331 glutamate synthase, small subunit gltD 0.40435228 ‐5.754339 ‐1.1972159 0.20805445 0 ‐1.2325765 ‐1.1646444 ‐1.1944269 STM3336 putative ManNAc kinase nanK 0.13808168 ‐1.7145517 ‐0.3675056 0.21434502 0.055790044 ‐0.3400754 ‐0.3430637 ‐0.41937774 STM3344 30S ribosomal subunit protein S9 rpsI 0.6781181 ‐1.5522492 ‐0.32076043 0.20664236 0.06573839 ‐0.31225324 ‐0.2942787 ‐0.35574937 STM3345 50S ribosomal subunit protein L13 rplM 0.5394953 ‐1.5666604 ‐0.36633584 0.23383231 0.066927865 ‐0.42418668 ‐0.39810398 ‐0.27671683 STM3346 putative ATPase yhcM ‐0.19449352 2.2489936 0.47426036 0.2108767 0 0.46733466 0.51619864 0.4392478 STM3347 putative periplasmic protein yhcB 0.18202876 1.6118252 0.41901252 0.25996152 0.04958284 0.27658775 0.5025476 0.47790214 STM3348 serine endoprotease degQ ‐0.47515002 1.6138811 0.4109477 0.2546332 0.04958284 0.29680672 0.52625495 0.40978143 STM3351 putative sodium ion pump oxaloacetate decarboxylase beta oadB 0.47321808 ‐1.8969579 ‐0.59574056 0.3140505 0.0654669 ‐0.34602475 ‐0.6961095 ‐0.74508744 STM3352 putative sodium ion pump oxaloacetate decarboxylase alpha oadA ‐0.15068413 ‐1.7228147 ‐0.42028627 0.24395327 0.056731287 ‐0.31769782 ‐0.43460757 ‐0.5085534 STM3353 putative sodium ion pump oxaloacetate decarboxylase gamma oadG 0.63738245 ‐2.3605113 ‐0.6863903 0.29078034 0 ‐0.4816189 ‐0.7889358 ‐0.78861606 STM3356 putative cation transporter ‐0.84726703 1.6132051 0.34528437 0.21403626 0.04958284 0.37959757 0.36113432 0.29512122 STM3359 malate dehydrogenase mdh 0.06865428 5.349108 1.0320538 0.19293942 0 1.0391147 1.0235662 1.0334805 STM3376 putative oxidoreductase yhdH 0.37864769 ‐1.9252613 ‐0.38043925 0.19760396 0.03424889 ‐0.38041863 ‐0.36449853 ‐0.3964006 STM3399 putative ferripyochelin binding protein yrdA 0.75414443 1.5964084 0.33414793 0.20931232 0.048099868 0.33387408 0.29805514 0.3705146 STM3400 putative periplasmic protein yrdB ‐0.19530067 1.5368217 0.38499892 0.25051633 0.066927865 0.36810875 0.50004303 0.28684494 STM3404 putative cytoplasmic protein smg ‐1.1222371 1.970463 0.4710404 0.23905061 0 0.55361795 0.37892056 0.48058265 STM3406 peptide deformylase def 0.15068413 2.2570117 0.47581294 0.21081546 0 0.45074987 0.5205464 0.45614257 STM3408 putative rRNA methylase sun 0.51471597 1.5143003 0.3354247 0.22150473 0.06573839 0.27524516 0.34158424 0.38944465 STM3409 Trk system transport of potassium trkA ‐0.9533757 2.1018822 0.42573324 0.20254856 0 0.45403755 0.41118976 0.4119724 STM3410 mechanosensitive channel mscL 0.107027 7.7003984 1.6406862 0.2130651 0 1.6509857 1.6773255 1.5937471 STM3411 putative cytoplasmic protein 0.6403776 2.6114893 0.56206405 0.2152274 0 0.61358094 0.5232863 0.549325 STM3444 regulatory or redox component complexing with Bfr bfd ‐0.080864854 1.6972271 0.44617307 0.26288354 0.05455575 0.29753736 0.5292295 0.5117523 STM3455 FKBP‐type peptidyl prolyl cis‐trans isomerase (rotamase) slyD 0.45096314 1.5787463 0.33144507 0.20994194 0.04670303 0.29044163 0.3634315 0.34046206 STM3468 acetylornithine transaminase (NAcOATase and DapATase) argD ‐0.57937014 ‐4.9745827 ‐1.0719284 0.21548107 0 ‐1.0901717 ‐1.1069815 ‐1.0186319 STM3494 putative NTP pyrophosphohydrolase yrfE ‐0.27923536 1.6730511 0.39433223 0.23569646 0.052916735 0.3264107 0.48532274 0.37126324 STM3505 ferrous iron transport protein A feoA 0.17860433 ‐3.7791817 ‐0.83861786 0.22190462 0 ‐0.8980078 ‐0.8358187 ‐0.78202707 STM3506 FeoB family, ferrous iron transport protein B feoB 0.34184274 ‐4.084264 ‐0.798303 0.19545823 0 ‐0.8008093 ‐0.7850094 ‐0.80909026 STM3507 putative cytoplasmic protein yhgG ‐0.7353798 ‐2.926362 ‐0.6313221 0.21573615 0 ‐0.65874517 ‐0.65858203 ‐0.5766391 STM3510 putative amidophosphoribosyltransferase yhgH 0.47819886 ‐1.9534088 ‐0.39899692 0.20425674 0.035703473 ‐0.40665218 ‐0.36850718 ‐0.42183143 STM3528 putative periplasmic phosphate‐binding protein ‐0.20990089 1.8143873 0.4996787 0.27539805 0.062375717 0.42640808 0.67299736 0.39963064 STM3541 low affinity gluconate permease gntU 0.12382674 ‐1.8159596 ‐0.38044965 0.20950337 0.061239734 ‐0.40383425 ‐0.39919758 ‐0.33831713 STM3547 putative transcriptional regulator of sugar metabolism ‐0.80572575 1.7613442 0.37545747 0.2131653 0.05861933 0.3454789 0.35628942 0.42460406 STM3549 putative inner membrane protein 0.21333815 2.6149595 0.5218723 0.19957185 0 0.52324367 0.54050964 0.50186354 STM3550 putative phosphotriesterase ‐0.58120793 1.8890399 0.4274388 0.22627304 0.033565152 0.44532394 0.35474345 0.482249 STM3551 gamma‐glutamyltranspeptidase ggt ‐0.37864769 3.7877216 0.8074597 0.2131782 0 0.85632825 0.79020727 0.7758436 STM3552 putative outer membrane protein yhhA ‐0.29703346 1.5481534 0.38999406 0.25190917 0.068245016 0.26605102 0.4760673 0.42786384 STM3559 putative cytoplasmic protein yhhV 0.44830734 ‐1.6243072 ‐0.3995211 0.24596402 0.048099868 ‐0.51195174 ‐0.36480522 ‐0.3218064 STM3562 ABC superfamily (membrane), branched‐chain amino acid transporter livM 0.72732615 ‐1.7891289 ‐0.39328074 0.2198169 0.060340617 ‐0.33340865 ‐0.43975687 ‐0.4066767 STM3585 putative ABC superfamily (atp_bind/membrane) transport protein yhhJ 0.29278332 ‐1.549129 ‐0.33445248 0.21589711 0.06573839 ‐0.376025 ‐0.28247398 ‐0.34485847 STM3608 putative tRNA‐processing ribonuclease yhjD ‐0.33938333 2.5381799 0.51426595 0.2026121 0 0.504887 0.5422027 0.49570817 STM3617 endo‐1,4‐D‐glucanase bcsC ‐0.20685117 1.6005901 0.40892595 0.2554845 0.048099868 0.5395899 0.37002033 0.3171676 STM3622 putative cytoplasmic protein yhjS ‐0.4742528 2.3276753 0.48388755 0.20788448 0 0.47895348 0.5198404 0.45286873 STM3630 ABC superfamily (peri_perm), dipeptide transport protein dppA ‐0.19732961 3.3539507 0.6884257 0.20525815 0 0.65638983 0.7135767 0.6953107 STM3641 putative lipase yhjY ‐0.25549942 2.5380428 0.6006069 0.23664176 0 0.50655806 0.66632545 0.6289372 STM3648 putative transcriptional regulator yiaG ‐0.27465343 2.8019512 0.776201 0.27702162 0 0.64083105 0.74478775 0.9429842 STM3666 paral putative oxidoreductase ysaA 0.011871857 ‐1.7150571 ‐0.39172906 0.22840583 0.055790044 ‐0.3849482 ‐0.3260673 ‐0.4641717 STM3679 putative cytoplasmic protein 0.49298185 ‐1.6969042 ‐0.5012656 0.29540005 0.055124886 ‐0.29648966 ‐0.65751076 ‐0.54979634 STM3682 selenocysteinyl‐tRNA‐specific translation factor selB ‐1.1542956 ‐1.6817443 ‐0.45353958 0.26968402 0.052916735 ‐0.46270218 ‐0.58953184 ‐0.3083847 STM3684 putative glutathione S‐transferase yibF ‐0.4000066 1.5722961 0.3495993 0.22234952 0.04670303 0.31454217 0.31675866 0.41749704 STM3686 mannitol‐1‐phosphate dehydrogenase mtlD ‐0.29463667 2.3630202 0.51300955 0.2170991 0 0.5595593 0.5188325 0.46063688 STM3689 putative cytoplasmic protein yibL 0.4466139 1.6536298 0.4465721 0.27005568 0.052023627 0.36531964 0.36450312 0.6098935 STM3695 putative tRNA/rRNA methyltransferase yibK 0.5674203 ‐1.8137153 ‐0.39065447 0.21538907 0.061239734 ‐0.38597736 ‐0.43957305 ‐0.34641305 STM3713 O‐antigen ligase rfaL ‐0.40543115 1.9103702 0.4311251 0.22567621 0.034698687 0.36301234 0.49145386 0.43890908 STM3715 lipopolysaccharide core biosynthesis rfaZ 0.17513816 2.534816 0.5261738 0.20757869 0 0.4886192 0.5517573 0.53814477 STM3717 UDP‐D‐glucose:(galactosyl)lipopolysaccharide glucosyltransferase rfaJ ‐0.7238866 1.9889339 0.5328845 0.26792467 0 0.5205779 0.40170062 0.676375 STM3719 UDP‐D‐galactose:(glucosyl)lipopolysaccharide‐1,6‐D‐galactosyltransferase rfaB 0.14179465 1.5872976 0.56814337 0.35793123 0.04736082 0.23581295 0.79257816 0.67603904 STM3721 lipopolysaccharide core biosynthesis phosphorylation of core heptose rfaP 0.34437576 1.7386192 0.4682747 0.26933715 0.057885446 0.62995374 0.3803654 0.39450496 STM3722 glucosyltransferase I rfaG ‐1.6554445 2.0911803 0.5393938 0.2579375 0 0.5888077 0.62728035 0.4020932 134 STM3727 50S ribosomal subunit protein L33 rpmG 0.1301892 1.605819 0.44745818 0.27864796 0.048099868 0.6258041 0.38240027 0.33417016 STM3728 50S ribosomal subunit protein L28 rpmB ‐0.3780471 1.955886 0.44447473 0.22724982 0.03676819 0.5031419 0.37100726 0.459275 STM3735 putative stress‐induced protein yicC ‐0.68675524 1.6156315 0.34351423 0.21261919 0.04958284 0.36955753 0.36587334 0.29511184 STM3739 putative DNA ligase yicF 0.17353666 1.6391077 0.36658975 0.22365202 0.050878678 0.33638847 0.4368734 0.3265074 STM3753 ATP binding protein sugR ‐0.47684246 2.1396935 0.48596856 0.22712064 0 0.43738025 0.56249774 0.4580277 STM3754 putative cytoplasmic protein 0.31969455 1.5200504 0.41399205 0.27235416 0.06573839 0.29049364 0.57427406 0.3772084 STM3756 putative cytoplasmic protein rmbA 0.51307684 1.7668608 0.3677635 0.20814514 0.05861933 0.3757983 0.33025235 0.39723983 STM3757 putative autotransported protein misL ‐0.41458035 1.5712994 0.4469973 0.28447622 0.04670303 0.63744277 0.37397614 0.329573 STM3767 putative cytoplasmic protein 0.5678712 ‐1.8977661 ‐0.5191424 0.27355447 0.0654669 ‐0.3511006 ‐0.57912034 ‐0.62720615 STM3781 putative sugar (pentulose and hexulose) kinase ‐0.52694124 1.9337174 0.46641704 0.24120228 0.035703473 0.37124303 0.47435084 0.5536573 STM3784 putative phosphotransferase system mannitol/fructose‐specific IIA domain ‐3.0451999 2.364518 0.53195083 0.22497222 0 0.60478884 0.48963878 0.5014249 STM3788 membrane protein, regulator of uhpT expression uhpC ‐0.13783324 ‐1.5452976 ‐0.3369816 0.21806906 0.06573839 ‐0.2906086 ‐0.39224416 ‐0.32809198 STM3794 putative regulatory protein, deoR family 0.63420165 1.7026069 0.3517111 0.2065721 0.055124886 0.37849623 0.35960653 0.31703052 STM3795 acetolactate synthase I, small subunit ilvN ‐0.04255068 4.1565914 1.04016 0.25024348 0 0.91801894 1.1181724 1.0842886 STM3796 acetolactate synthase I, large subunit, valine sensitive ilvB ‐0.33471116 5.550189 1.4274511 0.25718963 0 1.5609252 1.3317875 1.3896406 STM3832 putative permease ‐0.41137883 2.0627105 0.4464571 0.21644194 0 0.50030506 0.40592232 0.43314388 STM3835 DNA gyrase, subunit B (type II topoisomerase) gyrB 0.014867804 1.8083141 0.5025008 0.27788356 0.061239734 0.58903855 0.5949088 0.32355496 STM3859 putative shikimate / quinate 5‐dehydrogenase ‐0.29522222 2.1979892 0.4633829 0.21082129 0 0.5036455 0.42613268 0.46037054 STM3860 putative dipeptide/oligopeptide/nickel ABC‐type transport systems, periplasmic component 0.4650053 1.5305167 0.35714597 0.23334992 0.066927865 0.41193685 0.26801392 0.3914871 STM3862 N‐acetyl glucosamine‐1‐phosphate uridyltransferase and glucosamine‐1‐phosphate acetyl traglmU ‐0.25826892 1.9085512 0.45362625 0.23768094 0.034698687 0.36955515 0.5402315 0.4510921 STM3866 membrane‐bound ATP synthase, F1 sector, gamma‐subunit atpG ‐0.3545216 1.6940398 0.4262952 0.25164413 0.05455575 0.54671985 0.3996228 0.33254293 STM3877 asparagine synthetase A asnA ‐0.2263804 ‐7.9468703 ‐1.9373995 0.24379402 0 ‐1.8288294 ‐2.0108335 ‐1.9725355 STM3879 paral putative regulator protein yieN 0.13103093 1.9051694 0.46846965 0.24589397 0.034698687 0.5740368 0.4551856 0.3761866 STM3884 ABC superfamily (peri_perm), D‐ribose transport protein rbsB ‐0.15711944 1.8763212 0.39542574 0.21074523 0.0654669 0.42535704 0.35170707 0.40921313 STM3887 putative MFS family tranport protein (1st mdule) yieO ‐0.082485124 1.585647 0.33321476 0.21014436 0.04736082 0.30532005 0.37606826 0.31825593 STM3898 putative LysR type transcriptional regulator with pssR yifE ‐0.21383426 2.3108907 0.633534 0.27415144 0 0.47292084 0.7659487 0.66173244 STM3901 acetolactate synthase II, large subunit, fragment 1 ilvG ‐1.879907 2.9675903 0.6094899 0.2053821 0 0.6425514 0.59973615 0.58618224 STM3902 acetolactate synthase II, small subunit ilvM 0.68424237 4.168034 0.96123534 0.2306208 0 1.0454634 0.92444766 0.91379493 STM3903 branched‐chain amino‐acid aminotransferase ilvE 0.36235517 3.8437219 0.76985306 0.20028844 0 0.79254895 0.75233585 0.7646743 STM3904 dihydroxyacid dehydratase ilvD ‐0.48547572 1.9831517 0.5742589 0.28956884 0 0.775312 0.45393547 0.49352932 STM3905 threonine deaminase ilvA ‐0.5703434 2.0576208 0.49188125 0.2390534 0 0.5118394 0.3958778 0.5679266 STM3912 rep helicase, a single‐stranded DNA dependent ATPase rep 0.09942931 2.1033072 0.49100342 0.23344351 0 0.40508392 0.5574491 0.51047724 STM3919 modulator of enterobacterial common antigen (ECA) polysaccharide wzzE ‐0.21702328 1.6406711 0.36819875 0.2244196 0.050878678 0.38888365 0.4176267 0.29808593 STM3939 adenylate cyclase cyaA ‐0.28849924 4.398021 0.8866541 0.20160295 0 0.91051465 0.88454133 0.8649062 STM3941 putative inner membrane protein 0.15665773 2.06263 0.46457082 0.22523227 0 0.5347797 0.4101256 0.4488071 STM3942 putative cytoplasmic protein ‐0.54959726 2.0346022 0.5273971 0.25921386 0 0.42004734 0.5010525 0.66109145 STM3944 putative inner membrane protein 0.0356387 1.8969996 0.44918942 0.23678942 0.03424889 0.38673782 0.5444544 0.41637605 STM3947 diaminopimelate epimerase dapF ‐0.6192518 1.8873991 0.38624415 0.2046436 0.033565152 0.37373444 0.36652365 0.41847432 STM3957 outer membrane phospholipase A pldA ‐0.6526042 1.8269706 0.38733566 0.2120098 0.063013285 0.40118644 0.41951457 0.34130597 STM3964 regulator for metE and metH (LysR family) metR ‐0.21790259 2.4859245 0.5481714 0.22051008 0 0.496016 0.6067155 0.5417827 STM3965 5‐methyltetrahydropteroyltriglutamate‐homocysteine S‐methyltransferase metE 0.5000016 9.195377 2.0591905 0.22393757 0 2.0208678 2.130202 2.026502 STM3967 putative dienelactone hydrolase family dlhH 0.42949915 2.867417 0.6445667 0.22479 0 0.57621735 0.6570585 0.70042425 STM3970 S‐adenosylmethionine : 2‐DMK methyltransferase and 2‐octaprenyl‐6‐methoxy‐1,4‐benzoqui ubiE ‐0.47769812 2.48138 0.6148735 0.24779499 0 0.5451342 0.7330351 0.5664514 STM3972 putative regulator in ubiquinone biosynthesis aarF 0.65638953 1.9997739 0.41125435 0.20565042 0 0.38699812 0.4446431 0.40212184 STM3974 component of Sec‐independent protein secretion pathway tatB ‐0.042263385 1.7091753 0.36889693 0.21583329 0.055124886 0.3267777 0.4204216 0.35949153 STM3986 Trk family, potassium transport protein, requires TrkE trkH 0.27883244 1.8580741 0.38901678 0.20936559 0.06489263 0.43091 0.36631954 0.36982083 STM3994 putative molybdopterin‐guanine dinucleotide biosynthesis protein mobA ‐0.12210245 1.6856477 0.3811573 0.22611919 0.052916735 0.34198838 0.4565878 0.34489578 STM3999 DNA polymerase I, 3 ‐‐ 5 polymerase polA ‐0.34398723 1.6466826 0.4377981 0.26586673 0.050878678 0.37616727 0.5917273 0.34549972 STM4001 putative GTPase, involved in coordination of cell yihA 0.49538356 2.3654792 0.46261853 0.19557074 0 0.46204188 0.4504875 0.47532624 STM4002 putative cytoplasmic protein ‐0.5802446 6.0609818 1.8694432 0.30843902 0 1.8951077 1.6498793 2.0633426 STM4006 sensory kinase (phosphatase) in two‐component regulatory system glnL 0.24259792 ‐2.0877984 ‐0.5045588 0.24167028 0 ‐0.6108326 ‐0.4447654 ‐0.4580785 STM4007 glutamine synthetase glnA ‐0.092812985 ‐2.6353803 ‐0.59251535 0.22483106 0 ‐0.53651893 ‐0.5801261 ‐0.66090095 STM4010 putative hydrolase ‐0.5882759 2.4007227 0.48924688 0.2037915 0 0.46053627 0.49396023 0.5132441 STM4012 putative coproporphyrinogen III oxidase and related FeS 0.19134629 1.9572333 0.45540714 0.23267902 0.03676819 0.4891817 0.5094267 0.367613 STM4015 putative cytoplasmic protein 0.2744039 1.6393343 0.40781978 0.24877158 0.050878678 0.28797778 0.454913 0.4805686 STM4017 putative GPH family transport protein yihO ‐0.6100708 1.6875355 0.3963741 0.23488341 0.052916735 0.48487806 0.37679827 0.327446 STM4044 putative iron‐containing alcohol dehydrogenase 0.18566619 ‐2.3585281 ‐0.49964577 0.21184643 0 ‐0.45278054 ‐0.5214348 ‐0.524722 STM4050 DMT Superfamily, L‐rhamnose:H symporter protein rhaT 0.18909171 1.7020295 0.410316 0.24107455 0.055124886 0.36642 0.51521206 0.3493159 STM4051 putative outer membrane protein ‐0.6281051 1.847927 0.4098875 0.22180936 0.064440414 0.461429 0.347276 0.4209575 STM4052 putative C4‐dicarboxylate transport system 0.4620052 1.8644136 0.46624777 0.25007743 0.06489263 0.38197103 0.5864078 0.4303645 STM4055 superoxide dismutase, manganese sodA ‐0.49239075 4.3115897 0.9755554 0.22626351 0 0.89982533 1.0143545 1.0124865 STM4063 ABC superfamily (bind_prot), sulfate transport protein sbp ‐0.4593492 3.6809943 1.1947391 0.32456967 0 0.92472845 1.3605927 1.2988963 STM4068 putative regulatory protein, gntR family 0.931704 ‐1.9415044 ‐0.5420718 0.27920195 0.035160456 ‐0.4316753 ‐0.72215956 ‐0.47238067 STM4074 putative ABC‐type sugar, aldose transport system, ATPase ego ‐0.056709845 1.5847982 0.45291167 0.28578508 0.04736082 0.33004305 0.6452359 0.38345605 STM4075 putative ABC superfamily (membrane), sugar transport protein ydeY ‐0.9815406 1.6034166 0.36356896 0.22674643 0.048099868 0.28925765 0.38426402 0.41718525 STM4076 putative ABC superfamily (membrane), sugar transport protein ydeZ ‐0.19276725 2.3568122 0.71426153 0.30306256 0 0.51653886 0.9137485 0.7124973 STM4096 50S ribosomal subunit protein L31 rpmE 0.6940803 ‐2.40593 ‐0.5846065 0.24298567 0 ‐0.52524084 ‐0.6936451 ‐0.5349336 STM4098 putative arylsulfate sulfotransferase ‐0.15832898 2.107291 0.6554832 0.3110549 0 0.5901314 0.89293575 0.48338243 STM4100 cystathionine gamma‐synthase metB ‐0.6186724 1.9149498 0.5192227 0.27114168 0.034698687 0.3551766 0.58232796 0.62016344 STM4105 5,10‐methylenetetrahydrofolate reductase metF 0.082485124 4.9100404 1.136547 0.23147406 0 1.0520654 1.1641366 1.1934389 STM4108 glycerol dehydrogenase, NAD gldA ‐0.32403237 ‐1.7187896 ‐0.42860514 0.24936453 0.056731287 ‐0.49974674 ‐0.30726638 ‐0.47880226 STM4121 N‐acetyl‐gamma‐glutamylphosphate reductase argC 0.3298821 ‐7.00797 ‐1.8144642 0.25891438 0 ‐1.6799085 ‐1.9183506 ‐1.8451334 STM4122 acetylglutamate kinase argB 0.8724605 ‐5.5200133 ‐1.2989787 0.23532166 0 ‐1.2066184 ‐1.330715 ‐1.3596027 STM4123 argininosuccinate lyase argH ‐0.45369187 ‐6.326408 ‐1.4246911 0.22519748 0 ‐1.35849 ‐1.4856558 ‐1.4299273 STM4159 deoxyxylulose‐5‐P thi‐S‐COSH tyrosine thiH 0.6655571 1.9949859 0.43634397 0.21872032 0 0.49387768 0.4242009 0.39095336 STM4160 deoxyxylulose‐5‐P thi‐S‐COSH tyrosine thiG ‐0.12347267 2.7008054 0.59175986 0.21910496 0 0.5696071 0.6524479 0.5532246 STM4161 putative involved in thiamine biosynthesis ‐0.17311701 2.6730256 0.6788698 0.25397056 0 0.74364185 0.74524623 0.5477212 STM4162 catalyzes the adenylation of thisS as part thiF ‐0.16321859 2.0685506 0.45746613 0.22115298 0 0.42741707 0.5229101 0.4220712 STM4163 thiamin phosphate synthase (thiamine phosphate pyrophosphorylase) thiE ‐0.61755073 2.3483047 0.48944348 0.20842418 0 0.4782781 0.52834356 0.46170875 STM4165 regulator of sigma D, has binding activity rsd 0.4868646 2.2970204 0.5652766 0.24609125 0 0.5121794 0.50309974 0.68055075 STM4170 DNA‐binding protein HU‐alpha (HU‐2) hupA 0.1547093 3.0071814 0.65318567 0.2172086 0 0.6041425 0.6515002 0.70391434 STM4181 putative acetyltransferase yjaB ‐0.48628333 1.5604886 0.38863373 0.24904619 0.046063263 0.41277462 0.27361307 0.4795135 STM4182 homoserine transsuccinylase metA ‐0.15436698 3.9471924 0.88750505 0.22484463 0 0.83211875 0.9562479 0.87414855 STM4209 putative inner membrane protein ‐0.505967 ‐1.7779773 ‐0.42324895 0.2380508 0.05994943 ‐0.50856966 ‐0.33657166 ‐0.4246055 STM4220 aspartokinase III, lysine sensitive lysC ‐0.86451375 ‐3.3963428 ‐0.9882611 0.290978 0 ‐1.1065358 ‐1.0743078 ‐0.7839398 STM4222 putative outer membrane protein yjbE 0.11456228 ‐10.081721 ‐2.1054304 0.20883639 0 ‐2.0814438 ‐2.1460955 ‐2.0887516 STM4223 putative outer membrane lipoprotein yjbF ‐1.952237 ‐1.5435418 ‐0.42309836 0.27410877 0.06573839 ‐0.37885618 ‐0.5886514 ‐0.3017875 STM4224 putative periplasmic protein yjbG ‐0.06963306 ‐2.2580628 ‐0.4635481 0.20528574 0 ‐0.43143997 ‐0.47050652 ‐0.48869783 STM4237 SOS response regulator, transcriptional repressor (LexA family) lexA ‐0.15642636 1.8176259 0.4132672 0.22736648 0.062375717 0.4908214 0.36775026 0.3812299 STM4248 tyrosine aminotransferase, tyrosine repressible tyrB ‐0.90958524 2.0587034 0.52193683 0.25352696 0 0.48781145 0.43012685 0.6478722 STM4254 UvrA with UvrBC is a DNA excision uvrA ‐0.75989574 1.5824612 0.41460815 0.26200208 0.04736082 0.5232973 0.4462529 0.2742742 STM4256 ssDNA‐binding protein controls activity of RecBCD nuclease ssb ‐0.012055409 2.822107 0.59220576 0.20984524 0 0.5871153 0.5578599 0.6316421 STM4271 putative inner membrane protein 0.16376834 ‐1.8470995 ‐0.41584668 0.22513495 0.063013285 ‐0.42716506 ‐0.3473108 ‐0.47306418 STM4274 putative inner membrane protein yjcH 0.6100708 ‐1.6569892 ‐0.33754137 0.20370765 0.050878678 ‐0.3073611 ‐0.35714027 ‐0.34812275 STM4280 putative nitrate reductase, formate dependent nrfD 0.22428694 ‐1.5790939 ‐0.44720033 0.2832006 0.068245016 ‐0.6087446 ‐0.28045094 ‐0.4524054 STM4282 part of formate‐dependent nitrite reductase complex involved nrfG ‐0.2318009 ‐1.6900375 ‐0.42897272 0.25382438 0.05455575 ‐0.3483499 ‐0.38001975 ‐0.5585485 STM4285 formate dehydrogenase fdhF 0.0855047 ‐5.2187743 ‐1.3442297 0.25757575 0 ‐1.2277148 ‐1.3378628 ‐1.4671113 STM4306 putative anaerobic dimethyl sulfoxide reductase, subunit B 0.006172235 ‐3.1490297 ‐0.80663604 0.25615382 0 ‐0.7360135 ‐0.74178106 ‐0.9421135 STM4329 chaperone Hsp10, affects cell division mopB ‐0.21186993 ‐2.0601845 ‐0.48067027 0.23331419 0 ‐0.5202757 ‐0.39103302 ‐0.5307021 STM4336 putative entericidin B precursor ecnB ‐0.4503383 2.2616508 0.6320353 0.2794575 0 0.4911552 0.6025157 0.8024351 STM4339 outer membrane lipoprotein (lipocalin) blc 0.06498495 1.9442763 0.4079992 0.2098463 0.036121875 0.41673467 0.36725438 0.4400085 STM4343 fumarate reductase, anaerobic, flavoprotein subunit frdA 0.08171417 ‐2.0651295 ‐0.5069592 0.24548542 0 ‐0.43022296 ‐0.47210342 ‐0.6185513 STM4362 putative GTP‐ase, together with HflCK possibly involved hflX ‐0.1558558 2.901106 0.7587986 0.26155493 0 0.7876796 0.86858255 0.6201337 STM4363 with HflC, part of modulator for protease hflK ‐1.6163129 3.6108074 0.7583688 0.21002749 0 0.8000094 0.7273756 0.7477214 STM4389 putative outer membrane protein yjfY 0.894851 ‐1.958884 ‐0.4843642 0.24726538 0.035703473 ‐0.36662456 ‐0.5426558 ‐0.5438123 STM4406 putative cytoplasmic protein ytfK 0.93876207 3.1500947 1.0473622 0.33248594 0 0.7850865 1.075081 1.2819192 STM4414 inorganic pyrophosphatase ppa 0.23807266 2.3549054 0.51015383 0.21663454 0 0.45368612 0.5373738 0.53940153 STM4418 sugar (and other) transporter ‐1.0153017 2.0922332 0.40358648 0.19289747 0 0.3966816 0.4120458 0.40203202 STM4419 sugar (and other) transporter 0.58439744 2.1450062 0.43582895 0.20318307 0 0.46449316 0.41518277 0.4278109 STM4428 putative permease 0.19530067 ‐1.8720412 ‐0.5923989 0.31644544 0.064440414 ‐0.34634352 ‐0.7769375 ‐0.65391564 STM4442 putative cytoplasmic protein 0.28506687 ‐2.3116417 ‐0.5741389 0.24836846 0 ‐0.6668347 ‐0.4618653 ‐0.5937166 STM4446 putative selenocysteine synthase [L‐seryl‐tRNA(Ser) selenium transferase 0.30279577 ‐2.2090225 ‐0.5517769 0.24978328 0 ‐0.42905918 ‐0.6164485 ‐0.60982305 STM4447 putative periplasmic protein ‐0.21333815 ‐1.5569214 ‐0.3323978 0.21349683 0.066927865 ‐0.38117865 ‐0.3182876 ‐0.2977271 STM4469 ornithine carbamoyltransferase 1 argI ‐0.43788415 ‐5.1410637 ‐1.3976216 0.27185458 0 ‐1.3485008 ‐1.5603379 ‐1.2840261 135 STM4473 putative acetyltransferase yjgM ‐0.71215767 1.593907 0.36478534 0.22886238 0.048099868 0.28985777 0.4287503 0.37574795 STM4486 putative alcohol dehydrogenase yjgB ‐0.11949775 2.278952 0.5181439 0.2273606 0 0.5597197 0.5544405 0.44027153 STM4492 putative cytoplasmic protein ‐0.5941703 2.5838516 0.6488349 0.2511115 0 0.5707446 0.7728898 0.60287035 STM4495 putative type II restriction enzyme, methylase subunit 0.23842911 1.5136276 0.39394987 0.2602687 0.06573839 0.25195864 0.4843493 0.44554168 STM4498 putative inner membrane protein ‐0.7631232 1.9802327 0.40949884 0.2067933 0 0.38002673 0.44331577 0.40515405 STM4505 putative inner membrane or exported 0.12053465 2.2200248 0.578649 0.26064977 0 0.4717325 0.7163038 0.54791063 STM4511 putative transcriptional regulator, LysR family yjiE 3.0451999 ‐1.7070447 ‐0.50016266 0.29299915 0.055790044 ‐0.29897767 ‐0.650452 ‐0.55105835 STM4513 putative permease yjiG 0.38334697 ‐4.7692523 ‐0.9544537 0.20012648 0 ‐0.96606237 ‐0.9663083 ‐0.9309904 STM4514 putative inner membrane protein yjiH ‐0.5954039 ‐2.1606038 ‐0.5022019 0.23243591 0 ‐0.4175689 ‐0.52337974 ‐0.5656572 STM4519 putative NAD‐dependent aldehyde dehydrogenase ‐0.024576357 1.5270014 0.40365338 0.26434383 0.066927865 0.55251664 0.35538727 0.3030562 STM4533 methyl‐accepting chemotaxis protein I, serine sensor receptor tsr 0.15356995 ‐1.6729057 ‐0.9974906 0.5962623 0.052916735 ‐0.9134698 ‐1.7421912 ‐0.33681077 STM4549 putative cytoplasmic protein 0.39336935 2.7949016 0.56562847 0.20237868 0 0.54050124 0.567556 0.5888282 STM4550 ferric hydrozamate transport, involved in reduction of fhuF 0.03778016 3.8569243 0.7813237 0.20257688 0 0.77914 0.80690694 0.757924 STM4552 putative inner membrane protein ‐0.1356715 5.468598 1.6186746 0.29599446 0 1.443204 1.5985178 1.8143021 STM4561 hyperosmotically inducible periplasmic protein, RpoS‐dependent stationary phase osmY ‐0.8455967 2.8529289 0.61580104 0.21584871 0 0.58273304 0.5943737 0.6702963 STM4562 putative inner membrane protein ‐0.7222619 2.328125 0.62252986 0.26739538 0 0.69533205 0.46468645 0.707571 STM4573 putative fimbrial chaparone protein stjC ‐0.4490622 1.6897191 0.44662827 0.26432103 0.05455575 0.3577469 0.59769696 0.38444096 STM4593 putative fimbrial usher protein sthB ‐0.37704462 2.5734284 0.68401676 0.2657998 0 0.83054364 0.6540209 0.5674857 STM4594 putative fimbrial chaparone protein sthA ‐0.08171417 1.8201561 0.51402205 0.28240547 0.062375717 0.3393081 0.6615488 0.5412092 STM4595 putative fimbrial chaparone protein 0.21577792 1.952907 0.44954565 0.23019306 0.03676819 0.47992814 0.36690807 0.5018008 STM4596 putative inner membrane protein 0.5386312 2.088449 0.45491496 0.21782431 0 0.453717 0.50647706 0.4045508 STY0287 hypothetical protein ‐0.3905154 ‐2.3752172 ‐0.49395123 0.20796044 0 ‐0.5284297 ‐0.46068415 ‐0.49273983 STY0402 PrpD protein prpD 0.59466296 ‐2.3385806 ‐0.5209139 0.22274789 0 ‐0.49298972 ‐0.5892416 ‐0.48051035 STY0439 maltodextrin glucosidase malZ 0.52694124 ‐1.5636102 ‐0.41040137 0.2624704 0.066927865 ‐0.26598063 ‐0.5112237 ‐0.4539998 STY0586 putative membrane protein ybcI 0.4844363 ‐1.7372906 ‐0.3617383 0.2082198 0.056731287 ‐0.39932278 ‐0.33200687 ‐0.3538852 STY0861 hypothetical protein ‐0.18842188 ‐1.7608556 ‐0.49434984 0.2807441 0.05861933 ‐0.39604163 ‐0.67891777 ‐0.4080901 STY0936 putative virK protein ybjX ‐0.2103791 3.5299184 0.943098 0.26717275 0 0.8266219 1.0932217 0.9094505 STY0963 anaerobic dimethyl sulfoxide reductase chain B dmsB ‐0.17353666 ‐1.9120498 ‐0.43810558 0.22912875 0.033565152 ‐0.45513213 ‐0.3605968 ‐0.49858785 STY1164 putative membrane transporter ‐0.01806822 1.6345549 0.35074425 0.2145809 0.05046221 0.35195166 0.39548445 0.30479664 STY1284 putative invasin 0.17594515 1.6050096 0.45023513 0.28051865 0.048099868 0.6207646 0.30455282 0.42538792 STY1472 putative virulence effector protein srfA ‐0.45500827 ‐1.6420331 ‐0.39458135 0.24030048 0.05046221 ‐0.29640138 ‐0.41446215 ‐0.4728805 STY1488 respiratory nitrate reductase 2 alpha chain narZ ‐0.8157917 ‐1.8987545 ‐0.5004718 0.26357898 0.0654669 ‐0.5651388 ‐0.5857039 ‐0.35057256 STY1505 putative glycogen debranching protein glgX ‐0.012356399 ‐1.7237203 ‐0.37865144 0.21967104 0.056731287 ‐0.31610373 ‐0.41061938 ‐0.40923125 STY2099 high‐affinity zinc uptake system periplasmic binding protein yebL ‐0.04622489 6.638497 1.8014921 0.27137047 0 1.6600322 1.9473672 1.7970768 STY2115 putative copper homeostasis protein cutC 1.0694163 ‐3.090817 ‐0.74927926 0.2424211 0 ‐0.83848965 ‐0.75747293 ‐0.65187526 STY2258 putative ferredoxin pduS 0.10332791 ‐1.5463238 ‐0.49018532 0.31700045 0.06573839 ‐0.36159647 ‐0.36156255 ‐0.74739695 STY2303 putative reductase RfbI rfbI ‐0.27765492 2.282679 0.82277745 0.36044377 0 0.6925853 1.1637181 0.61202896 STY2535 O‐succinylbenzoic acid‐CoA ligase menE ‐0.21771874 ‐1.64059 ‐0.38969326 0.23753239 0.05046221 ‐0.3119127 ‐0.37656242 ‐0.48060465 STY2695 ethanolamine ammonia‐lyase heavy chain eutB 0.6988597 ‐1.5830407 ‐0.41469145 0.2619588 0.046063263 ‐0.2979307 ‐0.39554596 ‐0.55059767 STY2703 putative cobalamin adenosyltransferase ‐0.43592656 ‐1.9174988 ‐0.52570236 0.27416044 0.03424889 ‐0.38120845 ‐0.6780023 ‐0.5178964 STY2717 putative oxidoreductase aegA ‐0.3926839 ‐2.1972065 ‐0.59363675 0.27017796 0 ‐0.4300859 ‐0.67344296 ‐0.6773814 STY2751 GMP synthase (glutamine‐hydrolyzing) guaA ‐1.5188409 2.1293032 0.55082524 0.25868803 0 0.67157376 0.55280757 0.42809445 STY2893 putative exported protein iroE 1.4100732 4.2431254 0.8910266 0.20999299 0 0.93417346 0.86765563 0.87125075 STY2894 TonB‐dependent outer membrane siderophore receptor protein iroN 0.077165596 4.3721895 1.6631677 0.380397 0 1.2964964 1.9452901 1.7477167 STY2897 conserved hypothetical protein ‐0.45116913 ‐7.0437884 ‐1.5071532 0.21396911 0 ‐1.4992087 ‐1.4673667 ‐1.5548842 STY2966 putative exported protein ‐0.56153303 ‐5.3715653 ‐1.262799 0.23508957 0 ‐1.3324382 ‐1.1740903 ‐1.2818687 STY3034 hypothetical protein 0.2633421 ‐2.0251381 ‐0.53842866 0.26587257 0 ‐0.68828505 ‐0.42935696 ‐0.49764392 STY3470 argininosuccinate synthetase argG 0.9257506 ‐4.191836 ‐0.88805217 0.2118528 0 ‐0.8413535 ‐0.9153108 ‐0.9074922 STY3532 oxaloacetate decarboxylase alpha chain oadA 0.72089875 ‐2.112639 ‐0.5543712 0.26240698 0 ‐0.40848166 ‐0.60562116 ‐0.6490108 STY3533 oxaloacetate decarboxylase gamma chain oadG ‐0.08631868 ‐1.8961029 ‐0.45030677 0.23749068 0.0654669 ‐0.54803133 ‐0.39315587 ‐0.40973312 STY3724 thiamine biosynthesis protein thiS ‐0.044669397 1.6659126 0.3687843 0.22137074 0.052023627 0.34690958 0.4336048 0.3258385 STY3725 thiamine biosynthesis protein thiG 0.3761747 2.8552682 0.64458287 0.22575213 0 0.6056575 0.7192756 0.60881543 STY3769 cystathionine gamma‐synthase metB ‐0.31661856 3.3029058 0.6846172 0.20727725 0 0.7182417 0.68269473 0.6529152 STY4091 2,3‐bisphosphoglycerate‐independent phosphoglycerate mutase 0.47470537 ‐4.0558205 ‐1.2421782 0.3062705 0 ‐1.0078194 ‐1.3371959 ‐1.3815194 STY4154 putative DNA‐binding protein ‐0.3089121 1.7678808 0.6529806 0.36935782 0.05994943 0.51049954 0.43609375 1.0123487 STY4163 hypothetical protein ‐0.014090952 ‐1.6739954 ‐0.41327924 0.24688195 0.052916735 ‐0.29650614 ‐0.4657217 ‐0.4776099 STY4175 hypothetical protein 0.23624487 ‐3.4714706 ‐0.74050146 0.2133106 0 ‐0.70266485 ‐0.7875038 ‐0.7313358 STY4202 putative phosphosugar‐binding protein ‐0.8119977 2.0096915 0.43511128 0.21650651 0 0.49000984 0.4181711 0.39715287 STY4259 hypothetical protein 0.10265508 1.7132899 0.3831437 0.2236304 0.055790044 0.39459327 0.43763816 0.31719965 STY4260 gamma‐glutamyltranspeptidase precursor ggt ‐0.13645609 2.4212725 0.5848236 0.24153563 0 0.68399864 0.5683288 0.5021433 t0080 putative metabolite transport protein yaaU ‐0.5191252 1.5017532 0.35812873 0.23847376 0.08572143 0.34281677 0.45150468 0.28006473 t3166 hypothetical protein ‐0.54731643 ‐2.2515032 ‐0.49981746 0.22199278 0 ‐0.47960433 ‐0.56542253 ‐0.45442554 136
APPENDIX B
DATASET FOR FIGURE 12 137 Gene Expected Observed Observed Denominator Operon Locus Gene Name Numerator (r) q‐value (%) Symbol score (dExp) score (d) score (d) (s+s0) STM0732 succinate dehydrogenase, cytochrome b556 sdhC ‐0.16097945 0.32585317 0.07164832 0.21987917 12.94102 STM0733 succinate dehydrogenase, hydrophobic subunit sdhD 0.52972996 ‐1.1092175 ‐0.31271487 0.28192386 0.17665482 sdh STM0734 succinate dehydrogenase, flavoprotein subunit sdhA 0.7314146 ‐0.8225715 ‐0.17090602 0.2077704 0.6706345 STM0735 succinate dehydrogenase, Fe‐S protein sdhB 0.26868537 ‐0.46165362 ‐0.14950018 0.32383624 8.556413
fba STM3068 fructose‐bisphosphate aldolase fba ‐0.34157068 1.7177707 0.3701238 0.21546753 0.055790044
STM4221 glucosephosphate isomerase pgi ‐0.41912338 0.5373871 0.121118516 0.22538413 2.981996 pgi/pgm STM0698 phosphoglucomutase pgm ‐0.17831652 0.5294637 0.13027412 0.2460492 2.981996
gmd STM2109 GDP‐D‐mannose dehydratase in colanic acid gene cluster gmd ‐0.15905677 ‐1.2891157 ‐0.34493408 0.2675742 0.115076266
STM2098 putative glucose‐1‐phosphate uridylyltransferase (UDP‐glucose pyrophosphorylase), non‐catgalF STM2099 putative colanic acid biosynthesis protein wcaM STM2100 putative glycosyl transferase in colanic acid gene wcaL STM2101 putative galactokinase in colanic acid gene cluster wcaK ‐0.7955477 0.49970412 0.10571416 0.2115535 3.821398 STM2102 putative export protein in colanic acid gene wzxC STM2103 putative UDP‐glucose lipid carrier transferase/glucose‐1‐phosphate transferase in wcaJ ‐0.5923859 1.2691798 0.29942727 0.23592186 0.11737153 STM2104 phosphomannomutase in colanic acid gene cluster cpsG ‐2.2956998 0.3212012 0.086465225 0.26919335 14.038219 STM2105 mannose‐1‐phosphate in colanic acid gene cluster manC ‐0.43147963 ‐2.6516657 ‐0.66243654 0.24981903 0 STM2106 putative glycosyl transferase in colanic acid biosynthesis wcaI ‐0.06639378 ‐1.5617541 ‐0.35225782 0.22555268 0.066927865 STM2107 GDP‐mannose mannosyl hydrolase in colanic acid biosynthesis wcaH ‐0.08616231 ‐2.3840563 ‐0.5075489 0.21289301 0 wca STM2108 bifunctional GDP fucose synthetase in colanic acid wcaG 0.3645222 ‐1.8586746 ‐0.46265164 0.24891481 0.06410537 STM2109 GDP‐D‐mannose dehydratase in colanic acid gene cluster gmd ‐0.15905677 ‐1.2891157 ‐0.34493408 0.2675742 0.115076266 STM2110 putative acyltransferase in colanic acid biosynthesis wcaF STM2111 putative transferase in colanic acid biosynthesis wcaE STM2112 putative colanic acid polymerase wcaD STM2113 putative glycosyl transferase in colanic acid biosynthesis wcaC 0.33265916 ‐1.0247878 ‐0.2735066 0.26689097 0.22714518 STM2114 putative acyl transferase in colanic acid biosynthesis wcaB STM2115 putative glycosyl transferase in colanic acid biosynthesis wcaA 0.25384754 ‐1.6581541 ‐0.4503259 0.27158266 0.050878678 STM2116 putative tyrosine‐protein kinase in colanic acid export wzc STM2117 putative protein‐tyrosine‐phosphatase in colanic acid export wzb STM2118 putative polysaccharide export protein, outer membrane wza
STM3919 modulator of enterobacterial common antigen (ECA) polysaccharide wzzE ‐0.21702328 1.6406711 0.36819875 0.2244196 0.050878678 STM3920 UDP‐N‐acetyl glucosamine ‐2‐epimerase wecB ‐0.5249004 1.4984355 0.29216692 0.1949813 0.08572143 STM3921 UDP‐N‐acetyl‐D‐mannosaminuronic acid dehydrogenase wecC ‐0.1648354 1.0119336 0.19485374 0.19255586 0.199535 STM3922 dTDP‐glucose 4,6‐dehydratase rffG ‐0.379019 1.1267594 0.24137188 0.21421777 0.15733828 STM3923 glucose‐1‐phosphate thymidyl transferase rffH 0.75989574 ‐0.3923465 ‐0.091574974 0.23340331 14.038219 wec STM3924 lipopolysaccharide biosynthesis protein wecD ‐0.2744039 ‐0.68108827 ‐0.16207713 0.23796788 1.602521 STM3925 TDP‐4‐oxo‐6‐deoxy‐D‐glucose transaminase wecE ‐0.25473747 ‐0.57317686 ‐0.12583627 0.21954177 3.2794652 STM3926 O‐antigen translocase in LPS biosyntesis wzxE ‐0.27037552 0.24911368 0.06391327 0.25656268 18.641977 STM3927 putative inner membrane protein 0.40543115 0.59106064 0.1448034 0.24498908 1.9518311 STM3928 TDP‐Fuc4NAc:lipidII transferase wecF ‐0.004637463 1.0639365 0.2822519 0.26529017 0.18574002 STM3929 putative UDP‐N‐acetyl‐D‐mannosaminuronic acid transferase wecG
STM3606 putative transcriptional regulator (LuxR/UhpA familiy) yhjB STM3607 putative transcriptional regulator, LysR family yhjC ‐1.2774783 1.2618214 0.28907466 0.22909316 0.115076266 STM3608 putative tRNA‐processing ribonuclease yhjD ‐0.33938333 2.5381799 0.51426595 0.2026121 0 STM3609 putative MFS family transport protein yhjE 0.950021 0.42335746 0.123582125 0.29190964 7.0054545 STM3610 putative inner membrane protein yhjG 0.21675953 1.2370105 0.45271584 0.36597577 0.16040243 STM3611 putative Diguanylate cyclase/phosphodiesterase domain 3 yhjH STM3612 ketodeoxygluconokinase kdgK ‐0.13808168 ‐0.35020438 ‐0.072251335 0.20631191 16.321444 STM3613 putative Zn‐dependent peptidase yhjJ ‐0.17669298 0.39898506 0.13480397 0.3378672 8.556413 STM3614 DAACS family, C4‐dicarboxylic acids transport protein dctA 0.019353023 0.75786716 0.15860808 0.20928216 0.6706345 yhj/bcs STM3615 putative Diguanylate cyclase/phosphodiesterase yhjK ‐0.27506167 0.8503567 0.16695112 0.1963307 0.3835722 STM3616 putative TPR‐repeat‐containing protein yhjL STM3617 endo‐1,4‐D‐glucanase bcsC ‐0.20685117 1.6005901 0.40892595 0.2554845 0.048099868 STM3618 putative cellulose synthase yhjN ‐0.15356995 0.89733094 0.32254764 0.35945228 0.29865357 STM3619 glycosyltransferase, probably involved in cell wall biogenesis yhjO STM3620 putative ATPase involved in chromosome partitioning yhjQ 0.67170036 1.4742607 0.31383693 0.2128775 0.10496254 STM3621 putative cytoplasmic protein yhjR ‐0.885439 1.4697394 0.32386404 0.22035474 0.10378451 STM3622 putative cytoplasmic protein yhjS ‐0.4742528 2.3276753 0.48388755 0.20788448 0 STM3623 putative inner membrane protein yhjT ‐0.11016077 ‐0.5877265 ‐0.17164081 0.292042 2.981996 STM3624 putative inner membrane protein yhjU ‐0.12431578 0.5816348 0.14401408 0.24760222 2.0488043
STM1139 putative transcriptional regulator in curly assembly/transport, 2nd csgG 0.77964735 ‐3.1918595 ‐1.0043005 0.31464434 0 STM1140 curli production assembly/transport component, 2nd curli operon csgF ‐0.75900143 ‐3.496217 ‐0.8307732 0.23762059 0 STM1141 curli production assembly/transport component, 2nd curli operon csgE ‐0.86330074 ‐2.6320384 ‐0.8747101 0.3323318 0 csg STM1142 putative transcriptional regulator (LuxR/UhpA family) csgD 0.098342165 ‐4.3753157 ‐1.3654959 0.31209084 0 STM1143 minor curlin subunit precursor, nucleator for assembly csgB STM1144 curlin major subunit, coiled surface structures cryptic csgA STM1145 putative curli production protein csgC 0.16054967 ‐7.121766 ‐1.4728444 0.20680887 0
adr STM0385 putative diguanylate cyclase/phosphodiesterase domain 1 (aka yaiC ) adrA 0.59701335 ‐4.324508 ‐1.1396213 0.2635262 0
gly STM2555 serine hydroxymethyltransferase glyA ‐0.7095931 2.7489436 0.59083503 0.21493167 0 138
APPENDIX C
DATASET FOR FIGURE 13 139 Pathogenicity Expected Observed Observed Denominator Locus Gene Name Gene Symbol Numerator (r) q‐value (%) Island score (dExp) score (d) score (d) (s+s) PSLT037 Salmonella plasmid virulence: hydrophilic protein spvD PSLT038 Salmonella plasmid virulence: hydrophilic protein spvC PSLT039 Salmonella plasmid virulence: hydrophilic protein spvB 0.3451125 3.73863 0.8478979 0.22726588 0 spv PSLT040 Salmonella plasmid virulence: outer membrane protein spvA 0.12597384 3.69344 0.9168429 0.34995 0 PSLT041 Salmonella plasmid virulence: regulation of spv operon spvR 0.52864 1.7494527 0.57788384 0.3332265 0.058067188
STM1087 Pathogenicity island encoded protein: SPI3 pipA 0.533578 0.857898 0.21516998 0.258168 0.39057806 STM1088 Pathogenicity island encoded protein: SPI3 pipB 0.1795718 ‐0.9798491 ‐0.2721435 0.277684 0.25100356 STM1089 putative inner membrane protein Unknown STM1090 Pathogenicity island encoded protein: homologous to ipgE pipC 0.34778625 0.6241384 0.1232865 0.19741683 1.602521 STM1091 Salmonella outer protein: homologous to ipgD of sopB ‐0.67124 2.89835 0.549752 0.2416341 0 5 ‐ STM1092 putative cytoplasmic protein orfX SPI STM1093 putative cytoplasmic protein Unknown STM1094 Pathogenicity island encoded protein: SPI3 pipD ‐0.4367854 0.582196 0.13251573 0.267453 3.2794652 STM1095 Copper resistance histidine kiUnknownse copS STM1096 Copper resistance transcriptioUnknownl regulatory protein copR 0.4992586 ‐0.624824 ‐0.15457898 0.2474459 2.0488043 STM1097 putative periplasmic or exported protein Unknown ‐0.557762 ‐1.1292721 ‐0.3515194 0.27224 0.18036549
STM1379 putative amino acid permease orf48 STM1380 putative hydrolase or acyltransferase orf32 STM1381 putative cytoplasmic protein orf245 0.478286 0.65599614 0.15581225 0.237527 1.2710634 STM1382 putative regulatory protein, deoR family orf408 ‐0.34437576 0.33842635 0.7698345 0.2248594 11.978601 STM1383 TetrathioUnknownte reductase complex, subunit A ttrA ‐0.4692294 ‐1.693815 ‐0.21243665 0.19865376 0.19118953 STM1384 TetrathioUnknownte reductase complex, subunit C ttrC 0.382388 ‐1.8441163 ‐0.48361963 0.262257 0.063013285 STM1385 TetrathioUnknownte reductase complex, subunit B ttrB STM1386 TetrathioUnknownte reductase complex: sensory transduction histidine kiUnknowttrS ‐0.43564 ‐0.8197763 ‐0.2273156 0.2692583 0.6706345 STM1387 TetrathioUnknownte reductase complex: response regulator ttrR STM1388 putative cytoplasmic protein orf70 ‐0.4917346 0.81142 0.19661248 0.2423666 0.44346243 STM1389 putative inner membrane protein orf319 2.31332 1.3157438 0.2797925 0.21264967 0.1230616 STM1390 putative regulatory proteins, merR family orf242 STM1391 Secretion system regulator: transcriptoUnknownl activator, homologous with ssrB STM1392 Secretion system regulator:Sensor component ssrA 0.36591497 0.373257 0.94875835 0.2542196 9.568785 STM1393 Secretion system apparatus ssaB ‐3.5863433 ‐3.321381 ‐0.94357896 0.2849234 0 STM1394 Secretion system apparatus ssaC ‐0.32545796 ‐0.9836273 ‐0.21941125 0.223634 0.25100356 STM1395 Secretion system apparatus ssaD ‐0.39771888 ‐1.4643968 ‐0.3655539 0.24962762 0.099325456 STM1396 Secretion system effector ssaE 1.441267 ‐3.74352 ‐0.78974617 0.21319415 0 STM1397 Secretion system effector sseA 0.9723333 ‐4.8352513 ‐1.237889 0.2489697 0 STM1398 Secretion system effector sseB 0.41536158 ‐6.4116616 ‐1.57193 0.24516734 0 STM1399 Secretion system chaparone sscA ‐0.18371316 ‐5.22483 ‐1.1248634 0.2162347 0 2 ‐ STM1400 Secretion system effector sseC ‐0.92264754 ‐2.872765 ‐0.832631 0.2898113 0 SPI STM1401 Secretion system effector sseD ‐0.2912236 ‐2.187747 ‐0.48835576 0.22322313 0 STM1402 Secretion system effector sseE 0.35549143 ‐2.1521764 ‐0.58988625 0.2748823 0 STM1403 Secretion system chaparone sscB ‐0.4732188 0.358913 0.7282537 0.233796 10.890071 STM1404 Secretion system effector sseF STM1405 Secretion system effector sseG 0.743179 ‐0.7953813 ‐0.162677 0.237622 0.8168742 STM1406 Secretion system apparatus ssaG ‐0.5265974 ‐5.91822 ‐1.572854 0.2664949 0 STM1407 Secretion system apparatus ssaH ‐0.3911136 ‐11.97955 ‐2.4865324 0.277138 0 STM1408 Secretion system apparatus ssaI ‐0.2423272 ‐7.41666 ‐1.7376173 0.2343444 0 STM1409 Secretion system apparatus: homology with the yscJ/mxiJ/prgK ssaJ 0.28364876 ‐5.643275 ‐1.568448 0.277861 0 STM1410 putative cytoplasmic protein Unknown ‐0.6895825 ‐5.844457 ‐1.2747184 0.219617 0 STM1411 Secretion system apparatus ssaK 0.2181684 ‐3.228976 ‐0.98158574 0.339929 0 STM1412 Secretion system apparatus ssaL 0.9547462 ‐4.3237 ‐1.4888674 0.3446157 0 STM1413 Secretion system apparatus ssaM ‐0.716915 ‐3.9147432 ‐0.85478 0.2449561 0 STM1414 Secretion system apparatus: homology with the LcrD ssaV STM1415 Secretion system apparatus: homology with the YscN ssaN 0.785688 ‐1.398738 ‐0.4283639 0.3798185 0.12805222 STM1416 Secretion system apparatus ssaO ‐0.13117346 ‐0.8512679 ‐0.1888269 0.22178999 0.5286912 STM1417 Secretion system apparatus ssaP 0.18842188 0.4641686 0.9734219 0.29713 4.7937937 STM1418 Secretion system apparatus ssaQ ‐0.59271395 1.19356 0.22553737 0.233578 0.1685139 STM1419 Secretion system apparatus: homology with YscR of ssaR ‐0.131393 ‐7.5789514 ‐2.216393 0.26674393 0 STM1420 Secretion system apparatus: homology with YscS of ssaS 0.1898982 ‐2.9427886 ‐0.6748695 0.2293868 0 STM1421 Secretion system apparatus: homology with YscT of ssaT
STM2861 Salmonella iron transporter: fur regulated sitA 0.755373 7.42724 1.68272 0.22699997 0 STM2862 Salmonella iron transporter: fur regulated sitB ‐0.33848143 9.684762 1.985951 0.245632 0 STM2863 Salmonella iron transporter: fur regulated sitC ‐0.5332558 5.7489934 1.445996 0.2515266 0 STM2864 Salmonella iron transporter: fur regulated sitD ‐0.46562156 3.4989843 0.915324 0.2615962 0 STM2865 putative inner membrane protein avrA ‐0.267785 2.698598 0.5966483 0.22173147 0 STM2866 transcriptioUnknownl regulator sprB 0.3826 2.66538 0.863565 0.32417 0 STM2867 bacterial regulatory helix‐turn‐helix proteins, araC family hilC ‐0.1497325 1.2546563 0.3125714 0.24728456 0.115076266 STM2868 putative cytoplasmic protein Unknown STM2869 putative flagellar biosynthesis/type III secretory pathway protein orgA 2.392666 1.6843232 0.3551381 0.2184914 0.052916735 STM2870 putative inner membrane protein Unknown ‐0.3761747 2.429555 0.5277148 0.2172513 0 STM2871 cell invasion protein lipoprotein, may link inner prgK STM2872 cell invasion protein cytoplasmic prgJ 0.6737911 1.31495 0.385152 0.23712794 0.12110458 STM2873 cell invasion protein cytoplasmic prgI STM2874 cell invasion protein prgH ‐0.696366 2.439458 0.493937 0.24124567 0 STM2875 regulatory helix‐turn‐helix proteins, araC family hilD STM2876 invasion genes transcription activator hilA ‐0.3317754 2.583535 0.5453996 0.2111852 0 STM2877 cell invasion protein iagB STM2878 protein tyrosine phosphate sptP STM2879 chaparone, related to virulence sicP STM2880 putative cytoplasmic protein Unknown STM2881 putative acyl carrier protein iacP STM2882 cell invasion protein sipA ‐0.538284 0.748417 0.17691824 0.238878 0.70881206 STM2883 cell invasion protein sipD ‐0.4912687 1.28687 0.2348827 0.2282616 0.19118953 1
‐ STM2884 cell invasion protein sipC 0.2198736 1.554521 0.4571925 0.2616784 0.046063263
SPI STM2885 cell invasion protein sipB 0.63983226 0.4192444 0.9843971 0.2348268 7.0054545 STM2886 surface presentation of antigens secretory proteins sicA ‐0.772837 2.5279467 0.5134733 0.231186 0 STM2887 surface presentation of antigens secretory proteins spaS 0.3864253 0.6776876 0.21224698 0.31319296 1.1319548 STM2888 surface presentation of antigens secretory proteins spaR 0.3243237 0.4241646 0.9342445 0.222331 7.0054545 STM2889 surface presentation of antigens secretory proteins spaQ 0.798952 ‐0.39816448 ‐0.8193529 0.2578252 12.94102 STM2890 surface presentation of antigens secretory proteins spaP STM2891 surface presentation of antigens secretory proteins spaO STM2892 surface presentation of antigens secretory proteins invJ 0.8584856 ‐0.6327656 ‐0.14198452 0.22527337 2.0488043 STM2893 surface presentation of antigens secretory proteins invI STM2894 surface presentation of antigens secretory proteins invC ‐0.44472688 0.94338596 0.18169497 0.19259876 0.25100356 STM2895 surface presentation of antigens secretory proteins invB STM2896 invasion protein invA ‐0.26686937 0.4469964 0.167966 0.2387297 5.396542 STM2897 invasion protein invE STM2898 invasion protein outer membrane invG STM2899 invasion protein invF STM2900 invasion protein invH 0.3236683 0.87858 0.1874261 0.2345273 0.4960944 STM2901 putative cytoplasmic protein Unknown 0.496327 1.685345 0.533298 0.316382 0.052916735 STM2902 putative cytoplasmic protein Unknown STM2903 putative cytoplasmic protein Unknown STM2904 putative ABC‐type transport system Unknown 1.1462337 1.242791 0.269519 0.212999 0.199535 STM2905 putative acetyltransferase Unknown STM2906 putative cytoplasmic protein Unknown 0.8882618 1.156954 0.2792278 0.2413475 0.16223158 STM2907 serine/threonine specific protein phosphatase 2 pphB STM2908 putative cytoplasmic protein Unknown
STM3752 putative cytoplasmic protein Unknown 0.29431117 0.9432981 0.29729152 0.3151618 0.25100356 STM3753 ATP binding protein sugR ‐0.47684246 2.1396935 0.48596856 0.2271264 0 STM3754 putative cytoplasmic protein Unknown 0.31969455 1.5254 0.4139925 0.27235416 0.06573839 STM3755 putative cytoplasmic protein rhuM 0.4323464 1.948771 0.24619663 0.22486234 0.18036549 STM3756 putative cytoplasmic protein rmbA 0.5137684 1.766868 0.3677635 0.2814514 0.05861933 STM3757 putative autotransported protein misL ‐0.4145835 1.5712994 0.4469973 0.28447622 0.04670303 3 ‐ STM3758 putative inner membrane protein fidL SPI STM3759 putative transcriptioUnknownl regulatory protein marT 0.67124 0.7176173 0.1684743 0.23417416 0.8815512 STM3760 putative cytoplasmic protein Unknown 0.25594634 0.43751 0.9286179 0.21558158 7.0054545 STM3761 putative inner membrane protein slsA ‐0.6973895 ‐1.71379 ‐0.2424582 0.2265679 0.19118953 STM3762 putative inner membrane protein cigR ‐1.5135429 0.719244 0.172352 0.2424387 0.8815512 STM3763 Mg2 transport protein mgtB STM3764 Mg2 transport protein mgtC 0.38734964 1.3798 0.22465748 0.2164372 0.19118953 140
APPENDIX D
DATASET FOR FIGURE 15 141 Expected Observed Observed Denominator Operon Locus Gene Name Gene Symbol Numerator(r) q‐value (%) score (dExp) score(d) score(d) (s+s) STM0370 putative protein in propionate catabolism prpD ‐0.46287772 ‐1.4725568 ‐0.38424844 0.2693963 0.100403905
prp STM0371 putative acetyl‐CoA synthetase, propionate catabolism operon prpE 0.54299587 ‐1.85381 ‐0.5133654 0.28511778 0.06083684
STM1383 Tetrathionate reductase complex, subunit A ttrA ‐0.4692294 ‐1.693815 ‐0.21243665 0.19865376 0.19118953 STM1384 Tetrathionate reductase complex, subunit C ttrC 0.382388 ‐1.8441163 ‐0.48361963 0.262257 0.063013285 ttr STM1385 Tetrathionate reductase complex, subunit B ttrB STM1386 Tetrathionate reductase complex: sensory transduction histidine kinase ttrS ‐0.43564 ‐0.8197763 ‐0.2273156 0.2692583 0.6706345
STM2016 nicotinate‐nucleotide dimethylbenzimidazole‐P phophoribosyl transferase cobT ‐0.3596984 ‐0.6364274 ‐0.18234958 0.2865278 2.0488043 STM2017 cobalamin 5‐phosphate synthase cobS 0.125549 ‐1.613745 ‐0.379436 0.2348614 0.048099868 STM2018 bifunctional: cobinamide kinase cobinamide phosphate guanylyltransferase cobU STM2019 synthesis of vitamin B12 adenosyl cobalamide precursor cbiP STM2020 synthesis of vitamin B12 adenosyl cobalamide precursor cbiO ‐0.577434 ‐0.86849797 ‐0.271779 0.23854737 0.44346243 STM2021 synthesis of vitamin B12 adenosyl cobalamide precursor cbiQ STM2022 synthesis of vitamin B12 adenosyl cobalamide precursor cbiN 0.132948 ‐2.8734584 ‐0.6194955 0.21559231 0 STM2023 synthesis of vitamin B12 adenosyl cobalamide precursor cbiM ‐0.2681435 ‐1.193524 ‐0.21968375 0.2155135 0.22714518 STM2024 synthesis of vitamin B12 adenosyl cobalamide precursor cbiL 0.6821211 ‐1.911219 ‐0.48326436 0.25419956 0.0654669 STM2025 synthesis of vitamin B12 adenosyl cobalamide precursor cbiK ‐0.177487 ‐1.9498528 ‐0.54513216 0.2795766 0.035160456 cob ‐ STM2026 synthesis of vitamin B12 adenosyl cobalamide precursor cbiJ cbi STM2027 synthesis of vitamin B12 adenosyl cobalamide precursor cbiH ‐0.3415727 ‐1.622655 ‐0.32925114 0.229889 0.048099868 STM2028 synthesis of vitamin B12 adenosyl cobalamide precursor cbiG ‐1.1164812 ‐1.763159 ‐0.41459784 0.23514597 0.05861933 STM2029 synthesis of vitamin B12 adenosyl cobalamide precursor cbiF 0.18976788 ‐2.41728 ‐0.53393686 0.2288991 0 STM2030 synthesis of vitamin B12 adenosyl cobalamide precursor cbiT ‐0.263886 ‐1.5197679 ‐0.3129892 0.259454 0.10616762 STM2031 synthesis of vitamin B12 adenosyl cobalamide precursor cbiE ‐0.6444326 ‐1.4282357 ‐0.3276442 0.2294473 0.11451641 STM2032 synthesis of vitamin B12 adenosyl cobalamide precursor cbiD ‐0.2332939 ‐1.1972411 ‐0.384656 0.31773597 0.16223158 STM2033 synthesis of vitamin B12 adenosyl cobalamide precursor cbiC ‐0.23452298 ‐1.536577 ‐0.4781363 0.31116977 0.08572143 STM2034 synthesis of vitamin B12 adenosyl cobalamide precursor cibB ‐0.611676 ‐0.64688283 ‐0.14634614 0.22623284 1.9518311 STM2035 synthesis of vitamin B12 adenosyl cobalamide precursor cbiA ‐0.19833991 ‐0.72592443 ‐0.15292 0.273532 1.2710634
STM2036 Propanediol utilization: transcriptional regulation, AraC family pocR al scrit pion Tran STM2037 Propanediol utilization: propanediol diffusion facilitator pduF
STM2038 Propanediol utilization: polyhedral bodies pduA 0.81463695 ‐0.596994 ‐0.1662132 0.2918818 6.111435 STM2039 Propanediol utilization: polyhedral bodies pudB 0.2779956 ‐2.9346273 ‐0.6442693 0.2195442 0 STM2040 Propanediol utilization: dehydratase, large subunit pduC ‐0.691715 ‐1.337248 ‐0.2936185 0.219577 0.12110458 STM2041 Propanediol utilization: dehydratase, medium subunit pduD 0.49715197 ‐2.9236968 ‐0.664766 0.22711235 0 STM2042 Propanediol utilization: dehydratase, small subunit pduE STM2043 Propanediol utilization: diol dehydratase reactivation pduG ‐0.2545563 ‐2.4453 ‐0.769993 0.29452744 0 STM2044 Propanediol utilization: diol dehydratase reactivation pduH STM2045 Propanediol utilization: polyhedral bodies pduJ 0.78167754 ‐3.361834 ‐0.8561333 0.28197682 0 STM2046 Propanediol utilization: polyhedral bodies pduK 0.242989 ‐2.8958943 ‐0.7494269 0.25878945 0 STM2047 Propanediol utilization pduL STM2048 Propanediol utilization pduM 0.7955477 ‐2.593524 ‐0.5469762 0.21917 0 pdu STM2049 Propanediol utilization: polyhedral bodies pduN ‐0.66288 ‐3.332989 ‐0.746891 0.2114299 0 STM2050 Propanediol utilization: B12 related pduO 0.134613 ‐4.498622 ‐1.186744 0.2638166 0 STM2051 Propanediol utilization: CoA‐dependent propionaldehyde dehydrogenase pduP STM2052 Propanediol utilization: propanol dehydrogenase pduQ 0.6272232 ‐2.2732737 ‐0.517642 0.2272317 0 STM2053 Propanediol utilization: polyhedral bodies pduS 0.5557284 ‐2.489522 ‐0.59797454 0.2419843 0 STM2054 Propanediol utilization: polyhedral bodies pduT ‐0.7478967 ‐1.757235 ‐0.4866713 0.2769866 0.058067188 STM2055 Propanediol utilization: polyhedral bodies pduU ‐0.4263147 ‐1.2839699 ‐0.33875272 0.2638323 0.14613661 STM2056 Propanediol utilization pduV 0.2473526 ‐2.86925 ‐0.4437682 0.2123185 0 STM2057 Propanediol utilization: propionate kinase pduW ‐0.57325 0.5271 0.11952656 0.23892361 3.821398 STM2058 Propanediol utilization pduX 0.7679843 2.87743 0.422674 0.2313112 0 e STM2337 acetate kinase A (propionate kinase 2) ackA 0.5191252 ‐2.5375 ‐0.458568 0.2232548 0
Hous STM2338 phosphotransacetylase pta 0.75595593 ‐2.351337 ‐0.4913177 0.288388 0
STM2973 L‐1,2‐propanediol oxidoreductase fucO ‐0.5871229 0.56910187 0.1455015 0.25566864 2.304016 STM2974 L‐fuculose‐1‐phosphate aldolase fucA STM2975 L‐fucose permease pseudogene fucP STM2976 L‐fucose isomerase fucI 0.0894275 ‐2.0800235 ‐0.6155243 0.2959218 0 fuc STM2977 L‐fuculokinase fucK ‐0.102252536 ‐0.4770719 ‐0.110215545 0.23102501 7.600995 STM2978 conserved protein of fucose operon fucU ‐0.12107843 ‐0.89110214 ‐0.23629537 0.26517203 0.4182407 STM2979 positive regulator of the fuc operon (DeoR family transcriptional regulator) fucR 142
APPENDIX E
SIGNIFICANT MO GENES DATA FOR CHAPTER 4 143 All Significant Salmonella MO Genes (Delta=0.80701154, False Sig Genes=0, FDR=0%)
Log Ratio Locus GeneN GeneS 107808 107809 107810 107811 107812 107813 2 Ratio Means
PSLT012 putative bacterial regulatory proteins, luxR family orf7 ‐0.21873495 ‐0.33098617 ‐0.23817043 ‐1.0850646 ‐1.0817932 ‐0.86064273 ‐0.26263 0.833567 PSLT020 hypothetical protein 0.19118033 0.6662266 0.58284324 ‐0.63963336 ‐0.8767592 ‐0.9003971 0.480083 1.394824 PSLT023 DNA replication repA2 0.59046596 0.46488547 0.41520572 ‐0.6756516 ‐1.2608273 ‐1.1219376 0.490186 1.404626 PSLT036 putative transposase, IS200‐like 0.42819518 0.41039482 0.60164636 0.6962467 0.65043 0.6241986 0.480079 1.39482 PSLT042 putative integrase protein 0.5352007 0.51944155 0.46636653 ‐0.586795 ‐0.5008615 ‐0.35955667 0.507003 1.421095 PSLT043 putative phosphoribulokinase / uridine kinase family 0.52404296 0.5330904 0.5033524 ‐1.4889245 ‐1.3363144 ‐1.6471025 0.520162 1.434116 PSLT044 putative integrase protein rlgA 0.6716581 0.61639065 0.610975 ‐0.4208412 ‐0.91123503 ‐1.1832428 0.633008 1.550795 PSLT046 putative carbonic anhydrase 0.29661897 0.5118478 0.47765243 ‐0.7575558 ‐0.6575734 ‐0.68897706 0.428706 1.346026 PSLT047 putative cytoplasmic protein 0.39670837 0.48000222 0.5567938 0.23216134 ‐0.06946793 ‐0.54614925 0.477835 1.392652 PSLT052 plasmid partition protein A parA 0.37233824 0.5566913 0.31634837 ‐0.34044805 ‐0.45474067 ‐0.6530225 0.415126 1.333415 PSLT053 plasmid partition protein B parB 0.44112355 0.42865178 0.39327705 0.31699353 0.20886631 0.077271126 0.421017 1.338871 PSLT072 putative transglycosylase finP 0.27459073 0.60735095 0.4902862 ‐1.0760994 ‐1.0165291 ‐0.96350557 0.457409 1.373074 PSLT080 conjugative transfer: assembly traK ‐0.19855331 ‐0.4436235 ‐0.31377703 ‐0.8411851 ‐0.59166986 ‐0.5302125 ‐0.31865 0.801819 PSLT095 conjugative transfer: aggregate stability traN 0.5083317 0.49951515 0.3619898 ‐0.28462604 ‐0.80491954 ‐0.71326345 0.456612 1.372316 PSLT096 conjugative transfer trbE 0.30819207 0.4279481 0.3715972 ‐0.77392405 ‐0.7402496 ‐0.84005123 0.369246 1.291677 PSLT097 conjugative transfer: assembly traF 0.23419821 0.49506816 0.4314934 ‐0.93360496 ‐1.044014 ‐1.21234 0.38692 1.307599 PSLT098 conjugative transfer: fimbrial synthesis traQ 0.2876653 0.32006288 0.1999281 ‐0.93247354 ‐0.75738686 ‐0.967667 0.269219 1.205155 PSLT103 conjugative transfer: surface exclusion traT 0.5539146 0.47054815 0.43895933 ‐1.1038934 ‐1.4469562 ‐1.0903301 0.487807 1.402312 PSLT106 homologue of mvpA, Shigella flexneri 0.23498842 0.35477102 0.33978343 0.0844318 ‐0.062313866 ‐0.31416678 0.309848 1.239577 STM0003 homoserine kinase thrB ‐0.69281363 ‐1.2177294 ‐1.0278673 0.51616096 0.38311204 0.28184104 ‐0.97947 0.507166 STM0004 threonine synthase thrC ‐0.314873 ‐0.36514962 ‐0.41357788 0.83274347 0.43817458 0.35283428 ‐0.36453 0.77672 STM0012 chaperone Hsp70 in DNA biosynthesis/cell division dnaK ‐0.5170135 ‐0.66296506 ‐0.6681755 0.80367666 0.7522421 0.704346 ‐0.61605 0.652454 STM0023 fimbrial usher bcfC ‐0.33272958 ‐0.21676783 ‐0.282484 ‐0.16569032 ‐0.089326344 ‐0.21570423 ‐0.27733 0.825118 STM0027 fimbrial chaparone bcfG ‐0.5230399 ‐0.91175896 ‐0.9254414 ‐0.572756 ‐0.83642125 ‐0.8608931 ‐0.78675 0.57965 STM0064 dihydrodipicolinate reductase dapB ‐1.4498417 ‐1.5317243 ‐1.5456456 2.4256654 1.7328606 1.6991214 ‐1.50907 0.351337 STM0066 carbamoyl‐phosphate synthetase, glutamine‐hydrolysing small subunit carA ‐1.1434257 ‐1.2538745 ‐1.1086514 0.87991774 0.5956529 0.71649796 ‐1.16865 0.444837 STM0067 carbamoyl‐phosphate synthase, large subunit carB ‐1.053431 ‐1.2448778 ‐1.2725413 0.88545954 0.89565265 1.0044138 ‐1.19028 0.438217 STM0077 related to carnitine metabolism fixC ‐0.21692583 ‐0.42774284 ‐0.5170514 ‐0.0728656 ‐0.19386353 0.2334121 ‐0.38724 0.764591 STM0092 peptidyl‐prolyl cis‐trans isomerase, survival protein surA 0.3767992 0.28144532 0.26570287 1.0206679 1.0740172 1.1923009 0.307982 1.237975 STM0096 RNA polymerase associated protein, putative SNF2 family hepA ‐0.35401532 ‐0.5445657 ‐0.43465686 ‐0.24156623 ‐0.16503368 ‐0.23358908 ‐0.44441 0.734883 STM0108 thiamine‐binding periplasmic protein tbpA 0.23577571 0.33463296 0.26570046 1.0293115 1.1995857 1.1235733 0.278703 1.213104 STM0110 3‐isopropylmalate isomerase (dehydratase), subunit with LeuC leuD 1.5279573 1.7166674 1.583018 1.4300208 1.5770993 1.3194692 1.609214 3.050856 STM0113 2‐isopropylmalate synthase leuA 2.0958962 2.0898426 2.145787 1.6987354 1.1851902 1.4400281 2.110509 4.318435 STM0116 acetolactate synthase III, valine sensitive, large subunit ilvI 0.26020688 0.4106647 0.2518642 0.93679035 0.98173016 0.5206042 0.307579 1.237629 STM0120 putative S‐adenosyl methionine adenyltransferase yabC ‐0.22600807 ‐0.22315557 ‐0.22407691 1.1794915 0.9645097 0.99701464 ‐0.22441 0.855943 STM0134 UDP‐3‐O‐acyl N‐acetylglucosamine deacetylase lpxC ‐0.25837657 ‐0.28313807 ‐0.33918095 0.31029144 0.33947462 0.20077516 ‐0.29357 0.815883 STM0150 APC family, aromatic amino acid transporter aroP 0.33038053 0.36546996 0.44108745 0.42758867 0.153349 0.39013758 0.378979 1.300421 STM0153 pyruvate dehydrogenase, dihydrolipoyltransacetylase component aceF 0.43818256 0.34659097 0.21256778 1.0322548 0.9680674 0.9234585 0.332447 1.259147 STM0157 putative outer membrane protein yacH ‐0.40804002 ‐0.4874071 ‐0.43260288 0.45829695 0.5423217 0.6327726 ‐0.44268 0.735765 STM0167 putative periplasmic protein yacC ‐0.18872282 ‐0.29264215 ‐0.27398717 0.16680454 0.12027538 0.035354383 ‐0.25178 0.839857 STM0169 glucose dehydrogenase gcd 0.2772285 0.39958212 0.4279262 ‐0.015725844 ‐0.05477873 ‐0.007675674 0.368246 1.290782 STM0171 putative carbonic anhydrase yadF 1.1643332 1.417171 1.3067999 0.97402143 1.0766861 0.98444915 1.296101 2.455644 STM0172 putative ABC‐type multidrug transport system, ATPase component yadG 0.29700285 0.42260903 0.3322259 0.03287625 0.0646959 0.20375274 0.350613 1.275102 STM0178 putative PTS enzyme yadI ‐0.24664909 ‐0.28074655 ‐0.21187602 ‐0.2385491 ‐0.6072303 ‐0.3455686 ‐0.24642 0.842983 STM0181 pantothenate synthetase panC ‐0.43498638 ‐0.3594995 ‐0.3009579 ‐0.73306835 ‐0.5574113 ‐0.5896664 ‐0.36515 0.776389 STM0191 outer membrane protein receptor / transporter for fhuA 0.6176664 0.56935674 0.4045455 0.14433959 0.161439 0.29092133 0.530523 1.444453 STM0208 deoxyguanosine triphosphate triphosphohydrolase dgt 0.300246 0.31568775 0.2304402 0.47861534 0.3682905 0.12639475 0.282125 1.215984 STM0216 30S ribosomal subunit protein S2 rpsB ‐0.4021984 ‐0.54393405 ‐0.7115866 0.57341975 0.29930934 0.5275517 ‐0.55257 0.681803 STM0219 ribosome releasing factor frr 0.2711675 0.42408898 0.5943148 1.1404701 0.8477138 1.0069747 0.429857 1.3471 STM0221 undecaprenyl pyrophosphate synthetase (di‐trans,poly‐cis‐decaprenylcistransferase) uppS ‐0.23628573 ‐0.25281954 ‐0.28313074 0.19743674 0.23864031 0.3958258 ‐0.25741 0.836587 STM0223 putative membrane‐associated Zn‐dependent protease yaeL 0.3049555 0.31661424 0.3075448 0.6899292 0.7168318 0.6521502 0.309705 1.239454 STM0224 putative outer membrane antigen yaeT 0.43271163 0.52033836 0.30236128 1.415841 1.3570592 0.9922708 0.41847 1.33651 STM0225 histone‐like protein, located in outer membrane hlpA 0.5923797 0.6102872 0.6410853 0.17894988 0.18877642 0.2843624 0.614584 1.531117 STM0228 UDP‐N‐acetylglucosamine acetyltransferase lpxA 0.46926323 0.32102868 0.3484745 1.0336506 0.6345175 0.7105296 0.379589 1.300971 STM0245 putative outer membrane lipoprotein yaeC 0.7503361 0.9077048 0.6976756 0.1374862 ‐0.05216601 ‐0.28360838 0.785239 1.723378 STM0247 putative ABC superfamily (atp_bind) transport system abc 0.45306736 0.27486637 0.29837728 0.06541499 0.077230215 0.16295904 0.342104 1.267604 STM0259 putative methyltransferase in menaquinone/biotin biosynthesis yafE 0.5335188 0.54910225 0.48765448 ‐0.10479076 ‐0.22239582 ‐0.32202214 0.523425 1.437364 STM0300 putative fimbriae assembly chaparone safB 0.3435695 0.30105543 0.25424984 ‐0.059341572 ‐0.24911895 ‐0.36154994 0.299625 1.230824 STM0316 aminoacyl‐histidine dipeptidase (peptidase D) pepD 0.4249264 0.6467224 0.56409657 0.30107343 0.07402481 0.2727989 0.545248 1.459272 STM0319 transcriptional regulator of cryptic csgA gene for crl 0.38255042 0.48966178 0.43527973 0.59202254 0.32970014 0.2519256 0.435831 1.352689 STM0322 gamma‐glutamylphosphate reductase proA ‐0.42575482 ‐0.47432962 ‐0.46927315 0.93801695 0.001985377 ‐0.09746811 ‐0.45645 0.728776 STM0324 putative inner membrane protein ‐0.34722316 ‐0.32326004 ‐0.32992923 ‐0.52142775 ‐0.8202106 ‐0.9760636 ‐0.33347 0.793625 STM0351 putative cation efflux system protein ‐0.37917757 ‐0.66379964 ‐0.44164142 ‐0.13397627 ‐0.19225281 ‐0.2778022 ‐0.49487 0.709624 STM0352 putative cation efflux pump ‐0.5922731 ‐0.7305447 ‐0.58940333 ‐0.52192587 ‐0.07662028 ‐0.067977145 ‐0.63741 0.642867 STM0355 putative Copper chaperone ‐0.26525173 ‐0.3072882 ‐0.21923548 ‐1.4730307 ‐0.7093598 ‐0.71972054 ‐0.26393 0.832819 STM0362 putative cytoplasmic protein ‐0.37270135 ‐0.35836142 ‐0.21547908 ‐0.6839262 ‐0.7432704 ‐0.79809225 ‐0.31551 0.803565 STM0363 putative transcription regulator, AraC family 0.3706963 0.37361923 0.40769526 0.03719335 ‐0.073736854 ‐0.2841979 0.384004 1.304958 STM0369 putative citrate synthase prpC ‐0.60706687 ‐1.0282005 ‐0.84019566 ‐0.5843593 ‐0.7967985 ‐0.5542958 ‐0.82515 0.564422 STM0370 putative protein in propionate catabolism prpD ‐0.35205087 ‐0.5228659 ‐0.27782857 ‐0.19599861 ‐0.4814676 ‐0.3435003 ‐0.38425 0.766178 STM0377 putative outer membrane lipoprotein yaiW 0.25086525 0.25069094 0.26045486 0.34953326 0.105576865 0.2243431 0.254004 1.192512 STM0383 putative cytoplasmic protein yaiB ‐1.0665052 ‐0.96745145 ‐0.86840016 ‐0.54481554 ‐0.7013361 ‐0.8197837 ‐0.96745 0.511408 STM0385 putative diguanylate cyclase/phosphodiesterase domain 1 yaiC ‐1.035921 ‐1.2856466 ‐1.0972964 ‐0.5835514 ‐1.0542364 ‐0.85180116 ‐1.13962 0.453879 STM0388 shikimate kinase II aroL 0.6025709 0.70973486 0.6212581 1.2113078 0.88610744 0.6303237 0.644521 1.56322 STM0401 maltodextrin glucosidase malZ ‐0.3888723 ‐0.62017125 ‐0.49921197 0.06503034 0.059843328 0.1100638 ‐0.50275 0.705759 STM0402 putative thiol ‐ alkyl hydroperoxide reductase ‐0.26266083 ‐0.2559368 ‐0.21505938 ‐0.6453264 ‐0.70945585 ‐0.552541 ‐0.24455 0.844078 STM0405 tRNA‐guanine transglycosylase tgt ‐0.23448625 ‐0.32816613 ‐0.2688599 0.20476426 1.4769859 1.2148346 ‐0.27717 0.825208 STM0434 ketopantoate reductase apbA ‐0.23700683 ‐0.31890327 ‐0.3367807 0.62007135 0.46394312 0.51389384 ‐0.29756 0.813625 STM0436A IS903 transposase ‐0.37019327 ‐0.461738 ‐0.32148904 ‐0.26962534 ‐0.57110023 ‐0.51646316 ‐0.38447 0.766059 STM0447 peptidyl‐prolyl cis/trans isomerase, trigger factor a molecular tig 0.77709967 0.50235707 0.6469255 1.9144396 1.7988226 2.2050507 0.642127 1.560629 STM0448 proteolytic subunit of clpA‐clpP ATP‐dependent serine protease clpP 0.3406515 0.23828518 0.5413024 0.38613337 0.39837956 0.48524043 0.373413 1.295414 STM0452 peptidyl prolyl isomerase cypD 0.5217175 0.37075484 0.35298458 0.7027212 0.4547855 0.7326637 0.415152 1.333439 STM0457 putative hydrolase cof ‐0.199623 ‐0.4405928 ‐0.47523832 ‐0.18961263 ‐0.18991382 ‐0.26375663 ‐0.37182 0.772808 STM0458 putative cysteine synthase/cystathionine beta‐synthase ‐0.42223638 ‐0.2445751 ‐0.37689427 ‐0.2916745 ‐0.3193621 ‐0.39003247 ‐0.3479 0.785726 STM0460 putative ABC superfamily (atp) transporter mdlA ‐0.4450372 ‐0.51094645 ‐0.6286598 ‐0.7020355 ‐0.3485956 ‐0.4019517 ‐0.52821 0.693412 STM0461 putative ABC superfamily (atp&membrane) transporter mdlB ‐0.4977934 ‐0.66604364 ‐0.67152846 ‐0.6051969 ‐0.7758657 ‐0.6820164 ‐0.61179 0.654385 STM0462 regulatory protein, P‐II 2, for nitrogen assimilation glnK ‐2.2110238 ‐2.2586772 ‐2.2937286 ‐2.2217207 ‐2.6256282 ‐2.9934628 ‐2.25448 0.209573 STM0463 putative Amt family, ammonium transport protein amtB ‐2.5150805 ‐2.587126 ‐2.4561398 ‐2.7700706 ‐3.2622104 ‐3.0378387 ‐2.51945 0.17441 STM0469 putative 50S ribosomal protein L31 (second copy) rpmE2 1.3985962 1.5783657 1.7735767 ‐2.935089 ‐3.2296724 ‐3.5061345 1.583513 2.996987 STM0470 putative 50S ribosomal protein L36 (second copy) rpmJ2 1.5099168 1.5123256 1.6645528 ‐3.9113479 ‐3.6799922 ‐3.7337155 1.562265 2.953171 STM0472 maltose o‐acetyltransferase maa 0.2251964 0.33155555 0.41882786 ‐0.046616565 ‐0.3229667 ‐0.46000916 0.325193 1.252832 STM0475 RND family, acridine efflux pump acrB 0.39987427 0.31404147 0.24001056 0.2590296 ‐0.23273024 ‐0.0724034 0.317975 1.24658 STM0476 acridine efflux pump acrA 0.3923507 0.40799665 0.26487678 0.18720058 0.39140984 0.49807835 0.355075 1.279052 STM0485 putative cytoplasmic protein ybaB 0.42250806 0.66256225 0.6792037 1.3368509 1.0855744 1.02594 0.588091 1.503257 STM0488 adenylate kinase adk ‐0.55290645 ‐0.41970772 ‐0.6663243 0.6514215 0.62113297 0.2609175 ‐0.54631 0.684768 STM0498 putative copper‐transporting ATPase copA ‐0.63727254 ‐0.6506231 ‐0.69528997 ‐0.5962032 ‐0.2707283 ‐0.2668513 ‐0.66106 0.632413 STM0500 putative Membrane protein implicated in regulation of ybbJ ‐0.33343032 ‐0.619396 ‐0.62821084 ‐0.26874873 ‐0.09927541 ‐0.23757914 ‐0.52701 0.69399 STM0508 putative inner membrane protein ybbP ‐0.22696888 ‐0.2539097 ‐0.33893412 0.6334251 0.7281374 0.53804964 ‐0.27327 0.827441 STM0510 putative ABC‐type transport system ATPase component/cell division sfbA 1.4184393 1.588685 1.4249496 ‐0.004513601 ‐0.0848971 ‐0.06903442 1.477358 2.784384 STM0511 putative ABC‐type transport system ATPase component/cell division sfbB 0.44251212 0.37308457 0.40804917 0.26447338 0.08753406 0.06259792 0.407882 1.326737 STM0528 ureidoglycolate dehydrogenase allD ‐0.27818152 ‐0.28702745 ‐0.23388119 ‐0.4211586 ‐0.45683774 ‐0.5028857 ‐0.26636 0.831413 STM0530 putative cytoplasmic protein ylbE ‐0.42593813 ‐0.4512766 ‐0.51883566 ‐0.3809063 ‐0.32942057 ‐0.41091123 ‐0.46535 0.724295 STM0536 peptidyl‐prolyl cis‐trans isomerase B (rotamase B) ppiB 0.28459483 0.49165556 0.51679015 0.4785309 0.1927756 0.016317612 0.431014 1.34818 STM0558 putative glycosyltransferase yfdH 0.277786 0.2642377 0.4636148 ‐0.05028975 ‐0.119796574 ‐0.018137489 0.335213 1.261564 STM0562 putative transport protein ‐0.42998475 ‐0.4193589 ‐0.3444349 ‐0.5965487 ‐0.8350702 ‐0.8219256 ‐0.39793 0.758948 STM0570 outer membrane N‐acetyl phenylalanine beta‐naphthyl ester‐cleaving esterase apeE ‐0.37236246 ‐0.644741 ‐0.6217672 0.71657217 0.8763294 0.7615438 ‐0.54629 0.684779 144 STM0585 outer membrane porin, receptor for ferric enterobactin fepA 0.9580155 1.0559162 0.9598503 0.9709265 1.0320842 0.93534297 0.991261 1.987921 STM0587 putative cytoplasmic protein ybdZ 1.6586463 1.7351841 1.6181923 0.5550019 0.77824533 0.8829725 1.670674 3.183633 STM0603 putative aminotransferase ybdL 0.42625427 0.64241004 0.33061343 ‐0.19121508 ‐0.23664851 ‐0.16877598 0.466426 1.381682 STM0605 putative 3‐phosphoadenosine 5‐phosphosulfate sulfotransferase (PAPS reductase)/FAD synthybdN 0.3849634 0.48471278 0.425839 0.25178462 0.12766095 0.08455879 0.431838 1.348951 STM0607 periplasmic disulfide isomerase, thiol‐disulphide oxidase dsbG 0.5100641 0.70760614 0.53589386 0.6468124 0.81203794 0.5543116 0.584521 1.499541 STM0608 alkyl hydroperoxide reductase, C22 subunit detoxification of ahpC 0.35502318 0.4435194 0.49125957 0.15069991 ‐0.13732953 ‐0.15077637 0.429934 1.347172 STM0629 RNA chaperone, negative regulator of cspA transcription cspE ‐0.7889897 ‐0.880915 ‐0.6495976 ‐0.20864968 ‐0.2603843 ‐0.114142515 ‐0.77317 0.585131 STM0632 putative Sec‐independent protein secretion pathway component ybeC ‐1.1095876 ‐1.0312442 ‐0.96915185 ‐1.4278146 ‐1.6140355 ‐1.4850512 ‐1.03666 0.487454 STM0633 lipoate synthase, an iron‐sulfur enzyme lipA 0.26320487 0.33734098 0.33047995 0.24327846 0.18448736 0.08720529 0.310342 1.240002 STM0640 cell elongation specific transpeptidase of penicillin‐binding protein mrdA 0.22524922 0.47127283 0.471701 0.034822803 0.054687776 ‐0.023785954 0.389408 1.309856 STM0659 putative heatshock protein, homolog of hsp70 in hscC ‐0.42572558 ‐0.37190017 ‐0.3907563 ‐0.5145188 ‐0.33737367 ‐0.4556404 ‐0.39613 0.759895 STM0661 putative purine nucleoside hydrolase ybeK ‐0.5770081 ‐0.5427533 ‐0.62149066 ‐0.47829667 ‐0.3749117 ‐0.42480436 ‐0.58042 0.66877 STM0662 ABC superfamily (atp_bind), glutamate/aspartate transporter gltL ‐0.673679 ‐1.0342818 ‐1.0537351 ‐0.69161516 ‐1.0319647 ‐0.7187726 ‐0.92057 0.528302 STM0663 ABC superfamily (membrane), glutamate/aspartate transporter gltK ‐0.5092478 ‐0.53041124 ‐0.74785215 ‐0.37341556 ‐0.30032292 ‐0.80333817 ‐0.59584 0.66166 STM0664 ABC superfamily (membrane), glutamate/aspartate transporter gltJ ‐0.5555748 ‐0.5709684 ‐0.63115054 ‐0.6378293 ‐0.7115269 ‐0.9004852 ‐0.5859 0.666235 STM0665 ABC superfamily (bind_prot), glutamate/aspartate transporter gltI ‐0.66387933 ‐0.76356953 ‐0.7679571 ‐1.4089369 ‐1.6537793 ‐1.8124185 ‐0.7318 0.602151 STM0671 putative monooxygenase ubiF ‐0.3663575 ‐0.6821574 ‐0.56265086 1.0897584 1.1038402 1.1244713 ‐0.53706 0.689176 STM0680 asparagine synthetase B asnB ‐1.5608506 ‐1.6479359 ‐1.5424268 ‐0.0956105 ‐0.10355192 ‐0.023382738 ‐1.58374 0.333616 STM0685 Sugar Specific PTS family, n‐acetylglucosamine‐specific enzyme IIABC nagE ‐0.25067455 ‐0.3726625 ‐0.25038597 0.15950722 0.07047722 0.028475543 ‐0.29124 0.817199 STM0690 citrate utilization protein b citB ‐0.2981579 ‐0.48714057 ‐0.39032212 ‐0.40041003 ‐0.32748368 ‐0.31356326 ‐0.39187 0.762139 STM0692 putative transcriptional regulator, LysR family ‐0.25044683 ‐0.44280136 ‐0.39094642 ‐0.12072479 ‐0.20360208 ‐0.07248604 ‐0.3614 0.77841 STM0693 transcriptional repressor of iron‐responsive genes (Fur family) fur 0.58997774 0.91239756 0.831037 0.9073395 0.80599254 0.7938867 0.777804 1.714519 STM0730 citrate synthase gltA 0.6266423 0.619384 0.86853135 1.796742 1.4630904 1.5352359 0.704853 1.629978 STM0737 2‐oxoglutarate dehydrogenase (dihydrolipoyltranssuccinase E2 component) sucB 0.26151693 0.40387812 0.231357 2.2338598 2.410301 2.2622237 0.298917 1.230221 STM0741 cytochrome d terminal oxidase polypeptide subunit II cydB ‐0.30366108 ‐0.33722287 ‐0.368614 ‐0.41331273 ‐0.13948935 ‐0.24926664 ‐0.3365 0.791961 STM0749 tol protein required for outer membrane integrity pal 0.4004878 0.70452666 0.46171623 1.5477052 1.34555 1.2616546 0.522244 1.436187 STM0756 quinolinate synthetase, A protein nadA ‐0.3240194 ‐0.34578836 ‐0.30040222 ‐0.26702607 ‐0.13559411 ‐0.34239936 ‐0.3234 0.799182 STM0757 NMN family, nucleoside/purine/pyrimidine transporter pnuC ‐0.3011169 ‐0.2727079 ‐0.30462992 ‐0.077311166 ‐0.07028874 0.05537214 ‐0.29282 0.816306 STM0760 3‐deoxy‐D‐arabinoheptulosonate‐7‐phosphate synthase (DAHP synthetase, phenylalanine reparoG 0.54628253 0.40731314 0.5453931 0.95983857 0.1955221 0.13860117 0.499663 1.413883 STM0764 transcriptional regulator, lysR family 0.2849219 0.56606615 0.49930444 0.17560285 0.91956943 0.5009572 0.450097 1.366133 STM0768 Oxalacetate decarboxylase: beta chain dcoB ‐0.34293717 ‐0.890913 ‐0.94957954 0.26257965 0.093307786 0.14219761 ‐0.72781 0.60382 STM0771 putative ABC‐type cobalamin/Fe3 ‐siderophores transport system, ATPase component 0.4087879 0.26271224 0.4147616 ‐0.3103159 ‐0.23873681 ‐0.4349714 0.362087 1.285284 STM0772 phosphoglyceromutase 1 gpmA 0.6452878 0.5928036 0.6900711 ‐0.8919129 ‐0.89992064 ‐0.737573 0.642721 1.561271 STM0782 ABC superfamily (membrane), molybdate transporter modB ‐0.4180693 ‐0.33851707 ‐0.39626706 1.1440533 0.9742888 1.1510261 ‐0.38428 0.766159 STM0802 molybdopterin biosynthesis, protein A moaA 0.65986574 0.6332867 0.7044902 ‐0.02816065 ‐0.010397093 ‐0.14391999 0.665881 1.586537 STM0803 molybdopterin biosynthesis, protein B moaB 0.29125378 0.49719876 0.39910957 ‐1.042177 ‐0.9060325 ‐0.90210325 0.395854 1.315721 STM0804 molybdopterin biosynthesis, protein C moaC 0.3687425 0.1976365 0.36066052 ‐0.21917652 ‐0.30484277 ‐0.14593555 0.309013 1.23886 STM0807 putative permease ybhL 0.30521566 0.29398838 0.25006676 ‐0.09702353 ‐0.16546385 ‐0.3067349 0.28309 1.216798 STM0819 putative transcriptional repressor (TetR/AcrR family) ybiH ‐0.41621664 ‐0.17864455 ‐0.39408445 0.3378418 ‐0.12042255 0.16623312 ‐0.32965 0.79573 STM0822 putative transferase ybiB ‐0.442354 ‐0.3170274 ‐0.22195747 0.005124741 0.074902885 ‐0.033983357 ‐0.32711 0.79713 STM0826 putative SAM‐dependent methyltransferase ybiN ‐0.4781753 ‐0.7681317 ‐0.6186037 0.08266802 0.46681458 0.4464508 ‐0.62164 0.649933 STM0828 ABC superfamily (atp_bind), glutamine high‐affinity transporter glnQ ‐0.8392573 ‐0.6363069 ‐0.50710005 ‐0.57792866 ‐0.4704322 ‐0.34354207 ‐0.66089 0.632489 STM0829 ABC superfamily (membrane), glutamine high‐affinity transporter glnP ‐0.4746565 ‐0.53600425 ‐0.54333925 ‐0.40534726 ‐0.7341103 ‐0.8433608 ‐0.518 0.698339 STM0830 ABC superfamily (bind_prot), glutamine high‐affinity transporter glnH ‐1.635288 ‐1.5401719 ‐1.650116 ‐1.7286297 ‐1.7587894 ‐1.8504239 ‐1.60853 0.327933 STM0833 outer membrane protease, receptor for phage OX2 ompX 0.4758158 0.26884237 0.46976787 ‐1.3159094 ‐1.284921 ‐1.1680741 0.404809 1.323913 STM0837 putative periplasmic protein ybiS ‐0.22505845 ‐0.60718817 ‐0.3888678 0.7924875 0.21959558 1.0621192 ‐0.40704 0.75417 STM0844 putative pyruvate formate lyase activating enzyme pflE ‐0.30814725 ‐0.3479092 ‐0.23795207 ‐0.58763456 ‐0.52717257 ‐0.65537995 ‐0.298 0.813378 STM0845 molybdopterin biosynthesis moeB ‐0.29099888 ‐0.8327344 ‐0.31021452 ‐0.43077865 ‐0.14306134 ‐0.22562754 ‐0.47798 0.717981 STM0846 molybdopterin biosynthesis protein moeA ‐0.4043882 ‐0.5576657 ‐0.41715202 ‐0.33460942 ‐0.16004929 ‐0.17734632 ‐0.45974 0.72712 STM0850 putative ABC transporter periplasmic binding protein yliC ‐0.22125629 ‐0.7490953 ‐0.5501267 0.082801186 ‐0.065431945 ‐0.04659729 ‐0.50683 0.703769 STM0852 putative Fe‐S oxidoreductases family 1 yliG ‐0.4049356 ‐0.65422064 ‐0.5119743 ‐0.24739324 ‐0.3684934 ‐0.1422847 ‐0.52371 0.695581 STM0862 putative glutathione S‐transferase yliJ 0.31162846 0.32918483 0.27655312 ‐0.78265816 ‐1.0283278 ‐0.90984267 0.305789 1.236094 STM0873 putative inner membrane protein ybjC ‐0.17905602 ‐0.44594544 ‐0.4199509 ‐0.4170016 ‐0.74505764 ‐0.5799282 ‐0.34832 0.7855 STM0887 ABC superfamily (bind_prot), arginine 3rd transport system artJ ‐1.4173365 ‐1.4003847 ‐1.1767683 ‐1.0465586 ‐1.2539867 ‐1.3252928 ‐1.3315 0.397356 STM0891 ABC superfamily (atp&memb), arginine transport system artP ‐0.71155953 ‐0.5094942 ‐0.4639384 ‐0.048897367 ‐0.116677105 0.08669766 ‐0.56166 0.67752 STM0933 putative nucleoside‐diphosphate‐sugar epimerase ybjT ‐0.25646675 ‐0.53386205 ‐0.556527 0.08613055 0.25150496 0.50403845 ‐0.44895 0.732575 STM0934 L‐allo‐threonine aldolase ltaA ‐0.30666682 ‐0.5187434 ‐0.47626817 0.6707763 0.73030025 0.8241052 ‐0.43389 0.740262 STM0959 regulator for lrp regulon and high‐affinity branched‐chain lrp ‐0.4318177 ‐0.33552516 ‐0.38188127 1.0524905 0.62952006 0.6558956 ‐0.38307 0.766802 STM0965 anaerobic dimethyl sulfoxide reductase, subunit B dmsB ‐0.44168755 ‐0.57411414 ‐0.5876101 ‐0.90780324 ‐0.8215511 ‐0.94185776 ‐0.53447 0.690412 STM0966 anaerobic dimethyl sulfoxide reductase, subunit C dmsC ‐0.28122625 ‐0.3578153 ‐0.3033928 ‐0.2535967 ‐0.24641363 ‐0.42048126 ‐0.31414 0.804328 STM0973 pyruvate formate lyase I, induced anaerobically pflB ‐1.4719023 ‐1.5097382 ‐1.4523679 ‐3.645095 ‐3.5508404 ‐3.386212 ‐1.478 0.358985 STM0974 putative FNT family, formate transporter (formate channel focA ‐1.2823764 ‐1.2160076 ‐1.338426 ‐2.496082 ‐2.7509668 ‐2.8551254 ‐1.27894 0.412099 STM0985 tetraacyldisaccharide 4 kinase (lipid A 4kinase) lpxK ‐0.39834878 ‐0.22449249 ‐0.46480176 0.13554913 0.2625243 0.0740137 ‐0.36255 0.77779 STM0988 CTP:CMP‐3‐deoxy‐D‐manno‐octulosonate transferase kdsB ‐0.45908305 ‐0.34753028 ‐0.3542699 ‐0.11640237 ‐0.005751802 ‐0.081944585 ‐0.38696 0.764739 STM0989 mukF protein (killing factor KicB) ‐0.8264857 ‐0.52779496 ‐0.86790794 ‐0.3820342 ‐0.53006834 ‐0.7149592 ‐0.74073 0.598437 STM0995 putative periplasmic protein ycbB ‐0.35174665 ‐0.23928219 ‐0.32487994 0.19056635 0.39383805 0.33149144 ‐0.3053 0.809272 STM1066 ribosome modulation factor (involved in dimerization of rmf ‐1.0369891 ‐1.025873 ‐0.6459207 ‐2.939138 ‐2.43706 ‐2.2428668 ‐0.90293 0.5348 STM1068 putative protease lonH 0.40872064 0.44216406 0.41327387 0.7258578 0.74335986 0.49317136 0.421386 1.339214 STM1070 putative hydrogenase, membrane component ompA 1.1558242 1.0283022 0.74478096 ‐0.15404917 ‐0.26885107 ‐0.38527164 0.976302 1.967417 STM1076 methylglyoxal synthase mgsA ‐0.40152797 ‐0.51506615 ‐0.48631975 ‐0.74361235 ‐1.0801302 ‐0.8070471 ‐0.46764 0.723148 STM1077 putative periplasmic protein yccT ‐0.5581323 ‐0.5256422 ‐0.4948595 ‐0.75453085 ‐0.56906116 ‐0.7390381 ‐0.52621 0.694376 STM1079 putative inner membrane protein yccV 0.3499813 0.36906227 0.4714568 ‐0.31249458 ‐0.3919469 ‐0.63334495 0.396833 1.316615 STM1112 curved DNA‐binding protein cbpA ‐0.3099581 ‐0.5270556 ‐0.49807793 ‐0.4426769 ‐0.4222615 ‐0.25903344 ‐0.44503 0.734569 STM1139 putative transcriptional regulator in curly assembly/transport, 2nd csgG ‐0.7588283 ‐1.1782665 ‐1.0758065 ‐1.6324872 ‐2.0239973 ‐1.6082772 ‐1.0043 0.498512 STM1140 curli production assembly/transport component, 2nd curli operon csgF ‐0.9241674 ‐0.7570996 ‐0.8110525 ‐2.4841034 ‐2.324837 ‐2.4346235 ‐0.83077 0.562228 STM1141 curli production assembly/transport component, 2nd curli operon csgE ‐1.0519996 ‐0.9824834 ‐0.58964723 ‐2.2129786 ‐2.2709503 ‐2.066302 ‐0.87471 0.545363 STM1142 putative transcriptional regulator (LuxR/UhpA family) csgD ‐1.3281112 ‐1.1724006 ‐1.5959761 ‐2.0441546 ‐2.5151248 ‐2.4268098 ‐1.3655 0.388101 STM1145 putative curli production protein csgC ‐1.4600596 ‐1.4493257 ‐1.5091476 ‐1.74516 ‐1.4549979 ‐1.5759916 ‐1.47284 0.360271 STM1146 putative periplasmic protein ymdA ‐1.4272671 ‐1.1628419 ‐1.0917475 ‐1.1675874 ‐0.9190649 ‐1.0819148 ‐1.22729 0.42712 STM1147 putative ACR related to the C‐terminal domain ‐0.7126416 ‐0.9903692 ‐0.94709754 ‐0.60921794 ‐1.0801338 ‐0.9391641 ‐0.88337 0.5421 STM1150 periplasmic glucans biosynthesis protein mdoG 0.5415282 0.7216828 0.53028905 0.94543475 0.8897964 0.79126954 0.597833 1.513442 STM1152 putative outer membrane lipoprotein yceK ‐0.36696 ‐0.46095848 ‐0.4073095 ‐0.16921954 ‐0.23827368 ‐0.11798355 ‐0.41174 0.751715 STM1178 flagellar biosynthesis, cell‐proximal portion of basal‐body rod flgF ‐0.5251709 ‐0.5935623 ‐0.70547336 1.0958923 1.1005088 0.9917764 ‐0.60807 0.656074 STM1179 flagellar biosynthesis, cell‐distal portion of basal‐body rod flgG ‐0.41774648 ‐0.40301433 ‐0.46112373 1.3467141 1.4337074 1.5044321 ‐0.42729 0.743655 STM1180 flagellar biosynthesis, basal‐body outer‐membrane L (lipopolysaccharide layer) flgH ‐0.24669611 ‐0.45819262 ‐0.36717805 1.1339319 1.7485083 1.8011872 ‐0.35736 0.780594 STM1181 putative flagella basal body protein flgI ‐0.324302 ‐0.2887586 ‐0.2424051 1.9730844 2.096299 2.0200503 ‐0.28516 0.820653 STM1183 flagellar biosynthesis, hook‐filament junction protein 1 flgK ‐0.23739685 ‐0.2801575 ‐0.27900034 1.619831 1.6788012 1.5202569 ‐0.26552 0.8319 STM1204 outer membrane receptor for Fe(III)‐coprogen, Fe(III)‐ferrioxamine B fhuE 0.32385328 0.46183276 0.42694753 0.37853062 0.3217923 0.2793581 0.404211 1.323365 STM1210 putative esterase ycfP ‐0.3665278 ‐0.65324485 ‐0.37464687 0.08399701 ‐0.3701707 ‐0.11579435 ‐0.46481 0.724568 STM1211 respiratory NADH dehydrogenase 2 cupric reductase ndh 0.30300504 0.2696462 0.24299727 0.28233495 0.15257327 0.12216826 0.271883 1.207383 STM1214 putative outer membrane protein ycfR ‐0.47596112 ‐0.44852042 ‐0.3523592 ‐0.6465189 ‐0.5931529 ‐0.60973513 ‐0.42561 0.744522 STM1218 ABC transporter, ATP‐binding protein ycfV ‐0.3584991 ‐0.49531895 ‐0.4751201 ‐0.108652465 ‐0.1991152 ‐0.16417414 ‐0.44298 0.735614 STM1237 putative ribosomal large subunit pseudouridine synthase ymfC ‐0.3603536 ‐0.3645241 ‐0.34903866 ‐0.384855 ‐0.5160779 ‐0.2492648 ‐0.35797 0.780261 STM1238 isocitrate dehydrogenase in e14 prophage, specific for icdA 0.33846152 0.38819313 0.34394217 1.923276 1.6409713 1.7221025 0.356866 1.280641 STM1255 putative ABC transporter periplasmic binding protein 0.37114596 0.3023748 0.3604987 ‐0.046311248 0.12354395 ‐0.018276125 0.344673 1.269863 STM1261 putative cytoplasmic protein 0.27194655 0.56820977 0.43828702 ‐0.8873787 ‐1.1520764 ‐0.8446487 0.426148 1.343641 STM1263 putative periplasmic protein 2.2810953 2.2803102 2.2510886 ‐3.407243 ‐3.7447538 ‐4.084797 2.270831 4.826012 STM1274 putative inner membrane protein yeaQ 0.65378964 0.6692242 0.8762841 ‐0.6688221 ‐0.6933789 ‐0.4495114 0.733099 1.662206 STM1284 putative cytoplasmic protein yeaH 0.2744936 0.40142876 0.3414933 ‐0.30740705 ‐0.47545207 ‐0.3315415 0.339139 1.265001 STM1285 putative Ser protein kinase yeaG 0.68933046 0.7587421 0.6440396 ‐0.46575496 ‐0.41566285 ‐0.36063853 0.697371 1.621547 STM1289 putative enzymes related to aldose 1‐epimerase yeaD 0.21782845 0.27611786 0.24608544 ‐0.13277811 ‐0.32061452 ‐0.41818246 0.246677 1.186471 STM1295 protease IV, a signal peptide peptidase sppA ‐0.2943676 ‐0.45289037 ‐0.39618397 ‐0.58583647 ‐0.5792948 ‐0.5848898 ‐0.38115 0.767827 STM1300 putative periplasmic protein ‐0.24713163 ‐0.5175908 ‐0.41109887 0.27648553 ‐0.20017582 ‐0.04893046 ‐0.39194 0.762104 STM1304 arginine succinyltransferase astA ‐0.44366714 ‐0.64911693 ‐0.6599875 ‐0.7756207 ‐0.96686655 ‐0.9297423 ‐0.58426 0.666993 STM1305 succinylglutamic semialdehyde dehydrogenase astD ‐0.24514297 ‐0.41127566 ‐0.3780378 ‐0.63193977 ‐0.52545446 ‐0.57170576 ‐0.34482 0.787407 STM1310 NAD synthetase, prefers NH3 over glutamine nadE 0.29985374 0.38263682 0.37407726 ‐0.5443109 ‐0.49825403 ‐0.5621249 0.352189 1.276496 STM1335 50S ribosomal subunit protein L35 rpmI ‐1.4608428 ‐1.5701078 ‐1.8205353 0.19425759 0.16109267 0.096692316 ‐1.61716 0.325976 STM1336 50S ribosomal subunit protein L20 rplT ‐1.0606834 ‐1.1933404 ‐1.3318871 0.15193738 0.056686662 0.05046198 ‐1.1953 0.436695 STM1339 integration host factor (IHF), alpha subunit himA 0.29264265 0.24104732 0.32525933 ‐0.3852759 ‐0.2967572 ‐0.19504993 0.286316 1.219523 STM1340 ABC superfamily (membrane), vitamin B12 transport protein btuC ‐0.2934278 ‐0.345843 ‐0.2620518 ‐0.049118973 ‐0.15822318 ‐0.19683614 ‐0.30044 0.812004 145 STM1345 putative cytoplasmic protein ydiU 1.1109093 1.4927708 1.3023136 0.837666 0.87025166 0.8473188 1.301998 2.465701 STM1359 putative shikimate 5‐dehydrogenase ydiB 0.23921464 0.44171196 0.2541867 0.09182452 0.24539095 ‐2.26E‐04 0.311704 1.241173 STM1367 putative cytoplasmic protein ydiH ‐1.1607132 ‐1.217718 ‐0.95250094 ‐1.1420289 ‐1.0192692 ‐1.0349541 ‐1.11031 0.463194 STM1368 putative Na ‐dicarboxylate symporter 0.3481311 0.45733228 0.27683023 ‐0.3665625 ‐0.06849653 ‐0.077386834 0.360765 1.284106 STM1370 putative ABC transporter sufB 1.8288628 1.8384182 1.7571864 2.0679772 1.9349446 1.9260905 1.808156 3.501943 STM1373 selenocysteine lyase sufS 1.0143319 0.8581476 0.9030303 1.7707404 1.9531987 1.996953 0.92517 1.898908 STM1374 putative SufE protein probably involved in Fe‐S ynhA 0.6949266 0.8367215 0.78655946 1.3053304 1.282638 1.2608409 0.772736 1.708507 STM1378 pyruvate kinase I (formerly F), fructose stimulated pykF 1.0706054 1.076777 0.9540288 0.34609383 0.25985903 0.17014986 1.033804 2.047415 STM1384 Tetrathionate reductase complex, subunit C ttrC ‐0.3832782 ‐0.43991503 ‐0.62766564 ‐0.53071415 ‐0.41407105 ‐0.2703583 ‐0.48362 0.715181 STM1398 Secretion system effector sseB ‐1.6741128 ‐1.4779617 ‐1.5637157 ‐1.5679544 ‐1.726097 ‐1.6248128 ‐1.57193 0.336358 STM1400 Secretion system effector sseC ‐0.89993477 ‐0.95905095 ‐0.6318036 ‐1.0857143 ‐1.2127495 ‐1.1596113 ‐0.83026 0.562427 STM1402 Secretion system effector sseE ‐0.7404304 ‐0.5855545 ‐0.44367382 ‐1.4752728 ‐1.1332533 ‐1.2630181 ‐0.58989 0.664395 STM1407 Secretion system apparatus ssaH ‐2.5226486 ‐2.480366 ‐2.4565828 ‐3.276874 ‐3.4141567 ‐3.4247928 ‐2.48653 0.178435 STM1409 Secretion system apparatus: homology with the yscJ/mxiJ/prgK ssaJ ‐1.745902 ‐1.4621507 ‐1.4960818 ‐1.9544916 ‐1.8679796 ‐1.8298781 ‐1.56804 0.337265 STM1410 putative cytoplasmic protein ‐1.2823895 ‐1.324541 ‐1.2172247 ‐1.8518736 ‐2.1207027 ‐2.0425308 ‐1.27472 0.413306 STM1411 Secretion system apparatus ssaK ‐1.212782 ‐0.865683 ‐0.86629224 ‐1.5459058 ‐1.4453876 ‐1.4393945 ‐0.98159 0.506423 STM1412 Secretion system apparatus ssaL ‐1.1971893 ‐1.7317013 ‐1.5377116 ‐1.1985549 ‐1.706445 ‐1.4232875 ‐1.48887 0.356292 STM1413 Secretion system apparatus ssaM ‐0.77967024 ‐0.8322191 ‐0.78975403 ‐2.2722535 ‐1.7264606 ‐1.8331716 ‐0.80055 0.574131 STM1419 Secretion system apparatus: homology with YscR of ssaR ‐2.10759 ‐2.092133 ‐1.865195 ‐1.5756209 ‐2.0081894 ‐1.995713 ‐2.02164 0.246278 STM1427 cyclopropane fatty acyl phospholipid synthase cfa 0.53838634 0.5852242 0.549235 ‐1.1271503 ‐1.9751949 ‐1.5026411 0.557615 1.471834 STM1445 putative outer membrane lipoprotein slyB 0.54758734 0.6674519 0.6889855 0.65983456 0.31934425 0.25440368 0.634675 1.552588 STM1450 pyridoxal kinase 2/pyridoxine kinase pdxY 0.5507013 0.25061792 0.38647062 0.35734636 0.3821307 0.22372746 0.39593 1.315791 STM1451 glutathionine S‐transferase gst 0.41312236 0.4460167 0.54826 ‐0.70826876 ‐0.6502949 ‐0.7800278 0.469133 1.384277 STM1456 putative oxidoreductase ydgO ‐0.18982045 ‐0.3831436 ‐0.35884932 1.138298 1.0549725 1.025241 ‐0.3106 0.806304 STM1466 putative periplasmic protein ydgA 0.4062534 0.32921973 0.2527213 0.38519296 0.18928708 0.2782044 0.329398 1.256489 STM1478 putative periplasmic protein ydgH 0.36855495 0.3679174 0.36575988 0.7347037 0.85411257 0.74237645 0.367411 1.290035 STM1482 putative membrane transporter of cations and cationic ydgF ‐0.18909168 ‐0.42212728 ‐0.3997874 ‐0.10787598 ‐0.33845413 0.023952104 ‐0.337 0.791685 STM1486 putative MFS familty transport protein ynfM ‐0.23127855 ‐0.39081946 ‐0.45196387 ‐0.5932076 ‐0.7651399 ‐0.628818 ‐0.35802 0.780234 STM1489 putative dethiobiotin synthase ynfK ‐1.1623932 ‐1.1485412 ‐0.97866875 ‐0.52552414 ‐0.760583 ‐0.5617785 ‐1.09653 0.467639 STM1495 putative component of anaerobic dehydrogenases ynfI ‐0.19872937 ‐0.3369662 ‐0.32943332 ‐0.6292595 ‐0.54972446 ‐0.5097459 ‐0.28838 0.818823 STM1496 putative dimethylsulfoxide reductase ‐0.3685398 ‐0.37358811 ‐0.27664664 ‐0.5378545 ‐0.60932666 ‐0.63203114 ‐0.33959 0.790265 STM1497 putative dimethyl sulphoxide reductase ‐0.3500527 ‐0.55640876 ‐0.51866335 ‐0.7948172 ‐1.1683357 ‐0.8657208 ‐0.47504 0.719446 STM1509 putative cytoplasmic protein ydfZ ‐1.3511477 ‐1.210879 ‐0.81715876 ‐2.0551136 ‐2.1272924 ‐1.9854239 ‐1.1264 0.458059 STM1525 putative glutaminase yneH ‐0.31196776 ‐0.5324096 ‐0.4200531 0.46168852 0.2885842 0.37501928 ‐0.42148 0.74666 STM1554 putative coiled‐coil protein 0.43193775 0.44049537 0.4944495 0.47160825 0.2640034 0.33904615 0.455628 1.371379 STM1567 alcohol dehydrogenase, propanol preferring adhP 0.4718006 0.42413142 0.3675194 ‐0.26860577 ‐0.33799547 ‐0.37310302 0.42115 1.338995 STM1572 new outer membrane protein predicted bacterial porin nmpC ‐0.18370068 ‐0.2966894 ‐0.34496439 0.4717645 0.0995451 0.10905572 ‐0.27512 0.826383 STM1577 nitrate reductase 2, alpha subunit narZ ‐0.2248073 ‐0.4580479 ‐0.31478006 ‐0.3036716 ‐0.26014018 ‐0.19998862 ‐0.33255 0.794134 STM1586 putative periplasmic protein 1.0042905 1.1498488 1.263933 0.25987425 0.31525543 0.41740522 1.139357 2.202829 STM1592 putative cytoplasmic protein ydcY ‐0.38371983 ‐0.6083607 ‐0.4058153 ‐0.4082041 ‐0.45463413 ‐0.3126648 ‐0.46597 0.723987 STM1594 ssrAB activated gene srfB ‐0.44180423 ‐0.5306051 ‐0.6152019 0.138828 ‐0.2099058 0.024343297 ‐0.5292 0.692937 STM1595 ssrAB activated gene: predicted coiled‐coil structure srfC ‐0.6356835 ‐0.41037938 ‐0.36208963 0.142187 0.106389776 0.11309321 ‐0.46938 0.722273 STM1606 putative benzoate membrane transport protein ‐0.2536418 ‐0.32784393 ‐0.26576608 ‐0.5791322 ‐0.61242646 ‐0.6168841 ‐0.28242 0.822212 STM1612 putative cellulase protein ‐0.52231705 ‐0.7856752 ‐0.7000317 ‐1.3844473 ‐1.5026865 ‐1.395355 ‐0.66934 0.628794 STM1613 putative PTS system, enzymeIIB component ‐0.3519927 ‐0.3795157 ‐0.40696353 ‐0.9162813 ‐1.1813852 ‐0.9658277 ‐0.37949 0.768709 STM1614 putative PTS system enzyme IIC component ‐0.33452767 ‐0.6439114 ‐0.49038953 ‐0.4312252 ‐0.64045763 ‐0.45143804 ‐0.48961 0.712218 STM1615 putative nucleoside triphosphatase ‐0.2504369 ‐0.39927378 ‐0.5593485 ‐0.87528783 ‐0.8458499 ‐0.91353655 ‐0.40302 0.756274 STM1616 putative Sugar Specific PTS Enzyme II ‐0.5471751 ‐0.6508115 ‐0.69132197 ‐0.9636082 ‐1.3039311 ‐1.1980091 ‐0.62977 0.64628 STM1628 putative cytoplasmic protein ‐0.30046344 ‐0.3825925 ‐0.1886261 ‐4.07E‐04 ‐0.17345259 ‐0.003326796 ‐0.29056 0.817584 STM1645 putative outer membrane lipoprotein ynbE ‐0.4214404 ‐0.4550827 ‐0.3689802 ‐0.24922627 ‐0.5800033 ‐0.6674307 ‐0.41517 0.749932 STM1649 putative cytoplasmic protein ‐0.19018997 ‐0.399026 ‐0.3227409 ‐0.76038283 ‐0.75157917 ‐0.78606546 ‐0.30399 0.810012 STM1660 transcriptional regulation of aerobic, anaerobic respiration, osmotic fnr 0.2812335 0.39288732 0.4851172 0.5186295 0.41619164 0.36252376 0.386413 1.307139 STM1662 putative inner membrane protein ynaJ 0.532323 0.49079153 0.6095416 0.16564049 ‐0.26653215 ‐0.21402918 0.544219 1.45823 STM1682 thiol peroxidase tpx 0.6041635 0.75391585 0.6196073 1.0710678 1.1310829 1.1226921 0.659229 1.579238 STM1686 phage shock protein pspE ‐0.24195158 ‐0.2239119 ‐0.2397045 ‐0.6327867 ‐0.5577372 ‐0.6503412 ‐0.23519 0.849574 STM1713 transcriptional regulator for cysteine regulon (LysR familiy) cysB 0.3855786 0.58886385 0.3916322 0.3562029 0.30875078 0.14567114 0.455358 1.371123 STM1719 putative ribosomal large subunit pseudouridine synthase yciL ‐0.37572515 ‐0.30425462 ‐0.27576232 0.31031558 0.39768574 0.39678493 ‐0.31858 0.801858 STM1721 trpR controlled transcriptional unit in the 5 trpH ‐0.31108093 ‐0.29586965 ‐0.2603506 ‐0.36760768 ‐0.35555023 ‐0.47195932 ‐0.2891 0.818412 STM1726 tryptophan synthase, beta protein trpB 0.6247902 0.7092721 0.81449515 0.89797586 0.80832547 0.82315576 0.716186 1.642833 STM1727 tryptophan synthase, alpha protein trpA 0.42639452 0.30337414 0.2700325 0.39369184 0.01953881 0.15296096 0.333267 1.259863 STM1736 putative Acyl‐CoA hydrolase yciA ‐0.2479896 ‐0.22087821 ‐0.2577209 ‐0.24616353 ‐0.14075956 ‐0.3137594 ‐0.2422 0.845457 STM1743 ABC superfamily (atp‐binding), oligopeptide transport protein oppD 0.31725043 0.2979059 0.22481397 0.12536727 ‐0.055885192 ‐0.016461318 0.27999 1.214187 STM1749 iron‐dependent alcohol dehydrogenase of the multifunctional alcohol adhE ‐0.94126964 ‐1.0152637 ‐1.0613933 ‐3.373034 ‐2.9843004 ‐2.7309978 ‐1.00598 0.497933 STM1751 DNA‐binding protein HLP‐II (HU, BH2, HD, NS) hns 0.28761715 0.39059618 0.5427891 ‐0.038890112 ‐0.14976403 ‐0.05902101 0.407001 1.325927 STM1753 Response regulator in protein turnover: mouse virulence hnr 0.30030814 0.38211897 0.3175498 0.54183644 0.3932172 0.2300782 0.333326 1.259914 STM1754 putative phosphoesterase ychK 0.47854376 0.34373415 0.37279 0.75828016 0.958124 1.0925204 0.398356 1.318005 STM1780 phosphoribosylpyrophosphate synthetase prsA ‐0.30122158 ‐0.27414304 ‐0.3812938 0.81053585 0.5377214 0.43598494 ‐0.31889 0.801689 STM1781 putative SulP family transport protein ychM ‐0.43034276 ‐0.2892813 ‐0.40384802 0.1461771 ‐0.02610114 ‐0.10166211 ‐0.37449 0.771378 STM1782 putative inner membrane protein ychH ‐0.42107615 ‐0.33402443 ‐0.37810418 ‐0.18030512 ‐0.13911952 ‐0.16395706 ‐0.37773 0.769645 STM1793 putative cytochrome oxidase, subunit II ‐0.20705564 ‐0.40138167 ‐0.38687545 ‐0.627598 ‐0.99744743 ‐0.6675818 ‐0.33177 0.794561 STM1801 putative CPA1 family, Na:H transport protein ycgO ‐0.30309612 ‐0.3038189 ‐0.3510658 ‐0.2795044 ‐0.2943152 ‐0.5589706 ‐0.31933 0.801444 STM1804 putative cytoplasmic protein ycgB 0.3659159 0.30410102 0.18880795 0.05911469 0.048354328 0.16504192 0.286275 1.219487 STM1812 putative Fumarylacetoacetate (FAA) hydrolase family ycgM 0.6757513 0.4047032 0.48674396 0.05535708 0.053606264 0.07697686 0.522399 1.436342 STM1815 cell division inhibitor, a membrane ATPase, activates minD 0.64360964 0.539904 0.46649835 0.57414794 0.5769835 0.12150221 0.550004 1.46409 STM1823 putative cytoplasmic protein yoaH ‐0.40831774 ‐0.405646 ‐0.46832395 ‐0.15754999 ‐0.45120302 ‐0.45403653 ‐0.42743 0.743586 STM1825 putative NTP pyrophosphohydrolase yeaB ‐0.38418204 ‐0.38979676 ‐0.440912 ‐0.21480568 ‐0.16558334 ‐0.29719406 ‐0.40496 0.755255 STM1829 putative cytoplasmic protein ‐0.26884434 ‐0.42344797 ‐0.2660132 ‐0.3604281 ‐0.6645848 ‐0.5956276 ‐0.31944 0.801384 STM1837 cold shock protein, multicopy suppresses mukB mutants cspC ‐0.41805288 ‐0.49406308 ‐0.49191025 ‐0.2913259 ‐0.3668987 ‐0.23230623 ‐0.46801 0.722962 STM1838 putative cytoplasmic protein yobF ‐0.30826873 ‐0.44221333 ‐0.34613034 ‐0.49601406 ‐0.9558 ‐0.54831296 ‐0.36554 0.77618 STM1840 putative inner membrane protein yobG ‐0.582477 ‐0.57865244 ‐0.51988935 ‐0.33765703 ‐0.6450774 ‐0.5211667 ‐0.56034 0.678143 STM1851 putative cytoplasmic protein ‐0.30207226 ‐0.35991398 ‐0.28196493 ‐1.4156271 ‐1.2193029 ‐1.2874681 ‐0.31465 0.804046 STM1888 pyruvate kinase II, glucose stimulated pykA ‐0.45786908 ‐0.6001217 ‐0.33456108 ‐0.7494681 ‐0.7444827 ‐0.60186774 ‐0.46418 0.724881 STM1890 putative Peptidase yebA 0.7314299 0.6941771 0.91438 ‐1.1120312 ‐1.4507257 ‐0.8762661 0.779996 1.717126 STM1891 ABC superfamily (bind_prot) high affinity Zn transport znuA 1.3631965 1.3828597 1.453435 ‐3.1004639 ‐3.2172017 ‐3.3780866 1.39983 2.638706 STM1901 aspartate tRNA synthetase aspS ‐0.40783373 ‐0.58696544 ‐0.2616341 ‐0.3228629 ‐0.33112475 ‐0.18849096 ‐0.41881 0.748041 STM1902 putative isochorismatase yecD ‐0.3656827 ‐0.36847875 ‐0.43531647 ‐0.67360085 ‐0.5151873 ‐0.6069283 ‐0.38983 0.763222 STM1916 chemotaxis regulator, transmits chemoreceptor signals to flagelllar cheY ‐0.38359508 ‐0.43315798 ‐0.39431602 1.5257362 1.6956547 1.9617764 ‐0.40369 0.755923 STM1959 flagellar biosynthesis flagellin, filament structural protein fliC 0.39477825 0.5807938 0.6376977 2.3017983 2.3778193 2.6140275 0.537757 1.451713 STM1978 flagellar biosynthesis fliO ‐0.57403517 ‐0.664406 ‐0.5776367 0.075564675 0.36710957 0.4283571 ‐0.60536 0.657308 STM1990 putative permease yedA ‐0.28627598 ‐0.53123426 ‐0.44428456 ‐0.68307203 ‐0.73559564 ‐0.49098048 ‐0.4206 0.747115 STM2017 cobalamin 5‐phosphate synthase cobS ‐0.35943896 ‐0.31011033 ‐0.46746382 0.050599314 0.04789822 ‐0.20290194 ‐0.379 0.768968 STM2024 synthesis of vitamin B12 adenosyl cobalamide precursor cbiL ‐0.36653033 ‐0.5942693 ‐0.48899347 ‐0.6076826 ‐0.9152125 ‐0.813943 ‐0.48326 0.715357 STM2028 synthesis of vitamin B12 adenosyl cobalamide precursor cbiG ‐0.35900822 ‐0.5075034 ‐0.37728187 ‐0.4092767 ‐0.3165983 ‐0.46636346 ‐0.4146 0.750229 STM2031 synthesis of vitamin B12 adenosyl cobalamide precursor cbiE ‐0.37218127 ‐0.245728 ‐0.3650228 ‐0.5108238 ‐0.51285577 ‐0.54533434 ‐0.32764 0.796837 STM2039 Propanediol utilization: polyhedral bodies pudB ‐0.60162073 ‐0.6262743 ‐0.70491284 ‐0.6635016 ‐0.5572539 ‐0.5123162 ‐0.64427 0.639817 STM2053 Propanediol utilization: polyhedral bodies pduS ‐0.49494177 ‐0.6589297 ‐0.6400521 0.19818437 0.03671358 0.28584102 ‐0.59797 0.660681 STM2056 Propanediol utilization pduV ‐0.4730784 ‐0.3958133 ‐0.46033874 0.12201987 0.1591279 0.2229881 ‐0.44308 0.735564 STM2059 putative cytoplasmic protein yeeX 0.32313725 0.3182445 0.48112833 ‐1.7658125 ‐1.9565146 ‐1.7855941 0.37417 1.296094 STM2067 exonuclease I, 3 ‐‐ 5 specific deoxyribophosphodiesterase sbcB 0.2899644 0.4685992 0.24099086 0.17351031 0.15334004 ‐0.18637115 0.333185 1.259791 STM2071 ATP phosphoribosyltransferase hisG 1.4977757 1.2457414 1.2286866 0.19091474 ‐0.14521758 ‐0.11062954 1.324068 2.503711 STM2072 histidinal dehydrogenase (also histidinol dehydrogenase activity) hisD 0.62781864 0.60583025 0.55097926 0.05327945 0.07998438 0.04636184 0.594876 1.510343 STM2073 histidinol phosphate aminotransferase hisC 0.6341258 0.4897871 0.31570336 1.2940421 0.5775246 0.44503582 0.479872 1.39462 STM2076 N‐(5‐phospho‐L‐ribosyl‐formimino)‐5‐amino‐1‐(5‐phosphoribosyl)‐4‐imidazolecarboxamide ishisA ‐0.19402218 ‐0.42735654 ‐0.42955026 0.31025815 0.2162306 0.29324135 ‐0.35031 0.784416 STM2079 regulator of length of O‐antigen component of wzzB 0.25764465 0.44832304 0.326458 0.54390585 0.6638624 0.47716227 0.344142 1.269396 STM2081 gluconate‐6‐phosphate dehydrogenase, decarboxylating gnd 0.30357298 0.5028009 0.31710204 0.4266141 0.33291423 0.1856702 0.374492 1.296383 STM2083 LPS side chain defect: phosphomannomutase rfbK 0.4056601 0.53315276 0.58841336 0.5132727 0.49226788 0.59198165 0.509075 1.423138 STM2087 LPS side chain defect: abequosyltransferase rfbV 0.98017097 0.9868867 0.9106193 1.3449967 1.3260227 1.4699153 0.959226 1.944266 STM2090 LPS side chain defect: CDP‐6deoxy‐D‐xylo‐4‐hexulose‐3‐dehydrase rfbH 0.51607764 0.44115597 0.42561674 0.65423524 0.4146966 0.613847 0.46095 1.376448 STM2091 LPS side chain defect: CDP glucose 4,6‐dehydratase rfbG 0.29437086 0.305522 0.3116214 0.9596773 0.724822 0.79896784 0.303838 1.234424 STM2117 putative protein‐tyrosine‐phosphatase in colanic acid export wzb ‐0.14169501 ‐0.63931817 ‐0.55770266 ‐0.48187384 ‐0.7830294 ‐0.5893673 ‐0.44624 0.733954 146 STM2130 sensory kinase in two‐component regulatoyr system wtih baeS ‐0.23525706 ‐0.30325264 ‐0.3394083 ‐0.6639423 ‐0.65042436 ‐0.796252 ‐0.29264 0.816407 STM2139 putative inner membrane protein ‐1.4245783 ‐1.4444654 ‐1.3343866 ‐1.0207832 ‐0.9393163 ‐1.1401907 ‐1.40114 0.378629 STM2146 bifunctional enzyme: hydroxy‐phosphomethylpyrimidine kinase (HMP‐P kinase) hydroxy‐metthiD 0.8380818 0.9110559 0.86167157 0.35555798 0.26258653 0.36383238 0.87027 1.828005 STM2147 hydoxyethylthiazole kinase (THZ kinase) thiM 0.8900621 0.7898668 0.70109767 0.60119885 ‐0.002512962 0.029784463 0.793676 1.733485 STM2148 putative periplasmic protein 0.7350009 0.5211285 0.64384043 0.46631774 0.67152745 0.49984565 0.633323 1.551134 STM2199 outer membrane porin, receptor for colicin I cirA 0.42267513 0.34250376 0.29650134 1.9126965 1.9137075 1.8750834 0.353893 1.278005 STM2218 putative ABC‐type dipeptide/oligopeptide/nickel transport systems, permease component yejE ‐0.2229477 ‐0.47907624 ‐0.26018736 0.23921727 0.17514017 0.5090737 ‐0.32074 0.800661 STM2223 putative ATP‐dependent helicase yejH ‐0.34153134 ‐0.28165892 ‐0.48666865 ‐0.602654 ‐0.61617696 ‐0.80372417 ‐0.36995 0.773808 STM2224 50S ribosomal subunit protein L25 rplY ‐0.40191922 ‐0.4752816 ‐0.17719823 0.22545871 0.26638293 0.33103037 ‐0.35147 0.783787 STM2228 putative hydrolase of alkaline phosphatase superfamily yejM 0.30365953 0.49258414 0.4001365 0.4594475 0.4441329 0.20801595 0.398793 1.318405 STM2267 outer membrane protein 1b (ibc), porin ompC ‐0.3649795 ‐0.68441063 ‐0.5550241 ‐1.9298726 ‐1.9060316 ‐1.8553083 ‐0.5348 0.690252 STM2278 ribonucleoside‐diphosphate reductase 1, beta subunit nrdB 0.45811883 0.38812217 0.45650494 ‐0.01204091 0.15576616 0.15613848 0.434249 1.351207 STM2285 sn‐glycerol‐3‐phosphate dehydrogenase (anaerobic), membrane anchor subunit glpB ‐0.5205092 ‐0.48782656 ‐0.5498602 ‐0.20428927 ‐0.3382881 ‐0.54045844 ‐0.5194 0.697663 STM2297 putative DegT/DnrJ/EryC1/StrS family yfbE 0.32749838 0.28917238 0.20130165 0.15429819 ‐0.11762217 ‐0.20724286 0.272657 1.208031 STM2302 putative inner membrane protein ‐0.29371068 ‐0.39288747 ‐0.3338009 0.105254896 ‐0.2373996 ‐0.142814 ‐0.34013 0.789968 STM2309 bifunctional: 2‐oxoglutarate decarboxylase SHCHC synthase menD ‐0.5449582 ‐0.62357396 ‐0.5364034 ‐0.09010234 0.015949069 ‐0.13984679 ‐0.56831 0.674405 STM2316 NADH dehydrogenase I chain N nuoN ‐0.3797041 ‐0.71908444 ‐0.61559105 0.20472471 0.22401272 0.23394392 ‐0.57146 0.672936 STM2317 NADH dehydrogenase I chain M nuoM ‐0.46761006 ‐0.8066455 ‐0.8020342 0.36260724 0.39635876 ‐0.04449083 ‐0.6921 0.618954 STM2318 NADH dehydrogenase I chain L nuoL ‐0.8575317 ‐0.92838544 ‐1.0345399 0.92301166 0.9969052 0.9841413 ‐0.94015 0.521178 STM2320 NADH dehydrogenase I chain J nuoJ ‐0.6258309 ‐0.58527905 ‐0.3001663 1.0111129 1.5354394 1.2720251 ‐0.50376 0.705267 STM2321 NADH dehydrogenase I chain I nuoI ‐0.39599353 ‐0.57785195 ‐0.5341032 0.3335542 0.5885079 0.6079343 ‐0.50265 0.705809 STM2323 NADH dehydrogenase I chain G nuoG ‐0.55333656 ‐0.52553827 ‐0.41416374 0.66871697 0.7760612 0.8482847 ‐0.49768 0.708245 STM2324 NADH dehydrogenase I chain F nuoF ‐0.76764554 ‐1.3955622 ‐1.2866403 0.7578795 0.7946701 0.71211123 ‐1.14995 0.450641 STM2326 NADH dehydrogenase I chain C,D nuoC ‐0.90607184 ‐0.87389094 ‐0.7842597 0.7514559 0.64789313 0.71703404 ‐0.85474 0.552965 STM2327 NADH dehydrogenase I chain B nuoB ‐0.40745583 ‐0.36292687 ‐0.40497294 0.25386277 0.38418785 0.39346194 ‐0.39179 0.762186 STM2328 NADH dehydrogenase I chain A nuoA ‐0.5014692 ‐0.5934646 ‐0.56030476 0.7614176 0.57570356 0.48981956 ‐0.55175 0.682194 STM2337 acetate kinase A (propionate kinase 2) ackA ‐0.39079365 ‐0.47798032 ‐0.50672805 ‐0.3476028 ‐0.8295524 ‐0.5067927 ‐0.4585 0.727742 STM2338 phosphotransacetylase pta ‐0.4616236 ‐0.48115346 ‐0.5303182 ‐1.0072376 ‐0.8412558 ‐0.7478572 ‐0.49103 0.711516 STM2347 putative phosphoesterase yfcE 0.5325464 0.2414636 0.30317497 0.47926083 0.4151023 0.30556625 0.359062 1.282591 STM2352 ABC superfamily (membrane),histidine and lysine/arginine/ornithine transport protein hisM ‐0.3382629 ‐0.48924717 ‐0.31882894 ‐0.15360825 ‐0.61077553 ‐0.4950088 ‐0.38211 0.767313 STM2354 ABC superfamily (bind_prot), histidine transport protein hisJ ‐0.5936473 ‐0.7646353 ‐0.63680995 ‐0.69515795 ‐0.67024964 ‐0.56542164 ‐0.66503 0.630675 STM2355 ABC superfamily (bind_prot), lysine/arginine/ornithine transport protein argT ‐1.400604 ‐1.3309743 ‐1.3863664 ‐2.6482382 ‐2.515496 ‐2.4523265 ‐1.37265 0.386182 STM2362 amidophosphoribosyltransferase (PRPP amidotransferase) purF 0.54774284 0.8205257 0.5031891 1.9648407 2.1074753 1.8334143 0.623819 1.540949 STM2372 putative transport protein ‐0.19344439 ‐0.538076 ‐0.4004039 0.78080255 0.36654153 0.7381135 ‐0.37731 0.769873 STM2378 3‐oxoacyl‐[acyl‐carrier‐protein] synthase I fabB ‐0.70569223 ‐0.5307672 ‐0.67913485 ‐0.08790274 0.045238234 ‐0.06390487 ‐0.63853 0.642367 STM2381 putative cytoplasmic protein yfcM ‐0.33975238 ‐0.44699302 ‐0.48137915 0.5186413 0.25569984 0.29104447 ‐0.42271 0.746023 STM2387 phosphohistidine phosphatase sixA ‐0.4210802 ‐0.44985646 ‐0.513038 0.26960456 0.11712958 ‐0.08601441 ‐0.46132 0.726319 STM2389 paral putative acetyl‐CoA acetyltransferase yfcY ‐0.43354943 ‐0.735563 ‐0.5262327 ‐0.51674217 ‐0.44256973 ‐0.07579631 ‐0.56512 0.675902 STM2390 putative cytoplasmic protein yfcZ ‐1.0053508 ‐1.0411766 ‐0.97862315 ‐1.0113494 ‐1.1621034 ‐1.4432645 ‐1.00838 0.497103 STM2393 putative transport yfdC 0.33464143 0.43004054 0.22414994 ‐0.19638361 ‐0.16651835 ‐0.2655585 0.329611 1.256674 STM2402 putative aminotransferase yfdZ 0.55602515 0.5908321 0.53190136 0.2600624 0.26398492 0.023082407 0.559586 1.473846 STM2405 putative thiamine pyrophosphate enzymes ‐0.30937022 ‐0.3005613 ‐0.39667216 4.64E‐04 ‐0.018764509 ‐0.18700634 ‐0.33553 0.79249 STM2408 Nramp family, manganese/divalent cation transport prortein mntH 0.5733523 0.53790146 0.46242976 ‐0.038998865 ‐0.24948457 ‐0.25137687 0.524561 1.438496 STM2409 NUP family, nucleoside transport nupC 0.4415167 0.4327222 0.42390454 0.098293975 0.05965885 0.17366005 0.432714 1.349771 STM2428 cell division protein involved in FtsZ ring zipA 0.45122093 0.32291824 0.2700161 0.84455734 0.3571823 0.43619353 0.348052 1.272841 STM2430 subunit of cysteine synthase A and O‐acetylserine cysK 0.6733387 0.6188528 0.59673494 ‐0.63130504 ‐0.819051 ‐0.74938726 0.629642 1.547181 STM2431 PTS family, Hpr protein, phosphohistidinoprotein‐hexose phosphotransferase ptsH 0.33419007 0.2014798 0.49719268 ‐0.20622128 ‐0.10071657 ‐0.07020261 0.344288 1.269524 STM2432 General PTS family (Enzyme I) PEP‐protein phosphotransferase ptsI 0.5854015 0.41560653 0.43937817 0.6884998 0.5863998 0.53092635 0.480129 1.394868 STM2433 PTS family, glucose‐specific IIA component crr 0.35445872 0.3651713 0.34319264 0.07999854 0.039455757 0.02775653 0.354274 1.278342 STM2434 putative cytoplasmic protein 0.2990498 0.34132865 0.36836603 0.06625182 0.045512054 ‐0.19176048 0.336248 1.262469 STM2467 putative cobalamin adenosyltransferase, ethanolamine utilization eutT ‐0.5692435 ‐0.638844 ‐0.6675065 0.6006584 0.4766011 0.48291883 ‐0.6252 0.648331 STM2472 paral putative transferase maeB 0.31660816 0.631907 0.32096383 1.394403 1.3680007 0.95552915 0.42316 1.340861 STM2473 transaldolase A talA 0.5624847 0.68613225 0.54327565 0.11988245 0.013463078 0.017414007 0.597298 1.51288 STM2479 putative oxidoreductase aegA ‐0.3615075 ‐0.49790597 ‐0.5386727 ‐0.005572236 0.10283049 ‐0.06752354 ‐0.46603 0.723955 STM2498 uracil phosphoribosyltransferase upp ‐0.34565735 ‐0.43354815 ‐0.36561623 0.029761888 ‐0.2159622 ‐0.076321065 ‐0.38161 0.767582 STM2499 phosphoribosylaminoimidazole synthetase (AIR synthetase) purM ‐0.19817394 ‐0.26949763 ‐0.27411497 1.6319189 1.404445 1.4160644 ‐0.24726 0.842494 STM2510 GMP synthetase guaA 0.45461294 0.50390565 0.22497275 0.52327347 0.73832494 0.9471155 0.394497 1.314484 STM2511 IMP dehydrogenase guaB 0.5478117 0.32566613 0.4064823 0.27413726 0.2895384 0.51163965 0.426653 1.344112 STM2513 similar to the C‐terminal region of AIDA shdA ‐0.2064581 ‐0.4816775 ‐0.30287918 ‐0.4883459 0.07266714 0.15302329 ‐0.33034 0.79535 STM2521 putative inner membrane protein yfgM 0.38129607 0.30712685 0.2257414 0.8262161 0.6358742 0.60499936 0.304721 1.23518 STM2522 histidine tRNA synthetase hisS 0.3655798 0.28132844 0.3583133 0.7556656 1.0426716 0.8955026 0.335074 1.261442 STM2523 putative protein, involved in density‐dependent regulation of gcpE 0.65346134 0.19456767 0.5378542 0.30621108 0.5394509 0.5964574 0.461961 1.377413 STM2544 believed to be involved in assembly of yfhP 1.9767494 1.9268703 1.9821848 1.6390253 1.487708 1.5227687 1.961935 3.895841 STM2549 anaerobic sulfide reductase asrB ‐0.46834084 ‐0.59718376 ‐0.55395865 ‐0.75783175 ‐0.6825032 ‐0.59163463 ‐0.53983 0.687853 STM2551 putative inner membrane protein ‐0.50833637 ‐0.62913424 ‐0.54535985 ‐0.41308144 ‐0.6082869 ‐0.7965573 ‐0.56094 0.677859 STM2552 putative periplasmic or exported protein ‐0.37134042 ‐0.31807062 ‐0.21125828 ‐0.5125055 ‐0.5690386 ‐0.47179893 ‐0.30022 0.812127 STM2553 stationary phase inducible protein csiE ‐0.40518212 ‐0.6434078 ‐0.52824616 ‐0.7355737 ‐0.6372644 ‐0.51503503 ‐0.52561 0.694664 STM2555 serine hydroxymethyltransferase glyA 0.64363766 0.55979085 0.5690766 0.85604954 0.9068405 0.8827994 0.590835 1.506118 STM2567 putative periplasmic amino acid binding protein yfhD ‐0.26364854 ‐0.49239382 ‐0.25670066 0.23552082 0.22396353 0.25169766 ‐0.33758 0.791367 STM2579 gap repair gene recO ‐0.371346 ‐0.561585 ‐0.52674264 0.40875655 0.21271114 0.6226194 ‐0.48656 0.713726 STM2589 Gifsy‐1 prophage: similar to host specificity protein‐J ‐0.4698734 ‐0.6328658 ‐0.6162032 ‐0.16477494 ‐0.46521708 ‐0.24240327 ‐0.57298 0.672226 STM2592 Gifsy‐1 prophage: similar to phage tail component ‐0.393688 ‐0.36545414 ‐0.35795328 ‐0.1642597 ‐0.07226453 ‐0.33703125 ‐0.37237 0.772515 STM2602 Gifsy‐1 prophage: similar to DNA packaging protein ‐0.3195953 ‐0.6365987 ‐0.48812613 ‐0.5757709 ‐0.73887795 ‐0.65123403 ‐0.48144 0.716262 STM2604 Gifsy‐1 prophage: similar to head protein gpshp ‐0.51528144 ‐0.6633785 ‐0.65227646 ‐0.8489438 ‐0.92762154 ‐1.0008435 ‐0.61031 0.655055 STM2605 Gifsy‐1 prophage: similar to head‐tail preconnector gp5 ‐0.46762577 ‐0.6847157 ‐0.7068311 ‐0.6161648 ‐0.6992853 ‐0.51704144 ‐0.61972 0.650795 STM2606 Gifsy‐1 prophage: similar to head‐tail preconnector gp4 ‐0.4409544 ‐0.37403706 ‐0.5243789 ‐0.3866868 ‐0.33483467 ‐0.54304653 ‐0.44646 0.733843 STM2637 regulator of sigma E (sigma 24) factor rseC ‐0.3276338 ‐0.23637518 ‐0.2256565 ‐0.8565542 ‐0.7094124 ‐0.8726867 ‐0.26322 0.833225 STM2639 anti sigma E (sigma 24) factor, negative rseA ‐0.72710884 ‐0.83900166 ‐0.7159658 ‐0.21629183 ‐0.43168828 ‐0.33610797 ‐0.76069 0.590213 STM2642 putative transferase yfiC ‐0.21117067 ‐0.40218395 ‐0.39635748 ‐0.2691202 ‐0.48473087 ‐0.29618627 ‐0.33657 0.791921 STM2646 putative formate acetyltransferase yfiD ‐2.409216 ‐2.5270565 ‐2.4806406 ‐3.539058 ‐3.6892347 ‐3.8342152 ‐2.4723 0.180203 STM2663 putative lipoprotein yfiO 0.42493463 0.3290534 0.30795994 0.87684643 0.81144875 0.83785975 0.353983 1.278084 STM2667 bifuctional: chorismate mutase P prephenate dehydratase pheA 0.8552046 0.7936667 0.7369175 0.46165243 0.60133964 0.50020754 0.795263 1.735394 STM2669 bifunctional: chorismate mutase T prephenate dehydrogenase tyrA 1.3667911 1.3381793 1.1992822 0.88219213 0.9187685 0.909422 1.301418 2.464709 STM2670 3‐deoxy‐D‐arabinoheptulosonate‐7‐phosphate synthase (DAHP synthetase), tyrosine repress aroF 1.4136881 1.5990025 1.3860908 1.164331 1.1723489 0.9882371 1.46626 2.763048 STM2671 putative periplasmic protein yfiR 0.489211 0.31111732 0.40039545 0.29688472 0.06538507 0.11128916 0.400241 1.319729 STM2674 tRNA (guanine‐7‐)‐methyltransferase trmD 0.4924994 0.561775 0.354886 1.571607 0.8121499 0.79679686 0.46972 1.384841 STM2676 30S ribosomal subunit protein S16 rpsP 0.42766732 0.22290292 0.27952188 0.37897253 0.30458152 0.47828022 0.310031 1.239734 STM2690 putative outer membrane efflux protein ‐0.2827178 ‐0.34084126 ‐0.26870468 ‐0.47125855 ‐0.6280167 ‐0.31454402 ‐0.29742 0.813706 STM2746 putative Excinuclease ATPase subunit 0.59398854 0.48456725 0.820836 0.91573364 0.88280106 1.2101729 0.633131 1.550927 STM2763 putative integrase 0.21955983 0.34764314 0.51134974 ‐0.33998582 ‐0.24395336 ‐0.4226718 0.359518 1.282997 STM2771 Flagellar synthesis: phase 2 flagellin (filament structural fljB 0.59391034 0.86389077 0.62645835 4.4718914 3.0326958 3.278312 0.694753 1.618607 STM2773 putative glycosyl transferase, related to UDP‐glucuronosyltransferase iroB 1.4615705 1.4559537 1.3366925 ‐0.1385594 ‐0.06457027 ‐0.022934027 1.418072 2.672282 STM2774 putative ATP binding cassette (ABC) transporter iroC 1.4685358 1.3882108 1.4077921 1.0338286 0.83051705 0.97554153 1.421513 2.678663 STM2775 Similar to enterochelin esterase of E. coli iroD 0.88882965 0.9238883 0.88425475 1.4213401 1.660388 1.6496134 0.898991 1.864761 STM2776 putative hydrolase of the alpha/beta superfamily iroE 0.8541298 0.9028306 0.97993296 0.7055156 0.86182636 0.6533429 0.912298 1.882041 STM2777 TonB‐dependent siderophore receptor protein iroN 1.9108407 2.1902285 2.018897 0.21211101 0.26418743 0.21821526 2.039989 4.112423 STM2779 putative inner membrane protein ‐1.6570932 ‐1.5668646 ‐1.3951266 ‐1.5192282 ‐1.3188132 ‐1.1711544 ‐1.53969 0.343958 STM2780 Homolog of pipB, putative pentapeptide repeats (8 ‐1.0780922 ‐0.8139626 ‐0.97066003 ‐1.3445059 ‐1.1444677 ‐1.3973186 ‐0.95424 0.516114 STM2788 tricarboxylic transport ‐0.24668622 ‐0.5167338 ‐0.51041025 ‐0.03694854 ‐0.33182222 ‐0.039279483 ‐0.42461 0.74504 STM2799 DNA‐binding protein with chaperone activity stpA 0.51035285 0.7136659 0.6639277 1.2195485 1.4674598 1.3035315 0.629315 1.546831 STM2800 putative inner membrane protein ‐1.0397096 ‐1.0487089 ‐0.9491986 ‐1.1627603 ‐1.7866412 ‐1.4778053 ‐1.01254 0.495673 STM2805 glutaredoxin‐like protein hydrogen donor nrdH 1.4108615 1.5631614 1.6114173 0.2844111 0.23818079 0.09022212 1.52848 2.884818 STM2806 stimulates ribonucleotide reduction nrdI 1.5859082 1.6896712 1.5323713 0.5361342 0.5886238 0.54786766 1.60265 3.037007 STM2807 ribonucleoside diphosphate reductase 2, alpha subunit nrdE 1.3610189 1.1131215 1.3807477 1.2840371 1.6497548 1.5424218 1.284963 2.436758 STM2811 ABC superfamily (bind_prot), glycine/betaine/proline transport protein proX 0.28423262 0.24634005 0.27426836 1.0516843 1.2805676 1.3833369 0.26828 1.204371 STM2814 multidrug resistance secretion protein emrA ‐0.6603798 ‐0.61795837 ‐0.6030626 0.14563538 0.105465606 0.05179591 ‐0.62713 0.647462 STM2818 gamma‐glutamate‐cysteine ligase gshA 0.30802456 0.2622602 0.22540766 1.3915378 1.2543832 1.0112273 0.265231 1.201828 STM2820 putative phosphoglucomutase yqaB 0.5168176 0.22583568 0.35993382 0.42678532 0.6108107 0.5289412 0.367529 1.290141 STM2829 DNA strand exchange and recombination protein with recA 0.36601838 0.616091 0.48594844 1.2252629 1.1004763 0.8265971 0.489353 1.403815 STM2843 electron transport protein (FeS senter) from formate hydN ‐2.111915 ‐2.1141264 ‐2.1909368 ‐0.7292152 ‐0.3609178 ‐0.662025 ‐2.13899 0.227038 147 STM2844 putative periplasmic or exported protein ‐1.2787188 ‐1.2830478 ‐1.2518593 ‐0.172181 ‐0.263596 ‐0.3009187 ‐1.27121 0.414313 STM2846 processing of HycE (part of the FHL hycH ‐1.9982865 ‐2.2120636 ‐2.144421 ‐1.3907449 ‐1.029538 ‐0.9739851 ‐2.11826 0.230325 STM2849 hydrogenase 3, large subunit (part of FHL hycE ‐1.5778861 ‐1.6977483 ‐1.7120734 ‐0.10358425 ‐0.09148506 ‐0.16535304 ‐1.66257 0.315876 STM2851 hydrogenase 3, membrane subunit (part of FHL hycC ‐1.5309073 ‐1.5929081 ‐1.6289089 ‐0.6390652 ‐0.3003945 ‐0.3207277 ‐1.58424 0.3335 STM2854 guanine‐nucleotide binding protein in formate‐hydrogenlyase system, functions hypA ‐1.380965 ‐1.3377738 ‐1.5077561 ‐0.6757089 ‐0.86436427 ‐1.1842023 ‐1.40883 0.376617 STM2855 hydrogenase‐3 accessory protein, assembly of metallocenter hypB ‐1.510201 ‐1.5917325 ‐1.7514678 ‐1.2971075 ‐1.0884947 ‐1.2998145 ‐1.6178 0.325832 STM2856 putative hydrogenase expression/formation protein hypC ‐1.6043607 ‐1.3384742 ‐1.4685069 ‐1.3643197 ‐1.0714186 ‐1.1026849 ‐1.47045 0.36087 STM2857 putative hydrogenase expression/formation protein hypD ‐1.3017131 ‐1.5445496 ‐1.4773316 ‐1.7078265 ‐2.026192 ‐1.9283416 ‐1.4412 0.368261 STM2858 putative hydrogenase expression/formation protein hypE ‐1.2006162 ‐1.1917812 ‐1.2197933 ‐1.1196187 ‐0.9748724 ‐1.2857137 ‐1.20406 0.434051 STM2861 Salmonella iron transporter: fur regulated sitA 1.7026858 1.6050758 1.7330488 ‐1.8225362 ‐1.4510936 ‐1.3076658 1.68027 3.20488 STM2862 Salmonella iron transporter: fur regulated sitB 2.0106812 1.9755465 1.9555578 ‐1.4567972 ‐1.5760242 ‐1.6994305 1.980595 3.946559 STM2863 Salmonella iron transporter: fur regulated sitC 1.479524 1.534634 1.3238136 ‐1.2319107 ‐1.1149666 ‐1.2070023 1.445991 2.724498 STM2864 Salmonella iron transporter: fur regulated sitD 1.0156461 0.77281904 0.95749605 ‐0.57300925 ‐0.6943098 ‐0.82742065 0.91532 1.885988 STM2865 putative inner membrane protein avrA 0.6580734 0.54348016 0.5883913 0.22636618 0.16684346 0.15857702 0.596648 1.512199 STM2901 putative cytoplasmic protein 0.28170028 0.617756 0.7001731 0.37418702 0.13207701 0.19973299 0.53321 1.447145 STM2911 putative permease ‐0.36350116 ‐0.28299135 ‐0.4199722 0.64968485 0.60937476 0.4931611 ‐0.35549 0.781605 STM2924 sigma S (sigma 38) factor of RNA rpoS 1.0578645 0.65946704 0.5723216 1.0113361 0.8807009 0.9485627 0.763218 1.697272 STM2934 ATP‐sulfurylase, subunit 1 (ATP:sulfate adenylyltransferase) cysN 0.30372697 0.48952314 0.310964 1.7175845 1.5714319 1.5097268 0.368071 1.290626 STM2935 ATP‐sulfurylase, subunit 1 (ATP:sulfate adenylyltransferase) cysD 0.3542767 0.29968372 0.3409208 0.995818 0.83977145 0.903015 0.331627 1.258432 STM2938 putative cytoplasmic protein ‐0.18880545 ‐0.57485443 ‐0.3934032 ‐0.4256609 ‐0.614946 ‐0.59168684 ‐0.38569 0.765414 STM2939 putative cytoplasmic protein ygcH ‐0.20089796 ‐0.483565 ‐0.53419197 ‐0.12783015 ‐0.2431091 ‐0.17925814 ‐0.40622 0.754599 STM2946 3‐phosphoadenosine 5‐phosphosulfate (PAPS) reductase cysH ‐0.2020317 ‐0.42270452 ‐0.4029644 0.30678847 ‐0.061309233 0.14378427 ‐0.34257 0.788637 STM2951 putative Organic radical activating enzymes ygcF 0.62965447 0.71734643 0.33090457 0.9377197 0.94293815 0.70960456 0.559302 1.473556 STM2953 CTP synthetase pyrG 0.46347573 0.63191265 0.53153473 1.5831877 1.2341961 0.790129 0.542308 1.4563 STM2954 putative pyrophosphatase mazG 0.26385403 0.5658111 0.27409884 ‐0.06666602 0.24465722 0.040505618 0.367921 1.290492 STM2963 putative MFS superfamily, D‐glucarate permease 0.6211641 0.5561981 0.6033192 0.38301352 0.37756073 0.4378025 0.59356 1.508966 STM2971 L‐serine dehydratase (L‐threonine deaminase 2) sdaB ‐0.32765755 ‐0.43095577 ‐0.30523852 ‐0.037356358 0.37048268 0.12657136 ‐0.35462 0.782077 STM2976 L‐fucose isomerase fucI ‐0.40149662 ‐0.7043617 ‐0.7407146 ‐0.15369768 ‐0.3733546 ‐0.3041184 ‐0.61552 0.652693 STM2985 putative SufE protein probably involved in Fe‐S ygdK ‐0.23369008 ‐0.46151632 ‐0.40656316 ‐0.50069046 ‐0.66075945 ‐0.5349036 ‐0.36726 0.775255 STM2992 N‐alpha‐acetylglutamate synthase (amino‐acid acetyltransferase) argA ‐1.8826816 ‐2.0373597 ‐1.7753541 ‐0.9094354 ‐1.0514808 ‐0.7714091 ‐1.89847 0.268229 STM3003 General PTS system, enzyme I, transcriptional regulator ptsP 0.45904133 0.49615526 0.4057607 1.61506 1.5269563 1.6946888 0.453652 1.369503 STM3012 putative transcriptional regulator ‐0.19931345 ‐0.23968917 ‐0.27772453 ‐0.4509196 ‐0.19308375 ‐0.1738517 ‐0.23891 0.847386 STM3034 putative cytoplasmic protein 0.39470655 0.5751511 0.52478904 0.041727323 0.30389428 0.08183529 0.498216 1.412465 STM3040 lysine tRNA synthetase, constitutive lysS 0.5489557 0.705428 0.4235758 0.8250381 0.37911683 0.51252145 0.55932 1.473574 STM3047 putative cytoplasmic protein ygfY 0.22228152 0.28155047 0.33851743 ‐0.39068496 ‐0.45433235 ‐0.3793316 0.280783 1.214854 STM3048 putative aminomethyltransferase ygfZ 0.37370208 0.3103816 0.36433092 0.09927412 0.18745086 ‐0.0856364 0.349472 1.274094 STM3049 putative hemolysin yqfA ‐0.26975584 ‐0.25578 ‐0.34860906 ‐0.8640276 ‐0.6955426 ‐0.8497073 ‐0.29138 0.817119 STM3053 glycine cleavage complex protein P, glycine decarboxylase gcvP ‐0.28896147 ‐0.31050998 ‐0.30673265 ‐0.15525909 ‐0.18276502 ‐0.3426088 ‐0.30207 0.811089 STM3054 glycine cleavage complex protein H, carrier of gcvH ‐0.44275403 ‐0.3848467 ‐0.52412593 0.02444239 ‐0.061243914 ‐0.18869832 ‐0.45058 0.731751 STM3055 glycine cleavage complex protein T, aminomethyltransferase, tetrahydrofolate‐dependent gcvT ‐0.4154128 ‐0.34686542 ‐0.4907852 ‐0.08639197 ‐0.15058707 ‐0.32628548 ‐0.41769 0.748623 STM3060 putative cytoplasmic protein ygfE ‐1.2001287 ‐1.0961808 ‐1.0825833 0.1922612 0.16760007 0.14385821 ‐1.1263 0.45809 STM3062 D‐3‐phosphoglycerate dehydrogenase serA 0.8323728 0.74745554 0.5936536 0.62308353 0.19925058 0.16718918 0.724494 1.652321 STM3063 ribosephosphate isomerase, constitutive rpiA 0.5394156 0.44647112 0.42515892 0.54042345 0.7274467 0.54703075 0.470349 1.385444 STM3067 putative membrane protein, involved in stability of yggB 0.47451338 0.4381121 0.4382247 ‐0.050456624 ‐0.22115836 ‐0.45672375 0.450283 1.366309 STM3068 fructose‐bisphosphate aldolase fba 0.3727042 0.415672 0.32199523 ‐0.73165846 ‐0.6565856 ‐0.90815854 0.370124 1.292464 STM3073 putative ABC‐type cobalt transport system, permease component ‐0.7943754 ‐1.0122044 ‐1.05152 ‐1.5030166 ‐1.7414619 ‐1.6000873 ‐0.9527 0.516665 STM3074 putative ABC‐type cobalt transport system, ATPase component ‐0.493748 ‐0.44734427 ‐0.5929929 ‐0.24813941 ‐0.07105917 ‐0.14006026 ‐0.51136 0.70156 STM3075 putative ABC‐type cobalt transport system, ATPase component ‐0.499996 ‐0.46201798 ‐0.28025147 ‐0.20015813 ‐0.12247555 ‐0.17347944 ‐0.41409 0.750494 STM3076 transketolase 1 isozyme tktA ‐0.2935491 ‐0.7141154 ‐0.5902455 0.039647017 ‐0.14916487 ‐0.12813893 ‐0.53264 0.69129 STM3086 arginine decarboxylase speA 0.53480905 0.4557718 0.27149752 1.1257912 0.82378703 0.8655421 0.420693 1.33857 STM3091 MFS family, galactose:proton symporter galP 0.3331002 0.47443724 0.21365693 0.20429307 0.2514892 0.02743258 0.340398 1.266106 STM3128 putative oxidoreductase 0.50142735 0.29206783 0.27690646 ‐0.18091533 ‐0.32729176 ‐0.22772942 0.356801 1.280583 STM3150 putative Ni/Fe hydrogenases, small subunit hypO ‐0.19726229 ‐0.34846747 ‐0.46484947 0.25835583 0.033438966 0.2959998 ‐0.33686 0.791763 STM3165 2,5‐diketo‐D‐gluconate reductase A yqhE 0.20250544 0.32095325 0.37499368 ‐0.13356934 ‐0.2397828 ‐0.17741789 0.299484 1.230704 STM3175 putative bacterial regulatory helix‐turn‐helix proteins, araC family ‐0.31041464 ‐0.32097733 ‐0.36471972 ‐0.15913767 ‐0.16535844 ‐0.303867 ‐0.33204 0.794414 STM3178 putative sensory histidine kinase in regulatory system ygiY ‐0.38070723 ‐0.16367202 ‐0.497045 0.14814201 0.10543076 ‐0.24226819 ‐0.34714 0.78614 STM3198 putative inner membrane protein ‐0.22396512 ‐0.42934448 ‐0.3221091 ‐0.24545233 ‐0.5870015 ‐0.6201221 ‐0.32514 0.798221 STM3217 aerotaxis sensor receptor, senses cellular redox state aer 0.35210353 0.31415823 0.33692762 ‐0.13237587 ‐0.28828335 8.02E‐04 0.334396 1.26085 STM3222 putative integral membrane protein ygjQ 0.2223704 0.35430413 0.33712152 ‐0.17460038 ‐0.26037008 ‐0.17399216 0.304599 1.235075 STM3229 putative inner membrane protein yqjD 0.3128186 0.3589067 0.59789807 ‐0.42720148 ‐0.2842111 ‐0.27550352 0.423208 1.340906 STM3231 putative inner membrane protein yqjK 0.44499046 0.5090171 0.3568463 ‐0.09442147 ‐0.13439716 ‐0.43509114 0.436951 1.353741 STM3238 putative inner membrane protein yhaN ‐0.23153356 ‐0.27967775 ‐0.27294913 0.3655211 0.22990517 0.3426212 ‐0.26139 0.834286 STM3255 putative phosphotransferase system fructose‐specific component IIB 0.28756332 0.55266887 0.4851381 0.7379055 0.41182685 0.39430737 0.44179 1.358289 STM3272 putative ABC superfamily (membrane) transport protein yhbS ‐0.512472 ‐0.2669699 ‐0.28543532 ‐0.43123624 ‐0.27311894 ‐0.09063242 ‐0.35496 0.781892 STM3283 30S ribosomal subunit protein S15 rpsO ‐0.5601261 ‐0.48675564 ‐0.37208533 0.19555874 0.22505854 0.25455463 ‐0.47299 0.72047 STM3290 argininosuccinate synthetase argG ‐0.8604555 ‐0.8045967 ‐0.7496812 ‐0.027040191 ‐0.01537311 0.06927864 ‐0.80491 0.572397 STM3296 ATP‐dependent zinc‐metallo protease hflB 0.3639048 0.31723154 0.26751897 0.873671 0.6887258 0.6959391 0.316218 1.245063 STM3303 50S ribosomal subunit protein L27 rpmA 0.29266664 0.27417678 0.37332067 0.722275 0.80754155 0.8770581 0.313388 1.242622 STM3307 UDP‐N‐acetylglucosamine 1‐carboxyvinyltransferase murA 0.31915554 0.385592 0.33516544 0.86490834 0.8380177 0.68250495 0.346638 1.271594 STM3310 putative ABC superfamily (atp&memb), transport protein yrbC 0.45055595 0.6493985 0.37100726 1.0194108 1.4531128 1.1803452 0.490321 1.404757 STM3318 putative ABC superfamily (bind_prot) transport protein yhbN 0.21828444 0.24881084 0.34011468 0.72728646 0.6107526 0.72495925 0.26907 1.205031 STM3319 putative ABC superfamily (atp_bind) transport protein yhbG 0.55796766 0.51682436 0.24608935 0.90596527 0.61113596 0.61389375 0.440294 1.356881 STM3321 putative sigma N modulation factor yhbH 1.0253689 1.2957793 1.0338696 0.12469561 ‐0.14209625 ‐0.21633388 1.118339 2.170969 STM3322 sugar specific PTS family, enzyme IIA, also ptsN 0.35407287 0.44442272 0.31480545 0.5144853 0.2909794 ‐0.007488954 0.3711 1.293339 STM3323 putative P‐loop‐containing kinase yhbJ 0.4593303 0.5092408 0.3930682 0.87617284 0.41066575 0.21388516 0.45388 1.369719 STM3330 glutamate synthase, large subunit gltB ‐1.2374511 ‐1.1750478 ‐1.0209262 0.42223728 0.46917948 0.41576034 ‐1.14448 0.452354 STM3331 glutamate synthase, small subunit gltD ‐1.2325765 ‐1.1646444 ‐1.1944269 0.86034554 0.7685048 0.74538505 ‐1.19722 0.436116 STM3344 30S ribosomal subunit protein S9 rpsI ‐0.31225324 ‐0.2942787 ‐0.35574937 0.59703296 0.72727215 0.84410584 ‐0.32076 0.800648 STM3345 50S ribosomal subunit protein L13 rplM ‐0.42418668 ‐0.39810398 ‐0.27671683 0.3355869 0.5297364 0.5527854 ‐0.36634 0.77575 STM3346 putative ATPase yhcM 0.46733466 0.51619864 0.4392478 0.48856956 0.5567523 0.3359806 0.47426 1.389206 STM3347 putative periplasmic protein yhcB 0.27658775 0.5025476 0.47790214 0.7403273 0.653262 0.6178786 0.419012 1.337012 STM3348 serine endoprotease degQ 0.29680672 0.52625495 0.40978143 0.9529764 0.89315414 0.42084214 0.410948 1.329559 STM3351 putative sodium ion pump oxaloacetate decarboxylase beta oadB ‐0.34602475 ‐0.6961095 ‐0.74508744 0.32210544 0.26042974 0.28443214 ‐0.59574 0.661705 STM3353 putative sodium ion pump oxaloacetate decarboxylase gamma oadG ‐0.4816189 ‐0.7889358 ‐0.78861606 0.10544067 ‐0.15715173 0.053094957 ‐0.68639 0.621407 STM3356 putative cation transporter 0.37959757 0.36113432 0.29512122 ‐0.77252007 0.22669515 0.25414976 0.345284 1.270401 STM3376 putative oxidoreductase yhdH ‐0.38041863 ‐0.36449853 ‐0.3964006 ‐0.0674355 0.1674601 0.650326 ‐0.38044 0.768204 STM3404 putative cytoplasmic protein smg 0.55361795 0.37892056 0.48058265 ‐0.3222866 ‐0.36682993 ‐0.42427483 0.47104 1.386109 STM3409 Trk system transport of potassium trkA 0.45403755 0.41118976 0.4119724 0.081143364 0.0475558 0.034577005 0.425733 1.343255 STM3411 putative cytoplasmic protein 0.61358094 0.5232863 0.549325 0.38336587 ‐0.15478486 ‐0.0657317 0.562064 1.47638 STM3428 50S ribosomal subunit protein L5 rplE 0.27224478 0.408246 0.21400793 0.55655867 0.5555049 0.57440585 0.298166 1.229581 STM3444 regulatory or redox component complexing with Bfr bfd 0.29753736 0.5292295 0.5117523 1.82E‐04 ‐0.025506811 0.004482636 0.446173 1.362421 STM3455 FKBP‐type peptidyl prolyl cis‐trans isomerase (rotamase) slyD 0.29044163 0.3634315 0.34046206 0.028055783 0.012357877 0.022738952 0.331445 1.258273 STM3467 putative inner membrane protein yhfK ‐0.27054843 ‐0.34388548 ‐0.24580324 ‐0.07410044 ‐0.36324915 ‐0.25896966 ‐0.28675 0.819749 STM3468 acetylornithine transaminase (NAcOATase and DapATase) argD ‐1.0901717 ‐1.1069815 ‐1.0186319 ‐0.5776001 ‐0.8472112 ‐0.9248754 ‐1.07193 0.475683 STM3483 D‐ribulose‐5‐phosphate 3‐epimerase rpe 0.22289732 0.2771398 0.25279966 1.1238592 1.5802953 0.8778368 0.250946 1.189987 STM3487 shikimate kinase I aroK 0.23728496 0.50706136 0.38406584 1.4653877 1.4609106 1.3644738 0.376137 1.297862 STM3494 putative NTP pyrophosphohydrolase yrfE 0.3264107 0.48532274 0.37126324 1.1182879 1.1681563 0.9867609 0.394332 1.314334 STM3505 ferrous iron transport protein A feoA ‐0.8980078 ‐0.8358187 ‐0.78202707 ‐1.9934821 ‐1.9092382 ‐1.8104979 ‐0.83862 0.559179 STM3506 FeoB family, ferrous iron transport protein B feoB ‐0.8008093 ‐0.7850094 ‐0.80909026 ‐1.6182702 ‐1.514517 ‐1.5827016 ‐0.7983 0.575025 STM3507 putative cytoplasmic protein yhgG ‐0.65874517 ‐0.65858203 ‐0.5766391 ‐0.78440833 ‐0.9887308 ‐0.9772643 ‐0.63132 0.645585 STM3510 putative amidophosphoribosyltransferase yhgH ‐0.40665218 ‐0.36850718 ‐0.42183143 ‐0.49081504 ‐0.18121335 ‐0.94985723 ‐0.399 0.758385 STM3521 putative ribonucleoprotein related‐protein ‐0.41907156 ‐0.19010767 ‐0.36613894 ‐0.2944485 ‐0.34561506 ‐0.25370425 ‐0.32511 0.79824 STM3541 low affinity gluconate permease gntU ‐0.40383425 ‐0.39919758 ‐0.33831713 ‐0.19777584 0.014297553 ‐0.20688541 ‐0.38045 0.768198 STM3545 putative oxidoreductase yhhX 0.3654765 0.456926 0.22306515 1.4265004 1.4592677 1.38696 0.348489 1.273227 STM3547 putative transcriptional regulator of sugar metabolism 0.3454789 0.35628942 0.42460406 ‐1.5679135 0.1685269 0.027284415 0.375457 1.297251 STM3559 putative cytoplasmic protein yhhV ‐0.51195174 ‐0.36480522 ‐0.3218064 ‐0.8147165 ‐0.6967587 ‐0.6396708 ‐0.39952 0.75811 STM3562 ABC superfamily (membrane), branched‐chain amino acid transporter livM ‐0.33340865 ‐0.43975687 ‐0.4066767 1.1676672 0.695106 0.74952626 ‐0.39328 0.761396 STM3579 putative integral membrane protein yhhQ ‐0.26206633 ‐0.28131464 ‐0.31972826 0.8972435 0.9045855 1.2626444 ‐0.2877 0.819205 STM3583 putative Phosphopantetheinyl transferase acpT ‐0.23017658 ‐0.21891128 ‐0.23699446 0.6221992 1.0144118 0.95787734 ‐0.22869 0.853407 STM3592 putative POT family, peptide transport protein yhiP 0.42574438 0.24779528 0.3458033 0.2915216 0.100314565 0.44760516 0.339781 1.265564 148 STM3622 putative cytoplasmic protein yhjS 0.47895348 0.5198404 0.45286873 1.1361014 0.71533597 0.33328858 0.483888 1.398507 STM3630 ABC superfamily (peri_perm), dipeptide transport protein dppA 0.65638983 0.7135767 0.6953107 0.10715337 0.08700275 ‐0.06425898 0.688426 1.611524 STM3647 putative outer membrane lipoprotein yiaF 0.26586452 0.36045036 0.25343433 0.39822218 0.4916266 0.46281114 0.29325 1.225397 STM3649 major cold shock protein 7.4, transcriptional activator cspA 0.18005908 0.46725303 0.35170114 1.7636927 1.7109131 1.7175866 0.333004 1.259634 STM3650 putative periplasmic or exported protein 0.22452152 0.22606935 0.32060763 0.17822671 ‐0.12572524 ‐0.057249717 0.257066 1.195046 STM3659 putative inner membrane protein yiaB ‐0.1970659 ‐0.28612143 ‐0.3498788 0.18167017 ‐0.16547696 ‐0.13611113 ‐0.27769 0.824912 STM3663 gene transcribed divergently from malS bax ‐0.19354104 ‐0.29071295 ‐0.32134485 0.20326287 ‐0.047476996 ‐0.14926338 ‐0.26853 0.830163 STM3664 alpha‐amylase malS ‐0.24996409 ‐0.2857351 ‐0.34253663 ‐0.002784849 0.078710474 4.09E‐04 ‐0.29275 0.816347 STM3666 paral putative oxidoreductase ysaA ‐0.3849482 ‐0.3260673 ‐0.4641717 ‐0.42707002 ‐0.54028434 ‐0.6653222 ‐0.39173 0.762216 STM3679 putative cytoplasmic protein ‐0.29648966 ‐0.65751076 ‐0.54979634 ‐0.6548299 ‐0.61710554 ‐0.7088889 ‐0.50127 0.706487 STM3682 selenocysteinyl‐tRNA‐specific translation factor selB ‐0.46270218 ‐0.58953184 ‐0.3083847 ‐0.26028427 ‐0.1905019 ‐0.067840494 ‐0.45354 0.730249 STM3689 putative cytoplasmic protein yibL 0.36531964 0.36450312 0.6098935 0.07639939 ‐0.21415645 0.15354414 0.446572 1.362798 STM3693 putative transcriptional regulator for lct operon (GntR lldR ‐0.40226498 ‐0.21572231 ‐0.25337076 ‐0.2106168 ‐0.07665873 ‐0.05643029 ‐0.29045 0.817645 STM3694 L‐lactate dehydrogenase lldD ‐0.31891036 ‐0.38540933 ‐0.21543375 ‐0.21499631 ‐0.050316732 ‐0.11105678 ‐0.30658 0.808554 STM3695 putative tRNA/rRNA methyltransferase yibK ‐0.38597736 ‐0.43957305 ‐0.34641305 ‐0.31762493 ‐0.1700495 ‐0.037356976 ‐0.39065 0.762783 STM3699 serine acetyltransferase cysE 0.2519985 0.23225242 0.25430465 0.25100732 0.6143443 0.4956306 0.246185 1.186067 STM3713 O‐antigen ligase rfaL 0.36301234 0.49145386 0.43890908 1.906771 1.6350414 1.0828239 0.431125 1.348285 STM3727 50S ribosomal subunit protein L33 rpmG 0.6258041 0.38240027 0.33417016 1.5091441 1.1095043 1.1165243 0.447458 1.363636 STM3728 50S ribosomal subunit protein L28 rpmB 0.5031419 0.37100726 0.459275 0.8283098 0.82460684 0.77496606 0.444475 1.360819 STM3733 orotate phosphoribosyltransferase pyrE 0.22934297 0.43212935 0.260425 1.0674946 0.70575684 0.77110326 0.307299 1.237389 STM3738 putative inner membrane protein yigC 0.24687901 0.47976634 0.24572635 ‐0.44474292 ‐0.5762905 ‐0.37029564 0.324124 1.251904 STM3753 ATP binding protein sugR 0.43738025 0.56249774 0.4580277 0.6982648 0.39981353 0.04603538 0.485969 1.400526 STM3767 putative cytoplasmic protein ‐0.3511006 ‐0.57912034 ‐0.62720615 0.43108487 0.4718336 0.60070896 ‐0.51914 0.697787 STM3780 putative fructose‐bisphosphate aldolase class‐II 0.20207778 0.57365334 0.4473668 0.43595454 0.43045422 0.32178733 0.407699 1.326569 STM3794 putative regulatory protein, deoR family 0.37849623 0.35960653 0.31703052 0.51292825 0.26912284 0.28366348 0.351711 1.276073 STM3796 acetolactate synthase I, large subunit, valine sensitive ilvB 1.5609252 1.3317875 1.3896406 1.216307 1.1003712 0.9060913 1.427451 2.689711 STM3808 small heat shock protein ibpB ‐0.28224045 ‐0.41326177 ‐0.2579473 ‐0.46361297 ‐0.44752392 ‐0.4528699 ‐0.31782 0.802283 STM3810 putative outer membrane lipoprotein yidQ 0.28135958 0.27978045 0.4666824 0.059726506 ‐0.20296866 ‐0.011735023 0.342607 1.268046 STM3828 galactonate dehydratase in bifunctional: 2‐oxo‐3‐deoxygalactonate 6‐phosphate aldolase dgoA 0.21327987 0.3637907 0.2827768 0.54554945 0.53348064 0.3950154 0.286616 1.219776 STM3832 putative permease 0.50030506 0.40592232 0.43314388 ‐0.4325301 ‐0.25363237 ‐0.32690707 0.446457 1.36269 STM3842 putative Preprotein translocase subunit YidC yidC ‐0.23485981 ‐0.22943561 ‐0.2112078 0.29219565 0.4062164 0.49257448 ‐0.22517 0.855496 STM3850 putative oxidoreductase yieF 0.23937899 0.3455915 0.36063868 ‐0.04232111 ‐0.041951276 ‐0.35066804 0.315203 1.244187 STM3862 N‐acetyl glucosamine‐1‐phosphate uridyltransferase and glucosamine‐1‐phosphate acetyl traglmU 0.36955515 0.5402315 0.4510921 1.0702175 0.9851888 0.66823614 0.453626 1.369478 STM3866 membrane‐bound ATP synthase, F1 sector, gamma‐subunit atpG 0.54671985 0.3996228 0.33254293 1.437102 1.0038995 0.9538133 0.426295 1.343778 STM3877 asparagine synthetase A asnA ‐1.8288294 ‐2.0108335 ‐1.9725355 ‐0.7493705 ‐1.1015068 ‐1.0090463 ‐1.9374 0.261087 STM3879 paral putative regulator protein yieN 0.5740368 0.4551856 0.3761866 0.11855396 ‐0.3955661 0.075530075 0.46847 1.383641 STM3887 putative MFS family tranport protein (1st mdule) yieO 0.30532005 0.37606826 0.31825593 0.08260533 0.003871119 ‐0.2290431 0.333215 1.259817 STM3898 putative LysR type transcriptional regulator with pssR yifE 0.47292084 0.7659487 0.66173244 0.116377756 0.11979651 ‐0.030671012 0.633534 1.551361 STM3899 putative magnesium chelatase, subunit ChlI yifB 0.32598174 0.2897434 0.27166605 0.19326666 0.1352363 0.10118432 0.295797 1.227563 STM3901 acetolactate synthase II, large subunit, fragment 1 ilvG 0.6425514 0.59973615 0.58618224 0.6117585 0.62401396 0.6385095 0.60949 1.52572 STM3902 acetolactate synthase II, small subunit ilvM 1.0454634 0.92444766 0.91379493 0.80081606 0.38492376 0.60558546 0.961235 1.946976 STM3903 branched‐chain amino‐acid aminotransferase ilvE 0.79254895 0.75233585 0.7646743 0.65603364 0.3946524 0.4817307 0.769853 1.705096 STM3904 dihydroxyacid dehydratase ilvD 0.775312 0.45393547 0.49352932 1.5322919 1.1240008 1.3032608 0.574259 1.488912 STM3905 threonine deaminase ilvA 0.5118394 0.3958778 0.5679266 1.3083211 1.0906904 1.2207458 0.491881 1.406277 STM3909 ketol‐acid reductoisomerase ilvC ‐0.25719902 ‐0.60160685 ‐0.39823884 0.7675543 0.856862 1.0445279 ‐0.41901 0.747935 STM3918 undecaprenyl‐phosphate N‐acetylglucosaminyltransferase rfe 0.28181234 0.31976473 0.20916136 0.2355924 0.29574695 0.16008376 0.270246 1.206014 STM3919 modulator of enterobacterial common antigen (ECA) polysaccharide wzzE 0.38888365 0.4176267 0.29808593 0.90911055 0.9141631 0.60147023 0.368199 1.29074 STM3920 UDP‐N‐acetyl glucosamine ‐2‐epimerase wecB 0.2827122 0.28895012 0.30483842 0.05869467 0.62140656 0.43969116 0.292167 1.224478 STM3956 putative protein PaaI, possibly involved in aromatic yigI 0.29129466 0.37405178 0.2899537 0.50552374 0.38928434 0.29344177 0.318433 1.246976 STM3964 regulator for metE and metH (LysR family) metR 0.496016 0.6067155 0.5417827 0.08060953 0.0294121 ‐0.06707674 0.548171 1.462231 STM3965 5‐methyltetrahydropteroyltriglutamate‐homocysteine S‐methyltransferase metE 2.0208678 2.130202 2.026502 1.3302777 1.5007643 1.636712 2.059191 4.167524 STM3967 putative dienelactone hydrolase family dlhH 0.57621735 0.6570585 0.70042425 0.3934541 0.23191008 0.13222028 0.644567 1.56327 STM3970 S‐adenosylmethionine : 2‐DMK methyltransferase and 2‐octaprenyl‐6‐methoxy‐1,4‐benzoqui ubiE 0.5451342 0.7330351 0.5664514 1.9925156 1.8771598 1.2903749 0.614874 1.531424 STM3972 putative regulator in ubiquinone biosynthesis aarF 0.38699812 0.4446431 0.40212184 0.6121604 0.6710387 0.8239563 0.411254 1.329842 STM3973 component of Sec‐independent protein secretion pathway tatA 0.39415374 0.21388204 0.36006528 0.49250725 0.6424895 0.9343452 0.3227 1.250669 STM3974 component of Sec‐independent protein secretion pathway tatB 0.3267777 0.4204216 0.35949153 1.2409211 0.96708983 0.6855373 0.368897 1.291365 STM3986 Trk family, potassium transport protein, requires TrkE trkH 0.43091 0.36631954 0.36982083 0.42558333 0.49539125 0.6512143 0.389017 1.309501 STM3987 protoporphyrin oxidase hemG 0.4650082 0.2570255 0.34211197 0.7979541 0.6967339 0.5071127 0.354715 1.278733 STM3996 putative homoserine kinase type II, protein kinase yihE 0.36842012 0.5877408 0.24637876 0.4794375 0.736238 0.29896173 0.400847 1.320282 STM3998 putative endonuclease yihG 0.6362146 0.32162002 0.23502919 0.24990827 0.039901324 0.068191454 0.397621 1.317334 STM3999 DNA polymerase I, 3 ‐‐ 5 polymerase polA 0.37616727 0.5917273 0.34549972 0.86111623 0.68715334 0.30518755 0.437798 1.354535 STM4001 putative GTPase, involved in coordination of cell yihA 0.46204188 0.4504875 0.47532624 0.23006605 ‐0.038399022 0.15837023 0.462619 1.378041 STM4002 putative cytoplasmic protein 1.8951077 1.6498793 2.0633426 ‐3.046172 ‐3.429997 ‐3.3333795 1.869443 3.653915 STM4006 sensory kinase (phosphatase) in two‐component regulatory system glnL ‐0.6108326 ‐0.4447654 ‐0.4580785 1.014649 0.8775167 0.7090234 ‐0.50456 0.704876 STM4007 glutamine synthetase glnA ‐0.53651893 ‐0.5801261 ‐0.66090095 ‐0.8614913 ‐1.0806694 ‐1.1501278 ‐0.59252 0.663186 STM4021 putative isomerase yihS ‐0.2704055 ‐0.27652904 ‐0.22166605 ‐0.14612405 ‐0.25875008 ‐0.20933959 ‐0.2562 0.83729 STM4042 putative branched‐chain amino acid permease ‐0.31133318 ‐0.27132848 ‐0.3750686 0.043424353 0.24703322 0.14072745 ‐0.31924 0.80149 STM4044 putative iron‐containing alcohol dehydrogenase ‐0.45278054 ‐0.5214348 ‐0.524722 ‐0.31382 ‐0.29780543 ‐0.38358757 ‐0.49965 0.70728 STM4050 DMT Superfamily, L‐rhamnose:H symporter protein rhaT 0.36642 0.51521206 0.3493159 ‐0.05258342 0.003506932 ‐0.13109052 0.410316 1.328977 STM4068 putative regulatory protein, gntR family ‐0.4316753 ‐0.72215956 ‐0.47238067 ‐0.5438755 ‐0.7996518 ‐0.63016534 ‐0.54207 0.686784 STM4074 putative ABC‐type sugar, aldose transport system, ATPase ego 0.33004305 0.6452359 0.38345605 0.15237305 0.16123646 ‐0.050507206 0.452912 1.3688 STM4075 putative ABC superfamily (membrane), sugar transport protein ydeY 0.28925765 0.38426402 0.41718525 ‐0.265797 ‐0.14742954 ‐0.066055015 0.363569 1.286605 STM4080 putative ribulose‐5‐phosphate 3‐epimerase 0.34366462 0.20211396 0.28522003 ‐0.40540716 ‐0.30971038 ‐0.53250366 0.277 1.211672 STM4085 unknown function in glycerol metabolism glpX ‐0.24018738 ‐0.3257725 ‐0.29373208 ‐0.081974894 ‐0.25006828 ‐0.34049258 ‐0.28656 0.819852 STM4089 putative methyltransferase in menaquinone biosynthesis protein menG ‐0.32543272 ‐0.19806375 ‐0.2541264 ‐0.35762367 ‐0.55476916 ‐0.5807771 ‐0.25921 0.835547 STM4091 ATPase component of the HslUV protease hslU ‐0.21740294 ‐0.32428992 ‐0.26945928 0.18986104 ‐0.1350702 0.20300889 ‐0.27038 0.829099 STM4096 50S ribosomal subunit protein L31 rpmE ‐0.52524084 ‐0.6936451 ‐0.5349336 0.9467218 1.1588022 1.4138205 ‐0.58461 0.666831 STM4100 cystathionine gamma‐synthase metB 0.3551766 0.58232796 0.62016344 0.8253261 1.0059774 0.8184255 0.519223 1.433183 STM4103 putative cytoplasmic protein 0.4829309 0.17199175 0.51570684 0.69531804 0.47887748 0.5695407 0.39021 1.310584 STM4105 5,10‐methylenetetrahydrofolate reductase metF 1.0520654 1.1641366 1.1934389 0.0978407 0.00562335 ‐0.06088176 1.136547 2.198542 STM4106 catalase hydroperoxidase HPI(I) katG ‐0.22332722 ‐0.277701 ‐0.4115189 0.15668105 0.12392089 ‐0.045554634 ‐0.30418 0.809901 STM4110 General PTS family, enzyme I ptsA ‐0.3237488 ‐0.2876717 ‐0.5148504 1.2346344 1.1793113 0.982827 ‐0.37542 0.770879 STM4121 N‐acetyl‐gamma‐glutamylphosphate reductase argC ‐1.6799085 ‐1.9183506 ‐1.8451334 0.13672332 ‐0.16850032 ‐0.14625329 ‐1.81446 0.28431 STM4122 acetylglutamate kinase argB ‐1.2066184 ‐1.330715 ‐1.3596027 ‐0.1591417 0.27497667 ‐0.016878612 ‐1.29898 0.406414 STM4123 argininosuccinate lyase argH ‐1.35849 ‐1.4856558 ‐1.4299273 0.6250283 0.31935942 ‐0.008788543 ‐1.42469 0.372499 STM4147 preprotein translocase IISP family, membrane subunit secE 0.37733194 0.25517297 0.2670554 0.31977314 0.64295644 0.6141499 0.299853 1.231019 STM4151 50S ribosomal subunit protein L10 rplJ ‐0.32769844 ‐0.29879412 ‐0.45284906 ‐0.09704229 0.088375315 0.08313876 ‐0.35978 0.779283 STM4152 50S ribosomal subunit protein L7/L12 rplL ‐0.27338395 ‐0.21300955 ‐0.3425917 0.62130743 0.52880853 0.45028988 ‐0.27633 0.82569 STM4159 deoxyxylulose‐5‐P thi‐S‐COSH tyrosine thiH 0.49387768 0.4242009 0.39095336 0.3482004 0.4624054 0.44730914 0.436344 1.353171 STM4160 deoxyxylulose‐5‐P thi‐S‐COSH tyrosine thiG 0.5696071 0.6524479 0.5532246 0.43022105 0.564055 0.51288176 0.59176 1.507084 STM4161 putative involved in thiamine biosynthesis 0.74364185 0.74524623 0.5477212 1.0572369 0.97125435 0.83276814 0.67887 1.600885 STM4162 catalyzes the adenylation of thisS as part thiF 0.42741707 0.5229101 0.4220712 0.7624599 0.87814826 0.69689643 0.457466 1.373128 STM4163 thiamin phosphate synthase (thiamine phosphate pyrophosphorylase) thiE 0.4782781 0.52834356 0.46170875 0.98228496 1.009627 0.9916104 0.489443 1.403903 STM4170 DNA‐binding protein HU‐alpha (HU‐2) hupA 0.6041425 0.6515002 0.70391434 0.29124603 0.097995125 0.20224686 0.653186 1.572637 STM4181 putative acetyltransferase yjaB 0.41277462 0.27361307 0.4795135 0.045616366 ‐0.2692408 ‐0.17483352 0.388634 1.309153 STM4182 homoserine transsuccinylase metA 0.83211875 0.9562479 0.87414855 ‐0.3689904 ‐0.77333647 ‐0.9920574 0.887505 1.849974 STM4190 (alpha)‐aspartyl dipeptidase pepE ‐0.19743058 ‐0.3404635 ‐0.32733977 ‐0.68625724 ‐0.47755364 ‐0.43082675 ‐0.28841 0.818803 STM4201 putative phage tail protein ‐0.22076447 ‐0.44376224 ‐0.37578574 ‐0.041930385 ‐0.31664777 ‐0.19647604 ‐0.34677 0.786342 STM4220 aspartokinase III, lysine sensitive lysC ‐1.1065358 ‐1.0743078 ‐0.7839398 ‐0.067584634 ‐0.18820454 ‐0.12233027 ‐0.98826 0.504085 STM4222 putative outer membrane protein yjbE ‐2.0814438 ‐2.1460955 ‐2.0887516 ‐2.8885083 ‐2.8630266 ‐2.601704 ‐2.10543 0.232382 STM4226 putative inner membrane protein yjbA ‐0.3906223 ‐0.23616368 ‐0.29530108 ‐0.42360932 ‐0.43033835 ‐0.6432603 ‐0.30736 0.808118 STM4237 SOS response regulator, transcriptional repressor (LexA family) lexA 0.4908214 0.36775026 0.3812299 0.89199054 0.7649744 0.68065786 0.413267 1.331698 STM4248 tyrosine aminotransferase, tyrosine repressible tyrB 0.48781145 0.43012685 0.6478722 ‐0.06561804 ‐0.10670616 ‐0.05398615 0.521937 1.435882 STM4256 ssDNA‐binding protein controls activity of RecBCD nuclease ssb 0.5871153 0.5578599 0.6316421 0.87687755 0.63089496 0.65885246 0.592206 1.50755 STM4263 putative inner membrane protein yjcB 0.1971912 0.3038759 0.34870505 0.089991726 0.028018676 0.008216077 0.283257 1.216939 STM4270 putative transcriptional regulator, LysR family ‐0.30131537 ‐0.3492216 ‐0.20983638 ‐0.36365175 ‐0.4410995 ‐0.3154152 ‐0.28679 0.819723 STM4271 putative inner membrane protein ‐0.42716506 ‐0.3473108 ‐0.47306418 ‐0.62511533 ‐0.61022663 ‐0.7487976 ‐0.41585 0.749579 STM4274 putative inner membrane protein yjcH ‐0.3073611 ‐0.35714027 ‐0.34812275 ‐0.4655083 ‐0.2816491 ‐0.21799472 ‐0.33754 0.791389 STM4282 part of formate‐dependent nitrite reductase complex involved nrfG ‐0.3483499 ‐0.38001975 ‐0.5585485 0.75978756 0.52543026 0.35321736 ‐0.42897 0.742791 STM4331 putative outer membrane lipoprotein yjeI 0.28103364 0.37520134 0.2916052 0.09004359 0.042432725 ‐0.09096117 0.315947 1.244828 149 STM4333 putative aminomutase yjeK 0.34275535 0.3663677 0.2541502 0.19885266 0.31783143 0.28968376 0.321091 1.249275 STM4336 putative entericidin B precursor ecnB 0.4911552 0.6025157 0.8024351 ‐0.2815821 ‐0.3991241 ‐0.51115614 0.632035 1.54975 STM4343 fumarate reductase, anaerobic, flavoprotein subunit frdA ‐0.43022296 ‐0.47210342 ‐0.6185513 ‐0.21412861 ‐0.26285717 ‐0.34201923 ‐0.50696 0.703704 STM4351 putative arginine‐binding periplasmic protein 0.26687232 0.34219256 0.2355721 0.68633914 0.41939098 0.22016367 0.281546 1.215496 STM4356 putative sugar kinase yjeF ‐0.26104313 ‐0.4351466 ‐0.538389 0.7492662 0.9724459 1.2659442 ‐0.41153 0.751828 STM4362 putative GTP‐ase, together with HflCK possibly involved hflX 0.7876796 0.86858255 0.6201337 1.1325591 0.79570717 0.7112566 0.758799 1.692081 STM4363 with HflC, part of modulator for protease hflK 0.8000094 0.7273756 0.7477214 0.5571832 0.5122535 0.6720588 0.758369 1.691577 STM4374 putative inner membrane protein yjfL ‐0.4443888 ‐0.4237964 ‐0.2376784 ‐0.652044 ‐0.0996806 ‐0.4925044 ‐0.36862 0.774522 STM4375 putative inner membrane protein yjfM ‐0.27731678 ‐0.36688748 ‐0.25895834 ‐0.17989731 ‐0.46148422 ‐0.40780795 ‐0.30105 0.811659 STM4409 putative outer membrane protein ytfM 0.27382404 0.24136394 0.2284955 0.13155776 0.21557996 0.25771213 0.247894 1.187473 STM4414 inorganic pyrophosphatase ppa 0.45368612 0.5373738 0.53940153 0.3797464 ‐0.3178469 0.38645786 0.510154 1.424202 STM4419 sugar (and other) transporter 0.46449316 0.41518277 0.4278109 0.22889353 0.2702437 0.31595305 0.435829 1.352688 STM4446 putative selenocysteine synthase [L‐seryl‐tRNA(Ser) selenium transferase ‐0.42905918 ‐0.6164485 ‐0.60982305 0.66548145 0.8008127 0.578856 ‐0.55178 0.682179 STM4469 ornithine carbamoyltransferase 1 argI ‐1.3485008 ‐1.5603379 ‐1.2840261 ‐0.16654044 ‐0.58588463 ‐0.5805293 ‐1.39762 0.379554 STM4473 putative acetyltransferase yjgM 0.28985777 0.4287503 0.37574795 0.35791102 0.51642 0.2898662 0.364785 1.28769 STM4486 putative alcohol dehydrogenase yjgB 0.5597197 0.5544405 0.44027153 0.009001294 ‐0.2096884 ‐0.47505113 0.518144 1.432112 STM4490 putative Mrr restriction endonuclease 0.3887054 0.24690713 0.34024322 1.0261223 0.5276918 0.43209174 0.325285 1.252912 STM4492 putative cytoplasmic protein 0.5707446 0.7728898 0.60287035 1.3183347 1.072003 0.84367573 0.648835 1.567901 STM4498 putative inner membrane protein 0.38002673 0.44331577 0.40515405 0.48088077 0.47889808 0.20146409 0.409499 1.328224 STM4511 putative transcriptional regulator, LysR family yjiE ‐0.29897767 ‐0.650452 ‐0.55105835 ‐0.23040657 ‐0.4647893 ‐0.06686011 ‐0.50016 0.707027 STM4514 putative inner membrane protein yjiH ‐0.4175689 ‐0.52337974 ‐0.5656572 ‐0.031217387 ‐0.057554044 ‐0.2564576 ‐0.5022 0.706028 STM4549 putative cytoplasmic protein 0.54050124 0.567556 0.5888282 0.24952032 ‐0.31520516 ‐0.02025315 0.565628 1.480032 STM4550 ferric hydrozamate transport, involved in reduction of fhuF 0.77914 0.80690694 0.757924 0.18168716 0.1969045 0.1514706 0.781324 1.718707 STM4552 putative inner membrane protein 1.443204 1.5985178 1.8143021 0.11738137 ‐0.31504673 ‐0.18409345 1.618675 3.070928 STM4594 putative fimbrial chaparone protein sthA 0.3393081 0.6615488 0.5412092 ‐0.20185731 ‐0.2049984 ‐0.3331284 0.514022 1.428026 STM4598 response regulator (OmpR family) in two‐component regulatory arcA 0.26712856 0.25683007 0.21130179 ‐0.022407375 ‐0.14870913 ‐0.23917845 0.245087 1.185164 STY0070 citrate lyase alpha chain citF2 ‐0.18545978 ‐0.42093408 ‐0.50465536 ‐0.5581128 ‐0.5847175 ‐0.53381014 ‐0.37035 0.773595 STY0402 PrpD protein prpD ‐0.49298972 ‐0.5892416 ‐0.48051035 0.985427 0.4965236 0.6967143 ‐0.52091 0.69693 STY0439 maltodextrin glucosidase malZ ‐0.26598063 ‐0.5112237 ‐0.4539998 0.6373062 0.10209008 0.34853366 ‐0.4104 0.752414 STY0586 putative membrane protein ybcI ‐0.39932278 ‐0.33200687 ‐0.3538852 ‐0.42742905 ‐0.47057682 ‐0.4057785 ‐0.36174 0.778226 STY0936 putative virK protein ybjX 0.8266219 1.0932217 0.9094505 0.14976603 ‐0.38822445 ‐0.7432075 0.943098 1.922652 STY0963 anaerobic dimethyl sulfoxide reductase chain B dmsB ‐0.45513213 ‐0.3605968 ‐0.49858785 ‐0.8189377 ‐0.69091284 ‐0.9507103 ‐0.43811 0.738103 STY1472 putative virulence effector protein srfA ‐0.29640138 ‐0.41446215 ‐0.4728805 0.003883983 0.025953632 ‐0.17169361 ‐0.39458 0.76071 STY1488 respiratory nitrate reductase 2 alpha chain narZ ‐0.5651388 ‐0.5857039 ‐0.35057256 ‐0.50144684 ‐0.51809454 ‐0.43401277 ‐0.50047 0.706876 STY1505 putative glycogen debranching protein glgX ‐0.31610373 ‐0.41061938 ‐0.40923125 ‐0.92813474 ‐1.0527322 ‐0.9623939 ‐0.37865 0.769156 STY1567 putative dimethyl sulphoxide reductase subunit dmsB ‐0.21789041 ‐0.28208828 ‐0.34394017 ‐0.3544724 ‐0.47628576 ‐0.63092494 ‐0.28131 0.822846 STY2099 high‐affinity zinc uptake system periplasmic binding protein yebL 1.6600322 1.9473672 1.7970768 ‐3.3868663 ‐3.5019495 ‐3.6352866 1.801492 3.485805 STY2115 putative copper homeostasis protein cutC ‐0.83848965 ‐0.75747293 ‐0.65187526 ‐0.46578476 ‐0.5861411 ‐0.32073995 ‐0.74928 0.594901 STY2258 putative ferredoxin pduS ‐0.36159647 ‐0.36156255 ‐0.74739695 0.2783675 0.034208395 ‐0.27177742 ‐0.49019 0.711934 STY2261 putative propanediol utilization protein PduV pduV ‐0.33628783 ‐0.35360885 ‐0.6888912 ‐0.5082773 ‐0.4873949 ‐0.38296574 ‐0.4596 0.72719 STY2303 putative reductase RfbI rfbI 0.6925853 1.1637181 0.61202896 2.163033 1.9231256 1.4972976 0.822777 1.768808 STY2345 hypothetical protein ‐0.37001657 ‐0.31735414 ‐0.22864625 ‐0.22236492 ‐0.073161565 ‐0.027449075 ‐0.30534 0.809252 STY2703 putative cobalamin adenosyltransferase ‐0.38120845 ‐0.6780023 ‐0.5178964 0.5951261 0.49704218 0.5939658 ‐0.5257 0.694621 STY2717 putative oxidoreductase aegA ‐0.4300859 ‐0.67344296 ‐0.6773814 ‐0.17396946 ‐0.3890439 ‐0.42055735 ‐0.59364 0.66267 STY2751 GMP synthase (glutamine‐hydrolyzing) guaA 0.67157376 0.55280757 0.42809445 0.23781666 0.1643857 0.07279256 0.550825 1.464923 STY2867 hypothetical protein 0.19530237 0.37931833 0.29865903 0.6023217 0.53004766 0.28801653 0.291093 1.223567 STY2893 putative exported protein iroE 0.93417346 0.86765563 0.87125075 0.83267385 0.7676555 0.7568699 0.891027 1.854495 STY2894 TonB‐dependent outer membrane siderophore receptor protein iroN 1.2964964 1.9452901 1.7477167 0.34931105 0.36523324 0.3093109 1.663168 3.167112 STY2897 conserved hypothetical protein ‐1.4992087 ‐1.4673667 ‐1.5548842 ‐1.1871341 ‐1.3526785 ‐1.3884839 ‐1.50715 0.351805 STY3403 possible oxidoreductase 0.22387105 0.2886808 0.42742115 ‐0.32889977 ‐0.21418169 ‐0.1868183 0.313324 1.242568 STY3470 argininosuccinate synthetase argG ‐0.8413535 ‐0.9153108 ‐0.9074922 0.007016142 ‐0.10949153 ‐0.014826099 ‐0.88805 0.540343 STY3653 dihydroxyacid dehydratase ilvD 0.40515068 0.26249734 0.2621436 1.4708517 0.88730145 0.8937096 0.309931 1.239648 STY3724 thiamine biosynthesis protein thiS 0.34690958 0.4336048 0.3258385 1.424583 0.9494153 0.7918123 0.368784 1.291264 STY3725 thiamine biosynthesis protein thiG 0.6056575 0.7192756 0.60881543 0.69907445 0.65668464 0.52331895 0.644583 1.563287 STY4091 2,3‐bisphosphoglycerate‐independent phosphoglycerate mutase ‐1.0078194 ‐1.3371959 ‐1.3815194 0.02113587 ‐0.10393594 ‐0.092662506 ‐1.24218 0.422734 STY4175 hypothetical protein ‐0.70266485 ‐0.7875038 ‐0.7313358 ‐0.36298174 ‐0.58551556 ‐0.66896117 ‐0.7405 0.598531 STY4259 hypothetical protein 0.39459327 0.43763816 0.31719965 ‐0.15451665 ‐0.3308565 ‐0.3029147 0.383144 1.304181 STY4260 gamma‐glutamyltranspeptidase precursor ggt 0.68399864 0.5683288 0.5021433 ‐0.154856 0.14545798 ‐0.07953447 0.584824 1.499856 STY4754 D‐serine/D‐alanine/glycine transporter cycA 0.26940024 0.34920967 0.22701757 0.55573344 0.3729122 0.14492114 0.281876 1.215775 STY4846 putative outer membrane protein 0.33641014 0.40311894 0.23571685 ‐0.53900665 ‐0.9099165 ‐1.2299426 0.325082 1.252736 150
APPENDIX F
SIGNIFICANT LT2 GENES DATA FOR CHAPTER 4 151 All Significant Salmonella LT2 Genes (Delta=0.77666634, False Sig Genes=0, FDR=0%) Expected Log Ratio Observed Numerato Denomina q‐value Locus GeneN GeneS 107808 107809 107810 107811 107812 107813 2 Ratio score Means score(d) r(r) tor (s+s0) (%) (dExp) Obsolete Obsolete ‐0.024515491 0.109967075 ‐0.035030454 ‐0.3178753 ‐0.5590353 ‐0.47630873 ‐0.45107 0.731499 ‐0.60076 ‐1.38154 ‐0.45107 0.326501 0 PSLT002 putative phospholipase D ‐0.56913185 0.18585254 0.17598073 ‐0.7012004 ‐0.8732664 ‐0.84985125 ‐0.80811 0.571131 0.061582 ‐2.60992 ‐0.80811 0.309628 0 PSLT004 DNA replication repA3 0.26097435 ‐0.015408918 0.30341008 ‐0.44108105 ‐0.49048424 ‐0.44274163 ‐0.4581 0.727943 0.9208 ‐1.68452 ‐0.4581 0.271948 0 PSLT005 replication of plasmid tap 0.14039512 0.14760229 0.1447253 ‐0.46645153 ‐0.67465156 ‐0.728913 ‐0.62334 0.649167 ‐0.29929 ‐1.8566 ‐0.62334 0.335742 0 PSLT008 sdiA‐regulated geneputative bacterial regulatory helix‐turn‐helix proteins, araC srgC ‐0.08653011 ‐0.031123893 ‐0.07799622 ‐0.86112 ‐0.8363603 ‐1.0207927 ‐0.90609 0.533629 0.128603 ‐2.88984 ‐0.90609 0.313544 0 PSLT011 sdiA‐regulated gene putative thiol‐disulfide isomerase or thioredoxin srgA 0.017582217 0.062044326 0.06855492 ‐1.0260054 ‐1.2005081 ‐1.4041059 ‐1.21021 0.432207 ‐0.85605 ‐3.31558 ‐1.21021 0.365006 0 PSLT012 putative bacterial regulatory proteins, luxR family orf7 ‐0.21873495 ‐0.33098617 ‐0.23817043 ‐1.0850646 ‐1.0817932 ‐0.86064273 ‐1.00917 0.496833 0.870234 ‐3.05792 ‐1.00917 0.330018 0 PSLT015 putative outer membrane protein orf5 0.32027528 0.19406171 0.12695019 ‐0.63325745 ‐0.8036808 ‐0.58809394 ‐0.67501 0.626328 0.713429 ‐2.10027 ‐0.67501 0.321392 0 PSLT016 plasmid‐encoded fimbriaechaperone pefD 0.06589713 0.22573361 0.07201219 ‐0.3770909 ‐0.35168564 ‐0.4151503 ‐0.38131 0.767741 0.481909 ‐1.39067 ‐0.38131 0.274191 0 PSLT018 plasmid‐encoded fimbriae major fimbrial subunit pefA 0.20367016 0.11760886 0.2659146 ‐0.5968133 ‐0.7367811 ‐0.6808149 ‐0.67147 0.627867 0.118159 ‐2.26523 ‐0.67147 0.296424 0 PSLT020 hypothetical protein 0.19118033 0.6662266 0.58284324 ‐0.63963336 ‐0.8767592 ‐0.9003971 ‐0.8056 0.572125 0.398341 ‐2.37631 ‐0.8056 0.339011 0 PSLT023 DNA replication repA2 0.59046596 0.46488547 0.41520572 ‐0.6756516 ‐1.2608273 ‐1.1219376 ‐1.01947 0.493297 0.069159 ‐2.3584 ‐1.01947 0.432273 0 PSLT026 putative periplasmic protein ‐0.14326921 0.004133523 0.085149705 ‐0.8314 ‐0.65585476 ‐0.698623 ‐0.72863 0.603478 0.865692 ‐2.36108 ‐0.72863 0.308599 0 PSLT027 toxin addiction system: antidote ccdA 0.17466165 0.33300367 0.46012414 ‐0.55316913 ‐0.6941175 ‐0.3980606 ‐0.54845 0.683755 ‐1.45763 ‐1.60719 ‐0.54845 0.341246 0 PSLT036 putative transposase, IS200‐like 0.42819518 0.41039482 0.60164636 0.6962467 0.65043 0.6241986 0.656958 1.576755 0.863839 2.373382 0.656958 0.276803 0 PSLT042 putative integrase protein 0.5352007 0.51944155 0.46636653 ‐0.586795 ‐0.5008615 ‐0.35955667 ‐0.4824 0.715784 1.232557 ‐1.49818 ‐0.4824 0.321994 0 PSLT043 putative phosphoribulokinase / uridine kinase family 0.52404296 0.5330904 0.5033524 ‐1.4889245 ‐1.3363144 ‐1.6471025 ‐1.49078 0.35582 ‐0.07928 ‐4.31521 ‐1.49078 0.345471 0 PSLT044 putative integrase protein rlgA 0.6716581 0.61639065 0.610975 ‐0.4208412 ‐0.91123503 ‐1.1832428 ‐0.83844 0.559248 ‐0.414 ‐1.75103 ‐0.83844 0.478825 0 PSLT045 putative resolvase rlgA 0.14444664 0.24948385 0.20626752 ‐1.2752275 ‐1.2566822 ‐1.4972923 ‐1.34307 0.394182 0.701186 ‐4.03266 ‐1.34307 0.333048 0 PSLT046 putative carbonic anhydrase 0.29661897 0.5118478 0.47765243 ‐0.7575558 ‐0.6575734 ‐0.68897706 ‐0.70137 0.614988 0.5544 ‐2.45862 ‐0.70137 0.28527 0 PSLT048 alpha‐helical coiled coil protein tlpA 0.06846177 0.046543863 ‐0.005062324 ‐0.3740288 ‐0.6530334 ‐0.84832406 ‐0.62513 0.648362 ‐0.26489 ‐1.58914 ‐0.62513 0.393376 0 PSLT049 putative DNA polymerase III epsilon subunit (3‐5 ‐0.19189966 ‐0.15671502 ‐0.087829895 ‐1.0907441 ‐0.93230665 ‐0.8935997 ‐0.97222 0.509722 0.591169 ‐3.07608 ‐0.97222 0.316057 0 PSLT050 putative cytoplasmic protein ‐0.012879659 ‐0.09964181 ‐0.12937424 ‐1.0865803 ‐1.2578626 ‐1.0860307 ‐1.14349 0.452663 1.600897 ‐3.65408 ‐1.14349 0.312936 0 PSLT051 putative cytoplasmic protein samB 0.111188374 0.030347038 0.10145542 ‐1.1690465 ‐1.3365123 ‐1.1462287 ‐1.21726 0.430098 ‐1.05141 ‐3.8553 ‐1.21726 0.315737 0 PSLT052 plasmid partition protein A parA 0.37233824 0.5566913 0.31634837 ‐0.34044805 ‐0.45474067 ‐0.6530225 ‐0.48274 0.715619 0.313744 ‐1.39093 ‐0.48274 0.347061 0 PSLT055 mutagenesis by UV and mutagens related to samA 0.03915568 0.08042525 0.17513727 ‐0.44043934 ‐0.4705424 ‐0.61812747 ‐0.5097 0.702367 ‐0.94071 ‐1.64074 ‐0.5097 0.310654 0 PSLT068 putative ParB‐like nuclease domain 0.096520856 ‐0.21454842 ‐0.27145207 ‐0.37463763 ‐0.6261268 ‐0.47696564 ‐0.49258 0.710755 0.989512 ‐1.49826 ‐0.49258 0.328767 0 PSLT072 putative transglycosylase finP 0.27459073 0.60735095 0.4902862 ‐1.0760994 ‐1.0165291 ‐0.96350557 ‐1.01871 0.493557 0.428741 ‐3.53387 ‐1.01871 0.288271 0 PSLT077 conjugative transfer: fimbrial subunit traA 0.17014757 0.25809515 0.22106652 ‐0.7422059 ‐0.54335165 ‐0.5648818 ‐0.61681 0.65211 0.301009 ‐1.93508 ‐0.61681 0.318753 0 PSLT079 conjugative transfer: assembly traE ‐0.1526614 ‐0.028852222 0.03563294 ‐0.55611783 ‐0.57119286 ‐0.70043534 ‐0.60925 0.655538 0.736635 ‐2.02039 ‐0.60925 0.30155 0 PSLT080 conjugative transfer: assembly traK ‐0.19855331 ‐0.4436235 ‐0.31377703 ‐0.8411851 ‐0.59166986 ‐0.5302125 ‐0.65436 0.635359 1.234405 ‐1.86514 ‐0.65436 0.350834 0 PSLT083 conjugative transfer: trbD ‐0.31278655 ‐0.16835885 ‐0.2461052 ‐0.7080694 ‐0.7858825 ‐0.6939375 ‐0.7293 0.603198 0.470677 ‐2.56492 ‐0.7293 0.284335 0 PSLT085 conjugative transfer traR ‐0.14846921 ‐0.06893303 ‐0.114045255 ‐1.0022832 ‐1.0243008 ‐1.3184862 ‐1.11502 0.461684 ‐0.28705 ‐3.11738 ‐1.11502 0.357679 0 PSLT091 conjugative transfer: assembly traW ‐0.049170665 ‐0.1998216 ‐0.16829999 ‐0.61945295 ‐0.95396143 ‐1.08258 ‐0.88533 0.541363 ‐0.35589 ‐2.24831 ‐0.88533 0.393776 0 PSLT092 conjugative transfer: assembly traU 0.15605529 0.03967613 ‐0.00748688 ‐0.77961516 ‐1.084095 ‐0.97996753 ‐0.94789 0.518389 0.038165 ‐2.74675 ‐0.94789 0.345096 0 PSLT093 conjugative transfer: 0.008135702 0.25818804 0.08862781 ‐0.38843426 ‐0.7221319 ‐0.8119023 ‐0.64082 0.641347 0.351722 ‐1.6663 ‐0.64082 0.384577 0 PSLT095 conjugative transfer: aggregate stability traN 0.5083317 0.49951515 0.3619898 ‐0.28462604 ‐0.80491954 ‐0.71326345 ‐0.60094 0.659326 0.12158 ‐1.4442 ‐0.60094 0.416103 0 PSLT096 conjugative transfer trbE 0.30819207 0.4279481 0.3715972 ‐0.77392405 ‐0.7402496 ‐0.84005123 ‐0.78474 0.580456 0.044502 ‐2.75287 ‐0.78474 0.285063 0 PSLT097 conjugative transfer: assembly traF 0.23419821 0.49506816 0.4314934 ‐0.93360496 ‐1.044014 ‐1.21234 ‐1.06332 0.47853 ‐0.61534 ‐3.15721 ‐1.06332 0.33679 0 PSLT098 conjugative transfer: fimbrial synthesis traQ 0.2876653 0.32006288 0.1999281 ‐0.93247354 ‐0.75738686 ‐0.967667 ‐0.88584 0.541171 0.056153 ‐2.76156 ‐0.88584 0.320776 0 PSLT099 conjugative transfer trbB 0.34536356 0.40143034 0.122797824 ‐0.9666945 ‐1.2760592 ‐1.2982337 ‐1.18033 0.441251 0.29929 ‐3.25376 ‐1.18033 0.362759 0 PSLT100 conjugative transfer: assembly traH 0.18574595 0.40696064 0.2385979 ‐0.9970439 ‐1.0738035 ‐0.97136444 ‐1.01407 0.495147 0.340537 ‐3.53924 ‐1.01407 0.286522 0 PSLT103 conjugative transfer: surface exclusion traT 0.5539146 0.47054815 0.43895933 ‐1.1038934 ‐1.4469562 ‐1.0903301 ‐1.21373 0.431153 ‐0.04703 ‐3.25894 ‐1.21373 0.37243 0 PSLT107 putative cytoplasmic protein 0.096651144 0.16220076 0.11592378 ‐0.5798514 ‐0.61901164 ‐0.9647307 ‐0.7212 0.606594 ‐0.43169 ‐1.90773 ‐0.7212 0.37804 0 STM0004 threonine synthase thrC ‐0.314873 ‐0.36514962 ‐0.41357788 0.83274347 0.43817458 0.35283428 0.541251 1.455234 ‐0.2902 1.341179 0.541251 0.403563 0 STM0009 putative regulator yaaH ‐0.11071756 0.012572029 ‐0.17039281 0.8916415 0.87591946 0.67216027 0.81324 1.757154 ‐0.50458 2.491274 0.81324 0.326436 0 STM0012 chaperone Hsp70 in DNA biosynthesis/cell division dnaK ‐0.5170135 ‐0.66296506 ‐0.6681755 0.80367666 0.7522421 0.704346 0.753422 1.685786 ‐0.29209 2.648883 0.753422 0.28443 0 STM0013 heat shock protein, DnaJ and GrpE stimulates dnaJ 0.052890055 ‐0.05017231 ‐0.03275316 0.8971304 0.9123665 1.0958174 0.968438 1.956721 0.439491 3.030242 0.968438 0.319591 0 STM0018 putative exochitinase 0.27360895 0.08875282 0.15926483 ‐0.46230847 ‐0.7128606 ‐0.46364868 ‐0.54627 0.684787 0.23731 ‐1.61121 ‐0.54627 0.339045 0 STM0019 putative hydroxymethyltransferase 0.07337441 0.035043046 ‐0.020479208 ‐0.44477814 ‐0.58665085 ‐0.58377564 ‐0.5384 0.688533 ‐0.22329 ‐1.77944 ‐0.5384 0.302569 0 STM0024 fimbrial subunit bcfD ‐0.10704203 ‐0.3587687 ‐0.41533518 ‐0.41096395 ‐0.58373487 ‐0.53525835 ‐0.50999 0.702229 0.086029 ‐1.66011 ‐0.50999 0.3072 0 STM0027 fimbrial chaparone bcfG ‐0.5230399 ‐0.91175896 ‐0.9254414 ‐0.572756 ‐0.83642125 ‐0.8608931 ‐0.75669 0.591853 0.494818 ‐2.17447 ‐0.75669 0.347988 0 STM0028 putative thiol‐disulfide isomerase bcfH ‐0.08871317 ‐0.03893658 ‐0.09210748 ‐0.37815225 ‐0.45147872 ‐0.56505764 ‐0.4649 0.724523 0.074434 ‐1.49908 ‐0.4649 0.31012 0 STM0043 30S ribosomal subunit protein S20 rpsT ‐0.20089658 ‐0.2661108 ‐0.098945215 0.4716167 0.41125882 0.47513437 0.45267 1.368571 0.365644 1.637261 0.45267 0.27648 0 STM0048 FKBP‐type peptidyl‐prolyl cis‐trans isomerase (rotamase) slpA ‐0.016470363 0.008465212 ‐0.015216936 0.40721318 0.41153362 0.33195403 0.383567 1.304563 0.743661 1.362165 0.383567 0.281586 0 STM0049 regulates the activity of guanosine 3,5‐bispyrophosphate synthetase lytB ‐0.10075465 0.05489772 0.009544011 0.55788106 0.8107692 0.8278819 0.732177 1.661144 0.337449 2.134394 0.732177 0.343038 0 STM0064 dihydrodipicolinate reductase dapB ‐1.4498417 ‐1.5317243 ‐1.5456456 2.4256654 1.7328606 1.6991214 1.952549 3.870578 ‐0.06001 3.964501 1.952549 0.492508 0 STM0066 carbamoyl‐phosphate synthetase, glutamine‐hydrolysing small subunit carA ‐1.1434257 ‐1.2538745 ‐1.1086514 0.87991774 0.5956529 0.71649796 0.73069 1.659432 0.593543 2.161062 0.73069 0.338116 0 STM0067 carbamoyl‐phosphate synthase, large subunit carB ‐1.053431 ‐1.2448778 ‐1.2725413 0.88545954 0.89565265 1.0044138 0.928509 1.903307 0.095578 3.16017 0.928509 0.293816 0 STM0089 putative cytoplasmic protein apaG ‐0.03341754 ‐0.37726894 ‐0.17708895 0.7085653 0.86141175 0.7316711 0.767216 1.701982 1.071704 2.529416 0.767216 0.303317 0 STM0090 S‐adenosylmethionine‐6‐N,N‐adenosyl (rRNA) dimethyltransferase kasugamycin resistance ksgA ‐8.57E‐04 0.07971882 0.02302706 1.2748251 1.3571906 1.1179612 1.249992 2.378402 0.275075 3.835314 1.249992 0.325917 0 STM0091 NAD‐dependent dehydrogenase/carboxylase pyridoxine phosphate biosynthetic protein PdxJpdxA 0.112623245 0.25723776 0.29398572 1.7484965 1.782081 1.7441692 1.758249 3.382873 0.708205 6.567223 1.758249 0.267731 0 STM0092 peptidyl‐prolyl cis‐trans isomerase, survival protein surA 0.3767992 0.28144532 0.26570287 1.0206679 1.0740172 1.1923009 1.095662 2.137111 0.33358 3.575174 1.095662 0.306464 0 STM0093 Organic solvent tolerance protein imp 0.2644671 0.23846218 0.055939388 0.8907043 0.931686 0.25266615 0.691685 1.615169 ‐1.21286 1.454411 0.691685 0.475578 0 STM0094 DnaJ like chaperone protein djlA 0.19831209 ‐0.02423773 0.09690074 0.7086819 0.44692767 0.7739203 0.643177 1.561764 0.495699 1.808378 0.643177 0.355665 0 STM0107 putative binding‐protein‐dependent transport system inner membrane component yabK ‐0.2140608 ‐0.11707239 ‐0.23706743 1.1448509 1.1841683 1.0670031 1.132007 2.191635 0.077786 3.901099 1.132008 0.290177 0 STM0108 thiamine‐binding periplasmic protein tbpA 0.23577571 0.33463296 0.26570046 1.0293115 1.1995857 1.1235733 1.11749 2.169692 ‐0.12609 3.663932 1.11749 0.304998 0 STM0110 3‐isopropylmalate isomerase (dehydratase), subunit with LeuC leuD 1.5279573 1.7166674 1.583018 1.4300208 1.5770993 1.3194692 1.442196 2.717343 0.162481 4.365401 1.442197 0.33037 0 STM0113 2‐isopropylmalate synthase leuA 2.0958962 2.0898426 2.145787 1.6987354 1.1851902 1.4400281 1.441318 2.715688 0.709606 3.56763 1.441318 0.403999 0 STM0116 acetolactate synthase III, valine sensitive, large subunit ilvI 0.26020688 0.4106647 0.2518642 0.93679035 0.98173016 0.5206042 0.813042 1.756912 ‐0.50555 2.019765 0.813042 0.402543 0 STM0120 putative S‐adenosyl methionine adenyltransferase yabC ‐0.22600807 ‐0.22315557 ‐0.22407691 1.1794915 0.9645097 0.99701464 1.047005 2.066236 0.876007 3.244978 1.047005 0.322654 0 STM0125 phospho‐N‐acetylmuramoyl‐pentapeptide transferase mraY ‐0.17006904 0.09187374 ‐0.19211438 1.0492826 0.841995 0.7592049 0.883494 1.844838 ‐0.16342 2.583163 0.883494 0.34202 0 STM0127 essential cell division gene, stablilzes FtsZ ring ftsW ‐0.12006317 ‐0.011474098 ‐0.18126376 1.7430907 1.3378145 0.9643548 1.34842 2.546331 ‐0.45196 2.80562 1.34842 0.480614 0 STM0129 L‐alanine adding enzyme, UDP‐N‐acetyl‐muramate:alanine ligase murC ‐0.20283265 ‐0.047314465 ‐0.027416121 0.7847641 0.788876 0.71410125 0.76258 1.696522 ‐1.14584 2.723324 0.76258 0.280018 0 STM0131 cell division protein ingrowth of wall at ftsQ ‐0.19884682 ‐0.14612615 ‐0.076396585 1.0218602 1.2807578 0.9755648 1.092728 2.132769 ‐0.08476 3.11576 1.092728 0.35071 0 STM0132 ATP‐binding cell division protein, septation process, complexes ftsA ‐0.098191515 ‐0.155406 ‐0.25006297 0.62190914 0.77353925 0.7106285 0.702026 1.626787 0.330477 2.342176 0.702026 0.299732 0 STM0136 preprotein translocase secretion protein of IISP family secA 0.16311926 ‐0.06436498 0.14492969 0.8546085 1.0449086 1.0284092 0.975975 1.966971 1.880968 3.082485 0.975975 0.31662 0 STM0152 pyruvate dehydrogenase, decarboxylase component aceE 0.7129928 ‐4.26E‐05 0.5556925 1.3482674 1.0821278 1.1139914 1.181462 2.268065 0.632487 3.478389 1.181462 0.339658 0 STM0153 pyruvate dehydrogenase, dihydrolipoyltransacetylase component aceF 0.43818256 0.34659097 0.21256778 1.0322548 0.9680674 0.9234585 0.974594 1.965088 ‐0.19833 3.39195 0.974594 0.287325 0 STM0157 putative outer membrane protein yacH ‐0.40804002 ‐0.4874071 ‐0.43260288 0.45829695 0.5423217 0.6327726 0.544464 1.458478 0.729416 1.778551 0.544464 0.306128 0 STM0158 aconitate hydratase 2 acnB ‐0.14649121 ‐0.08231762 ‐0.19665106 1.3556936 1.6505774 1.4447147 1.483662 2.796577 0.448135 4.324608 1.483662 0.343074 0 STM0166 spermidine synthase (putrescine aminopropyltransferase) speE 0.119811065 0.05181466 0.19224705 0.45519966 0.32902807 0.36136717 0.381865 1.303025 ‐1.01347 1.300689 0.381865 0.293587 0 STM0168 putative multicopper oxidase cueO ‐0.25086978 ‐0.14035764 ‐0.31378183 ‐1.0482265 ‐0.7835071 ‐0.74054164 ‐0.85743 0.551937 0.378644 ‐2.43619 ‐0.85743 0.351953 0 STM0171 putative carbonic anhydrase yadF 1.1643332 1.417171 1.3067999 0.97402143 1.0766861 0.98444915 1.011719 2.016312 0.377207 3.508376 1.011719 0.288372 0 STM0173 putative ABC superfamily (membrane) transport protein yadH 0.20200182 ‐0.022789177 ‐0.038382508 ‐0.38512462 ‐0.3639681 ‐0.41794303 ‐0.38901 0.763652 ‐0.78615 ‐1.43308 ‐0.38901 0.271452 0 STM0177 putative fimbrial subunit stiA ‐0.17890756 ‐0.08671995 ‐0.04382514 ‐0.7245394 ‐0.65723234 ‐0.70912886 ‐0.69697 0.616868 ‐0.13855 ‐2.52425 ‐0.69697 0.276109 0 STM0181 pantothenate synthetase panC ‐0.43498638 ‐0.3594995 ‐0.3009579 ‐0.73306835 ‐0.5574113 ‐0.5896664 ‐0.62672 0.647649 0.35118 ‐2.02339 ‐0.62672 0.309735 0 STM0190 transpeptidase of penicillin‐binding protein 1b (peptidoglycan synthetase) mrcB 0.10777675 0.17487906 ‐0.003396956 0.8579666 0.79675347 0.616637 0.757119 1.690112 0.244168 2.307029 0.757119 0.328179 0 STM0193 ABC superfamily (bind _prot), hydroxamate‐dependent iron uptake fhuD 0.007443094 ‐0.11153896 ‐0.05192486 0.87246543 0.9673261 0.99694276 0.945578 1.92596 ‐0.23685 3.224012 0.945578 0.293292 0 STM0213 2,3,4,5‐tetrahydropyridine‐2‐carboxylate N‐succinyltransferase dapD ‐0.191328 ‐0.2754977 ‐0.08721535 1.0971526 0.8437279 1.0483469 0.996409 1.995028 ‐0.66863 2.988814 0.996409 0.333379 0 STM0216 30S ribosomal subunit protein S2 rpsB ‐0.4021984 ‐0.54393405 ‐0.7115866 0.57341975 0.29930934 0.5275517 0.46676 1.382003 0.182031 1.370746 0.46676 0.340516 0 STM0217 protein chain elongation factor EF‐Ts tsf 0.078738 0.1272982 0.060426794 1.1490176 1.0189682 0.80457145 0.990852 1.987359 ‐0.50764 2.781953 0.990852 0.356171 0 STM0219 ribosome releasing factor frr 0.2711675 0.42408898 0.5943148 1.1404701 0.8477138 1.0069747 0.998386 1.997764 0.597365 2.933237 0.998386 0.34037 0 STM0222 CDP‐diglyceride synthase cdsA 0.1391841 0.24969073 0.09907728 1.5885047 1.1740962 0.8087542 1.190452 2.282242 ‐0.47236 2.474989 1.190452 0.480993 0 STM0223 putative membrane‐associated Zn‐dependent protease yaeL 0.3049555 0.31661424 0.3075448 0.6899292 0.7168318 0.6521502 0.686304 1.609155 0.104747 2.50011 0.686304 0.274509 0 STM0224 putative outer membrane antigen yaeT 0.43271163 0.52033836 0.30236128 1.415841 1.3570592 0.9922708 1.255057 2.386766 ‐0.57737 3.232734 1.255057 0.388234 0 STM0227 (3R)‐hydroxymyristol acyl carrier protein dehydratase fabZ 0.32568344 0.23637791 0.2029817 0.6900964 0.41285872 0.50637925 0.536445 1.450394 ‐0.16902 1.590971 0.536445 0.337181 0 STM0228 UDP‐N‐acetylglucosamine acetyltransferase lpxA 0.46926323 0.32102868 0.3484745 1.0336506 0.6345175 0.7105296 0.792899 1.732553 ‐0.5921 2.097013 0.792899 0.378109 0 STM0229 tetraacyldisaccharide‐1‐P lpxB ‐0.013715944 ‐0.11588781 0.005734357 0.71775705 0.65910125 0.67716736 0.684675 1.60734 ‐0.79903 2.507112 0.684675 0.273093 0 STM0230 RNAse HII rnhB 0.05028361 ‐0.15517406 0.16715686 0.80364996 0.88572997 0.91760117 0.868994 1.826389 2.179022 2.999714 0.868994 0.289692 0 STM0236 cell cycle protein mesJ 0.013130277 ‐0.10385231 ‐0.08982612 0.60620975 0.38494682 0.5957402 0.528966 1.442894 0.097248 1.613574 0.528966 0.327822 0 STM0257 putative drug efflux protein (perhaps for chloramphenicol) ‐0.044888634 ‐0.24147615 ‐0.24537873 ‐0.43852103 ‐0.37103057 ‐0.3734191 ‐0.39432 0.760846 ‐0.14131 ‐1.41915 ‐0.39432 0.277859 0 STM0264 DNA polymerase III, epsilon subunit, 3‐5 exonucleolytic dnaQ ‐0.02997567 ‐0.1064646 0.013496813 0.5090484 0.325833 0.4978041 0.444229 1.360586 1.061023 1.410087 0.444229 0.315036 0 STM0289 putative cytoplasmic protein ‐0.15800431 ‐0.07536851 ‐0.036371242 1.4514205 1.3280559 0.8551662 1.211548 2.315859 ‐0.54133 2.769479 1.211548 0.437464 0 STM0313 DNA polymerase IV, devoid of proofreading, damage‐inducible dinP ‐0.18206458 0.16388059 0.054859973 ‐0.55591816 ‐0.44036174 ‐0.4913373 ‐0.49587 0.709133 0.377815 ‐1.71472 ‐0.49587 0.289185 0 STM0324 putative inner membrane protein ‐0.34722316 ‐0.32326004 ‐0.32992923 ‐0.52142775 ‐0.8202106 ‐0.9760636 ‐0.77257 0.585375 ‐0.54969 ‐1.98534 ‐0.77257 0.389136 0 STM0330 putative 3‐isopropylmalate isomerase (dehydratase), subunit with LeuC 0.24744545 0.20047584 0.26200908 ‐0.75975925 ‐0.97403556 ‐0.5715621 ‐0.76845 0.587047 ‐0.25634 ‐2.06565 ‐0.76845 0.372015 0 STM0337 putative fimbriae usher stbD ‐0.20143446 ‐0.26524666 ‐0.16202874 ‐0.4925068 ‐0.55290353 ‐0.39480707 ‐0.48007 0.716942 0.188743 ‐1.59065 ‐0.48007 0.30181 0 STM0355 putative Copper chaperone ‐0.26525173 ‐0.3072882 ‐0.21923548 ‐1.4730307 ‐0.7093598 ‐0.71972054 ‐0.96737 0.511437 ‐0.77298 ‐1.90204 ‐0.96737 0.508597 0 STM0362 putative cytoplasmic protein ‐0.37270135 ‐0.35836142 ‐0.21547908 ‐0.6839262 ‐0.7432704 ‐0.79809225 ‐0.74176 0.598008 ‐0.17628 ‐2.56919 ‐0.74176 0.288715 0 STM0369 putative citrate synthase prpC ‐0.60706687 ‐1.0282005 ‐0.84019566 ‐0.5843593 ‐0.7967985 ‐0.5542958 ‐0.64515 0.639426 1.714808 ‐1.94283 ‐0.64515 0.332068 0 STM0378 putative inner membrane protein yaiY ‐0.22987401 0.055511825 0.050791927 ‐0.66106755 ‐0.56807154 ‐0.5048042 ‐0.57798 0.669901 0.400907 ‐1.91937 ‐0.57798 0.30113 0 STM0383 putative cytoplasmic protein yaiB ‐1.0665052 ‐0.96745145 ‐0.86840016 ‐0.54481554 ‐0.7013361 ‐0.8197837 ‐0.68865 0.620436 ‐0.56586 ‐2.05333 ‐0.68865 0.335379 0 STM0384 induced by phosphate starvation psiF ‐0.24462359 ‐0.118161425 ‐0.03308993 ‐0.5045892 ‐0.4854659 ‐0.5983404 ‐0.52947 0.692812 ‐0.82656 ‐1.8218 ‐0.52947 0.290627 0 STM0385 putative diguanylate cyclase/phosphodiesterase domain 1 yaiC ‐1.035921 ‐1.2856466 ‐1.0972964 ‐0.5835514 ‐1.0542364 ‐0.85180116 ‐0.82986 0.562583 0.768363 ‐2.11664 ‐0.82986 0.392067 0 STM0388 shikimate kinase II aroL 0.6025709 0.70973486 0.6212581 1.2113078 0.88610744 0.6303237 0.909246 1.878064 ‐0.05615 2.145138 0.909246 0.423864 0 STM0392 putative exonuclease involved in removal of stalled rdgC 0.20761167 0.087086454 0.10785352 0.33080214 0.38405833 0.49439356 0.403085 1.322332 0.576001 1.326272 0.403085 0.303923 0 STM0399 LIVCS family, branched chain amino acid transporter brnQ 0.06495717 ‐0.026942851 0.013568372 0.47835243 0.671455 0.32832554 0.492711 1.407086 ‐0.3244 1.387675 0.492711 0.355062 0 STM0400 putative APC family, proline transporter proY ‐0.19994743 ‐0.15446708 ‐0.42936707 0.79900515 0.78537035 0.3985292 0.660968 1.581143 0.05056 1.707804 0.660968 0.387028 0 STM0402 putative thiol ‐ alkyl hydroperoxide reductase ‐0.26266083 ‐0.2559368 ‐0.21505938 ‐0.6453264 ‐0.70945585 ‐0.552541 ‐0.63577 0.643595 0.975941 ‐2.11012 ‐0.63577 0.301298 0 STM0405 tRNA‐guanine transglycosylase tgt ‐0.23448625 ‐0.32816613 ‐0.2688599 0.20476426 1.4769859 1.2148346 0.965528 1.952778 ‐0.29444 1.500231 0.965528 0.643586 0 STM0406 preprotein translocase IISP family, membrane subunit yajC 0.11962856 0.034208562 0.16036971 1.142839 0.7577437 0.9905058 0.963696 1.9503 1.258977 2.620717 0.963696 0.367722 0 STM0407 preprotein translocase, IISP family, part of the secD 0.11275097 0.37148115 0.09624046 1.1477289 1.2874233 1.0090208 1.148058 2.216153 ‐0.22272 3.415642 1.148058 0.336118 0 STM0418 transcription termination L factor nusB ‐0.113886215 ‐0.017852247 ‐0.025089113 0.90064746 0.8751357 1.1148609 0.963548 1.9501 ‐0.84382 2.904321 0.963548 0.331764 0 STM0422 1‐deoxyxylulose‐5‐phosphate synthase flavoprotein dxs 0.18474916 ‐0.028791165 0.005142221 0.87931055 0.6138723 0.645033 0.712739 1.638912 0.153391 2.099254 0.712739 0.33952 0 STM0425 sulfur transfer protein (from cys to ThiS thiI 0.09322556 ‐0.009968681 0.012762454 1.1883136 0.8481654 0.8839316 0.97347 1.963558 0.834841 2.676822 0.97347 0.363666 0 STM0434 ketopantoate reductase apbA ‐0.23700683 ‐0.31890327 ‐0.3367807 0.62007135 0.46394312 0.51389384 0.532636 1.44657 1.349896 1.764959 0.532636 0.301784 0 STM0439 protohaeme IX farnesyltransferase (haeme O biosynthesis) cyoE ‐0.063925184 ‐0.2491674 ‐0.33575934 1.2340465 1.2247059 1.1463679 1.201707 2.300116 0.096314 4.238075 1.201707 0.28355 0 STM0440 cytochrome o ubiquinol oxidase subunit IV cyoD ‐0.092447676 ‐0.19011502 ‐0.1998862 1.390631 1.3016087 1.2867326 1.326324 2.507629 1.113066 4.602279 1.326324 0.288189 0 STM0441 cytochrome o ubiquinol oxidase subunit III cyoC ‐0.043399356 0.18307544 0.06552855 1.495569 1.284953 1.3487186 1.376414 2.596222 0.384153 4.3269 1.376414 0.318106 0 STM0443 cytochrome o ubiquinol oxidase subunit II cyoA 0.020950954 0.1483014 ‐0.10590536 0.64498657 0.3547519 0.5125706 0.504103 1.418241 ‐2.30068 1.484227 0.504103 0.33964 0 STM0447 peptidyl‐prolyl cis/trans isomerase, trigger factor a molecular tig 0.77709967 0.50235707 0.6469255 1.9144396 1.7988226 2.2050507 1.972771 3.925213 0.806797 5.238511 1.972771 0.37659 0 STM0448 proteolytic subunit of clpA‐clpP ATP‐dependent serine protease clpP 0.3406515 0.23828518 0.5413024 0.38613337 0.39837956 0.48524043 0.423251 1.340946 ‐2.17902 1.475024 0.423251 0.286945 0 152 STM0449 specificity component of clpA‐clpP ATP‐dependent serine protease clpX 0.2764029 0.25895515 0.13220412 0.5881954 0.48591846 0.4034188 0.492511 1.406891 0.108928 1.592898 0.492511 0.309192 0 STM0450 DNA‐binding, ATP‐dependent protease la cleaves RcsA and lon 0.21014813 0.16719347 0.06442701 0.38362837 0.5674981 0.5316524 0.49426 1.408598 0.134997 1.58404 0.49426 0.312025 0 STM0452 peptidyl prolyl isomerase cypD 0.5217175 0.37075484 0.35298458 0.7027212 0.4547855 0.7326637 0.630057 1.547626 ‐1.49469 1.83257 0.630057 0.343811 0 STM0456 putative ABC transporter periplasmic binding protein ybaE 0.013862575 0.17962728 0.032708135 ‐0.45761234 ‐0.51768845 ‐0.76862204 ‐0.58131 0.668358 ‐0.77383 ‐1.65615 ‐0.58131 0.350999 0 STM0461 putative ABC superfamily (atp&membrane) transporter mdlB ‐0.4977934 ‐0.66604364 ‐0.67152846 ‐0.6051969 ‐0.7758657 ‐0.6820164 ‐0.68769 0.620846 ‐0.23815 ‐2.254 ‐0.68769 0.305099 0 STM0462 regulatory protein, P‐II 2, for nitrogen assimilation glnK ‐2.2110238 ‐2.2586772 ‐2.2937286 ‐2.2217207 ‐2.6256282 ‐2.9934628 ‐2.6136 0.163391 ‐0.49223 ‐5.46078 ‐2.6136 0.478613 0 STM0463 putative Amt family, ammonium transport protein amtB ‐2.5150805 ‐2.587126 ‐2.4561398 ‐2.7700706 ‐3.2622104 ‐3.0378387 ‐3.02337 0.122991 0.688729 ‐7.59637 ‐3.02337 0.398002 0 STM0468 putative diguanylate cyclase/phosphodiesterase domain 2 ylaB 0.18790144 ‐0.0858201 0.047930665 ‐0.3980607 ‐0.8186577 ‐0.7430714 ‐0.65326 0.63584 0.606334 ‐1.69589 ‐0.65326 0.385203 0 STM0469 putative 50S ribosomal protein L31 (second copy) rpmE2 1.3985962 1.5783657 1.7735767 ‐2.935089 ‐3.2296724 ‐3.5061345 ‐3.22363 0.107051 0.031971 ‐7.66393 ‐3.22363 0.420624 0 STM0470 putative 50S ribosomal protein L36 (second copy) rpmJ2 1.5099168 1.5123256 1.6645528 ‐3.9113479 ‐3.6799922 ‐3.7337155 ‐3.77502 0.073048 ‐2.1543 ‐11.592 ‐3.77502 0.325656 0 STM0485 putative cytoplasmic protein ybaB 0.42250806 0.66256225 0.6792037 1.3368509 1.0855744 1.02594 1.149455 2.218301 ‐0.73412 3.274653 1.149455 0.351016 0 STM0486 putative recombination protein, gap repair recR 0.1383543 0.3955859 0.31080914 1.2840316 1.691644 1.3031485 1.426275 2.687519 0.449981 3.670772 1.426275 0.388549 0 STM0488 adenylate kinase adk ‐0.55290645 ‐0.41970772 ‐0.6663243 0.6514215 0.62113297 0.2609175 0.511157 1.425193 0.280356 1.341006 0.511157 0.381175 0 STM0492 putative CPA2 family transport protein ybaL ‐0.18466538 ‐0.19477 ‐0.24703479 0.6109426 0.6944987 0.5525017 0.619314 1.536145 0.224191 2.085558 0.619314 0.296954 0 STM0508 putative inner membrane protein ybbP ‐0.22696888 ‐0.2539097 ‐0.33893412 0.6334251 0.7281374 0.53804964 0.633204 1.551006 ‐0.27096 2.038495 0.633204 0.310623 0 STM0513 putative ATPase ybbB 0.18248695 0.098355666 0.060930066 0.6815095 0.62595284 0.42622778 0.577897 1.492672 ‐0.8299 1.734064 0.577897 0.333261 0 STM0523 allantoinase allB 0.04045679 0.105447866 0.079972014 ‐0.4666402 ‐0.36191988 ‐0.4132611 ‐0.41394 0.750571 ‐0.97311 ‐1.44744 ‐0.41394 0.285982 0 STM0528 ureidoglycolate dehydrogenase allD ‐0.27818152 ‐0.28702745 ‐0.23388119 ‐0.4211586 ‐0.45683774 ‐0.5028857 ‐0.46029 0.726838 0.740171 ‐1.64741 ‐0.46029 0.279405 0 STM0542 bifunctional 5,10‐methylene‐tetrahydrofolate dehydrogenase and 5,10‐methylene‐tetrahydr folD ‐0.23547623 ‐0.17731822 ‐0.273221 ‐0.42355603 ‐0.46405047 ‐0.6619927 ‐0.51653 0.69905 ‐0.37721 ‐1.56804 ‐0.51653 0.329413 0 STM0546 outer membrane usher protein fimD ‐0.2289422 ‐0.026289761 ‐0.03212258 ‐0.35288966 ‐0.46591848 ‐0.4802229 ‐0.43301 0.740715 ‐0.06715 ‐1.46276 ‐0.43301 0.296022 0 STM0561 Sensor protein ‐0.16640389 ‐0.07622832 ‐0.14931792 ‐0.6220974 ‐0.73967624 ‐1.0528361 ‐0.80487 0.572414 ‐0.35217 ‐2.09441 ‐0.80487 0.384295 0 STM0562 putative transport protein ‐0.42998475 ‐0.4193589 ‐0.3444349 ‐0.5965487 ‐0.8350702 ‐0.8219256 ‐0.75118 0.594117 ‐0.10823 ‐2.25472 ‐0.75118 0.333159 0 STM0568 APC family, phenylalanene transporter pheP ‐0.12897126 ‐0.002069403 ‐0.14651653 0.4407517 0.44320828 0.38491824 0.422959 1.340675 0.450863 1.539247 0.422959 0.274783 0 STM0570 outer membrane N‐acetyl phenylalanine beta‐naphthyl ester‐cleaving esterase apeE ‐0.37236246 ‐0.644741 ‐0.6217672 0.71657217 0.8763294 0.7615438 0.784815 1.722872 1.333779 2.587478 0.784815 0.303313 0 STM0583 putative cytoplasmic protein ybdK 0.136302 0.19414575 0.27541468 1.2068516 1.2777793 1.1836523 1.222761 2.33393 0.355139 4.304554 1.222761 0.284062 0 STM0585 outer membrane porin, receptor for ferric enterobactin fepA 0.9580155 1.0559162 0.9598503 0.9709265 1.0320842 0.93534297 0.979451 1.971715 ‐0.30939 3.448774 0.979451 0.284 0 STM0587 putative cytoplasmic protein ybdZ 1.6586463 1.7351841 1.6181923 0.5550019 0.77824533 0.8829725 0.73874 1.668718 0.651029 2.095923 0.73874 0.352465 0 STM0592 ABC superfamily (membrane), ferric enterobactin (enterochelin) transporter fepD ‐0.089237794 ‐0.25716263 ‐0.33554307 1.6180853 1.4884098 1.8124847 1.63966 3.115924 0.818173 4.685789 1.63966 0.349922 0 STM0594 ABC superfamily (peri_perm), ferric enterobactin (enterochelin) tranporter fepB 0.15964195 0.25267553 0.14055583 0.84581584 0.7783631 0.6027718 0.742317 1.67286 ‐0.64549 2.261863 0.742317 0.328188 0 STM0595 isochorismate synthetase, enterochelin biosynthesis entC ‐0.041376133 ‐0.37923864 ‐0.3823051 0.6193428 0.36754686 0.49043092 0.49244 1.406822 0.496206 1.499314 0.49244 0.328444 0 STM0596 2,3‐dihydroxybenzoate‐AMP ligase entE ‐0.16569774 ‐0.13061993 ‐0.15019825 0.85804677 0.97658736 1.1256006 0.986745 1.981709 0.797175 2.961841 0.986745 0.333153 0 STM0597 2,3‐dihydro‐2,3‐dihydroxybenzoate synthetase, isochorismatase entB ‐0.03610212 0.057909448 ‐0.0426332 1.1064093 1.0510966 1.005625 1.054377 2.076821 ‐0.20792 3.701 1.054377 0.28489 0 STM0598 2,3‐dihydro‐2,3‐dihydroxybenzoate dehydrogenase entA 0.26830655 0.1754265 0.12275723 1.1252744 1.1405331 1.2029724 1.15626 2.228789 ‐1.0717 4.136627 1.15626 0.279518 0 STM0599 putative protein PaaI, possibly involved in aromatic ybdB ‐0.037574347 ‐0.11972696 ‐0.004524556 0.8244946 1.0012503 1.0899552 0.9719 1.961422 1.219369 2.911851 0.9719 0.333774 0 STM0600 carbon starvation protein cstA 0.006246797 ‐0.18393022 ‐0.119045444 1.3345076 1.445501 1.6780187 1.486009 2.80113 ‐0.88686 4.162956 1.486009 0.35696 0 STM0607 periplasmic disulfide isomerase, thiol‐disulphide oxidase dsbG 0.5100641 0.70760614 0.53589386 0.6468124 0.81203794 0.5543116 0.671054 1.592236 ‐0.31244 2.026559 0.671054 0.33113 0 STM0617 RNase I, cleaves phosphodiester bond between any rna ‐0.16996862 ‐0.2836915 ‐0.215731 ‐0.29312536 ‐0.7033897 ‐0.7252752 ‐0.57393 0.671784 ‐0.48515 ‐1.44824 ‐0.57393 0.396294 0 STM0626 response regulator in two‐component regulatory system with dpiA ‐0.07584326 ‐0.08754068 ‐0.1227667 ‐0.43145782 ‐0.5075876 ‐0.5681539 ‐0.5024 0.705932 0.019906 ‐1.70135 ‐0.5024 0.295296 0 STM0632 putative Sec‐independent protein secretion pathway component ybeC ‐1.1095876 ‐1.0312442 ‐0.96915185 ‐1.4278146 ‐1.6140355 ‐1.4850512 ‐1.50897 0.351363 0.870636 ‐4.85478 ‐1.50897 0.310821 0 STM0643 alpha ribazole‐5‐P phosphatase in cobalamin synthesis cobC 0.028894002 ‐0.2483012 ‐0.14774653 ‐0.824551 ‐0.89919317 ‐0.60410976 ‐0.77595 0.584003 ‐0.5101 ‐2.2535 ‐0.77595 0.344331 0 STM0645 putative Nicotinic acid mononucleotide adenylyltransferase nadD ‐0.10901003 0.027530616 ‐0.19411977 ‐0.44751242 ‐0.4768979 ‐0.674735 ‐0.53305 0.691093 ‐0.17819 ‐1.62962 ‐0.53305 0.327099 0 STM0648 leucine tRNA synthetase leuS 0.20801476 0.21691012 0.18741052 0.6466164 0.8099471 0.78945315 0.748672 1.680246 ‐0.18459 2.437724 0.748672 0.307119 0 STM0655 putative cytoplasmic protein ybeR 0.074464895 ‐0.022565901 5.07E‐04 ‐0.35918546 ‐0.59028405 ‐0.45415658 ‐0.46788 0.723029 0.083827 ‐1.44937 ‐0.46788 0.322814 0 STM0659 putative heatshock protein, homolog of hsp70 in hscC ‐0.42572558 ‐0.37190017 ‐0.3907563 ‐0.5145188 ‐0.33737367 ‐0.4556404 ‐0.43584 0.739261 0.516043 ‐1.41583 ‐0.43584 0.307836 0 STM0660 putative cytoplasmic protein ‐0.20414087 ‐0.2077432 ‐0.31832653 ‐0.3653211 ‐0.38457164 ‐0.48287573 ‐0.41092 0.752142 ‐0.77862 ‐1.40653 ‐0.41092 0.292153 0 STM0661 putative purine nucleoside hydrolase ybeK ‐0.5770081 ‐0.5427533 ‐0.62149066 ‐0.47829667 ‐0.3749117 ‐0.42480436 ‐0.426 0.74432 0.914592 ‐1.49161 ‐0.426 0.2856 0 STM0662 ABC superfamily (atp_bind), glutamate/aspartate transporter gltL ‐0.673679 ‐1.0342818 ‐1.0537351 ‐0.69161516 ‐1.0319647 ‐0.7187726 ‐0.81412 0.568756 0.982388 ‐2.23073 ‐0.81412 0.364955 0 STM0664 ABC superfamily (membrane), glutamate/aspartate transporter gltJ ‐0.5555748 ‐0.5709684 ‐0.63115054 ‐0.6378293 ‐0.7115269 ‐0.9004852 ‐0.74995 0.594625 ‐0.03031 ‐2.24557 ‐0.74995 0.333968 0 STM0665 ABC superfamily (bind_prot), glutamate/aspartate transporter gltI ‐0.66387933 ‐0.76356953 ‐0.7679571 ‐1.4089369 ‐1.6537793 ‐1.8124185 ‐1.62504 0.3242 ‐0.38247 ‐4.35543 ‐1.62504 0.373107 0 STM0671 putative monooxygenase ubiF ‐0.3663575 ‐0.6821574 ‐0.56265086 1.0897584 1.1038402 1.1244713 1.106023 2.152515 1.062088 4.160647 1.106023 0.26583 0 STM0688 putative lipoprotein ybfN ‐0.02801992 0.13353829 0.27169454 ‐0.41021413 ‐0.5384636 ‐0.41777337 ‐0.45548 0.729266 ‐0.68873 ‐1.53208 ‐0.45548 0.297297 0 STM0689 citrate‐proton symporter citA ‐0.19560848 ‐0.100571804 ‐0.067824185 ‐0.4198267 ‐0.5098769 ‐0.44878626 ‐0.4595 0.72724 0.176283 ‐1.62774 ‐0.4595 0.282291 0 STM0693 transcriptional repressor of iron‐responsive genes (Fur family) fur 0.58997774 0.91239756 0.831037 0.9073395 0.80599254 0.7938867 0.83574 1.784772 0.484351 2.864872 0.83574 0.29172 0 STM0717 putative inner membrane protein ‐0.12471457 ‐0.103127725 ‐0.014256021 ‐0.7044656 ‐0.48667648 ‐0.6289139 ‐0.60669 0.656704 1.206932 ‐1.8983 ‐0.60669 0.319595 0 STM0718 putative cytoplasmic protein 0.23774374 0.40668654 0.13502394 ‐0.6457012 ‐0.44293168 ‐0.52819157 ‐0.53894 0.688276 0.297018 ‐1.71348 ‐0.53894 0.31453 0 STM0730 citrate synthase gltA 0.6266423 0.619384 0.86853135 1.796742 1.4630904 1.5352359 1.598356 3.027981 0.926592 4.475867 1.598356 0.357105 0 STM0732 succinate dehydrogenase, cytochrome b556 sdhC 0.008798748 0.09971459 0.10643163 1.0731727 1.0892856 1.056166 1.072875 2.103621 ‐0.20282 4.043829 1.072875 0.265312 0 STM0733 succinate dehydrogenase, hydrophobic subunit sdhD ‐0.13162221 ‐0.44384727 ‐0.3626751 1.1050904 0.67024225 0.9964748 0.923936 1.897284 0.682928 2.391051 0.923936 0.386414 0 STM0734 succinate dehydrogenase, flavoprotein subunit sdhA ‐0.13651139 ‐0.20356365 ‐0.17264305 1.204875 1.7905883 1.6572974 1.55092 2.93004 0.946979 3.58181 1.55092 0.432999 0 STM0736 2‐oxoglutarate dehydrogenase (decarboxylase component) sucA 0.06386573 0.10227226 ‐0.022172369 1.8724911 1.76674 1.6305912 1.756607 3.379026 0.220052 5.392275 1.756607 0.325764 0 STM0737 2‐oxoglutarate dehydrogenase (dihydrolipoyltranssuccinase E2 component) sucB 0.26151693 0.40387812 0.231357 2.2338598 2.410301 2.2622237 2.302128 4.931847 ‐1.06209 7.415401 2.302128 0.310452 0 STM0738 succinyl‐CoA synthetase, beta subunit sucC 0.13465412 ‐0.09066245 ‐0.06626046 2.144797 2.0064297 1.9691268 2.040118 4.112791 ‐0.7027 6.598362 2.040118 0.309185 0 STM0739 succinyl‐CoA synthetase, alpha subunit sucD ‐0.05691173 0.06843569 0.12708043 1.5119464 1.7780126 1.6003435 1.630101 3.095346 0.47301 4.880773 1.630101 0.333984 0 STM0748 tol protein required for outer membrane integrity tolB 0.09232277 0.003675571 0.05527863 1.0028434 0.9691292 1.1500187 1.040664 2.057174 0.393064 3.343106 1.040664 0.311286 0 STM0749 tol protein required for outer membrane integrity pal 0.4004878 0.70452666 0.46171623 1.5477052 1.34555 1.2616546 1.38497 2.611665 0.35656 4.065728 1.38497 0.340645 0 STM0750 putative periplasmic protein ybgF ‐0.0552178 ‐0.11513294 ‐0.13074383 0.8464135 0.71751934 0.9059369 0.82329 1.769436 0.345638 2.644205 0.82329 0.311356 0 STM0772 phosphoglyceromutase 1 gpmA 0.6452878 0.5928036 0.6900711 ‐0.8919129 ‐0.89992064 ‐0.737573 ‐0.84314 0.557431 ‐1.02501 ‐2.73229 ‐0.84314 0.308581 0 STM0782 ABC superfamily (membrane), molybdate transporter modB ‐0.4180693 ‐0.33851707 ‐0.39626706 1.1440533 0.9742888 1.1510261 1.089789 2.12843 0.452556 3.475814 1.089789 0.313535 0 STM0783 ABC superfamily (atp_bind), molybdate transporter modC ‐0.15239358 ‐0.048083737 ‐0.19053271 0.784267 0.63934493 0.6057894 0.676467 1.598221 0.047033 2.178546 0.676467 0.310513 0 STM0795 7‐keto‐8‐aminopelargonic acid synthetase bioF 0.32754552 0.16651924 0.09135419 1.8587207 1.4728436 1.6029614 1.644842 3.127136 1.331985 4.456433 1.644842 0.369094 0 STM0803 molybdopterin biosynthesis, protein B moaB 0.29125378 0.49719876 0.39910957 ‐1.042177 ‐0.9060325 ‐0.90210325 ‐0.9501 0.517595 0.580918 ‐3.14813 ‐0.9501 0.3018 0 STM0811 putative negative regulator ybhN ‐0.1731959 ‐0.21476826 ‐0.24257632 ‐0.6489656 ‐0.4341976 ‐0.41296202 ‐0.49871 0.70774 1.854217 ‐1.50609 ‐0.49871 0.331128 0 STM0812 cardiolipin (CL) synthase ybhO ‐0.2027896 0.101249255 ‐0.055903517 ‐0.62175876 ‐0.5726015 ‐0.5017533 ‐0.56537 0.675782 0.542138 ‐1.94566 ‐0.56537 0.29058 0 STM0816 putative ABC superfamily (membrane) transport protein ybhS ‐0.121631615 ‐0.24367702 ‐0.21742254 ‐0.62156874 ‐0.7663998 ‐0.64496404 ‐0.67764 0.625185 0.120492 ‐2.25402 ‐0.67764 0.300638 0 STM0828 ABC superfamily (atp_bind), glutamine high‐affinity transporter glnQ ‐0.8392573 ‐0.6363069 ‐0.50710005 ‐0.57792866 ‐0.4704322 ‐0.34354207 ‐0.46397 0.72499 0.803895 ‐1.43426 ‐0.46397 0.323488 0 STM0829 ABC superfamily (membrane), glutamine high‐affinity transporter glnP ‐0.4746565 ‐0.53600425 ‐0.54333925 ‐0.40534726 ‐0.7341103 ‐0.8433608 ‐0.66094 0.632466 0.081805 ‐1.70618 ‐0.66094 0.38738 0 STM0830 ABC superfamily (bind_prot), glutamine high‐affinity transporter glnH ‐1.635288 ‐1.5401719 ‐1.650116 ‐1.7286297 ‐1.7587894 ‐1.8504239 ‐1.77928 0.291329 ‐0.0051 ‐6.0857 ‐1.77928 0.292371 0 STM0833 outer membrane protease, receptor for phage OX2 ompX 0.4758158 0.26884237 0.46976787 ‐1.3159094 ‐1.284921 ‐1.1680741 ‐1.2563 0.418616 ‐1.08777 ‐4.17707 ‐1.2563 0.300761 0 STM0837 putative periplasmic protein ybiS ‐0.22505845 ‐0.60718817 ‐0.3888678 0.7924875 0.21959558 1.0621192 0.691401 1.614851 0.210726 1.371388 0.691401 0.504162 0 STM0844 putative pyruvate formate lyase activating enzyme pflE ‐0.30814725 ‐0.3479092 ‐0.23795207 ‐0.58763456 ‐0.52717257 ‐0.65537995 ‐0.59006 0.664314 ‐1.37305 ‐2.01538 ‐0.59006 0.29278 0 STM0847 putative asparaginase ybiK ‐0.123217225 ‐0.16249698 ‐0.20412482 0.72973096 0.525086 0.31968203 0.524833 1.438767 ‐0.30862 1.402844 0.524833 0.374121 0 STM0862 putative glutathione S‐transferase yliJ 0.31162846 0.32918483 0.27655312 ‐0.78265816 ‐1.0283278 ‐0.90984267 ‐0.90694 0.533314 0.068114 ‐2.77622 ‐0.90694 0.326683 0 STM0865 putative permease ybjG ‐0.07805403 ‐0.1820682 ‐0.1218412 ‐0.37384605 ‐0.7777111 ‐0.71372145 ‐0.62176 0.649878 0.097612 ‐1.63159 ‐0.62176 0.381075 0 STM0871 putative inner membrane protein ybjM ‐0.16829391 ‐0.18227065 ‐0.10846 ‐0.39615297 ‐0.49150193 ‐0.49653733 ‐0.4614 0.726282 ‐0.44118 ‐1.59983 ‐0.4614 0.288404 0 STM0873 putative inner membrane protein ybjC ‐0.17905602 ‐0.44594544 ‐0.4199509 ‐0.4170016 ‐0.74505764 ‐0.5799282 ‐0.58066 0.668657 0.641659 ‐1.6569 ‐0.58066 0.350452 0 STM0874 oxygen‐insensitive NADPH nitroreductase mdaA 0.053176016 ‐0.060060628 0.035438962 0.36533445 0.34835386 0.37766808 0.363785 1.286798 ‐0.80558 1.376686 0.363785 0.264247 0 STM0878 ABC superfamily (atp_bind), putrescine transporter potG ‐0.14448799 ‐0.19592857 0.014923051 0.7473764 0.71340287 0.71976113 0.726847 1.655018 ‐1.03447 2.730687 0.726847 0.266177 0 STM0887 ABC superfamily (bind_prot), arginine 3rd transport system artJ ‐1.4173365 ‐1.4003847 ‐1.1767683 ‐1.0465586 ‐1.2539867 ‐1.3252928 ‐1.20861 0.432684 ‐0.77185 ‐3.56155 ‐1.20861 0.33935 0 STM0888 ABC superfamily (membrane), arginine 3rd transport system artM ‐0.13690579 ‐0.001789385 ‐0.06557214 ‐0.40076837 ‐0.54336035 ‐0.7508444 ‐0.56499 0.67596 ‐0.22676 ‐1.5809 ‐0.56499 0.357385 0 STM0890 ABC superfamily (bind_prot), arginine transport system artI 0.09460141 0.005221735 0.06740219 ‐0.9801959 ‐1.1065919 ‐1.3414176 ‐1.14274 0.4529 ‐0.36759 ‐3.1604 ‐1.14274 0.36158 0 STM0892 putative lipoprotein ybjP 0.07022612 0.005066474 0.03450497 ‐0.4114434 ‐0.4573738 ‐0.54452103 ‐0.47111 0.721408 ‐0.24014 ‐1.59821 ‐0.47111 0.294775 0 STM0908 Fels‐1 prophage ‐0.18527438 ‐0.26432416 ‐0.24639323 ‐0.6858905 ‐0.92513174 ‐0.86475366 ‐0.82526 0.564381 ‐1.07325 ‐2.51926 ‐0.82526 0.32758 0 STM0934 L‐allo‐threonine aldolase ltaA ‐0.30666682 ‐0.5187434 ‐0.47626817 0.6707763 0.73030025 0.8241052 0.741727 1.672177 ‐0.56166 2.469304 0.741727 0.300379 0 STM0937 hybrid cluster protein similar to prismane‐protein homolog hcp 0.13254821 0.048995327 ‐0.1514591 ‐0.8583821 ‐0.5006274 ‐0.5094654 ‐0.62282 0.649398 ‐2.88661 ‐1.66729 ‐0.62282 0.373556 0 STM0938 putative inner membrane protein ybjE ‐0.023494873 ‐0.27251658 ‐0.035935927 ‐0.7249376 ‐0.7377606 ‐0.78367907 ‐0.74879 0.595101 ‐0.58783 ‐2.737 ‐0.74879 0.273581 0 STM0948 putative cytoplasmic protein ‐0.3081 ‐0.112031065 ‐0.1351535 ‐0.7413598 ‐0.40463015 ‐0.47701064 ‐0.541 0.687294 0.339246 ‐1.51081 ‐0.541 0.358085 0 STM0954 putative inner membrane protein ‐0.37670466 ‐0.41688257 ‐0.037841357 0.5842649 0.7589663 0.73781437 0.693682 1.617406 ‐1.05863 2.231939 0.693682 0.310798 0 STM0958 thioredoxin reductase trxB 0.14916131 0.32061037 0.11702429 0.7431806 0.74079674 0.6101422 0.69804 1.622299 0.163417 2.329099 0.69804 0.299704 0 STM0959 regulator for lrp regulon and high‐affinity branched‐chain lrp ‐0.4318177 ‐0.33552516 ‐0.38188127 1.0524905 0.62952006 0.6558956 0.779302 1.7163 ‐0.11329 1.9852 0.779302 0.392556 0 STM0965 anaerobic dimethyl sulfoxide reductase, subunit B dmsB ‐0.44168755 ‐0.57411414 ‐0.5876101 ‐0.90780324 ‐0.8215511 ‐0.94185776 ‐0.8904 0.539463 0.425461 ‐3.05401 ‐0.8904 0.291552 0 STM0968 putative MFS family transport protein ycaD ‐0.022586863 ‐0.1905175 ‐0.32656303 ‐0.4322307 ‐0.5046901 ‐0.3367984 ‐0.42457 0.745059 0.236847 ‐1.39494 ‐0.42457 0.304367 0 STM0973 pyruvate formate lyase I, induced anaerobically pflB ‐1.4719023 ‐1.5097382 ‐1.4523679 ‐3.645095 ‐3.5508404 ‐3.386212 ‐3.52738 0.086727 ‐1.45026 ‐10.644 ‐3.52738 0.331398 0 STM0974 putative FNT family, formate transporter (formate channel focA ‐1.2823764 ‐1.2160076 ‐1.338426 ‐2.496082 ‐2.7509668 ‐2.8551254 ‐2.70072 0.153816 0.129443 ‐7.45239 ‐2.70072 0.362397 0 STM0975 putative cytoplasmic protein ycaO 0.19294322 0.040550433 0.21191859 0.37118307 0.49899256 0.58558655 0.485254 1.399832 1.5789 1.525848 0.485254 0.318023 0 STM0979 putative Zn‐dependent protease with chaperone function ycaL 0.004482293 0.005993511 0.03872211 0.6519776 0.73462725 0.90680647 0.76447 1.698746 0.786153 2.310902 0.76447 0.33081 0 STM0981 30S ribosomal subunit protein S1 rpsA 0.1129186 0.17974937 ‐0.07130914 0.58543766 0.59233326 0.3848109 0.520861 1.434811 ‐0.39786 1.60857 0.520861 0.323804 0 STM0982 integration host factor (IHF), beta subunit site‐specific himD 0.0826966 0.16687225 0.12247399 ‐0.5335145 ‐0.5428273 ‐0.7258174 ‐0.60072 0.659425 ‐0.15211 ‐1.88694 ‐0.60072 0.318356 0 STM0989 mukF protein (killing factor KicB) ‐0.8264857 ‐0.52779496 ‐0.86790794 ‐0.3820342 ‐0.53006834 ‐0.7149592 ‐0.54235 0.68665 ‐0.24373 ‐1.54055 ‐0.54235 0.352053 0 STM1009 Gifsy‐2 prophage exodeoxyribonuclease ‐0.016730106 ‐0.09943681 ‐0.10027532 ‐0.41747448 ‐0.5451697 ‐0.69797474 ‐0.55354 0.681346 0.419697 ‐1.64337 ‐0.55354 0.336831 0 STM1020 Gifsy‐2 prophage ‐0.053763438 ‐0.014017738 0.09729467 ‐0.37020394 ‐0.48221228 ‐0.62012684 ‐0.49085 0.711607 ‐0.70961 ‐1.49637 ‐0.49085 0.328025 0 STM1021 Gifsy‐2 prophage ‐0.30851012 ‐0.1425107 ‐0.2532696 ‐0.9262608 ‐0.8163984 ‐0.7411998 ‐0.82795 0.563328 0.433919 ‐2.67527 ‐0.82795 0.309484 0 STM1026 Gifsy‐2 prophage ‐0.035161383 ‐0.0825589 ‐0.07506792 ‐0.4949597 ‐0.568312 ‐0.47093445 ‐0.5114 0.70154 1.382548 ‐1.79416 ‐0.5114 0.285038 0 STM1027 Gifsy‐2 prophage ‐0.136989 ‐0.39771196 ‐0.33779973 ‐1.1598936 ‐1.4890867 ‐1.3726978 ‐1.34056 0.394868 0.764831 ‐3.80702 ‐1.34056 0.352129 0 STM1028 Gifsy‐2 prophage lysozyme 0.1707156 0.18303591 0.20381786 ‐0.86373496 ‐0.9796492 ‐0.98392576 ‐0.94244 0.520353 ‐0.68018 ‐3.1934 ‐0.94244 0.29512 0 STM1032 Gifsy‐2 prophage 0.01930838 ‐0.35201576 ‐0.30661643 ‐0.6955057 ‐0.6340615 ‐0.48082042 ‐0.60346 0.658172 0.309132 ‐1.88827 ‐0.60346 0.319584 0 STM1044 Gifsy‐2 prophage: superoxide dismutase precursor (Cu‐Zn) sodC ‐0.46788502 ‐0.0507874 ‐0.21940587 ‐1.2270298 ‐1.2665696 ‐1.2220559 ‐1.23855 0.423798 0.319488 ‐4.59009 ‐1.23855 0.269832 0 STM1045 Gifsy‐2 prophage probable minor tail protein 0.13166812 ‐0.017710516 0.075890236 ‐0.42943862 ‐0.5250911 ‐0.37995383 ‐0.44483 0.734672 0.944958 ‐1.49097 ‐0.44483 0.298348 0 STM1059 putative cytoplasmic protein ycbW ‐0.020034539 ‐0.057550106 ‐0.057470012 ‐0.5909608 ‐0.95165664 ‐0.91867226 ‐0.82043 0.566273 0.284636 ‐2.21213 ‐0.82043 0.370879 0 STM1061 putative N6‐adenine‐specific DNA methylase ycbY 0.021966599 ‐0.41774347 ‐0.4122924 0.44939023 0.74210215 0.76606804 0.65252 1.571912 0.187416 1.824976 0.65252 0.35755 0 STM1062 putative ATPase component of ABC transporters with uup 0.009675218 ‐0.0972533 ‐0.09807664 0.50852597 0.4733692 0.6642514 0.548716 1.462783 0.364934 1.745266 0.548716 0.314402 0 STM1064 paraquat‐inducible protein B pqiB 0.44150075 0.27339482 0.17079642 0.6643549 0.62101567 0.52863103 0.604667 1.520628 0.10765 2.04436 0.604667 0.295773 0 STM1066 ribosome modulation factor (involved in dimerization of rmf ‐1.0369891 ‐1.025873 ‐0.6459207 ‐2.939138 ‐2.43706 ‐2.2428668 ‐2.53969 0.17198 1.503153 ‐5.48301 ‐2.53969 0.463193 0 STM1067 beta‐hydroxydecanoyl thioester dehydrase (trans‐2‐decenoyl‐ACP isomerase) fabA 0.1901781 0.22569199 0.22145864 0.5574526 0.41634783 0.3668966 0.446899 1.363107 0.033196 1.428523 0.446899 0.31284 0 STM1068 putative protease lonH 0.40872064 0.44216406 0.41327387 0.7258578 0.74335986 0.49317136 0.65413 1.573666 ‐0.93727 1.944574 0.65413 0.336387 0 STM1072 putative DNA transformation protein yccR ‐0.006722272 0.11794678 0.14655764 ‐0.53495693 ‐0.44912842 ‐0.4041072 ‐0.46273 0.725611 0.955133 ‐1.57322 ‐0.46273 0.29413 0 STM1076 methylglyoxal synthase mgsA ‐0.40152797 ‐0.51506615 ‐0.48631975 ‐0.74361235 ‐1.0801302 ‐0.8070471 ‐0.87693 0.544525 0.258331 ‐2.44279 ‐0.87693 0.358987 0 STM1077 putative periplasmic protein yccT ‐0.5581323 ‐0.5256422 ‐0.4948595 ‐0.75453085 ‐0.56906116 ‐0.7390381 ‐0.68754 0.62091 0.794088 ‐2.18157 ‐0.68754 0.315159 0 STM1096 Copper resistance transcriptional regulatory protein copR ‐0.26226795 ‐0.1425537 ‐0.05891531 ‐0.53030914 ‐0.5812142 ‐0.49127528 ‐0.53427 0.69051 0.653291 ‐1.89599 ‐0.53427 0.281788 0 STM1097 putative periplasmic or exported protein ‐0.41177925 ‐0.3593518 ‐0.1443248 ‐1.4691228 ‐1.359782 ‐1.4977427 ‐1.44222 0.368002 ‐0.68188 ‐4.84312 ‐1.44222 0.297786 0 STM1098 4‐hydroxyphenylacetate catabolism hpaC ‐0.09466166 ‐0.051474757 ‐0.038535997 ‐0.9726101 ‐0.8137459 ‐0.9472928 ‐0.91122 0.531737 ‐0.82504 ‐2.9873 ‐0.91122 0.30503 0 STM1125 SSS family, major sodium/proline symporter putP ‐0.028754672 ‐0.12814485 ‐0.024961982 0.70970964 0.6148712 0.739097 0.687893 1.610929 ‐0.74017 2.345891 0.687893 0.293233 0 STM1139 putative transcriptional regulator in curly assembly/transport, 2nd csgG ‐0.7588283 ‐1.1782665 ‐1.0758065 ‐1.6324872 ‐2.0239973 ‐1.6082772 ‐1.75492 0.29629 0.983615 ‐4.49439 ‐1.75492 0.390469 0 STM1140 curli production assembly/transport component, 2nd curli operon csgF ‐0.9241674 ‐0.7570996 ‐0.8110525 ‐2.4841034 ‐2.324837 ‐2.4346235 ‐2.41452 0.187567 ‐0.91929 ‐7.97367 ‐2.41452 0.302812 0 STM1141 curli production assembly/transport component, 2nd curli operon csgE ‐1.0519996 ‐0.9824834 ‐0.58964723 ‐2.2129786 ‐2.2709503 ‐2.066302 ‐2.18341 0.220155 ‐1.04998 ‐6.89538 ‐2.18341 0.316648 0 STM1142 putative transcriptional regulator (LuxR/UhpA family) csgD ‐1.3281112 ‐1.1724006 ‐1.5959761 ‐2.0441546 ‐2.5151248 ‐2.4268098 ‐2.3287 0.199064 0.170016 ‐5.81757 ‐2.3287 0.400287 0 STM1145 putative curli production protein csgC ‐1.4600596 ‐1.4493257 ‐1.5091476 ‐1.74516 ‐1.4549979 ‐1.5759916 ‐1.59205 0.3317 0.242556 ‐4.68393 ‐1.59205 0.339896 0 STM1146 putative periplasmic protein ymdA ‐1.4272671 ‐1.1628419 ‐1.0917475 ‐1.1675874 ‐0.9190649 ‐1.0819148 ‐1.05619 0.480901 0.506618 ‐3.21386 ‐1.05619 0.328636 0 STM1147 putative ACR related to the C‐terminal domain ‐0.7126416 ‐0.9903692 ‐0.94709754 ‐0.60921794 ‐1.0801338 ‐0.9391641 ‐0.87617 0.544811 0.498948 ‐2.21652 ‐0.87617 0.395292 0 153 STM1148 putative phospholipase ymdC 0.054068517 ‐0.108016655 ‐0.14861533 0.82993424 0.6339539 0.48829114 0.650726 1.569959 0.116934 1.834431 0.650726 0.354729 0 STM1150 periplasmic glucans biosynthesis protein mdoG 0.5415282 0.7216828 0.53028905 0.94543475 0.8897964 0.79126954 0.8755 1.834644 ‐0.72112 2.910343 0.8755 0.300824 0 STM1155 lauroyl/myristoyl acyltransferase involved in lipid A biosynthesis htrB ‐0.1604228 ‐0.2713051 ‐0.18319903 ‐0.77662677 ‐0.7340871 ‐0.73484254 ‐0.74852 0.595214 ‐0.65951 ‐2.77429 ‐0.74852 0.269805 0 STM1164 putative outer membrane lipoprotein yceB 0.029775366 0.071547635 0.09752407 ‐0.66621584 ‐0.55567634 ‐0.6065725 ‐0.60949 0.655429 ‐0.6132 ‐2.11854 ‐0.60949 0.287693 0 STM1165 glutaredoxin 2 grxB 0.16463952 0.15097828 0.095054746 ‐0.72637826 ‐1.2202902 ‐1.0162948 ‐0.98765 0.504297 0.501619 ‐2.47503 ‐0.98765 0.399047 0 STM1166 putative MFS superfamily transport protein yceL ‐0.20057508 ‐0.13999118 ‐0.28870073 ‐0.589312 ‐0.5850855 ‐0.82377785 ‐0.66606 0.630226 ‐0.50391 ‐1.9905 ‐0.66606 0.334619 0 STM1174 flagellar biosynthesis, cell‐proximal portion of basal‐body rod flgB ‐0.24398626 ‐0.15891434 ‐0.31864962 1.061214 0.9175013 0.8054976 0.928071 1.90273 ‐0.44871 2.814404 0.928071 0.329758 0 STM1176 flagellar biosynthesis, initiation of hook assembly flgD ‐0.31164765 ‐0.12191109 ‐0.23948023 1.2616581 1.70193 1.486162 1.48325 2.795778 0.514035 3.874197 1.48325 0.382854 0 STM1178 flagellar biosynthesis, cell‐proximal portion of basal‐body rod flgF ‐0.5251709 ‐0.5935623 ‐0.70547336 1.0958923 1.1005088 0.9917764 1.062726 2.088875 ‐0.23132 3.648852 1.062726 0.291249 0 STM1179 flagellar biosynthesis, cell‐distal portion of basal‐body rod flgG ‐0.41774648 ‐0.40301433 ‐0.46112373 1.3467141 1.4337074 1.5044321 1.428285 2.691265 ‐0.03913 4.739471 1.428285 0.30136 0 STM1180 flagellar biosynthesis, basal‐body outer‐membrane L (lipopolysaccharide layer) flgH ‐0.24669611 ‐0.45819262 ‐0.36717805 1.1339319 1.7485083 1.8011872 1.561209 2.951011 1.1025 3.322225 1.561209 0.469929 0 STM1181 putative flagella basal body protein flgI ‐0.324302 ‐0.2887586 ‐0.2424051 1.9730844 2.096299 2.0200503 2.029811 4.083514 1.08522 6.959707 2.029811 0.291652 0 STM1183 flagellar biosynthesis, hook‐filament junction protein 1 flgK ‐0.23739685 ‐0.2801575 ‐0.27900034 1.619831 1.6788012 1.5202569 1.606296 3.044692 0.102881 5.318597 1.606296 0.302015 0 STM1185 RNase E rne 0.02921594 ‐0.18947308 ‐0.11561472 0.8085795 0.55627835 0.6062042 0.657021 1.576823 ‐0.23731 1.973703 0.657021 0.332887 0 STM1190 putative metal‐binding yceD 0.21810497 0.16459917 0.14148992 1.4886531 0.96983606 0.93328345 1.130591 2.189484 ‐0.25896 2.598513 1.130591 0.435091 0 STM1194 malonyl‐CoA‐[acyl‐carrier‐protein] transacylase fabD 0.117961995 ‐0.1920138 ‐0.18482763 0.9270183 0.71139777 0.91258305 0.850333 1.802917 1.003171 2.613658 0.850333 0.325342 0 STM1195 3‐oxoacyl‐[acyl‐carrier‐protein] reductase fabG 0.15777712 ‐0.012130227 ‐0.04840321 1.1013998 0.9370459 0.94289905 0.993782 1.991398 ‐0.10765 3.210042 0.993782 0.309585 0 STM1214 putative outer membrane protein ycfR ‐0.47596112 ‐0.44852042 ‐0.3523592 ‐0.6465189 ‐0.5931529 ‐0.60973513 ‐0.61647 0.652265 0.348475 ‐2.27045 ‐0.61647 0.271519 0 STM1220 putative regulator (NagC/XylR family) ycfX 0.058407985 ‐0.1285463 0.007555843 1.0009295 0.6888944 0.49127084 0.727032 1.65523 ‐0.02428 1.799111 0.727032 0.404106 0 STM1228 putative periplasmic protein ‐0.005889685 0.13874896 ‐0.04143879 ‐0.7370077 ‐0.6458873 ‐0.63049036 ‐0.67113 0.628015 ‐0.83264 ‐2.32234 ‐0.67113 0.288988 0 STM1232 adenylosuccinate lyase purB ‐0.31009138 0.03655681 ‐0.25444815 0.6595636 0.8379876 0.74038297 0.745978 1.677111 0.352689 2.42727 0.745978 0.307332 0 STM1238 isocitrate dehydrogenase in e14 prophage, specific for icdA 0.33846152 0.38819313 0.34394217 1.923276 1.6409713 1.7221025 1.762117 3.391954 0.487826 5.187824 1.762117 0.339664 0 STM1254 putative outer membrane lipoprotein 0.015791897 0.26073694 0.26242307 ‐0.72672886 ‐1.0188545 ‐1.1357363 ‐0.96044 0.5139 ‐0.47012 ‐2.54503 ‐0.96044 0.377379 0 STM1261 putative cytoplasmic protein 0.27194655 0.56820977 0.43828702 ‐0.8873787 ‐1.1520764 ‐0.8446487 ‐0.96137 0.51357 0.540127 ‐2.73195 ‐0.96137 0.351898 0 STM1263 putative periplasmic protein 2.2810953 2.2803102 2.2510886 ‐3.407243 ‐3.7447538 ‐4.084797 ‐3.7456 0.074553 ‐0.44092 ‐8.29878 ‐3.7456 0.451343 0 STM1274 putative inner membrane protein yeaQ 0.65378964 0.6692242 0.8762841 ‐0.6688221 ‐0.6933789 ‐0.4495114 ‐0.6039 0.657971 ‐0.6251 ‐1.81205 ‐0.6039 0.333271 0 STM1285 putative Ser protein kinase yeaG 0.68933046 0.7587421 0.6440396 ‐0.46575496 ‐0.41566285 ‐0.36063853 ‐0.41402 0.75053 0.745401 ‐1.44709 ‐0.41402 0.286105 0 STM1290 glyceraldehyde‐3‐phosphate dehydrogenase A gapA 0.03538778 ‐0.07432849 ‐0.23907097 ‐0.6706508 ‐0.68530047 ‐0.812011 ‐0.72265 0.605982 0.055222 ‐2.40382 ‐0.72265 0.300628 0 STM1295 protease IV, a signal peptide peptidase sppA ‐0.2943676 ‐0.45289037 ‐0.39618397 ‐0.58583647 ‐0.5792948 ‐0.5848898 ‐0.58334 0.667417 0.040866 ‐2.26284 ‐0.58334 0.257791 0 STM1304 arginine succinyltransferase astA ‐0.44366714 ‐0.64911693 ‐0.6599875 ‐0.7756207 ‐0.96686655 ‐0.9297423 ‐0.89074 0.539336 0.260035 ‐2.83405 ‐0.89074 0.3143 0 STM1305 succinylglutamic semialdehyde dehydrogenase astD ‐0.24514297 ‐0.41127566 ‐0.3780378 ‐0.63193977 ‐0.52545446 ‐0.57170576 ‐0.57637 0.670651 ‐0.6288 ‐2.01121 ‐0.57637 0.286578 0 STM1310 NAD synthetase, prefers NH3 over glutamine nadE 0.29985374 0.38263682 0.37407726 ‐0.5443109 ‐0.49825403 ‐0.5621249 ‐0.5349 0.690208 ‐0.02918 ‐1.94664 ‐0.5349 0.274779 0 STM1320 part of a kinase, putative domain shared ydjN 0.046802618 0.038091604 0.03691275 1.5665126 1.2462264 1.3662349 1.392991 2.626226 0.60163 3.989423 1.392991 0.349171 0 STM1324 putative cytoplasmic protein 0.095578276 0.12058025 0.19640777 ‐0.7960288 ‐1.0856298 ‐0.6835736 ‐0.85508 0.552836 0.871885 ‐2.27711 ‐0.85508 0.37551 0 STM1325 putative cytoplasmic protein ydiZ 0.15465511 ‐0.029846352 0.17462827 ‐1.171536 ‐1.1068064 ‐1.0095242 ‐1.09596 0.467826 ‐0.74436 ‐3.61902 ‐1.09596 0.302832 0 STM1326 6‐phosphofructokinase II pfkB 0.13333306 0.20857969 0.32062015 ‐0.5588714 ‐0.6502705 ‐0.5986638 ‐0.6026 0.658565 ‐1.0995 ‐2.13531 ‐0.6026 0.282208 0 STM1342 ABC superfamily (binding protein), vitamin B12 transport btuD ‐0.080898724 0.021437347 ‐0.019437123 ‐0.46719512 ‐0.41809595 ‐0.63415766 ‐0.50648 0.703936 0.073202 ‐1.57713 ‐0.50648 0.321142 0 STM1345 putative cytoplasmic protein ydiU 1.1109093 1.4927708 1.3023136 0.837666 0.87025166 0.8473188 0.851745 1.804683 0.706048 3.209131 0.851746 0.265413 0 STM1348 putative inner membrane protein ydiA ‐0.008475127 ‐0.11085564 0.00335303 ‐0.98782885 ‐1.0171635 ‐0.87472814 ‐0.95991 0.51409 ‐0.70344 ‐3.20854 ‐0.95991 0.299173 0 STM1350 Homolog of a plant pathogenicity factor ydiD ‐0.37968674 ‐0.02649557 ‐0.23027726 ‐0.69067895 ‐0.65585244 ‐0.6087594 ‐0.65176 0.636502 0.407475 ‐2.33201 ‐0.65176 0.279486 0 STM1353 putative electron transfer flavoprotein ydiR ‐0.21897374 ‐0.20456798 0.048657984 ‐0.57548267 ‐0.5184006 ‐0.50821173 ‐0.53403 0.690622 ‐1.16895 ‐1.93012 ‐0.53403 0.276683 0 STM1354 putative electron transfer flavoprotein ydiQ ‐0.17257172 0.07833293 ‐0.08649514 ‐0.6196425 ‐0.707356 ‐0.8314009 ‐0.71947 0.607322 ‐0.40641 ‐2.26834 ‐0.71947 0.317178 0 STM1367 putative cytoplasmic protein ydiH ‐1.1607132 ‐1.217718 ‐0.95250094 ‐1.1420289 ‐1.0192692 ‐1.0349541 ‐1.06542 0.477834 ‐0.94185 ‐3.6199 ‐1.06542 0.294322 0 STM1370 putative ABC transporter sufB 1.8288628 1.8384182 1.7571864 2.0679772 1.9349446 1.9260905 1.976337 3.934929 0.666454 6.551958 1.976337 0.301641 0 STM1373 selenocysteine lyase sufS 1.0143319 0.8581476 0.9030303 1.7707404 1.9531987 1.996953 1.906964 3.750191 1.571817 5.867172 1.906964 0.325023 0 STM1374 putative SufE protein probably involved in Fe‐S ynhA 0.6949266 0.8367215 0.78655946 1.3053304 1.282638 1.2608409 1.282936 2.433337 0.166026 4.776498 1.282937 0.268594 0 STM1375 putative LysM domain ynhG 0.2030428 0.0627239 0.10129302 1.1016718 0.56228167 0.43078968 0.698248 1.622533 ‐0.26159 1.51463 0.698248 0.461002 0 STM1388 putative cytoplasmic protein orf70 0.09683996 0.281905 0.21109246 0.99918956 0.7773908 0.2995659 0.692049 1.615576 ‐0.47545 1.497383 0.692049 0.462172 0 STM1391 Secretion system regulator: transcriptonal activator, homologous with ssrB ‐0.045912962 ‐0.07884433 ‐0.037779655 ‐0.4242109 ‐0.6474891 ‐0.61075556 ‐0.56082 0.677917 ‐0.43475 ‐1.72628 ‐0.56082 0.324872 0 STM1398 Secretion system effector sseB ‐1.6741128 ‐1.4779617 ‐1.5637157 ‐1.5679544 ‐1.726097 ‐1.6248128 ‐1.63962 0.320941 0.526659 ‐5.42925 ‐1.63962 0.301998 0 STM1400 Secretion system effector sseC ‐0.89993477 ‐0.95905095 ‐0.6318036 ‐1.0857143 ‐1.2127495 ‐1.1596113 ‐1.15269 0.449785 ‐1.10794 ‐3.93969 ‐1.15269 0.292584 0 STM1402 Secretion system effector sseE ‐0.7404304 ‐0.5855545 ‐0.44367382 ‐1.4752728 ‐1.1332533 ‐1.2630181 ‐1.29051 0.408805 0.451956 ‐3.63081 ‐1.29051 0.355435 0 STM1404 Secretion system effector sseF ‐0.08034967 0.07565084 0.06725627 ‐0.96691734 ‐0.7155965 ‐0.9358278 ‐0.87278 0.546093 0.290199 ‐2.60646 ‐0.87278 0.334852 0 STM1405 Secretion system effector sseG ‐0.18586467 ‐0.16700755 ‐0.133329 ‐0.3972213 ‐0.45908755 ‐0.3669683 ‐0.40776 0.753793 0.96431 ‐1.44156 ‐0.40776 0.282859 0 STM1407 Secretion system apparatus ssaH ‐2.5226486 ‐2.480366 ‐2.4565828 ‐3.276874 ‐3.4141567 ‐3.4247928 ‐3.37194 0.096593 ‐0.45741 ‐11.1145 ‐3.37194 0.303382 0 STM1409 Secretion system apparatus: homology with the yscJ/mxiJ/prgK ssaJ ‐1.745902 ‐1.4621507 ‐1.4960818 ‐1.9544916 ‐1.8679796 ‐1.8298781 ‐1.88412 0.27091 0.371105 ‐6.43887 ‐1.88412 0.292616 0 STM1410 putative cytoplasmic protein ‐1.2823895 ‐1.324541 ‐1.2172247 ‐1.8518736 ‐2.1207027 ‐2.0425308 ‐2.00504 0.249129 ‐0.07443 ‐5.97473 ‐2.00504 0.335586 0 STM1411 Secretion system apparatus ssaK ‐1.212782 ‐0.865683 ‐0.86629224 ‐1.5459058 ‐1.4453876 ‐1.4393945 ‐1.4769 0.359261 0.309392 ‐5.08752 ‐1.4769 0.290298 0 STM1412 Secretion system apparatus ssaL ‐1.1971893 ‐1.7317013 ‐1.5377116 ‐1.1985549 ‐1.706445 ‐1.4232875 ‐1.44276 0.367862 1.172099 ‐3.58283 ‐1.44276 0.402688 0 STM1413 Secretion system apparatus ssaM ‐0.77967024 ‐0.8322191 ‐0.78975403 ‐2.2722535 ‐1.7264606 ‐1.8331716 ‐1.94396 0.259902 ‐0.88532 ‐4.59825 ‐1.94396 0.422761 0 STM1419 Secretion system apparatus: homology with YscR of ssaR ‐2.10759 ‐2.092133 ‐1.865195 ‐1.5756209 ‐2.0081894 ‐1.995713 ‐1.85984 0.275507 ‐0.1716 ‐4.67408 ‐1.85984 0.397905 0 STM1427 cyclopropane fatty acyl phospholipid synthase cfa 0.53838634 0.5852242 0.549235 ‐1.1271503 ‐1.9751949 ‐1.5026411 ‐1.535 0.34508 0.532108 ‐3.0633 ‐1.535 0.501093 0 STM1428 putative MFS family transport protein ydhC ‐0.086790815 ‐0.105173916 ‐0.39397734 ‐0.7249601 ‐0.6731876 ‐0.6777504 ‐0.69197 0.61901 ‐2.79772 ‐2.5412 ‐0.69197 0.272299 0 STM1449 tyrosine tRNA synthetase tyrS 0.14966837 ‐0.02462159 ‐0.093539745 0.37887296 0.3974113 0.47508696 0.417124 1.335263 0.043799 1.462457 0.417124 0.285221 0 STM1451 glutathionine S‐transferase gst 0.41312236 0.4460167 0.54826 ‐0.70826876 ‐0.6502949 ‐0.7800278 ‐0.71286 0.610108 ‐0.72776 ‐2.43074 ‐0.71286 0.293271 0 STM1452 putative POT family, peptide transport protein ydgR ‐0.08561341 ‐0.09977127 ‐0.048650537 ‐0.7505755 ‐0.5336004 ‐0.563473 ‐0.61588 0.65253 1.107941 ‐1.90295 ‐0.61588 0.323646 0 STM1456 putative oxidoreductase ydgO ‐0.18982045 ‐0.3831436 ‐0.35884932 1.138298 1.0549725 1.025241 1.072837 2.103566 0.728686 3.704719 1.072837 0.289587 0 STM1467 mannose‐6‐phosphate isomerase manA 0.09934974 ‐0.06953407 0.16549467 ‐0.77736884 ‐0.75218385 ‐0.76715267 ‐0.76557 0.588222 ‐0.66391 ‐2.91021 ‐0.76557 0.263063 0 STM1471 sensory histidine kinase in two‐component regulatory system rstB ‐0.23468739 ‐0.255906 ‐0.08181926 ‐0.6600637 ‐0.62928545 ‐0.5765737 ‐0.62197 0.649781 ‐0.6998 ‐2.22033 ‐0.62197 0.280127 0 STM1472 putative periplasmic protein 0.001483276 ‐0.023751773 ‐0.1438854 ‐0.3646904 ‐0.4561633 ‐0.44944343 ‐0.42343 0.745649 ‐0.82839 ‐1.48477 ‐0.42343 0.285185 0 STM1477 putative amino acid transporter ydgI ‐0.3116799 ‐0.013351898 ‐0.069152325 ‐0.3696191 ‐0.86721665 ‐0.7860708 ‐0.6743 0.626635 0.376748 ‐1.64511 ‐0.6743 0.409882 0 STM1478 putative periplasmic protein ydgH 0.36855495 0.3679174 0.36575988 0.7347037 0.85411257 0.74237645 0.777064 1.71364 ‐1.41856 2.640046 0.777064 0.294337 0 STM1485 acid shock protein ‐0.055210296 ‐0.093497545 0.034639798 ‐0.96861243 ‐0.7401026 ‐0.8380957 ‐0.84894 0.555194 0.203677 ‐2.63697 ‐0.84894 0.321937 0 STM1486 putative MFS familty transport protein ynfM ‐0.23127855 ‐0.39081946 ‐0.45196387 ‐0.5932076 ‐0.7651399 ‐0.628818 ‐0.66239 0.631831 2.25206 ‐2.14961 ‐0.66239 0.308144 0 STM1489 putative dethiobiotin synthase ynfK ‐1.1623932 ‐1.1485412 ‐0.97866875 ‐0.52552414 ‐0.760583 ‐0.5617785 ‐0.61596 0.652495 ‐0.8068 ‐1.87329 ‐0.61596 0.328814 0 STM1495 putative component of anaerobic dehydrogenases ynfI ‐0.19872937 ‐0.3369662 ‐0.32943332 ‐0.6292595 ‐0.54972446 ‐0.5097459 ‐0.56291 0.676935 ‐0.29085 ‐1.93523 ‐0.56291 0.290874 0 STM1496 putative dimethylsulfoxide reductase ‐0.3685398 ‐0.37358811 ‐0.27664664 ‐0.5378545 ‐0.60932666 ‐0.63203114 ‐0.59307 0.66293 0.907938 ‐2.08736 ‐0.59307 0.284125 0 STM1497 putative dimethyl sulphoxide reductase ‐0.3500527 ‐0.55640876 ‐0.51866335 ‐0.7948172 ‐1.1683357 ‐0.8657208 ‐0.94296 0.520165 0.899718 ‐2.54659 ‐0.94296 0.370282 0 STM1500 putative outer membrane protein ynfD ‐0.2840113 ‐0.157557 ‐0.16994056 ‐0.73276037 ‐0.82988316 ‐0.68797207 ‐0.75021 0.594519 ‐1.32298 ‐2.52056 ‐0.75021 0.297634 0 STM1501 putative inner membrane lipoprotein ynfC ‐0.12229592 ‐0.09390689 ‐0.08647378 ‐0.60774875 ‐0.62542945 ‐0.7074547 ‐0.64688 0.638661 ‐0.46499 ‐2.25814 ‐0.64688 0.286465 0 STM1504 putative inner membrane lipoprotein ynfA ‐0.13590805 ‐0.23647597 ‐0.21969484 ‐0.8076601 ‐0.86296415 ‐0.9510768 ‐0.8739 0.54567 ‐0.86919 ‐2.93738 ‐0.8739 0.29751 0 STM1507 putative transport protein ydfJ ‐0.15804242 ‐0.15857194 ‐0.08365344 ‐0.601096 ‐0.44695082 ‐0.63138336 ‐0.55981 0.678391 1.942743 ‐1.78937 ‐0.55981 0.312853 0 STM1509 putative cytoplasmic protein ydfZ ‐1.3511477 ‐1.210879 ‐0.81715876 ‐2.0551136 ‐2.1272924 ‐1.9854239 ‐2.05594 0.240491 ‐3.5849 ‐6.92924 ‐2.05594 0.296706 0 STM1528 putative outer membrane protein ‐0.12595634 ‐0.35776296 ‐0.16172118 ‐0.50909084 ‐0.5601326 ‐0.44228798 ‐0.50384 0.705229 1.640155 ‐1.73815 ‐0.50384 0.28987 0 STM1532 putative dehydrogenase protein ‐0.15376502 ‐0.10208606 ‐0.04879934 ‐0.94183975 ‐0.68510705 ‐0.7221051 ‐0.78302 0.58115 1.442658 ‐2.33127 ‐0.78302 0.335876 0 STM1533 putative hydrogenase 0.06782231 0.15546015 0.13181192 ‐0.685314 ‐0.992452 ‐0.7613524 ‐0.81304 0.569181 0.88314 ‐2.33563 ‐0.81304 0.348102 0 STM1534 putative hydrogenase ‐0.13515557 ‐0.0418269 0.0409649 ‐0.6052997 ‐0.6744813 ‐0.7226432 ‐0.66747 0.629608 ‐0.03473 ‐2.30319 ‐0.66747 0.289804 0 STM1536 putative hydrogenase maturation protease ‐0.18552598 ‐0.20655942 ‐0.2750501 ‐0.5512554 ‐0.6772804 ‐0.726064 ‐0.65153 0.636603 0.394928 ‐2.11654 ‐0.65153 0.307829 0 STM1537 putative Ni/Fe‐hydrogenase 1 b‐type cytochrome subunit ‐0.2032689 ‐0.21031234 ‐0.17360745 ‐1.1877218 ‐1.1009934 ‐1.0048685 ‐1.09786 0.467209 ‐1.3522 ‐3.55804 ‐1.09786 0.308558 0 STM1539 putative hydrogenase‐1 small subunit ‐0.21789321 ‐0.033842675 ‐0.21605578 ‐0.794696 ‐0.72448015 ‐0.7767756 ‐0.76532 0.588324 0.274159 ‐2.76474 ‐0.76532 0.276813 0 STM1546 putative monooxygenase 0.20372333 0.10701732 0.15740846 ‐0.558984 ‐0.5951373 ‐0.60820156 ‐0.58744 0.665522 ‐0.07092 ‐2.17193 ‐0.58744 0.270469 0 STM1549 putative translation initiation inhibitor 0.106838144 0.20268254 0.22907755 ‐0.7320999 ‐0.6893947 ‐0.8041505 ‐0.74188 0.597959 0.135797 ‐2.56497 ‐0.74188 0.289236 0 STM1556 putative Na /H antiporter ‐0.007203043 ‐0.08502233 ‐0.11407895 ‐0.46775585 ‐0.6495617 ‐0.6261081 ‐0.58114 0.668435 ‐0.26093 ‐1.8576 ‐0.58114 0.312845 0 STM1558 putative glycosyl hydrolase ‐0.089331925 ‐0.06959273 ‐0.07084581 ‐0.50252587 ‐0.68266314 ‐0.67003536 ‐0.61841 0.651389 0.202816 ‐1.97067 ‐0.61841 0.313805 0 STM1559 putative glycosyl hydrolase ‐0.034019895 0.005380407 0.007884459 ‐0.5451603 ‐0.5296892 ‐0.52982485 ‐0.53489 0.690211 0.54408 ‐2.0503 ‐0.53489 0.260884 0 STM1565 30S ribosomal subunit protein S22 rpsV ‐0.42334127 ‐0.596213 ‐0.09476432 ‐1.666416 ‐1.6521345 ‐1.6026465 ‐1.6404 0.320768 ‐1.39684 ‐5.96355 ‐1.6404 0.275071 0 STM1571 putative permease yddG 0.09303354 ‐0.12684515 ‐0.039898522 ‐0.5169558 ‐0.78011316 ‐0.54541606 ‐0.61416 0.653309 2.357846 ‐1.81099 ‐0.61416 0.339131 0 STM1582 putative arylamine N‐acetyltransferase nhoA 0.09087757 0.17604361 0.14440401 ‐0.4605063 ‐0.6325657 ‐0.8063286 ‐0.63313 0.644774 ‐0.61466 ‐1.78056 ‐0.63313 0.35558 0 STM1585 putative outer membrane lipoprotein ‐0.08836462 0.099436425 0.06889076 0.32994342 0.60093623 0.5234561 0.484779 1.399371 0.070921 1.441363 0.484779 0.336333 0 STM1588 putative regulatory protein, gntR family yncC ‐0.23514542 0.041621055 0.023392105 ‐0.62129307 ‐0.778097 ‐0.8816995 ‐0.76036 0.590348 ‐0.64607 ‐2.2941 ‐0.76036 0.331444 0 STM1606 putative benzoate membrane transport protein ‐0.2536418 ‐0.32784393 ‐0.26576608 ‐0.5791322 ‐0.61242646 ‐0.6168841 ‐0.60281 0.658468 ‐0.01252 ‐2.25216 ‐0.60281 0.26766 0 STM1612 putative cellulase protein ‐0.52231705 ‐0.7856752 ‐0.7000317 ‐1.3844473 ‐1.5026865 ‐1.395355 ‐1.4275 0.371776 0.147938 ‐4.86409 ‐1.4275 0.293476 0 STM1613 putative PTS system, enzymeIIB component ‐0.3519927 ‐0.3795157 ‐0.40696353 ‐0.9162813 ‐1.1813852 ‐0.9658277 ‐1.02116 0.492718 ‐0.13897 ‐3.02902 ‐1.02116 0.337127 0 STM1614 putative PTS system enzyme IIC component ‐0.33452767 ‐0.6439114 ‐0.49038953 ‐0.4312252 ‐0.64045763 ‐0.45143804 ‐0.50771 0.703339 0.647298 ‐1.57487 ‐0.50771 0.322381 0 STM1615 putative nucleoside triphosphatase ‐0.2504369 ‐0.39927378 ‐0.5593485 ‐0.87528783 ‐0.8458499 ‐0.91353655 ‐0.87822 0.544036 0.119918 ‐3.18955 ‐0.87822 0.275344 0 STM1616 putative Sugar Specific PTS Enzyme II ‐0.5471751 ‐0.6508115 ‐0.69132197 ‐0.9636082 ‐1.3039311 ‐1.1980091 ‐1.15518 0.449009 0.08326 ‐3.24217 ‐1.15518 0.356299 0 STM1617 putative ribulose‐phosphate 3‐epimerase ‐0.19925678 ‐0.1544576 ‐0.089455344 ‐0.34568596 ‐0.45893317 ‐0.6631916 ‐0.48927 0.712385 ‐0.60427 ‐1.40332 ‐0.48927 0.348652 0 STM1627 alcohol dehydrogenase class III 0.3018156 ‐0.007162598 0.2390924 0.45413736 0.38278034 0.52605206 0.454323 1.37014 0.437683 1.529148 0.454323 0.297109 0 STM1632 putative inner membrane protein 0.10058872 0.031953044 0.17441356 ‐0.41350847 ‐0.5831861 ‐0.55534726 ‐0.51735 0.698655 ‐1.11307 ‐1.67813 ‐0.51735 0.308287 0 STM1638 putative SAM‐dependent methyltransferases 0.011606389 ‐0.004490397 ‐0.06840186 0.97099084 0.67011476 0.77110285 0.804069 1.746019 0.812388 2.336356 0.804069 0.344155 0 STM1639 cytochrome b(561) cybB ‐0.010859509 0.120846935 0.2399092 ‐0.46831122 ‐0.48407668 ‐0.35868126 ‐0.43702 0.738657 ‐1.12162 ‐1.48051 ‐0.43702 0.295184 0 STM1642 acyl carrier protein phosphodiesterase acpD ‐0.10919571 0.041565914 ‐0.21896222 ‐0.5127906 ‐0.7541382 ‐0.9500993 ‐0.73901 0.599151 ‐0.34981 ‐1.93349 ‐0.73901 0.382216 0 STM1647 fermentative D‐lactate dehydrogenase, NAD‐dependent ldhA ‐0.102360666 ‐0.05225767 ‐0.21389751 ‐1.1932006 ‐1.3984904 ‐1.7124944 ‐1.43473 0.369916 ‐0.30407 ‐3.52732 ‐1.43473 0.406748 0 STM1649 putative cytoplasmic protein ‐0.19018997 ‐0.399026 ‐0.3227409 ‐0.76038283 ‐0.75157917 ‐0.78606546 ‐0.76601 0.588042 ‐0.89562 ‐2.87871 ‐0.76601 0.266095 0 STM1660 transcriptional regulation of aerobic, anaerobic respiration, osmotic fnr 0.2812335 0.39288732 0.4851172 0.5186295 0.41619164 0.36252376 0.432448 1.349522 ‐1.03872 1.434129 0.432448 0.301541 0 STM1663 putative integral membrane protein ynaI ‐0.007718208 ‐0.10974138 ‐0.10466575 ‐0.3929026 ‐0.45954356 ‐0.5163247 ‐0.45626 0.728875 ‐0.33745 ‐1.56565 ‐0.45626 0.291416 0 STM1672 putative cytoplasmic protein 0.08616393 0.109365046 0.05195004 ‐0.4659009 ‐0.78160584 ‐0.83686554 ‐0.69479 0.617799 0.416648 ‐1.87123 ‐0.69479 0.371301 0 STM1676 putative aldo/keto reductase family ‐0.031380136 0.16731921 0.10788623 ‐0.7303201 ‐0.7757595 ‐0.6681624 ‐0.72475 0.605103 1.025006 ‐2.52582 ‐0.72475 0.286935 0 STM1680 putative carboxypeptidase ycjI ‐0.14750583 ‐0.27840137 ‐0.16082178 ‐0.517121 ‐0.7022351 ‐0.44785112 ‐0.55574 0.68031 ‐0.75053 ‐1.67552 ‐0.55574 0.33168 0 STM1682 thiol peroxidase tpx 0.6041635 0.75391585 0.6196073 1.0710678 1.1310829 1.1226921 1.108281 2.155886 0.471303 4.03726 1.108281 0.274513 0 STM1686 phage shock protein pspE ‐0.24195158 ‐0.2239119 ‐0.2397045 ‐0.6327867 ‐0.5577372 ‐0.6503412 ‐0.61362 0.653554 0.13329 ‐2.15952 ‐0.61362 0.284148 0 STM1690 phage shock protein negative regulatory gene for pspA ‐0.15976194 ‐0.010411385 ‐0.08804815 ‐1.5960633 ‐0.71834034 ‐0.97084504 ‐1.09508 0.468109 0.851866 ‐2.11967 ‐1.09508 0.51663 0 STM1692 ABC superfamily (periplasm), peptide transport protein sapA ‐0.1263535 ‐0.25867128 ‐0.25376248 ‐0.8616485 ‐0.6168595 ‐0.49295065 ‐0.65715 0.634128 0.673689 ‐1.805 ‐0.65715 0.364074 0 STM1697 putative Diguanylate cyclase/phosphodiesterase domain 2 0.27374637 0.016170513 0.10604738 ‐0.94297886 ‐0.93781877 ‐0.90692276 ‐0.92924 0.525135 0.257725 ‐3.48021 ‐0.92924 0.267007 0 STM1702 RNase II, mRNA degradation rnb 0.24852581 ‐0.061163615 0.1715302 0.56479317 0.5931013 0.57596654 0.577954 1.49273 ‐1.99489 2.189371 0.577954 0.263982 0 STM1714 DNA topoisomerase type I, omega protein topA 0.13929856 0.12498835 0.047933824 0.5281989 1.0019652 0.86759585 0.799253 1.7402 0.953883 2.014661 0.799253 0.396718 0 STM1726 tryptophan synthase, beta protein trpB 0.6247902 0.7092721 0.81449515 0.89797586 0.80832547 0.82315576 0.843152 1.793966 ‐0.95737 2.974149 0.843152 0.283494 0 STM1746 ABC superfamily (periplasm), oligopeptide transport protein with oppA 0.10556983 0.14339177 0.28086802 ‐0.5346366 ‐0.7749634 ‐0.8569063 ‐0.72217 0.606185 ‐0.34482 ‐2.04898 ‐0.72217 0.352453 0 STM1749 iron‐dependent alcohol dehydrogenase of the multifunctional alcohol adhE ‐0.94126964 ‐1.0152637 ‐1.0613933 ‐3.373034 ‐2.9843004 ‐2.7309978 ‐3.02944 0.122475 0.475452 ‐6.84684 ‐3.02944 0.442459 0 STM1754 putative phosphoesterase ychK 0.47854376 0.34373415 0.37279 0.75828016 0.958124 1.0925204 0.936308 1.913625 0.01751 2.653551 0.936308 0.352851 0 STM1761 nitrate reductase 1, cytochrome b(NR), gamma subunit narI ‐0.17575248 ‐0.091930225 ‐0.05066422 ‐1.1388326 ‐0.7310931 ‐0.6237552 ‐0.83123 0.562051 ‐1.29715 ‐2.0144 ‐0.83123 0.412643 0 STM1780 phosphoribosylpyrophosphate synthetase prsA ‐0.30122158 ‐0.27414304 ‐0.3812938 0.81053585 0.5377214 0.43598494 0.594747 1.510208 0.144566 1.618054 0.594747 0.36757 0 STM1784 putative GTP‐binding protein ychF 0.1969354 0.21479593 0.20464218 0.6455129 0.89789003 0.59121174 0.711538 1.637549 ‐0.09152 2.031603 0.711538 0.350235 0 STM1785 putative cytoplasmic protein 0.057605747 0.08438086 0.2458505 1.1502045 0.54018706 0.60706544 0.765819 1.700335 0.898357 1.705954 0.765819 0.44891 0 STM1792 putative cytochrome oxidase, subunit I ‐0.004706493 ‐0.24098572 ‐0.2690527 ‐0.59740245 ‐0.41082653 ‐0.5167275 ‐0.50832 0.703041 ‐0.17002 ‐1.64094 ‐0.50832 0.309773 0 STM1793 putative cytochrome oxidase, subunit II ‐0.20705564 ‐0.40138167 ‐0.38687545 ‐0.627598 ‐0.99744743 ‐0.6675818 ‐0.76421 0.588776 0.720654 ‐2.04916 ‐0.76421 0.372939 0 STM1797 putative transglycosylase‐associated protein ymgE ‐0.074945815 ‐0.18277146 ‐0.10639785 ‐0.42816684 ‐0.75552917 ‐0.61599755 ‐0.5999 0.659801 0.087958 ‐1.71109 ‐0.5999 0.350593 0 STM1802 alanine racemase 2, catabolic dadX 0.093311004 0.06541252 0.023002686 ‐0.60868037 ‐0.47967458 ‐0.7302695 ‐0.60621 0.656921 ‐0.85842 ‐1.84763 ‐0.60621 0.328101 0 154 STM1814 cell division inhibitor activated MinC inhibits FtsZ minC 0.20873626 0.22262585 0.16397606 0.81621933 0.31987524 0.5204162 0.55217 1.46629 0.813954 1.380741 0.55217 0.399909 0 STM1821 putative DNA helicase yoaA ‐0.23990272 ‐0.30401734 ‐0.029133506 ‐0.8018912 ‐0.53843874 ‐0.5280769 ‐0.6228 0.649408 ‐1.72392 ‐1.80343 ‐0.6228 0.345344 0 STM1829 putative cytoplasmic protein ‐0.26884434 ‐0.42344797 ‐0.2660132 ‐0.3604281 ‐0.6645848 ‐0.5956276 ‐0.54021 0.687669 ‐0.48343 ‐1.55314 ‐0.54021 0.34782 0 STM1838 putative cytoplasmic protein yobF ‐0.30826873 ‐0.44221333 ‐0.34613034 ‐0.49601406 ‐0.9558 ‐0.54831296 ‐0.66671 0.629942 ‐0.59482 ‐1.66228 ‐0.66671 0.401081 0 STM1840 putative inner membrane protein yobG ‐0.582477 ‐0.57865244 ‐0.51988935 ‐0.33765703 ‐0.6450774 ‐0.5211667 ‐0.5013 0.70647 ‐0.2769 ‐1.45284 ‐0.5013 0.345048 0 STM1844 heat shock protein, integral membrane protein htpX 0.069191605 0.1054979 0.04267285 1.3484325 0.9440111 0.74709153 1.013178 2.018353 0.243027 2.341238 1.013178 0.432753 0 STM1845 carboxy‐terminal protease for penicillin‐binding protein 3 prc 0.23165391 0.09220145 0.03891062 1.5405129 1.2421398 1.4411441 1.407932 2.653566 ‐0.14021 4.099158 1.407932 0.343469 0 STM1846 activator of proP proQ 0.07755703 ‐0.04104786 0.18038921 0.77866393 0.90958303 0.78325266 0.823833 1.770103 ‐0.70875 2.75857 0.823833 0.298645 0 STM1849 putative inner membrane protein ‐0.11267924 ‐0.24856229 ‐0.18332617 ‐0.45260203 ‐0.7098146 ‐0.60011125 ‐0.58751 0.665491 1.050737 ‐1.77889 ‐0.58751 0.330267 0 STM1851 putative cytoplasmic protein ‐0.30207226 ‐0.35991398 ‐0.28196493 ‐1.4156271 ‐1.2193029 ‐1.2874681 ‐1.30747 0.40403 1.080465 ‐4.17322 ‐1.30747 0.313299 0 STM1852 putative inner membrane lipoprotein yebW ‐0.18065819 ‐0.2861385 ‐0.2872012 ‐0.44179687 ‐0.7366514 ‐0.59125876 ‐0.5899 0.664388 1.289066 ‐1.73058 ‐0.5899 0.34087 0 STM1863 putative inner membrane protein 0.1864297 0.036686923 0.041368224 ‐0.5521444 ‐0.6372888 ‐0.7499136 ‐0.64645 0.638851 ‐0.7082 ‐2.06517 ‐0.64645 0.313024 0 STM1864 putative inner membrane protein 0.27213326 0.19440068 0.07415763 ‐0.69375944 ‐0.57718146 ‐0.33678567 ‐0.53591 0.689724 0.016659 ‐1.48515 ‐0.53591 0.360845 0 STM1874 putative inner membrane protein 0.14664434 0.100961916 0.19800717 1.0275615 1.5390232 1.2851639 1.283916 2.434991 1.396835 3.18276 1.283916 0.403397 0 STM1878 DNA exonuclease X, degrades ss and ds exoX 0.1810388 0.105976425 0.09778798 ‐0.44643223 ‐0.48117566 ‐0.55824053 ‐0.49528 0.709423 ‐0.87902 ‐1.71504 ‐0.49528 0.288788 0 STM1879 protease II ptrB 0.4198059 0.152566 ‐0.18538009 ‐0.40455627 ‐0.67309177 ‐0.50660735 ‐0.52809 0.693475 0.210057 ‐1.58105 ‐0.52809 0.334009 0 STM1888 pyruvate kinase II, glucose stimulated pykA ‐0.45786908 ‐0.6001217 ‐0.33456108 ‐0.7494681 ‐0.7444827 ‐0.60186774 ‐0.69861 0.616167 ‐1.07783 ‐2.29699 ‐0.69861 0.30414 0 STM1890 putative Peptidase yebA 0.7314299 0.6941771 0.91438 ‐1.1120312 ‐1.4507257 ‐0.8762661 ‐1.14634 0.45177 0.630338 ‐2.71345 ‐1.14634 0.422467 0 STM1891 ABC superfamily (bind_prot) high affinity Zn transport znuA 1.3631965 1.3828597 1.453435 ‐3.1004639 ‐3.2172017 ‐3.3780866 ‐3.23192 0.106438 0.361455 ‐9.61224 ‐3.23192 0.336229 0 STM1892 ABC superfamily (atp_bind) high affinity Zn transport znuC 0.25144094 0.24517128 0.09406786 ‐1.0330946 ‐1.088731 ‐1.1055045 ‐1.07578 0.474416 ‐2.0841 ‐3.87481 ‐1.07578 0.277633 0 STM1893 ABC superfamily (atp_bind) high affinity Zn transport zunB ‐0.03187781 ‐0.2856091 ‐0.24613762 ‐1.36795 ‐1.7113938 ‐1.6522384 ‐1.57719 0.335133 0.084761 ‐4.35983 ‐1.57719 0.361756 0 STM1894 Holliday junction helicase, subunit B ruvB ‐0.14616849 ‐0.3093324 ‐0.32275596 ‐0.52441055 ‐0.6152119 ‐0.6510335 ‐0.59689 0.66118 ‐0.1358 ‐2.03414 ‐0.59689 0.293434 0 STM1897 putative periplasmic protein yebB ‐0.2446566 0.04280575 0.004744758 ‐0.58817655 ‐0.48302406 ‐0.44973573 ‐0.50698 0.703695 0.544799 ‐1.7043 ‐0.50698 0.29747 0 STM1902 putative isochorismatase yecD ‐0.3656827 ‐0.36847875 ‐0.43531647 ‐0.67360085 ‐0.5151873 ‐0.6069283 ‐0.59857 0.660407 0.846233 ‐1.98419 ‐0.59857 0.30167 0 STM1904 putative inner membrane protein yecN ‐0.10861167 ‐0.07851224 ‐0.16326405 ‐0.5087431 ‐0.35234627 ‐0.4056329 ‐0.42224 0.746265 ‐0.22707 ‐1.39975 ‐0.42224 0.301655 0 STM1916 chemotaxis regulator, transmits chemoreceptor signals to flagelllar cheY ‐0.38359508 ‐0.43315798 ‐0.39431602 1.5257362 1.6956547 1.9617764 1.727722 3.312045 0.915163 4.515261 1.727722 0.382641 0 STM1917 methyl esterase, response regulator for chemotaxis (cheA cheB 0.021205017 ‐0.5573388 ‐0.035766583 2.082769 2.1655052 2.0335026 2.093926 4.269081 ‐1.64016 7.115864 2.093926 0.294262 0 STM1919 methyl accepting chemotaxis protein II, aspartate sensor‐receptor cheM ‐0.21584944 ‐0.3472248 ‐0.14102437 1.8705837 1.9050734 2.0245483 1.933402 3.819548 0.843816 6.393572 1.933402 0.302398 0 STM1920 purine‐binding chemotaxis protein regulation cheW ‐0.16131973 ‐0.58123994 0.008166656 2.2831492 1.9116014 1.9174606 2.037404 4.105061 ‐0.78793 5.380932 2.037404 0.378634 0 STM1921 sensory histitine protein kinase, transduces signal between cheA 0.106536426 ‐0.28617868 ‐0.06963351 3.0381498 2.9623184 3.0281928 3.009554 8.053153 0.286399 10.76604 3.009554 0.279542 0 STM1922 enables flagellar motor rotation, linking torque machinery motB ‐0.05808545 0.093669176 0.003069375 1.2339189 1.1990033 1.0977336 1.176885 2.260881 ‐0.11561 3.968071 1.176885 0.296589 0 STM1926 putative cytoplasmic protein ‐0.19881563 ‐0.40677258 ‐0.12561509 ‐1.4653237 ‐0.86791044 ‐0.9055835 ‐1.07961 0.473158 0.145794 ‐2.40492 ‐1.07961 0.448915 0 STM1927 putative universal stress protein yecG 0.046041377 ‐0.044514507 ‐0.08677584 ‐0.37884936 ‐0.6156154 ‐0.68871623 ‐0.56106 0.677804 0.030309 ‐1.60639 ‐0.56106 0.349267 0 STM1932 ferritin‐like protein ftnB ‐0.14805304 0.043752573 ‐0.10904165 ‐1.4604146 ‐1.3855908 ‐1.7150912 ‐1.52037 0.348598 ‐0.37864 ‐4.27694 ‐1.52037 0.35548 0 STM1936 putative cytoplasmic protein yecH ‐0.39661565 ‐0.27870166 ‐0.11134555 ‐0.5720005 ‐0.75935656 ‐0.76627064 ‐0.69921 0.61591 ‐0.93459 ‐2.18923 ‐0.69921 0.319385 0 STM1953 putative 1‐cyclopropane‐carboxylate deaminase yedO 0.14875863 0.06791354 0.122007385 1.4223013 1.0740879 1.4104686 1.302286 2.466193 ‐0.63034 3.520645 1.302286 0.3699 0 STM1956 sigma F (sigma 28) factor of RNA fliA 0.31583518 0.053942945 ‐0.017547473 1.156529 1.440264 1.3644723 1.320422 2.497391 0.14669 3.877133 1.320422 0.340567 0 STM1958 N‐methylation of lysine residues in flagellin fliB 0.1414723 0.3278289 0.24662276 1.0738633 1.1922829 0.9612492 1.075798 2.107888 ‐0.65103 3.336323 1.075799 0.32245 0 STM1959 flagellar biosynthesis flagellin, filament structural protein fliC 0.39477825 0.5807938 0.6376977 2.3017983 2.3778193 2.6140275 2.431215 5.393475 ‐0.49621 6.951228 2.431215 0.349753 0 STM1960 flagellar biosynthesis filament capping protein fliD 0.046875205 0.07710468 0.2806006 1.6295432 1.365571 1.6637 1.552938 2.934141 0.633763 4.437592 1.552938 0.349951 0 STM1970 flagellar biosynthesis, component of motor switching and fliG ‐0.33502188 ‐0.11381289 ‐0.3652626 0.6223094 0.61046654 0.48995155 0.574242 1.488895 0.357833 1.926772 0.574243 0.298034 0 STM1975 flagellar biosynthesis fliL ‐0.15826781 ‐0.03612866 ‐0.18180452 1.8774848 2.2947068 1.9960862 2.056093 4.158585 ‐0.12049 5.412593 2.056093 0.379872 0 STM1979 flagellar biosynthesis fliP ‐0.020009601 ‐0.20453846 ‐0.051829748 0.6913528 0.4050317 0.4412748 0.512553 1.426573 ‐0.66914 1.482397 0.512553 0.34576 0 STM1980 flagellar biosynthesis fliQ 0.017453767 ‐0.4703003 ‐0.10170686 0.91294384 0.42128915 0.5236481 0.619294 1.536123 0.094198 1.527165 0.619294 0.405518 0 STM1990 putative permease yedA ‐0.28627598 ‐0.53123426 ‐0.44428456 ‐0.68307203 ‐0.73559564 ‐0.49098048 ‐0.63655 0.64325 ‐0.00997 ‐1.92837 ‐0.63655 0.330097 0 STM1996 putative cold‐shock protein cspB 0.18569529 0.30097237 0.20967452 1.5791256 1.4667304 1.4199255 1.488594 2.806153 ‐0.21006 4.913029 1.488594 0.302989 0 STM2001 putative inner membrane protein yeeI 0.07780213 ‐0.052811924 0.10201301 ‐0.50360346 ‐0.56883603 ‐0.60503745 ‐0.55916 0.678698 ‐0.46284 ‐1.95902 ‐0.55916 0.285428 0 STM2006 putative branched chain amino acid transport protein ‐0.102783434 ‐0.052941978 ‐0.09161636 ‐0.79071563 ‐0.8204234 ‐1.0013149 ‐0.87082 0.546837 ‐0.43006 ‐2.70811 ‐0.87082 0.321559 0 STM2011 putative cytoplasmic protein ‐0.29447466 0.058238026 ‐0.04655777 ‐0.5200955 ‐0.42108572 ‐0.385836 ‐0.44234 0.73594 0.4769 ‐1.4947 ‐0.44234 0.295937 0 STM2021 synthesis of vitamin B12 adenosyl cobalamide precursor cboQ 0.026401527 0.039250746 0.03327545 ‐0.4720489 ‐0.39996484 ‐0.514378 ‐0.46213 0.725913 ‐0.5728 ‐1.59825 ‐0.46213 0.289148 0 STM2023 synthesis of vitamin B12 adenosyl cobalamide precursor cbiM ‐0.18780291 ‐0.19762504 ‐0.27362332 ‐0.4819454 ‐0.5443803 ‐0.52870744 ‐0.51834 0.698173 ‐0.32269 ‐1.8883 ‐0.51834 0.274503 0 STM2024 synthesis of vitamin B12 adenosyl cobalamide precursor cbiL ‐0.36653033 ‐0.5942693 ‐0.48899347 ‐0.6076826 ‐0.9152125 ‐0.813943 ‐0.77895 0.582792 0.888103 ‐2.24977 ‐0.77895 0.346234 0 STM2031 synthesis of vitamin B12 adenosyl cobalamide precursor cbiE ‐0.37218127 ‐0.245728 ‐0.3650228 ‐0.5108238 ‐0.51285577 ‐0.54533434 ‐0.523 0.695921 ‐0.06637 ‐1.95933 ‐0.523 0.26693 0 STM2035 synthesis of vitamin B12 adenosyl cobalamide precursor cbiA ‐0.12346863 ‐0.14128031 ‐0.18612704 ‐0.6427809 ‐0.6785252 ‐0.8296177 ‐0.71697 0.608372 ‐0.24808 ‐2.29059 ‐0.71697 0.313009 0 STM2039 Propanediol utilization: polyhedral bodies pudB ‐0.60162073 ‐0.6262743 ‐0.70491284 ‐0.6635016 ‐0.5572539 ‐0.5123162 ‐0.57769 0.670035 0.360469 ‐1.92196 ‐0.57769 0.300573 0 STM2059 putative cytoplasmic protein yeeX 0.32313725 0.3182445 0.48112833 ‐1.7658125 ‐1.9565146 ‐1.7855941 ‐1.83597 0.280102 0.122593 ‐5.80472 ‐1.83597 0.31629 0 STM2063 Hydrogen sulfide production: membrane anchoring protein phsC ‐0.08552289 0.07946232 ‐0.056804392 ‐0.6743178 ‐0.35142386 ‐0.82022935 ‐0.61532 0.652783 0.216705 ‐1.56071 ‐0.61532 0.394259 0 STM2070 putative dehydratase yeeZ 0.32365817 0.16975561 0.29050237 ‐0.41097435 ‐0.45042178 ‐0.3601026 ‐0.40717 0.754103 ‐0.7454 ‐1.44441 ‐0.40717 0.281892 0 STM2073 histidinol phosphate aminotransferase hisC 0.6341258 0.4897871 0.31570336 1.2940421 0.5775246 0.44503582 0.772201 1.707873 0.205016 1.48655 0.772201 0.519459 0 STM2079 regulator of length of O‐antigen component of wzzB 0.25764465 0.44832304 0.326458 0.54390585 0.6638624 0.47716227 0.561644 1.47595 ‐0.18252 1.809593 0.561644 0.31037 0 STM2080 UDP‐glucose/GDP‐mannose dehydrogenase udg 0.014545129 0.05432841 0.08512198 ‐0.64250344 ‐0.92977816 ‐0.9568699 ‐0.84305 0.557464 ‐0.34189 ‐2.36594 ‐0.84305 0.356328 0 STM2082 LPS side chain defect: bifunctional enzyme: undecaprenol‐phosphate rfbP ‐0.18199804 ‐0.16203153 ‐0.18614309 1.7216538 1.7367321 1.4169514 1.625112 3.084662 0.197338 4.515191 1.625112 0.359921 0 STM2083 LPS side chain defect: phosphomannomutase rfbK 0.4056601 0.53315276 0.58841336 0.5132727 0.49226788 0.59198165 0.532507 1.446441 ‐1.40501 1.861272 0.532507 0.286099 0 STM2087 LPS side chain defect: abequosyltransferase rfbV 0.98017097 0.9868867 0.9106193 1.3449967 1.3260227 1.4699153 1.380312 2.603246 0.759134 4.587505 1.380312 0.300885 0 STM2090 LPS side chain defect: CDP‐6deoxy‐D‐xylo‐4‐hexulose‐3‐dehydrase rfbH 0.51607764 0.44115597 0.42561674 0.65423524 0.4146966 0.613847 0.560926 1.475216 3.584895 1.700868 0.560926 0.329788 0 STM2091 LPS side chain defect: CDP glucose 4,6‐dehydratase rfbG 0.29437086 0.305522 0.3116214 0.9596773 0.724822 0.79896784 0.827822 1.775004 0.485894 2.54664 0.827822 0.325065 0 STM2096 TDP‐rhamnose synthetase rfbD 0.26496527 0.15737686 0.20318204 1.2561338 0.8229627 0.9822171 1.020438 2.028535 0.724796 2.669576 1.020438 0.382247 0 STM2117 putative protein‐tyrosine‐phosphatase in colanic acid export wzb ‐0.14169501 ‐0.63931817 ‐0.55770266 ‐0.48187384 ‐0.7830294 ‐0.5893673 ‐0.61809 0.651533 1.058628 ‐1.79748 ‐0.61809 0.343864 0 STM2130 sensory kinase in two‐component regulatoyr system wtih baeS ‐0.23525706 ‐0.30325264 ‐0.3394083 ‐0.6639423 ‐0.65042436 ‐0.796252 ‐0.70354 0.614064 ‐0.86384 ‐2.32752 ‐0.70354 0.30227 0 STM2139 putative inner membrane protein ‐1.4245783 ‐1.4444654 ‐1.3343866 ‐1.0207832 ‐0.9393163 ‐1.1401907 ‐1.03343 0.488547 0.421315 ‐3.29033 ‐1.03343 0.314081 0 STM2140 putative diacylglycerol kinase catalytic domain yegS 0.26698622 0.18609942 0.23534639 ‐0.6383152 ‐0.34186012 ‐0.69286036 ‐0.55768 0.679394 ‐0.94284 ‐1.52872 ‐0.55768 0.364802 0 STM2148 putative periplasmic protein 0.7350009 0.5211285 0.64384043 0.46631774 0.67152745 0.49984565 0.545897 1.459928 ‐1.1721 1.709635 0.545897 0.319306 0 STM2194 putative esterase yeiG 0.054421656 ‐0.03454032 ‐0.1072457 ‐0.33636925 ‐0.7749706 ‐0.6929472 ‐0.60143 0.659101 0.304822 ‐1.54063 ‐0.60143 0.390378 0 STM2199 outer membrane porin, receptor for colicin I cirA 0.42267513 0.34250376 0.29650134 1.9126965 1.9137075 1.8750834 1.900496 3.733415 ‐0.16757 7.079274 1.900496 0.268459 0 STM2200 APC family, lysine‐specific permease lysP 0.05140927 ‐0.116212964 ‐0.04760506 1.3873385 1.6515472 1.1871734 1.408686 2.654953 ‐0.24083 3.609915 1.408686 0.390227 0 STM2203 endonuclease IV nfo ‐0.045610104 ‐0.075764045 ‐0.17865808 0.7370712 0.6853415 0.35917997 0.593864 1.509284 ‐0.25123 1.58771 0.593864 0.374038 0 STM2214 putative lipoprotein, suppresses thermosensitivity of prc mutants spr 0.01517154 0.048784353 0.105388075 1.2080153 1.0828807 0.96607 1.085655 2.122339 0.810297 3.334251 1.085655 0.325607 0 STM2217 putative ABC‐type dipeptide/oligopeptide/nickel transport systems, permease component yejB ‐0.05366419 ‐0.10929663 ‐0.22557163 0.6320843 0.7185845 0.91006833 0.753579 1.68597 ‐0.13231 2.230302 0.753579 0.337882 0 STM2223 putative ATP‐dependent helicase yejH ‐0.34153134 ‐0.28165892 ‐0.48666865 ‐0.602654 ‐0.61617696 ‐0.80372417 ‐0.67419 0.626686 ‐0.4552 ‐2.10264 ‐0.67419 0.320637 0 STM2236 putative phage protein 0.18049029 0.2621859 0.1324489 ‐0.50787115 ‐1.0167085 ‐0.37465256 ‐0.63308 0.6448 0.707855 ‐1.40253 ‐0.63308 0.451382 0 STM2237 putative inner membrane protein ‐0.014838871 0.058021955 0.1272294 ‐0.45595673 ‐0.38579804 ‐0.42637488 ‐0.42271 0.746022 0.509064 ‐1.53108 ‐0.42271 0.276085 0 STM2267 outer membrane protein 1b (ibc), porin ompC ‐0.3649795 ‐0.68441063 ‐0.5550241 ‐1.9298726 ‐1.9060316 ‐1.8553083 ‐1.89707 0.268488 ‐0.94619 ‐6.83049 ‐1.89707 0.277736 0 STM2272 DNA gyrase, subunit A, type II topoisomerase gyrA 0.080137804 0.0748521 0.09637077 1.1776893 0.9506059 0.785593 0.971296 1.960601 ‐0.14457 2.629318 0.971296 0.36941 0 STM2280 putative permease 0.03252856 0.16715702 0.24949875 ‐0.61414075 ‐0.5495741 ‐0.65642756 ‐0.60671 0.656691 0.100917 ‐2.11533 ‐0.60671 0.286818 0 STM2299 paral putative transformylase yfbG ‐0.033254035 0.018600065 0.012057397 ‐0.5977108 ‐0.63679963 ‐0.64119536 ‐0.62524 0.648314 ‐0.08383 ‐2.31938 ‐0.62524 0.26957 0 STM2300 putative cytoplasmic protein 0.06925537 ‐0.12364325 ‐0.13452715 ‐0.24379787 ‐0.91190344 ‐0.8287754 ‐0.66149 0.632224 ‐0.45883 ‐1.4196 ‐0.66149 0.465971 0 STM2304 polymyxin resistance protein B pmrD ‐0.2081248 ‐0.20753814 ‐0.07757484 ‐0.8079383 ‐1.2756813 ‐1.07246 ‐1.05203 0.48229 0.722359 ‐2.6895 ‐1.05203 0.391161 0 STM2318 NADH dehydrogenase I chain L nuoL ‐0.8575317 ‐0.92838544 ‐1.0345399 0.92301166 0.9969052 0.9841413 0.968019 1.956153 0.669139 3.47517 0.968019 0.278553 0 STM2320 NADH dehydrogenase I chain J nuoJ ‐0.6258309 ‐0.58527905 ‐0.3001663 1.0111129 1.5354394 1.2720251 1.272859 2.4164 ‐0.18034 3.126571 1.272859 0.40711 0 STM2321 NADH dehydrogenase I chain I nuoI ‐0.39599353 ‐0.57785195 ‐0.5341032 0.3335542 0.5885079 0.6079343 0.509999 1.424049 ‐0.79409 1.481909 0.509999 0.34415 0 STM2323 NADH dehydrogenase I chain G nuoG ‐0.55333656 ‐0.52553827 ‐0.41416374 0.66871697 0.7760612 0.8482847 0.764354 1.69861 ‐0.89928 2.482348 0.764354 0.307916 0 STM2324 NADH dehydrogenase I chain F nuoF ‐0.76764554 ‐1.3955622 ‐1.2866403 0.7578795 0.7946701 0.71211123 0.754887 1.687499 0.503911 2.6996 0.754887 0.279629 0 STM2326 NADH dehydrogenase I chain C,D nuoC ‐0.90607184 ‐0.87389094 ‐0.7842597 0.7514559 0.64789313 0.71703404 0.705461 1.630666 0.805582 2.464919 0.705461 0.2862 0 STM2328 NADH dehydrogenase I chain A nuoA ‐0.5014692 ‐0.5934646 ‐0.56030476 0.7614176 0.57570356 0.48981956 0.60898 1.525181 ‐0.48876 1.812985 0.60898 0.335899 0 STM2331 putative aminotransferase (ortho), paral putative regulator yfbQ 0.10471456 0.153201 0.08440292 0.56494445 0.53034896 0.29456156 0.463285 1.378677 0.024279 1.359802 0.463285 0.3407 0 STM2333 putative response regulator yfbS ‐0.061281778 ‐0.39802796 ‐0.34647635 0.9858371 0.832419 1.0910722 0.969776 1.958537 ‐0.48435 2.931192 0.969776 0.330847 0 STM2337 acetate kinase A (propionate kinase 2) ackA ‐0.39079365 ‐0.47798032 ‐0.50672805 ‐0.3476028 ‐0.8295524 ‐0.5067927 ‐0.56132 0.677684 0.674475 ‐1.41204 ‐0.56132 0.397522 0 STM2338 phosphotransacetylase pta ‐0.4616236 ‐0.48115346 ‐0.5303182 ‐1.0072376 ‐0.8412558 ‐0.7478572 ‐0.86545 0.548875 0.973106 ‐2.60994 ‐0.86545 0.331597 0 STM2341 putative transketolase ‐0.018777054 ‐0.21977705 ‐0.041515693 ‐0.5971058 ‐0.7892743 ‐0.58608896 ‐0.65749 0.63398 ‐0.89046 ‐2.04368 ‐0.65749 0.321719 0 STM2347 putative phosphoesterase yfcE 0.5325464 0.2414636 0.30317497 0.47926083 0.4151023 0.30556625 0.399976 1.319486 0.184589 1.305159 0.399976 0.306458 0 STM2354 ABC superfamily (bind_prot), histidine transport protein hisJ ‐0.5936473 ‐0.7646353 ‐0.63680995 ‐0.69515795 ‐0.67024964 ‐0.56542164 ‐0.64361 0.640109 1.768047 ‐2.17804 ‐0.64361 0.295499 0 STM2355 ABC superfamily (bind_prot), lysine/arginine/ornithine transport protein argT ‐1.400604 ‐1.3309743 ‐1.3863664 ‐2.6482382 ‐2.515496 ‐2.4523265 ‐2.53869 0.172099 ‐0.78181 ‐8.09838 ‐2.53869 0.313481 0 STM2362 amidophosphoribosyltransferase (PRPP amidotransferase) purF 0.54774284 0.8205257 0.5031891 1.9648407 2.1074753 1.8334143 1.968577 3.913818 0.254927 5.878345 1.968577 0.334886 0 STM2363 membrane protein required for colicin V production cvpA ‐0.1076371 ‐0.01685051 0.001595976 1.1789459 1.3222896 1.2689024 1.256713 2.389506 ‐0.67369 4.223168 1.256713 0.297576 0 STM2366 acetylCoA carboxylase, beta subunit accD 0.22395338 ‐0.006877702 0.1717803 0.8641163 0.8240169 0.90332 0.863818 1.819848 0.992259 3.100089 0.863818 0.278643 0 STM2368 pseudouridylate synthase I truA 0.016327815 0.003586193 ‐0.05610269 1.2193966 0.8736367 0.50661016 0.866548 1.823295 ‐0.08796 1.877498 0.866548 0.461544 0 STM2369 putative aspartate‐semialdehyde dehydrogenase usg 0.15879549 0.4640597 0.14050888 1.7921561 1.6977626 1.6720469 1.720655 3.295861 ‐0.14794 5.887359 1.720655 0.292263 0 STM2372 putative transport protein ‐0.19344439 ‐0.538076 ‐0.4004039 0.78080255 0.36654153 0.7381135 0.628486 1.545942 0.644606 1.622736 0.628486 0.3873 0 STM2390 putative cytoplasmic protein yfcZ ‐1.0053508 ‐1.0411766 ‐0.97862315 ‐1.0113494 ‐1.1621034 ‐1.4432645 ‐1.20557 0.433597 ‐0.34282 ‐3.15337 ‐1.20557 0.382313 0 STM2392 lipoprotein precursor vacJ 0.08148945 0.4313549 0.15057379 0.6400065 0.75674677 0.47248212 0.623078 1.540158 0.100512 1.842092 0.623078 0.338245 0 STM2424 putative transcriptional regulator, LysR family yfeR ‐0.049995497 ‐0.4107043 ‐0.15914987 ‐0.4824844 ‐0.61319035 ‐0.47462806 ‐0.52343 0.695714 1.15779 ‐1.74081 ‐0.52343 0.300685 0 STM2428 cell division protein involved in FtsZ ring zipA 0.45122093 0.32291824 0.2700161 0.84455734 0.3571823 0.43619353 0.545978 1.460009 0.005098 1.342221 0.545978 0.406772 0 STM2430 subunit of cysteine synthase A and O‐acetylserine cysK 0.6733387 0.6188528 0.59673494 ‐0.63130504 ‐0.819051 ‐0.74938726 ‐0.73325 0.601548 ‐0.67102 ‐2.36117 ‐0.73325 0.310545 0 STM2432 General PTS family (Enzyme I) PEP‐protein phosphotransferase ptsI 0.5854015 0.41560653 0.43937817 0.6884998 0.5863998 0.53092635 0.601942 1.517758 1.247456 1.993871 0.601942 0.301896 0 STM2442 ABC superfamily (membrane), thiosulfate permease W protein cysW 0.06484899 0.0624721 0.14536904 0.8213127 0.7981536 0.6914933 0.77032 1.705648 ‐0.82168 2.604844 0.77032 0.295726 0 STM2443 ABC superfamily (membrane), thiosulfate transport protein cysU ‐0.039981093 ‐0.30424285 ‐0.28310165 0.6235134 0.39782253 0.620624 0.54732 1.461368 0.285647 1.656021 0.54732 0.330503 0 STM2467 putative cobalamin adenosyltransferase, ethanolamine utilization eutT ‐0.5692435 ‐0.638844 ‐0.6675065 0.6006584 0.4766011 0.48291883 0.520059 1.434014 0.007525 1.756421 0.520059 0.29609 0 STM2472 paral putative transferase maeB 0.31660816 0.631907 0.32096383 1.394403 1.3680007 0.95552915 1.239311 2.360857 0.403355 3.115059 1.239311 0.397845 0 STM2499 phosphoribosylaminoimidazole synthetase (AIR synthetase) purM ‐0.19817394 ‐0.26949763 ‐0.27411497 1.6319189 1.404445 1.4160644 1.484143 2.797509 ‐0.36564 4.501307 1.484143 0.329714 0 STM2500 polyphosphate kinase, component of RNA degradosome purN ‐0.061437722 ‐0.4162794 ‐0.23652318 0.48958057 0.42361504 0.6242828 0.512493 1.426513 0.997852 1.627998 0.512493 0.314799 0 STM2501 polyphosphate kinase, component of RNA degradosome ppk 0.15320905 0.14973487 0.19187717 0.6625556 0.29880738 0.4916377 0.484334 1.398939 0.64549 1.34232 0.484334 0.360818 0 STM2506 putative inner membrane protein 0.22724605 0.039916545 0.2442124 ‐0.74479675 ‐0.6381614 ‐0.5614981 ‐0.64815 0.638097 ‐0.842 ‐2.09827 ‐0.64815 0.308899 0 STM2510 GMP synthetase guaA 0.45461294 0.50390565 0.22497275 0.52327347 0.73832494 0.9471155 0.736238 1.665826 0.742156 1.94717 0.736238 0.378107 0 STM2512 exonuclease VII, large subunit xseA 0.22466974 0.2103931 0.05449734 0.8153534 0.7052006 0.6969059 0.739153 1.669196 ‐0.00167 2.51477 0.739153 0.293925 0 STM2521 putative inner membrane protein yfgM 0.38129607 0.30712685 0.2257414 0.8262161 0.6358742 0.60499936 0.68903 1.612199 ‐0.29779 2.120618 0.68903 0.324919 0 STM2522 histidine tRNA synthetase hisS 0.3655798 0.28132844 0.3583133 0.7556656 1.0426716 0.8955026 0.897947 1.863412 0.34981 2.65186 0.897947 0.33861 0 STM2523 putative protein, involved in density‐dependent regulation of gcpE 0.65346134 0.19456767 0.5378542 0.30621108 0.5394509 0.5964574 0.480706 1.395427 ‐1.08366 1.39523 0.480706 0.344536 0 STM2536 putative aminopeptidase pepB ‐0.040686227 ‐0.12126932 ‐0.09132061 1.0170218 1.0444963 1.1126822 1.058067 2.08214 0.066374 3.723151 1.058067 0.284186 0 STM2538 [2FE‐2S] ferredoxin, electron carrer protein, believed to fdx ‐0.10597995 ‐0.17619285 ‐0.031532355 1.7855537 1.7516148 1.7850844 1.774084 3.420209 ‐0.55078 6.644879 1.774084 0.266985 0 STM2540 co‐chaperone protein Hsc20, believed to be involved hscB 0.20873909 0.013661562 ‐0.042759415 1.6032605 1.0676236 1.3715297 1.347471 2.544657 0.821682 3.279781 1.347471 0.410842 0 STM2543 putative aminotransferase class‐V nifS 0.2126126 0.37317967 0.21135764 0.94592535 1.0509021 1.2741302 1.090319 2.129211 0.699038 3.092908 1.090319 0.352522 0 STM2544 believed to be involved in assembly of yfhP 1.9767494 1.9268703 1.9821848 1.6390253 1.487708 1.5227687 1.549834 2.927834 ‐0.44308 5.140763 1.549834 0.301479 0 STM2549 anaerobic sulfide reductase asrB ‐0.46834084 ‐0.59718376 ‐0.55395865 ‐0.75783175 ‐0.6825032 ‐0.59163463 ‐0.67732 0.625324 0.235805 ‐2.22953 ‐0.67732 0.303796 0 STM2551 putative inner membrane protein ‐0.50833637 ‐0.62913424 ‐0.54535985 ‐0.41308144 ‐0.6082869 ‐0.7965573 ‐0.60598 0.657027 0.323536 ‐1.65361 ‐0.60598 0.366456 0 STM2552 putative periplasmic or exported protein ‐0.37134042 ‐0.31807062 ‐0.21125828 ‐0.5125055 ‐0.5690386 ‐0.47179893 ‐0.51778 0.698445 ‐0.69721 ‐1.82353 ‐0.51778 0.283944 0 STM2553 stationary phase inducible protein csiE ‐0.40518212 ‐0.6434078 ‐0.52824616 ‐0.7355737 ‐0.6372644 ‐0.51503503 ‐0.62929 0.646494 0.156499 ‐1.96938 ‐0.62929 0.319538 0 STM2555 serine hydroxymethyltransferase glyA 0.64363766 0.55979085 0.5690766 0.85604954 0.9068405 0.8827994 0.881896 1.842796 ‐0.87023 3.261226 0.881897 0.270419 0 STM2571 putative aminotransferase ‐0.12592368 ‐0.43089432 ‐0.22789226 ‐0.7399156 ‐0.8007746 ‐0.8938684 ‐0.81152 0.569781 ‐0.62397 ‐2.70043 ‐0.81152 0.300515 0 155 STM2582 leader peptidase (signal peptidase I), serine protease lepB 0.09966997 0.20593268 0.05357113 0.5916567 0.6738609 0.50706035 0.590859 1.506144 0.193614 1.94424 0.590859 0.303902 0 STM2583 GTP‐binding elongation factor lepA 0.005809556 0.1014333 0.21773262 0.57178414 0.62521434 0.635363 0.610787 1.527092 ‐1.13131 2.217255 0.610787 0.27547 0 STM2600 Gifsy‐1 prophage: similar to minor tail protein ‐0.17638513 ‐0.2742328 ‐0.12595981 ‐0.9957277 ‐0.60188156 ‐0.6572079 ‐0.75161 0.593942 ‐1.0548 ‐1.98391 ‐0.75161 0.378851 0 STM2601 Gifsy‐1 prophage: similar to minor capsid protein ‐0.25034606 ‐0.12566397 ‐0.26800135 ‐0.79157364 ‐0.9375658 ‐1.125732 ‐0.95162 0.51705 ‐0.50162 ‐2.69988 ‐0.95162 0.352469 0 STM2602 Gifsy‐1 prophage: similar to DNA packaging protein ‐0.3195953 ‐0.6365987 ‐0.48812613 ‐0.5757709 ‐0.73887795 ‐0.65123403 ‐0.65529 0.634946 1.166575 ‐2.16356 ‐0.65529 0.302878 0 STM2604 Gifsy‐1 prophage: similar to head protein gpshp ‐0.51528144 ‐0.6633785 ‐0.65227646 ‐0.8489438 ‐0.92762154 ‐1.0008435 ‐0.9258 0.526387 0.423883 ‐3.09004 ‐0.9258 0.299609 0 STM2605 Gifsy‐1 prophage: similar to head‐tail preconnector gp5 ‐0.46762577 ‐0.6847157 ‐0.7068311 ‐0.6161648 ‐0.6992853 ‐0.51704144 ‐0.61083 0.65482 1.176908 ‐1.98047 ‐0.61083 0.308426 0 STM2613 Gifsy‐1 prophage ‐0.0664435 ‐0.038837463 ‐0.054674678 ‐0.5275034 ‐0.71590596 ‐1.0227988 ‐0.7554 0.592381 ‐0.02103 ‐1.8881 ‐0.7554 0.400086 0 STM2625 Gifsy‐1 prophage: similar to dnaC Homolog in 0.04889824 0.2679128 0.15600066 ‐0.81746256 ‐1.0576814 ‐1.2540472 ‐1.04306 0.485296 ‐0.54803 ‐2.73059 ‐1.04306 0.381993 0 STM2626 Gifsy‐1 prophage: similar to replication protein 15 0.002201933 0.12518373 0.008890197 ‐0.45344615 ‐0.49207753 ‐0.49332753 ‐0.47962 0.717168 1.099502 ‐1.78402 ‐0.47962 0.26884 0 STM2629 Gifsy‐1 prophage ‐0.018076448 ‐0.06352956 0.27539665 ‐0.58997846 ‐0.6300953 ‐0.47800833 ‐0.56603 0.675474 0.707396 ‐1.87888 ‐0.56603 0.301257 0 STM2637 regulator of sigma E (sigma 24) factor rseC ‐0.3276338 ‐0.23637518 ‐0.2256565 ‐0.8565542 ‐0.7094124 ‐0.8726867 ‐0.81288 0.569243 0.071744 ‐2.64185 ‐0.81288 0.307695 0 STM2638 anti sigma E (sigma 24) factor, negative rseB ‐0.012538897 0.06686209 ‐0.06068614 0.53380734 0.6663871 0.37579963 0.525331 1.439264 ‐0.30566 1.546266 0.525331 0.339742 0 STM2646 putative formate acetyltransferase yfiD ‐2.409216 ‐2.5270565 ‐2.4806406 ‐3.539058 ‐3.6892347 ‐3.8342152 ‐3.6875 0.077616 ‐0.22938 ‐10.8151 ‐3.6875 0.340959 0 STM2647 uracil‐DNA‐glycosylase ung ‐0.02925302 ‐0.025046064 ‐0.10279054 ‐0.9064514 ‐0.9081608 ‐1.0135117 ‐0.94271 0.520255 ‐0.34781 ‐3.23782 ‐0.94271 0.291155 0 STM2648 putative tRNA/rRNA methyltransferase yfiF ‐0.06344302 0.060515027 0.004911195 1.2615591 1.2526436 0.9548015 1.156335 2.228904 ‐0.08696 3.243129 1.156335 0.356549 0 STM2663 putative lipoprotein yfiO 0.42493463 0.3290534 0.30795994 0.87684643 0.81144875 0.83785975 0.842052 1.792598 ‐0.74825 3.064856 0.842052 0.274744 0 STM2665 ribosome associated factor, stabilizes ribosomes against dissociation yfiA ‐0.25310317 ‐0.13701907 0.07632942 ‐0.78871423 ‐0.6562085 ‐0.54647964 ‐0.6638 0.631213 0.869194 ‐2.03758 ‐0.6638 0.32578 0 STM2667 bifuctional: chorismate mutase P prephenate dehydratase pheA 0.8552046 0.7936667 0.7369175 0.46165243 0.60133964 0.50020754 0.521067 1.435016 2.03774 1.752069 0.521067 0.297401 0 STM2669 bifunctional: chorismate mutase T prephenate dehydrogenase tyrA 1.3667911 1.3381793 1.1992822 0.88219213 0.9187685 0.909422 0.903461 1.870548 0.138552 3.387289 0.903461 0.266721 0 STM2670 3‐deoxy‐D‐arabinoheptulosonate‐7‐phosphate synthase (DAHP synthetase), tyrosine repress aroF 1.4136881 1.5990025 1.3860908 1.164331 1.1723489 0.9882371 1.108306 2.155923 0.196317 3.509201 1.108306 0.315829 0 STM2674 tRNA (guanine‐7‐)‐methyltransferase trmD 0.4924994 0.561775 0.354886 1.571607 0.8121499 0.79679686 1.060185 2.085198 0.25576 2.0727 1.060185 0.511499 0 STM2678 putative cytochrome c‐type biogenesis protein (heme exporter corE 0.45198253 0.33105728 0.16392724 0.6109971 0.44705623 0.61621284 0.558089 1.472317 0.114597 1.792847 0.558089 0.311286 0 STM2681 molecular chaparone heat shock protein grpE ‐0.25207266 ‐0.219745 ‐0.16762441 0.51942676 0.58000386 0.38854185 0.495991 1.410289 ‐0.06811 1.588449 0.495991 0.312248 0 STM2692 putative HlyD family secretion protein ‐0.3458817 ‐0.105080955 ‐0.17565991 ‐0.30258146 ‐0.61178833 ‐0.5936708 ‐0.50268 0.705794 0.253112 ‐1.41228 ‐0.50268 0.355936 0 STM2746 putative Excinuclease ATPase subunit 0.59398854 0.48456725 0.820836 0.91573364 0.88280106 1.2101729 1.002903 2.004028 0.367586 2.787235 1.002903 0.35982 0 STM2771 Flagellar synthesis: phase 2 flagellin (filament structural fljB 0.59391034 0.86389077 0.62645835 4.4718914 3.0326958 3.278312 3.5943 12.07792 0.519337 5.132976 3.5943 0.700237 0 STM2774 putative ATP binding cassette (ABC) transporter iroC 1.4685358 1.3882108 1.4077921 1.0338286 0.83051705 0.97554153 0.946629 1.927364 0.011302 2.993816 0.946629 0.316195 0 STM2775 Similar to enterochelin esterase of E. coli iroD 0.88882965 0.9238883 0.88425475 1.4213401 1.660388 1.6496134 1.577114 2.983723 0.949245 4.726163 1.577114 0.333699 0 STM2776 putative hydrolase of the alpha/beta superfamily iroE 0.8541298 0.9028306 0.97993296 0.7055156 0.86182636 0.6533429 0.740228 1.67044 ‐0.24933 2.324938 0.740228 0.318386 0 STM2779 putative inner membrane protein ‐1.6570932 ‐1.5668646 ‐1.3951266 ‐1.5192282 ‐1.3188132 ‐1.1711544 ‐1.3364 0.396008 0.615961 ‐3.74747 ‐1.3364 0.356614 0 STM2780 Homolog of pipB, putative pentapeptide repeats (8 ‐1.0780922 ‐0.8139626 ‐0.97066003 ‐1.3445059 ‐1.1444677 ‐1.3973186 ‐1.29543 0.407415 ‐0.56441 ‐3.89304 ‐1.29543 0.332755 0 STM2784 tricarboxylic transport: regulatory protein tctE ‐0.0024338 ‐0.08608077 ‐0.031923085 ‐0.4754369 ‐0.5139672 ‐0.46975276 ‐0.48639 0.713811 0.980468 ‐1.80385 ‐0.48639 0.269638 0 STM2799 DNA‐binding protein with chaperone activity stpA 0.51035285 0.7136659 0.6639277 1.2195485 1.4674598 1.3035315 1.33018 2.51434 0.648303 4.048697 1.33018 0.328545 0 STM2800 putative inner membrane protein ‐1.0397096 ‐1.0487089 ‐0.9491986 ‐1.1627603 ‐1.7866412 ‐1.4778053 ‐1.47574 0.35955 0.304073 ‐3.38587 ‐1.47574 0.435851 0 STM2803 putative regulatory protein, gntR family ‐0.14893174 ‐0.35169092 ‐0.29418498 ‐0.7921751 ‐0.84443575 ‐0.79789424 ‐0.8115 0.569788 ‐0.135 ‐2.98018 ‐0.8115 0.272299 0 STM2806 stimulates ribonucleotide reduction nrdI 1.5859082 1.6896712 1.5323713 0.5361342 0.5886238 0.54786766 0.557542 1.471759 0.620905 2.052387 0.557542 0.271655 0 STM2807 ribonucleoside diphosphate reductase 2, alpha subunit nrdE 1.3610189 1.1131215 1.3807477 1.2840371 1.6497548 1.5424218 1.492071 2.812925 ‐0.46554 4.095908 1.492071 0.364283 0 STM2810 ABC superfamily (membrane), glycine/betaine/proline transport protein proW ‐0.08571178 0.037242457 ‐0.100272834 0.8111567 0.764251 0.6013942 0.725601 1.653589 ‐0.22603 2.272389 0.725601 0.319312 0 STM2811 ABC superfamily (bind_prot), glycine/betaine/proline transport protein proX 0.28423262 0.24634005 0.27426836 1.0516843 1.2805676 1.3833369 1.23853 2.359579 0.750531 3.50095 1.23853 0.35377 0 STM2817 quorum sensing protein, produces autoinducer ‐ acyl‐homoserine luxS 0.19017899 0.22966039 0.3912015 ‐0.39434144 ‐0.8224546 ‐0.88572073 ‐0.70084 0.615214 ‐0.5892 ‐1.70902 ‐0.70084 0.410083 0 STM2818 gamma‐glutamate‐cysteine ligase gshA 0.30802456 0.2622602 0.22540766 1.3915378 1.2543832 1.0112273 1.219049 2.327933 ‐0.05813 3.322129 1.21905 0.366948 0 STM2820 putative phosphoglucomutase yqaB 0.5168176 0.22583568 0.35993382 0.42678532 0.6108107 0.5289412 0.522179 1.436123 ‐1.31909 1.690006 0.522179 0.308981 0 STM2827 alanyl‐tRNA synthetase alaS 0.08696923 ‐0.045989398 0.009967996 0.43071222 0.3911952 0.36508504 0.395664 1.315548 ‐0.84855 1.43969 0.395664 0.274826 0 STM2829 DNA strand exchange and recombination protein with recA 0.36601838 0.616091 0.48594844 1.2252629 1.1004763 0.8265971 1.050779 2.071648 0.385875 2.813431 1.050779 0.373487 0 STM2830 putative cytoplasmic protein ygaD ‐0.05823111 0.002727301 0.0839029 0.51590735 0.7166603 0.77565557 0.669408 1.59042 1.083664 2.002018 0.669408 0.334367 0 STM2838 putative polysialic acid capsule expression protein gutQ 0.010391856 ‐0.17322683 0.045713007 0.96365744 0.81719846 0.92377216 0.901543 1.868062 ‐0.88161 3.010509 0.901543 0.299465 0 STM2843 electron transport protein (FeS senter) from formate hydN ‐2.111915 ‐2.1141264 ‐2.1909368 ‐0.7292152 ‐0.3609178 ‐0.662025 ‐0.58405 0.667087 ‐0.11693 ‐1.58284 ‐0.58405 0.368991 0 STM2846 processing of HycE (part of the FHL hycH ‐1.9982865 ‐2.2120636 ‐2.144421 ‐1.3907449 ‐1.029538 ‐0.9739851 ‐1.13142 0.456465 1.897161 ‐2.92812 ‐1.13142 0.386399 0 STM2854 guanine‐nucleotide binding protein in formate‐hydrogenlyase system, functions hypA ‐1.380965 ‐1.3377738 ‐1.5077561 ‐0.6757089 ‐0.86436427 ‐1.1842023 ‐0.90809 0.532889 ‐0.64461 ‐2.24687 ‐0.90809 0.404158 0 STM2855 hydrogenase‐3 accessory protein, assembly of metallocenter hypB ‐1.510201 ‐1.5917325 ‐1.7514678 ‐1.2971075 ‐1.0884947 ‐1.2998145 ‐1.22847 0.426769 ‐0.73811 ‐3.7713 ‐1.22847 0.325743 0 STM2856 putative hydrogenase expression/formation protein hypC ‐1.6043607 ‐1.3384742 ‐1.4685069 ‐1.3643197 ‐1.0714186 ‐1.1026849 ‐1.17947 0.441512 0.383309 ‐3.38335 ‐1.17947 0.348612 0 STM2857 putative hydrogenase expression/formation protein hypD ‐1.3017131 ‐1.5445496 ‐1.4773316 ‐1.7078265 ‐2.026192 ‐1.9283416 ‐1.88745 0.270284 ‐0.5179 ‐5.39426 ‐1.88745 0.3499 0 STM2858 putative hydrogenase expression/formation protein hypE ‐1.2006162 ‐1.1917812 ‐1.2197933 ‐1.1196187 ‐0.9748724 ‐1.2857137 ‐1.12673 0.457951 ‐0.06589 ‐3.26068 ‐1.12674 0.345552 0 STM2861 Salmonella iron transporter: fur regulated sitA 1.7026858 1.6050758 1.7330488 ‐1.8225362 ‐1.4510936 ‐1.3076658 ‐1.5271 0.346974 0.968613 ‐3.73227 ‐1.5271 0.409161 0 STM2862 Salmonella iron transporter: fur regulated sitB 2.0106812 1.9755465 1.9555578 ‐1.4567972 ‐1.5760242 ‐1.6994305 ‐1.57742 0.335081 ‐0.39493 ‐4.84174 ‐1.57742 0.325795 0 STM2863 Salmonella iron transporter: fur regulated sitC 1.479524 1.534634 1.3238136 ‐1.2319107 ‐1.1149666 ‐1.2070023 ‐1.18463 0.439938 ‐0.65329 ‐4.06649 ‐1.18463 0.291314 0 STM2864 Salmonella iron transporter: fur regulated sitD 1.0156461 0.77281904 0.95749605 ‐0.57300925 ‐0.6943098 ‐0.82742065 ‐0.69825 0.616321 ‐0.56358 ‐2.12092 ‐0.69825 0.329218 0 STM2911 putative permease ‐0.36350116 ‐0.28299135 ‐0.4199722 0.64968485 0.60937476 0.4931611 0.584074 1.499076 ‐0.23022 1.929727 0.584074 0.302672 0 STM2922 putative 3‐polyprenyl‐4‐hydroxybenzoate decarboxylase and related decarboxylase 0.007283965 ‐0.01565569 0.07242312 ‐0.73271036 ‐0.7122252 ‐0.7171739 ‐0.7207 0.606802 ‐0.77533 ‐2.75161 ‐0.7207 0.261921 0 STM2924 sigma S (sigma 38) factor of RNA rpoS 1.0578645 0.65946704 0.5723216 1.0113361 0.8807009 0.9485627 0.946867 1.927681 ‐0.59736 3.226448 0.946867 0.29347 0 STM2925 lipoprotein nlpD 0.1636027 0.26038495 0.22599287 0.36568114 0.6373582 0.7776076 0.593549 1.508954 0.411725 1.575808 0.593549 0.376663 0 STM2928 paral putative hydrogenase subunit ygbO 0.08241676 0.1496541 0.15939096 1.3575366 1.3299998 1.0254316 1.237656 2.358151 ‐0.28808 3.417437 1.237656 0.362159 0 STM2934 ATP‐sulfurylase, subunit 1 (ATP:sulfate adenylyltransferase) cysN 0.30372697 0.48952314 0.310964 1.7175845 1.5714319 1.5097268 1.599581 3.030553 0.342819 5.039931 1.599581 0.317382 0 STM2935 ATP‐sulfurylase, subunit 1 (ATP:sulfate adenylyltransferase) cysD 0.3542767 0.29968372 0.3409208 0.995818 0.83977145 0.903015 0.912868 1.882785 ‐0.01385 3.03213 0.912868 0.301065 0 STM2938 putative cytoplasmic protein ‐0.18880545 ‐0.57485443 ‐0.3934032 ‐0.4256609 ‐0.614946 ‐0.59168684 ‐0.5441 0.68582 0.646675 ‐1.72539 ‐0.5441 0.315348 0 STM2948 sulfite reductase, beta (flavoprotein) subunit cysJ 0.17232679 0.09527983 0.10417513 0.82691765 0.92148805 0.96029365 0.9029 1.869821 ‐0.53211 3.056969 0.9029 0.295358 0 STM2951 putative Organic radical activating enzymes ygcF 0.62965447 0.71734643 0.33090457 0.9377197 0.94293815 0.70960456 0.863421 1.819347 ‐1.55655 2.595408 0.863421 0.332672 0 STM2952 enolase eno ‐0.15794368 ‐0.17798114 ‐0.2562994 ‐0.45854482 ‐0.46459493 ‐0.58150333 ‐0.50155 0.706349 0.034731 ‐1.69576 ‐0.50155 0.295766 0 STM2953 CTP synthetase pyrG 0.46347573 0.63191265 0.53153473 1.5831877 1.2341961 0.790129 1.202504 2.301388 ‐0.49895 2.478196 1.202504 0.485234 0 STM2963 putative MFS superfamily, D‐glucarate permease 0.6211641 0.5561981 0.6033192 0.38301352 0.37756073 0.4378025 0.399459 1.319013 2.300679 1.452652 0.399459 0.274986 0 STM2985 putative SufE protein probably involved in Fe‐S ygdK ‐0.23369008 ‐0.46151632 ‐0.40656316 ‐0.50069046 ‐0.66075945 ‐0.5349036 ‐0.56545 0.675744 0.886855 ‐1.85749 ‐0.56545 0.304416 0 STM2992 N‐alpha‐acetylglutamate synthase (amino‐acid acetyltransferase) argA ‐1.8826816 ‐2.0373597 ‐1.7753541 ‐0.9094354 ‐1.0514808 ‐0.7714091 ‐0.91078 0.531899 ‐0.74281 ‐2.70579 ‐0.91078 0.336602 0 STM3001 thymidylate synthetase thyA ‐0.004866882 0.26829427 ‐0.013539204 1.0519418 0.948105 0.890139 0.963395 1.949893 0.409007 3.178687 0.963395 0.30308 0 STM3002 phosphatidylglycerol‐prolipoprotein diacylglyceryl transferase lgt ‐0.15134822 0.028634714 ‐0.11858269 0.9341656 0.7284123 0.5866112 0.74973 1.681478 ‐0.1279 2.102176 0.74973 0.356645 0 STM3003 General PTS system, enzyme I, transcriptional regulator ptsP 0.45904133 0.49615526 0.4057607 1.61506 1.5269563 1.6946888 1.612235 3.057251 0.8738 5.300085 1.612235 0.30419 0 STM3040 lysine tRNA synthetase, constitutive lysS 0.5489557 0.705428 0.4235758 0.8250381 0.37911683 0.51252145 0.572225 1.486815 0.557001 1.475218 0.572225 0.387892 0 STM3041 peptide chain release factor RF‐2 prfB 0.20445457 0.118721396 0.15328436 0.31896365 0.7021465 0.6573744 0.559495 1.473753 1.196408 1.485223 0.559495 0.376708 0 STM3047 putative cytoplasmic protein ygfY 0.22228152 0.28155047 0.33851743 ‐0.39068496 ‐0.45433235 ‐0.3793316 ‐0.40812 0.753607 ‐0.94698 ‐1.46232 ‐0.40812 0.279089 0 STM3049 putative hemolysin yqfA ‐0.26975584 ‐0.25578 ‐0.34860906 ‐0.8640276 ‐0.6955426 ‐0.8497073 ‐0.80309 0.573119 0.917672 ‐2.59327 ‐0.80309 0.309683 0 STM3058 proline aminopeptidase P II pepP ‐0.004089691 ‐0.00613397 ‐0.074968375 1.1865511 1.2101642 0.7337791 1.043498 2.061219 ‐0.15056 2.540414 1.043498 0.410759 0 STM3063 ribosephosphate isomerase, constitutive rpiA 0.5394156 0.44647112 0.42515892 0.54042345 0.7274467 0.54703075 0.604967 1.520944 ‐1.15668 1.908298 0.604967 0.317019 0 STM3066 putative LYSE family, amino acid transport protein yggA ‐0.2124776 0.100207396 0.031301398 0.39912364 0.56539404 0.3302064 0.431575 1.348705 ‐0.02263 1.325661 0.431575 0.325554 0 STM3068 fructose‐bisphosphate aldolase fba 0.3727042 0.415672 0.32199523 ‐0.73165846 ‐0.6565856 ‐0.90815854 ‐0.76547 0.588263 ‐0.39834 ‐2.31739 ‐0.76547 0.330314 0 STM3069 phosphoglycerate kinase pgk 0.14861359 0.29308948 0.2946258 ‐0.4568361 ‐0.39942473 ‐0.38106892 ‐0.41244 0.75135 0.555024 ‐1.48057 ‐0.41244 0.27857 0 STM3073 putative ABC‐type cobalt transport system, permease component ‐0.7943754 ‐1.0122044 ‐1.05152 ‐1.5030166 ‐1.7414619 ‐1.6000873 ‐1.61486 0.326498 0.039134 ‐4.96913 ‐1.61486 0.324978 0 STM3086 arginine decarboxylase speA 0.53480905 0.4557718 0.27149752 1.1257912 0.82378703 0.8655421 0.938373 1.916366 0.298515 2.679302 0.938373 0.350231 0 STM3099 putative protein transport yggR ‐0.061858002 0.024763463 ‐0.094669834 0.36173138 0.53561974 0.5765678 0.491306 1.405717 ‐0.40091 1.527662 0.491306 0.321607 0 STM3109 putative S‐adenosylmethionine‐dependent methyltransferase yggH ‐0.118700884 ‐0.32781953 ‐0.23102309 0.6009225 0.40339646 0.5492505 0.517856 1.431826 0.089904 1.644555 0.517857 0.314892 0 STM3115 putative inner membrane protein yqgA 0.02044422 ‐0.08933705 0.021162478 ‐0.3918133 ‐0.7512944 ‐0.519497 ‐0.5542 0.681034 0.717622 ‐1.53534 ‐0.5542 0.360964 0 STM3120 putative transcriptional regulator, LysR family 0.042138446 0.13966922 0.030387117 ‐0.46844065 ‐0.5192889 ‐0.7870097 ‐0.59158 0.663616 ‐0.54648 ‐1.66849 ‐0.59158 0.354561 0 STM3180 putative cytoplasmic protein ygiN 0.090776965 0.23736475 0.18766257 ‐0.8831592 ‐0.98961717 ‐0.87133825 ‐0.9147 0.530452 ‐0.54013 ‐3.11802 ‐0.9147 0.293361 0 STM3189 putative cytoplasmic protein ygiD ‐0.03154176 ‐0.08255189 ‐0.14289394 ‐0.44555646 ‐0.48397323 ‐0.60670054 ‐0.51208 0.701212 ‐0.43768 ‐1.68256 ‐0.51208 0.304344 0 STM3195 3,4 dihydroxy‐2‐butanone‐4‐phosphate synthase ribB ‐0.014588503 ‐0.003988799 0.02529741 1.4724897 1.0858337 1.001783 1.186702 2.276318 ‐0.1146 2.961656 1.186702 0.400689 0 STM3200 bifunctional putative sugar nucleotide transferase domain of rfaE 0.0378735 ‐0.15404993 ‐0.20141844 1.0107374 0.6274843 0.5105102 0.716244 1.642899 ‐0.2778 1.760598 0.716244 0.406819 0 STM3202 putative cytoplasmic protein ygiF ‐0.036254928 ‐0.33209553 0.11838128 0.9045049 0.6362264 1.3067031 0.949145 1.930728 0.28756 2.106485 0.949145 0.450582 0 STM3203 putative SH3 domain protein ygiM ‐0.03987757 ‐0.1330226 ‐0.06085754 0.4021744 0.3229126 0.43900347 0.38803 1.308605 0.332433 1.338034 0.38803 0.29 0 STM3208 putative O‐sialoglycoprotein endopeptidase gcp ‐0.1840618 ‐0.20660804 ‐0.09481134 1.6224974 1.5688049 1.5368252 1.576043 2.981509 ‐0.91516 5.613798 1.576043 0.280744 0 STM3209 30S ribosomal subunit protein S21 rpsU ‐0.074756615 0.11385263 0.18511528 0.9687112 0.8101795 0.799553 0.859481 1.814386 ‐0.58563 2.768495 0.859481 0.310451 0 STM3211 sigma D (sigma 70) factor of RNA rpoD 0.024191434 0.10382196 0.12358436 0.6024334 0.39776328 0.44121185 0.48047 1.395198 0.556409 1.510872 0.48047 0.318008 0 STM3221 putative metal‐dependent hydrolase ygjP ‐0.1397961 0.001734606 0.04273513 ‐0.46579698 ‐0.42401534 ‐0.5513716 ‐0.48039 0.716782 ‐0.18635 ‐1.63828 ‐0.48039 0.293232 0 STM3223 putative dehydrogenase ygjR 0.2381426 0.073373266 0.18642077 ‐0.668651 ‐0.7760198 ‐0.8261018 ‐0.75692 0.591757 ‐0.50906 ‐2.50476 ‐0.75692 0.302194 0 STM3225 putative dicarboxylate permease ygjU 0.37479806 0.3099094 0.13743226 ‐1.0302029 ‐1.0730301 ‐1.0650597 ‐1.0561 0.480931 ‐0.72942 ‐3.92748 ‐1.0561 0.2689 0 STM3250 galactarate dehydrogenase garD ‐0.6256263 ‐0.25812346 ‐0.1164927 ‐0.34901798 ‐0.48722446 ‐0.3887005 ‐0.40831 0.753503 ‐1.28122 ‐1.37556 ‐0.40831 0.296834 0.014971 STM3255 putative phosphotransferase system fructose‐specific component IIB 0.28756332 0.55266887 0.4851381 0.7379055 0.41182685 0.39430737 0.51468 1.428677 ‐0.37281 1.400577 0.51468 0.367477 0 STM3261 galactitol‐1‐phosphate dehydrogenase ‐0.20311347 0.21478082 0.058728024 0.43816087 0.6339922 0.3299853 0.467379 1.382596 ‐0.31535 1.355837 0.467379 0.344717 0 STM3265 putative endonuclease yraN ‐0.240176 ‐0.19994754 ‐0.17018883 0.61774576 1.1174277 1.2904097 1.008528 2.011857 0.850341 2.204815 1.008528 0.457421 0 STM3280 cysteine sulfinate desulfinase deaD 0.11226402 0.090695724 ‐0.075012125 0.7503863 0.68511885 0.5076172 0.647707 1.566677 ‐0.30101 1.973007 0.647707 0.328285 0 STM3282 polynucleotide phosphorylase, member of mRNA degradosome pnp 0.287719 0.27095413 0.16514485 1.3900466 1.01867 1.3603115 1.256343 2.388894 0.524708 3.35118 1.256343 0.374896 0 STM3285 ribosome‐binding factor, role in processing of 10S rbfA ‐0.005791862 ‐0.04465242 ‐0.017997647 0.60618097 0.55015844 0.5319397 0.56276 1.477092 ‐0.711 2.023674 0.56276 0.278088 0 STM3286 protein chain initiation factor IF‐2 infB 0.108974874 ‐0.012338016 ‐0.01067437 0.8832069 1.2870035 1.2373838 1.135865 2.197502 1.028654 2.966572 1.135865 0.382888 0 STM3288 putative cytoplasmic protein yhbC ‐0.11697027 0.20749073 0.14714777 1.3815571 1.3008317 1.2844783 1.322289 2.500626 0.480966 4.627315 1.322289 0.285757 0 STM3293 preprotein translocase IISP family, auxillary membrane component secG 0.01768721 0.019447526 0.1491869 1.2449843 1.5090841 1.5471741 1.433748 2.701475 1.845169 4.087434 1.433748 0.35077 0 STM3296 ATP‐dependent zinc‐metallo protease hflB 0.3639048 0.31723154 0.26751897 0.873671 0.6887258 0.6959391 0.752779 1.685035 ‐0.63598 2.380466 0.752779 0.316232 0 STM3303 50S ribosomal subunit protein L27 rpmA 0.29266664 0.27417678 0.37332067 0.722275 0.80754155 0.8770581 0.802292 1.743869 ‐0.53261 2.669778 0.802292 0.300509 0 STM3304 50S ribosomal subunit protein L21 rplU 0.14947657 0.18808955 0.28382948 0.82678646 0.9400084 1.1391729 0.968656 1.957017 0.930021 2.791047 0.968656 0.347058 0 STM3307 UDP‐N‐acetylglucosamine 1‐carboxyvinyltransferase murA 0.31915554 0.385592 0.33516544 0.86490834 0.8380177 0.68250495 0.795144 1.73525 ‐0.03551 2.543634 0.795144 0.312601 0 STM3310 putative ABC superfamily (atp&memb), transport protein yrbC 0.45055595 0.6493985 0.37100726 1.0194108 1.4531128 1.1803452 1.217623 2.325632 0.302409 3.184757 1.217623 0.382328 0 STM3318 putative ABC superfamily (bind_prot) transport protein yhbN 0.21828444 0.24881084 0.34011468 0.72728646 0.6107526 0.72495925 0.687666 1.610676 0.45741 2.337313 0.687666 0.294212 0 STM3319 putative ABC superfamily (atp_bind) transport protein yhbG 0.55796766 0.51682436 0.24608935 0.90596527 0.61113596 0.61389375 0.710332 1.63618 0.226032 2.009029 0.710332 0.35357 0 STM3330 glutamate synthase, large subunit gltB ‐1.2374511 ‐1.1750478 ‐1.0209262 0.42223728 0.46917948 0.41576034 0.435726 1.352591 ‐1.37684 1.59852 0.435726 0.272581 0 STM3331 glutamate synthase, small subunit gltD ‐1.2325765 ‐1.1646444 ‐1.1944269 0.86034554 0.7685048 0.74538505 0.791412 1.730767 0.510854 2.720968 0.791412 0.290857 0 STM3333 putative purine‐cytosine permease ‐0.07350284 0.0889527 0.1374948 0.44045606 0.44140106 0.31248042 0.398113 1.317783 ‐0.16058 1.333413 0.398113 0.298567 0 STM3341 stringent starvation protein B sspB 0.11391048 0.09031873 0.1314835 0.5373964 0.5705995 0.437884 0.515293 1.429285 0.557369 1.743073 0.515293 0.295623 0 STM3344 30S ribosomal subunit protein S9 rpsI ‐0.31225324 ‐0.2942787 ‐0.35574937 0.59703296 0.72727215 0.84410584 0.722804 1.650386 0.879025 2.209676 0.722804 0.327108 0 STM3345 50S ribosomal subunit protein L13 rplM ‐0.42418668 ‐0.39810398 ‐0.27671683 0.3355869 0.5297364 0.5527854 0.472703 1.387707 0.704058 1.456129 0.472703 0.32463 0 STM3346 putative ATPase yhcM 0.46733466 0.51619864 0.4392478 0.48856956 0.5567523 0.3359806 0.460434 1.375956 ‐0.24417 1.434307 0.460434 0.321015 0 STM3347 putative periplasmic protein yhcB 0.27658775 0.5025476 0.47790214 0.7403273 0.653262 0.6178786 0.670489 1.591613 0.2697 2.29516 0.670489 0.292132 0 STM3348 serine endoprotease degQ 0.29680672 0.52625495 0.40978143 0.9529764 0.89315414 0.42084214 0.755658 1.688401 ‐0.57334 1.782019 0.755658 0.424046 0 STM3370 RNase G cafA 0.32975817 0.20061354 0.060122635 1.1699529 0.91923195 0.8932288 0.994138 1.99189 0.086961 2.890129 0.994138 0.343977 0 STM3372 rod shape‐determining protein mreD 0.11135699 0.2793191 0.1755934 0.94404954 1.1231475 1.0040327 1.023743 2.033187 ‐0.04087 3.319728 1.023743 0.308382 0 STM3374 rod shape‐determining protein HSP70 class molecular chaperones mreB ‐0.049545288 0.06909308 ‐0.10524708 1.2637119 1.0159082 1.013385 1.097668 2.140085 ‐0.00852 3.240115 1.097668 0.338775 0 STM3377 putative nitrate reductase 0.16395642 0.004959014 0.019371338 0.8321907 0.7664692 0.888353 0.829004 1.776459 ‐0.4769 2.849101 0.829004 0.290971 0 STM3379 acetylCoA carboxylase, BCCP subunit, carrier of biotin accB 0.3264945 0.1647305 0.25905517 1.0537269 1.2477264 1.1608334 1.154096 2.225448 ‐0.98951 3.70076 1.154096 0.311854 0 STM3380 acetyl CoA carboxylase, biotin carboxylase subunit accC 0.0967396 0.18060349 0.068293154 0.69413424 1.0396188 0.99623066 0.909995 1.879038 0.658374 2.497213 0.909995 0.364404 0 STM3403 putative DNA topoisomerase yrdD 0.28743678 0.2726006 0.110935025 0.6499722 0.38813308 0.35735843 0.465155 1.380465 ‐0.10475 1.33441 0.465155 0.348584 0 STM3407 10‐formyltetrahydrofolate:L‐methionyl‐tRNA(fMet) N‐formyltransferase fmt 0.14425322 0.23554099 0.15461309 0.8723259 0.7963802 0.49501544 0.721241 1.648599 ‐0.28565 1.944216 0.721241 0.370967 0 STM3414 50S ribosomal subunit protein L17 rplQ ‐0.21090123 ‐0.13917804 ‐0.16408038 0.47248608 0.6622497 0.5642593 0.566332 1.480754 0.403972 1.823703 0.566332 0.310539 0 156 STM3415 RNA polymerase, alpha subunit rpoA ‐0.17111461 ‐0.32143748 ‐0.239364 0.40389606 0.540604 0.564277 0.502926 1.417084 0.665133 1.644979 0.502926 0.305734 0 STM3418 30S ribosomal subunit protein S13 rpsM ‐0.066201754 0.001316099 ‐0.13031937 0.43502557 0.5317855 0.48192284 0.482911 1.397561 0.315353 1.702273 0.482911 0.283686 0 STM3420 preprotein translocase of IISP family, membrane subunit secY ‐0.029094636 ‐0.40166813 ‐0.46753326 0.56648 0.38486713 0.5876388 0.512995 1.42701 0.263122 1.602588 0.512995 0.320104 0 STM3421 50S ribosomal subunit protein L15 rplO 0.023761628 ‐0.003743239 0.030900303 0.4057411 0.5109895 0.47595713 0.464229 1.37958 ‐0.64166 1.619256 0.464229 0.286693 0 STM3426 30S ribosomal subunit protein S8, and regulator rpsH 0.156887 ‐0.07459578 0.027831098 0.38986868 0.5357284 0.5916262 0.505741 1.419853 ‐2.35785 1.600999 0.505741 0.315891 0 STM3427 30S ribosomal subunit protein S14 rpsN 0.14298563 0.044006325 0.07243931 1.017614 0.7627185 0.7287779 0.83637 1.785552 ‐0.56292 2.410986 0.83637 0.3469 0 STM3428 50S ribosomal subunit protein L5 rplE 0.27224478 0.408246 0.21400793 0.55655867 0.5555049 0.57440585 0.562156 1.476475 0.552608 2.146603 0.562157 0.261882 0 STM3429 50S ribosomal subunit protein L24 rplX 0.1746039 0.17433919 0.002341535 0.58207536 0.46410722 0.3929964 0.479726 1.394479 ‐0.2497 1.543085 0.479726 0.310888 0 STM3430 50S ribosomal subunit protein L14 rplN 0.13766943 0.12731695 0.1843003 0.37834528 0.36636478 0.48344076 0.409384 1.328118 ‐0.90794 1.397503 0.409384 0.292939 0 STM3431 30S ribosomal subunit protein S17 rpsQ ‐0.0887727 ‐0.040331673 0.05516144 0.33699328 0.468183 0.49178082 0.432319 1.349401 ‐1.38255 1.422585 0.432319 0.303897 0 STM3433 50S ribosomal subunit protein L16 rplP 0.0771694 0.11529771 ‐0.016960746 0.8118268 0.866603 0.74783975 0.808757 1.751701 ‐0.37111 2.788162 0.808757 0.290068 0 STM3434 30S ribosomal subunit protein S3 rpsC ‐0.04383161 ‐0.18462062 ‐0.18147409 0.7072566 0.6380355 0.71248406 0.685925 1.608734 ‐0.62802 2.451992 0.685925 0.279742 0 STM3435 50S ribosomal subunit protein L22 rplV 0.02788896 0.09586572 ‐0.05151192 0.8675472 0.82554907 0.73800594 0.810367 1.753658 ‐0.37363 2.757218 0.810367 0.293908 0 STM3436 30S ribosomal subunit protein S19 rpsS 0.13707714 ‐0.00233156 0.024264153 0.47191405 0.5576356 0.6335334 0.554361 1.468518 0.96709 1.833 0.554361 0.302434 0 STM3437 50S ribosomal subunit protein L2 rplB 0.2131876 0.26937285 0.072163686 1.2741129 1.0043688 0.8330089 1.037164 2.052189 ‐0.11816 2.699985 1.037164 0.384137 0 STM3438 50S ribosomal subunit protein L23 rplW 0.16592273 0.06168102 0.04589028 0.88793 0.925726 0.6928181 0.835491 1.784465 ‐0.5448 2.547884 0.835491 0.327916 0 STM3439 50S ribosomal subunit protein L4, regulates expression rplD 0.16622669 ‐0.07109449 ‐0.038105242 0.6980796 0.44608715 0.58348465 0.575884 1.49059 ‐0.46067 1.752576 0.575884 0.328593 0 STM3440 50S ribosomal subunit protein L3 rplC 0.067706786 0.12034215 0.005215909 0.5133172 0.5191262 0.5149952 0.515813 1.4298 ‐0.56479 2.003346 0.515813 0.257476 0 STM3441 30S ribosomal subunit protein S10 rpsJ ‐0.08544141 0.024410091 ‐0.003385578 0.4772821 0.5419155 0.6356286 0.551609 1.465719 ‐1.10013 1.828235 0.551609 0.301717 0 STM3446 protein chain elongation factor EF‐G, GTP‐binding fusA 0.18110873 0.117635965 0.08852364 1.3127447 1.2558875 1.236176 1.268269 2.408725 ‐0.8103 4.550601 1.268269 0.278704 0 STM3447 30S ribosomal subunit protein S7, initiates assembly rpsG ‐0.078892924 ‐0.043607447 ‐0.08896896 0.7281382 0.7104598 0.63126135 0.689953 1.613231 ‐0.47413 2.416344 0.689953 0.285536 0 STM3448 30S ribosomal subunit protein S12 rpsL ‐0.15138279 ‐0.20287304 ‐0.18437465 0.56427264 0.39691463 0.43030784 0.463832 1.3792 ‐0.13652 1.511409 0.463832 0.306887 0 STM3453 FKBP‐type peptidyl‐prolyl cis‐trans isomerase (rotamase) fkpA 0.13268282 0.2703331 0.2590825 0.96936053 0.8613894 0.81345856 0.881403 1.842166 ‐0.72674 2.919967 0.881403 0.301854 0 STM3468 acetylornithine transaminase (NAcOATase and DapATase) argD ‐1.0901717 ‐1.1069815 ‐1.0186319 ‐0.5776001 ‐0.8472112 ‐0.9248754 ‐0.78323 0.581065 ‐0.71901 ‐2.16973 ‐0.78323 0.36098 0 STM3483 D‐ribulose‐5‐phosphate 3‐epimerase rpe 0.22289732 0.2771398 0.25279966 1.1238592 1.5802953 0.8778368 1.193997 2.287857 ‐0.61861 2.586974 1.193997 0.461542 0 STM3485 membrane protein damX 0.40057707 0.2942246 0.14190911 0.82500184 0.9361938 1.1599814 0.973726 1.963906 0.441179 2.748666 0.973726 0.354254 0 STM3487 shikimate kinase I aroK 0.23728496 0.50706136 0.38406584 1.4653877 1.4609106 1.3644738 1.430257 2.694948 0.410167 4.954701 1.430257 0.288667 0 STM3493 transpeptidase of penicillin‐binding protein 1a (peptidoglycan synthetase) mrcA 0.027661547 0.026157668 ‐0.034723267 1.0460325 1.0722368 0.61331016 0.910526 1.879731 ‐0.45119 2.250713 0.910527 0.40455 0 STM3494 putative NTP pyrophosphohydrolase yrfE 0.3264107 0.48532274 0.37126324 1.1182879 1.1681563 0.9867609 1.091068 2.130317 ‐0.33358 3.521238 1.091068 0.309854 0 STM3505 ferrous iron transport protein A feoA ‐0.8980078 ‐0.8358187 ‐0.78202707 ‐1.9934821 ‐1.9092382 ‐1.8104979 ‐1.90441 0.267126 0.263943 ‐6.17056 ‐1.90441 0.308628 0 STM3506 FeoB family, ferrous iron transport protein B feoB ‐0.8008093 ‐0.7850094 ‐0.80909026 ‐1.6182702 ‐1.514517 ‐1.5827016 ‐1.57183 0.336382 0.435592 ‐5.49226 ‐1.57183 0.28619 0 STM3507 putative cytoplasmic protein yhgG ‐0.65874517 ‐0.65858203 ‐0.5766391 ‐0.78440833 ‐0.9887308 ‐0.9772643 ‐0.9168 0.529682 ‐0.90625 ‐2.84695 ‐0.9168 0.322029 0 STM3529 putative glycerol dehydrogenase ‐0.018010184 0.1032425 0.2209399 ‐0.60592294 ‐0.6886082 ‐0.55081296 ‐0.61511 0.652878 ‐1.19641 ‐2.07955 ‐0.61511 0.295792 0 STM3545 putative oxidoreductase yhhX 0.3654765 0.456926 0.22306515 1.4265004 1.4592677 1.38696 1.424243 2.683736 0.250595 5.148109 1.424243 0.276654 0 STM3554 ABC superfamily (atp_bind), sn‐glycerol 3‐phosphate transport protein ugpC ‐0.04468284 ‐0.26788393 ‐0.097273536 0.40960887 0.4329138 0.33226907 0.391597 1.311845 ‐0.93936 1.368422 0.391597 0.286167 0 STM3559 putative cytoplasmic protein yhhV ‐0.51195174 ‐0.36480522 ‐0.3218064 ‐0.8147165 ‐0.6967587 ‐0.6396708 ‐0.71705 0.608341 0.579981 ‐2.33346 ‐0.71705 0.307289 0 STM3560 ABC superfamily (atp_bind), branched‐chain amino acid transporter livF ‐0.16427407 ‐0.3524308 ‐0.2516342 1.2833763 1.3266482 1.5995159 1.40318 2.644839 0.062796 3.955862 1.40318 0.354709 0 STM3562 ABC superfamily (membrane), branched‐chain amino acid transporter livM ‐0.33340865 ‐0.43975687 ‐0.4066767 1.1676672 0.695106 0.74952626 0.870766 1.828634 0.942842 2.149887 0.870766 0.405029 0 STM3563 ABC superfamily (membrane), branched‐chain amino acid transporter livH ‐0.00253958 ‐0.16058128 ‐0.09113365 0.5935828 0.61582816 0.6754202 0.628277 1.545718 ‐0.43392 2.242403 0.628277 0.28018 0 STM3564 ABC superfamily (bind_prot), branched‐chain amino acid transporter livK ‐0.010174342 ‐0.028692126 0.011515966 1.2721968 1.210193 1.286044 1.256145 2.388566 ‐0.55502 4.501173 1.256145 0.279071 0 STM3565 putative acetyltransferase yhhK ‐0.008102455 0.07012291 ‐0.008915209 0.71416783 0.8418233 0.926609 0.827533 1.774649 0.848555 2.606479 0.827533 0.317491 0 STM3566 putative cytoplasmic protein ‐0.12003672 ‐0.18484004 ‐0.29097027 0.92943585 0.6644095 0.73091805 0.774921 1.711097 0.679647 2.310736 0.774921 0.335357 0 STM3569 putative integral membrane cell division protein ftsX ‐0.121858135 ‐0.13931735 ‐0.19150385 0.5935469 0.5677569 0.3352809 0.498862 1.413098 ‐0.58275 1.476454 0.498862 0.337878 0 STM3579 putative integral membrane protein yhhQ ‐0.26206633 ‐0.28131464 ‐0.31972826 0.8972435 0.9045855 1.2626444 1.021491 2.030016 0.660554 2.714242 1.021491 0.376345 0 STM3581 putative MFS family transport protein yhhS ‐0.23966552 ‐0.15919942 ‐0.26792803 0.6503621 0.670634 0.49067158 0.603889 1.519808 0.294078 1.931456 0.603889 0.31266 0 STM3582 putative PerM family permease yhhT ‐0.17338857 ‐0.06607158 ‐0.23319583 1.1769857 1.239285 0.96768475 1.127985 2.185533 0.021029 3.338294 1.127985 0.337893 0 STM3583 putative Phosphopantetheinyl transferase acpT ‐0.23017658 ‐0.21891128 ‐0.23699446 0.6221992 1.0144118 0.95787734 0.864829 1.821124 0.104247 2.286955 0.864829 0.378158 0 STM3588 putative periplasmic protein yhiN 0.09012696 0.17638624 0.12930581 1.6446699 1.6807184 1.11275 1.479379 2.788288 ‐0.4713 3.367128 1.479379 0.439359 0 STM3589 PiT family, low‐affinity phosphate transporter pitA 0.22636662 0.075264834 0.08798218 0.5316787 0.8371307 0.96918947 0.779333 1.716337 ‐0.41172 2.022602 0.779333 0.385312 0 STM3591 universal stress protein A uspA 0.100602835 0.2301181 0.1864977 ‐0.9589353 ‐1.1389306 ‐1.3391746 ‐1.14568 0.451977 ‐0.30336 ‐3.13398 ‐1.14568 0.365567 0 STM3593 putative SAM‐dependent methyltransferase yhiQ 0.047663294 0.05877624 ‐0.048142686 1.3996212 1.6575541 1.3547417 1.470639 2.771446 ‐0.47301 4.200615 1.470639 0.350101 0 STM3596 putative cytoplasmic protein yhiR 0.201224 0.28259528 0.19151321 0.76100385 0.87566894 0.6427716 0.759815 1.693273 ‐0.25311 2.352485 0.759815 0.322984 0 STM3605 putative phage endolysin 0.1079073 0.1118315 0.2380045 ‐0.6818135 ‐0.85911566 ‐0.45678973 ‐0.66591 0.630293 ‐0.70119 ‐1.78929 ‐0.66591 0.372163 0 STM3622 putative cytoplasmic protein yhjS 0.47895348 0.5198404 0.45286873 1.1361014 0.71533597 0.33328858 0.728242 1.656619 ‐0.57059 1.493549 0.728242 0.487592 0 STM3644 biotin sulfoxide reductase bisC 0.14470662 0.19645415 0.1428582 1.5618557 1.4502966 1.095863 1.369338 2.583521 ‐0.61357 3.455931 1.369338 0.396229 0 STM3646 2‐keto‐D‐gluconate reductase yiaE 0.24432333 0.18313937 0.22066365 0.29687464 0.8787694 0.5413387 0.572328 1.486921 1.033219 1.348426 0.572328 0.424441 0 STM3647 putative outer membrane lipoprotein yiaF 0.26586452 0.36045036 0.25343433 0.39822218 0.4916266 0.46281114 0.450887 1.36688 0.0312 1.59119 0.450887 0.283364 0 STM3649 major cold shock protein 7.4, transcriptional activator cspA 0.18005908 0.46725303 0.35170114 1.7636927 1.7109131 1.7175866 1.730731 3.318959 0.42765 6.354972 1.730731 0.272343 0 STM3655 glycine tRNA synthetase, beta subunit glyS 0.30582297 0.17720874 0.02626356 0.7584689 0.5775694 0.30078572 0.545608 1.459635 ‐0.41665 1.403189 0.545608 0.388834 0 STM3656 glycine tRNA synthetase, alpha subunit glyQ 0.36266342 0.41440406 0.12351569 0.6817451 0.52612275 0.30909896 0.505656 1.419768 ‐0.36326 1.389893 0.505656 0.363809 0 STM3665 valine‐pyruvate aminotransferase avtA 0.1534823 0.13930215 0.18358889 0.5673434 0.6090645 0.49966124 0.55869 1.472931 ‐0.67193 1.942413 0.55869 0.287627 0 STM3666 paral putative oxidoreductase ysaA ‐0.3849482 ‐0.3260673 ‐0.4641717 ‐0.42707002 ‐0.54028434 ‐0.6653222 ‐0.54423 0.685759 0.045402 ‐1.67683 ‐0.54423 0.324555 0 STM3679 putative cytoplasmic protein ‐0.29648966 ‐0.65751076 ‐0.54979634 ‐0.6548299 ‐0.61710554 ‐0.7088889 ‐0.66027 0.632758 0.639963 ‐2.33821 ‐0.66027 0.282385 0 STM3683 selenocysteine synthase (with SelD) selA ‐0.15914151 ‐0.19465336 ‐0.29391286 1.0289332 0.80916214 0.7335391 0.857211 1.811533 ‐0.45086 2.489417 0.857212 0.344342 0 STM3696 putative transcriptional regulator ‐0.13165651 ‐0.2929532 ‐0.263262 ‐0.46893784 ‐0.48872402 ‐0.37355036 ‐0.44374 0.735227 0.126095 ‐1.52327 ‐0.44374 0.291305 0 STM3700 glycerol‐3‐phosphate dehydrogenase (NAD ) gpsA 0.3124642 0.18166745 0.082764484 1.5715777 1.1473793 0.7342488 1.151069 2.220783 ‐0.4197 2.313833 1.151069 0.497473 0 STM3701 molecular chaperone in protein export secB 0.037450768 0.085822046 0.023267388 0.57160187 0.6174447 0.39696622 0.528671 1.4426 0.035514 1.637165 0.528671 0.322919 0 STM3703 putative Rhodanese‐related sulfurtransferases yibN 0.12468472 0.07792352 0.092866965 1.2429237 0.89182585 0.7405136 0.958421 1.943182 ‐0.29628 2.369068 0.958421 0.404556 0 STM3713 O‐antigen ligase rfaL 0.36301234 0.49145386 0.43890908 1.906771 1.6350414 1.0828239 1.541545 2.911062 ‐0.46753 3.094522 1.541545 0.498153 0 STM3723 lipopolysaccharide core biosynthesis modification of heptose region rfaQ 0.19400369 0.34150213 0.23618971 1.0832036 0.6196684 0.46239242 0.721755 1.649187 ‐0.05103 1.632598 0.721755 0.44209 0 STM3727 50S ribosomal subunit protein L33 rpmG 0.6258041 0.38240027 0.33417016 1.5091441 1.1095043 1.1165243 1.245058 2.37028 0.206924 3.210497 1.245058 0.387808 0 STM3728 50S ribosomal subunit protein L28 rpmB 0.5031419 0.37100726 0.459275 0.8283098 0.82460684 0.77496606 0.809294 1.752354 ‐0.44367 2.965024 0.809294 0.272947 0 STM3730 flavoprotein affecting synthesis of DNA and pantothenate dfp 0.06676046 0.10776893 0.15122965 0.64047354 0.32047513 0.54447114 0.501807 1.415986 0.266171 1.431458 0.501807 0.350556 0 STM3731 deoxyuridinetriphosphatase dut ‐0.04612479 ‐0.030110795 ‐0.15081427 0.88178676 1.0015429 0.955422 0.946251 1.926858 0.224551 3.255938 0.946251 0.290623 0 STM3732 putative transcriptional regulator (TetR/ArcR family) ttk 0.05935783 0.2986477 0.09886001 0.8049446 0.93363255 0.7464978 0.828358 1.775664 0.29266 2.66332 0.828358 0.311025 0 STM3733 orotate phosphoribosyltransferase pyrE 0.22934297 0.43212935 0.260425 1.0674946 0.70575684 0.77110326 0.848118 1.800151 ‐0.05172 2.310646 0.848118 0.367048 0 STM3734 RNase PH rph 0.019597685 0.077178694 0.23095728 0.5203567 0.5639603 0.637919 0.574079 1.488726 0.858425 1.979159 0.574079 0.290062 0 STM3738 putative inner membrane protein yigC 0.24687901 0.47976634 0.24572635 ‐0.44474292 ‐0.5762905 ‐0.37029564 ‐0.46378 0.725086 0.321095 ‐1.46778 ‐0.46378 0.315972 0 STM3740 guanylate kinase gmk 0.15725826 0.3728713 0.22955245 0.8462617 0.83134234 0.9367947 0.871466 1.829521 0.315924 3.018624 0.871466 0.288697 0 STM3741 RNA polymerase, omega subunit rpoZ 0.14028324 0.18378332 0.28171414 0.7753145 0.56308615 0.6088408 0.64908 1.568168 0.52061 2.026896 0.649081 0.320234 0 STM3742 bifunctional : (p)ppGpp synthetase II also guanosine‐3,5‐bis spoT ‐0.056992415 ‐0.25012997 ‐0.2844884 0.5152583 0.35582075 0.52016604 0.463748 1.37912 0.993629 1.497257 0.463748 0.309732 0 STM3743 putative tRNA/rRNA methyltransferase spoU ‐0.16272414 ‐0.015153673 ‐0.18987694 0.4675559 0.54671586 0.2914016 0.435224 1.352121 0.273153 1.314066 0.435224 0.331205 0 STM3746 GltS family, glutamate transport protein gltS ‐0.027708873 0.10655096 ‐0.12550037 0.7002074 0.6240892 0.3462079 0.556835 1.471038 ‐0.0039 1.532583 0.556835 0.363331 0 STM3762 putative inner membrane protein cigR 0.1902197 0.071109936 0.25572044 ‐0.59304273 ‐0.77539563 ‐0.6598723 ‐0.6761 0.625853 ‐1.61551 ‐2.18795 ‐0.6761 0.309012 0 STM3767 putative cytoplasmic protein ‐0.3511006 ‐0.57912034 ‐0.62720615 0.43108487 0.4718336 0.60070896 0.501209 1.415399 0.727759 1.633288 0.501209 0.306871 0 STM3773 putative NtrC family transcriptional regulators, ATPase domain 0.15289244 0.35352457 0.30111754 0.540291 0.48780385 0.4386067 0.488901 1.403375 ‐0.12718 1.714788 0.488901 0.285108 0 STM3780 putative fructose‐bisphosphate aldolase class‐II 0.20207778 0.57365334 0.4473668 0.43595454 0.43045422 0.32178733 0.396065 1.315914 0.654424 1.352116 0.396065 0.292923 0 STM3790 response regulator (repressor) in two‐component regulatory system uhpA ‐0.20300399 ‐0.23561907 ‐0.084135115 0.63575506 0.85417336 0.37672183 0.622217 1.539238 ‐0.81989 1.580257 0.622217 0.393744 0 STM3796 acetolactate synthase I, large subunit, valine sensitive ilvB 1.5609252 1.3317875 1.3896406 1.216307 1.1003712 0.9060913 1.074257 2.105637 ‐0.39007 3.102563 1.074257 0.346248 0 STM3797 ilvB operon leader peptide ivbL 0.30770418 0.0621715 0.2673648 ‐0.5445204 ‐0.60196054 ‐0.59754527 ‐0.58134 0.668342 0.885319 ‐2.1201 ‐0.58134 0.274205 0 STM3803 putative cytoplasmic protein yidF 0.18201616 0.007583045 ‐0.23177125 ‐0.53644156 ‐0.74233145 ‐0.4259721 ‐0.56825 0.674435 ‐0.6246 ‐1.63079 ‐0.56825 0.348449 0 STM3808 small heat shock protein ibpB ‐0.28224045 ‐0.41326177 ‐0.2579473 ‐0.46361297 ‐0.44752392 ‐0.4528699 ‐0.45467 0.729678 ‐0.96994 ‐1.7455 ‐0.45467 0.26048 0 STM3828 galactonate dehydratase in bifunctional: 2‐oxo‐3‐deoxygalactonate 6‐phosphate aldolase dgoA 0.21327987 0.3637907 0.2827768 0.54554945 0.53348064 0.3950154 0.491348 1.405758 ‐0.05931 1.616055 0.491349 0.304042 0 STM3839 50S ribosomal subunit protein L34 rpmH ‐0.31835505 ‐0.10970761 ‐0.13283214 1.121832 1.1214676 1.1418061 1.128369 2.186114 0.316915 4.299051 1.128369 0.262469 0 STM3840 RNase P, protein component (protein C5), processes rnpA ‐0.1544575 ‐0.16499291 ‐0.27050206 1.3615233 1.405014 1.1863526 1.31763 2.492563 0.279636 4.084684 1.31763 0.322578 0 STM3851 putative xanthine/uracil permeases family yieG ‐0.14575565 ‐0.21347322 ‐0.031739704 0.8828982 0.96764827 0.95135605 0.933968 1.910523 0.742813 3.315306 0.933968 0.281714 0 STM3862 N‐acetyl glucosamine‐1‐phosphate uridyltransferase and glucosamine‐1‐phosphate acetyl traglmU 0.36955515 0.5402315 0.4510921 1.0702175 0.9851888 0.66823614 0.907881 1.876287 ‐0.30482 2.401418 0.907881 0.37806 0 STM3864 membrane‐bound ATP synthase, F1 sector, epsilon‐subunit atpC ‐0.011487707 ‐0.029106656 ‐0.07965923 1.0321796 0.99560744 0.9898409 1.005876 2.008162 0.48811 3.739228 1.005876 0.269006 0 STM3865 membrane‐bound ATP synthase, F1 sector, beta‐subunit atpD 0.01870176 0.13035516 ‐0.06819548 0.7332065 0.8959317 0.5588629 0.729334 1.657873 ‐0.60933 2.065678 0.729334 0.353072 0 STM3866 membrane‐bound ATP synthase, F1 sector, gamma‐subunit atpG 0.54671985 0.3996228 0.33254293 1.437102 1.0038995 0.9538133 1.131605 2.191023 ‐0.41275 2.765537 1.131605 0.409181 0 STM3867 membrane‐bound ATP synthase, F1 sector, alpha‐subunit atpA 0.10773366 0.061710186 0.08329395 0.89879 0.8716521 0.8813822 0.883941 1.84541 ‐0.89217 3.352232 0.883942 0.263687 0 STM3868 membrane‐bound ATP synthase, F1 sector, delta‐subunit atpH 0.22998466 0.44132522 0.17325944 1.1519117 1.0365077 0.91901296 1.035811 2.050266 ‐0.22183 3.207017 1.035811 0.322983 0 STM3869 membrane‐bound ATP synthase, F0 sector, subunit b atpF 0.048203807 0.19851294 0.0882226 0.961933 0.96212155 0.88443506 0.936163 1.913433 ‐0.20944 3.324281 0.936163 0.281614 0 STM3870 membrane‐bound ATP synthase, F0 sector, subunit c atpE 0.009046757 0.11437796 0.021699624 0.65336937 0.7971888 0.6472277 0.699262 1.623674 0.159499 2.29458 0.699262 0.304745 0 STM3871 membrane‐bound ATP synthase, F0 sector, subunit a atpB 0.24357018 0.1995768 0.04752768 1.5409764 1.056537 1.4860215 1.361178 2.568949 0.282757 3.328926 1.361178 0.408894 0 STM3875 initiation of chromosome replication mioC 0.21495241 0.17961408 0.21395944 1.5702454 1.2295758 1.2453265 1.348383 2.546265 ‐0.55737 3.676329 1.348383 0.366774 0 STM3877 asparagine synthetase A asnA ‐1.8288294 ‐2.0108335 ‐1.9725355 ‐0.7493705 ‐1.1015068 ‐1.0090463 ‐0.95331 0.516447 ‐0.27829 ‐2.63962 ‐0.95331 0.361154 0 STM3885 ribokinase rbsK 0.3601816 0.39282104 0.15744178 0.5545818 0.41455597 0.5954437 0.521527 1.435474 0.178185 1.679526 0.521527 0.310521 0 STM3900 ilvGEDA operon leader peptide ilvL ‐0.23719585 ‐0.3070986 0.0417315 ‐0.71283674 ‐0.38508698 ‐0.57018745 ‐0.55604 0.680168 ‐2.25206 ‐1.58584 ‐0.55604 0.350627 0 STM3901 acetolactate synthase II, large subunit, fragment 1 ilvG 0.6425514 0.59973615 0.58618224 0.6117585 0.62401396 0.6385095 0.624761 1.541955 ‐1.88097 2.371179 0.624761 0.263481 0 STM3902 acetolactate synthase II, small subunit ilvM 1.0454634 0.92444766 0.91379493 0.80081606 0.38492376 0.60558546 0.597108 1.512682 0.892174 1.588552 0.597108 0.375882 0 STM3903 branched‐chain amino‐acid aminotransferase ilvE 0.79254895 0.75233585 0.7646743 0.65603364 0.3946524 0.4817307 0.510806 1.424846 0.459504 1.535835 0.510806 0.332592 0 STM3904 dihydroxyacid dehydratase ilvD 0.775312 0.45393547 0.49352932 1.5322919 1.1240008 1.3032608 1.319851 2.496404 ‐0.59117 3.529914 1.319851 0.373905 0 STM3905 threonine deaminase ilvA 0.5118394 0.3958778 0.5679266 1.3083211 1.0906904 1.2207458 1.206586 2.307908 ‐0.70605 3.782734 1.206586 0.318972 0 STM3909 ketol‐acid reductoisomerase ilvC ‐0.25719902 ‐0.60160685 ‐0.39823884 0.7675543 0.856862 1.0445279 0.889648 1.852724 ‐1.75215 2.637024 0.889648 0.337368 0 STM3919 modulator of enterobacterial common antigen (ECA) polysaccharide wzzE 0.38888365 0.4176267 0.29808593 0.90911055 0.9141631 0.60147023 0.808248 1.751084 ‐0.26617 2.250454 0.808248 0.359149 0 STM3921 UDP‐N‐acetyl‐D‐mannosaminuronic acid dehydrogenase wecC 0.20276114 0.18865238 0.19314767 1.0837299 1.0751495 0.87831944 1.0124 2.017264 ‐0.21073 3.135962 1.0124 0.322835 0 STM3922 dTDP‐glucose 4,6‐dehydratase rffG 0.2537869 0.19174887 0.2785799 0.7698976 0.623928 0.33736098 0.577062 1.491808 ‐0.44457 1.507509 0.577062 0.382792 0 STM3927 putative inner membrane protein 0.04580798 0.24182725 0.14677499 0.4962595 0.62923944 0.5452565 0.556918 1.471124 0.515429 1.890564 0.556919 0.294578 0 STM3928 TDP‐Fuc4NAc:lipidII transferase wecF 0.14082524 0.40528783 0.3006426 0.57902503 0.7906797 0.73144406 0.700383 1.624936 0.027061 2.196991 0.700383 0.318792 0 STM3936 uroporphyrinogen III methylase hemX ‐0.21156333 0.12881263 ‐0.006796745 0.8144221 0.5928944 0.272307 0.559875 1.474141 ‐0.181 1.355257 0.559875 0.413113 0 STM3946 putative outer membrane lipoprotein yifL 0.1862601 0.26797107 0.4029051 0.6939396 0.5428045 0.53333163 0.590025 1.505273 ‐0.50861 1.917044 0.590025 0.307779 0 STM3949 putative integrase/recombinase, site‐specific xerC 0.13264139 ‐0.00340049 0.04418981 1.0018001 0.7039443 0.65936977 0.788371 1.727124 0.065893 2.170405 0.788371 0.363237 0 STM3952 MIT family, Mg2 /Ni2 /Co2 transport protein (Mg transport corA ‐0.06012455 0.373126 0.18432376 0.5917475 0.5367442 0.34873492 0.492409 1.406792 0.430821 1.495227 0.492409 0.32932 0 STM3965 5‐methyltetrahydropteroyltriglutamate‐homocysteine S‐methyltransferase metE 2.0208678 2.130202 2.026502 1.3302777 1.5007643 1.636712 1.489251 2.807432 0.656237 4.324233 1.489251 0.344397 0 STM3970 S‐adenosylmethionine : 2‐DMK methyltransferase and 2‐octaprenyl‐6‐methoxy‐1,4‐benzoqui ubiE 0.5451342 0.7330351 0.5664514 1.9925156 1.8771598 1.2903749 1.720017 3.294402 ‐0.57998 3.635352 1.720017 0.473136 0 STM3972 putative regulator in ubiquinone biosynthesis aarF 0.38699812 0.4446431 0.40212184 0.6121604 0.6710387 0.8239563 0.702385 1.627193 0.854953 2.202754 0.702385 0.318867 0 STM3973 component of Sec‐independent protein secretion pathway tatA 0.39415374 0.21388204 0.36006528 0.49250725 0.6424895 0.9343452 0.689781 1.613038 ‐0.59043 1.789451 0.689781 0.385471 0 STM3974 component of Sec‐independent protein secretion pathway tatB 0.3267777 0.4204216 0.35949153 1.2409211 0.96708983 0.6855373 0.964516 1.951409 ‐0.02541 2.318101 0.964516 0.41608 0 STM3978 putative oxidoreductase yigC 0.25310853 ‐0.06369869 ‐0.00989898 0.7984362 0.25809354 0.6248028 0.560444 1.474723 0.006476 1.35041 0.560444 0.415018 0 STM3986 Trk family, potassium transport protein, requires TrkE trkH 0.43091 0.36631954 0.36982083 0.42558333 0.49539125 0.6512143 0.524063 1.437999 0.363257 1.62529 0.524063 0.322443 0 STM3987 protoporphyrin oxidase hemG 0.4650082 0.2570255 0.34211197 0.7979541 0.6967339 0.5071127 0.667267 1.588062 ‐0.66513 1.956845 0.667267 0.340991 0 STM3996 putative homoserine kinase type II, protein kinase yihE 0.36842012 0.5877408 0.24637876 0.4794375 0.736238 0.29896173 0.504879 1.419004 0.344184 1.319532 0.504879 0.38262 0 STM3999 DNA polymerase I, 3 ‐‐ 5 polymerase polA 0.37616727 0.5917273 0.34549972 0.86111623 0.68715334 0.30518755 0.617819 1.534554 ‐0.40397 1.471229 0.617819 0.419934 0 STM4002 putative cytoplasmic protein 1.8951077 1.6498793 2.0633426 ‐3.046172 ‐3.429997 ‐3.3333795 ‐3.26985 0.103676 ‐0.72065 ‐8.81328 ‐3.26985 0.371014 0 STM4006 sensory kinase (phosphatase) in two‐component regulatory system glnL ‐0.6108326 ‐0.4447654 ‐0.4580785 1.014649 0.8775167 0.7090234 0.867063 1.823946 0.33435 2.519574 0.867063 0.344131 0 STM4007 glutamine synthetase glnA ‐0.53651893 ‐0.5801261 ‐0.66090095 ‐0.8614913 ‐1.0806694 ‐1.1501278 ‐1.03076 0.489451 ‐0.10893 ‐3.00752 ‐1.03076 0.342728 0 STM4062 6‐phosphofructokinase I pfkA 0.23692147 0.23283237 0.19542523 ‐0.8576517 ‐0.88586307 ‐0.8942313 ‐0.87925 0.54365 0.245833 ‐3.29535 ‐0.87925 0.266815 0 157 STM4068 putative regulatory protein, gntR family ‐0.4316753 ‐0.72215956 ‐0.47238067 ‐0.5438755 ‐0.7996518 ‐0.63016534 ‐0.6579 0.633801 1.139377 ‐1.98835 ‐0.6579 0.330877 0 STM4081 triosephosphate isomerase tpiA 0.08820934 0.11121911 0.060286928 ‐0.79814637 ‐1.0640477 ‐1.1518017 ‐1.00467 0.498386 ‐0.14579 ‐2.77477 ‐1.00467 0.362071 0 STM4088 putative cytoplasmic protein yiiU ‐0.4223067 ‐0.26139188 ‐0.03552375 ‐0.6951794 ‐0.6350564 ‐0.46052048 ‐0.59692 0.661165 0.445113 ‐1.83035 ‐0.59692 0.326123 0 STM4089 putative methyltransferase in menaquinone biosynthesis protein menG ‐0.32543272 ‐0.19806375 ‐0.2541264 ‐0.35762367 ‐0.55476916 ‐0.5807771 ‐0.49772 0.708224 0.047875 ‐1.52582 ‐0.49772 0.326201 0 STM4096 50S ribosomal subunit protein L31 rpmE ‐0.52524084 ‐0.6936451 ‐0.5349336 0.9467218 1.1588022 1.4138205 1.173115 2.25498 0.906253 3.001989 1.173115 0.390779 0 STM4100 cystathionine gamma‐synthase metB 0.3551766 0.58232796 0.62016344 0.8253261 1.0059774 0.8184255 0.883243 1.844517 ‐0.76617 2.784945 0.883243 0.317149 0 STM4101 aspartokinase II in bifunctional enxyme: aspartokinase II metL 0.11339356 0.20083217 0.035536792 0.6148853 0.7424174 0.91816837 0.75849 1.691719 0.659505 2.207044 0.75849 0.343668 0 STM4103 putative cytoplasmic protein 0.4829309 0.17199175 0.51570684 0.69531804 0.47887748 0.5695407 0.581245 1.49614 ‐0.62619 1.824923 0.581245 0.318504 0 STM4110 General PTS family, enzyme I ptsA ‐0.3237488 ‐0.2876717 ‐0.5148504 1.2346344 1.1793113 0.982827 1.132258 2.192015 ‐0.77651 3.408847 1.132258 0.332153 0 STM4112 PTS system fructose‐like IIC component frwC ‐0.021079062 ‐0.03662912 ‐0.022082517 0.492473 0.53179514 0.5148206 0.51303 1.427044 1.104254 1.920479 0.51303 0.267136 0 STM4118 putative Integral membrane protein yijP ‐0.009622546 0.023690742 0.10472735 1.115939 1.4263332 1.5023652 1.348212 2.545965 1.494692 3.605404 1.348213 0.373942 0 STM4119 phosphoenolpyruvate carboxylase ppc ‐0.017977186 ‐0.084627435 ‐0.31016555 1.2117127 0.81977683 0.5193365 0.850275 1.802845 ‐0.32354 1.863812 0.850275 0.456202 0 STM4125 regulatory protein sensor for oxidative stress, regulates oxyR 0.17255981 0.2267895 0.107635334 1.0420253 0.5638604 0.30808458 0.63799 1.55616 ‐0.05402 1.355011 0.63799 0.470838 0 STM4137 UDP‐N‐acetylenolpyruvoylglucosamine reductase murB 0.2412864 0.3411356 0.19636619 1.1494392 1.0200086 0.68865937 0.952702 1.935495 ‐0.12158 2.424448 0.952702 0.392956 0 STM4138 bifunctional: biotin‐[acetylCoA carboxylase] holoenzyme synthetase biotin operon birA 0.20755552 0.5247538 0.2071292 1.0865655 0.8850802 0.6860805 0.885909 1.847928 0.546482 2.385577 0.885909 0.37136 0 STM4139 pantothenate kinase coaA 0.18044613 0.33875772 0.06666341 0.7064172 0.74266016 0.6682729 0.705783 1.63103 0.919289 2.54588 0.705783 0.277226 0 STM4147 preprotein translocase IISP family, membrane subunit secE 0.37733194 0.25517297 0.2670554 0.31977314 0.64295644 0.6141499 0.525626 1.439559 ‐1.31041 1.464093 0.525627 0.359012 0 STM4150 50S ribosomal subunit protein L1, regulates synthesis rplA ‐0.009967902 0.12469781 ‐0.036103617 0.9806079 1.0134511 0.98505104 0.993037 1.99037 0.317348 3.7327 0.993037 0.266037 0 STM4152 50S ribosomal subunit protein L7/L12 rplL ‐0.27338395 ‐0.21300955 ‐0.3425917 0.62130743 0.52880853 0.45028988 0.533469 1.447405 ‐0.08011 1.748085 0.533469 0.305173 0 STM4159 deoxyxylulose‐5‐P thi‐S‐COSH tyrosine thiH 0.49387768 0.4242009 0.39095336 0.3482004 0.4624054 0.44730914 0.419305 1.337283 0.867473 1.438104 0.419305 0.291568 0 STM4160 deoxyxylulose‐5‐P thi‐S‐COSH tyrosine thiG 0.5696071 0.6524479 0.5532246 0.43022105 0.564055 0.51288176 0.502386 1.416554 ‐0.16183 1.704512 0.502386 0.294739 0 STM4161 putative involved in thiamine biosynthesis 0.74364185 0.74524623 0.5477212 1.0572369 0.97125435 0.83276814 0.953753 1.936905 ‐0.21855 2.969932 0.953753 0.321136 0 STM4162 catalyzes the adenylation of thisS as part thiF 0.42741707 0.5229101 0.4220712 0.7624599 0.87814826 0.69689643 0.779168 1.716141 ‐0.2087 2.523742 0.779168 0.308735 0 STM4163 thiamin phosphate synthase (thiamine phosphate pyrophosphorylase) thiE 0.4782781 0.52834356 0.46170875 0.98228496 1.009627 0.9916104 0.994507 1.9924 ‐0.76483 3.770296 0.994507 0.263774 0 STM4172 zinc‐resistance associated protein zraP ‐0.1561097 ‐0.015572153 ‐0.10101194 ‐0.9327319 ‐0.68908715 ‐0.56765115 ‐0.72982 0.602978 0.5179 ‐2.01004 ‐0.72982 0.36309 0 STM4182 homoserine transsuccinylase metA 0.83211875 0.9562479 0.87414855 ‐0.3689904 ‐0.77333647 ‐0.9920574 ‐0.71146 0.610701 ‐0.19417 ‐1.6234 ‐0.71146 0.438255 0 STM4188 B12‐dependent homocysteine‐N5‐methyltetrahydrofolate transmethylase, repressor of metEmetH 0.20014055 0.060896266 0.004278254 0.70330346 0.7226151 0.82178986 0.749236 1.680903 0.421906 2.561909 0.749236 0.292452 0 STM4190 (alpha)‐aspartyl dipeptidase pepE ‐0.19743058 ‐0.3404635 ‐0.32733977 ‐0.68625724 ‐0.47755364 ‐0.43082675 ‐0.53155 0.691813 1.465145 ‐1.59016 ‐0.53155 0.334273 0 STM4199 putative cytoplasmic protein ‐0.1392753 ‐0.13274455 ‐0.10709991 ‐0.58733094 ‐0.6224291 ‐0.528743 ‐0.5795 0.669195 0.154063 ‐2.04715 ‐0.5795 0.283076 0 STM4218 putative inner membrane protein ‐0.2195201 ‐0.18488295 ‐0.21319446 ‐0.39921743 ‐0.5148394 ‐0.5157363 ‐0.4766 0.71867 ‐0.39306 ‐1.61865 ‐0.4766 0.294441 0 STM4222 putative outer membrane protein yjbE ‐2.0814438 ‐2.1460955 ‐2.0887516 ‐2.8885083 ‐2.8630266 ‐2.601704 ‐2.78441 0.145147 0.19133 ‐8.01501 ‐2.78441 0.3474 0 STM4226 putative inner membrane protein yjbA ‐0.3906223 ‐0.23616368 ‐0.29530108 ‐0.42360932 ‐0.43033835 ‐0.6432603 ‐0.49907 0.707563 ‐0.0942 ‐1.52215 ‐0.49907 0.327871 0 STM4233 chorismate pyruvate lyase ubiC ‐0.12871805 0.023418335 0.041092947 0.52969265 0.56418645 0.41168126 0.501853 1.416032 0.445576 1.662195 0.501853 0.301922 0 STM4234 p‐hydroxybenzoate: octaprenyltransferase ubiA 0.048525788 0.20326346 ‐0.005566194 0.36930713 0.51416093 0.47677785 0.453415 1.369278 ‐0.06916 1.515597 0.453415 0.299166 0 STM4237 SOS response regulator, transcriptional repressor (LexA family) lexA 0.4908214 0.36775026 0.3812299 0.89199054 0.7649744 0.68065786 0.779208 1.716188 ‐0.19734 2.456752 0.779208 0.31717 0 STM4245 quinone oxidoreductase, NADPH dependent qor ‐0.09936339 ‐0.25282648 ‐0.10849875 ‐0.77310276 ‐0.8810941 ‐0.64505816 ‐0.76642 0.587875 ‐0.58622 ‐2.36571 ‐0.76642 0.323969 0 STM4256 ssDNA‐binding protein controls activity of RecBCD nuclease ssb 0.5871153 0.5578599 0.6316421 0.87687755 0.63089496 0.65885246 0.722208 1.649705 0.00997 2.165515 0.722208 0.333504 0 STM4271 putative inner membrane protein ‐0.42716506 ‐0.3473108 ‐0.47306418 ‐0.62511533 ‐0.61022663 ‐0.7487976 ‐0.66138 0.632273 0.247332 ‐2.20703 ‐0.66138 0.299669 0 STM4282 part of formate‐dependent nitrite reductase complex involved nrfG ‐0.3483499 ‐0.38001975 ‐0.5585485 0.75978756 0.52543026 0.35321736 0.546145 1.460179 ‐0.28036 1.461952 0.546145 0.373572 0 STM4299 GPH family, melibiose permease II melB 0.03857644 ‐0.058848847 ‐0.050801385 ‐0.74538815 ‐0.51585025 ‐0.6467351 ‐0.63599 0.643499 1.038719 ‐1.97372 ‐0.63599 0.322229 0 STM4330 chaperone Hsp60 with peptide‐dependent ATPase activity, affects mopA ‐0.078556 ‐0.14903623 ‐0.1830112 1.4066368 1.3344876 1.0810019 1.274042 2.418382 6.89E‐04 3.594001 1.274042 0.354491 0 STM4356 putative sugar kinase yjeF ‐0.26104313 ‐0.4351466 ‐0.538389 0.7492662 0.9724459 1.2659442 0.995885 1.994304 0.284089 2.456784 0.995885 0.405361 0 STM4358 N‐acetylmuramoyl‐l‐alanine amidase II, a murein hydrolase amiB 0.084567875 ‐0.08013403 ‐0.07075234 0.47241879 0.5631526 0.76438445 0.599985 1.515701 ‐0.38057 1.754233 0.599985 0.342021 0 STM4360 delta(2)‐isopentenylpyrophosphate tRNA‐adenosine transferase miaA 0.21154094 0.11492931 0.47787622 0.5184273 0.37730786 0.5192869 0.471674 1.386718 ‐1.20392 1.557023 0.471674 0.302933 0 STM4362 putative GTP‐ase, together with HflCK possibly involved hflX 0.7876796 0.86858255 0.6201337 1.1325591 0.79570717 0.7112566 0.879841 1.840172 ‐0.19517 2.288637 0.879841 0.384439 0 STM4363 with HflC, part of modulator for protease hflK 0.8000094 0.7273756 0.7477214 0.5571832 0.5122535 0.6720588 0.580499 1.495366 ‐1.73589 1.913742 0.580499 0.303332 0 STM4378 putative inner membrane protein yjfN ‐0.08648893 0.06479884 ‐0.047556624 ‐0.43526262 ‐0.37957746 ‐0.44299832 ‐0.41928 0.747798 0.161829 ‐1.52064 ‐0.41928 0.275726 0 STM4380 putative hydrolase of the alpha/beta superfamily yjfP 0.15110746 0.049971323 ‐0.10394158 ‐0.616622 ‐0.49003586 ‐0.42832986 ‐0.51166 0.701414 ‐1.60559 ‐1.64432 ‐0.51166 0.31117 0 STM4385 putative PTS enzyme IIsga subunit ptxA ‐0.17311272 ‐0.30231303 ‐0.24611764 0.41039428 0.39502704 0.477002 0.427474 1.344877 0.53003 1.521762 0.427474 0.280908 0 STM4386 putative hexulose phosphate synthase (arabino hexulose phosphate sgaH ‐0.09369197 ‐0.41996542 ‐0.37748674 0.97509044 0.8751564 1.0705723 0.973606 1.963743 1.168948 3.118872 0.973606 0.312166 0 STM4391 30S ribosomal subunit protein S6 rpsF 0.2568282 0.23183334 0.09631286 0.9645099 0.9792134 0.8653081 0.936344 1.913672 ‐0.27901 3.211935 0.936344 0.29152 0 STM4392 primosomal replication protein N priB 0.16337097 0.16544451 0.017810205 0.9178786 0.8114638 0.6617667 0.797036 1.737528 ‐0.3893 2.415014 0.797036 0.330034 0 STM4394 50S ribosomal subunit protein L9 rplI 0.17027046 0.10517608 0.13777104 1.0980852 1.1089771 1.0507216 1.085928 2.12274 ‐0.85704 3.96858 1.085928 0.273631 0 STM4415 fructose‐bisphosphatase fbp 0.31432876 0.22913125 0.1297009 1.0985059 0.8416824 0.77107865 0.903756 1.87093 0.833273 2.544107 0.903756 0.355235 0 STM4436 putative endonuclease ‐0.07797606 ‐0.013048857 ‐0.018706404 ‐0.6232457 ‐0.5166787 ‐0.4909864 ‐0.54364 0.686039 0.947851 ‐1.83513 ‐0.54364 0.296239 0 STM4446 putative selenocysteine synthase [L‐seryl‐tRNA(Ser) selenium transferase ‐0.42905918 ‐0.6164485 ‐0.60982305 0.66548145 0.8008127 0.578856 0.681717 1.604047 0.391923 2.128136 0.681717 0.320335 0 STM4450 putative inner membrane protein ‐0.013533389 ‐0.1349672 ‐0.018422266 ‐0.5365105 ‐0.65171814 ‐0.34277293 ‐0.51033 0.70206 ‐0.79648 ‐1.47542 ‐0.51033 0.34589 0 STM4452 anaerobic ribonucleoside‐triphosphate reductase nrdD ‐0.015759228 0.06448343 ‐1.13E‐04 ‐0.7143738 ‐0.9242318 ‐1.0140898 ‐0.88423 0.541776 ‐0.90963 ‐2.56633 ‐0.88423 0.344552 0 STM4459 aspartate carbamoyltransferase, regulatory subunit (allosteric regulation) pyrI ‐0.15205932 ‐0.02226476 0.007731194 ‐0.5128814 ‐0.65781504 ‐0.8329326 ‐0.66788 0.629433 ‐0.1565 ‐1.91766 ‐0.66788 0.348277 0 STM4460 aspartate carbamoyltransferase, catalytic subunit pyrB ‐0.1911988 0.1065385 ‐0.16156189 ‐0.84438145 ‐0.73007506 ‐0.79527605 ‐0.78991 0.57838 0.37631 ‐2.73462 ‐0.78991 0.288856 0 STM4466 putative carbamate kinase ‐0.2684855 ‐0.16979168 ‐0.26766735 ‐0.40891954 ‐0.51845723 ‐0.6452463 ‐0.52421 0.695341 ‐0.2044 ‐1.61777 ‐0.52421 0.324032 0 STM4475 valine tRNA synthetase valS ‐0.13678817 ‐0.07033009 ‐0.09689432 0.68650246 1.1021756 1.0792964 0.955991 1.939912 0.958626 2.447145 0.955991 0.390656 0 STM4480 putative permease yjgQ 0.063486755 0.037087753 0.11353091 0.47087058 0.6197956 0.6118738 0.567513 1.481967 1.016714 1.866053 0.567513 0.304125 0 STM4482 GntP family, L‐idonate transport protein idnT 0.07238632 ‐0.09336653 0.03562069 ‐0.47078454 ‐0.41564474 ‐0.3407426 ‐0.40906 0.753115 ‐0.10336 ‐1.39404 ‐0.40906 0.293434 0 STM4490 putative Mrr restriction endonuclease 0.3887054 0.24690713 0.34024322 1.0261223 0.5276918 0.43209174 0.661969 1.58224 ‐0.25576 1.504795 0.661969 0.439906 0 STM4492 putative cytoplasmic protein 0.5707446 0.7728898 0.60287035 1.3183347 1.072003 0.84367573 1.078004 2.111114 ‐0.72869 2.744378 1.078005 0.392805 0 STM4509 putative cytoplasmic protein 0.03042349 ‐0.006757003 0.14729406 ‐0.56696653 ‐0.53948337 ‐0.56994706 ‐0.5588 0.678867 ‐0.99363 ‐2.10514 ‐0.5588 0.265446 0 STM4516 putative inner membrane protein yjiN ‐0.00796756 ‐0.119048804 0.006749298 ‐0.44633076 ‐0.5882699 ‐0.47674745 ‐0.50378 0.705255 ‐0.27507 ‐1.68548 ‐0.50378 0.298896 0 STM4545 putative inner membrane protein ‐0.036689278 ‐0.038779516 ‐0.031494915 ‐0.52909815 ‐0.50999796 ‐0.73008275 ‐0.58973 0.664469 ‐0.65442 ‐1.80818 ‐0.58973 0.326144 0 STM4563 putative phosphoesterase yjjU ‐0.24502057 ‐0.06639686 ‐0.042895477 0.33520892 0.37847388 0.39397 0.369218 1.291652 0.443675 1.3508 0.369218 0.273333 0 STM4581 putative ABC superfamily (atp_bind) transport protein yjjK 0.26470044 0.15528566 0.03081108 0.8739493 0.61789674 0.7724137 0.754753 1.687343 1.049982 2.285807 0.754753 0.330191 0 STM4586 transcriptional regulator (AraC/XylS family) rob 0.18556161 0.21676244 0.33318102 0.6667123 0.53899324 0.47461933 0.560108 1.47438 ‐0.1097 1.79408 0.560108 0.312198 0 STY0070 citrate lyase alpha chain citF2 ‐0.18545978 ‐0.42093408 ‐0.50465536 ‐0.5581128 ‐0.5847175 ‐0.53381014 ‐0.55888 0.678829 ‐0.0424 ‐2.06648 ‐0.55888 0.27045 0 STY0277 hypothetical transcriptional regulator yafC 0.14265087 ‐0.1521154 ‐0.15672413 ‐0.5587351 ‐0.47637355 ‐0.3457794 ‐0.4603 0.726837 0.287052 ‐1.44862 ‐0.4603 0.317748 0 STY0402 PrpD protein prpD ‐0.49298972 ‐0.5892416 ‐0.48051035 0.985427 0.4965236 0.6967143 0.726222 1.654301 0.763535 1.82627 0.726222 0.397653 0 STY0414 possible efflux pump ‐0.13029566 ‐0.14258891 ‐0.054987572 ‐0.94529253 ‐0.82980275 ‐0.7351139 ‐0.83674 0.559909 0.909626 ‐2.64353 ‐0.83674 0.316522 0 STY0586 putative membrane protein ybcI ‐0.39932278 ‐0.33200687 ‐0.3538852 ‐0.42742905 ‐0.47057682 ‐0.4057785 ‐0.43459 0.739902 0.627103 ‐1.58152 ‐0.43459 0.274795 0 STY0963 anaerobic dimethyl sulfoxide reductase chain B dmsB ‐0.45513213 ‐0.3605968 ‐0.49858785 ‐0.8189377 ‐0.69091284 ‐0.9507103 ‐0.82019 0.566369 ‐0.22005 ‐2.47978 ‐0.82019 0.330749 0 STY0968 pyruvate formate‐lyase 1 activating enzyme pflA 0.001969404 0.090691045 0.23764208 ‐0.44380128 ‐0.49522695 ‐0.37079692 ‐0.43661 0.73887 ‐1.08522 ‐1.49601 ‐0.43661 0.291849 0 STY1106 putative transcriptional regulator (pseudogene) 0.1654252 0.28281456 0.22824402 0.68875647 0.5618475 0.61749583 0.6227 1.539754 0.409719 2.129053 0.6227 0.292477 0 STY1228 conserved hypothetical protein ‐0.054740768 0.104661934 0.1468477 0.47063702 0.8555985 0.6568269 0.661021 1.581201 0.477337 1.801646 0.661021 0.366898 0 STY1314 TonB protein tonB 0.16541308 ‐0.006781798 0.2806966 0.30481392 0.51482433 0.5652554 0.461631 1.377098 ‐0.84012 1.375957 0.461631 0.335498 0 STY1431 putative cytochrome ‐0.1300409 ‐0.005602882 ‐0.15537688 ‐1.0654176 ‐1.2203649 ‐1.2829632 ‐1.18958 0.43843 ‐0.39887 ‐3.71271 ‐1.18958 0.320408 0 STY1488 respiratory nitrate reductase 2 alpha chain narZ ‐0.5651388 ‐0.5857039 ‐0.35057256 ‐0.50144684 ‐0.51809454 ‐0.43401277 ‐0.48452 0.714736 ‐0.99226 ‐1.72147 ‐0.48452 0.281455 0 STY1505 putative glycogen debranching protein glgX ‐0.31610373 ‐0.41061938 ‐0.40923125 ‐0.92813474 ‐1.0527322 ‐0.9623939 ‐0.98109 0.506598 0.009529 ‐3.34942 ‐0.98109 0.292912 0 STY1509 hypothetical protein 0.20744097 0.07347412 0.1599974 ‐0.45644525 ‐0.66976887 ‐0.6092868 ‐0.5785 0.66966 ‐0.83674 ‐1.8122 ‐0.5785 0.319226 0 STY1567 putative dimethyl sulphoxide reductase subunit dmsB ‐0.21789041 ‐0.28208828 ‐0.34394017 ‐0.3544724 ‐0.47628576 ‐0.63092494 ‐0.48723 0.713395 0.109704 ‐1.4512 ‐0.48723 0.335742 0 STY1602 hypothetical protein 0.026873764 0.29755065 0.31107032 0.83338255 0.8232579 0.675483 0.777374 1.714009 0.432441 2.533988 0.777375 0.306779 0 STY2099 high‐affinity zinc uptake system periplasmic binding protein yebL 1.6600322 1.9473672 1.7970768 ‐3.3868663 ‐3.5019495 ‐3.6352866 ‐3.50803 0.087897 ‐0.03647 ‐10.7107 ‐3.50803 0.327527 0 STY2115 putative copper homeostasis protein cutC ‐0.83848965 ‐0.75747293 ‐0.65187526 ‐0.46578476 ‐0.5861411 ‐0.32073995 ‐0.45756 0.728219 1.253116 ‐1.37621 ‐0.45756 0.332475 0.014971 STY2194 putative membrane protein ‐0.019149879 ‐0.14559393 ‐0.13401514 ‐0.51458967 ‐0.5499998 ‐0.40678453 ‐0.49046 0.711799 1.225879 ‐1.64133 ‐0.49046 0.298817 0 STY2202 putative membrane protein ‐0.21152759 ‐0.22645791 ‐0.05109429 ‐0.5148607 ‐0.5383166 ‐0.50320315 ‐0.51879 0.697955 ‐0.98239 ‐1.9498 ‐0.51879 0.266075 0 STY2261 putative propanediol utilization protein PduV pduV ‐0.33628783 ‐0.35360885 ‐0.6888912 ‐0.5082773 ‐0.4873949 ‐0.38296574 ‐0.45955 0.727215 1.134446 ‐1.56037 ‐0.45955 0.294511 0 STY2303 putative reductase RfbI rfbI 0.6925853 1.1637181 0.61202896 2.163033 1.9231256 1.4972976 1.861152 3.632977 ‐0.33048 4.132102 1.861152 0.450413 0 STY2703 putative cobalamin adenosyltransferase ‐0.38120845 ‐0.6780023 ‐0.5178964 0.5951261 0.49704218 0.5939658 0.562045 1.47636 ‐0.51934 1.949834 0.562045 0.288253 0 STY2769 putative DNA‐binding protein yfgA 0.11913918 0.18139827 0.22403127 0.8209639 1.2088264 1.1399691 1.056586 2.080004 ‐0.03397 2.815867 1.056587 0.375226 0 STY2867 hypothetical protein 0.19530237 0.37931833 0.29865903 0.6023217 0.53004766 0.28801653 0.473462 1.388437 ‐0.54408 1.3497 0.473462 0.350791 0 STY2893 putative exported protein iroE 0.93417346 0.86765563 0.87125075 0.83267385 0.7676555 0.7568699 0.785733 1.723968 1.553892 2.811958 0.785733 0.279426 0 STY2897 conserved hypothetical protein ‐1.4992087 ‐1.4673667 ‐1.5548842 ‐1.1871341 ‐1.3526785 ‐1.3884839 ‐1.30943 0.40348 ‐0.53584 ‐4.12074 ‐1.30943 0.317766 0 STY2906 putative exported protein ‐0.0854197 ‐0.24294394 ‐0.28493676 ‐0.4172547 ‐0.6227864 ‐0.52880716 ‐0.52295 0.695948 ‐0.1432 ‐1.65935 ‐0.52295 0.315154 0 STY3050 lipoprotein NlpD precursor nlpD 0.19060674 0.088254474 0.25072965 0.53283197 0.5166268 0.6816841 0.577048 1.491793 0.922408 1.87185 0.577048 0.308277 0 STY3296 hypothetical protein 0.21762614 0.16871466 0.17844664 ‐0.84779716 ‐0.7772739 ‐0.8087798 ‐0.81128 0.569875 ‐0.51543 ‐2.93788 ‐0.81128 0.276146 0 STY3467 protein chain initiation factor 2 infB 0.1128122 0.18285123 ‐0.015049658 1.4079425 1.1620206 0.8900322 1.153332 2.22427 ‐0.68293 2.84548 1.153332 0.405321 0 STY3653 dihydroxyacid dehydratase ilvD 0.40515068 0.26249734 0.2621436 1.4708517 0.88730145 0.8937096 1.083954 2.119838 ‐0.27573 2.413039 1.083954 0.449207 0 STY3709 phosphoribosylaminoimidazolecarboxamide formyltransferase and IMP cyclohydrolase (bifunpurH ‐0.23100583 ‐0.031957548 0.040262125 0.80629796 0.7513476 0.7758266 0.777824 1.714543 ‐1.22123 2.863397 0.777824 0.271644 0 STY3710 phosphoribosylglycineamide synthetase purD ‐0.17272185 ‐0.2504813 ‐0.35219258 1.3910269 1.1928164 1.3390877 1.307644 2.475369 ‐0.23581 4.150081 1.307644 0.315089 0 STY3724 thiamine biosynthesis protein thiS 0.34690958 0.4336048 0.3258385 1.424583 0.9494153 0.7918123 1.05527 2.078107 ‐0.03197 2.366458 1.05527 0.445928 0 STY3725 thiamine biosynthesis protein thiG 0.6056575 0.7192756 0.60881543 0.69907445 0.65668464 0.52331895 0.626359 1.543665 0.472357 2.029002 0.626359 0.308703 0 STY3804 putative carbohydrate kinase ‐0.08348141 0.03675181 ‐0.11607615 ‐0.3569091 ‐0.38829818 ‐0.4418674 ‐0.39569 0.760125 0.293705 ‐1.4104 ‐0.39569 0.280552 0 STY3808 periplasmic sulphate binding protein sbp 0.036801267 ‐0.31776533 ‐0.43881777 1.527675 1.0408645 1.1840522 1.250864 2.379839 0.775325 3.125631 1.250864 0.400196 0 STY3827 L‐rhamnose isomerase rhaA 0.063002154 ‐0.06389031 ‐0.11265572 ‐0.36148068 ‐0.53162616 ‐0.43974763 ‐0.44428 0.734949 ‐0.29266 ‐1.45706 ‐0.44428 0.304919 0 STY3864 hypothetical protein 0.25604105 0.24235685 0.15011619 ‐0.48472005 ‐0.6431972 ‐0.6195285 ‐0.58248 0.667814 0.238149 ‐1.90911 ‐0.58248 0.305106 0 STY4175 hypothetical protein ‐0.70266485 ‐0.7875038 ‐0.7313358 ‐0.36298174 ‐0.58551556 ‐0.66896117 ‐0.53915 0.688175 0.324395 ‐1.55344 ‐0.53915 0.34707 0 STY4517 conserved hypothetical protein 0.010962895 ‐0.058584455 0.300675 ‐0.40354007 ‐0.34922576 ‐0.5040589 ‐0.41894 0.747973 ‐1.84517 ‐1.39135 ‐0.41894 0.301105 0 STY4627 probable terminase subunit 0.01838409 0.035011154 ‐0.036598165 ‐0.73977816 ‐0.747407 ‐0.8286975 ‐0.77196 0.585621 0.266777 ‐2.71623 ‐0.77196 0.284203 0 STY4655 Vi polysaccharide export protein vexA 0.06558213 0.20682047 0.2547191 1.001506 1.0413368 1.0839763 1.042273 2.05947 0.46067 3.728244 1.042273 0.279561 0 STY4846 putative outer membrane protein 0.33641014 0.40311894 0.23571685 ‐0.53900665 ‐0.9099165 ‐1.2299426 ‐0.89296 0.53851 ‐0.21816 ‐1.96088 ‐0.89296 0.455386 0