Genome sequence of H. marismortui Supplementary material

Genome sequence of Haloarcula marismortui: supplementary material

Evolutionary comparison of Halobacterium sp. NRC-1 and H. marismortui genomes. Using a mutual best match procedure we identified 1,708 potential orthologous gene pairs between the 4,242 predicted protein sequences (see below for proteome description) from H. marismortui and the 2,627 annotated protein sequences from Halobacterium sp. NRC-1. The vast majority of these orthologous pairs (viz. 1,475 pairs) are located in the main chromosomes (H. marismortui Chromosome I and Halobacterium sp. NRC-1 Chromosome). This is significantly greater than the 996 pairs expected assuming a random distribution of unannotated genes among all chromosomes. In contrast, there are very few orthologous pairs distributed among the remaining replicons: no clear one-to-one relationship exists between the minor H. marismortui replicons and the two smaller Halobacterium sp. NRC-1 replicons. Nevertheless, after suppressing the orthologous pairs observed in comparing the large chromosomes in each of the two halophiles, among all of the other pair-wise comparisons of replicons, some statistically significant excess of orthologous pairs is observed when comparing pNRC200 to Chromosome II, pNG600 and pNG500, as well as in the comparison of pNRC100 to Chromosome II and pNG600. ADHoRe automatically detects genomic regions with statistically significant conserved gene content and order, paying special attention to micro-rearrangements. Following an all-against-all sequence similarity search, ADHoRe detects diagonal clusters of conserved order and orientation, then deletes statistically insignificant clusters, enriches the remaining clusters with compatible singletons, and finally merges compatible clusters in opposite orientations. The final clusters depict genomic regions of micro-colinearity that evolved from a common ancestor by rearrangement. GRIMM calculates solutions to the pairwise genome rearrangement problem, i.e. to find an optimal scenario transforming one genome into another via rearrangement events. For circular chromosomes, the most common rearrangement event is the reversal (or inversion). The reversal distance between two genomes is the minimum number of reversals it takes to get from one genome to the other. For a given pair of genomes, the reversal distance is unique, but there are usually many possible reversal scenarios with this distance. However, it is possible that this mathematical notion of reversal distance could underestimate the actual number of steps that occurred biologically. Genome sequence of H. marismortui Supplementary material

H. marismortui encodes genes that may play a role in DNA transfer between cells. An interesting finding among the smaller replicons is an operon on pNG500 potentially involved in a DNA transfer system (conjugation). This operon encodes eight proteins including plasmid transfer complex proteins (TrwB2 and TraD), a relaxase (Rlx) for plasmid mobilization, and two CopG family proteins; CopG family proteins are involved in regulation of plasmid copy number. DNA transfer among halophiles has been observed and identification of genes that are responsible for the process may facilitate study of this process in archaea.

Construction of the Function Association Network. 1. Inference of functional associations among proteins using comparative genomics. A. Domain fusion association. Two or more genes that are individually translated in one genome but translated as a single polypeptide in other genomes are predicted to be functionally related and that they may physically interact in the former (Marcotte et al. 1999). Using this strategy a total of 1,267 domain fusion associations were detected among 499 proteins encoded in H. marismortui genome. B. Phylogenetic pattern association. This type of association predicts functional coupling of proteins on the basis of similar profiles relating to the presence or absence of pairs of orthologs in fully sequenced genomes (Eisenberg et al. 2000). We identified in H. marismortui, upon analyzing 90 fully sequenced genomes, 5,322 putative phylogenetic pattern associations among 671 proteins. 2. Operons. In prokaryotes genes that are functionally associated are often organized in the form of operons of closely linked genes that are co-transcribed from a single promoter. This gene arrangement enables coordinate regulation of the genes in the operon and may also facilitate appropriate stoichiometry of the translated proteins. In fact the first or the last gene in an operon often encodes a transcription regulator of all genes in that operon. These transcriptional regulators are key in deciphering the gene regulatory networks that control the individual physiological processes. We have hypothesized that 952 genes are organized into 616 operons in the H. marismortui genome by ascertaining the chromosomal proximity of these genes (Moreno-Hagelsieb and Collado-Vides 2002; Zheng et al. 2002). In at least 33 of Genome sequence of H. marismortui Supplementary material

the 616 operons that we identified, the first or the last gene encodes a putative transcriptional regulator. 3. Protein families. A total of 1,448 pairwise similarities were inferred by comparing the entire H. marismortui predicted proteome to itself using BLASTP. Considering a BLASTP score cut- off of 10e-40, there are 218 protein families in H. marismortui ranging from two proteins up to 31 proteins per family.

Oxidative phosphorylation. Four subunits of succinate dehydrogenase, at least 18 genes required for biogenesis of NADH dehydrogenase and twenty-one cytochrome genes are encoded in the genome. These include three genes encoding cytochromes P450 involved in the oxidative degradation of environmental toxins and mutagens and one gene encoding a di-haem cytochrome c peroxidase which reduces hydrogen peroxide to water. At least five cytochrome biogenesis proteins were also identified. Nine genes encoding all of the subunits of an ATP synthase were also detected.

Lipid Metabolism, cell envelope components and transporters. Archaeal lipids and their metabolism differ substantially from their bacterial and eukaryotic counterparts and are thus one of the distinguishing characteristics of all known organisms in the archaeal domain of life (Koga et al. 1998). Archaeal lipids are characterized by ether linkages between isoprenoid alcohol tail and glycerol-1-phosphate, rather than ester linkages between fatty acids and glycerol-3- phosphate (Kates 1993). The synthesis of archaeal membrane lipids must therefore use different chemical pathways than those used by bacterial and eukaryotic organisms. Genes involved in the synthesis of isoprenoid precursors, isopentenyl pyrophosphate and dimethylallyl pyrophosphate, have been identified in the mevalonate pathway. However, one key enzyme in the synthesis of membrane lipids geranylgeranyl pyrophosphate (GGPP) synthase which generates the 20 carbon GGPP via the elongation of farnesyl pyrophosphate by isopentenyl pyrophosphate has not been identified. In addition, the enzymes involved in forming ether linkages between GGPP and glycerol-1-phosphate have also not been identified. This suggests that the enzymes catalyzing these steps in H. marismortui have either diverged significantly in their sequence such that they are no longer detectable at the level of sequence similarity. The other possibility is that an entirely different biochemical pathway exists in H. marismortui and the associated enzymes are Genome sequence of H. marismortui Supplementary material

yet to be characterized. Nevertheless, phosopholipid transferases PssA and PgsA are present for the formation of phospholipids. Other genes involved in lipid physiology, including the synthesis of other important apolar lipids such as beta-carotene (retinal precursor), squalene, and bacterioruberins (photoprotectants) have also been identified. Four genes encoding cell surface glycoprotein were identified including one that matched an S-layer protein in Methanothermobacter thermautotrophicus. These proteins as in all archaeal halophiles, such as Halobacterium sp. NRC-1, may assemble outside the cell membrane as a layer of sulfated- glycoproteins, which is primarily responsible for maintaining cell morphology. Finally, all enzymes of the β-oxidation pathway for the breakdown of fatty acids are present in H. marismortui.

Altogether at least 259 proteins with roles in the transport of small molecules including symporters, antiporters, ABC transporters, and permeases are distributed among five of the nine replicons (pNG500: 3, pNG600: 10, pNG700: 42, Chromosome I: 183, Chromosome II: 21). In the pNG600 mini-chromosome we identified ten cation transport proteins of different specificities (copper, zinc, mercury, cadmium), a mercuric reductase, and several metal-ion dependent transcription regulators suggesting that this replicon may be primarily responsible for handling stress offered by high concentrations of heavy metals in the natural environment of H. marismortui. For protein translocation across the membrane eight proteins (SecY, SecF, SecD, Sec11a and b, SecE, Sec61 beta, Srp10 and Srp54) of the sec-dependent and at least three proteins (TatC1, TatC2 and TatD) of the twin-arginine protein translocation (Tat) pathway are encoded in the H. marismortui predicted proteome. Other proteins that may participate in protein translocation include four bacterial type II secretion proteins (GspE1-E4) and one type IV secretion protein (VirB11). Of the four gspE genes, one (gspE3) is encoded in an operon with five genes encoding flagellar proteins suggesting that it may play a role in flagellar biogenesis. The genome also encodes an ortholog (CsaA) of an export-related chaperone that also has tRNA-binding activity (Kawaguchi et al. 2001). A total of 41 metal ion transporters were identified including active potassium uptake proteins (Trk), potassium channel proteins (Pch), and sodium-dependent symporters and antiporters. We also identified ABC transporters for a variety of solutes including spermidine/putrescine, sugars, peptides, sulfate ions and phosphate ions. All 13 proteins Genome sequence of H. marismortui Supplementary material

mediating oligopeptide or dipeptide transport are encoded on Chromosome I.

Arginine fermentation in Halobacterium sp. NRC-1 and H. marismortui. In Halobacterium sp. NRC-1 arginine is fermented by the arginine deiminase (ADI) pathway into ornithine and citrulline (Ruepp et al. 1995). Ornithine accumulates in the cell and is utilized for importing additional arginine via an ornithine/arginine antiporter (Storch et al. 1999) believed to be comprised of at least one protein YhdG (Baliga et al. 2002; Storch et al. 1999). Subsequent breakdown of citrulline yields equimolar amounts of ATP. While arginase genes have been detected in at least three other fully sequenced archaeal genomes –Methanopyrus kandleri AV19, Pyrococcus abyssi GE5, and Pyrococcus furiosus DSM 3638, thus far only Sulfolobus tokodaii and H. marismortui contain urease coding genes. However, S. tokodaii catabolizes arginine through the arginine deiminase (ADI) pathway which unlike the arginase pathway does not yield urea. Both Halobacterium sp. NRC-1 and H. marismortui can also convert arginine to agmatine via the action of ArgDC (Pyruvoyl-dependent arginine decarboxylase). In both organisms the agmatine can be further acted upon by agmatinase (SpeB) to yield putrescine . Agmatine, putrescine and spermidine are polyamines that participate in a number of cellular processes such as chromatin condensation, maintenance of DNA structure, RNA processing, translation and protein activation (Childs et al. 2003).

Organization of arginine metabolism genes in Halobacterium sp. NRC-1. An analysis of gene organization within a single genome and across multiple genomes can provide important insights into gene function and regulation (see above). For example, the physical organization in the Halobacterium sp. NRC-1 genome of arginine breakdown and synthesis genes, as described below, correlates with the coordinated regulation of the two pathways with several other aspects of metabolism such as pyrimidine and glutamate metabolism and phototrophy (Baliga et al. 2002). Three genes, argG, argH and arcB play a central role in the synthesis of arginine from ornithine and carbamoyl phosphate. Similarly, three genes arcA, arcB and arcC encode enzymes for fermentation of arginine by the arginine deiminase (ADI) pathway back to ornithine and carbamoyl phosphate. The two arginine synthesis genes argG and argH in Halobacterium sp. NRC-1 are organized as an operon on the large chromosome; in contrast, the third gene arcB, Genome sequence of H. marismortui Supplementary material

which encodes a function central to both the synthesis and the fermentation (ADI) pathways, is in an operon on the mini-chromosome pNRC200 with the two arginine fermentation genes arcA and arcC. Furthermore, all arginine fermentation genes including arcB are segregated on pNRC200 in a gene cluster along with a putative repressor of arginine fermentation arcR, an arginyl-tRNA synthetase gene and two genes of pyrimidine synthesis. Finally, the coordinated regulation of arginine metabolism with isoprenoid biosynthesis and phototrophy in Halobacterium sp. NRC-1 (Baliga et al. 2002) is reflected in the operon-like organization of the arginine metabolism gene argB with mvk which encodes mevalonate kinase –an isoprenoid biosynthesis enzyme. This coordinate regulation may be mediated by a common transcription regulator especially in cases where the genes are co-transcribed in the form of operons (Baliga et al. 2002).

Further Analysis of Unique Rhodopsin Xop2 Yet another potentially interesting feature of this protein is the double change to F and W, respectively, at positions Y83 and F189, two residues highly conserved in all archaeal opsins (Figure E in supplement). Although it is not clear whether or not this has any functional consequences, the side chains of these two residues again contribute, on the extracellular side of the protein, key hydrogen bonds that are thought to be functionally significant in the structural transitions that occur during the late portion of the bacteriorhodopsin photocycle. Indeed, enough uncertainty exists about the function of this protein that biochemical and physiological tests will have to be conducted to clarify its function.

Retinal Biosynthesis The multiple homologous carotenoid biosynthesis enzymes in Halobacterium sp. NRC-1 has been correlated to presence of two parallel biochemical pathways, of which only one pathway is under the regulatory control of Bat –the transcriptional regulator of purple membrane biogenesis (Baliga et al. 2001; Peck et al. 2001). In Halobacterium sp. NRC-1 the gene encoding Bat is co- transcribed with brp which encodes beta-carotene lyase and located in a gene cluster along with bop (bacterioopsin), crtB1 (phytoene synthase) and blp (function unknown). All of the genes in this cluster are under the control of Bat (Baliga et al. 2001). Although the H. marismortui genome encodes multiple Bat-like transcription regulators capable of sensing redox-potential and Genome sequence of H. marismortui Supplementary material

light, intriguingly, in the H. marismortui genome we did not detect a single ortholog of Bat co- localizing with any of the bacterioopsin or carotenoid biosynthesis genes.

Additional Photoreceptors For example, we find that rrnAC3205 encodes a PRC-barrel domain containing protein and rrnAC3204 (hcp1, halocyanin precursor-like) co-localized to the same regions of the Chromosome I, which as described for the genes of denitrification and arginine metabolism, often indicates functional coupling and coordinate regulation. Although we cannot determine the precise role of these photosynthesis proteins the presence of the antenna-complex and halocyanin proteins as well as their chromosomal organization clearly points to interesting photobiology.

A comparison of signaling proteins in H. marismortui and Halobacterium sp. NRC-1 In comparing the sensory proteins in H. marismortui with that of Halobacterium sp. NRC-1 it is evident that H. marismortui has more than twice the expected complement of proteins containing PAS, PAC, and GAF domains. Indeed, the number of such domains is 3-4 folds greater than in Halobacterium sp. NRC-1 suggesting that H. marismortui may have the ability to discriminate among a larger complement of conditions with respect to quality and quantity of light and redox conditions. The number of chemotaxis-like receptor proteins seems to be roughly similar to those found in Halobacterium sp. NRC-1. In concert with the abundance of light and redox sensors, H. marismortui has also evolved a comparatively large number of both response regulator proteins and histidine kinases to communicate the sensory information to the gene regulatory components. Therefore, it is not surprising that many of these “extra” response regulatory domains and histidine kinases are associated directly with PAS, PAC, or GAF domains.

Motility. Halobacterium sp. NRC-1 can physically relocate, in search of favorable environments, using the environment sensors that can, through common intermediate transducers, communicate changes in light (Luecke et al. 2001; Perazzona et al. 1996; Perazzona and Spudich 1999), oxygen (HtrVIII) (Brooun et al. 1998), and nutrient concentrations (Kokoeva and Oesterhelt 2000; Storch et al. 1999) to the flagellar apparatus. Halobacterium sp. NRC-1 can also synthesize buoyant gas-filled vesicles (Halladay et al. 1992) to facilitate its vertical mobility. Given the presence of the large number of sensors, transducers, and response regulators it seems Genome sequence of H. marismortui Supplementary material

that H. marismortui is equally capable of relocating in response to changes in environmental factors. Like in Halobacterium sp. NRC-1, nearly a full complement of chemotaxis genes (minus cheZ) has also been identified in H. marismortui. In addition, all flagellar genes including two copies of flagellin precursor A (flaA1 and A2) are present in H. marismortui. It is interesting to note that, in contrast to their Halobacterium sp. counterparts, laboratory cultures of H. marismortui used in this study did not exhibit motility suggesting that the expression of the motility genes may be restricted to specific environmental conditions as reported for Geobacter metallireducens (Childers et al. 2002). All the chemotaxis and flagellar genes with the exception of flaA1, which is located on pNG100, are encoded on Chromosome I. Finally, we did not detect any gas vesicle biogenesis genes in H. marismortui.

DNA replication, repair and recombination. Replication. Subsequent to binding of Mcm and Cdc6 proteins to origin of replication, the DNA helix is unwound, presumably through the helicase activity of Mcm (Chong et al. 2000), and DNA replication initiates. The resulting ssDNA molecules are stabilized during replication by the single strand binding protein Rpa (Kelly et al. 1998). Lastly, the sliding clamp PcnA (proliferating cell nuclear antigen) (De Felice et al. 1999) is recruited by the clamp loader replication factor C protein (RfcC) (Pisani et al. 2000). At least one copy each of the ssDNA stabilizing replication protein A homolog (RpaA) and a related protein (Rpa) are encoded on Chromosome I. One large subunit (RfcB) and two small subunits (RfcC1 and RfcC2) of the replication factor C have also been identified along with a single copy of pcnA. The small (Pri1) and large (Pri2) subunits of the DNA primase (Desogus et al. 1999) are encoded on Chromosome I. For DNA polymerization two subunits each for two DNA polymerases PolA (PolA1 and PolA2) and PolB (PolB1 and PolB2) have been identified. The autonomous replication in Halobacterium sp. NRC-1 of the pNRC100 mini- chromosome harboring the replication protein H (repH) gene has suggested that this gene is important in the replication and perhaps the maintenance of this mini-replicon (Ng and DasSarma 1993). At least three repH orthologs were identified on three of the nine replicons in H. marismotui: pNG200 (repH1), pNG300 (repH2), pNG400 (repH3). Interestingly, all replicons in H. marismortui, with exception of pNG300, encode either one or more copies of cdc6 or a single copy of repH. pNG300 on the other hand encodes one copy each of cdc6 and repH. These Genome sequence of H. marismortui Supplementary material

observations suggest that in halophilic archaea the presence on each replicon of at least one copy of either cdc6 or repH is necessary for DNA replication and/or replicon maintenance. Repair and recombination. Halophiles thrive in an environment that exposes them to unusually high doses of a variety of DNA damaging agents such as ultraviolet radiation, dessication/rehydration cycles, and chemical mutagens (primarily due to their concentration by evaporation). Consequently, they have evolved robust DNA repair and recombination mechanisms to counter the high incidence of DNA damage (Baliga et al. 2004). The H. marismortui genome sequence analysis has identified genes for several DNA repair and recombination pathways such as nucleotide excision repair (NER), photoreactivation, mismatch repair (MMR), and base excision repair. In addition to the four bacterial NER proteins (UvrA-D) a second UvrB-like protein and a UV DNA damage endonuclease (UvsE) are also present. Photoreactivation of pyrimdine dimers may be catalyzed by two putative photolyases –Phr1 and Phr2. However, in Halobacterium sp. NRC-1 only one of these two proteins (Phr2) is functional as a photolyase (Baliga et al. 2004); Phr1, on the other hand, may function as a cryptochrome and mediate cellular responses to blue light as has been reported for some organisms (Hitomi et al. 2000). The H. marismortui genome also encodes eukaryotic NER proteins Rad2, Rad3, Rad24, and Rad25. With respect to MMR, H. marismortui, like Halobacterium sp. NRC-1, does not encode a d(GATC)-specific methylase or a MutH endonuclease. However, it encodes a d(CTAG) methylase and six RecJ homologs which in Halobacterium sp. NRC-1 have been implicated in a novel MMR pathway (Baliga et al. 2004). All other MMR pathway genes such as MutL, MutS, MutT are present. Among the base excision repair proteins uracil DNA glycosylase, DNA-3- methyladenine glycosylase, A/G specific adenine glycosylase (MutY), 8-oxoguanine DNA glycosylase, and an AP-endonuclease/AP-lyase have also been detected. Other putative repair and recombination proteins identified include RadA, RadB, Holliday junction DNA helicase, Holliday junction resolvase, endonuclease III, endonuclease IV, endonuclease V, exonuclease VII and a staphylococcus nuclease homolog.

Transcription. RNA polymerase. Altogether 13 genes encoding RNA polymerase subunits were detected in H. marismortui including two RpoM proteins. These genes are organized as three operons: operon Genome sequence of H. marismortui Supplementary material

1: [rpoH, rpoC, rpoA, rpoB, rpoB1]; operon 2: [rpoD, rpoK, rpoN] and operon 3: [rpoE’, rpoE’’]. The other RNA polymerase genes rpoD (rpb3 in NRC-1), rpoK and rpoN are located in the large ribosomal protein gene cluster. These chromosomal organization features of the RNA polymerase genes are conserved between the two halophiles. Regulators and other transcription factors. We searched for transcriptional regulators using two primary methods 1) HMMER searches for similarities to Pfam families of transcription factors and 2) Rosetta-predicted structural similarities to transcription factors and/or DNA-binding proteins in the PDB. Overall 192 domains matched Pfam families involved in transcriptional regulation, while 61 proteins had Rosetta-predicted three dimensional structures with similarities to characterized transcription factor or DNA-binding folds (Table F in supplement). Many of the three-dimensional folds and Pfam families identified are multifunctional with some representing non-regulatory DNA binding functions and thus this number may be an overestimate of proteins that are true transcriptional regulators in H. marismortui. The majority of the 61 DNA-binding folds identified by Rosetta are helix-turn-helix motifs and slight variants of the basic HTH fold, the most common being CATH fold class 1.10.10.10 (closely followed in abundance by other small helical folds such as 1.10.10.60). [CATH is a database of classification of protein domain structures where each of the four numbers represent in order Class(C), Architecture(A), Topology(T) and Homologous superfamily (H) (Orengo et al. 1997). For example, 1.10.10.10 is a classification for "winged helix" repressor DNA binding domain and 1.10.10.60 is Homeodomain-like DNA-binding protein]. Likewise, the majority of transcriptional regulators predicted by Pfam are also small helical domains, predominantly HTH folds. This abundance of HTH transcriptional regulators is also a ubiquitous feature of the Halobacterium sp. NRC-1 proteome with PF04937 being the most common HTH-type transcription factor family in both genomes. It is interesting to note that with the completion of H. marismortui genome sequence we have added 30 new members to the PF04937 domain family which prior to this genome contained only 39 members, suggesting that several uncharacterized families of proteins await discovery in archaeal genomes extant and yet to be sequenced. Since the function of many DNA-binding proteins is to regulate gene expression via protein- DNA interactions the precise biological function of all predicted transcription factors and transcriptional regulators identified in this manner remains unknown until the cognate binding Genome sequence of H. marismortui Supplementary material

sites in the genome of the transcriptional factors and regulators is discovered and the correlation between regulator binding and gene expression is understood. Therefore, we await experimental data such as genome-wide transcription factor localization and genome-wide gene expression analysis to provide detailed functional information concerning these putative transcriptional regulators.

RNA processing in archaea. Subsequent to their transcription from DNA both protein-coding mRNAs and non-coding tRNAs and rRNAs undergo maturation through one or more processing steps. RNA processing in archaea occurs through processes catalyzed by proteins analogous to those in eukaryotes. In fact, the extent of rRNA modification in archaea, for example, is on a par with that observed in eukaryotic rRNAs (Omer et al. 2003). We provide below an account of several proteins encoded in the H. marismortui genome that are implicated, based on their functional annotations, in processing of rRNAs, tRNAs and mRNAs.

Translation. Ribosomal proteins. Fifty nine ribosomal protein encoding genes were identified. Except for 14 genes which are distributed as singletons throughout the genome, the remainder 45 genes are arranged in operons with other genes. tRNAs and translation factors. Altogether forty-eight of the fifty tRNA genes predicted by tRNAScan program were present on Chromosome I. One copy each of tRNALys and tRNAGlu were identified on Chromosome II and pNG600, respectively. All eighteen amino acid-tRNA- synthetase genes and the aspartyl and glutamyl amidotransferase are encoded in Chromosome I. Eighteen translation factor-encoding genes were identified; these include eleven translation initiation factor subunits (eif1A1, eif1A2, eif2A, eif2B2, eif2B1, eif2BA, eif2BD1, eif2BD2, eif2G, eif5A, and infB), three translation elongation factor subunits (eef1a, eef1b, and fusA), one translation initiation inhibition factor (tii), and three translation termination factors (nusA1, nusA2, and nusG). With the exception of tii, which is encoded on pNG700, all of the other translation factors are encoded on Chromosome I. Protein folding, unfolding, and degradation. At least seven chaperones were identified, viz. four DnaJ proteins as well as the DnaK and TorD proteins. These chaperone proteins along with four Cdc48 proteins may function in protein folding and unfolding. Protein degradation in H. Genome sequence of H. marismortui Supplementary material marismortui may be processed through a proteasome comprised of the four proteasome subunit proteins (PsmA1-4) encoded on Chromosome I. Two subunits of a proteasome activating nucleotidase are also encoded on Chromosome I. Seven heat-shock proteins Hsp5, HspC, Hsp20a and b, HtpX3 and 4, and GrpE, also presumed to be involved in degradation of unfolded proteins were identified. FIGURES (in supplement) A. The linear maps for the nine replicons in H. marismortui (not drawn to scale). In the linear map forward encoded genes are indicated in red, orange and yellow indicating, in order, proteins with BLASTP matches to characterized proteins, uncharacterized proteins and no proteins in public databases. Likewise, reverse coding genes are indicated in nave blue, green and sky blue. The location of the genes in the six reading frames is indicated by their proximity to the navy blue line. Location of ISH elements are indicated on the aqua blue line above each line of the map. B. Frequency distribution of distances between consecutive genes in the main chromosomes of H. marismortui (N=2788) and Halobacterium sp. NRC-1 (N=1794). Distances between overlapping genes were excluded from this analysis. X axis: intergenic distance in bp; Y axis: fraction of gene pairs separated by such distance. C. Analysis of nucleotide skews on the largest chromosome of (A) Halobacterium sp. NRC-1 and (B) H. marismortui. G/C skew (blue, thick lines) and A/T skew (red, thin lines) are plotted along the chromosomes and expressed as Z-scores, i.e. standard deviations from the mean skew observed in shuffled sequences. Some relevant genes relevant to DNA replication are positioned. Large font indicates genes orthologous between the two graphed chromosomes. D. H. marismortui function association network. (A) The complete network of H. marismortui. The circular nodes represent protein-coding genes encoded in the H. marismortui genome. The lines (edges) connecting the nodes represent among those genes functional associations deciphered through comparative genomics approaches as described in the text. The nodes shaded blue have some associated domain information, while those shaded yellow have weak or no domain information. (B) All genes with no obvious orthologs in public databases linked to at least one gene with some domain Genome sequence of H. marismortui Supplementary material

information. (See Table B for list of associations; this visualization is also available as a Cytoscape webstart on http://halo.systemsbiology.net). E. Structural re-arrangements of key residues in the extracellular side of bacteriorhodopsin during the transition between the O-intermediate and ground- state. The structures shown are the halide-free (blue) and bromide-bound (purple) structures of the D85S mutant of bacteriorhodopsin. The halide-free structure of the D85S mutant is analogous to the O-intermediate structure of the wild-type protein (Rouhani et al. 2001). Conversely, the bromide-bound state is analogous to the wild-type ground state in this mutant (Facciotti et al. 2003). The relative amino acid side-chain positions of the corresponding residues are nearly identical in the two states. Note that in Xop2, residues homologous to Y83 and F189 in bacteriorhodopsin have been replaced by F and W, respectively.

TABLES (in supplement) A. List of functional associations among H. marismortui proteins (see text for details). [Note to reviewers: This table is over 200 pages long and has not been included in this submission; it can be downloaded from the H. marismortui genome website [http://halo.systemsbiology.net] B. Function Annotations. C. Proteins in H. marismortui implicated in the denitrification process (see text for details). D. Proteins in H. marismortui implicated in arginine metabolism (see text for details). E. Sensory and response domains in H. marismortui proteins. Start and end refer to the amino acid residues over which a domain match was identified. Note that some proteins may have multiple unique identifications by different methods for the same domain type. F. Putative transcription regulators in H. marismortui. A. Transcriptional regulators deciphered from Rosetta structure prediction. Predicted transcription factor and DNA binding proteins derived from Rosetta ab initio 3-dimensional structure predictions are shown. For each protein, the Rosetta predicted structure (within the top five ranked predictions) match to a DNA binding fold is shown. Note that each protein may have more than one Rosetta prediction. For each prediction we give the fold class (CATH Genome sequence of H. marismortui Supplementary material

code), the Z-score (strength of structure-structure match between predicted structure and the PDB), and the probability that the fold identification is correct (based on Bonneau et al, JMB, 2002). B. Transcriptional regulators deciphered from Pfam matches. We present the matches to DNA binding proteins and transcription regulators by the corresponding Pfam families, show the start and stop for each match with respect to the H. marismortui query sequence, and the e-value associated with each match.

REFERENCES (in supplement)

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1 10001 20001 30001 40001 50001 60001 70001 80001 90001 100001 110001 120001 130001 140001 150001 160001 170001 180001 190001 200001 210001 220001 230001 240001 trn1 trn2 trn3 trn4 rps11P rpl13P rpoK 8 htr 17 20 24 29 ugpC3 37 42 trp4 47 49 dpd 54 rps13P rpoD rps9P eno 71 74 mvk 79 idsA arsA1 hsp5 ferB etfA1 95 102 rpl24E 107 sdr ilvB1 cysK2 140 151 163 proS gltB 171 rfbU 190 purB 195 aglA2 210 214 216 221 232 236 qacE cat 247 250 252 266 gbp1 phoD 5 9 14 trmH 22 26 30 35 ocd1 ctaB 46 48 51 citG rps17E rps4P rpl18E rpoN rps2P 72 cyc htlD23 argB1 80 82 gltX lipC etfB2 ydiS 96 rpl7AE ndk 121 zip 135 139 pdhA1 157 165 168 170 gldA 181 adh3 yfmO2 202 208 211 pimT 220 arcR ykfB2 238 hadL trkA4 248 251 265 268 hisD 274

accC2 accA nac adh11 tfbA gatE fumC 34 39 srp19 50 57 mer3 99 101 msrB 111 pai1 115 117 120 aroC aroA 131 133 eif2B1 nhaC2 cysT2 148 153 epf2b 159 161 172 176 nhaC5 htr 185 188 argE 199 aldY2 dapD dapA1 217 219 223 225 ocd3 nhaC1 234 mer2 folP3 253 255 ksgA 259 262 264 imd1 275 277 birA 3 6 ywfD1 15 boa 25 rad2 36 40 coxB1 mrp1 htlD22 alkK1 100 108 110 112 114 116 119 udg2 126 htl 132 136 sdhA2 potA3 tppA 150 154 158 160 167 173 pop ubiE2 folP 187 purH odc 200 203 dapB 213 rpoM 222 aglA1 iunH2 228 231 otsA trkA pfk3 metE hemK 258 eef1b 263 271 276 rpl21E 250001 260001 270001 280001 290001 300001 310001 320001 330001 340001 350001 360001 370001 380001 390001 400001 410001 420001 430001 440001 450001 460001 470001 480001 490001 ISH15 trn5 trn6 ISH15 494 cpdB3 286 290 293 297 300 yqjM1 pepQ fofB leuA2 ilvN 333 leuD htlD21 deoR2 346 350 354 htlD2 lbp 372 ssrA pcy 391 394 usp15 405 410 kinA6 414 418 426 yidJ traB purM 443 cdd galE top6B 469 sucD 476 trp5 481 483 486 araL1 491 sirR 498 copA4 hcp2 tyrA surE 518 524 hisC2 pgsA 535 539 tnp pykA gpdA gpdC 284 287 pri1 294 zntA3 ghmP 312 323 327 ilvB2 ilvC leuC 338 ipmD pfk4 348 ubiA 355 serA4 htr 374 387 nosZ nosD2 nosY1 htr12 fbr3 411 oye 417 TrmB2 427 tot 437 psmA3 manB2 udp2 arg1 top6A sucC 475 477 480 yajO yqjF htlD19 pip 492 495 497 503 505 hcp9 513 516 519 525 531 tnp tpiA 541 pfk1 glcK gpdB 564

279 281 285 eif2BD1 htrA1 301 305 purD1 rpoM 316 318 crtI2 325 343 347 dnaJ3 358 hlx7 asd dbp 373 377 glnP gabT gdhA1 397 400 408 rhoM gtl 423 425 exoM 433 435 440 yjlD1 gyrA 460 462 464 468 478 zurM ycdH 509 alaS2 521 523 527 hlx4 dinB tyrS 549 htr 558 usp14 278 280 283 288 291 299 ilvD 306 311 314 htlC ubiA 324 328 fba 349 dcuC 359 363 366 tnp 376 glnQ2 glnH1 arg2 arcR1 399 403 lemA doxD4 421 424 lpg3 432 act 439 441 451 gyrB 461 ligA gspE4 sir2 484 zurA 506 hpcEa 520 522 526 cheC1 538 542 cdc6j glpK 557 xop2 pepC

500001 510001 520001 530001 540001 550001 560001 570001 580001 590001 600001 610001 620001 630001 640001 650001 660001 670001 680001 690001 700001 710001 720001 730001 740001 trn7 trn8 trn9 trn10 565 567 569 571 fadD1 578 phrH1 rad25 620 629 631 nudB 640 acs1 657 apa 667 htlD17 nfi mamA1 mal citE1 695 708 trpD2 713 porA 720 726 728 usp29 hat2 749 icfA1 trkH3 cat 769 774 776 acdE doxD1 786 789 cdc48b 795 801 cdc48c tnp 824 827 ech2 menF ech1 htlD15 856 858 860 862 nop56/58 gcs2 566 568 570 catD htlD18 579 590 619 626 sppA 632 638 bdhA 654 658 663 672 675 677 mamB 688 cinA aroE trpE1 ilvE2 usp6 porB phr1 727 737 hat1 743 750 trkA1 usp17 fbp2 gdhA2 777 acdF 785 pssA 791 htlD16 800 805 nosY 817 livM 829 834 menD alkK3 pebP 857 folA1 tfeA 863 fib 867

575 tnp 583 586 589 592 594 596 598 601 604 606 608 610 613 615 622 624 627 rffH2 mcmA1 641 645 647 652 655 ama 662 665 668 673 Rad3a 682 aspC4 696 secE 702 704 715 mop 724 729 731 733 hcp8 nthA 744 guaB3 aroK trkH2 761 764 767 paaH 778 783 793 purF cdlM 803 808 811 813 818 821 823 sodA 835 dnaJ cinR ykfB1 849 851 853 576 582 585 588 591 593 595 597 599 602 605 607 609 612 614 pecE 623 625 sun gloA2 639 642 646 651 cysH ferA3 660 664 666 669 arsA2 tbpE 683 692 nusG htr18 ftsZ1 nce1 717 723 725 730 petB1 734 736 742 745 752 756 760 762 766 acdB 773 usp30 est hat4 snp 802 806 nitA 812 tnp 819 mogA 830 phrB1 836 840 menE menA 850 852 galE4 600 603 750001 760001 770001 780001 790001 800001 810001 820001 830001 840001 850001 860001 870001 880001 890001 900001 910001 920001 930001 940001 950001 960001 970001 980001 990001 trn11 trn12 ISH4 trn13 trn14 trn15 coaD2 872 875 coxA4 bioB bioF 889 892 cpdB2 905 907 910 926 928 930 936 938 949 951 953 957 961 tnp htr8 989 994 1001 1007 rfbB1 1012 dpm2 1023 1032 1037 lgtD 1045 tnp 1056 prk1 1069 1071 1073 capB 1079 cysE2 1090 1092 sdhA1 cbiA2 1105 1111 871 acdA panB 881 gdhA3 886 frt 893 900 ibp potA4 911 pyrE2 acaB4 935 937 948 950 moxR1 hel dapA2 963 975 985 htlD13 1000 1002 1008 rffG lpg2 1022 1024 1033 1038 1044 cdc6i 1055 stbB prkA spoVR cyp2 1075 1077 acdG alkA sdhC sdhB 1101 1103 1110

869 coxB3 cbiA1 891 acaB3 899 accA 912 TrmB1 sorD 919 921 923 925 argK 939 htr 944 946 956 959 kinA7 966 969 971 977 980 ssuE1 984 mutY mgtC1 mutT6 998 1003 1006 1013 1015 1018 1021 1026 lolC nps 1034 1036 1041 1046 1048 1050 1052 1060 1062 1064 fadD3 1080 1082 tnp 1089 1099 1106 purD2 1113 876 coxC scs 895 897 901 fabG1 913 915 gfo4 920 922 924 931 mcmA3 940 943 945 955 icfA2 962 pelA hypE aor3 974 979 981 983 nce2 htlD14 992 folD1 glyA suhB1 1009 1014 1016 dpm1 moxR6 1027 1029 1031 1035 1039 1042 1047 1049 1051 1059 trwB1 1063 1065 1078 rffH1 hbd1 1086 kinA4 1100 trkH1 1112 htlD12

1000001 1010001 1020001 103001 1040001 1050001 1060001 1070001 1080001 1090001 1100001 1110001 1120001 1130001 1140001 1150001 1160001 1170001 1180001 1190001 1200001 1210001 1220001 1230001 1240001 rrlB−3 rrlA−3 rrs−3 trn16 trn17 1321 1324 1116 1119 1123 trxB3 rpaA yhcR1 1143 hcp5 coxA3 1164 acyP 1172 1183 1194 petB2 narG 1202 narJ prp 1209 1219 1221 1223 1228 metK 1235 1243 1254 1257 alkK 1263 korB 1272 mcmA2 1281 1284 1288 cysS 1295 moeA2 adh9 1304 1308 1316 1319 1323 fdhF 1334 1337 1344 kinA1 1352 mutT5 1368 ccmC hcp6 1380 1383 1387 purL 1395 1400 adh4 1115 hlx1 thyX eif2B2 1130 1135 yprA4 mutS3 coxB2 1155 ogg 1168 mutT1 cysT1 1195 1197 narH 1203 1205 mrp2 1218 1220 moxR4 minD2 cytH thiI 1253 1256 cheC2 acdD korA asnC2 guaB2 1277 purA htpX5 1291 1293 corA moeA3 1303 1307 epf2a aor2 1322 1326 fdoH 1335 acs 1345 1350 tfbB 1366 ccmB 1374 13791381 gluTR 1388 hisF cyoC1401 dph5

1117 tfbH 1128 1132 1140 blp 1147 1150 1156 1158 1160 1162 1165 katG2 psmA4 1176 1178 1181 moaE moaB1 1190 boa 1211 hmoA 1216 pyrI 1226 slyD cysK1 eif1A2 1244 1246 1248 gspE2 lrp 1260 1264 1276 1279 1282 1289 1297 thuA 1309 1312 mobA 1329 1331 1338 1340 1347 rnp 1353 gatA1 asnB nirJ 1365 ccmF ccpA ccmE 1382 1386 1391 1393 1397 1403 1405 1125 1127 ribG fbp1 oye 1146 1149 1151 1157 pknA1 1161 1163 hflX 1173 rpp14 1177 1179 thiC moaC 1189 1191 rbnBN1 moz dmsA 1217 pyrB 1229 ilvA1 nikR 1242 1245 1247 1249 aspB1 1255 cdc6h 1266 coxA1 1280 1285 1290 yjlD2 1305 recJ1 moaA 1325 torD 1336 1339 1342 1348 1351 htpX6 gatC 1361 1364 ccdA trxA7 soxA2 pan1a 1385 1389 1392 rpoL 1398 usp28

1250001 1260001 1270001 1280001 1290001 1300001 1310001 1320001 1330001 1340001 1350001 1360001 1370001 1380001 1390001 1400001 1410001 1420001 1430001 1440001 1450001 1460001 1470001 1480001 1490001 trn18 trn19 trn20 ISH16c ISH19d trn21 trn22 ndhG6 1412 rpl1P rpL12P 1421 1423 1427 rps3AE aspC3 1441 1445 nolB ndHG5 nolD nolC nuoL2 ndhG3 1464 1469 doxD5 sacB parA4 kinA8 1493 1502 1510 1513 1516 1525 1529 radB 1543 1545 1548 1557 tnp 1561 1563 cdc6f wcaH galE8 tnp graD4a 1613 mch nrdA 1628 1632 1635 gatB 1650 1666 rpl11P rpl10E 1420 1422 rps15P 1428 ribE 1436 1444 purE nuoB ndhG4 1453 ndhD 1460 1465 trxB2 1476 1480 cheW2 1492 htlD11 tatD 1512 pyrF 1521 1528 1531 1542 spoVT/abrB 1547 1549 1558 tnp 1562 cdc6g 1570 rfbB2 1579 1581 1586 1615 1617 htlD10 1631 1633 1636 topA aspS 1670

1408 1410 1419 1425 purK atpC2 taqD pld 1459 1462 1466 tnp 1473 1475 scrB fapE2 dmd msrA2 nifS gcvH 1501 pstB1 pstC1 rps8E trpG1 trpF 1522 yfmJ2 1530 1534 1537 1539 1541 1550 1552 1555 1564 1566 1574 1576 1578 icsA glmS1 secY rps5P rpl32E rpl5P rpl14P rps3P rpl2P 1612 1620 1623 1627 hlx6 1637 smc2 1641 1644 1647 yhdG asnC3 1655 1658 1660 boa 1665 rpoP 1671 cyo gloA1 drg 1424 fbr2 dpm5 14371439 1443 1461 1463 1467 acrR1474 fdfT 1481 yjlD4 cadT oye3 gcvP1 gcvT2 1503 pstA2 phoX 1514 trpE2 trpD3 1523 cdc48d phoU2 trkA2 1538 1540 tnp 1551 1553 1556 tnp 1567 1575 tnp 1582 lpb2 1588 rpl15P rpl18P rpl6P rps4E rps17P rpl22P rpl23P rpl3 gbp2 1621 soxA3 1629 1634 1638 1640 1643 1646 1649 trkA5 1654 1656 hop 1662 1664 1667 1672 rpl30P rpl19E rps8P rpl24P rpl29P rps19P rpl4 rpl37AE 1500001 1510001 1520001 1530001 1540001 1550001 1560001 1570001 1580001 1590001 1600001 1610001 1620001 1630001 1640001 1650001 1660001 1670001 1680001 1690001 1700001 1710001 1720001 1730001 1740001 trn23 trn24 1673 16781681 1686 1688 1692 guaA2 moxR2 moeA1 uppS rimI 1724 1727 valS 1732 1735 1739 rfcB maeB serA2 1767 1770 1775 1777 hutU hutI dapF htlC metS 1802 gntR pnm cctA3 1820 1823 1838 1844 1846 1849 1851 1853 1855 1858 1861 1864 1868 nhaC3 dpg zim 1878 1887 1895 1898 apt2 1906 1915 1921 1930 ispD 1935 cobQ 1940 1952 yusZ1 eif2BD2 1674 pfdB 1684 boa 1689 1693 1696 1701 1712 1718 csaA panF 1728 1730 1733 1737 mvaS htr15 1756 tenA 1769 1771 dcd2 aknG hutG hutH ppsA gadD 1801 1803 1808 1813 1818 lysE 1837 1843 1845 1848 18501852 1854 1856 1860 mutT4 soxB trp1 1872 tfbD aroD minD6 gbp5 1896 crtI1 dsbB1 lon azlC trzA2 cobS hisC1 cobI minD1 1944 1953 glpA lpg1

tnp 1683 1691 1700 1703 pgp hemA NirH cspD5 1717 1721 1734 1742 1745 glnH2 ccp gptA 1759 atoE psmA1 1774 1781 1783 1786 1793 1807 1810 1814 1817 1824 1826 1828 yurF 1833 1835 smc1 1842 1867 aroB trpA trpC 1891 ldc brp 1907 fbr1 nadM glpQ2 1922 1924 speB1 1941 phrB2 1946 1948 gspE1 1959 1682 leuA1 1699 1702 1704 cad hemX 1713 dnaG 1731 1738 1743 glnQ1 1750 1755 1758 1760 1764 psmA2 1780 thi1 1784 1792 htlD9 1809 1811 1816 1822 idr 1827 1829 polB1 1834 tnp yhcR2 1859 1871 deoC2 trpB 1890 1892 1899 1904 nthD 1911 1916 1918 1923 mhpC eif5A 1942 1945 1947 1950 malQ graD4b cspD 1750001 1760001 1770001 1780001 1790001 1800001 1810001 1820001 1830001 1840001 1850001 1860001 1870001 1880001 1890001 1900001 1910001 1920001 1930001 1940001 1950001 1960001 1970001 1980001 1990001 trn25 trn26 1963 glcD1 aldY4 ech5 hbd2 anf 1991 1993 1996 usp9 2002 2009 2011 2017 msrA1 cdc48a 2032 pkn nifU2 oppB oppD1 2045 2049 2053 2059 2061 2071 trp2 2076 dhp 2088 2098 entB1 rli 2107 htlD7 2112 uvrA 2119 2123 bchP sseA2 epf1 tcmJ 2142 dcd3 2161 2167 2169 2173 cheB cheR 2209 rps6E 2214 2224 dppF dppB1 2231 2237 2240 2242 1965 arcR5 aacC aph maoC1 1989 1992 1994 1999 2001 ftsZ3 2010 2012 nuoC 2026 2031 htlA troR oppA oppC2 oppF 2048 2050 moaD 2060 rpl15E vacB 2074 2081 2086 uvsE 2099 2102 2106 2108 sec61b 2113 2117 2121 2125 2127 2131 2136 trxA8 prp1 2160 mgsA 2168 adh14 pepB2 cheA3 cpcE2 htlD6 2213 2221 2225 dppD oppC1 2234 2239 2241 2243

1961 arcR6 1968 gcdH alkK4 1983 acdC rbnBN2 2005 2007 xthA katG1 2021 2025 xop1 htlD8 sppA 2052 serA3 2062 blh crtB nusA1 2079 2083 2085 2089 htr 2094 2101 2105 2114 2124 2135 2140 2144 pstB2 pstC2 2151 mutT2 2156 acnB exsB ptpS 2171 2175 2178 gnd gspE3 flaG fapE1 cheA1 2195 flaB 2200 cheW1 2216 phoR 2222 2226 2235 2244 malA gloA3 1970 adh5 1978 fabG 1995 1998 2006 2014 2016 lpl 2022 2028 2035 2046 tfbF 2054 2058 aor1 crtY boa 2078 2080 2084 2087 moeB cxp argE 2104 trxA3 2115 sseA1 imd3 thiE phoU1 pstA1 yqgG 2152 2154 rimI 2164 pepB4 fdx galE9 fer2 fapJ flpH 2190 cheD cheY 2197 2199 kaiC1 dcd1 2217 usp5 usp2 pyrC entB2 2155 2000001 2010001 2020001 2030001 2040001 2050001 2060001 2070001 2080001 2090001 2100001 2110001 2120001 2130001 2140001 2150001 2160001 2170001 2180001 2190001 2200001 2210001 2220001 2230001 2240001 trn27trn28 trn29 trn30 trn31 ISH8 trn32 trn33 trn34 trn35 trn36 trn37 rps27AE 2246 crcB1 2255 gapB gvpE coaD1 phrH2 2289 2291 2293 cca 2306 2308 coxA2 2316 mcm1 boa repC 2331 glcD2 cspD3 2345 ugpC1 rpl10E rimK pgk hisH1 htlD5 engB 2380 phrH3 2390 2393 2395 2398 2400 2402 2412 2415 htr18 2434 2436 scm moxR3 2444 2446 thiD 2453 2460 2470 aldY2 2476 2479 ech3 rfcC2 2492 2494 2500 phzC/phzF trk 2514 2519 2251 crcB2 2260 2266 norB copG1 2288 2290 2292 2294 2304 2307 2310 2312 2317 2319 2324 2328 2332 cspD4 rfbA amy 2354 2358 gapA ribC hisI1 gbp4 2379 2381 2387 2392 tnp 2397 2399 2401 2403 metB 2416 24332435 mer1 2441 2443 sui1 2448 2450 usp10 ark2 yusM eif1A1 htlD4 act 2485 rps24E gcp ham1 htr14 gfo5 lgl pchB thrC4

eif2BA 2249 2254 pcm1 pepB1 2265 2268 2273 2277 2281 tnp 2287 2296 aup rpa 2305 2313 2315 2322 2326 tnp 2335 2340 2342 2347 2353 2356 hsp20b 2368 2375 tnp cdc6 2389 2396 rps10p−1 2407 2410 fusA cbiO 2421 rps12P rpoC rpoB rpoH serA5 2456 trxA1 2462 2464 2466 2469 2475 2482 nadE1 2497 2499 2505 2507 citZ 2516 2518 csd2 2250 pcm2 2259 2263 uvrD 2271 2275 cbiQ1 cbiM 2286 2295 2297 hpyA 2303 2309 trp3 2320 2323 2327 hspC 2337 2341 malG malE1 2355 usp16 2365 2373 2377 2384 2386 2391 2404 eef1a hom 2411 cbiQ2 bioY rps7P nusA2 rpoA rpoB tnaA 2452 2457 maa scp2 2465 2468 2472 2481 2483 2496 trkA6 araC 2506 ilvA2 2513 2517

2250001 2260001 2270001 2280001 2290001 2300001 2310001 2320001 2330001 2340001 2350001 2360001 2370001 2380001 2390001 2400001 2410001 2420001 2430001 2440001 2450001 2460001 2470001 2480001 2490001 trn38 trn39 trn40 trn41 hisA mutS4 2535 2537 2539 2542 mutL gcvT4 2563 2571 2582 2588 cobW/P47K_1 2599 yrdC dip3 2611 2614 glnB cheA2 hemL prsA 2632 hit2 2642 phoT2 rad24 2664 inb 2688 polA2 2694 2699 2702 mdh polA1 2718 2722 pepB3 2731 2735 2740 2744 2748 2752 2754 2757 mcm2 2765 minD4 2772 glnA 2795 2801 2805 2810 manB3 2530 ark1 2536 2538 2541 2546 kdgK 2558 2566 manB1 2586 2589 2597 prxS hdrD hemB 2612 amt asnC4 2624 2629 aldY1 udg1 minD5 nthB 2659 fer ort 2686 2689 2692 2695 glyS eif4A cdc6d cysD 2720 2724 2729 2734 2736 ywfD2 2745 2751 prt rad24a 2759 2764 2766 2770 2775 2785 fprA 2803 2806

pyrE1 hisI2 fer1 2528 2544 2549 2554 pca alaS1 2567 2569 rpiA 2576 2578 imp 2584 cstA 2594 2596 2600 2604 2607 htr 2626 htr 2641 2644 2647 rbsC 2654 yufN lysC 2666 2669 gltCP argB2 rimK argH 2684 serA1 2705 2708 gbp3 sec11b rad3b 2723 2730 2733 2739 2743 2749 2755 htr6 tfbI matE2 asnC1 rbn 2786 trm1 2791 yusZ3 udg3 2798 rpl40E 2807 usp21 2520 2523 2525 ylnA 2543 2547 2553 hisB 2559 rfcC1 pmm 2570 2575 upp 2579 2581 2587 arsA3 2595 2598 2603 2606 ark3 nirA1 narB ileS 2643 comA leuS1 2653 2655 usp20 2665 thrC3 arcB argD argC 2680 argG 2685 2698 2707 2709 sec11a serB1 cat htr 2732 glbN manC 2746 2750 2758 tmpC 2773 2777 pap2a dip2 2787 htlD25 2792 hisH2 2797 2799 2804 serS

2500001 2510001 2520001 2530001 2540001 2550001 2560001 2570001 2580001 2590001 2600001 2610001 2620001 2630001 2640001 2650001 2660001 2670001 2680001 2690001 2700001 2710001 2720001 2730001 2740001 rrs−1 trn42 rrlA−1 rrlB−1 trn43 trn44 rnp mutT3 2819 2821 2828 rpoE trzA3 ahcY pri2 2848 tatC2 mutS2 2863 potD2 potB2 phaJ1 2877 2880 2883 2885 2888 2901 2907 radA 2916 2918 2922 2932 2935 2938 ocd2 leuS2 top1 trpS pheT 2973 2978 2980 2982 2984 2986 nirA2 uvrB cbiT cbiF fabG6 cbiH 3010 3012 3014 cbiC 3024 3027 hpcEb aspC2 ligB 3056 3058 3061 metA panE 3070 rub 3083 3085 cysG2 3090 3094 3097 mthK ftsH phnP eif2G rpoE’ 2831 2838 2842 2846 ftsJ gpmB cdc6c 2866 potA2 potC2 2876 2878 2881 2884 phaC 2894 htpX1 2908 yvaI 2917 2920 2923 2933 boa cctB 2945 brr2 endA pheS 2971 2974 2979 2981 2983 2985 2990 2993 2997 cbiL cbiG cobH 3009 cbiK tup1 cobN cbiJ napA iunH1 3043 3048 htlD3 3057 3060 metY 3066 3069 3072 3080 3084 hemC cysG1 3092 3096 3100

2813 2816 2822 2826 2834 2836 2845 2849 pcnA 2855 tatC1 2864 dip1 2882 cctA2 2893 2896 cspD2 nmd3 gsp 2919 2925 gfo1 2931 2940 2943 bcp3 pheA 2952 2954 pdhB1 lipA 2962 pyrD 2977 2988 2995 3015 hmcA cbiX 3028 3032 gfo6 aldY3 htpX3 3042 3053 3055 3067 ribA 3075 3079 pspA2 edp nifU1 csd 2812 aca2 2817 2824 2832 hisG 2843 hjr 2850 nirK 2856 trmU 2865 2875 2889 2892 2895 galE2 2902 galE6 2913 guaA3 2927 2930 mutS1 2942 2944 hsp20a 2951 lpdA2 pdhC2 pdhA3 2960 2968 2970 2976 2987 2989 3007 3016 3022 yfmJ1 3030 3033 3035 3037 uvrC nosY2 3054 moxR5 ilvE1 3074 3077 3082 3098 3101 3103

2750001 2760001 2770001 2780001 2790001 2800001 2810001 2820001 2830001 2840001 2850001 2860001 2870001 2880001 2890001 2900001 2910001 2920001 2930001 2940001 2950001 2960001 2970001 2980001 2990001 trn45 trn46 trn47 ISH14 3109 rpl39E 3115 dpa 3123 3125 3134 3137 soxA1 3150 atpI atpE atpF ntpB atpD minD3 usp19 3175 3178 3180 hisS truA pan1 argDC 3202 3206 3212 secD 3221 graD4c ugd2 3251 3254 3257 tgt 3263 nce3 tmk trh5 hlx5 cyp1 3315 3319 3321 3324 3328 3333 3337 kinA5 noxA2 3355 3357 3359 htlD2 trh3 3368 3370 3378 3384 338 gufA rpl31E 3116 3119 srp54 3133 cat 3140 3142 atpG atpC1 ntpC ntpA bop 3163 3168 3172 3176 rps19 3181 3185 pepF 3198 3200 3205 3211 secF BacA 3231 glmS2 3247 3253 3256 tgt 3262 purU 3278 trkA3 nirD 3309 3314 3317 rnhA ipp 3325 3330 3335 bcp2 3351 3354 3356 3358 carB 3362 3366 htlA hemV htlD1 tnp

3107 3111 eda trxA4 livG−9 3130 hat3 3143 adk etfA2 3149 erf1 3167 3170 pyrH 3182 3187 3192 3195 malE2 infB 3207 pgi rnhB mic 3222 usp22 3227 boa 3236 3240 3242 galE5 3248 3250 3260 pstB3 3267 3269 3271 purC sop1 3282 ftsZ5 3287 3291 3294 oppD2 dppB 3300 ppiB1 trpD1 3311 3318 ftsZ4 hcp3 3332 3336 dnaK 3341 cmk adk thrB carA fecE lpdA1 3383 3105 3108 3114 mdcM 3127 3129 3132 3139 3144 fps etfB1 ubiE1 3165 argS lysS thiL 3186 deoR1 ugpC 3196 3201 hcp1 3208 3213 3217 3220 3224 3226 acs5 acs3 rffH3 3241 galE7 sqdB 3249 galE1 3264 modB purQ 3270 pap2b 3279 htr 3283 nolA 3288 3292 ykfD oppC dppA 3302 3304 3310 arsC 3322 3327 3331 dnaJ2 3338 grpE truB htlB kinA3 3352 3371 hemU 3382 ntrC

3000001 3010001 3020001 3030001 3040001 3050001 3060001 3070001 3080001 3090001 3100001 3110001 3120001 3130001 trn48 kaiC2 3397 3399 pgm 3406 3415 3418 map 3424 doxD2 3432 3435 3438 3443 3446 3451 3454 3461 3463 arsB 3469 pyrG 3473 3481 3487 pqqE 3491 3503 adh2 3516 3519 pan2 3549 3552 3390 usp4 3398 3400 3405 mvaA 3416 3420 hit1 cef 3430 udp1 3437 3439 3445 3450 3452 ykfB3 thrS 3464 3468 3470 guaA1 3477 3482 3488 boa2 3502 thrC1 usp7 dgs htpX4 3548 trzA4 usp1 Chromosome I ppnK usp24 3401 kptA nadB 3411 3414 icd 3428 3431 pch2 3441 arsR 3449 3457 usp26 3474 3476 moaB2 idi 3493 aspB2 3499 3504 dnaJ1 3511 rpl44E 3522 3524 3526 3528 nuoL1 3532 mnhG2 dfp 3541 3543 3393 3396 3402 nadC1 nadA 3413 3417 3422 deoC1 3433 3440 asbA 3448 bcp1 3458 pspA1 3475 3479 fabG2 3486 3494 yqeF 3501 usp3 3510 eif2A 3515 3517 apt1 3525 3527 3529 ndhG2 3534 mnhE 3540 3542 trxB4 rps27E mnhG1 3536 1 10001 20001 30001 40001 50001 60001 70001 80001 90001 100001 110001 120001 130001 140001 150001 160001 170001 180001 190001 200001 210001 220001 230001 240001 rrlB−4 ISH17b 7002 7007 galE3 7016 7023 7025 fucA dgoA1 yvbT 7040 csbC 7051 7055 cctA1 prp2 7068 fabG7 trxB1 usp23 qad 7092 camH1 adh7 7105 7109 7111 nthC ureC ureG ureE 7133 noxA1 usp31 nosL fdhA 7154 7160 hyuA 7166 arcR3 7178 7183 ndhG1 7194 7196 lpb1 7201 7204 7206 7216 7224 7226 rps17E 7238 7001 7006 7008 ttuD 7019 7024 7026 rhaB adh10 7039 7041 7046 7052 fmdA 7064 speB2 7069 rnh 7082 7085 7090 7095 7102 7104 7106 7110 7114 ureB ureA ureD ureF trxA2 7141 7144 7146 7152 oye2 7161 hyuB 7168 7172 7179 7186 phnM 7195 7197 7200 7202 7205 7207 7220 7225 nadE2 7229 7239

7004 7009 7011 dpm3 7018 adh1 7034 trh2 7045 7048 7050 7056 7058 usp12 7065 qgd 7075 7081 7086 7091 7098 7100 7107 7113 sdt 7119 7121 7130 7132 7138 7140 7149 guaB1 gudB boa nhaC4 tnp sojA 7177 7181 7185 7188 gfo2 7198 7208 7212 rfbX 7217 7219 7222 7231 phnD2glmU 7241 7003 7005 7010 ugd1 7017 kdgR1 fabG3 ndhF 7044 7047 7049 7054 dsbD prrC cat1 7071 7074 7076 htr8 7087 7094 cpt adh8 7108 7115 7118 7120 7122 7131 ctpA usp13 7148 nosD1 htlD24 7158 7167 7170 7174 7176 7180 7182 cdc6k 7190 7193 7203 7210 7213 gfo3 rffH4 7221 boa phnC1 ern1 7237 7240

250001 260001 270001 280001 290001 300001 310001 320001 330001 340001 350001 360001 370001 380001 390001 400001 410001 ISH19c 7249 7253 mer4 7260 7264 7267 7269 7272 fhuG1 7277 7280 glcD3 yafB 7295 7298 7301 7303 7311 adhC 7317 pch1 folD2 arcR2 7346 7348 potC1 aldA nitB 7357 gcvT5 yeaW gcvT1 usp25 7377 7385 ptsA ptsI rbsA 7254 trzA1 7262 7266 7268 7270 trxB5 fhuG2 7279 lctP 7292 7294 mox 7299 ppk tetR 7313 7315 7320 betL1 cysE1 arcR4 potA1 potB1 adh13 7353 7355 folA2 gcvT3 7368 ilvA3 betL2 fhs ptsC hpr ptsB pNG700 dsrE/dsrF_2 xdhD2 amaB 7251 thrC2 7263 adh12 7285 7287 adh6 tehB 7304 7307 7310 cobW/P47K_2 nuoF 7322 trpE3 gltP serB2 fabG5 7337 7339 camH2 7345 7360 7364 7374 7378 ftc 7383 7386 7394 7396 dsrE/dsrF_1 7245 cutC 7250 pbuX pyrC fadD2 7282 7286 7288 htpX2 7300 matE1 7309 7312 fdhG ern2 trpG2 7329 7332 7334 7336 7338 7340 msmK 7358 metF 7365 7376 folP2 folE 7384 7393 7395 tnp xdhD1 1 10001 20001 30001 40001 50001 60001 70001 80001 90001 100001 110001 120001 130001 140001 150001 160001 170001 180001 190001 200001 210001 220001 230001 240001 rrlB−2 rrlA−2 rrs−2 ISH11 ISH11 trn49 ISH11 ISH20 dISH8 ISH17c 5 10 14 flaA1 21 25 31 nadC2 usp11 exoVIIB 45 apbE 51 65 75 78 80 85 87 93 aldY6 98 100 103 105 107 116 121 124 129 133 136 140 tnp tnp tfbC 152 156 158 161 169 173 181 185 187 usp1 ilvB3 212 215 220 kdgR2 iclR paaK1 aldY5 ech6 fapS zntA2 275 278 287 phoT1 294 3 tnp 13 15 19 22 27 34 37 xseA2 43 47 50 64 71 76 79 84 86 89 tnp hcp7 99 suhB2 104 ugpC2 115 120 123 127 130 134 138 142 145 147 151 155 157 160 168 170 178 tnp 186 188 193 galE10 214 acs2 221 232 aca1 maoC2 253 citE2 269 273 trxA5 286 288 292 295

6 9 16 20 24 tnp 30 40 tnp 53 56 59 61 cdc6a 68 speE 74 81 83 96 109 112 114 118 132 141 162 164 cbp 172 176 179 184 190 195 lpdA3 pdhB2 202 204 aspC1 208 gabD livG−10 228 230 234 hbd3 acaB2 247 paaC paaA maoC3 accC1 acs4 ubiD 271 274 281 guaA4 285 kinA2 cdc6b 7 11 17 23 26 29 33 44 52 55 58 60 parA3 67 69 73 77 82 aldY7 108 111 gatA 117 tnp 137 154 163 166 171 imd2 177 oye1 189 191 196 pdhC1 pdhA2 203 205 207 218 224 227 229 paaK2 ech4 acaA paaI 248 pacF 255 pccB acdH 266 268 272 280 282 284 usp27 297

250001 260001 270001 280001 ISH8 tnp 306 ugpB ugpE glpQ1 phnC2 322 cpdB1 330 336 304 307 312 315 phnD1 phnE ftsZ2 328 parA5 Chromosome II oye 302 308 fmn mgtC2 324 331 334 hlx2 305 acaB1 araL2 323 327 333

1 10001 20001 30001 40001 50001 60001 70001 80001 90001 100001 110001 120001 130001 140001 150001 trn50 6027 6030 6076 exoVIIA 6099 6129 6139 6004 6006 6009 6014 6021 6024 6026 trxA6 6042 acnA 6055 copA1 6065 tfbG 6075 6085 6091 xseA1 6097 6102 6104 6107 6111 6115 6120 tfbE 6128 6132 6135 6138 6141 6145 6147 6151 merA copA5 6164 6166 6168 6170 6180 6183 6001 6005 6007 parA2 6016 6023 6025 6028 usp32 merP 6054 copA2 hcp4 6066 6074 6077 6084 6090 6093 6096 6101 6103 trwB3 6108 6113 6117 6121 6124 6127 6131 6134 6136 6140 6142 6144 6146 6149 6153 6158 6163 ltrC 6167 6169 6173 6181 pNG600 6003 6011 cadA trzA5 6032 6034 6036 6038 6041 6044 copA3 6050 6057 6060 6062 6068 Trx 6078 6080 6082 6086 6088 6092 6109 6122 6126 6150 6155 6160 6172 polB2 6178 6182 6185 6188 6190 6002 6010 6017 6020 6031 6033 6035 6037 6040 6043 6045 6047 6051 6058 6061 pan1b dsbB2 6071 czcD zntA1 6083 6087 6089 6098 6119 6125 mrr hyrA1 copG2 616 cdc6m 6177 6179 cdc6l 6187 6189

1 10001 20001 30001 40001 50001 60001 70001 80001 90001 100001 110001 120001 130001 ISH11 ISH17a ISH15 ISH8 ISH19a ISH13 dISH11 dISH8 ISH6 ISH19b dISH18 dISH20 ISH17b ISH16b ISH16a dISH8 ISH18 ISH21 dISH11 5009 5011 5014 5020 tnp 5036 5039 tnp 5049 5051 tnp tnp tnp 5063 5068 5074 tnp 5083 5085 trwB2 5089 traD 5093 5101 5106 5110 5114 tnp tnp 5131 5133 5136 csg1 5140 5144 5146 tnp 5010 5013 sojE 5021 5026 5037 5041 5048 5050 5053 5055 5057 5061 5067 5071 tnp 5082 5084 5086 5088 rlx 5092 5096 5102 5109 abrB 5119 tnp tnp tnp 5134 tnp tnp 5141 5145 pNG500 5003 5006 5015 5017 5023 cdc6o 5029 5033 5035 tnp 5046 usp8 5062 5065 5069 tnp 5077 5081 5095 5103 5105 5108 5112 5116 5120 cdc6n 5125 5135 tnp 5001 5004 tnp 5016 5018 5024 5028 5031 5034 5040 tnp doxD3 5059 htl 5066 5070 5073 5078 5094 5099 5104 5107 5111 5115 5118 sojD tnp 5126 tnp

1 10001 20001 30001 40001 50001 1 10001 20001 30001 1 10001 20001 30001 1 10001 20001 30001 ISH4 ISH9 ISH8 3019 3024 3027 4004 4007 parA1 4016 boa 4023 4029 4035 4045 4047 4050 cas4 cas2 3005 3008 3012 3014 3018 3021 3025 3028 3030 sojB 3041 3043 3046 3051 mcm3 2002 2007 2015 2029 2032 papSR 2043 1007 1012 1018 1021 cdc6q flaA2 1041 tnp 4005 4011 4013 4018 4021 4027 4034 4044 4046 cas3 4051 cas1 3004 3007 3010 cdc6p 3017 3023 3026 repH2 3032 3039 3042 3044 3050 3052 3054 2001 boa 2008 2021 2030 yprA1 2041 1006 1011 1016 1019 1022 1025 1040 pNG400 pNG300 pNG200 pNG100 tnp 4008 4010 4015 htlD25 4024 4026 4030 4033 40374039 4042 3009 3015 3040 3049 2005 2009 2011 sojC 2017 2019 repH1 2023 2026 2035 2038 2040 2044 1002 1004 1008 1013 1017 1023 10301032 1035 4002 4006 4009 4014 cpcE1 4022 4025 4028 tnp repH3 4038 4041 4043 3011 tnp 3048 2004 2006 2010 2013 parB rpL36 2020 2024 2027 2033 2037 2039 2042 1001 1003 1005 1009 1014 tnp 1027 1028 1033 1039 2025 2028 1029 1034 0.16 H. marismortui

0.14 Halobacterium NRC-1

0.12

0.1

F r a c t i o n 0.08

0.06

0.04

0.02

0 1 10 100 1000 10000

Intergenic distance (bp) A. Halobacterium NRC-1 22

18

14 gyrB,A orc8 orc6 orc7

10

6

2

Z-score -2 0 200000 400000 600000 800000 1000000 1200000 1400000 1600000 1800000 2000000

-6

-10

-14

-18 GC skew B. Haloarcula marismortui AT skew

10 (orc7) cdc6i cdc6g,f cdc6d cdc6c

6

2

Z-score 0 500000 1000000 1500000 2000000 2500000 3000000 -2

-6

gyrA,B cdc6j cdc6h cdc6e -10 A

B rrnAC0131 pNG3032 pNG4021 tup1 pNG4046 pNG3039

pNG4047 boa rrnAC1392 sojB rrnAC2917 rrnAC1086 rrnAC3012 rrnAC3270

rrnAC1391 rrnAC3271 rrnAC0464

boa cas3 rrnAC3181 cbiK parA5 yhcR2 tnp rrnB0336 rrnAC0869 endrrAnAC3084 htl_ tpiA dnaG rrnAC0629 rrnAC1525 rrnAC2791 nustAaq2D rpL12P yrhrncARC10238 rrnAC2519 rrnAC3180 pNG4050 rrnAC0314 rpl18E parA3 eif5A rrnAC0930 rrnAC3010 gapB rrnAC1664 rrnAC0262 pNG6044 rrnB0333 eef1bcmk rrnAC0210 nmd3 rrnB0331 rps6E rrnAC2098"rpoE""""" pNG6043 rpoM rps27AE bchP

rps8E rpoE' pfdB rrnB0061 adk pNG4051 rrnAC1681 hmvng2868 rrnAC1588 mcm3 rps27E rrnAC0214 rrnAC0277

pNG3054 trh3 pNG3052 pNG7132

rad24a tnp cbiH pNG3051 pri rrnAC3366 rrnAC0276 pNG5069

brr2

rrnAC0293 tnp

pNG5070 rrnAC2749

rrnAC0817

yprA1

rrnAC2876 yprA3

pNG6078 narH rrnAC1220 hemL tyrA rrnB0047 rrnAC0920 pNG5046 pNG6077 rrnAC0911 catD pNG5125 pNG2026

apbE pNG5031

rrnAC1202 pNG5136 pNG2023 czcD rrnAC0513 rrnAC0919 rrnAC1221 rrnAC2629 tnp pNG6076 rrnAC0910 rrnAC0571 tnp

rrnB0050

rrnAC1055 rrnAC1203 pNG6080 pNG5057 tnp surE rrnB0051 gfo4 tnp pNG2024 moxR4 prsA rrnAC1581 pNG6075 potA4 rrnAC0570

tnp narJ tnp zntA1

aor2 pNG6177 rrnAC0985 rrnAC0594 nosZ rrnAC0110 rrnAC0935 pNG5006 ilvC pNG7396 ftsZ5 rrnAC1062

hat7 tnp rrnAC1319 rrnAC0281 rrnAC0333 trwB3 rrnAC0391 rrnAC0111 rrnAC0936 rrnAC0595 rrnAC3283 trwB1 pNG6178 pNG7395 hmvng2059

rrnAC1321 leuC tnp pNG6104 rrnAC0937 nosD2 rrnAC0112 rrnAC3282 hat5 rrnAC0596 pNG7394 rrnAC1322 pNG6179

rrnAC3056 rrnB0186 rrnAC1552 rrnAC3413 gbp3 fdoH nirJ pNG5078 hcp8 rrnAC1027 rrnAC2930 rrnAC1846 rrnAC2523 pNG1035 srp19 rrnAC1119 rrnAC0040

rrnAC3414 hmvng1910 pNG1034 rrnAC1026 rrnB0187 rrnAC0734 rrnAC3057 rrnAC1555 rrnAC1334 rrnAC1364 flaA2 rrnAC2708 repH hpyA hlx1 hisI2 pNG1033 gfo1 virB 11 moxR6 rrnB0188 hmvng2364 rrnAC0733 rrnAC3058 pNG7195

rrnAC1194 rrnAC2792 rrnAC2850 guaA1 rrnAC0264 rrnAC0003 rrnAC0901 sojE pNG7174 rrnAC0949 rpaA dmsA rrnAC1654 acs4 pNG5003 pNG3044 rrnAC3098 trzA4 pNG2013 pNG7285 pNG7286 rrnAC1135 rrnAC1216 rrnAC1655 rrnB0266 pNG5004 pNG3043 pNG5020 sojA rrnAC0950 accA sojC pNG7287 rrnAC3552 accA rrnAC3473 rrnAC0263 rrnAC2849 pNG3042 edp rrnAC1195 yusZ3

csg1 cadA coxA3 coxA4 nhaC1 rrnB0196 tfeA ccmC rnhA rrnAC3294 pNG1013 pNG1028 pNG4009 parA1 pNG4014 pNG4038 pNG4041 pNG5036 pNG5055 pNG5086 pNG6004 pNG6010 pNG6040 pNG6127 pNG6128 rrnAC1374 rrnAC3321 ykfD pNG1014 pNG1029 pNG4010 pNG4013 pNG4015 pNG4039 pNG4042 pNG5037 tnp trwB2 pNG6005 pNG6011 pNG6041 rrnAC1408 pNG6017 rrnAC1155 rrnAC0881 rrnAC0228 lpdA3 rrnAC0862

pNG6185 qad hmvng1986 gudB pNG7200 pNG7224 rrnAC0099 rrnAC0187 rrnAC0232 rrnAC3454 rrnAC0374 rrnAC0408 rrnAC0531 rrnAC0549 rrnAC0608 rrnAC0622 rrnAC0791 rrnAC0851 rrnAC0627 rrnAC0723 nitA rrnAC1023 rrnAC1048 pNG6187 pNG7090 trmH pNG7158 pNG7201 pNG7225 rrnAC0100 rrnAC0188 ykfB2 ykfB3 ssrA rrnAC0897 acaB3 lemA pgsA glpK rrnAC0609 rrnAC0623 cdc48b rrnAC0852 sun rrnAC0724 rrnAC0811 rrnAC1024 rrnAC1049

capBrrnAC1077 rrnAC1r1r6n1AC1162 rrnAC1r1r7n8AC1179 rrnAC1r2r1n8AC1219 rrnAC1r3r2n6AC1327 mchrrnAC1617 rrnAC1r6rn4A6C1647 rrnAC1r7r5n9AC1760 rrnAC1r7rn6A9C1770 hmvng284c7omA rrnAC1r6rn7A3C1674 rrnAC1922nif3 minDr1rnAC1940 rrnAC1r9rn4A5C1946 rrnAC2r0rn1A1C2012 rrnAC204s6ppA rrnAC209e9ntB1 rrnAC2102 rli rrnAC2r2rn3A7C2239 rrnAC2r3rn8A0C2381 rrnAC2r5rn8A8C2589 mutTrr2nAC2154 rrnAC2r2rn8A9C2290 rrnAC2r3rn9A2C2393 rrnAC2h5m7v8ng1908

rrnAC2r6rn6A5C2666 rrnAC276m6inD4 rrnAC2r8rn5A5C2856 rrnAC2r8rn6A4C2865 rrnAC288p5haC rrnAC2r8rn9A5C2896 rrnAC2r9rn4A3C2944 rrnAC3r0rn1A5C3016 rrnAC3r2rn4A0C3241 rrnAC3461thrS rrnB0069speE rrnB010rr9nB0111 rrnB0142 tnp pNG50p2N3G5024 pNG7378folP2 rrnAC2r9rn7A9C2980 rrnB00r1r3nB0014 rrnB00r8rn1B0082 rrnB0166cbp ubiDrrnB0268 rrnB02r8r4nB0285 pNG4030tnp pNG50p9N2G5093 pNG60p5N0G6051 rrnAC0r1rn3A9C0140

rrnAC0r1rn5A3C0154 rrnAC0r5rn8A5C0586 rrnAC0r9rn8A0C0981 rrnAC1rr0n0A1C1002 rrnAC1r0rn6A4C1065 rrnAC1r1rn2A7C1128 rrnAC114m3utS3 thirIrnAC1235 pyrrFrnAC1516 rrnAC1r8rn1A0C1811 pNG7r2r8n0AC3486 rrnAC3r3rn3A7C0793 rrnB02p7N4G7154 rrnAC1r2rn8A9C1285 rrnAC2r0rn4A8C2049 rrnAC2r0rn6A0C2061 rrnAC2rr2n4A1C2242 rrnAC256p7mm rrnAC3r2rn5A6C3257 rrnAC3rr4n5A1C3452 rrnB01r3rn4B0136 Helix C

Helix F Y83 I119

Helix D P186 W189 G122

Helix E W138

Helix C

Helix F Y83 I119

W189 P186 Helix D

G122

W138 Helix E ORF Gene name EC number(s) Putative function pNG1015 transcription regulato pNG1020 tnp phage integrase pNG1024 cdc6q Cell division control protein 6 homolog 6 (CDC6 homolog 6 pNG1026 flaA2 Flagellin A protein pNG1040 Putative helicase pNG2003 boa Bacterio-opsin activator-like protein pNG2006 padR transcription regulato pNG2014 sojC Chromosome partitioning protein, membrane-associated ATPase pNG2016 parB ParB-like nuclease pNG2018 rpL36 Similar to H. sapiens and R.norvegicus 60S ribosomal protein L3 pNG2022 repH1 pNRC100 replication protein H homolog pNG2033 putative membrane-bound metal-dependent hydrolase pNG2034 yprA1 ATP-dependant helicase pNG2036 papSR 1.8.99.4 Phosphoadenosine phosphosulfate reductase pNG2039 Ribbon-helix-helix protein, copG family pNG2042 transcription regulato pNG3007 transcription regulato pNG3010 putative Helix-hairpin-helix motif DNA-binding protei pNG3013 cdc6p Cell division control protein 6 homolog pNG3029 repH2 pNRC100 replication protein H homolog pNG3034 tnp Transposase and inactivated derivatives pNG3037 sojB Putative plasmid partitioning protein So pNG3053 mcm3 MCM / cell division control protein 21 pNG4001 tnp Putative ISH4 transposase (VNG0918H pNG4003 tnp Putative transposase (VNG6486H) (VNG6040H pNG4012 parA1 Chromosome partitioning protein ParA pNG4017 cpcE1 Phycocyanin alpha phycocyanobilin lyase-lik pNG4019 htlD Similar to ESCHERICHIA COLI protein kinase GP:GI-606149 (HTR-like protein pNG4020 boa Bacterio-opsin activator-like protein pNG4025 transcription regulato pNG4032 tnp Putative ISH8 transposase pNG4036 repH3 pNRC100 replication protein H homolog pNG4042 DNA binding protein, putative transcriptional regulato pNG4043 transcription regulato pNG4049 cas3 CRISPR-associated protein, TM1801 family pNG4051 putative helicase pNG4052 cas4 CRISPR-associated protein Cas4 pNG4053 cas1 CRISPR-associated protein Cas1 pNG4054 cas2 CRISPR-associated protein Cas2 pNG5001 abcP-1 ABC transporter, permease protein pNG5003 yvrO-1 ABC transporter, ATP-binding protein pNG5007 tnp Putative transposase pNG5012 tnp Probable transposase for insertion sequence element ISH1 pNG5013 Sugar-specific transcriptional regulato pNG5019 sojE Similar to BACILLUS SUBTILIS SOJ (SPO0A activation inhibitor pNG5022 tnp Transposase pNG5027 cdc6o Cell division control protein 6 pNG5042 tnp Transposase pNG5043 tnp Putative ISH8 transposase pNG5045 tnp Putative transposase (VNG6486H) (VNG6040H pNG5047 doxD3 terminal quinol oxidase subun pNG5052 usp8 Universal stress protein pNG5054 tnp Probable transposase for insertion sequence element ISH1 pNG5056 tnp Putative transposase pNG5058 tnp Putative ISH8 transposase (VNG6331H pNG5061 putative collagenase pNG5064 htl Htr-like protein pNG5065 Putative lipid/cholesterol transpor pNG5066 3.2.1.18 putative exo-alpha-sialidase pNG5067 DNA binding protein tetR family pNG5071 transcription regulato pNG5072 tnp Putative transposase (VNG6486H) (VNG6040H pNG5075 tnp Transposase pNG5076 tnp Putative transposase (VNG6486H) (VNG6040H pNG5087 trwB2 bacterial conjugation protein pNG5088 Ribbon-helix-helix protein, copG family pNG5089 Ribbon-helix-helix protein, copG family pNG5090 rlx Relaxase/mobilization nuclease domain pNG5091 traD TraD protein pNG5113 abrB transcriptional regulator, AbrB family pNG5119 Putative transcriptional regulato pNG5121 sojD Similar to BACILLUS SUBTILIS SOJ (SPO0A activation inhibitor pNG5122 cdc6n Cell division control protein 6 pNG5123 tnp Transposase pNG5124 tnp Probable transposase for insertion sequence element ISH1 pNG5127 tnp Transposase pNG5128 tnp Transposase pNG5130 tnp putative transposase pNG5131 transcription regulato pNG5132 tnp Probable transposase for insertion sequence element ISH1 pNG5133 Putative transcriptional regulato pNG5137 tnp Transposase pNG5138 csg1 Cell surface glycoprotein pNG5139 tnp putative transposase pNG5140 Putative transcriptional regulato pNG5142 tnp Putative transposase pNG5143 tnp Putative ISH8 transposase (VNG6331H pNG6011 sigma-70 like region 4 HTH domain pNG6012 parA2 Partition protein, ParA homolog pNG6016 xerD Site-Specific Recombinase, Xerd pNG6019 cadA Cadmium transporting P-type ATPase pNG6021 Putative transcriptional regulato pNG6022 trzA5 N-ethylammeline chlorohydrolase pNG6023 putative metal ion permease pNG6029 trxA6 Thioredoxin pNG6030 Putative Copper Binging Protein pNG6033 ABC transporter, ATP-binding protein pNG6034 transcription regulato pNG6036 mitN 2.1.1.41 Sterol 24-C-methyltransferase pNG6039 usp32 putative Universal stress protein family pNG6044 pNG6046 copA3 3.6.3.4 Copper-transporting ATPase pNG6047 putative metal-binding transcription regulato pNG6048 merP Mercuric Transport Protein pNG6049 acnA 4.2.1.3 Aconitate hydratase I pNG6055 Putative cation binding protein pNG6056 copA2 Copper transporting ATPase CopA pNG6059 copA1 Copper-transporting ATPase copA pNG6063 hcp4 Halocyanin precursor -like pNG6067 pan1b Membrane protein Pan1 pNG6069 dsbB2 Disulfide bond formation protein DsbB pNG6070 Trx DSBA-like thioredoxin pNG6072 tfbG Transcription initiation factor IIB (TFIIB pNG6074 transcription regulato pNG6079 czcD Cation efflux system protein pNG6081 zntA1 Zinc-transporting ATPase pNG6091 transcription regulato pNG6092 transcription regulato pNG6094 xseA1 3.1.11.6 Probable exodeoxyribonuclease VII large subuni pNG6095 exoVIIA 3.1.11.6 Exonuclease VII small subunit pNG6105 trwB3 Transfer complex protein pNG6107 traG/traD bacterial conjugation protein pNG6123 tfbE Transcription initiation factor IIB 5 (TFIIB 5 pNG6134 transcription regulato pNG6135 ctpC Cation-transporting ATPase pNG6143 mrr Mrr restriction system protein homolog pNG6154 hyrA1 Monooxygenase pNG6155 Transcriptional regulato pNG6156 merA 1.16.1.1 Mercuric reductase pNG6157 copG2 Transcriptional regulator, CopG family pNG6161 copA5 Copper-transporting ATPase CopA pNG6165 ltrC LtrC-like protein pNG6174 cdc6m Cell division control protein 6 homolog 6 (CDC6 homolog 6 pNG6176 polB2 2.7.7.7 DNA polymerase B2, exonuclease domain pNG6184 cdc6l Cell division control protein 6 pNG6185 putative DEAD/H helicase pNG7003 Sulfatase pNG7005 glycosyl transferase pNG7006 chitin-binding protein pNG7008 gtr-1 2.4.1.- Glycosyl transferase pNG7009 ypjH-1 Glycosyl transferase, group 1 pNG7011 wecB 5.1.3.14 UDP-N-acetylglucosamine 2-epimerase pNG7012 ugd1 UDP-glucose 6-dehydrogenase pNG7013 dpm3 Dolichyl-phosphate beta-D-mannosyltransferas pNG7014 galE3 5.1.3.2 UDP-glucose 4-epimerase pNG7015 ttuD 1.1.1.81 Putative hydroxypyruvate reductase pNG7017 4Fe-S protein pNG7021 kdgR1 Transcriptional regulato pNG7022 adh1 1.1.1.1;1.6.5.5 Zinc-binding dehydrogenase pNG7023 rbsB-1 Putative ABC transporter, substrate-binding protei pNG7024 sugA Sugar ABC transporter, permease protein (Y4OQ pNG7025 malFG-1 Sugar ABC transporter, permease protein pNG7026 msmX-1 Multiple sugar ABC transporter ATP-binding protei pNG7027 fucA 4.1.2.17 L-fuculose phosphate aldolase pNG7029 rhaB 2.7.1.5 Rhamnulokinase pNG7030 fabG3 1.1.1.100 3-oxoacyl-[acyl-carrier protein] reductase pNG7031 dgoA1 Mandelate racemase / muconate lactonizing enzyme family pNG7032 adh10 1.1.1.1;1.6.5.5 Zinc-binding dehydrogenase pNG7033 yvbT 1.14.14.3 Alkanal monooxygenase homolog pNG7037 ndhF 1.6.99.5 Potential NADH-quinone oxidoreductase subunit 5 pNG7038 trh2 Transcription regulato pNG7039 putative iron transport protein pNG7043 csbC Probable metabolite transport protein CsbC pNG7044 Fructosamine kinase pNG7045 putative DNA binding domain pNG7046 transcription regulato pNG7050 drrA-1 ABC transporter, ATP-binding protein pNG7052 rdxA Nitroreductase family protein pNG7057 dsbD Cytochrome C biogenesis protein pNG7059 prrC Regulatory protein PrrC pNG7060 fmdA Formamidase pNG7061 cctA1 Thermosome alpha subunit (Thermosome subunit 1) (Chaperonin alpha subun pNG7062 usp12 Universal stress protein pNG7063 cat1 Cationic amino acid transporte pNG7065 putP-1 Probable sodium:solute symporte pNG7066 prp2 Phosphate regulatory protein homolog pNG7067 speB2 3.5.3.11 Agmatinase pNG7071 fabG Oxidoreductase pNG7072 fabG7 1.1.1.100 3-oxoacyl-[acyl-carrier protein] reductase 1 pNG7073 qgd 1.1.99.17 Quinoprotein Glucose Dehydrogenase pNG7077 rnh 3.1.26.4 RNaseH pNG7078 trxB1 1.8.1.9 Thioredoxin reductase pNG7082 3.1.6.- Sulfatase pNG7083 usp23 putative Universal stress protein family pNG7084 htr8 MCP domain signal transducer (membrane pNG7085 Heavy-metal-associated protein pNG7088 qad 1.1.99.- Quinohemoprotein Alcohol Dehydrogenase pNG7096 camH1 3.5.2.10 Creatinine amidohydrolase pNG7098 putative membrane-bound metal-dependent hydrolase pNG7099 cpt 2.7.8.- CDP-alcohol phosphatidyltransferase pNG7101 adh8 1.1.1.1;1.1.1.2 Alcohol dehydrogenase pNG7103 adh7 1.1.1.1 putative Zinc-binding dehydrogenase pNG7105 Glycosyl transferase group 1 pNG7110 putative permease pNG7116 nthC 4.2.99.18 Endonuclease III pNG7117 sdt Sodium-dependent transporter pNG7118 livF-1 Branched-chain amino acid ABC transporter, ATP-binding protei pNG7119 livG-1 Branched-chain amino acid ABC transporter, ATP binding protei pNG7120 livM-1 Branched-chain amino acid transport system / permease componen pNG7121 livH-1 Branched-chain amino acid ABC transporter, permease protei pNG7122 livJ Putative ABC transporter substrate-binding protei pNG7123 ureB 3.5.1.5 Urease beta subunit pNG7124 ureC 3.5.1.5 Urease alpha subunit pNG7125 ureA 3.5.1.5 Urease gamma subunit pNG7126 ureG Urease accessory protein UreG pNG7127 ureD Urease accessory protein UreD pNG7128 ureE Urease accessory protein UreE pNG7129 ureF 3.5.1.5. Urease accessory protein F, UreF pNG7134 trxA2 Thioredoxin pNG7136 noxA1 NADH oxidase pNG7137 ctpA Cation-transporting ATPase pNG7139 usp13 Universal stress protein pNG7142 usp31 Universal stress protein pNG7145 nosL NosL protein pNG7146 transcription regulato pNG7149 drrA-2 ABC transporter, ATP-binding protein pNG7150 nosD1 copper-binding protein pNG7151 fdhA Formate dehydrogenase alpha subuni pNG7153 guaB1 1.1.1.205 Inosine-5'-monophosphate dehydrogenase pNG7155 htlD Similar to ESCHERICHIA COLI protein kinase GP:GI-606149 (HTR-like protein pNG7156 oye2 11-domain light and oxygen sensing his kinas pNG7157 gudB 1.4.1.3 NAD(P)-specific glutamate dehydrogenase pNG7159 boa Bacterio-opsin activator-like protein pNG7160 CopG family ribbon-helix-helix transcription regulato pNG7161 mntH Putative Mn transporter, NRAMR family pNG7164 hyuA 3.5.2.9 N-methylhydaintoinase A pNG7165 hyuB 3.5.2.9 N-methylhydantoinase B pNG7167 Sensor histidine kinase pNG7169 nhaC4 Na+/H+ antiporter pNG7171 arcR3 Transcription regulator pNG7173 tnp Transposase pNG7175 sojA Putative plasmid partitioning protein So pNG7176 tnp phage integrase pNG7178 sdt-2 Sodium-dependent transporter pNG7180 transcription regulator, tetR family pNG7182 sialidase pNG7183 transcription regulator, tetR family pNG7187 cdc6k Cell division control protein 6 homolog 1 (CDC6 homolog 1 pNG7188 HTH DNA binding domain protein pNG7189 ndhG1 NADH dehydrogenase/oxidoreductase pNG7190 Ferrichrome-Binding protein pNG7191 gfo2 Putative glucose-fructose oxidoreductase pNG7192 phnM Phosphonate metabolism protein pNG7194 transcription regulato pNG7196 dpm4 Dolichyl-phosphate beta-D-mannosyltransferas pNG7198 wlaE Glycosyl transferase, group 1 pNG7199 lpb1 LPS biosynthesis protein pNG7200 ypjH-2 Glycosyltransferase pNG7203 3.1.6.- Sulfatase pNG7204 putative sulfatase pNG7205 2.4.1.- Glycosyl transferase pNG7206 N-acetylgalactosamine-4-sulfatase. pNG7210 putative carbohydrate binding module (family 6) protei pNG7214 rfbX Probable export protein pNG7215 gfo3 glucose fructose oxidoreductase pNG7218 rffH4 Glucose-1-phosphate thymidylyltransferase pNG7223 boa Bacterio-opsin activator-like protein pNG7227 nadE2 6.3.5.1 NH(3)-dependent NAD(+) synthetase pNG7228 rps17E Ribosomal protein S17e pNG7229 Cytosine Deaminase pNG7231 phnD1 Phosphonates ABC transporter, permease protein pNG7233 phnC1 Phosphonate transporter, ATP binding protein pNG7234 phnD2 Phosphate ABC transporter, phosphate-binding protei pNG7235 ern1 Endoribonuclease L-PSP (ssRNase pNG7236 glmU 2.7.7.23 UDP-N-acetylglucosamine pyrophosphorylase pNG7239 selD Putative selenophosphate synthase pNG7242 dsrE/dsrF_2 intracellular sulfur reduction protein pNG7243 dsrE/dsrF_1 intracellular sulfur reduction protein pNG7244 xdhD1 1.-.-.- Possible hypoxanthine oxidase XdhD pNG7245 iorA Isoquinoline 1-oxidoreductase, alpha subun pNG7246 xdhD2 1.-.-.- Possible hypoxanthine oxidase xdhD pNG7247 cutC Carbon monoxide dehydrogenase, small subun pNG7248 amaB 3.5.1.- N-carbamoyl-L-amino acid amidohydrolase pNG7249 ureX 3.5.1.5 urease subunit pNG7250 bmp-1 Basic membrane protein pNG7251 bmp-2 Basic membrane protein pNG7252 rbsA Ribose ABC transporter ATP-binding pNG7253 rbsC-1 Sugar ABC transporter permease protein pNG7254 rbsC-2 Sugar ABC transporter, permease protein pNG7255 mer4 F420-dependent N5,N10-methylene-tetrahydromethanopterin reductas pNG7256 pbuX Xanthine permease pNG7257 thrC2 4.2.3.1 Threonine synthase pNG7258 pyrC 3.5.2.3 Dihydroorotase pNG7259 trzA1 N-ethylammeline chlorohydrolase pNG7265 fadD2 Putative long-chain-fatty-acid-CoA ligase pNG7272 Retinal pigment epithelial membrane protein pNG7273 trxB5 Thioredoxin reductase pNG7275 fhuG1 Ferrichrome ABC transporter permease protein pNG7276 fhuG2 Ferrichrome ABC transporter ATP-binding protein pNG7278 adh12 1.1.1.1 Alcohol dehydrogenase pNG7279 Putative pyridine nucleotide-disulphide oxidoreductas pNG7283 lctP L-lactate permease pNG7284 glcD3 Putative oxidoreductase pNG7288 putative phosphoesterase pNG7289 adh6 1.1.1.1;1.6.5.5 Zinc-binding dehydrogenase pNG7291 htpX2 3.4.24.- Probable protease HtpX homolog pNG7293 yafB Aldehyde reductase pNG7295 3-beta hydroxysteroid dehydrogenase/isomerase famil pNG7296 mox 1.14.14.3 Alkanal monooxygenase (luciferase-like pNG7297 tehB Tellurite resistance protein pNG7301 pphA 3.1.3.16 Serine/threonine protein phosphatase pNG7302 ppk 2.7.4.1 Polyphosphate kinase pNG7305 matE1 Multi Antimicrobial Extrusion family drug/sodium antiporters pNG7307 putative tetR family regulator pNG7308 tetR transcription regulato pNG7310 PRC-barrel domain, posible photosystem reaction centre subunit H pNG7313 putative protease pNG7314 adhC 1.1.1.1 Formaldehyde dehydrogenase pNG7316 cobW/P47K_2 Cobalamin synthesis protein/P47K pNG7318 fdhG Formate dehydrogenase alpha subuni pNG7319 nuoF Putative NADH dehydrogenase I, F subun pNG7321 ern2 Endoribonuclease L-PSP (ssRNase pNG7323 pch1 Potassium channel homolog pNG7324 betL1 Glycine betaine transporter BetL pNG7325 trpG2 4.1.3.27 Anthranilate synthase component II pNG7327 trpE3 4.1.3.27 Anthranilate synthase component pNG7328 folD2 1.5.1.5;3.5.49 Methylenetetrahydrofolate dehydrogenase pNG7330 cysE1 2.3.1.30 Serine acetyltransferase pNG7331 gltP Proton/sodium-glutamate symport protein pNG7333 serB2 Phosphoserine phophotase pNG7334 tii Translation initiation inhibito pNG7335 fabG5 1.1.1.100 3-oxoacyl-[acyl-carrier protein] reductase pNG7336 pcaB N-acylamino acid racemase pNG7338 malFG-2 ABC transporter, permease protein pNG7339 malFG-3 Sugar ABC transport system, permease protein pNG7340 putative extracellular solute binding protei pNG7341 camH2 3.5.2.10 Creatinine amidohydrolase pNG7342 msmK Multiple sugar ABC transporter ATP-binding protei pNG7343 arcR2 Transcription regulato pNG7344 arcR4 Transcription regulato pNG7346 potD1 Spermidine/putrescine transporter, substrate binding protei pNG7347 potA1 Putrescine ABC transporter, ATP-binding protein pNG7349 potB1 Spermidine/putrescine ABC transporter, permease protein pNG7350 potC1 Spermidine/putrescine ABC transporter, permease protein (PotC pNG7351 adh13 1.1.1.1;1.6.5.5 Zinc-binding dehydrogenase pNG7352 aldA 1.2.1.3 Aldehyde dehydrogenase pNG7353 sugar transporter pNG7354 nitB 3.5.5.1 Nitrilase pNG7357 Putative transcriptional regulato pNG7359 folA2 1.5.1.3 Dihydrofolate reductase pNG7361 gcvT5 2.1.2.10 Probable aminomethyltransferase pNG7363 metF 1.7.99.5 5,10-methylenetetrahydrofolate reductase pNG7365 htrA2 serine protease pNG7366 gcvT3 1.5.3.1;2.1.2.10Sacrosine dehydrogenase/glycine cleavage T-protei pNG7367 yeaW 1.14.1.- Putative dioxygenase alpha subunit YeaW pNG7370 gcvT1 1.5.3.1;2.1.2.10Sacrosine dehydrogenase/glycine cleavage T-protei pNG7371 ilvA3 4.2.1.16 Threonine dehydratase pNG7373 usp25 Universal stress protein pNG7375 betL2 Glycine betaine transporte pNG7379 folP2 2.5.1.15 Dihydropteroate synthase pNG7380 fhs 6.3.4.3 Formyltetrahydrofolate synthetase pNG7381 ftc 4.3.1.4 Formimidoyltetrahydrofolate cyclodeaminase pNG7382 folE 3.5.4.16 GTP cyclohydrolase I pNG7387 ptsC 2.7.1.69 sugar Phosphotransferase system, IIC componen pNG7388 ptsA 2.7.1.69 Sugar Phosphotransferase system, IIA componen pNG7389 hpr Phosphocarrier protein Hpr pNG7391 ptsI 2.7.3.9 Phosphoenolpyruvate-protein phosphotransferase pNG7392 ptsB 2.7.1.69 Phosphotransferase system, IIB componen pNG7395 gtr-6 2.4.1.- Glycosyltransferase pNG7397 tnp Putative transposase (VNG6486H) (VNG6040H rrnAC0001 birA Biotin-(acetyl-CoA carboxylase) ligase rrnAC0002 accC2 6.3.4.16 Carbamoyl phosphate synthase L chain rrnAC0004 accA Acetyl-CoA carboxylase alpha subun rrnAC0006 Putative DNA binding rrnAC0010 nac Sodium-and chloride-dependent transporte rrnAC0011 ywfD1 1.1.1.47 Glucose 1-dehydrogenase rrnAC0012 adh11 1.1.1.1;1.6.5.5 Zinc-binding dehydrogenase rrnAC0013 htr MCP domain signal transducer (membrane rrnAC0014 sop2 Sensory rhodopsin 1 rrnAC0016 tfbA Transcription initiation factor IIB (TFIIB rrnAC0018 trmH RNA methyltransferase,TrmH family, group rrnAC0019 boa Bacterio-opsin activator-like protein rrnAC0023 gatE 6.3.5.- Glutamyl-tRNA(Gln) amidotransferase subunit E rrnAC0026 hat7 Putative Acetyltransferase (GNAT) rrnAC0028 fumC 4.2.1.2 Fumarate hydratase, class-II rrnAC0029 Sugar ABC transporter, permease protein rrnAC0030 yurM ABC transporter, permease protein rrnAC0031 ugpC3 Sugar ABC transporter, ATP-binding protein (UGPC rrnAC0032 rad2 DNA repair protein Rad2 rrnAC0038 ocd1 4.3.1.12 Ornithine cyclodeaminase rrnAC0041 srp19 Signal recognition particle 19 kDa protein (Srp19 rrnAC0043 coxB1 1.9.3.1 Cytochrome c oxidase subunit II rrnAC0044 ctaB Heme synthase rrnAC0045 trp4 ABC transporter, ATP-binding protein homolog rrnAC0048 ABC transporter, ATP-binding protein rrnAC0049 ABC transporter ATP-binding domain rrnAC0051 2.7.8.- sugar transferase rrnAC0052 dpd 1.3.1.2 Dihydropyrimidine Dehydrogenase rrnAC0053 citG CitG family protein rrnAC0054 rrnAC0055 rps17E 30S ribosomal protein S17e rrnAC0056 mrp1 Mrp protein homolog rrnAC0058 rps13P 30S ribosomal protein S13P rrnAC0059 rps4P 30S ribosomal protein S4P rrnAC0061 rps11P 30S ribosomal protein S11P rrnAC0062 rpoD DNA-directed RNA polymerase, subunit D rrnAC0064 rpl18E 50S ribosomal protein L18e rrnAC0065 rpl13P 50S ribosomal protein L13P rrnAC0066 rps9P 30S ribosomal protein S9P rrnAC0067 rpoN 2.7.7.6 DNA-directed RNA polymerase subunit N rrnAC0068 rpoK 2.7.7.6 DNA-directed RNA polymerase subunit K rrnAC0069 eno 4.2.1.11 Enolase rrnAC0070 rps2P 30S ribosomal protein S2P rrnAC0073 cyc 1.14.14.1;1.6.2Cytochrome P450 rrnAC0075 htlD Similar to ESCHERICHIA COLI protein kinase GP:GI-606149 (HTR-like protein rrnAC0077 mvk 2.7.1.36 Mevalonate kinase rrnAC0078 argB1 2.7.2.8 Acetylglutamate kinase rrnAC0080 predicted hydrolase (COG0595) rrnAC0081 idsA 2.5.1.1;2.5.1.10Geranylgeranyl diphosphate synthase rrnAC0083 arsA1 3.6.3.16 arsenical pump-driving ATPase rrnAC0085 gltX 6.1.1.18 Glutaminyl-tRNA synthetase rrnAC0086 htlD Similar to ESCHERICHIA COLI protein kinase GP:GI-606149 (HTR-like protein rrnAC0087 hsp5 Heat shock protease protein rrnAC0088 lipC Lipase/esterase rrnAC0089 ferB Ferredoxin rrnAC0090 etfB2 Electron transfer flavoprotein beta subun rrnAC0091 etfA1 Electron transfer flavoprotein alpha-subun rrnAC0094 ydiS Flavoprotein, probably electron transpor rrnAC0096 hat-1 Acetyl transferase, GNAT family rrnAC0097 mer3 N5,N10-methylenetetrahydromethanopterin reductase rrnAC0098 alkK1 Medium-chain acyl-CoA ligase rrnAC0102 npd 2-nitropropane dioxygenase-related protei rrnAC0103 rpl7AE 50S ribosomal protein L7Ae rrnAC0104 rpl24E 50S ribosomal protein L24e rrnAC0106 ndk 2.7.4.6 Nucleoside diphosphate kinase rrnAC0107 Glutaredoxin like rrnAC0109 msrB 1.8.4.6 Peptide methionine sulfoxide reductase msrB rrnAC0110 betA Oxidoreductase, GMC family rrnAC0113 pai1 Sporulation regulator homolog rrnAC0114 guaB5 Inosine-5'-monophosphate dehydrogenase related protein V rrnAC0123 udg2 3.2.2.- uracil DNA glycosylase superfamily protein rrnAC0124 aroC 4.2.3.5 Chorismate synthase rrnAC0127 aroA 2.5.1.19 3-phosphoshikimate 1-carboxyvinyltransferase rrnAC0128 sdr short chain dehydrogenase rrnAC0129 zip Zinc transporter rrnAC0130 htl Signal-transducing histidine kinase homolo rrnAC0131 RecA/helicase homology rrnAC0132 1.5.1.7;1.5.1.10lysine-ketoglutarate reductase/saccharopine dehydrogenas rrnAC0134 ilvB1 4.1.3.18 Acetolactate synthase large subunit rrnAC0137 cysK2 2.5.1.47 Cysteine synthase rrnAC0138 eif2B1 Probable translation initiation factor 2 beta subunit (eIF-2-beta rrnAC0141 sdhA2 1.3.99.1 Succinate dehydrogenase flavoprotein subuni rrnAC0143 nhaC2 Na+/H+ antiporter rrnAC0145 potA3 Spermidine/putrescine ABC transporter, ATP-binding protei rrnAC0146 cysT2 Sulfate transport system permease protein rrnAC0147 tppA Thiamin-binding periplasmic protein precursor homolo rrnAC0149 pdhA1 1.2.4.1;1.2.4.4 Pyruvate dehydrogenase E1 component, alpha subuni rrnAC0155 epf2b mRNA 3'-end processing factor homolog rrnAC0161 Putative transcriptional regulato rrnAC0166 proS 6.1.1.15 Proline-tRNA synthetase rrnAC0167 putative Patatin-like phospholipase rrnAC0169 gltB 1.4.1.13 Glutamate synthase large subunit rrnAC0172 transcription regulato rrnAC0173 bglX-1 Beta-glucosidase rrnAC0175 gldA 1.1.1.6;1.1.1.26Glycerol-1-phosphate dehydrogenase [NAD(P)] rrnAC0178 pop Prolyl oligopeptidase family protein rrnAC0179 rfbU LPS biosynthesis rrnAC0180 nhaC5 Na+/H+ antiporter rrnAC0181 rad25-1 DNA repair helicase rrnAC0182 ubiE2 Ubiquinone/menaquinone biosynthesis methyltransferase Ubi rrnAC0183 htr Heme-based aerotactic transducer HemAT rrnAC0184 folP 2.5.1.15 Dihydropteroate synthase rrnAC0187 Transporter, putative Bifunctional purine biosynthesis protein PurH [Includes: Phosphoribosylaminoimidazolecarboxamide formyltransfera rrnAC0189 purH 3.5.4.10;2.1.2.3(EC 2.1.2.3) (AICAR transformylase); IMP cyclohydrolase rrnAC0191 adh3 1.1.1.1;1.6.5.5 Zinc-binding dehydrogenase rrnAC0192 purB 4.3.2.2 Adenylosuccinate lyase rrnAC0194 yfmO2 Multidrug resistance protein homolog rrnAC0196 argE 3.5.1.16 Acetylornithine deacetylase rrnAC0198 odc 4.1.1.17;4.1.1.2Ornithine Decarboxylase rrnAC0199 Sigma-70, region 4 like DNA binding protein rrnAC0201 aldY2 1.2.1.3 Aldehyde dehydrogenase rrnAC0204 dapD 2.3.1.117 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase rrnAC0205 aglA2 Alpha-glucosidase rrnAC0206 dapB 1.3.1.26 Dihydrodipicolinate reductase rrnAC0207 dapA1 4.2.1.52 Dihydrodipicolinate synthase rrnAC0210 putative RNA binding protein rrnAC0215 pimT L-isoaspartyl protein carboxyl methyltransferas rrnAC0218 rpoM DNA-directed RNA-polymerase subunit M rrnAC0223 camH3 3.5.2.10 Creatinine amidohydrolase rrnAC0224 aglA1 3.2.1.20 Alpha-glucosidase rrnAC0226 iunH2 3.2.2.1 Inosine-uridine preferring nucleoside hydrolase rrnAC0227 ocd3 4.3.1.12 Ornithine cyclodeaminase rrnAC0229 nhaC1 Na+/H+ antiporter rrnAC0230 arcR Transcription regulato rrnAC0231 transcription regulato rrnAC0233 ykfB2 Chloromuconate cycloisomerase rrnAC0237 otsA Trehalose-6-phosphate synthase rrnAC0239 mer2 N5,N10-methylenetetrahydromethanopterin reductase rrnAC0240 qacE Quaternary ammonium compound-resistance protein rrnAC0241 hadL 3.8.1.2 2-haloalkanoic acid dehalogenase rrnAC0243 trkA7 TRK potassium uptake system protein rrnAC0244 cat Cationic amino acid transporte rrnAC0245 trkA4 Trk potassium uptake system protein rrnAC0246 folP3 2.5.1.15 Dihydropteroate synthase rrnAC0247 putative light-sensing histidine kinas rrnAC0248 phosphotransferase rrnAC0249 pfk3 2.7.1.11 phosphofructokinase rrnAC0251 yvrO-2 ABC transporter, ATP-binding protein rrnAC0252 abcS-2 ABC transporter, permease protein rrnAC0254 metE 2.1.1.14 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase rrnAC0255 2.1.1.14 Methionine synthase, vitamin-B12 independen rrnAC0256 hemK Protoporphyrinogen oxidase rrnAC0257 ksgA 2.1.1.- Dimethyladenosine transferase rrnAC0259 rpb4 RNA polymerase Rpb4 (RNAP sub F) rrnAC0260 rpl21E 50S ribosomal protein L21e rrnAC0261 eef1b Elongation factor 1-beta (EF-1-beta) (aEF-1beta rrnAC0264 hbd-1 1.1.1.35 3-hydroxyacyl-CoA dehydrogenase rrnAC0265 apl 3.1.21.2; 4.2.99AP-endonuclease/AP-lyase rrnAC0267 imd1 1.1.1.205 Inosine Monophosphate Dehydrogenase rrnAC0268 yrbE Oxidoreductase rrnAC0269 gbp1 GTP-binding protein rrnAC0272 hisD 1.1.1.23 Histidinol dehydrogenase rrnAC0273 phoD 3.1.3.1 Alkaline phosphatase D rrnAC0274 putative HesB-like protein rrnAC0275 ddeA Dodecin rrnAC0278 membrane-bound metal-dependent hydrolase rrnAC0282 cpdB3 3.1.4.16 2',3'-cyclic-nucleotide 2'-phosphodiesterase rrnAC0286 rrnAC0289 eif2BD1 Translation initiation factor eIF-2B subunit delt rrnAC0292 pri1 2.7.7.- Eukaryotic-type DNA primase small subunit rrnAC0296 htrA1 Serine protease HtrA rrnAC0298 zntA3 Zinc-transporting ATPase rrnAC0301 signal transducing his kinase rrnAC0302 ilvD 4.2.1.9;4.2.1.12Dihydroxy-acid dehydratase rrnAC0303 ghmP GHMP kinases putative ATP-binding protein rrnAC0304 yqjM1 NADH-dependent flavin oxidoreductase rrnAC0307 purD1 6.3.4.13 Phosphoribosylamine--glycine ligase rrnAC0313 rpoM 2.7.7.6 DNA-directed RNA-polymerase subunit M rrnAC0317 htlC Htr-like protein rrnAC0318 putative carotenoid biosynthesis protei rrnAC0320 ubiA prenyltransferase rrnAC0321 crtI2 1.3.99.- Phytoene dehydrogenase rrnAC0322 pepQ 3.4.11.9 Xaa-Pro aminopeptidase rrnAC0326 fofB Fosfomycin resistance protein FofB rrnAC0329 leuA2 2.3.3.13 2-isopropylmalate synthase 2 rrnAC0330 ilvB2 Acetolactate synthase, large subuni rrnAC0331 ilvN 2.2.1.6 Acetolactate synthase small subunit rrnAC0332 ilvC 1.1.1.86 Ketol-acid reductoisomerase rrnAC0334 leuC 4.2.1.33 3-isopropylmalate dehydratase large subunit rrnAC0336 leuD 4.2.1.33 3-isopropylmalate dehydratase small subunit rrnAC0339 htlD Similar to ESCHERICHIA COLI protein kinase GP:GI-606149 (HTR-like protein rrnAC0340 ipmD 1.1.1.85 3- Isopropylmalate Dehydrogenase rrnAC0341 deoR2 Transcriptional regulator, DeoR family rrnAC0342 pfk4 2.7.1.11 1-phosphofructokinase rrnAC0345 fba 4.1.2.13 Fructose-bisphosphate aldolase rrnAC0351 ubiA putative UbiA prenyltransferase rrnAC0353 dnaJ3 Chaperone protein DnaJ rrnAC0356 htlD Similar to ESCHERICHIA COLI protein kinase GP:GI-606149 (HTR-like protein rrnAC0357 dcuC C4-dicarboxylate anaerobic carrier rrnAC0358 imp-1 immunogenic protein rrnAC0359 1.14.13.2 4-hydroxybenzoate 3-monooxygenase rrnAC0361 hlx7 HoxA-like transcriptional regulato rrnAC0362 serA4 1.1.1.95 Phosphoglycerate dehydrogenase rrnAC0365 asd 1.2.1.11 Aspartate-semialdehyde dehydrogenase rrnAC0367 dbp DNA binding protein eukaryotic-like rrnAC0369 tnp Transposase rrnAC0370 lbp leucine-binding protein rrnAC0371 htr MCP domain signal transducer (membrane rrnAC0375 ssrA Integrase/recombinase rrnAC0376 transcription regulato rrnAC0377 yckA-1 Amino acid ABC transporter, permease protein rrnAC0379 glnQ2 Glutamine ABC transporter (ATP-binding protein rrnAC0380 glnP Glutamine-binding periplasmic protein of glutamine ABC transporte rrnAC0381 glnH1 Glutamine ABC transporter, permease protein rrnAC0382 gabT 4-aminobutyrate aminotransferase rrnAC0383 arg2 3.5.3.1 Arginase rrnAC0384 gdhA1 1.4.1.3 NADP-specific glutamate dehydrogenase rrnAC0385 arcR1 Transcription regulato rrnAC0389 pcy copper-binding plastocyanin like protei rrnAC0390 nosZ 1.7.99.6 Nitrous-oxide reductase rrnAC0392 nosD2 copper binding protein rrnAC0394 nosF-1 ABC transporter, ATP-binding protein rrnAC0396 nosY1 ABC-type transport system involved in multi-copper enzyme maturation, permease componen rrnAC0402 usp15 universal stress protein rrnAC0404 htr12 MCP domain signal transducer (soluble rrnAC0407 fbr3 Cytochrome-like protein rrnAC0409 lemA LemA protein rrnAC0410 ark-4 Sensory transduction histidine kinas rrnAC0411 rre-1 Response regulator receive rrnAC0412 kinA6 Signal-transducing histidine kinas rrnAC0413 oye gaf-pac Signal-transducing histidine kinase homolo rrnAC0414 putative RNA methylase rrnAC0415 rhoM putative intramembrane serine protease rrnAC0416 doxD4 terminal quinol oxidase subun rrnAC0417 transcription regulato rrnAC0419 gtl Glycosyl transferase-like rrnAC0420 TrmB2 Sugar-specific transcriptional regulato rrnAC0421 gtr-2 Predicted glycosyltransferase rrnAC0423 Arylsulfatase rrnAC0426 putative sulfatase rrnAC0427 putative polysaccharide biosynthesis protei rrnAC0428 yidJ Putative sulfatase rrnAC0429 lpg3 LPS glycosyltransferase rrnAC0430 exoM Succinoglycan biosynthesis protein rrnAC0431 tot Transmembrane oligosaccharyl transferase rrnAC0434 act Acyl-CoA thioester hydrolase rrnAC0435 transcription regulato rrnAC0436 traB putative plasmid transfer protein rrnAC0437 metallopeptidase rrnAC0438 purM 6.3.3.1 Phosphoribosylformylglycinamidine cyclo-ligase rrnAC0440 transcription regulato rrnAC0442 psmA3 Proteasome, subunit alpha rrnAC0444 manB2 5.4.2.2;5.4.2.8 Phosphoglucomutase/Phosphomannomutase rrnAC0446 cdd 3.5.4.5 Cytidine deaminase rrnAC0448 udp2 2.4.2.3 Uridine phosphorylase rrnAC0450 yjlD1 NADH dehydrogenase rrnAC0452 galE 5.1.3.2 UDP-glucose 4-epimerase rrnAC0453 arg1 3.5.3.1 Arginase rrnAC0455 gyrA 5.99.1.3 DNA gyrase subunit A rrnAC0456 gyrB 5.99.1.3 DNA gyrase subunit B rrnAC0457 top6B 5.99.1.3 Type II DNA topoisomerase VI subunit B rrnAC0459 top6A 5.99.1.3 Type II DNA topoisomerase VI subunit A rrnAC0460 pknA2 Serine/threonine protien kinase related protei rrnAC0463 ligA 6.5.1.1 DNA ligase rrnAC0466 gspE4 Type II secretion system protein rrnAC0470 sir2 Transcriptional regulator, Sir2 family rrnAC0472 sucC 6.2.1.5 Succinyl-CoA synthetase beta chain rrnAC0474 sucD 6.2.1.5 Succinyl-CoA synthetase alpha chain rrnAC0475 signal transducing his kinase rrnAC0476 transcription regulator/DNA-binding protein rrnAC0477 membrane associated histidine kinase rrnAC0479 trp5 ABC transporter, ATP-binding protein rrnAC0482 yajO Putative NAD(P)H-dependent xylose reductase rrnAC0485 yqjF Hypothetical protein yqjF rrnAC0487 htlD Similar to ESCHERICHIA COLI protein kinase GP:GI-606149 (HTR-like protein rrnAC0488 araL1 Arabinose operon protein araL rrnAC0489 pip 3.2.-.- putative intracellular protease rrnAC0496 sirR Transcription represso rrnAC0500 zurM ABC transporter, permease protein rrnAC0501 zurA Zinc uptake system ATP-binding protein ZurA rrnAC0502 ycdH Adhesion protein rrnAC0503 transcription regulato rrnAC0504 copA4 Copper-transporting ATPase CopA rrnAC0506 phr2 cryptochrome/photolyase rrnAC0508 hcp2 Halocyanin precursor-like protein rrnAC0510 hcp9 Halocyanin precursor-like rrnAC0511 hpcEa 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase rrnAC0512 tyrA 1.3.1.12 Prephenate dehydrogenase rrnAC0514 surE 3.1.3.2 Acid phosphatase SurE rrnAC0517 alaS2 6.1.1.7 Alanyl-tRNA synthetase rrnAC0522 bcp-1 Peroxiredoxin rrnAC0524 Putative sec-independent transolcation pro rrnAC0525 Glucose-methanol-choline family oxidoreductas rrnAC0526 putative membrane-bound metal-dependent hydrolase rrnAC0528 cheC1 Chemotaxis protein CheC rrnAC0529 hisC2 2.6.1.9 Histidinol-phosphate aminotransferase rrnAC0532 pgsA 2.7.8.5 CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase rrnAC0534 tnp Transposase rrnAC0535 HTH DNA-binding protein rrnAC0536 hlx4 HoxA-like transcriptional regulato rrnAC0537 tpiA 5.3.1.1 Triosephosphate isomerase rrnAC0538 rrnAC0540 dinB 2.7.7.7 DNA polymerase IV rrnAC0542 2.1.1.- methyltransferase rrnAC0543 tyrS Tyrosyl-tRNA synthetase rrnAC0544 tnp Transposase rrnAC0545 pfk1 2.7.1.11 phosphofructokinase rrnAC0546 pykA 2.7.1.40 Pyruvate kinase rrnAC0547 glcK 2.7.1.2 Glucokinase rrnAC0548 cdc6j Cell division control protein 6 homolog 6 (CDC6 homolog 6 rrnAC0550 glpK 2.7.1.30 Glycerol kinase rrnAC0552 htr MCP domain signal transducer (soluble rrnAC0554 gpdA 1.1.99.5 Glycerol-3-phosphate dehydrogenase rrnAC0555 gpdB Glycerol-3-phosphate dehydrogenase chain B rrnAC0556 gpdC Glycerol-3-phosphate dehydrogenase chain C rrnAC0558 HAMP domain protein (signal transducer rrnAC0559 xop2 opsin of unknown function rrnAC0561 usp14 universal stress protein rrnAC0562 pepC 4.1.1.31 Phosphoenolpyruvate carboxylase rrnAC0566 livK-1 Branched chain amino acid ABC transporter, branched chain amino acid-binding prote rrnAC0567 livG-2 Branched-chain amino acid ABC transporter, ATP-binding protei rrnAC0568 livF-2 Branched-chain amino acid ABC transporter, ATP-binding protei rrnAC0569 livH-2 Branched-chain amino acid ABC transporter, permease protei rrnAC0570 livM-2 Branched-chain amino acid ABC transporter, permease protei rrnAC0572 catD 3.1.1.24 3-oxoadipate enol-lactone hydrolase rrnAC0573 fadD1 Long-chain fatty-acid-CoA ligase rrnAC0574 htlD Similar to ESCHERICHIA COLI protein kinase GP:GI-606149 (HTR-like protein rrnAC0575 dgoA4 Mandelate racemase/muconate lactonizing enzyme family rrnAC0578 Putative DNA binding rrnAC0581 tnp phage integrase/site-specific recombinase rrnAC0583 Ribbon-helix-helix protein, copG family rrnAC0584 phrH1 PhiH1 repressor homolog rrnAC0589 putative Phage integrase rrnAC0616 pecE 3.1.1.11 Pectinesterase rrnAC0617 rad25 DNA repair protein Rad25 rrnAC0626 msbA-1 ABC transporter, ATP-binding protein rrnAC0628 sun tRNA and rRNA cytosine-C5-methylases rrnAC0630 sppA 3.4.21.- Putative signal peptide peptidase SppA rrnAC0633 rffH2 2.7.7.24 Glucose-1-phosphate thymidylyltransferase rrnAC0634 nudB NTP pyrophosphohydrolase rrnAC0635 gloA2 Lactoylglutathione lyase and related lyase rrnAC0637 mcmA1 Methylmalonyl-CoA mutase, subunit alpha rrnAC0638 ppiB2 5.2.1.8 Peptidylprolyl isomerase rrnAC0639 Acetyltransferase (GNAT) family rrnAC0640 transcription regulato rrnAC0641 livF-3 Branched-chain amino acid ABC transporter, ATP-binding protei rrnAC0642 livG-3 Branched-chain amino acid ABC transporter, ATP-binding protei rrnAC0645 livM-3 Branched-chain amino acid ABC transporter, permease protei rrnAC0646 livH-3 Branched-chain amino acid ABC transporter, permease protei rrnAC0647 abcS-1 ABC transporter substrate-binding protein rrnAC0648 bdhA D-beta-hydroxybutyrate dehydrogenase rrnAC0650 acs1 6.2.1.1 Acyl-coenzyme A synthetases rrnAC0651 sugar transporter rrnAC0653 cysH 1.8.99.4;1.8.4.8 Phospho-Adenylyl-Sulfate Reductase rrnAC0656 ferA3 Ferredoxin rrnAC0657 1.14.13.2 P-Hydroxybenzoate Hydroxylase rrnAC0659 ama N-acyl-L-amino acid amidohydrolase rrnAC0660 rps10p Ribosomal protein S10p rrnAC0661 apa Diadenosine tetraphosphate pyrophosphohydrolas rrnAC0665 abcP-2 ABC transporter, permease protein rrnAC0666 ABC transporter, ATP-binding protein rrnAC0669 polX DNA polymerase IV (Family X) rrnAC0674 htlD Similar to ESCHERICHIA COLI protein kinase GP:GI-606149 (HTR-like protein rrnAC0676 nfi 3.1.21.7 Endonuclease V rrnAC0677 yusZ4 Short-chain dehydrogenase/oxidoreductase rrnAC0678 arsA2 Arsenical pump-driving ATPase rrnAC0680 Rad3a Helicase TATA-box binding protein E (TATA-box factor E) (TATA sequence-binding protein E) (TBP E) (Box A binding protein E rrnAC0681 tbpE (BAP E) rrnAC0684 mamA1 5.4.99.1 Methylaspartate mutase S chain rrnAC0685 mamB Methylaspartate mutase rrnAC0687 mal 4.3.1.2 Methylaspartate ammonia-lyase rrnAC0690 citE1 4.1.3.6 Citrate lyase beta chain rrnAC0691 aspC4 2.6.1.1 Aspartate aminotransferase rrnAC0693 cinA Competence/damage-inducible protein CinA rrnAC0695 putative membrane-bound metal-dependent hydrolase rrnAC0698 nusG Transcription antitermination protein NusG rrnAC0700 secE Protein translocase SecE rrnAC0701 htr18 MCP domain signal transducer (membrane) rrnAC0702 Leucine/Isoleucine/Valine-Binding Protein rrnAC0703 ftsZ1 Cell division protein FtsZ rrnAC0706 nce1 Na+/Ca2+-exchanging protein rrnAC0707 aroE 1.1.1.25 Shikimate 5-dehydrogenase rrnAC0709 trpE1 4.1.3.27 Anthranilate synthase component I rrnAC0710 trpD2 4.1.3.27 Anthranilate synthase, component II rrnAC0711 ilvE2 Branched-chain amino acid aminotransferase rrnAC0713 Rieske [2Fe-2S] domain containing oxidoreductase rrnAC0716 usp6 Universal stress protein rrnAC0717 1.18.1.3 FAD/NAD binding oxidoreductase rrnAC0718 porA 1.2.7.3;1.2.7.1 Pyruvate ferredoxin oxidoreductase, subunit alph rrnAC0719 porB 1.2.7.3;1.2.7.1 Pyruvate ferredoxin oxidoreductase, subunit bet rrnAC0720 ubiE3 ubiE/COQ5 methyltransferase familiy protein rrnAC0721 phr1 Photolyase/cryptochrome rrnAC0722 mop Molybdenum-pterin binding protein rrnAC0723 putative membrane-bound metal-dependent hydrolase rrnAC0727 EC:2.7.1.23 ATP-NAD kinase rrnAC0731 Cytochrome b(C-terminal)/b6 rrnAC0732 petB1 Cytochrome b6 rrnAC0733 Rieske [2Fe-2S] domain protein rrnAC0735 hcp8 Halocyanin precursor-like rrnAC0738 usp29 Universal stress protein rrnAC0739 nthA 4.2.99.18 Endonuclease III rrnAC0740 hat1 Acetyltransferase rrnAC0741 hat2 Probable acetyltransferase rrnAC0742 top2 Topoisomerase DNA binding C4 zinc finger rrnAC0743 putative PRC-barrel domain rrnAC0745 yyaI Acetyltransferase, GNAT family rrnAC0748 guaB3 1.1.1.205 Inosine-5'-monophosphate dehydrogenase rrnAC0751 icfA1 Carbonic anhydrase rrnAC0753 aroK 2.7.1.71 Shikimate kinase rrnAC0754 trkA1 Trk potassium uptake system protein rrnAC0755 trkH3 TRK potassium uptake system protein rrnAC0757 trkH2 Potassium uptake protein TrkH rrnAC0758 usp17 universal stress protein rrnAC0759 cat Cationic amino acid transporte rrnAC0764 csg3 Cell surface protein rrnAC0766 putative cell surface protein rrnAC0768 DNA binding, putative transcriptional regulato rrnAC0770 acdB 1.3.99.- Acyl-coA dehydrogenase rrnAC0771 paaH 1.1.1.35 3-hydroxybutyryl-CoA dehydrogenase rrnAC0772 fbp2 3.1.3.11 Fructose-1,6-bisphosphatase rrnAC0775 gdhA2 1.4.1.3 NAD(P)-specific Glutamate dehydrogenase rrnAC0779 acdE 1.3.99.- Acyl-CoA dehydrogenase rrnAC0780 acdF 1.3.99.- Acyl-CoA dehydrogenase rrnAC0781 usp30 universal stress protein rrnAC0784 doxD1 terminal quinol oxidase rrnAC0788 pssA CDP-diacylglycerol-serine O phosphatidyltransferas rrnAC0789 putative PAS/PAC sensing his kinase rrnAC0790 est Carboxylesterase rrnAC0792 cdc48b Cell division control protein 48 rrnAC0794 htlD Similar to ESCHERICHIA COLI protein kinase GP:GI-606149 (HTR-like protein rrnAC0796 hat4 Putative acetyltransferase rrnAC0797 purF 2.4.2.14 Amidophosphoribosyl transferase rrnAC0798 snp snRNP homolog rrnAC0799 cdlM Endoglucanase rrnAC0806 putative C2H2 Zinc finger DNA-binding protein rrnAC0807 cdc48c Cell division control protein 48 rrnAC0810 nitA Nitrilase rrnAC0814 nosY Membrane protein NosY precurso rrnAC0815 tnp Probable transposase rrnAC0816 tnp Transposase rrnAC0819 2-domain regulatory protein rrnAC0821 2.7.1.23 ATP-NAD kinase rrnAC0822 mogA Molybdenumm Cofactor Biosynthesis Protein rrnAC0824 livH-4 Branched-chain amino acid ABC transporter, permease protei rrnAC0825 livM High-affinity branched-chain amino acid transport (High-affinity branched-chain amino acid transport prote rrnAC0827 livG-4 Branched-chain amino acid ABC transporter, ATP-binding protei rrnAC0829 livF-4 Branched-chain amino acid ABC transporter, ATP-binding protei rrnAC0831 sodA 1.15.1.1 Superoxide dismutase [Mn] 2 rrnAC0832 phrB1 4.1.99.3 Deoxyribodipyrimidine photolyase rrnAC0833 ech2 4.2.1.17 Enoyl-CoA hydratase rrnAC0836 csg2 Surface glycoprotein precursor rrnAC0837 menF 5.4.99.6 Menaquinone-specific isochorismate synthase rrnAC0838 menD 2-succinyl-6-hydroxy-2, 4-cyclohexadiene-1-carboxylate synthas rrnAC0839 dnaJ Chaperone protein DnaJ rrnAC0841 ech1 4.2.1.17 Enoyl-CoA hydratase rrnAC0842 cinR Transcription repressor CinR rrnAC0843 menE 6.2.1.26 O-succinylbenzoic acid--CoA ligase rrnAC0844 ykfB1 Chloromuconate cycloisomerase rrnAC0845 menA 1,4-dihydroxy-2-naphthoate octaprenyltransferas rrnAC0847 alkK3 Medium-chain acyl-CoA ligase rrnAC0848 htlD Similar to ESCHERICHIA COLI protein kinase GP:GI-606149 (HTR-like protein rrnAC0854 pebP Phosphatidylethanolamine-binding protein rrnAC0855 galE4 5.1.3.2 UDP-glucose 4-epimerase rrnAC0858 3.1.6.8 Arylsulfatase rrnAC0859 folA1 1.5.1.3 Dihydrofolate reductase rrnAC0861 tfeA Transcription initiation factor IIE alpha subun rrnAC0864 nop56/58 Archaeal nucleolar protein homolog rrnAC0865 fib Fibrillarin-like pre-rRNA processing protein rrnAC0866 gcs2 6.3.2.2 gamma-glutamylcysteine synthetase rrnAC0867 transcription regulato rrnAC0868 coaD2 2.7.7.3 Phosphopantetheine adenylyltransferase rrnAC0869 putative Transcription factor TFIIB repeat rrnAC0872 putative DNA binding domain rrnAC0874 acdA 1.3.99.- Acyl-CoA dehydrogenase rrnAC0875 putative haloacid dehalogenase-like hydrolase rrnAC0878 panB 2.1.2.11 3-methyl-2-oxobutanoate hydroxymethyltransferase rrnAC0879 coxB3 Cytochrome c oxidase subunit I rrnAC0880 coxA4 1.9.3.1 Cytochrome C oxidase subunit I rrnAC0882 coxC Cytochrome c oxidase subunit II rrnAC0883 bioB 2.8.1.6 Biotin synthase rrnAC0884 gdhA3 1.4.1.2 NAD-specific Glutamate Dehydrogenase rrnAC0885 bioF 2.3.1.47 8-amino-7-oxononanoate synthase rrnAC0887 cbiA1 Cobyrinic acid a,c-diamide synthase rrnAC0888 scs 6.2.1.5 Succinyl-Coa Synthetase rrnAC0890 frt ferritin rrnAC0894 cpdB2 3.1.4.16 2',3'-cyclic-nucleotide 2'-phosphodiesterase rrnAC0896 acaB3 2.3.1.9 3-ketoacyl-CoA thiolase rrnAC0903 accA Acetyl-CoA carboxylase alpha subun rrnAC0904 fabG1 1.1.1.100 3-oxoacyl-[acyl-carrier protein] reductase rrnAC0906 ibp Iron-binding protein rrnAC0907 sfuB Iron ABC transporter, permease protein rrnAC0908 potA4 Spermidine/putrescine ABC transporter, ATP-binding protei rrnAC0912 gtr-3 Glycosyltransferase rrnAC0913 rrnAC0914 TrmB1 Sugar-specific transcriptional regulator TrmB rrnAC0917 sorD 1.1.1.140 sorbitol dehydrogenase rrnAC0918 gfo4 oxidoreductase rrnAC0920 msmX-2 Sugar ABC transporter, ATP-binding protein rrnAC0921 malFG-4 Putative sugar ABC transporter permease protein rrnAC0922 malFG-5 Putative ABC transporter permease protein rrnAC0923 rbsB-2 Sugar ABC transporter, substrate binding protein rrnAC0925 yajO2 Oxidoreductase, aldo/keto reductase family rrnAC0927 pyrE2 2.4.2.10 Orotate phosphoribosyltransferase rrnAC0929 acaB4 2.3.1.16 3-ketoacyl-CoA thiolase rrnAC0933 argK ArgK protein rrnAC0934 mcmA3 Putative methylmalonyl-CoA mutase rrnAC0935 gtr-8 Putative glycosyltransferase rrnAC0937 ybaN 3.5.1.- Polysaccharide deacetylase rrnAC0939 dpm6 Dolichyl-phosphate-mannose-protein mannosyltransferase rrnAC0940 2.4.1.- Glycosyl transferase rrnAC0942 htr MCP domain signal transducer (membrane rrnAC0944 Putative sugar transporte rrnAC0951 glycosyl transferase rrnAC0952 moxR1 Methanol dehydrogenase regulatory protei rrnAC0954 hel DNA helicase rrnAC0958 icfA2 Carbonic anhydrase rrnAC0959 yprA3 ATP-dependent DNA helicase rrnAC0960 dapA2 4.2.1.52 Dihydrodipicolinate synthase rrnAC0962 pcm3 2.1.1.77 Protein-L-Isoaspartate O-Methyltransferase rrnAC0964 (kinA) Signal-transducing histidine kinase homolo rrnAC0965 pelA Cell division protein pelota rrnAC0967 hypE Hydrogenase expression/formation protein rrnAC0970 aor3 Flavin-containing amine-oxidoreductas rrnAC0971 csg4 Cell surface glycoprotein (S-layer protein) related protei rrnAC0972 tnp Putative ISH4 transposase (VNG0918H rrnAC0976 htr8 MCP domain signal transducer (membrane rrnAC0979 putative nuclease rrnAC0982 ssuE1 1.5.1.29 NADPH-dependent FMN reductase rrnAC0984 mamA2 5.4.99.1 Methylaspartate mutase S chain rrnAC0986 nce2 Na+/Ca2+-exchanging protein rrnAC0987 mutY 3.2.2.1 A/G-specific adenine glycosylase rrnAC0988 htlD Similar to ESCHERICHIA COLI protein kinase GP:GI-606149 (HTR-like protein rrnAC0990 mgtC1 Magnesium transporter accessory protein rrnAC0991 htlD Similar to ESCHERICHIA COLI protein kinase GP:GI-606149 (HTR-like protein rrnAC0992 DNA binding domain, similar to hmvng1864 rrnAC0995 mutT6 Mut/nudix family protein rrnAC0996 folD1 1.5.1.5;3.5.4.9 Methylenetetrahydrofolate dehydrogenase rrnAC0999 glyA 2.1.2.1 Serine hydroxymethyltransferase rrnAC1004 suhB1 3.1.3.25 Inositol-1-monophosphatase rrnAC1010 rfbB1 4.2.1.46 dTDP-glucose 4-6-dehydratase rrnAC1011 rffG 4.2.1.46 dTDP-glucose dehydratase rrnAC1015 gtr-7 2.4.1.- Glycosyltransferase rrnAC1017 lpg2 LPS glycosyltransferase rrnAC1018 2.4.1.- glycosyltransferase rrnAC1019 dpm1 Dolichyl-phosphate beta-D-mannosyltransferas rrnAC1020 dpm2 Dolichyl-P-glucose synthetase rrnAC1022 rrnAC1025 moxR6 Methanol dehydrogenase regulatory protei rrnAC1028 lolC putative permease rrnAC1029 ABC transporter, ATP-binding protein rrnAC1030 nps putative sodium/phosphate symporte rrnAC1039 yafB-2 Oxidoreductase, aldo/keto reductase family rrnAC1042 msbA-2 ABC transporter, ATP-binding protein rrnAC1043 lgtD Glycosyl transferase rrnAC1044 3.5.1.- putative Acetamidase/Formamidase rrnAC1047 putative membrane-bound metal-dependent hydrolase rrnAC1049 transcription regulato rrnAC1053 cdc6i Cell division control protein 6 homolog 6 (CDC6 homolog 6 rrnAC1054 tnp Putative transposase (VNG6486H) (VNG6040H rrnAC1057 stbB Plasmid stability protein StbB rrnAC1061 trwB1 Transfer complex protein rrnAC1067 prk1 Protein kinase rrnAC1068 prkA Kinase anchor protein rrnAC1070 spoVR Stage V sporulation protein R homolog rrnAC1072 cyp2 Cytochrome P450 rrnAC1074 fadD3 Long-chain fatty-acid-CoA ligase rrnAC1076 capB Mur ligase family CapB protein rrnAC1081 rffH1 Glucose-1-phosphate thymidylyltransferase rrnAC1083 hbd1 1.1.1.35;4.2.1. 3-hydroxyacyl-CoA dehydrogenase rrnAC1084 acdG 1.3.99.- Acyl-CoA dehydrogenase rrnAC1085 tnp Transposase rrnAC1087 cysE2 2.3.1.30 Serine acetyltransferase rrnAC1088 alkA DNA-3-methyladenine glycosylase rrnAC1091 sdhC Succinate dehydrogenase subunit C rrnAC1093 sdhB 1.3.99.1 Succinate dehydrogenase iron-sulfur protein subuni rrnAC1096 kinA4 Signal-transducing histidine kinase homolo rrnAC1097 sdhA1 1.3.99.1 Succinate dehydrogenase flavoprotein subuni rrnAC1102 cbiA2 Cobyrinic acid a, c-diamide synthase rrnAC1107 trkH1 Potassium uptake protein, TrkH family rrnAC1109 purD2 6.3.4.13 Phosphoribosylamine-glycine ligase rrnAC1111 Highly conserved protein containing a thioredoxin domain rrnAC1113 bglX-2 Beta-D-glucosidase rrnAC1114 htlD Similar to ESCHERICHIA COLI protein kinase GP:GI-606149 (HTR-like protein rrnAC1118 hlx1 HoxA-like transcriptional regulato rrnAC1121 thyX 2.1.1.- Thymidylate synthase ThyX rrnAC1124 eif2B2 Probable translation initiation factor 2 beta subunit (eIF-2-beta rrnAC1126 tfbH Transcription initiation factor IIB (TFIIB rrnAC1129 trxB3 1.6.4.5 Thioredoxin reductase rrnAC1131 ribG 1.1.1.- 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine 1-reductas rrnAC1133 rpaA Replication Protein A rrnAC1137 yhcR1 Phosphoesterase rrnAC1138 fbp1 3.1.3.11 Fructose-b1,6-isphosphatase rrnAC1139 yprA4 ATP-dependent helicase rrnAC1144 mutS3 DNA mismatch repair protein rrnAC1145 blp Bacterio-opsin linked produc rrnAC1149 ctpB Cation transporting ATPase rrnAC1152 hcp5 Halocyanin precursor-like rrnAC1153 coxB2 1.9.3.1 Cytochrome c oxidase subunit II rrnAC1154 coxA3 1.9.3.1 Cytochrome c oxidase polypeptide I rrnAC1157 putative DNA-binding protein with a phosphopeptide binding mot rrnAC1158 Protein phosphatase 2C like phosphatase rrnAC1159 pknA1 2.7.1.37 Serine/threonine-protein kinase pknA rrnAC1160 von Willebrand factor type A like metal binding protein rrnAC1163 estA Phospholipase/carboxylesterase rrnAC1166 ogg 3.2.2.- 8-oxoguanine DNA glycosylase rrnAC1167 acyP 3.6.1.7 Acylphosphatase rrnAC1169 hflX GTP-binding protein HflX rrnAC1171 katG2 1.11.1.6 Peroxidase/catalase HPI rrnAC1174 psmA4 3.4.25.1 Proteasome alpha subunit rrnAC1175 rpp14 RNaseP_Subunit14 rrnAC1177 rnp30 ribonuclease P, subunit p30 rrnAC1180 mutT1 3.6.1.- Mut/nudix family protein rrnAC1182 thiC Thiamine biosynthesis protein ThiC rrnAC1184 cysT1 Sulfate transport system permease protein rrnAC1186 moaE Molybdenum cofactor biosynthesis protein rrnAC1187 moaC Molybdenum cofactor biosynthesis protein C rrnAC1188 moaB1 Molybdenum cofactor biosynthesis protein B rrnAC1191 metal-dependent phosphohydrolase rrnAC1193 boa Bacterio-opsin activator-like protein rrnAC1195 petA Putative Rieske iron-sulfur protein rrnAC1196 petB2 Cytochrome B6 rrnAC1199 narG 1.7.99.4 Nitrate reductase, alpha chain rrnAC1200 narH 1.7.99.4 Nitrate reductase, beta chain rrnAC1204 narJ Chaperone protein rrnAC1205 putative ABC-type phosphate transport system, permease componen rrnAC1206 prp protein phosphatase rrnAC1208 mrp2 Mrp protein rrnAC1210 rbnBN1 Ribonuclease BN-like rrnAC1213 moz Molybdopterin oxidoreductase rrnAC1214 hmoA Molybdopterin oxidoreductase rrnAC1215 dmsA Dimethylsulfoxide reductase rrnAC1217 transcription regulato rrnAC1222 moxR4 Methanol dehydrogenase regulatory protei rrnAC1224 pyrI 2.1.3.2 Aspartate carbamoyltransferase regulatory chain rrnAC1225 pyrB 2.1.3.2 Aspartate carbamoyltransferase rrnAC1227 minD2 Cell division inhibitor MinD homolog rrnAC1230 slyD 5.2.1.8 Peptidyl-prolyl cis-trans isomerase rrnAC1231 ilvA1 4.2.1.16 Threonine dehydratase rrnAC1232 cytH 4.6.1.1 Adenylate cyclase rrnAC1233 metK 2.5.1.6 S-adenosylmethionine synthetase rrnAC1234 thiI Probable thiamine biosynthesis protein Th rrnAC1236 cysK1 4.2.99.8 Cysteine synthase rrnAC1238 nikR Putative nickel responsive regulato rrnAC1241 eif1A2 Translation initiation factor 1A (aIF-1A rrnAC1250 gspE2 Type II secretion system protein rrnAC1251 aspB1 2.6.1.1 Aspartate aminotransferase rrnAC1252 lrp Leucine responsive regulatory protein rrnAC1257 Caffeoyl-CoA O-methyltransferase rrnAC1258 cheC2 Chemotaxis protein CheC rrnAC1259 alkK2 Medium-chain-fatty-acid--CoA ligase rrnAC1261 acdD 1.3.99.- Acyl-coA dehydrogenase rrnAC1262 cdc6h Cell division control protein 6 homolog 2 (CDC6 homolog 2 rrnAC1267 korA 1.2.7.3;1.2.7.1 2-oxoglutarate ferredoxin oxidoreductase, subunit alph rrnAC1268 korB 1.2.7.3;1.2.7.1 Putative 2-ketoglutarate ferredoxin oxidoreductase (Beta rrnAC1269 asnC2 Transcription regulator, AsnC family rrnAC1274 guaB2 1.1.1.205 Inosine Monophosphate Dehydrogenase/GMP reductas rrnAC1275 mcmA2 Methylmalonyl-CoA mutase, subunit alpha rrnAC1278 coxA1 1.9.3.1 Cytochrome c oxidase polypeptide I rrnAC1283 purA 6.3.4.4 Adenylosuccinate synthetase rrnAC1287 htpX5 3.4.24.- Probable protease HtpX homolog 2 rrnAC1289 chelatase rrnAC1292 cysS 6.1.1.16 Cysteinyl-tRNA synthetase rrnAC1296 corA Magnesium Mg(2+)/cobalt Co(2+) transport protein rrnAC1298 moeA2 Molybdopterin biosynthesis protein moeA rrnAC1299 moeA3 Molybdopterin biosynthesis protein moeA rrnAC1300 adh9 1.1.1.1 Alcohol dehydrogenase rrnAC1301 yjlD2 NADH dehydrogenase rrnAC1302 thuA Trehalose utilization-related protein rrnAC1303 transcription regulato rrnAC1307 Putative transcriptional regulato rrnAC1308 Glutaredoxin rrnAC1310 epf2a mRNA 3'-end processing factor homolog rrnAC1311 recJ1 RecJ Exonuclease rrnAC1312 cysT3 Sulfate transporter family, permease rrnAC1314 moaA Molybdenum cofactor biosynthesis protein A rrnAC1317 mobA Molybdopterin-guanine dinucleotide biosynthesis protein rrnAC1318 aor2 Aldehyde ferredoxin oxidoreductase rrnAC1330 torD Cytoplasmic chaperone TorD rrnAC1331 fixX Putative ferridoxin protein rrnAC1332 fdhF Formate dehydrogenase alpha subuni rrnAC1333 fdoH Formate dehydrogenase-O, iron-sulfur subun rrnAC1338 arcR-6 Transcription regulato rrnAC1339 Fumarylacetoacetate (FAA) hydrolase family protein rrnAC1346 kinA1 Signal-transducing histidine kinase homolo rrnAC1347 putative Mechanosensitive ion channe rrnAC1349 Rnp RNAse P Rpr2/Rpp21 subunit rrnAC1350 gtr-4 Putative sugar transferase rrnAC1351 putative sugar transporte rrnAC1352 gtr-5 Glycosyltransferase rrnAC1354 htpX6 3.4.24.- Probable protease HtpX homolog 2 rrnAC1355 gatA1 6.3.5.- Glutamyl-tRNA(Gln) amidotransferase subunit A rrnAC1356 gatC 6.3.5.- Glutamyl-tRNA(Gln) amidotransferase subunit C rrnAC1357 tfbB Transcription initiation factor IIB (TFIIB rrnAC1358 mutT5 Mut/nudix family protein rrnAC1359 asnB 6.3.5.4 Asparagine synthetase rrnAC1363 nirJ Heme biosynthesis protein rrnAC1367 ccdA Cytochrome c-type biogenesis protein CcdA rrnAC1368 trp-6 ABC transporter, ATP-binding protein rrnAC1369 ccmB Cytochrome C-type biogenesis protein, heme exporter protein B rrnAC1370 ccmF Cytochrome c-type biogenesis protein CcmF rrnAC1371 trxA7 Thioredoxin rrnAC1372 ccpA Cytochrome c551 peroxidase rrnAC1373 ccmC Heme exporter protein C rrnAC1375 soxA2 Putative sulfite oxidase rrnAC1376 ccmE Cytochrome c-type biogenesis protein CcmE rrnAC1377 hcp6 Halocyanin precursor like rrnAC1378 pan1a Membrane protein Pan1 rrnAC1384 gluTR 1.2.1.- Glutamyl-tRNAGlu reductase rrnAC1390 purL 6.3.5.3 Phosphoribosylformylglycinamidine synthase I rrnAC1391 Similar to ESCHERICHIA COLI protein kinase GP:GI-606149 (HTR-like protein rrnAC1394 hisF 4.1.3.- Imidazole glycerol phosphate synthase subunit hisF rrnAC1396 rpoL 2.7.7.6 DNA-directed RNA polymerase subunit L rrnAC1397 Putative DNA binding rrnAC1399 cyoC 1.9.3.1 Cytochrome c oxidase polypeptide III rrnAC1402 adh4 1.1.1.1 Alcohol dehydrogenase rrnAC1404 usp28 universal stress protein rrnAC1405 predicted methyltransferase rrnAC1406 dph5 2.1.1.98 Diphthine synthase rrnAC1407 cyo Cytochrome oxidase subunit I homolog rrnAC1409 gloA1 4.4.1.5 Lactoylglutathione lyase rrnAC1411 drg GTP-binding protein Drg rrnAC1414 rpl11P 50S ribosomal protein L11P rrnAC1415 rpl1P 50S ribosomal protein L1P rrnAC1417 rpl10E 50S ribosomal protein L10E rrnAC1418 rpL12P 50S ribosomal protein L12P ('A' type) rrnAC1426 rps15P 30S ribosomal protein S15P rrnAC1427 recJ2 putative Exonuclease Recj rrnAC1429 rps3AE 30S ribosomal protein S3Ae rrnAC1430 fbr2 Cytochrome-like protein rrnAC1431 purK 4.1.1.21 Phosphoribosylaminoimidazole carboxylase ATP binding subun rrnAC1432 dpm5 2.4.1.-;2.4.1.10Dolichyl-phosphate-mannose-protein mannosyltransferase rrnAC1433 ribE 2.5.1.9 6,7-dimethyl-8-ribityllumazine synthase rrnAC1434 aspC3 2.6.1.1 Aspartate aminotransferase rrnAC1435 atpC2 3.6.3.14 ATP synthase subunit C rrnAC1438 taqD Glycerol-3-phosphate cytidyltransferase rrnAC1441 recJ3 putative exonuclease, recJ like rrnAC1442 pld Phospholipase D rrnAC1444 xup Xanthine/uracil permease family protein rrnAC1446 purE 4.1.1.21 Phosphoribosylaminoimidazole carboxylase, catalytic subun rrnAC1447 nolB 1.6.5.- NAD(P)H-quinone oxidoreductase chain 3 rrnAC1448 nuoB NADH dehydrogenase I, B subuni rrnAC1449 ndHG5 NADH dehydrogenase/oxidoreductase rrnAC1450 ndhG4 NADH dehydrogenase/oxidoreductase rrnAC1451 nolD NADH dehydrogenase/oxidoreductase-like protein rrnAC1452 ndhG6 1.6.5.- NAD(P)H-quinone oxidoreductase chain 6 rrnAC1454 nolC NADH dehydrogenase/oxidoreductase-like protein rrnAC1455 nuoL2 NADH dehydrogenase I, L subuni rrnAC1456 ndhD NADH dehydrogenase subunit 4 rrnAC1458 ndhG3 NADH dehydrogenase/oxidoreductase rrnAC1459 Metallo-beta-lactamase superfamily protein rrnAC1468 tnp Phage integrase rrnAC1470 trxB2 1.8.1.9 Thioredoxin Reductase rrnAC1471 doxD5 terminal quinol oxidase subun rrnAC1472 acrR transcription regulator, acrR family rrnAC1477 fdfT 2.5.1.21 Farnesyl-diphosphate farnesyltransferase rrnAC1478 sacB 2.4.1.10 Levansucrase rrnAC1479 scrB Sucrose-6-phosphate hydrolase rrnAC1482 fapE2 Flagella-related protein E rrnAC1483 parA4 Chromosome partitioning protein parA rrnAC1484 cheW2 Chemotaxis signal transduction protein CheW rrnAC1485 yjlD4 1.6.99.3 NADH dehydrogenase rrnAC1486 (kinA) Signal-transducing histidine kinase homolo rrnAC1489 dmd 4.1.1.33 Diphosphomevalonate decarboxylase rrnAC1490 cadT Cobalamin adenosyltransferase rrnAC1491 msrA2 1.8.4.6 Peptide methionine sulfoxide reductase msrA 1 rrnAC1494 htlD Similar to Escherichia coli protein kinase GP:GI-606149 (Htr-like protein rrnAC1495 oye3 putative light- and oxygen-sensing transcription regulato rrnAC1497 nifS 4.4.1.16 Selenocysteine lyase rrnAC1498 gcvP1 1.4.4.2 Glycine dehydrogenase subunit 1 rrnAC1499 gcvH Probable glycine cleavage system H protein rrnAC1500 gcvT2 2.1.2.10 Probable aminomethyltransferase rrnAC1501 pas-pac-pac sensing his kinase rrnAC1504 tatD 3.5.1.-; 3.5.2.5 TatD related DNase rrnAC1505 pstB1 Phosphate ABC transporter, ATP-binding protein rrnAC1507 pstA2 Phosphate ABC transporter, permease protein rrnAC1508 pstC1 Phosphate ABC transporter, permease protein rrnAC1509 phoX Phosphate ABC transporter phosphate-binding protei rrnAC1510 prp3 Phosphate regulatory protein homolog rrnAC1511 rps8E 30S ribosomal protein S8e rrnAC1515 pyrF 4.1.1.23 Orotidine 5'-phosphate decarboxylase rrnAC1517 trpG1 4.1.3.27 Anthranilate synthase, component II rrnAC1518 trpE2 4.1.3.27 Anthranilate synthase component I rrnAC1519 trpF 5.3.1.24 N-(5'-phosphoribosyl)anthranilate isomerase rrnAC1520 trpD3 2.4.2.18 Anthranilate phosphoribosyltransferase rrnAC1526 yfmJ2 1.6.5.5 Quinone oxidoreductase rrnAC1527 cdc48d Cell division control protein 48 rrnAC1532 radB DNA repair and recombination protein RadB rrnAC1533 phoU2 Phosphate transport system regulatory protein PhoU rrnAC1536 trkA2 Potassium uptake protein TrkA rrnAC1541 putative DNA binding domain rrnAC1544 spoVT/abrB transcription regulato rrnAC1546 tnp Transposase rrnAC1559 tnp Transposase rrnAC1560 tnp Putative transposase (VNG6486H) (VNG6040H rrnAC1565 tnp transposase rrnAC1568 cdc6g Cell division control protein 6 rrnAC1569 cdc6f Cell division control protein 6 homolog 2 (CDC6 homolog 2 rrnAC1570 trp-7 ABC transporter, ATP-binding protein rrnAC1571 wcaH 3.6.1.- GDP-mannose mannosyl hydrolase rrnAC1572 rfbB2 4.2.1.46 DTDP-glucose-4,6-dehydratase rrnAC1573 galE8 UDP-glucose 4-epimerase rrnAC1577 tnp Putative transposase rrnAC1580 tnp Putative transposase (VNG6486H) (VNG6040H rrnAC1583 icsA LPS glycosyltransferase rrnAC1584 lpb2 LPS biosynthesis protein rrnAC1585 graD4a Glucose-1-phosphate thymidylyltransferase rrnAC1587 glmS1 2.6.1.16 Glucosamine--fructose-6-phosphate aminotransferase [isomerizing rrnAC1589 secY Protein translocase subunit SecY rrnAC1590 rpl15P 50S ribosomal protein L15P rrnAC1591 rpl30P 50S ribosomal protein L30P rrnAC1592 rps5P 30S ribosomal protein S5P rrnAC1593 rpl18P 50S ribosomal protein L18P (HSal18) rrnAC1594 rpl19E 50S ribosomal protein L19e rrnAC1595 rpl32E 50S ribosomal protein L32E rrnAC1596 rpl6P 50S ribosomal protein L6P rrnAC1597 rps8P 30S ribosomal protein S8P rrnAC1598 rpl5P 50S ribosomal protein L5P (HSal5) rrnAC1600 rps4E 30S ribosomal protein S4e rrnAC1601 rpl24P 50S ribosomal protein L24P rrnAC1602 rpl14P 50S ribosomal protein L14P rrnAC1603 rps17P Ribosomal protein S17p rrnAC1604 rpl29P 50S ribosomal protein L29P rrnAC1605 rps3P 30S ribosomal protein S3P (HS4) (HHAS3) rrnAC1606 rpl22P 50S ribosomal protein L22P rrnAC1607 rps19P 30S ribosomal protein S19P rrnAC1608 rpl2P 50S ribosomal protein L2P rrnAC1609 rpl23P 50S ribosomal protein L23P rrnAC1610 rpl4 50S ribosomal protein L4 rrnAC1611 rpl3 50S Ribosomal protein L3 rrnAC1612 nucleic acid methylase rrnAC1616 mch 3.5.4.27 N(5),N(10)-methenyltetrahydromethanopterin cyclohydrolase rrnAC1619 gbp2 GTP-binding protein homolog rrnAC1620 haloacid dehalogenase-like hydrolase rrnAC1622 nrdA 1.17.4.1 Ribonucleoside-diphosphate reductase alpha chain rrnAC1624 soxA3 Probable sulfite oxidase rrnAC1626 htlD Similar to ESCHERICHIA COLI protein kinase GP:GI-606149 (HTR-like protein rrnAC1630 hlx6 HoxA-like transcriptional regulato rrnAC1639 smc2 Chromosome segregation protein rrnAC1642 gatB 6.3.5.- Glutamyl-tRNA(Gln) amidotransferase subunit B rrnAC1645 topA 5.99.1.2 DNA topoisomerase I rrnAC1650 pcrB PcrB protein rrnAC1651 yhdG Amino acid transporter rrnAC1652 trkA5 Trk potassium uptake system protein rrnAC1653 asnC3 Transcription regulator, Asn family rrnAC1655 nosF-2 ABC transporter, ATP-binding protein rrnAC1656 Nitrite/nitrate reduction protein rrnAC1657 aspS 6.1.1.12 Aspartyl-tRNA synthetase rrnAC1659 hop Halorhodopsin precursor (HR rrnAC1660 yafB-3 Oxidoreductase, aldo/keto reductase family rrnAC1663 boa Bacterio-opsin activator-like protein rrnAC1668 rpoP 2.7.7.6 DNA-directed RNA polymerase subunit P rrnAC1669 rpl37AE 50S ribosomal protein L37ae rrnAC1676 tnp Transposase and inactivated derivatives rrnAC1680 pfdB Prefoldin beta subunit (GimC beta subunit rrnAC1687 boa Bacterio-opsin activator-like protein rrnAC1690 leuA1 2.3.3.13 2-isopropylmalate synthase 2 rrnAC1693 membrane bound his kinase A rrnAC1694 guaA2 6.3.5.2 GMP synthase [glutamine-hydrolyzing] rrnAC1698 moxR2 Methanol dehydrogenase regulatory protei rrnAC1700 3.1.6.- sulfatase rrnAC1701 hat6 Putative Acetyltransferase (GNAT) rrnAC1703 Hsp20 rrnAC1705 moeA1 Molybdenum cofactor biosynthesis protein rrnAC1706 pgp 3-phosphoglycerate kinase rrnAC1707 cad 4.2.1.96 Pterin-4-alpha-carbinolamine dehydratase rrnAC1708 hemA 2.3.1.37 Glutamyl-tRNA reductase rrnAC1709 hemX Uroporphyrin-III C-methyltransferase rrnAC1711 NirH Heme biosynthesis protein NirH rrnAC1714 cspD5 Cold shock protein rrnAC1715 cspD1 Cold shock protein rrnAC1716 uppS 2.5.1.31 Undecaprenyl pyrophosphate synthetase rrnAC1719 rimI Pab N-terminal acetyltransferase rrnAC1720 dnaG dnaG rrnAC1722 csaA Protein secretion chaperonin CsaA rrnAC1726 panF Pantothenate permease rrnAC1729 valS 6.1.1.9 Valyl-tRNA synthetase rrnAC1732 SOR/SNZ family rrnAC1740 mvaS 4.1.3.5 Hydroxymethylglutaryl-CoA synthase rrnAC1744 rfcB Replication factor C large subuni rrnAC1745 yckA-2 Amino acid ABC transporter, permease protein rrnAC1747 glnQ1 Glutamine ABC transporter (ATP-binding protein rrnAC1749 glnH2 Glutamine ABC transporter, permease protein rrnAC1750 argT Amino acid ABC transporter, amino acid-binding protein rrnAC1751 ccp Cytochrome aa3 controlling protein rrnAC1752 htr15 MCP domain signal transducer (soluble rrnAC1754 maeB 1.1.1.40 NAD-dependent malate dehydrogenase rrnAC1757 gptA Purine phosphoribosyltransferase rrnAC1760 transporter, possibly hexose rrnAC1761 atoE Short chain fatty acids transporte rrnAC1762 serA2 1.1.1.95 D-3-phosphoglycerate dehydrogenase rrnAC1764 HTH DNA-binding protein rrnAC1765 tenA Transcriptional activator tenA rrnAC1767 tenA-2 Transcriptional regulator, putative rrnAC1769 putP-2 Sodium-solute symporter, putative rrnAC1772 psmA1 Proteasome, subunit alpha rrnAC1773 psmA2 3.4.25.1 Proteasome alpha subunit rrnAC1776 dcd2 3.5.4.13 Deoxycytidine triphosphate deaminase rrnAC1777 DNA binding protein rrnAC1779 aknG Alkanonic acid methyltransferase rrnAC1782 thi1 Putative thiazole biosynthetic enzyme rrnAC1786 HTH DNA-binding protein rrnAC1787 hutU 4.2.1.49 Urocanate hydratase rrnAC1789 hutG 3.5.3.8 Probable formimidoylglutamase rrnAC1790 hutI 3.5.2.7 Imidazolonepropionase rrnAC1791 hutH 4.3.1.3 Histidine ammonia-lyase rrnAC1792 ruvB Holliday junction DNA helicase rrnAC1794 dapF 5.1.1.7 Diaminopimelate epimerase rrnAC1795 ppsA 2.7.9.2 Phosphoenolpyruvate synthase rrnAC1797 htlC Htr-like protein rrnAC1798 gadD Glutamate decarboxylase rrnAC1800 metS 6.1.1.10 Methionyl-tRNA synthetase rrnAC1805 gntR transcription regulato rrnAC1806 htlD Similar to ESCHERICHIA COLI protein kinase GP:GI-606149 (HTR-like protein rrnAC1812 pnm N-methyltransferase homolog rrnAC1813 2.4.1.- glycosyl transferase rrnAC1815 cctA3 Thermosome alpha subunit (Thermosome subunit 1) (Chaperonin alpha subun rrnAC1818 Putative hydrolase rrnAC1821 lysE L-lysine exporter rrnAC1824 Acetyltransferase (GNAT) family rrnAC1825 idr Iron-dependent represso rrnAC1830 yurF ABC transporter, ATP-binding protein rrnAC1831 polB1 2.7.7.7 DNA polymerase B, elongation subuni rrnAC1836 tnp Phage integrase/site-specific recombinase rrnAC1840 smc1 structural maintenance of chromosomes rrnAC1841 yhcR2 Phosphoesterase rrnAC1848 virB11 Type IV secretion system protein rrnAC1856 putative RNA binding protein rrnAC1858 Aldo/keto reductase rrnAC1860 sugar transporter rrnAC1863 mutT4 Mut/nudix family protein rrnAC1865 soxB Sarcosine oxidase rrnAC1867 putative hsp20 rrnAC1869 trp1 ABC transporter, ATP-binding protein rrnAC1870 nhaC3 Na+/H+ antiporter rrnAC1872 radical HhH rrnAC1873 dpg Dolichol-P-glucose synthetase rrnAC1875 tfbD Transcription initiation factor IIB (TFIIB rrnAC1876 zim CTAG modification methylase rrnAC1877 aroD 4.2.1.10 3-dehydroquinate dehydratase rrnAC1879 aroB 4.6.1.3 3-dehydroquinate synthase rrnAC1880 minD6 Septum site-determining protein minD (Cell division inhibitor minD rrnAC1881 deoC2 Deoxyribose-phosphate aldolase rrnAC1884 trpA 4.2.1.20 Tryptophan synthase alpha chain rrnAC1885 trpB 4.2.1.20 Tryptophan synthase beta chain rrnAC1886 trpC 4.1.1.48 Indole-3-glycerol phosphate synthase rrnAC1887 hat5 Putative Acetyltransferase (GNAT) rrnAC1888 gbp5 GTP-binding protein rrnAC1892 DSBA-like thioredoxin domain rrnAC1893 ldc LD-carboxypeptidase rrnAC1895 Putative DNA binding rrnAC1901 brp Bacteriorhodopsin related protein rrnAC1902 crtI1 1.3.99.- Phytoene dehydrogenase rrnAC1903 apt2 2.4.2.7 Adenine phosphoribosyltransferase rrnAC1905 dsbB1 Disulfide bond formation protein rrnAC1906 tas Probable oxidoreductase rrnAC1907 putative sugar transporte rrnAC1908 nthD 4.2.99.18 Endonuclease III rrnAC1910 fbr1 Cytochrome-like protein Fbr rrnAC1913 nadM 2.7.7.1 Nicotinamide-nucleotide adenylyltransferase rrnAC1914 lon 3.4.21.53 ATP-dependent protease LA rrnAC1915 putative protease rrnAC1916 6-O-methylguanine DNA methyltransferase, DNA binding domain rrnAC1917 glpQ2 3.1.4.46 Glycerophosphoryl diester phosphodiesteras rrnAC1918 dhs 2.5.1.46 Probable deoxyhypusine synthase 1 rrnAC1920 azlC Branched-chain amino acid transport protein AzlC rrnAC1923 nif3 NIF3 (NGG1p interacting factor 3) rrnAC1925 mhpC 3.7.1.- 2-hydroxy-6-ketonona-2,4-dienedioic acid hydrolase rrnAC1926 trzA2 N-ethylammeline chlorohydrolase rrnAC1927 speB1 3.5.3.11 Agmatinase rrnAC1929 eif5A Translation initiation factor 5A (eIF-5A) (Hypusine-containing protei rrnAC1930 putative CobD/Cbib protein rrnAC1931 cobS Cobalamin-5-phosphate synthase rrnAC1932 ispD 2.7.7.60 4-diphosphocytidyl-2C-methyl-D-erythritol synthas rrnAC1934 hisC1 2.6.1.9 Histidinol-phosphate aminotransferase rrnAC1936 cobI 2.5.1.17 Cobalamin adenosyltransferase rrnAC1938 cobQ Cobyric acid synthase rrnAC1939 minD1 Cell division inhibito rrnAC1943 phrB2 4.1.99.3 Deoxyribodipyrimidine photolyase rrnAC1951 gspE1 Type II secretion system protein rrnAC1953 DNA binding protein rrnAC1954 yusZ1 Oxidoreductase rrnAC1955 glpA Glycerol-3-phosphate dehydrogenase subunit A (EC1.1.99.5 rrnAC1956 eif2BD2 Translation initiation factor eIF-2B subunit delt rrnAC1957 malQ 2.4.1.25 4-alpha-glucanotransferase rrnAC1958 lpg1 LPS glycosyltransferase rrnAC1960 graD4b Glucose-1-phosphate thymidylyltransferase rrnAC1961 cga-1 Glucoamylase rrnAC1962 malA Putative alpha-D-1,4-glucosidase rrnAC1964 arcR6 Transcription regulato rrnAC1965 aceB malate synthase rrnAC1966 gloA3 4.4.1.5 Lactoylglutathione lyase rrnAC1967 glcD1 Glycolate oxidase subunit GlcD rrnAC1971 arcR5 Transcription regulato rrnAC1972 gcdH 1.3.99.7 Glutaryl-CoA dehydrogenase rrnAC1973 aldY4 1.2.1.3 Aldehyde dehydrogenase rrnAC1974 aacC 2.3.1.81 Aminoglycoside N3'-acetyltransferase rrnAC1975 adh5 1.1.1.1 Alcohol dehydrogenase rrnAC1977 alkK4 Medium-chain fatty acid--CoA ligase rrnAC1979 ech5 4.2.1.17 Enoyl-CoA hydratase/isomerase rrnAC1980 aph aminoglycoside phosphotransferase rrnAC1982 hbd2 1.1.1.35;4.2.1. 3-hydroxybutyryl-CoA dehydrogenase rrnAC1983 acdI 1.3.99.3 Acyl-CoA dehydrogenase rrnAC1984 fabG4 1.1.1.100 3-oxoacyl-[acyl-carrier protein] reductase rrnAC1985 maoC1 Monoamine oxidase regulatory protein rrnAC1986 acdC 1.3.99.- Acyl-CoA dehydrogenase rrnAC1987 anf ABC transporter substrate-binding protein rrnAC1989 livH-5 Branched-chain amino acid ABC transporter, permease protei rrnAC1991 livM-4 Branched-chain amino acid ABC transporter, permease protei rrnAC1992 livG-5 Branched-chain amino acid ABC transporter, ATP-binding protei rrnAC1993 livF-5 Branched-chain amino acid ABC transporter, ATP-binding protei rrnAC1996 putative DNA binding domain rrnAC1997 rbnBN2 Ribonuclease BN rrnAC1999 spaT Aminotransferase, class V rrnAC2000 usp9 Universal stress protein family rrnAC2004 ftsZ3 Cell division protein FtsZ rrnAC2014 methyltransferase rrnAC2015 xthA 3.1.21.2 Probable endonuclease IV rrnAC2017 transcription regulato rrnAC2018 katG1 1.11.1.6 Peroxidase/catalase rrnAC2019 lpl 6.3.4.- Lipoate protein ligase rrnAC2022 transcription regulato rrnAC2023 nuoC NADH dehydrogenase I chain C, D rrnAC2024 msrA1 1.8.4.6 Peptide methionine sulfoxide reductase MsrA rrnAC2027 cdc48a Cell division cycle protein 48 rrnAC2030 xop1 Bacteriorhodopsin precursor (BR rrnAC2032 thioesterase of unknown specificity rrnAC2034 htlA Htr-like protein rrnAC2036 pkn Serine/threonine protein kinase rrnAC2037 troR Iron-dependent represso rrnAC2038 nifU2 NifU-like domain protein rrnAC2039 oppA Oligopeptide ABC transporter, solute-binding protei rrnAC2040 oppB Oligopeptide ABC transporter, permease protein rrnAC2041 oppC2 Oligopeptide transport system permease protein OppC rrnAC2042 oppD1 Oligopeptide ABC transporter, ATPase componen rrnAC2043 oppF Oligopeptide ABC transporter, ATP-binding protein rrnAC2044 htlD Similar to ESCHERICHIA COLI protein kinase GP:GI-606149 (HTR-like protein rrnAC2047 sppA 3.4.21.- Protease IV homolog rrnAC2048 mocA oxidoreductase rrnAC2051 tfbF Transcription initiation factor IIB (TFIIB rrnAC2052 transcription regulato rrnAC2056 serA3 1.1.1.95 D-3-phosphoglycerate dehydrogenase rrnAC2057 moaD Molybdopterin converting factor, subunit rrnAC2064 aor1 Aldehyde ferredoxin oxidoreductase rrnAC2065 rpl15E 50S ribosomal protein L15e rrnAC2066 blh Brp-like homolog rrnAC2067 crtY Lycopene cyclase rrnAC2069 crtB 2.5.1.32;2.5.1.2Phytoene synthase rrnAC2070 boa putative light- and oxygen-sensing transcription regulato rrnAC2072 vacB 3.1.-.- Ribonuclease R rrnAC2073 trp2 ABC transporter, ATP-binding protein rrnAC2075 nusA1 transcription anti-termination facto rrnAC2083 yadH ABC transporter, permease protein rrnAC2084 nosF-3 ABC transporter, ATP-binding protein rrnAC2087 putative PUA domain RNA-binding protein rrnAC2090 moeB Molybdopterin biosynthesis protein MoeB rrnAC2091 htr MCP domain signal transducer (soluble rrnAC2092 cxp Probable carboxypeptidase rrnAC2094 Amidase-related protein rrnAC2095 argE 3.5.1.16 Acetylornithine deacetylase rrnAC2096 uvsE 3.-.-.- UV DNA damage endonuclease rrnAC2100 entB1 3.3.2.1 Isochorismatase rrnAC2103 rli RNase L inhibitor rrnAC2108 npdG-1 1.6.8.- F420-dependent NADP reductase rrnAC2109 htlD Htr-like protein rrnAC2110 trxA3 Thioredoxin rrnAC2111 sec61beta component of the Sec61/SecYEG protein secretory system rrnAC2116 uvrA Excinuclease ABC, subunit A rrnAC2121 Pentapeptide repeats of unknown function rrnAC2126 bchP Geranylgeranyl hydrogenase rrnAC2128 sseA1 2.8.1.1 Thiosulfate sulfurtransferase rrnAC2129 sseA2 Thiosulfate sulfurtransferase rrnAC2133 epf1 mRNA 3'-end processing factor rrnAC2137 tcmJ Tetracenomycin polyketide synthesis protei rrnAC2139 imd3 1.1.1.205 Inosine Monophosphate Dehydrogenase rrnAC2140 sdr2 Oxidoreductase, short-chain dehydrogenase/reductase fami rrnAC2141 trxA8 thioredoxin rrnAC2143 thiE 2.5.1.3 Thiamine-phosphate pyrophosphorylase rrnAC2144 transcrption regulator rrnAC2145 phoU1 Phosphate transport system regulatory protein PhoU rrnAC2146 pstB2 Phosphate ABC transporter, ATP-binding protein rrnAC2147 pstA1 Phosphate ABC transporter, permease protein rrnAC2148 pstC2 Phosphate ABC transporter, permease protein rrnAC2149 yqgG Phosphate ABC transporter binding rrnAC2150 prp1 Phosphate regulatory protein homolog rrnAC2152 putative Rhodanese rrnAC2153 mutT2 Mut/nudix family protein rrnAC2157 rimI Pab N-terminal acetyltransferase rrnAC2158 acnB 4.2.1.3 Aconitate hydratase rrnAC2159 dcd3 3.6.1.23 Probable deoxyuridine 5'-triphosphate nucleotidohydrolase rrnAC2160 Putative DNA binding rrnAC2162 mgsA 4.2.3.3 Methylglyoxal synthase rrnAC2163 exsB Succinoglycan biosynthesis ExsB protei rrnAC2166 ptpS 4.2.3.12 6-pyruvoyl tetrahydropterin synthase rrnAC2170 pepB4 Aminopeptidase rrnAC2172 adh14 1.1.1.1 Alcohol dehydrogenase rrnAC2174 fdx Ferredoxin rrnAC2175 seb Selenium-binding protein rrnAC2176 galE9 UDP-glucose 4-epimerase rrnAC2178 rfbB3 4.2.1.46 Dtdp-Glucose 4,6-Dehydratase rrnAC2179 fer2 2Fe-2S iron-sulfur cluster binding domain rrnAC2180 gnd 1.1.1.44 6-phosphogluconate dehydrogenase rrnAC2181 pepB2 Aminopeptidase rrnAC2183 fapJ Flagella accessory protein J rrnAC2184 gspE3 Type II secretion system protein rrnAC2186 flpH Flagella-related protein H rrnAC2187 flaG Putative flagella-related protein G rrnAC2190 flaF Archaeal flagellar protein F rrnAC2191 fapE1 Flagella-related protein E rrnAC2192 cheD Chemotaxis protein CheD rrnAC2193 cheA1 CheA histidine kinase (Chemotaxis protein rrnAC2194 cheY Chemotaxis protein CheY rrnAC2198 flaB Flagellin B precursor rrnAC2202 kaiC1 Circadian regulator rrnAC2203 cheW1 Chemotaxis protein CheW rrnAC2204 cheB 3.1.1.61 Protein-glutamate methylesterase rrnAC2205 cheA3 2.7.3.- Chemotaxis protein cheA rrnAC2206 cheR 2.1.1.80 Chemotaxis protein methyltransferase CheR rrnAC2207 cpcE2 Phycocyanin alpha phycocyanobilin lyase-lik rrnAC2211 htlD Similar to ESCHERICHIA COLI protein kinase GP:GI-606149 (HTR-like protein rrnAC2212 rps6E 30S ribosomal protein S6e rrnAC2215 dcd1 Deoxycytidine triphosphate deaminase rrnAC2217 recJ4 RecJ-like exonuclease (DHH/DHHA1 family protein rrnAC2219 phoR PhoR protein homolog rrnAC2220 usp5 Universal stress protein rrnAC2222 Acetyltransferase (GNAT) family rrnAC2223 usp2 Universal stress protein family rrnAC2227 dppF Dipeptide ABC transporter ATP-binding rrnAC2228 dppD Dipeptide ABC transporter ATP-binding rrnAC2229 dppB1 Dipeptide ABC transporter permease rrnAC2230 oppC1 Oligopeptide transport system permease protein OppC rrnAC2232 pyrC 3.5.2.3 Dihydroorotase rrnAC2236 entB2 Isochorismatase rrnAC2241 2.4.2.19 Quinolinate phosphoribosyl transferase rrnAC2244 putative ZIP domain Zinc transporte rrnAC2245 M50 family metallopeptidase rrnAC2247 eif2BA Translation initiation factor eIF-2B alpha subun rrnAC2248 csd2 4.4.1.- Probable cysteine desulfurase rrnAC2252 crcB1 integral membrane protein possibly involved in chromosome condensatio rrnAC2253 crcB2 Integral membrane protein possibly involved in chromosome condensatio rrnAC2256 pcm2 2.1.1.77 Protein-L-isoaspartate O-methyltransferase 2 rrnAC2258 pcm1 2.1.1.77 Protein-L-isoaspartate O-methyltransferase 1 rrnAC2261 pepB1 Aminopeptidase rrnAC2262 gapB 1.2.1.59 Glyceraldehyde 3-phosphate dehydrogenase rrnAC2267 uvrD Repair helicase rrnAC2270 gvpE Transcriptional regulator PadR-like family rrnAC2272 norB Cytochrome B subunit of nitric oxide reductase rrnAC2277 dox Dioxgenase rrnAC2278 coaD1 2.7.7.3 Phosphopantetheine adenylyltransferase rrnAC2280 cbiQ1 Cobalt transport protein rrnAC2282 cbiM Cobalamin biosynthesis protein CbiM rrnAC2283 copG1 Transcriptional regulator, CopG family rrnAC2284 tnp Phage integrase/site-specific recombinase rrnAC2285 phrH2 PhiH1 repressor homolog rrnAC2298 cca 2.7.7.25 tRNA nucleotidyltransferase rrnAC2299 aup Acetoin utilization protein rrnAC2301 hpyA Archaeal histone A1 rrnAC2302 rpa Replication A related protein rrnAC2310 coxB4 1.9.3.1 Cytochrome C oxidase subunit II, membrane domai rrnAC2311 coxA2 1.9.3.1 Cytochrome c oxidase, subunit I rrnAC2314 trp3 ABC transport protein rrnAC2318 mcm1 MCM / cell division control protein 21 rrnAC2321 boa Bacterio-opsin activator-like protein rrnAC2325 repC replication factor C rrnAC2329 tnp phage integrase rrnAC2333 hspC Small heat shock protein rrnAC2334 glcD2 Putative oxidoreductase rrnAC2337 2.7.3.- Histidine Kinase rrnAC2338 cspD4 Cold shock protein rrnAC2339 cspD3 Cold shock protein rrnAC2343 rfbA Glucose-1-phosphate thymidylyltransferase rrnAC2346 malG Maltose ABC transporter, permease protein rrnAC2347 malFG-6 ABC-type sugar transport systems, permease components rrnAC2349 malE1 Maltose ABC transporter, maltose-binding protein rrnAC2350 amy 3.2.1.- Alpha amylase rrnAC2352 ugpC1 Sugar ABC transporter, ATP-binding protein (UGPC rrnAC2353 cga-2 3.2.1.3 Glucan 1,4-alpha-glucosidase (Glucoamylase) rrnAC2354 transcription regulato rrnAC2356 gst1 Glutathione S-transferase rrnAC2357 rpl10E 50S ribosomal protein L10e rrnAC2359 usp16 Universal stress protein rrnAC2360 rimK Ribosomal protein S6 modification protein rrnAC2361 hsp20b Putative heat shock protein rrnAC2363 gapA 1.2.1.12 Glyceraldehyde 3-phosphate dehydrogenase rrnAC2364 pgk 2.7.2.3 Phosphoglycerate kinase rrnAC2367 ribC 2.5.1.9 Ribiflavin synthase alpha chain rrnAC2369 hisH1 Imidazoleglycerol-phosphate synthase rrnAC2371 hisI1 3.6.1.31 Phosphoribosyl-ATP pyrophosphatase rrnAC2372 htlD Similar to ESCHERICHIA COLI protein kinase GP:GI-606149 (HTR-like protein rrnAC2374 gbp4 GTP-binding protein rrnAC2378 engB Probable GTP-binding protein EngB rrnAC2380 putative Serine/threonine phosphatase rrnAC2382 tnp phage integrase rrnAC2383 phrH3 PhiH1 repressor homolog rrnAC2385 cdc6e Orc / cell division control protein 6 rrnAC2394 tnp Putative ISH8 transposase rrnAC2405 rps10P 30S ribosomal protein S10P rrnAC2406 eef1a Elongation factor 1-alpha (EF-1-alpha) (Elongation factor Tu) (EF-Tu rrnAC2408 hom 1.1.1.3 Homoserine dehydrogenase rrnAC2412 putative peptidase rrnAC2413 fusA Elongation factor G (EF-G) rrnAC2414 metB 4.2.99.9;2.5.1.4Cystathionine gamma-synthase rrnAC2416 putative light and redox sensing histidine kinas rrnAC2417 cbiQ2 Cobalt transport protein rrnAC2418 cbiO Cobalt transport ATP-binding protein rrnAC2420 bioY dethiobiotin synthesis rrnAC2423 rps7P 30S ribosomal protein S7P rrnAC2424 rps12P 30S ribosomal protein S12P (HmaS12) rrnAC2425 htr18 MCP domain signal transducer (membrane rrnAC2426 nusA2 Transcription termination factor NusA rrnAC2427 rpoC 2.7.7.6 RNA polymerase Rpb1, domain 5 rrnAC2428 rpoA DNA-directed RNA polymerase subunit A rrnAC2429 rpoB 2.7.7.6 DNA-directed RNA polymerase, beta subunit rrnAC2430 rpoB DNA-directed RNA polymerase, subunit B rrnAC2432 rpoH 2.7.7.6 DNA-directed RNA polymerase subunit H rrnAC2435 Putative phosphoesterase rrnAC2437 mer1 F420-dependent N5,N10-methylene-tetrahydromethanopterin reductas rrnAC2439 tnaA 4.1.99.1 Tryptophanase rrnAC2440 scm 24-sterol C-methyltransferase rrnAC2442 moxR3 Methanol dehydrogenase regulatory protei rrnAC2443 rrnAC2445 sui1 Protein translation factor SUI1 homolog rrnAC2446 putative glycyl aminopeptidase rrnAC2449 thiD 2.7.4.7 Phosphomethylpyrimidine kinase rrnAC2450 trxA9 thioredoxin rrnAC2451 serA5 1.1.1.95 Phosphoglycerate dehydrogenase rrnAC2455 usp10 putative Universal stress protein rrnAC2458 trxA1 Thioredoxin rrnAC2459 maa 2.3.1.79 Maltose O-acetyltransferase rrnAC2461 ark2 Adaptive-response sensory-kinase rrnAC2463 scp2 Sterol Carrier Protein rrnAC2464 livF-6 Branched-chain amino acid ABC transporter, ATP-binding protei rrnAC2465 livG-6 Branched-chain amino acid ABC transporter, ATP-binding protei rrnAC2466 livM-5 Branched-chain amino acid ABC transporter, permease protei rrnAC2468 livH-6 Branched chain amino acid transporter, permease protei rrnAC2470 prr 5.1.1.4 Proline racemase rrnAC2471 yusM Proline dehydrogenase rrnAC2472 boa-8 Similar to Halobacterium Bat (Bacterio-opsin activatior-like protein rrnAC2473 aldY2 1.2.1.3 Aldehyde dehydrogenase rrnAC2474 eif1A1 Translation initiation factor 1A (aIF-1A rrnAC2476 prk2 protein kinase rrnAC2477 htlD Similar to ESCHERICHIA COLI protein kinase GP:GI-606149 (HTR-like protein rrnAC2480 act Acyl-CoA thioester hydrolase rrnAC2484 ech3 4.2.1.17 Enoyl-CoA hydratase rrnAC2486 nadE1 6.3.5.1 NH(3)-dependent NAD(+) synthetase rrnAC2487 rfcC2 Replication factor C small subuni rrnAC2488 rps24E 30S ribosomal protein S24e rrnAC2489 rps27AE 30S ribosomal protein S27ae rrnAC2490 gcp 3.4.24.57 O-sialoglycoprotein endopeptidase rrnAC2493 ham1 Ham1 protein rrnAC2494 yqjQ Oxidoreductase, short chain dehydrogenase/reductase famil rrnAC2495 htr14 MCP domain signal transducer (membrane rrnAC2498 trkA6 TRK potassium uptake system protein rrnAC2500 Metallo-beta-Lactamase like rrnAC2501 gfo5 oxidoreductase rrnAC2502 phzC/phzF Phenazine biosynthesis-like protein rrnAC2503 araC Transcriptional regulator, AraC family rrnAC2504 lgl 4.4.1.5 Putative lactoyglutathione lyase rrnAC2505 putative polysaccharide biosynthesis protei rrnAC2508 ilvA2 4.2.1.16 Threonine dehydratase rrnAC2510 trk trk active potasium channe rrnAC2511 citZ 2.3.3.1 Citrate synthase II rrnAC2512 pchB potassium channel-related protein rrnAC2515 thrC4 4.2.99.2 Threonine synthase rrnAC2519 putative DNA binding protein rrnAC2520 gstN Glutathione S-transferase, N-terminal domain rrnAC2521 pyrE1 2.4.2.10 Orotate phosphoribosyltransferase rrnAC2522 manB3 5.4.2.2;5.4.2.8 Phosphoglucomutase/Phosphomannomutase rrnAC2524 hisI2 3.5.4.19 Phosphoribosyl-AMP cyclohydrolase rrnAC2526 fer1 Ferredoxin rrnAC2527 ylnA Anion permease rrnAC2529 hisA 5.3.1.16 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomeras rrnAC2530 Putative methytransferase rrnAC2532 mutS4 DNA mismatch repair protein MutS rrnAC2533 ark1 Adaptive-response sensory-kinase rrnAC2535 trp-11 ABC transporter, ATP-binding protein rrnAC2550 mutL DNA mismatch repair protein mutL rrnAC2551 kdgK 2.7.1.45 2-keto-3-deoxygluconate kinase rrnAC2552 gcvT4 2.1.2.10 Aminomethyltransferase rrnAC2553 2Fe-2S iron-sulfur cluster binding domain rrnAC2555 hisB 4.2.1.19 Imidazoleglycerol-phosphate dehydratase rrnAC2557 pca 3-oxoadipate enol-lactone hydrolase/4-carboxymuconolactone decarboxylas rrnAC2558 nhaC6 Na+/H+ antiporter rrnAC2561 alaS1 6.1.1.7 Alanyl-tRNA synthetase rrnAC2565 rfcC1 Replication factor C small subuni rrnAC2566 Acetyltransferase (GNAT) family rrnAC2568 pmm 5.4.2.2;5.4.2.8 Phosphoglucomutase/phospho-mannomutase rrnAC2569 putative nuclease rrnAC2570 purE-2 NCAIR mutase (PurE)-related protein rrnAC2572 rpiA 5.3.1.6 Ribose 5-phosphate isomerase A rrnAC2574 manB1 5.4.2.2;5.4.2.8 Phosphoglucomutase/Phosphomannomutase rrnAC2577 upp 2.4.2.9 Uracil phosphoribosyltransferase rrnAC2580 imp Immunogenic protein rrnAC2586 phosphate transporter family protein rrnAC2590 cstA Carbon starvation protein CstA rrnAC2592 arsA3 3.6.3.16 arsenical pump-driving ATPase rrnAC2593 cobW/P47K_1 Cobalamin synthesis protein/P47K rrnAC2599 gst2 Glutathione S-transferase rrnAC2601 prxS AhpC/TSA family peroxiredoxins (Prxs rrnAC2602 yrdC DNA binding protein rrnAC2605 hdrD Heterodisulfide reductase rrnAC2606 mthK2 Potassium channel protein, putative rrnAC2608 dip3 Competence-damage protein CinA-like rrnAC2610 hemB 4.2.1.24 Delta-aminolevulinic acid dehydratase rrnAC2616 ark3 Adaptive-response sensory-kinase rrnAC2618 htr MCP domain signal transducer (soluble rrnAC2619 amt Ammonium transporter rrnAC2621 glnB Nitrogen regulatory protein P-I rrnAC2622 asnC4 Transcription regulator, AsnC family rrnAC2623 cheA2 CHEA histidine kinase (Chemotaxis protein rrnAC2624 ABC transporter, substrate-binding protein rrnAC2625 nirA1 Ferredoxin-nitrite reductase rrnAC2626 putative transporter rrnAC2627 narB 1.7.99.4 Nitrate reductase rrnAC2628 hemL 5.4.3.8 Glutamate-1-semialdehyde 2,1-aminomutase rrnAC2630 prsA 2.7.6.1 Ribose-phosphate pyrophosphokinase rrnAC2631 aldY1 1.2.1.3 Aldehyde dehydrogenase rrnAC2632 Sodium symporter transmembrane region rrnAC2633 htr MCP domain signal transducer (soluble rrnAC2634 ileS 6.1.1.5 Isoleucyl-tRNA synthetase rrnAC2636 udg1 3.2.2.- uracil DNA glycosylase superfamily protein rrnAC2638 hit2 Histidine triad protein rrnAC2639 minD5 Cell Division Inhibitor rrnAC2645 comA Competence-like protein rrnAC2648 nthB 4.2.99.18 Endonuclease III rrnAC2650 leuS1 6.1.1.4 Leucyl-tRNA synthetase rrnAC2651 rbsC Ribose ABC transporter permease rrnAC2653 rbsC-4 Sugar ABC transporter, permease protein rrnAC2654 rbsA-2 Sugar ABC transporter ATP binding protein rrnAC2655 rbsA Sugar ABC transporter, ATP binding protein rrnAC2656 yufN ABC transporter (Lipoprotein) rrnAC2657 phoT2 Sodium-dependent phosphate transporte rrnAC2658 usp20 Universal Stress Protein rrnAC2661 rad24 DNA repair protein rrnAC2662 fer Ferredoxin rrnAC2663 lysC 2.7.2.4 Aspartokinase rrnAC2667 thrC3 Threonine synthase rrnAC2669 Putative DNA binding rrnAC2670 ort 2.4.2.10 Orotate Phosphoribosyltransferase rrnAC2671 inb Oxidoreductase homolog rrnAC2672 arcB 2.1.3.3 Ornithine carbamoyltransferase rrnAC2674 gltCP 3.4.17.11 Glutamate Carboxypeptidase rrnAC2675 argD 2.6.1.11 Acetylornithine aminotransferase rrnAC2676 argB2 2.7.2.8 Acetylglutamate kinase rrnAC2678 argC 1.2.1.38 N-acetyl-gamma-glutamyl-phosphate reductase rrnAC2679 rimK Ribosomal protein S6 modification protein rrnAC2681 argH 4.3.2.1 Argininosuccinate lyase rrnAC2683 argG 6.3.4.5 Argininosuccinate synthase rrnAC2691 polA2 2.7.7.7 DNA polymerase II large subunit rrnAC2692 oxygen and light sensing his kinas rrnAC2696 serA1 1.1.1.95 D-3-phosphoglycerate dehydrogenase rrnAC2699 1.1.1.205 putative inosine monophosphate dehydrogenas rrnAC2701 glyS 6.1.1.14 Glycyl-tRNA synthetase rrnAC2704 eif4A ATP-dependent RNA helicase homolog eIF-4A rrnAC2706 mdh 1.1.1.37 L-malate dehydrogenase rrnAC2710 gbp3 GTP-binding protein homolog rrnAC2711 cdc6d Cell division control protein 6 homolog rrnAC2712 sec11a Signal sequence peptidase rrnAC2713 sec11b Signal sequence peptidase rrnAC2714 polA1 2.7.7.7 DNA polymerase II small subunit rrnAC2716 cysD 4.2.99.10 O-acetylhomoserine (thiol)-lyase rrnAC2717 serB1 3.1.3.3 Phosphoserine phosphatase rrnAC2719 rad3b Helicase rrnAC2721 cat cation efflux protein rrnAC2722 yhcR3 phosphoesterase rrnAC2723 Putative Bacterial regulatory protein, arsR family rrnAC2726 pepB3 Aminopeptidase rrnAC2728 htr putative HAMP and MCP domain signal transduce rrnAC2737 glbN Cyanoglobin rrnAC2740 TRAM domain protein rrnAC2741 ywfD2 1.1.1.47 glucose dehydrogenase rrnAC2742 manC Mannose-1-phosphate guanylyltransferas rrnAC2748 Ribbon-helix-helix protein, copG family rrnAC2749 putative helicase rrnAC2753 prt 2.4.2.- phosphoribosyltransferase rrnAC2756 rad24a rad24a plus uvrB domain rrnAC2759 nso Transporter, sodium/sulfate symporter family rrnAC2760 htr6 MCP domain signal transducer (membrane rrnAC2761 tmpC Membrane lipoprotein tmpC precursor (Membrane protein C) (35 kDa antigen) (Lipoprotein TpN35 rrnAC2762 mcm2 Cell division control protein 21 rrnAC2768 minD4 cell division inhibito rrnAC2769 tfbI Transcription initiation factor IIB (TFIIB rrnAC2773 ssuE2 1.5.1.29 NADPH-dependent FMN reductase rrnAC2776 matE2 Multi Antimicrobial Extrusion (MATE) drug/sodium antiporters rrnAC2777 DNA binding protein, putative transcriptional regulato rrnAC2779 asnC1 Transcription regulator, AsnC family rrnAC2780 glnA 6.3.1.2 Glutamine synthetase rrnAC2781 pap2a 3.1.3.9 Glucose-6-phosphatase rrnAC2782 rbn Ribonuclease BN rrnAC2783 dip2 DNA damage-inducible protein rrnAC2785 transcription regulato rrnAC2788 trm1 2.1.1.32 N(2),N(2)-dimethylguanosine tRNA methyltransferase rrnAC2789 htl_ Similar to ESCHERICHIA COLI protein kinase GP:GI-606149 (HTR-like protein rrnAC2793 yusZ3 Oxidoreductase rrnAC2794 hisH2 2.4.2.- Imidazole glycerol phosphate synthase subunit HisH rrnAC2796 udg3 3.2.2.- uracil DNA glycosylase superfamily protein rrnAC2797 ern3 Endoribonuclease L-PSP rrnAC2800 fprA Flavoprotein (Hydroxyacylglutathione hydrolase-like protein rrnAC2802 rpl40E 50S ribosomal protein L40E rrnAC2805 hyrA2 Monooxygenase rrnAC2808 serS 6.1.1.11 Seryl-tRNA synthetase rrnAC2809 usp21 Universal stress protein rrnAC2811 mthK Potassium Channel Related Protein rrnAC2814 mutT3 MutT/nudix family protein rrnAC2815 aca2 2.3.1.9 Acetyl-coA acetyltransferase rrnAC2818 ftsH 3.4.24.- Cell division protein FtsH rrnAC2820 phnP ATP-binding protein PhnP rrnAC2827 eif2G Translation initiation factor eIF-2 subunit gamm rrnAC2829 rpoE' DNA-directed RNA polymerase subunit E rrnAC2830 rpoE" DNA-directed RNA polymerase subunit E' rrnAC2834 Putative RNA methylase rrnAC2835 hisG 2.4.2.17 ATP phosphoribosyltransferase rrnAC2836 dld sugar (and other) transporte rrnAC2837 trzA3 N-ethylammeline chlorohydrolase rrnAC2840 ahcY 3.3.1.1 Adenosylhomocysteinase rrnAC2844 pri2 Eukaryotic-type DNA primase, large subuni rrnAC2847 hjr Holliday junction resolvase rrnAC2850 pcbD-1 Hydrolase, alpha/beta hydrolase fold family rrnAC2851 pcnA DNA polymerase sliding clamp (Proliferating cell nuclear antigen homolog) (PCNA rrnAC2853 nirK nitrite reductase, copper containing rrnAC2854 ftsJ 2.1.1.- Ribosomal RNA large subunit methyltransferase J rrnAC2857 tatC1 Sec-independent protein translocase protein TatC rrnAC2858 tatC2 Sec-independent protein translocase TatC rrnAC2859 gpmB 5.4.2.4; 5.4.2.1Phosphoglycerate mutase rrnAC2860 trmU 2.1.1.61 tRNA methyl transferase rrnAC2861 mutS2 Mismatch repair protein rrnAC2862 cdc6c Cell division control protein 6 rrnAC2867 dip1 DNA damage-inducible protein rrnAC2868 potD2 Spermidine/putrescine ABC transporter, spermidine/putrescine binding prote rrnAC2870 potA2 Spermidine/putrescine ABC transporter, ATP-binding protei rrnAC2872 potB2 Spermidine/putrescine ABC transporter, permease protein rrnAC2873 potC2 Spermidine/putrescine ABC transporter permease rrnAC2874 phaJ1 4.2.1.- (R)-specific enoyl -CoA hydratase rrnAC2876 rad24-2 3.6.1.- Putative ski2-type helicase rrnAC2880 yqjM2 NADH-dependent flavin oxidoreductase rrnAC2882 maoC1 MaoC family protein rrnAC2886 phaC POLY(3-hydroxyalkanoate) synthase rrnAC2891 cctA2 Thermosome alpha subunit (Thermosome subunit 1) (Chaperonin alpha subun rrnAC2897 galE2 5.1.3.2 UDP-glucose 4-epimerase rrnAC2900 cspD2 Cold shock protein rrnAC2901 uvrB putative uvrB rrnAC2902 putative methyltransferase rrnAC2903 nmd3 putative nonsense mediated mRNA decay protein rrnAC2904 galE6 UDP-glucose 4-epimerase rrnAC2906 htpX1 3.4.24.- Probable protease htpX homolog rrnAC2910 radA DNA repair and recombination protein RadA rrnAC2912 gsp General stress protein 69 rrnAC2914 yvaI Acetyltransferase homolog rrnAC2924 guaA3 6.3.5.2 GMP synthase (glutamine-hydrolyzing) rrnAC2927 yafB-4 Oxidoreductase rrnAC2929 gfo1 Glucose-fructose oxidoreductase rrnAC2936 boa Bacterio-opsin activator-like protein rrnAC2937 mutS1 DNA mismatch repair protein MutS rrnAC2939 cctB Thermosome beta subunit (Thermosome subunit 2) (Chaperonin beta subun rrnAC2941 ocd2 4.3.1.12 Ornithine cyclodeaminase rrnAC2945 signal-transducing histidine kinas rrnAC2947 leuS2 6.1.1.4 Leucyl-tRNA synthetase rrnAC2948 bcp3 Bacterioferritin comigratory protein rrnAC2949 hsp20a Small heat shock protein rrnAC2950 pheA 4.2.1.51 Prephenate dehydratase rrnAC2951 yccK 1.- Oxidoreductase rrnAC2953 lpdA2 1.8.1.4 Dihydrolipoamide dehydrogenase rrnAC2955 pdhC2 2.3.1.12 Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase comple rrnAC2956 pdhB1 1.2.4.1 Pyruvate Dehydrogenase rrnAC2957 pdhA3 1.2.4.1;1.2.4.4 Pyruvate dehydrogenase E1 component, alpha subuni rrnAC2959 lipA Lipoic acid synthetase (Lip-syn) (Lipoate synthase rrnAC2961 brr2 Pre-mRNA splicing helicase rrnAC2962 Putative haloacid dehalogenase-like hydrolas rrnAC2963 top1 Topoisomerase DNA binding C4 zinc finge rrnAC2964 endA 3.1.27.9 tRNA intron endonuclease rrnAC2965 trpS 6.1.1.2 Tryptophanyl-tRNA synthetase rrnAC2966 pheS 6.1.1.20 Phenylalanyl-tRNA synthetase alpha chain rrnAC2967 pheT 6.1.1.20 Phenylalanyl-tRNA synthetase beta chain rrnAC2969 pyrD 1.3.3.1 Dihydroorotate dehydrogenase rrnAC2992 nirA2 Ferredoxin-nitrite reductase rrnAC2996 uvrB UvrABC system protein B rrnAC2997 membrane bound his kinase A rrnAC2998 cbiT 1.-.-.- Precorrin-8W decarboxylase rrnAC3000 cbiL Precorrin-2 C20-methyltransferase rrnAC3001 cbiF Cobalamin biosynthesis precorrin-3 methylas rrnAC3003 cbiG Cobalamin biosynthesis protein G rrnAC3004 fabG6 1.1.1.100 3-oxoacyl-[acyl-carrier protein] reductase rrnAC3005 cobH 2.1.1.131 Precorrin-3B C17-methyltransferase rrnAC3008 cbiH 2.1.1.131 Precorrin-3B C17-methyltransferase rrnAC3011 cbiK 4.99.1.- colbalt chelase thioredoxin rrnAC3013 tup1 Tup1 like Transcriptional Represso rrnAC3018 hmcA Protoporphyrin IX magnesium chelatase rrnAC3019 cobN Cobalamin biosynthesis protein rrnAC3020 cbiC 5.4.1.2 Precorrin-8X methylmutase rrnAC3021 cbiJ Precorrin-3 methylase rrnAC3023 cbiX putative cobalamin biosynthesis protei rrnAC3025 napA Sodium/proton antiporter, putative rrnAC3026 yfmJ1 1.6.5.5 Quinone Oxidoreductase rrnAC3031 iunH1 Inosine-uridine preferring nucleoside hydrolas rrnAC3032 dgoA2 Mandelate racemase/muconate lactonizing enzyme family protei rrnAC3033 Metallo-beta-lactamase rrnAC3034 gfo6 Glucose-fructose oxidoreductase rrnAC3036 aldY3 Aldehyde dehydrogenase rrnAC3038 htpX3 Heat shock protein X rrnAC3039 hpcEb 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase rrnAC3041 uvrC UvrABC system protein C rrnAC3046 aspC2 Aspartate aminotransferase rrnAC3049 ligB 6.5.1.2 DNA ligase rrnAC3050 htlD Similar to ESCHERICHIA COLI protein kinase GP:GI-606149 (HTR-like protein rrnAC3052 nosY2 ABC-type transport system involved in multi-copper enzyme maturation, permease componen rrnAC3053 ABC transporter, ATP-binding protein rrnAC3062 moxR5 Methanol dehydrogenase regulatory protei rrnAC3063 metY O-acetylhomoserine (thiol)-lyase rrnAC3064 metA 2.3.1.31 Homoserine O-acetyltransferase rrnAC3068 panE 1.1.1.169 2-dehydropantoate 2-reductase rrnAC3069 dgoA3 Mandelate racemase/muconate lactonizing enzyme family rrnAC3071 ilvE1 Branched-chain amino acid aminotransferase rrnAC3073 ribA 3.5.4.25 GTP cyclohydrolase II / 3,4-dihydroxy-2-butanone 4-phosphate synthas rrnAC3078 rub rubredoxin rrnAC3086 hemC 4.3.1.8 Porphobilinogen deaminase rrnAC3087 cysG2 2.1.1.107 Uroporphyrin-III C-methyltransferase rrnAC3088 cysG1 Uroporphyrin-III C-methyltransferase rrnAC3089 pspA2 transcription regulato rrnAC3094 recJ5 RecJ-like exonuclease (DHH/DHHA1 family protein rrnAC3099 edp Proteinase IV homolog rrnAC3101 2.1.1.- methyltransferase rrnAC3102 nifU1 NifU-like protein rrnAC3104 csd1 4.4.1.- Probable cysteine desulfurase rrnAC3108 tpr tetratricopeptide repeat (TPR) protein rrnAC3109 2'-5' RNA ligase rrnAC3110 gufA Metal transporter family GufA protein rrnAC3112 rpl39E 50S ribosomal protein L39e rrnAC3113 rpl31E 50S ribosomal protein L31e rrnAC3118 dpa Signal recognition particle recepto rrnAC3119 LPXTG-motif cell wall anchor domain protein rrnAC3121 eda 4.1.2.14 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolas rrnAC3122 mdcM Malonate transporter rrnAC3124 srp54 Signal recognition 54 kDa protein (SRP54 rrnAC3125 usp33 universal stress protein rrnAC3126 trxA4 Thioredocxin rrnAC3127 livF-7 Branched-chain amino acid ABC transporter, ATP-binding protei rrnAC3128 livG-9 Branched-chain amino acid ABC transporter, ATP-binding protei rrnAC3129 livM-6 Branched-chain amino acid ABC transporter, permease protei rrnAC3130 livH-7 Branched-chain amino acid ABC transporter, permease protei rrnAC3132 livK-2 Branched-chain amino acid ABC transporter, amino acid-binding protei rrnAC3135 cat Divalent cation transporter rrnAC3138 hat3 putative GNAT-family histone acetyltransferase rrnAC3139 maoC2 MaoC family protein rrnAC3140 nuc endonuclease, Staphylococcal nuclease homologu rrnAC3141 soxA1 Sulfite Oxidase rrnAC3143 putative haloacid dehalogenase-like hydrolase rrnAC3145 adk Adenylate kinase rrnAC3146 fps farnesyl-pyrrophosphate synthase rrnAC3147 etfA2 Electron transfer flavoprotein alpha-subun rrnAC3148 etfB1 Electron transfer flavoprotein, beta subun rrnAC3151 ubiE1 Ubiquinone/menaquinone biosynthesis methyltransferas rrnAC3152 atpG 3.6.3.14 Vacuolar (H+)-ATPase G subuni rrnAC3154 atpI 3.6.3.14 V-type ATP synthase subunit I rrnAC3155 atpC1 3.6.3.14 H+ ATP synthase sununit C rrnAC3156 atpE 3.6.3.14 V-type ATP synthase subunit E rrnAC3157 ntpC 3.6.3.14 V-type ATP synthase subunit C rrnAC3158 atpF 3.6.3.14 V-type ATP synthase subunit F rrnAC3159 ntpA 3.6.1.34 V-type sodium ATP synthase subunit A rrnAC3160 ntpB 3.6.1.34 V-type sodium ATP synthase subunit B rrnAC3161 bop Bacteriorhodopsin rrnAC3162 atpD 3.6.3.14 V-type ATP synthase subunit D rrnAC3164 erf1 Peptide chain release factor eRF1 rrnAC3166 minD3 Septum site-determining protein MinD rrnAC3167 Putative DNA binding rrnAC3168 pcbD-2 Probable hydrolase rrnAC3169 argS 6.1.1.19 Arginyl-tRNA synthetase rrnAC3170 M50 metallopeptidase rrnAC3171 usp19 Universal stress protein rrnAC3173 lysS 6.1.1.6 Lysyl-tRNA synthetase rrnAC3174 pyrH 2.7.4.- Probable uridylate kinase rrnAC3177 thiL Thiamine monophosphate kinase rrnAC3179 rps19E 30S ribosomal protein S19E rrnAC3183 hisS 6.1.1.21 Histidyl-tRNA synthetase rrnAC3188 truA 4.2.1.70 tRNA pseudouridine synthase A rrnAC3189 pepF 3.4.24.- Oligoendopeptidase F rrnAC3190 pan1 Proteasome-activating nucleotidase 1 (Proteasome regulatory subunit 1 rrnAC3191 deoR1 Transcriptional regulator of sugar metabolism rrnAC3194 ugpC Sn-glycerol-3-phosphate transport system ATP-bindin rrnAC3195 malFG-7 Sugar ABC transporter, permease protein rrnAC3196 malFG-8 ABC transporter, permease protein rrnAC3197 malE2 Trehalose/maltose binding protein rrnAC3198 pkn-2 putative cell surface protein OR Serine/threonine protein kinase-related prote rrnAC3199 argDC 4.1.1.19 Pyruvoyl-dependent arginine decarboxylase rrnAC3203 infB Translation initiation factor IF-2 rrnAC3204 hcp1 Halocyanin precursor-like rrnAC3205 PRC-barrel domain, posible photosystem reaction centre subunit H rrnAC3207 Ribbon-helix-helix protein, copG family rrnAC3210 pgi 5.3.1.9 Glucose-6-phosphate isomerase rrnAC3214 secF Protein-export membrane protein SecF rrnAC3215 secD Protein-export membrane protein SecD rrnAC3216 rnhB 3.1.26.4 RNAase HII rrnAC3218 mic Mechanosensitive ion channe rrnAC3219 BacA Bacitracin resistance protein rrnAC3225 usp22 Universal stress protein rrnAC3226 ssf Sodium/solute symporter rrnAC3228 acs5 6.2.1.1 putative Acetyl-coenzyme A synthetase rrnAC3229 boa Bacterio-opsin activator-like protein rrnAC3230 acs3 6.2.1.1 Acyl-coenzyme A synthetases rrnAC3232 graD4c Glucose-1-phosphate thymidylyltransferase rrnAC3235 glmS2 2.6.1.16 Glucosamine-fructose-6-phosphate aminotransferase [isomerizing rrnAC3236 Sugar transferase involved in lipopolysaccharide synthes rrnAC3238 rffH3 2.7.7.24 Glucose-1-phosphate thymidylyltransferase rrnAC3239 ugd2 1.1.1.22 UDP-glucose 6-dehydrogenase rrnAC3240 putative membrane-bound metal-dependent hydrolase rrnAC3243 galE7 UDP-glucose 4-epimerase rrnAC3245 galE5 5.3.1.2 UDP-glucose 4-epimerase rrnAC3246 sqdB UDP-sulfoquinovose synthase rrnAC3249 guaB4 Inosine-5'-monophosphate dehydrogenase related protein IV rrnAC3250 codA Cytosine deaminase (Cytidine/deoxycytidylate deaminase family protein rrnAC3251 yjlD3 NADH dehydrogenase rrnAC3258 tgt Archaeosine tRNA-ribosyltransferase rrnAC3259 galE1 5.1.3.2 UDP-glucose 4-epimerase rrnAC3261 tgt Archaeosine tRNA-ribosyltransferase rrnAC3264 Putative molybdenum-binding protein (transcriptional regulato rrnAC3265 pstB3 Phosphate ABC transporter, ATP-binding protein rrnAC3266 modB Molybdenum ABC transporter, permease protein rrnAC3267 Molybdate Transport Protein rrnAC3268 purQ 6.3.5.3 Phosphoribosylformylglycinamidine synthase rrnAC3271 small putative GAF containing sensor rrnAC3272 purU 3.5.1.10;2.1.2.2Formyltetrahydrofolate deformylase rrnAC3274 pap2b 3.1.3.9 Glucose-6-phosphatase rrnAC3275 purC 6.3.2.6 Phosphoribosylaminoimidazole-succinocarboxamide synthase rrnAC3276 nce3 Na+/Ca2+-exchanging protein rrnAC3280 sop1 Sensory rhodopsin I (SR-I rrnAC3281 htr MCP domain signal transducer (soluble rrnAC3284 ftsZ5 Cell division protein rrnAC3285 nolA NADH dehydrogenase/oxidoreductase-like protein rrnAC3286 tmk 2.7.4.9 Thymidylate kinase rrnAC3289 trkA3 TRK potassium uptake system protein rrnAC3290 trh5 Transcription regulato rrnAC3295 ykfD Oligopeptide ABC transporter ATP-binding rrnAC3296 oppD2 Oligopeptide ABC transporter, ATPase componen rrnAC3297 oppC Oligopeptide ABC transporter, permease protein rrnAC3298 dppB Dipeptide ABC transporter permease rrnAC3299 dppA Dipeptide ABC transporter dipeptide-binding rrnAC3303 ppiB1 5.2.1.8 Peptidyl-prolyl cis-trans isomerase slr1251 rrnAC3304 yfhM Epoxide hydrolase-related protein rrnAC3306 trpD1 2.4.2.18 Anthranilate phosphoribosyltransferase rrnAC3307 nirD Heme biosynthesis protein rrnAC3308 hlx5 HoxA-like transcriptional regulato rrnAC3310 transcription regulato rrnAC3312 cyp1 1.14.14.1;1.6.2Cytochrome P450 rrnAC3316 arsC Putative arsenate reductase rrnAC3320 rnhA ribonuclease H-like protein rrnAC3322 transcription regulato rrnAC3323 ipp 3.6.1.1 Inorganic pyrophosphatase rrnAC3325 3.1.6.- sulfatase, Arylsulfatase A like rrnAC3326 ftsZ4 Cell division protein rrnAC3329 hcp3 Halocyanin precursor-like rrnAC3334 dnaJ2 Chaperone protein DnaJ rrnAC3337 Putative transcriptional regulato rrnAC3339 dnaK Chaperone protein dnaK rrnAC3340 grpE Heat shock protein, GrpE protein (HSP-70 cofactor rrnAC3342 truB 4.2.1.70 tRNA pseudouridine synthase B rrnAC3343 cmk 2.7.4.14 Cytidylate kinase rrnAC3344 htlB Htr-like protein rrnAC3345 bcp2 Bacterioferritin comigratory protein rrnAC3346 adk 2.7.4.3 Adenylate kinase rrnAC3347 kinA3 Signal-transducing histidine kinase homolo rrnAC3348 thrB 2.7.1.39 Homoserine kinase rrnAC3349 kinA5 Signal-transducing histidine kinase homolo rrnAC3353 noxA2 NADH oxidase rrnAC3360 carB 6.3.5.5 Carbamoylphosphate synthetase, large subuni rrnAC3361 htlD Similar to ESCHERICHIA COLI protein kinase GP:GI-606149 (HTR-like protein rrnAC3363 carA 6.3.5.5 Carbamoyl-phosphate synthase small chain rrnAC3365 trh3 Transcription regulato rrnAC3370 signal transducing histidine kinas rrnAC3371 yprA2 ATP-dependant helicase rrnAC3372 fecE Iron (III) ABC transporter ATP-binding protein rrnAC3374 hemU Iron(III) dicitrate transport system permease protein FecD rrnAC3375 hemV Iron (III) ABC transporter ATP-binding rrnAC3378 6.3.3.2 5-formyltetrahydrofolate cyclo-ligase rrnAC3379 htlD Similar to ESCHERICHIA COLI protein kinase GP:GI-606149 (HTR-like protein rrnAC3381 lpdA1 1.8.1.4 Dihydrolipoamide dehydrogenase rrnAC3384 DNA binding protein, putative transcriptional regulato rrnAC3385 ntrC signal receiver domain-protein (PF00072 rrnAC3387 tnp Transposase rrnAC3391 ppnK 2.7.1.23 Probable inorganic polyphosphate/ATP-NAD kinase rrnAC3392 kaiC2 Circadian regulator rrnAC3394 usp4 Universal stress protein rrnAC3395 usp24 Universal stress protein family rrnAC3399 DNA binding protein, putative transcriptional regulato rrnAC3403 pgm 5.4.2.1 2,3-bisphosphoglycerate-independent phosphoglycerate mutase rrnAC3404 kptA 2.7.-.- Probable RNA 2'-phosphotransferase rrnAC3405 Acetyltransferase (GNAT) family rrnAC3408 nadC1 2.4.2.19 nicotinate-nucleotide pyrophosphorylase rrnAC3409 nadB 1.4.3.16 L-aspartate oxidase rrnAC3410 nadA Quinolinate synthetase A rrnAC3411 3.5.-.-;3.5.1.25 metal dependent Amidohydrolase superfamily protein rrnAC3412 mvaA 1.1.1.34 3-hydroxy-3-methylglutaryl-coenzyme A reductase rrnAC3415 rrnAC3419 icd 1.1.1.42 Isocitrate dehydrogenase rrnAC3420 ans Asparaginase family protein rrnAC3421 map 3.4.11.18 Methionine aminopeptidase rrnAC3423 hit1 Histidine triad protein rrnAC3424 Rieske [2Fe-2S] domain protein rrnAC3425 cef Cation efflux system protein (Zinc/cadmium rrnAC3427 doxD2 terminal quinol oxidase subun rrnAC3429 deoC1 4.1.2.4 Deoxyribose-phosphate aldolase rrnAC3434 udp1 2.4.2.3 Uridine phosphorylase rrnAC3436 pch2 Potassium channel homolog rrnAC3441 hat5 GNAT family Acetyltransferase rrnAC3442 asbA 3.5.1.1 L-asparaginase rrnAC3447 arsR transcription regulato rrnAC3451 Putative DNA binding rrnAC3455 ykfB3 Chloromuconate cycloisomerase rrnAC3456 bcp1 Bacterioferritin comigrating protein rrnAC3458 Anhydrase, family 3 protein rrnAC3460 usp26 Universal stress protein rrnAC3462 thrS 6.1.1.3 Threonyl-tRNA synthetase rrnAC3466 arsB Arsenite transport protein rrnAC3467 pspA1 transcription regulato rrnAC3471 pyrG 6.3.4.2 CTP synthase rrnAC3472 guaA1 6.3.5.2 GMP synthase (glutamine-hydrolyzing) rrnAC3474 Metallo-beta-lactamase superfamily protein rrnAC3476 yafB-5 Oxidoreductase, aldo/keto reductase family rrnAC3480 moaB2 Molybdenum cofactor biosynthesis protein B rrnAC3482 ark-6 Putative signal-transducing histidine kinas rrnAC3483 fabG2 3-oxoacyl-[acyl-carrier protein] reductase rrnAC3484 idi 5.3.3.2 Probable isopentenyl-diphosphate delta-isomerase rrnAC3489 pqqE Coenzyme PQQ synthesis protein rrnAC3490 boa2 Bacterio-opsin activator-like protein rrnAC3494 putative Bacterial regulatory protein, arsR family rrnAC3495 aspB2 2.6.1.1 Aspartate aminotransferase rrnAC3497 yqeF 2.3.1.9 Acetyl-coA acetyltransferase rrnAC3501 transcription regulato rrnAC3504 Flavin containing amine oxidoreductase rrnAC3505 thrC1 4.2.99.2 Threonine synthase rrnAC3506 adh2 1.1.1.1;1.6.5.5 Alcohol dehydrogenase rrnAC3507 usp3 Universal stress protein 3 rrnAC3508 usp7 Universal stress protein rrnAC3509 dnaJ1 chaperone rrnAC3511 nop10P Nucleolar RNA-binding protein, Nop10p family rrnAC3512 eif2A Probable translation initiation factor 2 alpha subunit (eIF-2-alpha rrnAC3513 rps27E 30S ribosomal protein S27e rrnAC3514 rpl44E 50S ribosomal protein L44E rrnAC3518 dgs Dolichol-P-glucose transferase rrnAC3519 GtrA-like family protein rrnAC3523 apt1 2.4.2.7 Adenine phosphoribosyltransferase rrnAC3529 NADH-Ubiquinone/plastoquinone (complex I rrnAC3530 nuoL1 NADH dehydrogenase I, L subuni rrnAC3531 ndhG2 NADH dehydrogenase/oxidoreductase rrnAC3533 mnhG1 putative Na/H antiporter rrnAC3535 mnhG2 Multisubunit Na+/H+ antiporter, MnhG subun rrnAC3537 mnhE Na/H antiporter subunit rrnAC3539 dfp Pantothenate metabolism flavoprotein rrnAC3544 htpX4 3.4.24.- Protease heat shock protein HtpX rrnAC3545 trxB4 Thioredoxin reductase rrnAC3546 pan2 Proteasome-activating nucleotidase 2 (Proteasome regulatory subunit 2 rrnAC3549 putative HD family metal dependent phosphohydrolase rrnAC3551 trzA4 Chlorohydrolase family protein rrnAC3553 usp18 universal stress protein rrnB0004 cdc6b Cell division control protein 6 homolog 1 (CDC6 homolog 1 rrnB0006 Acetamidase/formamidase family protein rrnB0008 tnp Probable transposase for insertion sequence element ISH1 rrnB0018 flaA1 Flagellin A precursor rrnB0027 Acetyltransferase (GNAT family) rrnB0028 tnp Probable transposase for insertion sequence element ISH1 rrnB0029 yhcR4 phosphoesterase rrnB0033 Tautomerase rrnB0036 nadC2 Sodium dependent transporter rrnB0038 usp11 Universal stress protein rrnB0041 xseA2 3.1.11.6 Probable exodeoxyribonuclease VII large subuni rrnB0042 exoVIIB 3.1.11.6 Exonuclease VII small subunit rrnB0046 tnp phage integrase rrnB0049 apbE thiamin biosynthesis protein rrnB0052 regulatory protein, arsR family rrnB0062 parA3 Chromosome partitioning protein, ParA family ATPase rrnB0063 cdc6a Cell division control protein 6 homolog 1 (CDC6 homolog 1 rrnB0070 speE 2.5.1.16 Spermidine synthase rrnB0074 transcription regulato rrnB0075 2.4.1.- glycosyl transferase rrnB0083 ski-1 Putative 2-component system sensor kinase rrnB0087 ski-2 Sensor protein rrnB0089 transcription regulato rrnB0092 aldY7 1.2.1.3 Aldehyde dehydrogenase rrnB0094 tnp Putative transposase (VNG6486H) (VNG6040H rrnB0095 aldY6 1.2.1.3 Aldehyde dehydrogenase rrnB0097 hcp7 Halocyanin precursor-like rrnB0102 suhB2 3.1.3.25 Inositol-1-monophosphatase rrnB0103 rbsB-3 Putative ABC transporter, substrate binding protei rrnB0104 malFG-9 Sugar ABC transport system, permease protein rrnB0105 malFG-10 Sugar ABC transporter, permease protein rrnB0106 ugpC2 Sugar ABC transporter, ATP-binding subuni rrnB0107 very putative carbbohydrate responsive phospholipas rrnB0112 putative DNA binding domain rrnB0113 gatA2 6.3.5.- Glutamyl-tRNA(Gln) amidotransferase subunit A rrnB0122 tnp Probable transposase for insertion sequence element ISH1 rrnB0133 putative redox sensing protein rrnB0143 tnp Probable transposase rrnB0146 tnp Putative ISH8 transposase (VNG6331H rrnB0148 tfbC Tanscription initiation factor IIB (TFIIB rrnB0156 putative light and redox sensing histidine kinas rrnB0157 padR like DNA binding protein rrnB0167 cbp Calcium-binding protein homology rrnB0171 putative acyltransferase rrnB0175 imd2 1.1.1.205 Inosine Monophosphate Dehydrogenase rrnB0180 oye1 putative 22-domain light- and oxygen-sensing histidine kinas rrnB0183 tnp Transposase rrnB0187 putative cupin rrnB0192 usp1 Universal stress protein 1 rrnB0197 lpdA3 1.8.1.4 Dihydrolipoamide dehydrogenase rrnB0198 pdhC1 Dihydrolipoamide S-acetyltransferase component of pyruvate dehydrogenase complex E rrnB0199 pdhB2 1.2.4.1 Pyruvate Dehydrogenase rrnB0200 pdhA2 1.2.4.1 Pyruvate dehydrogenase E1 component, alpha subuni rrnB0202 livF-8 Branched-chain amino acid ABC transporter, ATP-binding protei rrnB0203 livG-8 Branched-chain amino acid ABC transporter, ATP-binding protei rrnB0204 livM-7 High-affinity branched-chain amino acid transport protei rrnB0205 livH-8 Branched-chain amino acid ABC transporter, permease protei rrnB0206 aspC1 2.6.1.1 Aspartate aminotransferase rrnB0207 putative extracellular ligand binding protei rrnB0209 ilvB3 4.1.3.18 Acetolactate synthase large subunit rrnB0210 galE10 UDP-glucose 4-epimerase rrnB0212 pepB5 Aminopeptidase rrnB0214 bacterial luciferase family monooxygenase rrnB0215 thioesterase rrnB0217 acs2 6.2.1.1 Acyl-coenzyme A synthetases rrnB0218 npdG-2 F420-dependent NADP reductase rrnB0219 gabD Succinate-semialdehyde dehydrogenase rrnB0221 putative metal dependent phosphohydrolase rrnB0222 kdgR2 Transcription regulator KdgR rrnB0224 livF-9 Branched-chain amino acid ABC transporter, ATP-binding protei rrnB0225 livG-10 Branched-chain amino acid ABC transporter, ATP-binding protei rrnB0227 livH-9 Branched-chain amino acid ABC transporter, permease protei rrnB0229 pga-1 3.5.1.11 Penicillin acylase (Penicillin amidase) rrnB0230 pga-2 3.5.1.11 Penicillin G amidase rrnB0231 paaK2 6.2.1.30 Phenylacetyl-CoA ligase rrnB0235 iclR Transcriptional regulator, IclR family rrnB0237 ech4 4.2.1.17 Enoyl-CoA hydratase rrnB0238 hbd3 1.1.1.35 3-hydroxyacyl-CoA dehydrogenase rrnB0240 aca1 2.3.1.9 Acetyl-coA acetyltransferase rrnB0241 acaA 2.3.1.41 Acyl carrier protein synthase rrnB0242 acaB2 2.3.1.9;2.3.1.163-ketoacyl-CoA thiolase rrnB0243 paaK1 Phenylacetyl-coenzyme A ligase rrnB0244 paaI Phenylacetic acid degradation protein Paa rrnB0245 maoC2 Monoamine oxidase regulatory protein rrnB0246 aldY5 1.2.1.3 Aldehyde dehydrogenase rrnB0249 paaC Phenylacetic acid degradation protein PaaC rrnB0250 pacF PacF protein rrnB0252 paaA Phenylacetic acid degradation protein PaaA rrnB0253 boa-12 transcription regulato rrnB0254 ech6 4.2.1.17 Enoyl-CoA hydratase rrnB0255 amidohydrolase rrnB0257 citE2 4.1.3.6;4.1.2.20Citrate lyase, beta chain rrnB0259 fapS 2.1.1.79 Cyclopropane-fatty-acyl-phospholipid synthas rrnB0260 maoC3 Molybdenum cofactor biosynthesis protein rrnB0261 pccB Propionyl-CoA carboxylase, beta subun rrnB0263 accC1 6.4.1.16 Carbamoyl phosphate synthase L chain rrnB0264 acdH 1.3.99.3 Acyl-CoA dehydrogenase rrnB0265 acs4 6.2.1.1 Acyl-coenzyme A synthetases rrnB0267 ubiD 3-octaprenyl-4-hydroxybenzoate carboxy-lyas rrnB0270 zntA2 Zinc-transporting ATPase rrnB0275 putative-iron binding protein rrnB0277 trxA5 thioredoxin rrnB0283 guaA4 6.3.5.2 GMP synthase rrnB0290 phoT1 Sodium-dependent phosphate transporte rrnB0291 usp27 Universal stress protein rrnB0295 gaf only light sensing his kinase rrnB0296 kinA2 Signal-transducing histidine kinase homolo rrnB0297 rre-2 Two-component response regulato rrnB0299 oye nineteen domain light and oxygen sensing his kinas rrnB0301 hlx2 HoxA-like transcriptional regulato rrnB0302 rre-3 Response regulator rrnB0303 tnp Putative ISH8 transposase rrnB0309 acaB1 2.3.1.9 3-ketoacyl-CoA thiolase rrnB0310 fmn Fmn oxidoreductase protein rrnB0311 ugpB Glycerol-3-phosphate-binding protein rrnB0312 ugpA ABC transporter, permease protein rrnB0314 ugpE Sn-glycerol-3-phosphate transport system permease rrnB0315 msmX-3 Sugar ABC transporter, ATP-binding protein rrnB0316 glpQ1 3.1.4.46 Glycerophosphoryl diester phosphodiesterase rrnB0317 araL2 unknown L-arabinose operon protein AraL rrnB0318 mgtC2 Magnesium transporter accessory protein rrnB0319 phnD1 ABC tranporter, phosphate-binding protein rrnB0320 phnC2 Phosphonates ABC transporter, ATP-binding protein rrnB0321 phnE Phosphonate ABC tranporter permease protein rrnB0322 phnD2 Phosphonates ABC transporter, permease protein rrnB0324 pqsH Fad-dependent monooxygenase rrnB0325 ftsZ2 Cell division protein rrnB0326 cpdB1 2', 3'-cyclic nucleotide 2'-phosphodiesterase rrnB0335 parA5 parA/minD like Bacterial Cell Division Regulato Genes implicated in denitrification ORF GENE Function rrnAC2619 amt Ammonium transporter rrnAC2779 asnC1 Transcription regulator, AsnC family rrnAC2622 asnC4 Transcription regulator, AsnC family rrnAC3005 cobH Precorrin-3B C17-methyltransferase rrnAC1215 dmsA Dimethylsulfoxide reductase pNG7151 fdhA Formate dehydrogenase alpha subunit pNG7318 fdnG Formate dehydrogenase alpha subunit rrnAC2621 glnB Nitrogen regulatory protein P-II rrnAC1252 lrp Leucine responsive regulatory protein rrnAC1186 moaE Molybdenum cofactor biosynthesis protein rrnAC1317 mobA Molybdopterin-guanine dinucleotide biosynthesis protein A rrnAC1705 moeA1 Molybdenum cofactor biosynthesis protein rrnAC2486 nadE1 NH(3)-dependent NAD(+) synthetase rrnAC2627 narB Nitrate reductase rrnAC1199 narG Nitrate reductase, alpha chain rrnAC1200 narH Nitrate reductase, beta chain rrnAC1204 narJ Chaperone protein rrnAC2625 nirA1 Ferredoxin-nitrite reductase rrnAC2992 nirA2 Ferredoxin-nitrite reductase rrnAC2853 nirK nitrite reductase, copper containing rrnAC0810 nitA Nitrilase rrnAC0392 nosD2 copper binding protein rrnAC0396 nosY1 ABC-type transport system involved in multi-copper enzyme maturation, permease component rrnAC3052 nosY2 ABC-type transport system involved in multi-copper enzyme maturation, permease component rrnAC0390 nosZ Nitrous-oxide reductase pNG7136 noxA1 NADH oxidase rrnAC3353 noxA2 NADH oxidase rrnAC0389 pcy copper-binding plastocyanin like protein rrnAC0616 pecE Pectinesterase rrnAC1196 petB2 Cytochrome B6 pNG6034 pNG6034 transcription regulator pNG6047 pNG6047 putative metal-binding transcription regulator rrnAC1206 prp protein phosphatase rrnAC2829 rpoE' DNA-directed RNA polymerase subunit E' rrnAC0391 rrnAC0394 ABC transporter, ATP-binding protein rrnAC0394 rrnAC1655 ABC transporter, ATP-binding protein rrnAC0811 rrnAC2084 ABC transporter, ATP-binding protein rrnAC1194 rrnAC1195 Putative Rieske iron-sulfur protein rrnAC1195 rrnAC0391 unknown rrnAC1197 rrnAC0811 unknown rrnAC1202 rrnAC1194 unknown rrnAC1203 rrnAC1197 unknown rrnAC1205 rrnAC1202 unknown rrnAC1655 rrnAC1203 unknown rrnAC2084 rrnAC1205 putative ABC-type phosphate transport system, permease component rrnAC2699 rrnAC2699 putative inosine monophosphate dehydrogenase rrnAC3053 rrnAC3053 ABC transporter, ATP-binding protein rrnAC2073 trp2 ABC transporter, ATP-binding protein rrnAC0479 trp5 ABC transporter, ATP-binding protein rrnAC0450 yjlD1 NADH dehydrogenase rrnAC1301 yjlD2 NADH dehydrogenase Genes implicated in arginine catabolism ORF GENE Function rrnAC2672 arcB Ornithine carbamoyltransferase rrnAC0453 arg1 Arginase rrnAC0383 arg2 Arginase rrnAC0078 argB1 Acetylglutamate kinase rrnAC2676 argB2 Acetylglutamate kinase rrnAC2678 argC N-acetyl-gamma-glutamyl-phosphate reductase rrnAC2675 argD Acetylornithine aminotransferase rrnAC2683 argG Argininosuccinate synthase rrnAC2681 argH Argininosuccinate lyase rrnAC0933 argK ArgK protein rrnAC3363 carA Carbamoyl-phosphate synthase small chain rrnAC3360 carB Carbamoylphosphate synthetase, large subunit rrnAC1929 eif5A Translation initiation factor 5A (eIF-5A) (Hypusine-containing protein) rrnAC0384 gdhA1 NADP-specific glutamate dehydrogenase rrnAC0775 gdhA2 NAD(P)-specific Glutamate dehydrogenase rrnAC2674 gltCP Glutamate Carboxypeptidase pNG7157 gudB NAD(P)-specific glutamate dehydrogenase rrnAC0637 mcmA1 Methylmalonyl-CoA mutase, subunit alpha rrnAC1275 mcmA2 Methylmalonyl-CoA mutase, subunit alpha rrnAC0934 mcmA3 Putative methylmalonyl-CoA mutase rrnAC0077 mvk Mevalonate kinase rrnAC2426 nusA2 Transcription termination factor NusA rrnAC2679 rimK Ribosomal protein S6 modification protein rrnAC2829 rpoE' DNA-directed RNA polymerase subunit E' rrnAC2460 rrnAC2460 Unknown rrnB0068 rrnB0068 Unknown rrnB0069 rrnB0069 Unknown rrnAC1927 speB1 Agmatinase rrnB0070 speE Spermidine synthase rrnAC0710 trpD2 Anthranilate synthase, component II pNG7325 trpG2 Anthranilate synthase component II pNG7125 ureA Urease gamma subunit pNG7123 ureB Urease beta subunit pNG7124 ureC Urease alpha subunit pNG7127 ureD Urease accessory protein UreD pNG7128 ureE Urease accessory protein UreE pNG7129 ureF Urease accessory protein F, UreF pNG7126 ureG Urease accessory protein UreG rrnAC2873 potC2 Spermidine/putrescine ABC transporter permease rrnAC0908 potA4 Spermidine/putrescine ABC transporter, ATP-binding protein rrnAC2870 potA2 Spermidine/putrescine ABC transporter, ATP-binding protein rrnAC2868 potD2 Spermidine/putrescine ABC transporter, spermidine/putrescine binding protein pNG7349 potB1 Spermidine/putrescine ABC transporter, permease protein pNG7347 potA1 Putrescine ABC transporter, ATP-binding protein rrnAC0145 potA3 Spermidine/putrescine ABC transporter, ATP-binding protein rrnAC2872 potB2 Spermidine/putrescine ABC transporter, permease protein pNG7350 potC1 Spermidine/putrescine ABC transporter, permease protein (PotC) pNG7067 speB2 Agmatinase rrnAC0223 camH3 Creatinine amidohydrolase pNG7096 camH1 Creatinine amidohydrolase pNG7341 camH2 Creatinine amidohydrolase rrnAC0198 odc Ornithine Decarboxylase rrnAC2941 ocd2 Ornithine cyclodeaminase rrnAC0227 ocd3 Ornithine cyclodeaminase rrnAC0038 ocd1 Ornithine cyclodeaminase Proteins with PAS, PAC, GAF, and Histidine Kinase domains PF00015: Methyl accepting chemotaxis (MCP) PF00072: Response regulator receiver domain Gene Name start stop e-value Gene Name start stop e-value rrnAC0013 469 757 2.00E-59 pNG7156 12 133 5.30E-12 rrnAC2760 475 763 5.90E-56 pNG7159 11 131 8.20E-07 rrnAC0976 338 628 3.00E-56 rrnAC1626 100 224 8.30E-21 rrnAC2425 484 772 9.70E-64 rrnAC2204 5 135 6.60E-25 rrnAC0701 508 796 1.30E-63 rrnAC3379 37 157 3.20E-10 pNG7084 337 630 1.20E-47 rrnAC0848 8 129 7.80E-22 rrnAC1752 376 636 4.40E-39 rrnAC2533 5 129 2.20E-11 rrnAC0183 235 492 1.20E-46 rrnAC3361 5 126 4.80E-22 rrnAC0552 163 437 3.90E-42 rrnAC0574 19 138 0.0014 rrnAC2728 466 756 1.00E-54 rrnAC0075 13 133 1.60E-14 rrnAC2495 259 547 5.30E-59 rrnAC2372 8 132 1.10E-23 rrnAC3281 137 395 9.10E-63 rrnAC2416 21 145 2.90E-26 rrnAC0404 161 432 7.30E-23 rrnAC1806 8 136 2.10E-18 rrnAC0942 155 443 3.80E-58 rrnAC2044 8 129 8.90E-29 rrnAC0371 420 619 0.0078 pNG7155 4 124 3.60E-25 rrnAC2091 70 327 5.90E-48 rrnAC3050 113 234 3.50E-22 rrnAC2633 14 288 7.80E-24 pNG7223 22 146 3.50E-23 rrnAC2618 48 303 7.40E-23 rrnAC0487 7 132 6.70E-26 rrnAC0356 9 133 1.10E-23 rrnAC1142 4 128 9.40E-27 PF00512: Histidine kinase (N-terminal) domain rrnB0296 7 133 3.20E-15 Gene Name start stop e-value rrnAC2109 7 132 7.90E-22 pNG7156 1100 1161 1.50E-16 rrnAC0411 10 140 4.20E-17 rrnAC1626 731 792 2.10E-13 rrnAC2211 9 130 1.60E-26 rrnAC3379 451 514 6.00E-16 rrnAC0339 9 130 9.90E-24 rrnAC0848 546 607 2.30E-14 rrnAC0475 6 126 0.00088 rrnAC3440 341 409 0.00036 rrnAC0674 63 187 1.90E-22 rrnAC2692 487 546 7.50E-11 rrnAC2194 2 119 2.20E-35 rrnAC2533 427 488 3.70E-17 rrnAC1118 7 121 8.00E-27 rrnAC3361 804 865 9.50E-17 rrnAC0536 24 138 3.60E-19 rrnAC0086 583 647 4.90E-12 rrnAC1495 8 120 7.40E-05 rrnAC0574 404 465 1.50E-13 rrnAC1663 74 188 0.059 rrnAC0075 524 585 5.40E-19 rrnAC3308 7 121 2.50E-22 rrnAC0991 430 494 1.60E-13 rrnAC0301 4 117 0.00096 rrnAC2372 427 488 5.80E-16 rrnAC0794 5 131 0.00065 rrnAC2416 831 892 2.60E-13 rrnAC0794 5 131 0.0024 rrnAC2219 111 170 1.30E-11 pNG4019 9 126 2.10E-22 rrnAC1806 393 454 3.00E-13 rrnAC0412 7 133 3.40E-14 rrnAC0247 177 238 5.20E-12 rrnAC0361 5 119 2.60E-13 rrnAC2044 532 593 9.60E-15 rrnB0301 119 231 1.10E-22 pNG7155 438 499 2.20E-18 rrnAC3271 5 124 3.10E-05 rrnAC3050 628 689 2.40E-07 rrnB0297 6 135 8.20E-14 rrnAC0410 417 484 7.30E-07 rrnAC1494 3 122 9.30E-19 rrnAC0487 256 319 2.10E-14 rrnAC2168 4 116 1.80E-11 rrnAC2477 146 207 6.40E-12 rrnB0299 1746 1814 7.80E-10 rrnAC1391 201 266 7.00E-13 PF00672: HAMP domain rrnB0156 750 814 0.00049 Gene Name start stop e-value rrnAC1096 251 310 1.10E-08 rrnAC0013 291 360 3.60E-16 rrnAC2461 159 220 6.00E-12 rrnAC2760 297 366 1.10E-16 rrnAC0477 167 228 4.20E-14 rrnAC2425 280 350 3.80E-10 rrnAC0988 435 505 6.20E-17 rrnAC0701 304 374 4.80E-12 rrnAC1114 349 410 1.40E-15 rrnAC2728 288 357 5.40E-15 rrnB0296 144 208 0.0003 rrnAC2495 60 130 3.80E-08 rrnB0180 2097 2165 0.0076 rrnAC0371 331 399 4.20E-10 rrnAC0475 135 191 0.00014 rrnB0156 251 319 0.0001 rrnAC3370 178 242 0.00859999 rrnAC0988 341 410 5.90E-18 rrnAC0789 358 420 2.30E-05 rrnAC0558 53 122 1.00E-05 rrnAC2945 254 313 0.0014 rrnAC1495 1082 1147 9.10E-05 rrnAC3482 348 409 0.00085 PF00785: PAC domain rrnAC0301 251 310 0.0018 Gene Name start stop e-value rrnB0133 477 541 0.0019 pNG7156 346 385 0.0058 rrnAC0413 307 367 0.0027 pNG7156 635 677 0.0014 rrnAC0794 308 369 4.40E-13 pNG7156 891 933 1.80E-07 rrnB0295 444 509 0.0011 rrnAC1626 310 352 2.30E-05 rrnAC0964 176 237 0.0033 rrnAC1626 435 477 0.0017 rrnAC1486 194 255 0.0022 rrnAC1626 559 601 2.40E-09 rrnAC0412 144 204 0.0057 rrnAC1626 683 725 4.00E-05 rrnAC1501 378 448 0.0005 rrnAC0848 330 372 8.00E-19 rrnAC3349 863 927 0.039 rrnAC2692 282 323 1.60E-10 rrnAC1693 107 169 0.0076 rrnAC2533 372 414 4.70E-08 rrnAC3347 128 193 0.0093 rrnAC3361 211 252 0.0032 rrnAC2997 147 211 0.0052 rrnAC3361 493 536 1.50E-07 rrnAC3361 620 662 8.00E-05 rrnAC3361 753 791 0.014 PF02518: Histidine kinase (C-terminal) domain rrnAC0086 293 335 0.023 Gene Name start stop e-value rrnAC0086 404 445 0.079 pNG7156 1199 1299 4.90E-21 rrnAC0086 528 570 5.70E-11 rrnAC0456 33 179 4.90E-36 rrnAC0574 225 266 1.20E-12 rrnAC0457 42 191 3.30E-17 rrnAC0574 349 391 9.40E-07 rrnAC2205 392 534 1.40E-32 rrnAC0075 222 263 0.0037 rrnAC2550 48 161 0.00011 rrnAC0075 346 388 2.20E-17 rrnAC1626 829 934 1.70E-28 rrnAC0075 471 511 0.0069 rrnAC3379 552 670 1.70E-28 rrnAC0991 376 417 0.0047 rrnAC0848 644 745 2.70E-29 rrnAC2416 229 271 0.004 PF02518: Histidine kinase (C-terminal) domain cont. PF00785: PAC domain cont. Gene Name start stop e-value Gene Name start stop e-value rrnAC3440 446 545 0.009 rrnAC2416 528 569 7.20E-06 rrnAC2692 584 684 1.30E-21 rrnAC2416 654 696 0.00015 rrnAC2533 525 645 5.80E-30 rrnAC2416 777 818 7.10E-09 rrnAC3361 902 1004 5.20E-27 rrnAC1806 214 256 1.20E-07 rrnAC0086 685 800 7.90E-29 rrnAC1806 340 380 6.10E-05 rrnAC0574 502 628 1.50E-18 rrnAC1687 214 255 0.04 rrnAC0075 622 722 4.10E-25 rrnAC2044 221 263 1.00E-05 rrnAC0991 531 635 3.60E-28 rrnAC2044 349 389 1.20E-08 rrnAC2372 525 641 1.30E-26 pNG7155 383 425 1.90E-08 rrnAC2416 929 1045 1.60E-24 rrnAC3050 324 366 1.80E-05 rrnAC2219 209 324 1.20E-27 rrnAC0410 81 121 0.0024 rrnAC1806 491 624 4.60E-24 rrnAC0356 211 248 0.089 rrnAC0247 275 396 8.90E-20 rrnAC0356 334 375 0.0084 rrnAC2044 636 781 6.90E-23 rrnAC2477 93 133 0.0015 pNG7155 542 646 2.10E-24 rrnB0299 200 242 8.20E-05 rrnAC3050 732 835 9.50E-28 rrnB0299 741 778 0.034 rrnAC0410 526 636 8.30E-39 rrnB0299 984 1024 0.041 rrnAC0487 357 459 7.00E-17 rrnB0299 1109 1150 5.90E-09 rrnAC2477 246 347 5.80E-24 rrnB0299 1237 1280 9.00E-10 rrnB0299 1856 1966 1.80E-36 rrnB0299 1366 1407 7.50E-08 rrnAC1391 303 405 1.30E-24 rrnAC1391 147 188 0.094 rrnB0156 856 963 1.60E-23 rrnB0156 411 450 0.00075 rrnAC1096 349 449 3.50E-19 rrnAC1096 79 119 0.091 rrnAC2461 257 373 4.20E-27 rrnAC1096 197 238 0.00028 rrnAC0477 265 396 3.00E-27 rrnAC2461 105 146 3.10E-06 rrnAC0988 542 642 8.70E-27 rrnAC1142 213 253 0.074 rrnAC1114 446 575 1.20E-21 rrnB0180 365 405 0.00042 rrnB0296 252 366 6.10E-25 rrnB0180 489 529 0.088 rrnB0180 2203 2306 1.50E-14 rrnB0180 729 771 6.80E-17 rrnAC0475 231 329 5.90E-18 rrnB0180 1024 1066 6.50E-09 rrnAC3370 284 391 1.20E-30 rrnB0180 1151 1195 0.00073 rrnAC0789 461 569 2.30E-14 rrnB0180 1277 1320 3.20E-10 rrnAC2945 360 462 3.90E-14 rrnB0180 1533 1575 6.50E-13 rrnAC1495 1187 1293 7.30E-24 rrnB0180 1810 1852 0.0022 rrnAC3482 451 561 6.00E-14 rrnB0180 1929 1970 0.00029 rrnAC0301 347 447 6.50E-17 rrnB0180 2050 2091 0.00025 rrnB0133 581 684 9.30E-21 rrnAC1495 348 390 0.0062 rrnAC0413 413 519 2.60E-27 rrnAC1495 636 678 5.40E-08 rrnAC2789 451 553 5.10E-22 rrnAC1495 908 948 0.00011 rrnAC0130 360 465 2.20E-20 rrnAC1663 396 438 8.20E-09 rrnB0295 550 656 3.60E-21 rrnAC1663 525 568 4.40E-12 rrnAC2616 322 427 3.70E-22 rrnAC3482 300 342 9.70E-05 rrnAC0964 278 385 2.50E-19 rrnAC0413 260 301 0.041 rrnAC1486 296 404 3.30E-15 rrnAC0130 207 249 1.40E-08 rrnAC0412 249 355 1.30E-24 rrnAC1501 210 252 0.015 rrnAC1501 488 595 1.80E-11 rrnAC1501 332 372 0.085 rrnAC2694 226 331 6.70E-20 rrnAC3347 82 122 4.20E-05 rrnAC3349 969 1075 2.10E-23 pNG7167 142 184 0.0029 rrnAC1693 216 320 2.40E-08 rrnAC3347 234 342 8.00E-16 rrnAC1346 299 406 4.30E-14 PF01590: GAF domain rrnAC2997 252 358 7.80E-18 Gene Name start stop e-value rrnAC2337 262 409 3.40E-14 pNG7156 412 548 3.20E-11 pNG7156 955 1085 0.071 pNG7159 401 532 1.10E-05 PF00989: PAS domain pNG7159 577 718 6.00E-07 Gene Name start stop e-value rrnAC3379 299 436 1.50E-09 pNG7156 146 208 0.016 rrnAC0848 394 524 1.70E-05 pNG7156 689 758 0.015 rrnAC2692 345 472 0.0024 pNG7156 820 881 2.90E-09 rrnAC2533 159 287 6.40E-07 rrnAC1626 364 426 0.0069 rrnAC3361 274 404 2.20E-09 rrnAC1626 485 547 7.30E-11 rrnAC0086 447 591 0.082 rrnAC1626 609 671 1.50E-13 rrnAC2372 276 405 0.0014 rrnAC1752 163 228 0.0001 rrnAC2416 305 443 0.0016 rrnAC3379 161 229 0.067 rrnAC0247 32 162 1.30E-07 rrnAC0848 135 200 3.30E-06 rrnAC1687 446 585 0.0017 rrnAC0848 255 321 0.00036 pNG7155 155 298 1.60E-11 rrnAC2692 210 273 2.10E-08 pNG7223 173 315 2.80E-10 rrnAC2533 298 363 0.011 pNG7223 344 481 1.10E-11 rrnAC3361 139 201 4.30E-05 pNG7223 675 816 0.035 rrnAC3361 548 612 0.019 rrnAC0410 261 395 0.0066 rrnAC0404 24 87 2.10E-11 rrnAC0356 402 540 0.0019 rrnAC0086 230 292 1.80E-09 rrnB0299 269 405 4.70E-10 rrnAC0086 457 518 9.10E-09 rrnB0299 1434 1570 5.00E-06 rrnAC0574 278 340 0.00093 rrnB0299 1594 1724 2.00E-06 rrnAC0075 271 337 0.0021 rrnB0156 600 735 0.041 rrnAC0075 400 462 2.20E-07 rrnAC2070 165 296 1.20E-06 rrnAC0991 195 254 0.083 rrnB0180 149 283 2.50E-07 rrnAC0991 303 365 7.20E-12 rrnB0180 798 939 0.0017 rrnAC2372 142 204 0.0016 rrnB0180 1597 1722 0.03 rrnAC2416 457 519 1.60E-07 rrnAC2211 167 298 5.60E-07 rrnAC1806 142 204 0.032 rrnAC0019 152 288 3.70E-15 rrnAC1687 141 203 2.70E-08 rrnAC0019 445 582 0.013 rrnAC2044 142 205 0.081 rrnAC1495 417 552 0.00055 rrnAC2044 275 339 1.90E-06 rrnAC1495 700 824 1.50E-08 rrnAC2044 401 463 3.40E-08 rrnAC1663 600 743 0.00047 pNG7155 312 374 3.40E-05 rrnAC0413 36 171 2.80E-05 PF00989: PAS domain cont. PF01590: GAF domain cont. Gene Name start stop e-value Gene Name start stop e-value rrnAC3050 374 439 0.038 rrnAC0794 158 286 0.00059 rrnAC0410 8 72 1.30E-06 rrnB0295 141 273 0.00018 rrnAC0410 133 197 0.027 rrnAC0964 28 151 0.011 rrnAC0487 135 197 4.00E-05 rrnAC3271 150 281 1.10E-13 rrnAC0356 139 205 0.00014 rrnAC0356 260 324 0.045 rrnAC2477 20 85 0.055 rrnB0299 10 73 0.077 rrnB0299 127 187 6.50E-10 rrnB0299 419 481 0.014 rrnB0299 545 608 0.0057 rrnB0299 669 731 1.90E-05 rrnB0299 915 975 7.40E-05 rrnB0299 1162 1226 2.20E-05 rrnB0156 336 402 2.00E-05 rrnAC1096 10 72 3.80E-08 rrnAC1096 124 187 0.011 rrnAC2461 34 96 3.80E-08 rrnAC1114 231 293 0.067 rrnAC1142 138 203 0.022 rrnAC1142 262 327 2.50E-08 rrnAC2070 6 66 0.078 rrnB0180 293 354 1.40E-08 rrnB0180 413 475 1.90E-09 rrnB0180 654 720 0.0002 rrnB0180 953 1014 0.05 rrnB0180 1332 1395 4.80E-14 rrnB0180 1458 1523 0.0056 rrnB0180 1736 1800 0.00046 rrnB0180 1857 1919 0.00065 rrnB0180 1975 2041 0.038 rrnAC2211 312 375 0.024 rrnAC0339 143 206 4.40E-09 rrnAC0674 197 258 0.00011 rrnAC0019 295 358 0.037 rrnAC1495 148 210 2.70E-07 rrnAC1495 276 340 3.90E-05 rrnAC1495 562 624 4.10E-10 rrnAC1495 834 896 0.014 rrnAC1495 960 1026 0.058 rrnAC1663 322 384 2.20E-06 rrnAC1663 450 514 0.054 rrnB0133 347 410 1.50E-07 rrnAC2789 240 301 0.0036 rrnAC0130 135 197 2.70E-11 rrnAC2616 103 166 0.0022 rrnAC1486 77 138 4.20E-11 rrnAC1501 131 186 0.011 rrnAC3349 598 662 0.023 rrnAC3347 7 70 0.026 A. Transcriptional regulators deciphered from Rosetta matches Cyclin A domain 1 like, TFIIB-like "Winged helix" repressor DNA binding domain (HTH) Gene name CATH I.D., Z-score, Probability Gene name CATH I.D., Z-score, Probability rrnAC2059 1.10.472.10,10.003618,0.428198 rrnB0084 1.10.10.10,6.3166937,0.402512 1.10.10.10,7.0476996,0.428564 1.10.10.10,7.1844317,0.456303 rrnAC2987 1.10.472.10,10.668899,0.561162 rrnAC0583 1.10.10.10,6.4040300,0.325012 1.10.10.60,6.5944764,0.339512 rrnAC3319 1.10.472.10,10.888133,0.450718 rrnB0007 1.10.10.10,7.1844317,0.350016 rrnAC1658 1.10.472.10,8.1323365,0.334127 rrnAC1147 1.10.10.10,7.2244547,0.352026 rrnB0185 1.10.472.10,8.1439717,0.347310 rrnAC0625 1.10.10.10,7.2360304,0.430226 1.10.10.10,5.6776870,0.325134 1.10.10.10,7.4903582,0.448287 rrnAC1963 1.10.472.10,8.2489460,0.400757 rrnAC0116 1.10.10.10,7.5344570,0.337471 rrnAC3359 1.10.472.10,8.3102932,0.348436 rrnAC3417 1.10.10.10,7.5404154,0.329536 1.10.472.10,8.7259440,0.37916 rrnB0114 1.10.472.10,8.4204319,0.357316 pNG2009 1.10.10.10,7.7678901,0.389429 pNG6053 1.10.472.10,8.4762485,0.385119 pNG3007 1.10.10.10,7.7774391,0.333087 rrnB0328 1.10.472.10,8.5239949,0.341826 rrnAC0025 1.10.10.10,7.9502897,0.387222 1.10.10.10,7.9038409,0.404731 rrnAC3470 1.10.472.10,8.8502856,0.383714 rrnAC2281 1.10.10.10,7.9751366,0.362329 pNG3005 1.10.472.10,8.8508538,0.322573 rrnAC2396 1.10.10.10,8.1009524,0.337038 rrnAC2135 1.10.472.10,8.8552536,0.357576 rrnAC2591 1.10.10.10,8.2136530,0.438271 rrnAC2686 1.10.10.10,8.3831686,0.358225 Classic zinc finger pNG4044 1.10.10.10,8.7094984,0.397792 Gene name CATH I.D., Z-score, Probability pNG1037 1.10.10.10,8.7432908,0.460002 rrnAC0582 3.30.160.60,6.7390678,0.339400 rrnAC0483 1.10.10.10,8.8973467,0.439155 lambda repressor-like DNA-binding domains Homeodomain-like Gene name CATH I.D., Z-score, Probability Gene name CATH I.D., Z-score, Probability rrnAC0288 1.10.260.10,6.3604714,0.307902 pNG7299 1.10.260.10,6.6220014,0.382065 rrnAC2251 1.10.10.60,6.3031714,0.391845 1.10.472.10,6.8042272,0.316579 pNG7309 1.10.10.60,6.5540825,0.302340 pNG5134 1.10.10.60,6.6595357,0.319028 Cyclin A domain 1 like, TFIIB-like rrnAC0363 1.10.10.60,6.7499816,0.338069 Gene name CATH I.D., Z-score, Probability rrnB0089 1.10.10.60,7.0747325,0.378860 1.10.10.60,7.2983001,0.394145 rrnAC2059 1.10.472.10,10.003618,0.428198 rrnAC1712 1.10.10.60,7.1725275,0.352306 rrnAC2987 1.10.472.10,10.668899,0.561162 rrnAC1994 1.10.10.60,7.7778424,0.326608 rrnAC3319 1.10.472.10,10.888133,0.450718 pNG6037 1.10.10.60,8.1240629,0.387675 rrnAC1658 1.10.472.10,8.1323365,0.334127 rrnB0185 1.10.472.10,8.1439717,0.347310 Probable RNA binding domain rrnAC1963 1.10.472.10,8.2489460,0.400757 Gene name CATH I.D., Z-score, Probability rrnAC3359 1.10.472.10,8.3102932,0.348436 rrnAC0095 3.30.70.330,6.9361750,0.309190 3.30.70.330,8.5533252,0.410636 rrnB0114 1.10.472.10,8.4204319,0.357316 pNG6053 1.10.472.10,8.4762485,0.385119 rrnB0328 1.10.472.10,8.5239949,0.341826 COMPLEX (TRANSCRIPTION REGULATION/DNA) (Nuclear rrnAC3470 1.10.472.10,8.8502856,0.383714 factor-appa-b p52; Transcription factor nfkb) pNG3005 1.10.472.10,8.8508538,0.322573 Gene name CATH I.D., Z-score, Probability rrnAC2135 1.10.472.10,8.8552536,0.357576 rrnAC3499 1.10.15.20,5.9527819,0.345372 Classic zinc finger lambda repressor-like DNA-binding domains Gene name CATH I.D., Z-score, Probability Gene name CATH I.D., Z-score, Probability rrnAC0582 3.30.160.60,6.7390678,0.339400 rrnAC0288 1.10.260.10,6.3604714,0.307902 pNG7299 1.10.260.10,6.6220014,0.382065 1.10.472.10,6.8042272,0.316579 B. Transcriptional regulators deciphered from Pfam matches PF00096: C2H2 zinc finger PF01022: Bacterial regulatory protein, arsR family (HTH) Gene name start stop bitScore e-value Gene name start stop bitScore e-value rrnAC0806 13 35 18.2 0.017 rrnAC1805 107 196 5.8 0.054 pNG2032 13 40 12.4 0.43 rrnAC0578 10 90 14.8 0.0069 rrnAC0476 3 25 15.9 0.084 pNG7194 11 90 4.4 0.073 rrnAC1397 32 55 23 0.00063 rrnAC2078 11 97 -1.2 0.26 rrnAC2751 4 27 18.1 0.019 rrnAC0914 16 94 -3.1 0.4 rrnAC3399 17 108 13 0.01 PF00320: GATA zinc finger pNG6142 1 77 -1.9 0.3 Gene name start stop bitScore e-value rrnAC3494 17 89 20.1 0.0021 pNG3023 60 96 -9.7 0.4 rrnAC1379 18 107 0.5 0.17 pNG6160 21 116 27.3 3.00E-05 PF00356: Bacterial regulatory proteins, lacI family rrnB0089 25 97 3.3 0.094 (HTH) rrnAC1256 266 362 -3 0.39 Gene name start stop bitScore e-value rrnAC0001 2 93 0.8 0.17 rrnAC0312 100 127 11.9 0.087 pNG7045 32 115 13.7 0.0089 rrnAC2622 17 44 8.2 0.26 rrnAC0961 32 116 28.5 1.30E-05 rrnAC2723 32 132 24.9 0.00017 PF00440: Bacterial regulatory proteins, tetR family pNG7312 33 116 1 0.16 (HTH): rrnB0118 35 135 18.1 0.0033 Gene name start stop bitScore e-value rrnAC0867 41 127 4.7 0.067 rrnAC2777 10 56 42.8 6.80E-10 pNG4023 43 125 1.8 0.13 pNG5131 1 46 43.6 3.90E-10 rrnAC3191 4 91 6.8 0.043 pNG7180 15 61 40.5 3.40E-09 pNG6075 51 150 5.9 0.052 pNG7308 16 62 43.8 3.40E-10 rrnB0014 53 136 2.5 0.11 pNG5071 16 62 24.2 0.00015 rrnB0052 66 157 40.1 4.40E-09 rrnAC1472 17 63 40.9 2.50E-09 rrnAC0161 68 147 22 0.0012 rrnAC3384 18 64 66.4 5.30E-17 pNG7343 7 101 0.2 0.19 pNG7183 18 64 42.7 7.50E-10 pNG7021 7 106 5.5 0.057 pNG5067 18 64 39.3 7.50E-09 pNG7146 71 151 5.5 0.056 rrnAC0019 763 813 -5.9 0.29 pNG6021 72 159 13.1 0.01 pNG7307 9 55 54 2.90E-13 rrnAC3447 7 81 37.2 3.20E-08 rrnB0222 9 79 9.4 0.023 PF01047: MarR family (HTH) Gene name start stop bitScore e-value PF01325: Iron dependent repressor, N-terminal DNA binding rrnAC0842 10 112 -22.4 0.24 domain (HTH) rrnAC3501 11 107 1 0.0032 Gene name start stop bitScore e-value rrnAC3310 11 109 -17 0.087 rrnAC3074 101 161 -6 0.18 rrnAC0230 11 112 -9 0.02 rrnAC1653 10 68 -7.2 0.24 rrnB0222 12 192 -26.1 0.47 rrnAC1269 1 56 8.5 0.0064 pNG6047 13 120 -19 0.13 rrnAC0341 1 58 -9.6 0.41 rrnAC0006 13 150 -7.6 0.016 rrnAC1825 1 60 61.6 1.50E-15 rrnAC1942 18 110 -25.9 0.45 pNG7038 1 60 -3.3 0.097 pNG7046 26 119 -17.5 0.095 rrnAC2037 1 60 56.5 5.10E-14 pNG7133 28 132 -18.3 0.11 rrnAC0496 1 62 84.9 1.50E-22 rrnAC2669 31 120 -24.2 0.32 pNG6011 4 58 -7.5 0.25 rrnAC2966 3 176 -13.8 0.048 rrnB0222 5 64 -0.4 0.05 rrnAC0503 4 99 2.1 0.0026 rrnAC1645 908 963 -9.1 0.36 rrnAC3082 58 162 -7.2 0.014 rrnAC1338 9 64 -0.9 0.056 pNG6034 6 101 -9.4 0.022 pNG6091 77 167 -23.8 0.31 PF02573: N-terminal HTH domain of molybdenum-binding protein rrnAC2285 8 104 -17.9 0.1 (HTH): rrnAC1645 909 1111 -23.9 0.31 Gene name start stop bitScore e-value rrnAC3074 97 312 -6.5 0.013 rrnAC3264 7 106 58.9 9.40E-15 PF01381: Helix-turn-helix 3 (HTH) PF01638: Transcriptional regulator Gene name start stop bitScore e-value Gene name start stop bitScore e-value rrnAC0872 109 166 15.7 0.081 rrnB0301 23 114 86.4 5.10E-23 rrnAC2519 132 185 38.5 1.30E-08 rrnAC0417 26 115 73.7 3.30E-19 rrnAC2428 182 238 14.1 0.12 rrnAC1303 26 117 119.7 4.80E-33 rrnAC1777 20 68 24.9 0.00017 pNG6155 39 114 26.6 1.90E-08 rrnAC1742 27 81 37.8 2.20E-08 rrnAC1764 40 92 19.4 0.0076 PF03551: Transcriptional regulator PadR-like family rrnAC2762 685 735 45.3 1.20E-10 Gene name start stop bitScore e-value rrnAC0535 94 148 47 3.70E-11 pNG6092 12 91 73.6 3.70E-19 rrnAC0440 9 63 53.3 4.80E-13 rrnAC3322 15 93 63.6 3.70E-16 pNG5119 1 79 32.3 8.70E-07 PF01402: Ribbon-helix-helix protein, copG family pNG1015 17 95 14.9 4.50E-05 Gene name start stop bitScore e-value pNG2042 17 95 9.8 0.00014 rrnAC3207 10 51 24.6 0.0002 pNG3007 17 95 -14.2 0.033 pNG6157 1 41 15.4 0.036 rrnB0161 1 81 63.8 3.30E-16 rrnAC1238 1 42 19 0.0097 rrnAC2383 18 86 -21.7 0.18 rrnAC2002 1 42 21.8 0.0014 pNG4025 19 101 1 0.0011 pNG5088 1 42 14.2 0.049 rrnAC1971 23 84 -14 0.031 rrnAC2856 1 43 7.1 0.33 rrnAC0435 2 81 76.4 5.10E-20 rrnAC0323 1 43 11 0.12 pNG2006 2 81 68.3 1.40E-17 rrnB0151 14 56 14.9 0.041 rrnAC0992 2 81 79.5 5.90E-21 pNG7160 2 43 44.7 1.80E-10 pNG6058 2 81 68.8 9.90E-18 rrnAC0583 2 43 12.6 0.076 rrnB0157 2 81 45.4 1.10E-10 pNG2039 25 66 25.6 0.0001 pNG6074 3 72 -8.8 0.0098 pNG5089 4 45 15.7 0.033 rrnB0074 39 115 -7.2 0.0069 rrnAC2748 53 94 22.9 0.00067 pNG6172 53 133 -22.8 0.23 rrnAC1567 61 102 18.3 0.016 pNG4043 5 83 -8.4 0.0088 rrnB0134 67 108 16.6 0.026 pNG4042 5 85 57.5 2.50E-14 rrnAC0316 7 48 11.2 0.11 rrnB0112 5 85 46.1 7.10E-11 pNG5140 5 85 31 1.20E-06 PF01614: Bacterial transcriptional regulator (HTH) rrnAC1521 6 101 -20.9 0.15 Gene name start stop bitScore e-value rrnAC2270 65 143 24.7 4.90E-06 rrnAC2801 104 289 -86.1 0.36 rrnB0084 6 84 -20.8 0.15 rrnB0235 104 290 121.9 1.00E-33 rrnAC1964 8 75 -24.3 0.33 rrnB0222 63 246 65.7 8.90E-17 rrnAC0768 8 84 20 1.40E-05 rrnAC0230 64 246 107.5 2.30E-29 rrnAC0913 9 77 -10.4 0.014 pNG7343 64 249 148.6 9.80E-42 rrnAC1338 64 250 194.9 1.10E-55 PF04967: HTH DNA binding domain (HTH) (bat like, found in rrnAC1964 65 250 150.6 2.40E-42 Halobacterium) pNG7021 65 251 139.4 5.60E-39 Gene name start stop bitScore e-value rrnAC0385 69 258 190.8 1.90E-54 rrnAC2160 151 203 62 1.10E-15 pNG7171 73 262 172.8 5.00E-49 rrnAC1895 154 206 56.9 3.80E-14 pNG7344 77 274 86.6 4.30E-23 rrnAC1217 155 207 80 4.20E-21 rrnAC1971 79 265 134.9 1.30E-37 rrnAC1786 156 208 63.9 3.10E-16 rrnAC1996 156 208 73.1 5.00E-19 PF02796: Helix-turn-helix (HTH) pNG7357 157 209 65.2 1.20E-16 Gene name start stop bitScore e-value rrnAC3490 158 210 79.3 7.10E-21 pNG4015 28 68 3.1 0.43 rrnAC3451 158 210 64.8 1.60E-16 rrnAC1941 5 52 4.6 0.27 rrnAC1953 159 211 81.7 1.30E-21 pNG5137 82 117 4.7 0.27 rrnB0253 160 212 68.5 1.30E-17 rrnAC2354 9 55 3.9 0.34 rrnAC1193 161 213 87.5 2.30E-23 rrnAC2022 162 214 57.4 2.80E-14 rrnAC3486 167 219 78.1 1.60E-20 PF02954: Bacterial regulatory protein, Fis family (HTH) rrnAC0640 171 223 74 2.80E-19 Gene name start stop bitScore e-value rrnAC0564 171 223 71.8 1.30E-18 rrnAC2519 124 160 -0.3 0.44 pNG6134 181 233 62.4 8.30E-16 rrnB0269 184 230 1.4 0.28 pNG7188 182 234 73.7 3.30E-19 PF04967: HTH DNA binding domain (HTH) (bat like, found in Halobacterium) (contd) Gene name start stop bitScore e-value rrnAC2936 183 235 97.3 2.70E-26 rrnAC2472 183 235 67.2 3.00E-17 rrnB0269 184 236 67.5 2.50E-17 rrnAC0376 184 236 83.7 3.40E-22 rrnAC3167 185 237 88.3 1.40E-23 rrnAC0231 189 241 87.8 2.00E-23 rrnAC2017 190 242 46.8 4.30E-11 rrnAC1541 192 244 59.4 6.70E-15 rrnAC2785 2 44 30.3 1.70E-06 rrnAC0199 42 86 -9.2 0.048 rrnAC2070 468 520 70.2 3.80E-18 rrnAC3229 495 547 92.7 6.30E-25 rrnAC1687 759 811 81.5 1.50E-21 rrnAC0019 759 811 82.4 8.20E-22 pNG7159 890 942 74.7 1.70E-19 rrnAC1663 913 965 87.8 1.90E-23 pNG7223 988 1040 72.8 6.30E-19