articles The genome sequence of the plant pathogen Xylella fastidiosa

The Xylella fastidiosa Consortium of the Organization for Nucleotide Sequencing and Analysis*,Sa˜o Paulo, Brazil

* A full list of authors appears at the end of this paper ......

Xylella fastidiosa is a fastidious, xylem-limited bacterium that causes a range of economically important plant diseases. Here we report the complete genome sequence of X. fastidiosa clone 9a5c, which causes citrus variegated chlorosis—a serious disease of orange trees. The genome comprises a 52.7% GC-rich 2,679,305-base-pair (bp) circular chromosome and two plasmids of 51,158 bp and 1,285 bp. We can assign putative functions to 47% of the 2,904 predicted coding regions. Efficient metabolic functions are predicted, with sugars as the principal energy and carbon source, supporting existence in the nutrient-poor xylem sap. The mechanisms associated with pathogenicity and virulence involve toxins, antibiotics and ion sequestration systems, as well as bacterium–bacterium and bacterium–host interactions mediated by a range of proteins. Orthologues of some of these proteins have only been identified in animal and human pathogens; their presence in X. fastidiosa indicates that the molecular basis for bacterial pathogenicity is both conserved and independent of host. At least 83 genes are bacteriophage-derived and include virulence-associated genes from other bacteria, providing direct evidence of phage-mediated horizontal gene transfer.

Citrus variegated chlorosis (CVC), which was first recorded in Brazil meningitidis10 (53.7%). This may reflect the lack of previous in 1987, affects all commercial sweet orange varieties1. Symptoms complete genome sequences from phytopathogenic bacteria. Plas- include conspicuous variegations on older leaves, with chlorotic mid pXF1.3 contains only two ORFs, one of which encodes a areas on the upper side and corresponding light brown lesions, with replication-associated protein. Plasmid pXF51 contains 64 ORFs, gum-like material on the lower side. Affected fruits are small, of which 5 encode proteins involved in replication or plasmid hardened and of no commercial value. A strain of Xylella fastidiosa stability and 20 encode proteins potentially involved in conjugative was first identified as the causal bacterium in 1993 (ref. 2) and found transfer. One ORF encodes a protein similar to the virulence- to be transmitted by sharpshooter leafhoppers in 1996 (ref. 3). CVC associated protein D (VapD), found in many other bacterial control is at present limited to removing infected shoots by pruning, pathogens11. Four regions of pXF51 present significant DNA simi- the application of insecticides and the use of healthy plants for new larity to parts of transposons found in plasmids from other bacteria, orchards. In addition to CVC, other strains of X. fastidiosa cause a suggesting interspecific horizontal exchange of genetic material. range of economically important plant diseases including Pierce’s The principal paralogous families are summarized in Table 2. The disease of grapevine, alfalfa dwarf, phony peach disease, periwinkle complete list of ORFs with assigned function is shown in Table 3. wilt and leaf scorch of plum, and are also associated with diseases in Seventy-five proteins present in the 21 completely sequenced mulberry, pear, almond, elm, sycamore, oak, maple, pecan and genomes in the COG database12 (as of 15th March 2000) were coffee4. The triply cloned X. fastidiosa 9a5c, sequenced here, was also found in X. fastidiosa. Each of these sequences was used to derived from the pathogenic culture 8.1b obtained in 1992 in Bordeaux (France) from CVC-affected Valencia sweet orange Table 1 General features of the Xylella fastidiosa 9a5c genome twigs collected in Macaubal (Sa˜o Paulo, Brazil) on May 21, 1992 (ref. 2). Strain 9a5c produces typical CVC symptoms on inoculation Main chromosome into experimental citrus plants5, and into Nicotiana tabacum (S. A. Length (bp) 2,679,305 G+C ratio 52.7% Lopes, personal communication) and Catharantus roseus (P. Brant- Open reading frames (ORFs) 2,782 Monteiro, personal communication)—two novel experimental Coding region (% of chromosome size) 88.0% hosts. Average ORF length (bp) 799 ORFs with functional assignment 1,283 ORFs with matches to conserved 310 General features of the genome hypothetical proteins The basic features of the genome are listed in Table 1 and a detailed ORFs without significant data base match 1,083 Ribosomal RNA operons 2 map is shown in Fig. 1. The conserved origin of replication of the (16SrRNA-Ala-TGC-tRNA-Ile-GAT- large chromosome has been identified in a region between the tRNA-23SrRNA-5SrRNA) putative 50S ribosomal protein L34 and gyrB genes containing tRNAs 49 (46 different sequences 6 corresponding to all 20 amino acids) dnaA, dnaN and recF . The Escherichia coli DnaA box consensus tmRNA 1 sequence TTATCCACA is found on both DNA strands close to ...... Plasmid pXF51 dnaA. In addition, there are typical 13-nucleotide (ACCACCAC- Length (bp) 51,158 CACCA) and 9-nucleotide (two TTTCATTGG and two TTTTA- G+C ratio 49.6% TATT) sequences in other intergenic sequences of this region. This Open reading frames (ORFs) 64 7 Protein coding region (% of plasmid size) 86.9% region is coincident with the calculated GC-skew signal inversion . ORFs with functional assignment 30 We have designated base 1 of the X. fastidiosa genome as the first Tof ORFs with matches to conserved 8 hypothetical proteins the only TTTTAT sequence found between the ribosomal protein ORFs without significant data base match 24 L34 gene and dnaA...... Plasmid pXF1.3 The overall percentage of open reading frames (ORFs) for which a Length (bp) 1,285 putative biological function could be assigned (47%) was slightly G+C ratio 55.6% below that for other sequenced genomes such as Thermotoga Open reading frames (ORFs) 2 8 9 ORFs with functional assignment 1 maritima (54%), Deinococcus radiodurans (52.5%) and Neisseria ......

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Table 2 Largest families of paralogous genes source of energy and anabolic precursors. The glyoxylate cycle is

Family Number of genes absent and the pentose phosphate pathway is incomplete. In the (total number of families = 312) (total number of genes = 853) latter pathway, genes for neither 6-phosphogluconic dehydrogenase ...... ATP-binding subunits of ABC transporters 23 nor transaldolase were identified. Reductases/dehydrogenases 12 Two-component system, regulatory proteins 12 Small molecule metabolism Hypothetical proteins 10 Transcriptional regulators 9 X. fastidiosa exhibits extensive biosynthetic capabilities, pre- Fimbrial proteins 9 sumably an absolute requirement for a xylem-dwelling bacterium. Two-component system, sensor proteins 9 ...... Most of the genes found in E. coli necessary for the synthesis of all amino acids from chorismate, pyruvate, 3-phosphoglycerate, glu- tamate and oxaloacetic acid16 were identified. However, some genes in X. fastidiosa are bi-functional, such as phosphoribosyl-AMP generate a phylogenetic tree of the 22 organisms. In 69% of such cyclohydrolase/phosphoribosyl-ATP pyrophosphatase (XF2213), trees, X. fastidiosa was grouped with Haemophilus influenzae and aspartokinase/homoserine dehydrogenase I (XF2225), imidazole- E. coli, consistent with a phylogenetic analysis undertaken with the glycerolphosphate dehydratase/histidinol-phosphate phosphatase 16S rRNA gene13. (XF2217) and a new diaminopimelate decarboxylase/aspartate One ORF, a cytosine methyltransferase (XF1774), is interrupted kinase (XF1116) that would catalyse the first and the last steps of by a Group II intron. The intron was identified on the basis of the lysine biosynthesis. In addition, the gene for acetylglutamate kinase presence of a reverse transcriptase-like gene (as in other Group II (XF1001) has an acetyltransferase domain at its carboxy-terminal introns), conserved splice sites, conserved sequence in structure V end that would compensate for the missing acetyltransferase in the and conserved elements of secondary structure14. Group II introns arginine biosynthesis pathway. Other missing genes include phos- are rare in prokaryotes, but have been found in different evolutive phoserine phosphatase, cystathionine ␤-lyase, homoserine O-suc- lineages including E. coli, cyanobacteria and proteobacteria15. cinyltransferase and 2,4,5-methyltetrahydrofolate-homocysteine methyltransferase. The first two enzymes are also absent in the Transcription, translation and repair Bacillus subtilis genome, the third is absent in Haemophilus influ- The basic transcriptional and translational machinery of X. fasti- enzae and the fourth is missing in both genomes12. We thus presume diosa is similar to that of E. coli16. Recombinational repair, nucleo- that alternative, unidentified enzymes complete the biosynthetic tide and base-excision repair, and transcription-coupled repair are pathways in these organisms and in X. fastidiosa. present with some noteworthy features. For example, no photolyase The pathways for the synthesis of purines, pyrimidines and was found, indicating exclusively dark repair. Although the main nucleotides are all complete. X. fastidiosa is also apparently capable genes of the SOS pathway, recA and lexA, are present, ORFs of both synthesizing and elongating fatty acids from acetate. Again, corresponding to the three DNA polymerases induced by SOS in however, some E. coli enzymes were not found, such as holo acyl- E. coli (DNA polymerases II, IVand V)17 are missing, indicating that carrier-protein synthase (also absent in Synechocystis sp.,H.influenzae the mutational pathway itself may be distinct. and Mycoplasma genitalium) and enoyl-ACP reductase (NADPH) (FabI) (also absent from M. genitalium, Borrelia burgdorferi and Energy metabolism Treponema pallidum)12. Even though X. fastidiosa is, as its name suggests, a fastidious X. fastidiosa appears to be capable of synthesizing an extensive organism, energy production is apparently efficient. In addition variety of enzyme cofactors and prosthetic groups, including biotin, to all the genes for the glycolytic pathway, all genes for the folic acid, pantothenate and coenzyme A, ubiquinone, glutathione, tricarboxylic acid cycle and oxidative and electron transport thioredoxin, glutaredoxin, riboflavin, FMN, FAD, pyrimidine chains are present. ATP synthesis is driven by the resulting chemi- nucleotides, porphyrin, thiamin, pyridoxal 5Ј-phosphate and lipo- osmotic proton gradient and occurs by an F-type ATP synthase. ate. In a number of the synthetic pathways, one or more of the Fructose, mannose and glycerol can be utilized in addition to enzymes present in E. coli are absent, but this is also true for at least glucose in the glycolytic pathway. There is a complete pathway for one other sequenced Gram-negative bacterial genome in each case12. hydrolysis of cellulose to glucose, consisting of 1,4-␤-cellobiosidase, We therefore again infer that the missing enzymes are either not endo-1,4-␤-glucanase and ␤-glucosidase, suggesting that cellulose essential or replaced by unknown proteins with novel structures. breakdown may supplement the often low concentrations of mono- saccharides in the xylem18. Two lipases are encoded in the genome, Transport-related proteins but there is no ␤-oxidation pathway for the hydrolysis of fatty acids, A total of 140 genes encoding transport-related proteins were presumably precluding their utilization as an alternative carbon and identified, representing 4.8% of all ORFs. For comparison, E. coli, energy source. Likewise, although enzymes required for the break- B. subtilis and M. genitalium have around 10% of genes encoding down of threonine, serine, glycine, alanine, aspartate and glutamate transport proteins, whereas Helicobacter pylori, Synechocystis sp. and are present, pathways for the catabolism of the other naturally Methanococcus jannaschii have 3.5–5.4% (ref. 19). Transport sys- occurring amino acids are incomplete or absent. tems are central components of the host–pathogen relationship The gluconeogenesis pathway appears to be incomplete. Phos- (Fig. 2). There are a number of ion transporters and transporters for phoenolpyruvate carboxykinase and the gluconeogenic enzyme the uptake of carbohydrates, amino acids, peptides, nitrate/nitrite, fructose-1,6-bisphosphatase, which are required to bypass the sulphate, phosphate and vitamin B12. Many different transport irreversible step in glycolysis, are not present. The absence of the first is compensated by the presence of phosphoenolpyruvate synthase and malate oxidoreductase, which together can generate Figure 1 Linear representation of the main chromosome and plasmids pXF51 and Q phosphoenolpyruvate from malate. There appears, however, to be pXF1.3 of the Xylella fastidiosa genome. Genes are coloured according to their no known compensating pathway for the absence of fructose-1,6- biological role. Arrows indicate the direction of transcription. Genes with frameshift and bisphosphatase. It is possible that among the large number of point mutations are indicated with an X. Ribosomal RNA genes, the tmRNA, the principal unidentified X. fastidiosa genes there are non-homologous genes repeats, prophages and the group II intron are indicated by coloured lines. Transfer RNAs that compensate for steps in such critical pathways. Barring this are identified by a single letter identifying the amino acid. Pie chart represents the possibility, however, the absence of a functional gluconeogenesis distribution of the number of genes according to biological role. The numbers below pathway implies a strict dependence on carbohydrates both as a protein-producing genes correspond to gene IDs.

152 © 2000 Macmillan Magazines Ltd NATURE | VOL 406 | 13 JULY 2000 | www.nature.com articles families are represented and include both small and large mechano- system controlling transcription of fimbrial subunits, presumably in sensitive conductance ion channels, a monovalent cation:proton response to host cues, and pilG, H, I, J and chpA, which encode a antiporter (CAP-2) and a glycerol facilitator belonging to the chemotactic system transducing environmental signals to the pilus major intrinsic protein (MIP) family. In addition, 23 ABC machinery. transport systems comprising 41 genes can be identified. X. fasti- In addition to the EPS and fimbriae, which are likely to have diosa appears to possess a phosphotransferase system (PTS) that central roles in the clumping of bacteria and in adhesion to the typically mediates small carbohydrate uptake. There are both the xylem walls, we also identified outer membrane protein homo- enzyme I and HPr components of this system, as well as a gene logues for afimbrial adhesins. Although fimbrial adhesins are well supposedly involved in its regulation (pstK or hprK); however, there characterized as crucial virulence factors in both plant and human is no PTS permease—an essential component of the phosphotrans- pathogens25, afimbrial adhesins, which are directly associated with ferase complex. The functionality of the system therefore remains in the bacterial cell surface, have been hitherto associated only with question. human and animal pathogens, where they promote adherence to There are five outer membrane receptors, including siderophores, epithelial tissue. Of the three putative adhesins of this kind iden- ferrichrome-iron and haemin receptors, which are all associated tified in X. fastidiosa, two exhibit significant similarity to each with iron transport. The energizing complexes, TonB–ExbB–ExbD other (XF1981, XF1529) and to the hsf and hia gene products of and the paralogous TolA–TolR–TolQ, essential for the functioning H. influenzae26. The third (XF1516) is similar to the uspA1 gene of the outer membrane receptors, are also present. In all, 67 genes product of Moraxella catarrhalis27. All these proteins share the encode proteins involved in iron metabolism. We propose that in X. common C-terminal domain of the autotransporter family28. fastidiosa the uptake of iron and possibly of other transition metal Direct experimentation will be required to establish whether these ions such as manganese causes a reduction in essential micro- adhesins promote binding to plant cell structures or components of nutrients in the plant xylem, contributing to the typical symptoms the insect vector foregut, or both. Nevertheless, their presence in the of leaf variegation. X. fastidiosa genome adds to the increasing evidence for the The X. fastidiosa genome encodes a battery of proteins that generality of mechanisms of bacterial pathogenicity, irrespective mediate drug inactivation and detoxification, alteration of potential of the host organism29. drug targets, prevention of drug entry and active extrusion of We also identified three different haemagglutinin-like genes. drugs and toxins. These include ABC transporters and transport Again, similar genes have not previously been identified in plant processes driven by a proton gradient. Of the latter, eight belong to pathogens. These genes (XF2775, XF2196, XF0889) are the largest in the hydrophobe/amphiphile efflux-1 (HAE1) family, which act as the genome and exhibit highest similarity to a Neisseria meningitidis multidrug resistance factors. putative secreted protein10.

Adhesion Intervessel migration X. fastidiosa is characteristically observed embedded in an extra- Movement between individual xylem vessels is crucial for effective cellular translucent matrix in planta20. Clumps of bacteria form colonization by X. fastidiosa. For this to occur, degradation of the pit within the xylem vessels leading to their blockage and symptoms of membrane of the xylem vessel is required. Of the known pectolytic the disease such as water-stress leaf curling. We deduce, from our enzymes capable of this function, a polygalacturonase precursor analysis of the complete genome sequence, that the matrix is and a cellulase were identified, although the former contains an composed of extracellular polysaccharides (EPSs) synthesized by authentic frameshift. These genes exhibited highest similarity to enzymes closely related to those of Xanthomonas campestris pv orthologues in Ralstonia solanacearum—which causes wilt disease campestris (Xcc) that produce what is commercially known as in tomatoes—where the polygalacturonase genes are required for xanthan gum. In comparison with Xcc, however, we did not find wild-type virulence. gumI (encoding glycosyltransferase V, which incorporates the terminal mannose), gumL (encoding ketalase which adds pyruvate Toxicity to the polymer) or gumG (encoding acetyltransferase which adds We identified five haemolysin-like genes: haemolysin III (XF0175), acetate), suggesting that Xylella gum may be less viscous than its which belongs to an uncharacterized protein family, and four others Xanthomonas counterpart. (XF0668, XF1011, XF2407, XF2759) which belong to the RTX toxin Positive regulation of the synthesis of extracelullar enzymes and family that contains tandemly repeated glycine-rich nonapeptide EPS in Xanthomomas is effected by proteins coded by the rpf motifs at the C-terminal domain. One of these ORFs is closely (regulation of pathogenicity factors) gene cluster21. Mutations in related to bacteriocin, an RTX toxin also found in the plant any of these genes in Xanthomomas results in failure to synthesize bacterium Rhizobium leguminosarum30. RTX or RTX-like proteins the EPS. In consequence, the strain becomes non-pathogenic21. are important virulence factors widely distributed among Gram- X. fastidiosa contains genes that encode RpfA, RpfB, RpfC and RpfF, negative pathogenic bacteria31. suggesting that both bacteria may regulate the synthesis of patho- There are two Colicin-V-like precursor proteins. Colicin V is an genic EPS factors through similar mechanisms. antibacterial polypeptide toxin produced by E. coli, which acts Fimbria-like structures are readily apparent upon electron micro- against closely related sensitive bacteria32. The precursors consist scopical observation of X. fastidiosa within both its plant and insect of 102-amino-acid peptides (XF0262, XF0263) that have the typical hosts22. Because of the high velocity of xylem sap passing through conserved leader 15-amino-acid motif, and have some similarity narrow portions of the insect foregut, fimbria-mediated attachment with Colicin V from E. coli at the remaining C-terminal portion. may be essential for insect colonization. Indeed, in the insect The necessary apparatus for Colicin biosynthesis and secretion is mouthparts the bacteria are attached in ordered arrays, indicating also present. Interestingly, in E. coli most of the genes necessary for specific and polarized adhesion23. In addition, fimbriae are thought biogenesis and export of Colicin V are in a gene cluster present in a to be involved in both plant–bacterium and bacterium–bacterium plasmid, whereas in X. fastidiosa these genes are dispersed in the interactions during colonization of the xylem itself. We identified 26 chromosome. genes encoding proteins responsible for the biogenesis and function We found four genes that may function in polyketide biogenesis: of Type 4 fimbria filaments. This type of fimbria is found at the poles polyketide synthase (PKS), pteridine-dependent deoxygenase, of a wide range of bacterial pathogens where they act to mediate daunorubicin C-13 ketoreductase and a NonF-related protein. adhesion and translocation along epithelial surfaces24. The genes These genes belong to the synthesis pathways of frenolicin, rapa- include pilS and pilR homologues, which encode a two-component mycin, daunorubicin and nonactin, respectively. These pathways

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Figure 2 A comprehensive view of the biochemical processes involved in Xylella fastidiosa represent symporters and antiporters (H+ or Na+ porters, unless noted otherwise). pathogenicity and survival in the host xylem. The principal functional categories are shown 2,5DDOL, 2,5-dichloro-2,5-cyclohexadiene-1,4-dol; EPS, exopolysaccharides; MATE, in bold, and the bacterial genes and gene products related to that function are arranged multi-antimicrobial extrusion family of transporters multidrug efflux gene (XF2686); MFS, within the coloured section containing the bold heading. Transporters are indicated as major facilitator superfamily of transporters; Pbp, ␤-lactamase-like penicillin-binding follows: cylinders, channels; ovals, secondary carriers, including the MFS family; paired protein (XF1621); RND, resistance-nodulation-cell division superfamily of transporters; dumbbells, secondary carriers for drug extrusion; triple dumbbells, ABC transporters; ROS, reactive oxygen species. bulb-like icon, F-type ATP synthase; squares, other transporters. Icons with two arrows

154 © 2000 Macmillan Magazines Ltd NATURE | VOL 406 | 13 JULY 2000 | www.nature.com articles include many more enzymes, which we did not find; however, some pathogenicity mechanisms. Some of these have not previously been of the genes listed lie close to ORFs without significant database postulated to occur in phytopathogens, providing new insights into matches, suggesting that at least one (as yet undiscovered) poly- the generality of these processes. Indeed, the availability of this first ketide pathway may be functional. complete plant pathogen genome sequence will now allow the initiation of the detailed comparison of animal and plant pathogens Prophages at the whole-genome level. In addition, the information contained Bacteriophages can mediate the evolution and transfer of virulence in the sequence should provide the basis for an accelerated and factors and occasional acquisition of new traits by the bacterial host. rational experimental dissection of the interactions between X. Because as much as 7% of the X. fastidiosa genome sequenced fastidiosa and its hosts that might lead to fresh insights into Ⅺ corresponds to double-stranded (ds) DNA phage sequences, mostly potential approaches to the control of CVC. from the Lambda group, we suspect that this route may have been of particular importance for this bacterium. It is noteworthy that Methods a very high percentage of phage-related sequences has also been The sequencing and analysis in this project were carried out by a network of 34 biology laboratories and one bioinformatics centre. The network is called the Organization for detected in a second vascular-restricted plant pathogen, 42 33 Nucleotide Sequencing and Analysis (ONSA) , and is entirely located in the state of Sa˜o Spiroplasma citri . We identified four regions, with a high density Paulo, Brazil. of ORFs homologous to phage sequences, that we considered to be prophages, in addition to isolated phage sequences dispersed Sequencing and assembly ϳ throughout the genome. Two of these prophages (each 42 kbp, The sequence was generated using a combination of ordered cosmid and shotgun designated XfP1 and XfP2) are similar to each other, lie in opposite strategies43. A cosmid library was constructed, providing roughly 15-fold genome cover- orientations in distinct regions and appear to belong to the dsDNA, age, containing 1,056 clones with average insert size of 40 kilobases (kb). High-density tailed-phage group. Both appear to contain most of the genes colony filters of the library were made, and a physical map of the genome was constructed 44 responsible for particle assembly, although we know of no reports using a strategy of hybridization without replacement . A total of 113 cosmid clones was selected for sequencing on the basis of the hybridization map and end-sequence analysis. of phage particle release from X. fastidiosa cultures. In prophage The cosmid sequences were assembled into 15 contigs covering 90% of the genome. XfP1, we found two ORFs between tail genes V and W that are Additionally, shotgun libraries with different insert sizes (0.8–2.0 kb and 2.0–4.5 kb) were similar to ORF118 and vapA from the virulence-associated region of constructed from nebulized or restricted genomic DNA cloned into plasmids, and the animal pathogen Dichelobacter nodosus, which by homology sequenced to achieve a 3.74-fold coverage of high-quality sequence (29,140 reads). Most of 34 the sequencing was performed with BigDye terminators on ABI Prism 377 DNA encode a killer and a suppressor protein . Interestingly, in prophage sequencers. XfP2, we found two other ORFs also between tail genes V and W Cosmid and shotgun sequences were assembled into six contigs. We identified sequence that are similar to hypothetical ORFs of Ralstonia eutropha trans- gaps by linking information from forward and reverse reads, and closed either by primer poson Tn4371 (ref. 35). The other two identified prophages, XfP3 walking or insert subcloning. The remaining physical gaps were closed by combinatorial PCR and by lambda clones selected from a ␭Dash library by end-sequencing. The and XfP4, are also similar in sequence to each other and to the collinearity between the genome and the obtained sequence was confirmed by digestion of H. influenzae cryptic prophage ␾flu (ref. 36). They both contain a genomic DNAwith AscI, NotI, SfiI, SmiI and SrfI, followed by comparison of the digestion 14,317-bp exact repeat. Few particle-assembly genes were found in pattern with the electronic digestion of the generated sequence. In addition, sequences these regions, suggesting that these prophages are defective. An ORF from both ends of most cosmid clones and 236 ␭ clones were used to confirm the orientation and integrity of the contigs. The sequence was assembled using similar to hicB from H. influenzae, a component of the major pilus phred+phrap+consed45. All consensus bases have quality with Phred value of at least 20. gene cluster in some isolates, was found in XfP4 (ref. 37). There are no unexplained high quality discrepancies, each consensus base is confirmed by The presence of virulence-associated genes from other organisms at least one read from each strand, and the overall error estimate is less than 1 in every within the prophage sequences is strong evidence for a direct role for 10,000 bases. bacteriophage-mediated horizontal gene transfer in the definition of the bacterial phenotype. ORF prediction and annotation ORFs were determined using glimmer 2.0 (ref. 46) and the glimmer post-processor RBSfinder (S. L. Salzberg, personal communication). A few ORFs were found by hand Absence of avirulence genes guided by BLAST41 results. Annotation was carried out in a cooperative way, mostly by Phytopathogenic bacteria generally have a limited host range, often comparison with sequences in public databases, using BLAST41 and tRNAscan-SE (ref. 47) confined to members of a single species or genus. This specificity is and was based on the functional categories for E. coli48. Only one tmRNA was located defined by the products of the so-called avirulence (avr) genes (K. Williams, personal communication). To help annotate transport proteins, we built a custom BLAST41 database using sequences from http://www-biology.ucsd.edu/ϳmsaier/ present in the pathogen, which are injected directly into host cells, transport/toc.html and compared our ORFs with these sequences. Phylogenetic trees for 38–40 41 on infection, through a type III secretory system . BLAST conserved COGs12 were built using ClustalX49 for multiple alignment and Phylip50. searches with all known avr and type III secretory system sequences Paralogous gene families (Table 2) were determined using BLASTX with the E-value failed to identify genes encoding proteins with significant simi- cut-off equal to e-5 and such that at least 60% of the query sequence and at least 30% of the larities in the genome of X. fastidiosa. Although the variability of avr subject sequence were aligned. genes amongst bacteria might account for this apparent lack, the Received 24 March; accepted 24 May 2000. high level of similarity of some components of the type III secretory 1. Rosseti, V. et al. Pre´sence de bacte´ries dans le xyle`me d’orangers atteints de chlorose varie´ge´e, une system argues against this. We suspect that these genes are, in fact, nouvelle maladie des agrumes au Bre´sil. C. R. Acad. Sci. 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NATURE | VOL 406 | 13 JULY 2000 | www.nature.com © 2000 Macmillan Magazines Ltd 155 articles

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Authors: A. J. G. Simpson1, F.C. Reinach2, P. Arruda3, F. A. Abreu4, M. Acencio5, R. Alvarenga2, L. M. C. Alves6, J. E. Araya7, G. S. Baia2, C. S. Baptista8, M. H. Barros8, E. D. Bonaccorsi2, S. Bordin9, J. M. Bove´ 10, M. R. S. Briones7, M. R. P. Bueno11, A. A. Camargo1,L.E.A. Camargo12, D. M. Carraro12, H. Carrer12, N. B. Colauto13, C. Colombo14, F. F. Costa9, M. C. R. Costa15, C. M. Costa-Neto16, L. L. Coutinho12, M. Cristofani17, E. Dias-Neto1, C. Docena2, H. El-Dorry2, A. P. Facincani6, A. J. S. Ferreira2, V. C. A. Ferreira18, J. A. Ferro6, J. S. Fraga4,S.C. Franc¸a19, M. C. Franco20, M. Frohme21, L. R. Furlan22, M. Garnier10, G. H. Goldman23, M. H. S. Goldman24, S. L. Gomes2, A. Gruber4,P.L.Ho25, J. D. Hoheisel21, M. L. Junqueira26, E. L. Kemper3, J. P. Kitajima27, J. E. Krieger26, E. E. Kuramae28, F. Laigret10, M. R. Lambais12,L.C.C. Leite25, E. G. M. Lemos6, M. V. F. Lemos29, S. A. Lopes19, C. R. Lopes13, J. A. Machado30†, M. A. Machado17, A. M. B. N. Madeira4,H.M.F. Madeira12†, C. L. Marino13, M. V. Marques8, E. A. L. Martins25, E. M. F. Martins18, A. Y. Matsukuma2, C. F. M. Menck8, E. C. Miracca5, C. Y. Miyaki11, C. B. Monteiro-Vitorello12, D. H. Moon20, M. A. Nagai5, A. L. T. O. Nascimento25, L. E. S. Netto11, A. Nhani Jr6, F. G. Nobrega8†, L. R. Nunes31, M. A. Oliveira32, M. C. de Oliveira33, R. C. de Oliveira31, D. A. Palmieri13, A. Paris13, B. R. Peixoto2, G. A. G. Pereira32, H. A. Pereira Jr6, J. B. Pesquero16, R. B. Quaggio2, P. G. Roberto19, V. Rodrigues34, A. J. de M. Rosa34, V. E. de Rosa Jr28,R.G.deSa´ 34, R. V. Santelli2, H. E. Sawasaki14, A. C. R. da Silva2, A. M. da Silva2, F. R. da Silva3,27, W. A. Silva Jr15, J. F. da Silveira7, M. L. Z. Silvestri2, W. J. Siqueira14, A. A. de Souza17, A. P. de Souza3, M. F. Terenzi23, D. Truffi12, S. M. Tsai20, M. H. Tsuhako18, H. Vallada35, M. A. Van Sluys33, S. Verjovski-Almeida2, A. L. Vettore3, M. A. Zago15, M. Zatz11, J. Meidanis27 & J. C. Setubal27.

Addresses: 1,Instituto Ludwig de Pesquisa sobre o Caˆ ncer, Rua Prof. Antonio Prudente,109 – 4o andar, 01509-010, Sa˜ o Paulo - SP,Brazil; 2, Departamento de Bioquı´mica, Instituto de Quı´mica, Universidade de Sa˜ o Paulo, Av. Prof. Lineu Prestes, 748, 05508-900, Sa˜ o Paulo - SP,Brazil; 3, Centro de Biologia Molecular e Engenharia Gene´ tica, Universidade Estadual de Campinas, Caixa Postal 6010,13083-970, Campinas – SP,Brazil; 4, Laborato´ rio de Biologia Molecular, Departamento de Patologia, Faculdade de Medicina Veterina´ ria e Zootecnia, Universidade de Sa˜ o Paulo, Av. Prof. Dr. Orlando Marques de Paiva, 87, 05508-000, Sa˜ o Paulo – SP,Brazil; 5, Disciplina de Oncologia, Departamento de Radiologia, Faculdade de Medicina, Universidade de Sa˜ o Paulo, Av. Dr. Arnaldo, 455, 01296-903, Sa˜ o Paulo – SP, Brazil; 6, Departamento de Tecnologia,Faculdade de Cieˆ ncias Agra´ rias e Veterina´ rias de Jaboticabal, Universidade Estadual Paulista, Via

156 © 2000 Macmillan Magazines Ltd NATURE | VOL 406 | 13 JULY 2000 | www.nature.com articles de Acesso Prof. Paulo D. Castellane s/n, Km 5,14884-900, Jaboticabal – SP, Brazil; 7, Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de Sa˜ o Paulo, Rua Botucatu, 862, 04023-062, Sa˜ o Paulo – SP,Brazil; 8, Departamento de Microbiologia, Instituto de Cieˆ ncias Biome´ dicas, Universidade de Sa˜ o Paulo, Av. Prof. Lineu Prestes,1374, 05508-900, Sa˜ o Paulo – SP,Brazil; 9, Hemocentro, Faculdade de Cieˆ ncias Me´ dicas, Universidade Estadual de Campinas,13083-97, Campinas – SP, Brazil; 10, Institut National de la Recherche Agronomique et Universite´ Victor Se´ galen Bordeaux 2, 71 Avenue Edouard Bourleaux, Laboratoire de Biologie Cellulaire et Mole´ culaire, 33883 Vilenave d’Ornon Cedex, France; 11, Departamento de Biologia, Instituto de Biocieˆ ncias, Universidade de Sa˜ o Paulo, Rua do Mata˜ o, 277,05508-900, Sa˜ o Paulo – SP,Brazil; 12, Escola Superior de Agricultura Luiz de Queiroz, Universidade de Sa˜ o Paulo, Av. Pa´ dua Dias,11,13418-900, Piracicaba – SP,Brazil; 13, Departamento de Gene´ tica, Instituto de Biocieˆ ncias, Universidade Estadual Paulista, Distrito de Rubia˜ o Junior,18618-000, Botucatu – SP,Brazil; 14, Centro de Gene´ tica, Biologia Molecular e Fitoquı´mica, Instituto Agronoˆ mico de Campinas, Av. Bara˜ o de Itapura,1481, Caixa Postal 28,13001-970, Campinas – SP, Brazil; 15, Departamento de Clı´nica Me´ dica, Faculdade de Medicina de Ribeira˜ o Preto, Universidade de Sa˜ o Paulo, Av. Bandeirantes, 3900,14049-900, Ribeira˜ o Preto – SP,Brazil; 16, Departamento de Biofı´sica, Escola Paulista de Medicina, Universidade Federal de Sa˜ o Paulo, Rua Botucatu, 862, 04023-062, Sa˜ o Paulo – SP, Brazil; 17, Centro de Citricultura Sylvio Moreira, Instituto Agronoˆ mico de Campinas, Caixa Postal 04,13490-970, Cordeiro´ polis – SP, Brazil; 18, Laborato´ rio de Bioquı´mica Fitopatolo´ gica e Laborato´ rio de Imunologia, Instituto Biolo´ gico, Av. Cons. Rodrigues Alves,1252, 04014-002, Sa˜ o Paulo – SP,Brazil; 19, Departamento de Biotecnologia de Plantas Medicinais, Universidade de Ribeira˜ o Preto, Av. Costa´ bile Romano, 2201,14096-380, Ribeira˜ o Preto – SP,Brazil; 20,Centro de Energia Nuclear na Agricultura, Universidade de Sa˜ o Paulo, Av. Centena´ rio, 303, Caixa Postal 96,13400-970, Piracicaba – SP,Brazil; 21, Funktionelle Genomanalyse, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 506, D-69120, Heidelberg, Germany; 22, Departamento de Melhoramento e Nutric¸a˜ o Animal, Faculdade de Medicina Veterina´ ria e Zootecnia, Universidade Estadual Paulista, Fazenda Lageado, Caixa Postal 560,18600-000, Botucatu - SP, Brazil; 23, Departamento de Cieˆ ncias Farmaceˆ uticas , Faculdade de Cieˆ ncias Farmaceˆ uticas de Ribeira˜ o Preto, Universidade de Sa˜ o Paulo, Av. do Cafe´ s/n,14040-903, Ribeira˜ o Preto – SP, Brazil; 24, Departamento de Biologia, Faculdade de Filosofia, Cieˆ ncias e Letras de Ribeira˜ o Preto, Universidade de Sa˜ o Paulo, Av. Bandeirantes, 3900,14040-901,Ribeira˜ o Preto – SP,Brazil; 25, Centro de Biotecnologia, Instituto Butantan, Av. Vital Brasil,1500, 05503-900, Sa˜ o Paulo – SP, Brazil; 26, Laborato´ rio de Gene´ tica e Cardiologia Molecular/LIM 13, Instituto do Corac¸a˜ o (InCor), Faculdade de Medicina, Universidade de Sa˜ o Paulo, Av. Dr. Ene´ as de Carvalho Aguiar, 44, 05403-000, Sa˜ o Paulo – SP, Brazil; 27, Instituto de Computac¸a˜ o, Universidade Estadual de Campinas, Caixa Postal 6176,13083-970, Campinas – SP, Brazil; 28, Departamento de Produc¸a˜ o Vegetal, Faculdade de Cieˆ ncias Agronoˆ micas, Universidade Estadual Paulista, Fazenda Lageado, Caixa Postal 237,18603-970, Botucatu – SP, Brazil; 29, Departamento de Biologia Aplicada a` Agropecua´ ria, Faculdade de Cieˆ ncias Agra´ rias e Veterina´ rias de Jaboticabal, Universidade Estadual Paulista, Via de Acesso Prof. Paulo Donato Castellane,14884-900, Jaboticabal – SP,Brazil; 30, Hospital do Caˆ ncer – A.C. Camargo, R. Antonio Prudente, 211, 01509-010, Sa˜ o Paulo – SP, Brazil; 31, Nu´ cleo Integrado de Biotecnologia, Universidade de Mogi das Cruzes, Av. Dr. Caˆ ndido Xavier de Almeida Souza, 200, 08780-911,Mogi das Cruzes – SP,Brazil; 32, Departamento de Gene´ tica e Evoluc¸a˜ o, Instituto de Biologia, Universidade Estadual de Campinas, Caixa Postal 6010,13083-970, Campinas– SP, Brazil; 33, Departamento de Botaˆ nica, Instituto de Biocieˆ ncias, Universidade de Sa˜ o Paulo, Rua do Mata˜ o, 277, 05508-900, Sa˜ o Paulo - SP,Brazil; 34, Departamento de Parasitologia, Microbiologia e Imunologia, Faculdade de Medicina de Ribeira˜ o Preto, Universidade de Sa˜ o Paulo, Av. Bandeirantes, 3900,14049-900, Ribeira˜ o Preto – SP,Brazil; 35, Departamento de Psiquiatria, Instituto de Psiquiatria, Faculdade de Medicina, Universidade de Sa˜ o Paulo, Rua Dr. Ovı´deo Pires de Campos s/n, Sala 4051 (3o. andar), 05403-010, Sa˜ o Paulo – SP, Brazil. † Present addresses: Novartis Seeds LTDA, Av. Prof. Vicente Rao, 90, 04706-900, Sa˜o Paulo – SP, Brazil (J. A. Machado); Centro de Cieˆncias Agra´rias e Ambientais, Pontifı´cia Universidade Cato´lica do Parana´, BR-376, Km 14, Caixa Postal 129, 83010-500, Sa˜o Jose´ dos Pinhais – PR, Brazil (H. M. F. Madeira); Instituto de Pesquisa e Desenvolvimento, Universidade do Vale do Paraı´ba, Av. Shishimi Hifumi, 2911, 12244-000, Sa˜o Jose´ dos Campos – SP, Brazil (F. G. Nobrega).

NATURE | VOL 406 | 13 JULY 2000 | www.nature.com © 2000 Macmillan Magazines Ltd 157 articles 1215000 135000 945000 270000 2295000 1485000 810000 1080000 1755000 1350000 1890000 2025000 405000 2160000 1620000 2430000 540000 675000 2565000 1120 1119 2414 L 1397 1398 2133 2134 1396 2413 1395 1691 1692 1257 1258 1259 1690 984 985 986 1256 2685 2686 2687 2132 2131 983 2130 2411 2412 982 2684 2129 2265 2266 2267 2268 2264 981 709 710 711 712 713 2263 708 1687 1688 1689 548 549 550 547 2127 2128 1686 546 1685 1975 1976 1977 1978 1979 2410 2126 545 1684 131 132 133 134 2125 130 543 2124 1974 542 544 541 1526 539 540 249 250 251 252 253 254 255 256 257 258 384 385 386 387 388 389 390 391 392 1388 1389 1390 1391 1392 1393 1394 538 248 1387 247 246 1523 1524 1525 1527 1528 1529 383 REPEAT-IN-XfP3-AND-XfP4 1678 126 127 128 129 703 704 705 706 707 1522 2120 2121 2122 2123 S 702 LR-3 701 1521 700 1250 1251 1252 1253 1254 1255 1520 2119 LR-6 XfP4 699 698 2118 534 535 536 537 1826 LR-6 1249 2117 533 XfP1 1674 1675 1676 1677 1679 1680 1681 1682 1683 695 696 697 1247 1248 1673 380 381 382 694 1246 379 693 1672 2115 2116 2676 2677 2678 2679 2680 2681 2682 2683 1671 692 2255 2256 2257 2258 2259 2260 2261 2262 1670 2542 2543 2544 2545 2546 2547 2548 2549 2550 2551 2552 691 2675 690 1669 688 2541 2254 972 973 974 975 976 977 978 979 980 2674 2253 2540 1964 1965 1966 1967 1968 1969 1970 19711972 1973 2114 2406 2407 2408 2409 971 2673 2113 2405 1963 970 2539 2112 2404 1516 1517 1518 1519 LR-5 2403 968 969 2402 V 526 527 528 529 530 531 532 2401 2670 2671 2672 2110 2111 2669 1241 1242 1243 1244 1245 1515 2109 2668 2667 525 2108 C 2666 1663 1664 1665 1666 16671668 2679305 1513 1514 2782 2665 1240 2535 2536 2537 2538 683 684 685 686 687 689 1662 965 1239 1512 1661 1660 1238 1237 2534 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 1116 1117 1118 682 1236 2105 2106 2107 2662 2663 2664 1235 2104 2246 2247 2248 2249 2250 2251 2252 1658 1659 1105 2661 1817 1818 1819 1820 1821 1822 1823 1824 1825 1827 1828 1829 1830 1831 1832 1833 1834 1835 1836 1837 1838 K 2103 2660 2245 1657 1816 521 522 523 524 114 115 116 117 118 119 120 121 122 123 124 125 2102 2659 1378 1379 1380 1381 1382 1383 1384 1385 1386 679 680 681 113 2658 1655 1656 1956 1957 1958 1959 1960 1961 1962 1377 2657 678 959 960 961 962 963 964 966 967 520 1654 2656 V 2395 2396 2397 2398 2399 2400 958 233 234 235 236 237 238 239 240 241 242 243 244 245 1955 2655 1653 1652 518 519 2654 1651 2778 2779 2780 2781 2099 2100 2101 2653 2394 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 M 517 829 1813 1814 1815 1102 1103 1104 109 110 111 112 956 957 2777 2241 2242 2243 2244 2098 1101 2528 2529 2530 2531 2532 2533 515 516 2392 2393 108 1100 955 2391 514 2527 2240 1099 1812 2239 2389 2390 1503 2388 1096 1097 1098 1811 1095 1810 1645 1646 1647 1648 1649 1650 1809 1093 1094 1644 1808 1092 227 228 229 230 231 232 LR-7 1807 E 1090 1091 LR-5 1368 1369 1370 1371 1372 1373 1374 1375 1376 1089 S 2645 2646 2647 2648 2649 2650 2651 2652 1367 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 2521 2522 2523 2524 2525 2526 Q 2520 1806 2519 2518 360 1227 1228 1229 1230 1231 1232 1233 1234 1087 1088 2517 1226 2516 2515 1086 99 100 101 102 103 104 105 106 107 LR-4 2514 1085 LR-1 2641 26422643 2644 2513 2774 2775 2776 1084 98 Y G T 1802 1803 1804 1805 2383 2384 2385 2386 2387 2640 2773 1801 2382 2381 2772 W 2510 2511 2512 667 668 669 670 671 672 673 674 675 676 677 2380 2639 2771 2509 2379 2508 2378 1081 1082 1083 2638 666 2377 27692770 500 502 816 817 818 819 820 821 822 823 824 825 826 827 828 2637 2768

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345

2081 2082 2083 2084 2085 2086 20872088 2089 2090 2091 2092 2093 2094 2095 2096 2097 2080 2.44 1071 1072 1073 2222 2223 2224 2225 2226 2227 2079 1350 1351 480 481 1070 2078 2758 2759 2760 2077 N 342 343 344 2221 2757 1349 341 2631 2076 2756 1932 1933 1934 1935 1936 1937 1938 2075 2755 650 651 652 653 654 655 656 657 658 659 660 661 662 2074 649 2073 1931 2072 1781 1782 1783 1784 178517861787 1788 2071 2496 2497 2498 2499 2500 2501 2502 478 479 2495 1930 924 925 926 927 928 929 930 2494 1929 1209 1210 1211 1212 1213 1214 646 2752 2753 2754 1780 1482 1483 1484 1485 1486 1487 1488 1489 1490 1491 2493 923 1779 2492 1208 2751 2068 2069 2070 2628 2629 2630 1481 1207 644 645 647 648 1206 2067 2491 1778 338 339 340 2750 1927 1928 477 1344 1345 1346 1347 1348 2066 1205 2490 643 337 2749 2065 642 2627 336 1204 2064 2489 335 1343 S 334 1342 333 2063 1203 1926 Frameshift/Point mutation (FSPM) Intron (letter indicates amino acid) tRNA 1776 1777 1341 331 A 474 1340 330 332 2213 2214 2215 2216 2217 2218 2219 2220 640 641 2212 1200 1201 1202 1620 1621 1622 1623 1624 1625 1626 1627 1628 1629 1630 1631 1632 1633 1634 329 1061 1062 1063 1064 1065 1066 1067 1068 1069 202 203 204 205 206 207 208 209 210 211 212 213 214 215216 217 639 1478 2211 A 2745 2746 2747 2748 201 638 1199 2357 2358 2359 2360 2361 2362 2363 2364 2365 2366 2367 2368 2369 2370 2371 2372 2373 1619 LE 2210 2744 2356 918 1775 1923 1924 1925 637 1060 917 919 920 921 922 2485 2486 2487 2488 1059 71 72 73 74 75 76 77 78 79 80 81 82 83 85 84 86 87 88 89 90 91 92 93 94 96 95 97 916 LR-3 1617 1618 1337 1338 1339 1922 1 1058 2484 1336 2354 2355 1616 1057 2623 2624 2625 2626 2353 1056 2622 469 470 471 472 473 475 476 2352 2621 1055 468 2351 2059 2060 2061 2062 2482 2483 Transport Mobile genetic elements Pathogenicity and adaptation Conserved hypothetical Hypothetical 1614 1615 195 196 197 198 199 200 1772 1773 1774 1613 194 rRNA-operon I 1771 1195 1196 1197 1198 2058 A 1473 1474 1475 1476 1477 1479 1480 2481 1194 2057 2056 1472 2055 2479 2480 2739 2740 2741 2742 2743 2617 2618 2619 2620 2348 2349 2350 2478 2347 2616 2204 2205 2206 2207 2208 2209 2346 1609 1610 1611 1612 2203 2345 2738 463 464 465 466 467 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 2737 462 1191 1192 1193 789 70 2613 2614 2615 2201 2202 2612 1608 788 Macromolecule metabolism processing DNA processing RNA Cell structure Undefined category Cellular processes 787 1329 1330 13311332 1333 1334 1335 2611 D V 2200 1328 69 R 2199 2198 1327 903 2049 2050 2051 2052 2053 2054 1326 622 627 2048 315 620 621 623 624 625 626 628 629 630 631 632 633 634 635 636 2733 2734 2735 2736 2469 2470 2471 2472 2473 2474 2475 2476 2477 1 kb 900 901 902 904 905 906 907 908 909 910 911 912 913 914 915 1761 1762 1764 1765 1766 1767 1768 1769 1770 183 184 185 186 187 188 189 190 191 192 193 781 782 783 784 785 786 1044 1051 Intermediary metabolism Energy metabolism Regulatory functions Biosynthesis of small molecules Amino acid biosynthesis Nucleotide biosynthesis 2468 619 182 1760 1905 1909 1918 899 G 2732 1321 1322 1323 1324 1325 618 2338 2339 2340 2341 2342 2343 2344 617 1186 1187 1188 1189 1190 2731 1759 1600 1601 1602 1603 1604 1605 1606 1607 1320 2730 1758 2337 1599 LR-7 1598 L 1597 2336 1041 1042 1043 1045 1046 1047 1048 1049 1050 1052 1053 1054 1596 1756 1763 180 181 2335 1595 1040 2728 2729 2605 2606 2607 2608 2609 2610 2465 2466 2467 1594 2604 60 61 62 63 64 65 66 67 68 179 2727 2464 59 1593 58 2463 1592 2726 57 2462 1591 2602 2603 56 55 449 450 451 452 453 454 455 456 457 458 459 460 461 1183 1184 1185 1590 448 1589 2601 51158 L 2195 2196 2197 2037 2038 2039 2040 2041 2042 2043 2044 2045 2046 2047 307 308 309 310 311 312 313 314 316 317 318 319 320 321 322 323 324 325 326 327328 2194 2193 306 2036 2459 2460 2461 305 775 776 777 778 779 780 2458 L 304 2192 774 1586 1587 1588 773 444 445 446 447 1585 2191 443 2034 2035 2190 772 2189 771 302 303 2033 2188 301 1035 1036 1037 1038 1039 2032 2187 2031 1034 1033 2029 1582 1583 1584 1581 XfP3 2028 1580 1579 2027 2030 REPEAT-1 REPEAT-1 767 768 769 770 2026 766 2324 2325 2326 2327 2328 2329 2330 2331 2332 2333 2334 1308 1309 1310 1311 1312 1313 1314 1315 1316 1317 1318 1319 606 607 608 609 610 611 612 613 614 615 616 2183 2184 2185 2186 605 LR-7 170 171 172 173 174 175 176 177 178 2323 2182 2181 2322 2180 2720 2721 2722 2723 2724 2725 2321 2719 1175 1176 1177 1178 1179 1180 1181 1182 2718 1307 1029 1030 1031 1032 2320 1574 1575 1576 1577 1578 1306 1174 2319 REPEAT-IN-XfP3-AND-XfP4 1573 2318 1028 1446 1447 1448 1449 1450 1451 1452 1453 1454 1455 1456 1457 1458 1459 1460 1461 1462 1463 1464 1465 1466 1467 1468 1469 1470 1471 2317 rRNA-operon 294 295 296 297 298 299 300 I A 1445 2316 F 1171 1172 1173 2315 1887 1888 1889 1890 1891 1892 1893 1894 1895 1896 1897 1898 1899 1900 1901 1902 1903 1904 19061907 1908 1910 1911 1912 1913 1914 1915 1916 1917 1919 1920 192 1170 tmRNA 1169 LR-2 1168 42 43 44 45 46 47 48 49 50 51 52 53 54 1738 1739 1740 1741 1742 1743 1744 1745 1746 1747 1748 1749 1750 1751 1752 1753 1754 1755 1757 1886 1167 1568 1569 1570 1571 1572 1885 41 1166 1567 1884 1737 1566 1165 1883 2311 2312 2313 2314 1565 2018 2019 2020 2021 2022 2023 2024 2025 1164 1564 1163 1881 1882 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 2017 1024 1025 1026 1027 2173 2174 2175 2176 2177 2178 2179 1563 1162 2310 1023 2172 1161 1880 G 1160 427 1879 1022 2015 2016 1159 1561 1562 1021 755 756 757 758 759 760 761 762 763 764 765 2014 1158 1157 1020 1156 1437 1438 1439 1440 14411442 1443 1444 1019 754 1732 1733 1734 1735 1736 1560 1155 2012 2013 2169 2170 2171 1018 1436 1875 1876 1877 1878 2011 2582 2583 2584 2585 2586 2587 2588 2589 2590 2591 2592 2593 2594 2595 2596 2597 2598 2599 2600 1559 1154 1731 1017 1558 1153 164 165 166 167 168 169 1874 2168 1557 1556 1294 12951296 1297 1298 1299 1300 1301 1302 1303 1304 1305 2167 2581 1873 R 1152 2305 2306 2307 2308 2309 163 1434 1435 1293 1872 LR-1 2304 2440 1433 1014 1015 1016 751 752 753 1432 1013 2008 2009 2010 1431 750 1430 2007 1150 1151 1869 1870 1871 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 1868 2438 2439 2441 2442 2443 2444 2445 2446 2447 2448 2449 2450 2451 2452 2453 2454 2455 2456 2457 1149 2164 2165 2166 1727 1728 1729 1730 35 1867 2163 1148 878 2162 158 160 2437 1147 1726 LR-4 1866 2300 2301 2302 2303 2004 2005 2006 1865 2003 2299 284 285 286 287 288 289 290 291 292 293 746 1864 2002 283 745 747 748 749 2159 2160 2161 P 2298 1863 2001 744 2297 2158 1862 1861 1723 1724 1725 29 30 31 32 33 34 1286 1287 1288 1289 1290 1291 1292 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 1722 1859 1860 1010 1011 1012 2156 2157 28 582 2295 2296 1721 S 1009 419 420 421 422 423 424 425 426 1998 1999 2000 1285 1720 580 581 1008 1284 K 418 2294 871 1997 579 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 1007 M 1858 578 2293 24 24 25 26 27 23 2292 2154 2155 416 417 23 1718 1719 2570 2571 2572 2573 2574 2575 2576 2577 2578 2579 2580 740 741 742 743 22 415 2153 2569 739 21 738 20 21 22 1140 1141 1142 1143 1144 1145 1146 19 G 575 576 577 2567 2568 1548 1549 1550 1551 1552 1553 1554 1555 574 1139 2703 2704 2705 2706 2707 2708 2709 2710 2711 2712 2713 2714 2715 2716 2717 2566 1422 1423 1424 1425 1426 1427 1428 1429 2702 2565 1421 572 573 1420 2150 2151 2152 571 1137 1138 1278 1279 1280 1281 1282 1283 1716 1717 2149 1547 1992 1993 1994 1995 1996 1418 1419 2148 1136 1417 411 412 413 414 1277 1276 1135 733 734 735 736 737 1134 2561 2562 2563 2564 1275 1545 1546 1991 2285 2286 2287 2288 2289 2290 2291 2560 1274 732 2284 273 274 275 276 277 278 279 280 281 282 1273 1715 410 1544 1543 272 1714 1272 2699 2700 2701 1542 271 1541 270 1271 1413 1414 1415 1416 730 731 2282 2283 1712 1713 1131 1132 1133 2698 1412 R 2281 861 862 863 864 865 866 867 868 869 870 872 873 874 875 876 877 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 1411 729 565 566 567 568 569 570 1130 1711 1538 1539 1540 1410 1129 998 999 1000 1001 1002 1003 1004 1005 1006 860 1987 1988 1989 1990 564 2425 2426 2427 2428 2429 2430 2431 2432 2433 2434 2435 2436 1710 2279 2280 2424 1537 997 LR-2 2278 1986 561 562 563 11 12 13 14 15 16 17 18 19 20 Main Chromosome Gene Map Plasmid pXF51 Gene Map Plasmid pXF1.3 Gene Map 403 266 267 268 269 10 XfP1 2140 2141 2142 2143 2144 2145 2146 2147 560 855 856 857 858 859 REPEAT-2 559 1847 1848 1849 1850 1851 1852 1853 1854 1855 1856 1857 REPEAT-2 1846 P 558 1405 1406 1407 1408 1409 2275 2276 2277 1265 1266 1267 1268 1269 1270 2139 723 724 725 726 727 728 2274 265 722 721 XfP4 1404 720 992 993 994 995 996 556 557 1703 1704 1705 1706 1707 1708 1709 400 401 402 404 405 406 407 408 409 719 263 264 1264 555 1702 399 991 1701 262 1263 717 718 1262 716 1530 1531 1532 1533 1534 1535 1536 1124 1125 1126 1127 1128 1981 1982 1983 1984 1985 1699 1700 2553 2554 2555 2556 2557 2558 2559 396 397 398 1401 1402 1403 1698 2135 2136 2137 2138 395 1123 851 852 853 854 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 159 161 162 1260 1261 714 715 1697 2270 2271 2272 2273 1400 850 393 394 987 988 989 990 259 260 261 1696 1529 137 2416 2417 2418 2419 2420 2421 2422 2423 1399 1840 1841 1842 1843 1844 1845 2 M 2552 1121 1122 849 2688 2689 2690 2691 2692 2693 2694 2695 2696 2697 2134 551 552 553 554 Q 1259 1980 1 2 3 4 5 6 7 8 9 10 14 11 13 12 15 16 17 18 136 2 3 4 5 6 7 8 9 1695 1839 2269 1694 713 1 135 986 550 1398 392 2415 T 848 1979 1120 1693 2687 258 1838 1 134 2414 2268 1 1 1285 1 810001 135001 945001 675001 270001 405001 540001 1080001 2160001 1350001 1620001 1890001 1755001 1215001 2565001 2025001 1485001 2295001 2430001

158 © 2000 Macmillan Magazines Ltd NATURE | VOL 406 | 13 JULY 2000 | www.nature.com articles (traG/virB11) 41% pyrophosphohydrolase/thiamine phosphate synthase (mutT/thiE1)the biotin operon/biotin acetyl-CoA-carboxylase synthetase (birA/bioR/dhbB) 43% 40% XF0591 virulence factorXF2420 virulence factor (mviN)XF0754 virulence protein (acvB)XF2679 virulence protein (acvB)XF0749 virulence regulator (xrvA)XF1493 virulence regulator (xrvA)XF0506 virulence-associated protein E (vapE)XF2121 virulence-associated protein E (vapE)ORFS WITH UNDEFINED CATEGORY 39% 31% 39% 32% 48% XF2149 28% 47% ApaG protein (apaG/corD)XF1828 46% ATPaseXF0961 bacterioferritin comigratory protein (bcp)XF1120 bifunctional DGTP- 51% XF1796 bifunctional transcriptional repressor of 45% XF1624 carboxylesterase (estB)XF0063 competence protein F (comF)XF1179 competence related protein (comM)XF1078 DNA uptake protein (comA)XF2243 GTP binding protein (lepA)XF1213 28% GTP-binding elongation factor protein (typA)XF0088 52% 69% GTP-binding protein (hflX)XF0465 37% GTP-binding protein (yfgK)XF1430 37% GTP-binding protein (yihA)XF2422 GTP-binding protein (yhbZ) 35% XF2641 GTP-binding proteinXF1668 69% HicB-related proteinXF1192 integral membrane proteinXF1927 54% integral membrane proteinXF2645 46% isopentenyl monophosphate kinase (ipk)XF0145 52% oxidoreductase (ydfG)XF1744 55% oxidoreductase 50% XF1723 dehydrogenase (yrpG) sugar-phosphate XF1724 dehydrogenase (yrpG) sugar-phosphate 49% 68% 55% ---% 38% 55% pXF51 genes: FUNCTIONS INTERMEDIARY METABOLISM/REGULATORY 50% XFa0001 transcriptional regulatorXFa0057 transcriptional regulator (korA) 71% MACROMOLECULE METABOLISM/DNA METABOLISM/Replication XFa0061 40% single-strand binding protein (ssb)XFa0003 31% topoisomerase I (topA/supX)MACROMOLECULE METABOLISM/DNA METABOLISM/Recombination 54% XFa0019 site-specific recombinase (rin) 35% FUNCTIONS MOBILE GENETIC ELEMENTS/PLASMID-RELATED XFa0002 conjugal transfer protein (traL/virB1)XFa0005 91% conjugal transfer protein (trbC/virB2)XFa0006 conjugal transfer protein (traA/virB3)XFa0007 46% conjugal transfer protein (traB/virB4)XFa0008 32% conjugal transfer protein (traC/virB5)XFa0011 39% conjugal transfer protein (traD/virB6)XFa0012 43% conjugal transfer protein (traE/virB8)XFa0013 28% conjugal transfer protein (traO/virB9)XFa0014 23% conjugal transfer protein (traF/virB10)XFa0015 33% conjugal transfer protein 34% 40% XFa0016 conjugal transfer protein (traG/virD4)XFa0036 conjugal transfer protein (trbN)XFa0037 conjugal transfer protein (trbL)XFa0039 35% conjugal transfer protein (trbJ)XFa0040 conjugal transfer protein (trbI)XFa0041 conjugal transfer protein (trbH)XFa0042 76% conjugal transfer protein (trbG)XFa0043 45% conjugal transfer protein (trbF)XFa0044 54% conjugal transfer protein (trbE)XFa0047 52% nickase (taxC)XFa0027 44% plasmid maintenance protein (pemK)XFa0060 65% plasmid replication protein (incC)XFa0059 47% plasmid replication/partition proteinXFa0029 48% ---% plasmid stabilization protein (parE) VIRULENCE, AND ADAPTATION/OTHER PATHOGENICITY, 32% 34% 76% XFa0052 virulence-associated protein D (vapD) 30% 64% pXF1.3 genes: FUNCTIONS MOBILE GENETIC ELEMENTS/PLASMID-RELATED XFb0001 replication protein 41% protein (ohr)(tolC/mtcB/mukA/refI)protein (hecB)(oxyR) 33% protein (cutA/cycY/cutA1) 70% 26% (acrA/mtcA/lir) 37% (ahpC) 81% (ahpF)(sodA/sodM)(thdF/trmE) 42% 70% 77% 57% protein (hlyB) 47% (engXCA) 61% 33% (uspA1)(czcD)(hspA) 28% (imp/ostA)(mdoH)(mdoG) 53% 38% 29% 37% 36% precursor (xpsD/pefD)(xpsE/pefE)precursor (xpsG/pefG)precursor (xpsH) 68% precursor (xpsI/pefI)precursor (xpsJ/pefJ) 78% 81% 67% 55% 56% XF1827 organic hydroperoxide resistance XF2586 outer membrane export factor XF2550 outer membrane hemolysin activator XF1532 oxidative stress transcriptional regulator XF1038 peptide synthaseXF2276 peptide synthaseXF0619 periplasmic divalent cation tolerance XF1729 phenylacetaldehyde dehydrogenaseXF1131 PmbA protein (pmbA/tldE)XF2135 polyketide synthase (PKS) (frnE)XF2093 precursor of drug resistance protein 61% XF0769 pteridine-dependent deoxygenase (rapK)XF1530 23% subunit C of alkyl hydroperoxide reductase 26% 35% 34% XF1531 45% subunit F of alkyl hydroperoxide reductase XF2614 superoxide dismutase [MN] (sodA/sod)XF1921 superoxide dismutase [MN] precursor 78% XF2778 thiophene and furan oxidation protein XF1898 protein (tolA) TolA XF1897 protein precursor (tolB) TolB XF1900 protein (tolQ/fii) TolQ XF1899 protein (tolR) TolR XF0009 protein (tonB) TonB XF1957 protein (tonB) TonB XF2287 protein (tonB) TonB XF2327 protein (tonB) 40% TonB XF2605 protein (tonB) TonB XF2397 toxin secretion ABC transporter ATP-binding 21% 48% XF1841 undecaprenol kinase (bacA) CELL VIRULENCE, AND ADAPTATION/HOST 34% PATHOGENICITY, 72% DEGRADATION WALL 26% 29% XF1267 28% 1,4-beta-cellobiosidase (cbhA)XF0818 36% endo-1,4-beta-glucanase (engXCA) 38% XF2708 endo-1,4-beta-glucanase (egl)XF0810 extracellular endoglucanase precursor XF0845 64% family 3 glycoside hydrolase (xylA) 46% XF2466 polygalacturonase precursor (pglA) VIRULENCE, AND 47% PATHOGENICITY, ADAPTATION/EXOPOLYSACCHARIDES 45% ---% XF2370 GumB protein (gumB)XF2369 GumC protein (gumC)XF2367 GumD protein (gumD)XF2366 GumE protein (gumE)XF2365 GumF protein (gumF)XF2364 GumH protein (gumH)XF2362 GumJ protein (gumJ)XF2361 GumK protein (gumK)XF2360 GumM protein (gumM) 67% VIRULENCE, AND ADAPTATION/SURFACE 62% PATHOGENICITY, 73% PROTEINS 61% XF0889 44% hemagglutinin-like secreted protein (pspA) 64% XF2196 25% hemagglutinin-like secreted protein (pspA) 65% XF2775 hemagglutinin-like secreted protein (pspA) 35% 69% XF1529 69% surface protein (hsf) 35% XF1981 surface protein (hsf)XF1516 surface-exposed outer membrane protein VIRULENCE, AND PATHOGENICITY, CONDITIONS ATYPICAL ADAPTATION/ADAPTATION, XF0432 BrkB protein (brk)XF0866 22% cobalt-zinc-cadmium resistance protein 24% XF0285 heat shock protein (htrA/degP/ptd)XF2625 heat shock protein (htpX)XF2234 low molecular weight heat shock protein XF1379 43% luciferaseXF0837 organic solvent tolerance precursor XF1623 33% periplasmic glucan biosynthesis protein 53% XF2682 periplasmic glucan biosynthesis protein XF0785 sulfur deprivation response regulator (sac1)XF0858 22% survival protein (surE)XF2622 temperature acclimation protein B (tapB)XF0418 toluene tolerance protein (ttg2D)XF0419 85% toluene tolerance protein (ttg2C)XF0420 toluene tolerance protein (ttg2B) 31% XF0421 toluene tolerance protein (ttg2A) VIRULENCE, AND ADAPTATION/OTHER 24% PATHOGENICITY, 41% 60% XF0290 42% aconitase (rpfA) 50% XF1424 chitinase (chi)XF1527 general secretory pathway protein D XF1517 general secretory pathway protein E XF1518 general secretory pathway protein F (xpsF)XF1519 general secretory pathway protein G 66% XF1520 general secretory pathway protein H 79% XF1521 general secretory pathway protein I 43% XF1522 general secretory pathway protein J XF1523 general secretory pathway protein K (pefK)XF1524 general secretory pathway protein L (pefL) 60% XF1020 pathogenicity-related protein 60% XF0720 proteic killer active protein (higB)XF0721 proteic killer suppression protein (higA)XF0223 queuine tRNA-ribosyltransferase (tgt/vacC)XF0287 61% regulator of pathogenicity factors (rpfB) 40% XF1114 regulator of pathogenicity factors (rpfC) 33% XF1115 48% regulator of pathogenicity factors (rpfF) 72% XF1987 protein (vacB) VacB 59% 67% 46% dehydrogenase (linC)protein (ampG) 39% 38% protein (cvaB)ATP-binding 40% reductase (ncr) 40% XF2127 phage-related proteinXF2132 phage-related proteinXF2290 phage-related proteinXF2291 phage-related proteinXF2292 phage-related proteinXF2294 phage-related proteinXF2295 phage-related proteinXF2479 phage-related proteinXF2482 phage-related protein 24% XF2484 phage-related protein 34% XF2501 phage-related protein 57% XF2504 phage-related protein 47% XF2505 phage-related protein 50% XF2511 phage-related protein 32% XF2522 phage-related protein 53% XF2523 phage-related protein 32% XF2524 phage-related protein 21% XF2526 phage-related protein 41% XF2527 phage-related protein 27% XF2528 phage-related protein 44% XF0500 phage-related repressor protein (racR) 34% XF0696 phage-related repressor protein (rpcI) 28% XF1658 phage-related repressor protein (CI) 41% XF1706 50% phage-related tail fiber protein (gp37) 52% XF0725 29% phage-related tail protein (gpI) 43% XF0730 phage-related tail protein (gpT) 50% 24% XF0731 25% phage-related tail protein (gpU) 21% XF0732 phage-related tail protein (gpX) 56% XF0733 phage-related tail protein (gpD)XF2480 phage-related tail protein (gpX) 35% XF2481 21% phage-related tail protein (gpU)XF2487 40% phage-related tail protein (gpI)XF0508 41% phage-related terminase large subunit (gp2)XF0711 25% 32% phage-related terminase large subunit (gp2)XF2500 28% 41% phage-related terminase large subunit (gp2) 28% 40% FUNCTIONS MOBILE GENETIC ELEMENTS/PLASMID-RELATED 35% XF2045 conjugal transfer protein (trbN)XF2046 conjugal transfer protein (trbL)XF2048 conjugal transfer protein (trbJ)XF2049 conjugal transfer protein (trbI)XF2050 conjugal transfer protein (trbH)XF2051 76% conjugal transfer protein (trbG)XF2052 conjugal transfer protein (trbF) 45% XF2053 conjugal transfer protein (trbE) ---% XF2054 conjugal transfer protein (trbD) 53% XF2055 conjugal transfer protein (trbC) 45% XF2056 conjugal transfer protein (trbB) 65% XF2058 conjugal transfer protein (traF) 49% XF2059 conjugal transfer protein (traE) ---% XF2060 conjugal transfer protein (traD) 68% XF1759 conserved plasmid protein 52% XF2066 conserved plasmid protein (yacB) 69% XF2161 conserved plasmid protein 59% XF2061 DNA primase (traC) 73% XF2444 pheromone shutdown protein (traB) 43% XF1589 plasmid stabilization protein 35% XF1590 plasmid stabilization proteinXF2031 35% plasmid stabilization protein (parD)XF2032 31% plasmid stabilization protein (parE)XF1574 30% plasmid-related protein (traN)XF1679 plasmid-related protein (traN)XF1945 81% 50% protein (virK) VirK 75% 62% 44% AND INTRON- MOBILE GENETIC ELEMENTS/TRANSPOSON- FUNCTIONS RELATED 34% 34% XF2063 DNA-invertase (rin)XF1930 resolvase (tnpR)XF1775 reverse transcriptaseXF1931 transposase (tnpA)XF2303 transposase (tnpA) 35% XF0325 transposase OrfAXF0535 transposase OrfAXF0326 transposase OrfBXF0536 transposase OrfB ---% VIRULENCE, AND ADAPTATION/TOXIN PATHOGENICITY, ---% PRODUCTION AND DETOXIFICATION ---% ---% XF1726 2,5-dichloro-2,5-cyclohexadiene-1,4-diol 71% XF0243 64% acriflavin resistance protein (yerP)XF2386 64% acriflavin resistance protein (yegN)XF2385 ---% acriflavin resistance protein D (yegN)XF2407 35% bacteriocinXF0165 23% beta-lactamase induction signal transducer 42% 50% XF1621 beta-lactamase-like protein (pbp)XF0010 biopolymer transport ExbB protein (exbB)XF0011 biopolymer transport ExbD1 protein (exbD1)XF0012 81% 78% biopolymer transport ExbD2 protein (exbD2)XF2232 82% catalase/peroxidase (cpeB) 24% XF2083 cation efflux system protein (czcA)XF0262 colicin V precursor (cvaC)XF0263 colicin V precursor (cvaC)XF1948 colicin V production protein (cvpA)XF1220 27% 24% colicin V secretion ABC transporter 66% XF1216 colicin V secretion protein (cvaA)XF2084 31% component of multidrug efflux system (mexE) 28% XF1341 36% copper homeostasis protein (cutC)XF0132 31% copper resistance protein A precursor (copA)XF0133 61% copper resistance protein B precursor (copB) 25% XF1741 38% daunorubicin C-13 ketoreductase (dnrU)XF2148 47% dimethyladenosine transferase (ksgA/rsmA)XF2416 48% drug tolerance protein (lytB) 31% XF0993 drug:proton antiporter (tetV)XF1765 drug:proton antiporter (mmr)XF1029 glutaryl-7-ACA acylase precursor (gaa)XF1890 glutathione peroxidase-like protein (gpo)XF1210 glutathione S-transferase (gst)XF0175 60% 50% hemolysin III protein 64% XF2398 24% hemolysin secretion protein D (hlyD)XF0668 33% hemolysin-type calcium binding protein (frpC) 32% XF1011 hemolysin-type calcium binding protein (frpC) 30% XF2759 hemolysin-type calcium binding protein (frpC) 38% 35% 39% XF1934 HetI protein (hetI)XF0244 membrane fusion protein (mexC)XF2384 membrane fusion protein precursor (mtrC)XF2686 multidrug efflux protein (ydhE) 37% XF2094 48% multidrug-efflux transporter (acrF/envD)XF1732 NAD(P)H-dependent 2-cyclohexen-1-one 25% 50% XF1137 NonF-related protein (nonF) 34% 35% 34% permease (btuE)channel (mscL)ion channel (yggB) 44% 52% 35% (minE)protein (soj) 48% 27% (gpV)(gpW)(gpJ)(gpJ)(gpW)(gpV)protein (fIR2) 32% protein (fIR2) 40% (fIIR2) 46% 46% 40% 46% 32% 46% 41% XF1913 type V secretory pathway protein (mttC)CELLULAR PROCESSES/TRANSPORT/Other 46% XF0875 protein (yusC) ABC transporter ATP-binding XF0944 protein (yjjK) 48% ABC transporter ATP-binding XF1077 protein (ycfV) ABC transporter ATP-binding 69% XF1081 protein (msbA) ABC transporter ATP-binding 55% XF1223 41% protein (yadG) ABC transporter ATP-binding XF1302 54% protein ABC transporter ATP-binding XF1409 protein ABC transporter ATP-binding XF1475 protein (ynhD) ABC transporter ATP-binding XF1602 63% protein ABC transporter ATP-binding 42% XF2133 protein (yheS) ABC transporter ATP-binding 60% XF2568 45% protein (rfbE) ABC transporter ATP-binding XF2582 protein ABC transporter ATP-binding 31% 45% XF2617 protein (uup) ABC transporter ATP-binding XF2695 protein (ftsE) ABC transporter ATP-binding 49% XF1474 ABC transporter membrane protein (ynhC) 42% 47% XF1476 ABC transporter membrane protein 33% XF0874 ABC transporter permease proteinXF2567 ABC transporter permease protein (rfbD)XF1604 ABC transporter vitamin B12 uptake 69% 35% XF0406 48% export protein (ygjT)XF0039 large-conductance mechanosensitive XF0589 permeaseXF2301 polysaccharide export protein (mrp)XF1258 small conductance mechanosensitive XF2251 solute:Na+ symporter (ppa)XF0281 63% transport protein (yueF)XF0651 54% transport protein (yxaH)XF1728 transport proteinCELLULAR PROCESSES/CELL DIVISION 58% XF0659 cell cycle protein (mesJ)XF0286 cell division inhibitor (sulA) 28% XF1322 24% cell division inhibitor (minC)XF0093 33% cell division protein (hflB/ftsH/mrsC/tolZ)XF0094 cell division protein (ftsJ/mrsF)XF0791 64% cell division protein (ftsL)XF0796 27% cell division protein (ftsW)XF0800 cell division protein (ftsQ) 39% 42% XF0801 cell division protein (ftsA/divA) 35% XF0802 52% cell division protein (ftsZ)XF1450 cell division protein (ftsK)XF1910 cell division protein (ftsY)XF2557 30% cell division protein (zipA)XF2694 44% 45% cell division protein (ftsX/ftsS)XF1320 32% cell division topological specificity factor XF1657 59% cell filamentation protein (fic)XF2281 50% chromosome partitioning proteinXF2282 45% chromosome partitioning protein (parA) 31% XF1785 27% chromosome partitioning related 49% XF2247 GTP binding protein (era) 38% XF1084 43% partition protein (parA)XF1321 septum site-determining protein (minD) AND MOBILITY CELLULAR PROCESSES/CHEMOTAXIS 68% XF1952 chemotaxis-related protein kinase (chpA) 51% FUNCTIONS MOBILE GENETIC ELEMENTS/PHAGE-RELATED 42% AND PROPHAGES 32% XF0089 protein (hfq) host factor-I XF0719 phage-related baseplate assembly protein XF0723 phage-related baseplate assembly protein XF0724 phage-related baseplate assembly protein XF2488 92% phage-related baseplate assembly protein XF2489 phage-related baseplate assembly protein XF2492 phage-related baseplate assembly protein XF0727 phage-related contractile tail sheath XF2485 phage-related contractile tail sheath XF0728 phage-related contractile tail tube protein XF0683 phage-related DNA polymerase (dpoL)XF2525 phage-related DNA polymerase (dpoL)XF0513 phage-related endolysin (lycV)XF0631 50% phage-related integrase (int)XF0678 49% phage-related integrase (int)XF1642 phage-related integrase (int)XF1718 phage-related integrase (int)XF2288 phage-related integrase (int) 46% XF2530 phage-related integrase (int)XF1564 28% phage-related lysozyme (lycV)XF1669 27% phage-related lysozyme (lycV)XF2314 28% phage-related lysozyme (lycV)XF0713 91% phage-related portal protein (gp4)XF2498 26% phage-related portal protein (gp4)XF0485 28% phage-related protein 43% XF0680 phage-related protein 43% XF0682 phage-related protein 25% 42% XF0684 phage-related protein 25% XF0685 phage-related proteinXF0686 phage-related proteinXF0704 phage-related proteinXF0705 phage-related proteinXF0707 phage-related protein 34% XF0710 phage-related protein 56% XF1555 phage-related protein 50% XF1570 phage-related protein 49% XF1573 phage-related protein 53% XF1645 phage-related protein 41% XF1663 phage-related protein 32% XF1675 phage-related protein 32% XF1678 phage-related protein 44% XF1763 phage-related protein 27% XF1786 phage-related protein 34% XF1864 phage-related protein 29% XF1869 phage-related protein 27% XF1870 phage-related protein 31% XF1875 phage-related protein 47% XF1876 phage-related protein 29% 27% 30% 42% 48% 37% 35% 36% 36% (fimD) 36% protein (yclF)(phoX)(pstC/phoW) 35% (pstA/phoT)(cysU/cysT)protein (nrtD)protein (pstB/phoT) 50% 67% protein (cysA) 53% 50% 46% 65% (kgtP/witA) 61% (citN/citH)(phbH) 64% 60% 52% protein (corA)protein (natA) 33% transport (ybiL)transport (yncD)subunit 47% protein (ccmA) 47% (ccmB) 23% (ccmC)(secA/prlD/azi/pea) 50% (secY/prlA) 41% 50% 60% 48% (tatC/mttB) 55% 47% XF2538 fimbrial assembly protein (pilC)XF2539 fimbrial proteinXF2542 fimbrial proteinXF0083 fimbrial subunit precursorXF0487 fimbrillinXF0538 56% fimbrillinXF0539 fimbrillin (fimA)XF1791 fimbrillinXF0081 outer membrane usher protein precursor XF1953 42% pilus biogenesis protein (pilJ)XF1954 pilus biogenesis protein (pilI) 48% XF2544 pilus biogenesis protein (pilB) 53% XF1955 pilus protein (pilG)XF0031 PilX protein (pilX)XF0032 PilY1 gene product (pilY1)XF1224 46% PilY1 gene product (pilY1) 38% 37% XF2537 33% pre-pilin leader peptidase (xpsO) 37% 55% XF0029 pre-pilin leader sequence (pilV)XF1632 twitching motility protein (pilU) 48% XF1633 twitching motility protein (pilT)XF0677 type 4 fimbriae assembly protein (pilZ)XF0479 76% 32% type IV pilin (pilE) 82% 30% 33% CELLULAR PROCESSES/TRANSPORT/Amino acids, amines 62% 28% 60% 74% XF0408 amino acid transporter (yhdG)XF2730 amino acid transporter (rhtC)XF2207 cationic amino acid transporterXF2208 cationic amino acid transporterXF1891 di-tripeptide ABC transporter membrane XF0656 43% 35% glutamate symport protein (gltT)XF1937 28% 43% proton glutamate symport protein (gltP) 41% CELLULAR PROCESSES/TRANSPORT/Anions 35% XF0411 28% ABC transporter nitrate permease (nrtB)XF2141 ABC transporter phosphate binding protein 26% XF2142 ABC transporter phosphate permease XF2143 ABC transporter phosphate permease XF1344 ABC transporter sulfate binding protein (sbp) 64% XF1345 ABC transporter sulfate permease XF1346 ABC transporter sulfate permease (cysW)XF0412 nitrate ABC transporter ATP-binding 49% XF2144 phosphate ABC transporter ATP-binding XF1347 sulfate ABC transporter ATP-binding CELLULAR PROCESSES/TRANSPORT/Carbohydrates, organic acids, alcohols XF2446 ABC transporter sugar permeaseXF2447 ABC transporter sugar permease (lacF)XF2448 protein (malE) ABC transporter sugar-binding 24% XF0087 alpha-ketoglutarate permease symporter 37% XF0976 40% C4-dicarboxylate transport protein (dctA)XF1462 glucose/galactose transporter (gluP)XF1609 66% glucose/galactose transporter (gluP)XF2267 glycerol uptake facilitator protein (glpF)XF1406 HPr kinase/phosphatase (ptsK) 31% XF0320 Mg++/citrate complex transporter 39% 48% XF1402 phosphotransferase system enzyme I (phbI)XF1403 40% phosphotransferase system HPr enzyme 36% XF1067 protein sugar ABC transporter ATP-binding 53% CELLULAR PROCESSES/TRANSPORT/Cations XF2328 ABC transporter sodium permease (natB)XF1844 ammonium transporter (amtB)XF0395 27% bacterioferritin (bfr)XF2140 cation:proton antiporter (ybaL)XF2134 ferric enterobactin receptor (bfeA)XF2137 ferric enterobactin receptor (bfeA)XF0932 ferrous iron transport protein 57% XF0933 ferrous iron transport protein B (feoB)XF1426 22% ion transporter 57% XF0900 22% magnesium and cobalt transport 52% XF1015 61% manganese transport protein (mntH2)XF1401 47% Mg++ transporter (mgtE)XF1398 Na+/H+ exchange proteinXF2019 64% Na+:H+ antiporter (yjcE)XF0324 periplasmic iron-binding protein (afuA)XF0901 polar amino acid transporter (ybeX)XF1903 potassium uptake protein (kup/trkD)XF2329 24% sodium ABC transporter ATP-binding 48% 26% XF0599 46% 24% receptor for iron TonB-dependent 48% 42% XF1496 receptor for iron TonB-dependent XF0367 voltage-gated potassium channel beta peptide secretion CELLULAR PROCESSES/TRANSPORT/Protein, XF2455 heme ABC transporter ATP-binding XF2456 heme ABC transporter membrane protein XF2457 heme ABC transporter membrane protein XF2261 oligopeptide transporterXF0806 preprotein translocase SecA subunit XF1172 preprotein translocase SecY subunit XF2639 preprotein translocase subunit (secE)XF0224 subunit (yajC) preprotein translocase YajC XF2685 protease IV (sppA) 40% 36% XF0225 protein-export membrane protein (secD) 33% XF0226 protein-export membrane protein (secF)XF0304 protein-export membrane protein (secG) 44% XF1801 protein-export protein (secB) 38% XF0562 sec-independent protein translocase 43% XF0073 signal recognition particle protein (ffh) 40% 63% 43% lipoprotein precursor (pcp/lpp) 29% precursor (slt/sltY)peptidoglycan transglycosylase (mtgA) 25% precursor (amiC) 50% (lolB/hemM)(pal/ompP6) 45% transferase (mraY/murX) 29% (mreB/envB/rodY) 37% precursor (yjbJ) 59% (pentapeptide) pyrophosphoryl-undecaprenol (murG)(murC) 77% (mpl)ligase (murD) 42% 2,6-diaminopimelate ligase (murE)diaminopimelate--D-alanyl-D-alanyl ligase (murF/mra) 43% reductase (murB) 47% (uppS/rth) 53% 29% 50% 41% aldolase (kdsA) 43% transferase (kdtA/waaA)cytidylyltransferase (kdsB) 51% (dmt) 44% 44% 50% related protein(rfbD)(htrB/waaM) 34% (htrB/waaM) 24% 75% (kpsF)(opsX) 40% 26% N-acyltransferase (lpxD/firA/ssc)N-acyltransferase (lpxD/firA)acyltransferase (lpxD) 41% acetylglucosamine deacetylase (lpxC) 28% carboxyvinyltransferase (murA/murZ) 45% 59% (lpxA) 73% 62% 31% 44% XF1046 outer membrane antigen (oma)XF0384 outer membrane hemin receptor (phuR)XF0343 outer membrane protein (mopB)XF0872 outer membrane protein (ompW) 22% XF0873 outer membrane proteinXF1053 outer membrane protein (ompP1) 37% XF1123 outer membrane proteinXF1739 31% outer membrane protein (romA)XF2345 30% outer membrane protein (smpA)XF1024 outer membrane protein H.8 precursor 28% XF1811 outer membrane protein Slp precursor (slp)XF1547 peptidoglycan-associated outer membrane 31% 43% 42% 43% XF0033 38% PilE protein (pilE) 34% XF0975 polyphosphate-selective porin O (oprO)XF0321 porin O precursor (oprO)XF0028 pre-pilin like leader sequence (fimT) 23% XF1363 soluble lytic murein transglycosylase 37% CELL STRUCTURE/MUREIN SACCULUS, PEPTIDOGLYCAN XF0852 alanine racemase (alr) 23% XF0799 37% D-alanine--D-alanine ligase B (ddlB/ddl)XF0855 lipoprotein (nlpD/lppB)XF0416 lipoprotein precursor (vacJ) 51% XF1715 monofunctional biosynthetic XF0759 N-acetylmuramoyl-L-alanine amidase XF2646 45% outer membrane lipoprotein precursor 36% XF1896 39% outer membrane protein P6 precursor XF1614 penicillin binding protein (pbp4)XF0368 penicillin-binding protein 1A (mrcA/ponA)XF0884 penicillin-binding protein 1B (ponB)XF1312 39% penicillin-binding protein 2 (mrdA/pbp2)XF0792 penicillin-binding protein 3 (ftsI/pbpB)XF0795 39% phospho-N-acetylmuramoyl-pentapeptide- 38% 41% XF2185 43% rare lipoprotein A (rlpA)XF1309 rod shape-determining protein XF1311 rod shape-determining protein (mreD)XF0907 soluble lytic murein transglycosylase XF0797 32% UDP-N-acetylglucosamine--N-acetylmuramyl- 30% XF0798 UDP-N-acetylmuramate--alanine ligase XF0276 UDP-N-acetylmuramate-L-alanine ligase XF1118 UDP-N-acetylmuramoylalanine--D-glutamate XF0793 UDP-N-acetylmuramoylalanyl-D-glutamate-- XF0794 UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6 XF2572 UDP-N-acetylpyruvoylglucosamine XF1050 undecaprenyl pyrophosphate synthetase POLYSACCHARIDES, CELL STRUCTURE/SURFACE AND ANTIGENS LIPOPOLYSACCHARIDES, XF1289 2-dehydro-3-deoxyphosphooctonate XF0105 3-deoxy-D-manno-octulosonic acid XF2299 3-deoxy-manno-octulosonate XF1419 acetyltransferase (lpxD/firA/omsA)XF0918 acyl-[ACP]-UDP-N-acetylglucosamine (lpxA)XF1994 32% beta 1,4 glucosyltransferaseXF0612 dolichol-phosphate mannosyltransferase 26% XF1638 dolichyl-phosphate mannose synthase XF0257 dTDP-4-dehydrorhamnose 3,5-epimerase 29% XF0258 dTDP-4-keto-L-rhamnose reductase (rfbC)XF0255 dTDP-glucose 4,6-dehydratase (rfbB)XF0611 54% dTDP-glucose 4-6-dehydratase (rfbB)XF1637 glycosyl transferase (spsQ)XF1082 lipid A 4’-kinase (lpxK) 76% XF0104 lipid A biosynthesis lauroyl acyltransferase 63% XF1348 lipid A biosynthesis lauroyl acyltransferase XF1042 lipid A disaccharide synthase (lpxB/pgsB) 29% XF0879 lipopolysaccharide biosynthesis protein (rfbU) 26% XF2434 45% lipopolysaccharide core biosynthesis proteinXF0980 37% 38% lipopolysaccharide synthesis enzyme (kdtB)XF0778 56% O-antigen acetylase (oafA)XF1413 polysialic acid capsule expression protein XF2154 saccharide biosynthesis regulatory protein XF0176 sugar transferaseXF1045 UDP-3-O-(R-3-hydroxymyristoyl)-glucosamine 26% XF1646 UDP-3-O-(R-3-hydroxymyristoyl)-glucosamine XF0486 UDP-3-O-[3-hydroxymyristoyl] glucosamine N- XF0803 UDP-3-O-[3-hydroxymyristoyl] N- XF1415 UDP-N-acetylglucosamine 1- 43% XF1043 UDP-N-acetylglucosamine acyltransferase STRUCTURES CELL STRUCTURE/SURFACE XF0077 fimbrial adhesin precursor (mrkD)XF0078 fimbrial adhesin precursor (mrkD)XF0080 fimbrial adhesin precursor (fimA/pilA)XF0369 fimbrial assembly membrane protein (pilM)XF0370 61% fimbrial assembly membrane protein (pilN) 30% XF0371 29% fimbrial assembly membrane protein (pilO) 44% 32% XF0372 fimbrial assembly protein (pilP) 43% XF0373 fimbrial assembly protein (pilQ)XF0478 fimbrial assembly protein (pilY1) 38% 34% 33% (msrA/pms) 59% O-methyltransferase (pcm) 34% binding subunit Clpx (clpX/lopC)subunit (clpP/lopP)(clpB/htpM) 73% (clpA/lopD)(lon/capR/deg/muc/lopA) 73% 64% 69% 61% (dpm1)phosphatidyltransferase (pgsA) 49% 24% protein 1C precursor (pbpC)(dadA/dadR) 47% (rfbA) 54% (vipA/tviB)(lgt/umpA) 78% pyrophosphorylase (glmU) 52% 49% 48% transglycosylase (mltB) 36% XF1940 peptide methionine sulfoxide reductase XF2642 peptidyl tRNA hydrolase (pth)XF0644 peptidyl-prolyl cis-trans isomerase (mip)XF0652 peptidyl-prolyl cis-trans isomerase (slyD)XF0838 38% peptidyl-prolyl cis-trans isomerase (surA)XF1191 43% peptidyl-prolyl cis-trans isomerase (ppiD)XF1212 32% peptidyl-prolyl cis-trans isomerase (ppiB/ppi) 60% XF1605 49% 25% peptidyl-prolyl cis-trans isomeraseXF0442 phosphatidyltransferase (ptr)XF0926 polypeptide deformylase (def/fms)XF2156 protein phosphatase (yloO)XF1446 36% protein transferase (aat)XF2585 protein-L-isoaspartate 55% XF1051 37% ribosome recycling factor (frr)XF2244 signal peptidase I (lepB)XF1437 thiol:disulfide interchange protein (dsbA) 35% XF0353 translation initiation inhibitor 39% 51% MACROMOLECULE METABOLISM/PROTEIN METABOLISM/Chaperones 58% XF0616 10kDa chaperonin (groES/htpA) 40% XF0615 54% 60kDa chaperonin (mopA/groEL)XF1452 chaperone (lolA)XF2233 DnaJ protein (dnaJ)XF2339 DnaJ protein (dnaJ)XF2340 59% DnaK protein (dnaK/grpF/groP/seg)XF0991 77% DnaK supressorXF0978 heat shock protein G (htpG)XF2341 heat shock protein GrpE (grpE)XF1186 72% peptidyl-prolyl cis-trans isomerase (tig)MACROMOLECULE METABOLISM/PROTEIN 32% degradation METABOLISM/Protein 41% 32% 59% 58% 38% XF2260 alanyl dipeptidyl peptidaseXF0138 aminopeptidase A/I (pepA/xerB/carP)XF1488 aminopeptidase N 48% XF2009 aminopeptidase P (pepP)XF1188 47% Clp protease ATP ATP-dependent XF1187 Clp protease proteolytic ATP-dependent 30% XF0381 Clp protease subunit ATP-dependent XF1443 Clp protease subunit ATP-dependent 46% 36% XF1189 serine proteinase La ATP-dependent XF2704 carboxyl-terminal protease (ctpA)XF1282 carboxypeptidase related proteinXF0156 cysteine protease (cpr6)XF0015 dipeptidyl-peptidaseXF1484 heat shock protein (hslV/htpO) 41% XF1485 heat shock protein (hslU/htpI) 33% XF0452 integral membrane protease (hflK/hflA)XF0453 integral membrane proteinase (hflC)XF0280 leucine aminopeptidase (pepA) 33% XF0435 O-sialoglycoprotein endopeptidase (gcp) 65% 28% XF0127 oligopeptidase A (prlC/opdA/optA) 36% XF1479 66% 63% peptidase (ptrB/tlp)XF1944 28% peptidyl-dipeptidase (dcp)XF2241 periplasmic protease (mucD) 34% XF0220 50% proline dipeptidase (pepQ)XF1510 proline imino-peptidase (pip/xap)XF2330 proteinase (slpD)XF0267 serine protease (pspB)XF1026 serine protease (pspB)XF1851 53% 47% serine protease 81% XF1823 44% tail-specific protease (prc/tsp)XF0816 33% zinc protease MACROMOLECULES MACROMOLECULE METABOLISM/OTHER METABOLISM/Polysaccharides 28% 39% XF2714 22% 27% alpha-L-fucosidase (fucA1)XF2278 dolichol-phosphate mannosyltransferase XF0887 mannosyltransferase (mtfA) 25% MACROMOLECULES MACROMOLECULE METABOLISM/OTHER METABOLISM/Phospholipids 40% 36% XF2310 CDP-diacylglycerol-glycerol-3-phosphate 3- 31% XF1031 glycerol-3-phosphate acyltransferase (plsB) 37% CELL STRUCTURE/MEMBRANE COMPONENTS/Inner membrane XF2780 protein 60kDa inner-membrane XF1640 ankyrin-like protein (ank2)XF2235 bifunctional penicillin-binding XF0082 chaperone protein precursor (ecpD)XF0851 D-amino acid dehydrogenase subunit 40% XF2334 diacylglycerol kinase (dgkA)XF0340 40% 26% disulfide bond formation protein B (dsbB)XF2433 epimerase/dehydratase protein (capD)XF0256 33% glucose-1-phosphate thymidylyltransferase XF0375 37% inner membrane protein (yjdB)XF0103 membrane protein 54% XF0764 membrane proteinXF0777 membrane protein (actII-3)XF2230 penicillin-binding protein 6 precursor (dacC)XF0151 47% phosphomannomutase (algC) 36% XF1183 polysaccharide biosynthetic protein XF2333 prolipoprotein diacylglyceryl transferase XF1310 22% rod shape-determining protein (mreC) 25% XF1313 45% rod shape-determining protein (mrdB/rodA) 36% XF1979 48% transmembrane protein (ampE)XF1140 37% UDP-N-acetylglucosamine CELL STRUCTURE/MEMBRANE COMPONENTS/Outer membrane constituents 28% XF2392 autolytic lysozyme (lyc)XF0847 beta-hexosaminidase precursor (nahA)XF2184 membrane-bound lytic 37% 30% synthase D (rluD/sfhB)(prmA)(rimK)synthase (rsuA) 54% acetyltransferase (rimI) 46% 42% 38% ---% (glyQ/glyS(A))(glyS/glyS(B)) 74% (pheT) 39% chain (pheS)ribosyltransferase-isomerase (queA) 52% transferase (miaA/trpX) 59% 42% (truA/hisT/asuC/leuK) 49% 52% (rpoB/groN/nitB/rif/ron)(rho/nitA/psuA/rnsC/tsu) 67% 72% subunit-relatedprotein phosphatase (stp1) 50% (prfA/sueB/uar) 40% 61% MACROMOLECULE METABOLISM/RNA - maturation and modification METABOLISM/Ribosomes XF0108 16S rRNA processing protein (rimM)XF2607 ribonuclease E (rne/ams/hmp1)XF1125 ribonuclease G (cafA/rng)XF0939 ribosomal large subunit pseudouridine 36% XF2201 ribosomal protein L11 methyltransferase 43% XF2532 ribosomal protein S6 modification XF1200 53% ribosomal small subunit pseudouridine XF0236 ribosomal-binding factor A (rbfA)XF0441 ribosomal-protein-alanine XF2358 RNA methyltransferase (ygcA)XF1972 tRNA/rRNA methylase (yibK) 35% XF1985 tRNA/rRNA methyltransferase (yjfH)MACROMOLECULE METABOLISM/RNA tRNA synthetases, METABOLISM/Aminoacyl 50% 38% tRNA modification 57% XF0124 alanyl-tRNA synthetase (alaS/lovB)XF0147 arginyl-tRNA synthetase (argS)XF2563 asparaginyl-tRNA synthetase (asnS/tss)XF1856 aspartyl-tRNA synthetase (aspS)XF0995 56% cysteinyl-tRNA synthetase (cysS) 66% XF1338 glutaminyl-tRNA synthetase (glnS)XF0822 glutamyl-tRNA synthetase (gltX) 40% XF1960 glycyl-tRNA synthetase alpha chain 53% 46% XF1959 54% glycyl-tRNA synthetase beta chain XF2222 54% histidyl-tRNA synthetase (hisS)XF2418 isoleucyl-tRNA synthetase (ileS/ilvS)XF2176 leucyl-tRNA synthetase (leuS)XF1112 lysyl-tRNA synthetase (lysU)XF2555 lysyl-tRNA synthetase (yjeA/genX) 54% XF0927 36% methionyl-tRNA formyltransferase (fmt)XF0549 methionyl-tRNA synthetase (metG)XF0742 phenylalanyl-tRNA sinthetase beta chain 56% 58% 47% XF0741 56% phenylalanyl-tRNA synthetase alpha 54% XF0445 prolyl-tRNA synthetase (proS/drpA)XF0751 ribonuclease D (rnd)XF2781 ribonuclease P (rnpA)XF1314 S-adenosylmethionine: tRNA 55% XF2286 seryl-tRNA synthetase (serS)XF0736 threonyl-tRNA synthetase (thrS)XF0109 tRNA (guanine-N1-)-methyltransferase (trmD) 51% XF1362 tRNA adenylyltransferase (cca)XF0090 tRNA delta(2)-isopentenylpyrophosphate 31% 37% XF1440 59% 59% tRNA methyltransferase (trmU/asuE)XF1373 tRNA pseudouridine synthase A 52% XF0237 tRNA pseudouridine synthase B (truB) 55% XF2475 tRNA/rRNA methyltransferaseXF0428 tryptophanyl-tRNA synthetaseXF0169 42% tyrosyl-tRNA synthetase (tyrS)XF0134 valyl-tRNA synthetase (valS) METABOLISM/RNA MACROMOLECULE METABOLISM/RNA 41% synthesis, modification, DNA transcription 34% 53% XF0192 RNA helicase (rhlE) ATP-dependent XF0252 51% -dependent RNA helicase (deaD) ATP XF2696 RNA helicase (rhlB/mmrA) ATP-dependent XF0234 55% N utilization substance protein A (nusA) 52% XF0227 52% polynucleotide adenyltransferase (pcnB)XF2606 pseudouridylate synthase (rluC) 56% XF1176 48% RNA polymerase alpha subunit (rpoA)XF2633 RNA polymerase beta subunit XF2632 87% RNA polymerase beta’ subunit (rpoC/tabB)XF1502 48% RNA polymerase omega subunit (rpoZ) 71% XF2638 transcription antitermination factor (nusG)XF0955 transcription termination factor (nusB/ssyB) 60% XF2699 43% 49% transcription termination factor Rho XF1108 transcriptional elongation factor (greA) METABOLISM/RNA MACROMOLECULE METABOLISM/RNA 62% degradation XF1257 oligoribonuclease (orn)XF0239 polynucleotide phosphorylase (pnp)XF2615 ribonucleaseXF2158 ribonuclease H (rnhA/rnh)XF1041 ribonuclease HII (rnhB)XF2246 64% ribonuclease III (rnc)XF1505 ribonuclease PH (rph)XF2146 ribonuclease T (rnt) 58% MACROMOLECULE METABOLISM/PROTEIN and modification METABOLISM/Translation 60% XF1018 55% arginine-tRNA-protein transferase (ate1)XF1436 disulfide oxidoreductase (dsbA) 44% XF1834 50% 25% disulphide isomerase 63% XF2629 elongation factor G (fusA)XF2203 47% elongation factor P (yeiP)XF2473 elongation factor P (efp)XF2579 38% (tsf) elongation factor Ts XF2628 (tufA) elongation factor Tu XF2640 (tufB) elongation factor Tu XF2553 initiation factor eIF-2B, alpha 70% 30% XF1445 39% initiation factor IF-1 (infA)XF0235 initiation factor IF-2 (infB) 63% XF0737 initiation factor IF-3 (infC) 50% XF0857 82% L-isoaspartate O-methyltransferase (pcm)XF2417 82% lipoprotein signal peptidase (lspA)XF2298 47% low molecular weight phosphotyrosine XF0576 73% metallopeptidaseXF0111 49% 45% methionine aminopeptidase (map)XF2649 60% peptide chain release factor 1 XF1111 peptide chain release factor 2 (prfB)XF0174 peptide chain release factor 3 (prfC) 60% 66% 62% 37% DNA (alkB) 28% (xseA)(mutM/fpg)(mutM/fpg)DNA helicase (ruvB)DNA helicase (ruvA)endodeoxyribonuclease (ruvC) 41% 51% 69% 52% 51% 42% DNA methylaseDNA methylase (hsdM)DNA methylaseDNA methylase (hsdM)endonuclease 44% endonuclease (hsdR1) ---% endonuclease 53% endonuclease (hsdR) 61% specificity determinantspecificity determinant 20% ---% specificity determinant (hsdS)specificity determinant (hsdS) 42% 53% 27% 24% 21% 24% XF0760 DNA mismatch repair protein MutL (mutL)XF0148 DNA repair protein (radC) 42% XF1378 DNA repair protein (radA/sms)XF1299 DNA repair system specific for alkylated XF1326 DNA-3-methyladenine glycosidase (mag1)XF1806 DNA-damage-inducible protein (dinD/pcsA) 35% XF2081 ---% DNA-damage-inducible protein (dinJ) 61% XF0647 41% endonuclease III (nth)XF2426 excinuclease ABC subunit A (uvrA)XF0967 57% excinuclease ABC subunit B (uvrB)XF2311 excinuclease ABC subunit C (uvrC)XF0164 exodeoxyribonucleaseXF2022 70% exodeoxyribonuclease I (sbcB/xonA/cpeA)XF1933 83% exodeoxyribonuclease II I (xthA) 43% XF0660 50% exodeoxyribonuclease small subunit (xseB)XF0755 exodeoxyribonuclease VII large subunit 39% 67% XF0071 formamidopyrimidine DNA glycosylase 46% XF0170 43% formamidopyrimidine DNA glycosylase XF1902 holliday junction binding protein, XF1904 holliday junction binding protein, XF1905 holliday junction resolvase, XF1716 mismatch repair protein (mutS)XF0045 transcription-repair coupling factor (mfd)XF2692 uracil-DNA glycosylase (ung) 49% MACROMOLECULE METABOLISM/DNA modification METABOLISM/Restriction, 54% XF1368 adenine-specific methylaseXF2297 55% DNA methylaseXF0641 DNA methyltransferase (sfiIM)XF1774 DNA methyltransferase (gene with intron)XF0924 DNA processing chain A (smf/dprA) ---% XF0935 methyltransferaseXF1968 methyltransferase (kpnIM) 46% XF1804 site-specific DNA-methyltransferase (sphIM) 31% 39% XF2313 37% site-specific DNA-methyltransferaseXF2724 type I restriction-modification system (hsdM) 25% XF0297 type I restriction-modification system 40% 41% XF2723 type I restriction-modification system 33% XF2728 type I restriction-modification system 37% XF2742 type I restriction-modification system XF0295 type I restriction-modification system XF2721 type I restriction-modification system XF2725 type I restriction-modification system XF2739 type I restriction-modification system XF0296 type I restriction-modification system XF2722 type I restriction-modification system XF2726 type I restriction-modification system XF2741 type I restriction-modification system MACROMOLECULE METABOLISM/RNA proteins METABOLISM/Ribosomal XF2438 30S ribosomal protein S1 (rpsA/ssyF)XF1151 30S ribosomal protein S10 (rpsJ)XF1174 30S ribosomal protein S11 (rpsK)XF2631 30S ribosomal protein S12 (rpsL) 67% XF1173 30S ribosomal protein S13 (rpsM)XF1165 30S ribosomal protein S14 (rpsN) 72% XF0238 30S ribosomal protein S15 (rpsO/secC) 86% XF0107 30S ribosomal protein S16 (rpsP)XF1161 81% 30S ribosomal protein S17 (rpsQ) 85% XF2560 62% 30S ribosomal protein S18 (rpsR) 62% XF1156 30S ribosomal protein S19 (rpsS)XF2580 30S ribosomal protein S2 (rpsB) 65% XF2421 30S ribosomal protein S20 (rpsT) 51% XF0434 30S ribosomal protein S21 (rpsU) 70% XF1158 30S ribosomal protein S3 (rpsC) 60% XF1175 30S ribosomal protein S4 (rpsD)XF1169 60% 30S ribosomal protein S5 (rpsE/spc) 54% XF2561 30S ribosomal protein S6 (rpsF) 67% XF2630 30S ribosomal protein S7 (rpsG/rps7)XF1166 67% 30S ribosomal protein S8 (rpsH/rps8) 71% XF1536 84% 30S ribosomal protein S9 (rpsI/rps9)XF2636 50S ribosomal protein L1 (rplA/rpl1) 60% XF2635 67% 50S ribosomal protein L10 (rplJ) 56% XF2637 50S ribosomal protein L11 (rplK/relC) 68% XF1537 50S ribosomal protein L13 (rplM) 64% XF1162 50S ribosomal protein L14 (rplN)XF1171 50S ribosomal protein L15 (rplO) 69% XF1159 43% 50S ribosomal protein L16 (rplP)XF1177 50S ribosomal protein L17 (rplQ) 71% XF1168 50S ribosomal protein L18 (rplR)XF0110 80% 50S ribosomal protein L19 (rplS)XF1155 48% 50S ribosomal protein L2 (rplB)XF0740 69% 50S ribosomal protein L20 (rplT)XF2424 80% 50S ribosomal protein L21 (rplU)XF1157 53% 50S ribosomal protein L22 (rplV)XF1154 65% 50S ribosomal protein L23 (rplW)XF1163 50S ribosomal protein L24 (rplX) 69% XF2643 72% 50S ribosomal protein L25 (rplY)XF2423 53% 50S ribosomal protein L27 (rpmA)XF1206 63% 50S ribosomal protein L28 (rpmB) 52% XF1160 50S ribosomal protein L29 (rpmC)XF1152 48% 50S ribosomal protein L3 (rplC/rpl3)XF1170 48% 50S ribosomal protein L30 (rpmD) 64% XF1534 50S ribosomal protein L31 (rpmE) 71% XF1816 50S ribosomal protein L32 (rpmF) 50% 61% XF1207 50S ribosomal protein L33 (rpmG)XF2782 50S ribosomal protein L34 (rpmH) 47% XF0739 50S ribosomal protein L35 (rpmI) 57% XF2440 50S ribosomal protein L36 (rpmJ) 75% XF1153 50S ribosomal protein L4 (rplD) 73% XF1164 50S ribosomal protein L5 (rplE/rpl5) 76% XF1167 50S ribosomal protein L6 (rplF)XF2634 60% 50S ribosomal protein L7/L12 (rplL) 65% XF2559 50S ribosomal protein L9 (rplI) 63% 54% 67% 52% 52% transferase subunit alpha (accA)transferase subunit beta (accD/dedB/usg) 62% 64% (fabA)acetyl-CoA carboxilase (accB/fabE)acetyl CoA carboxylase (accC/fabG) 53% 76% 63% proenzyme (speD) 66% (holC)(dnaX/dnaZ/dnaZX)(dnaE/polC) 40% 34% flavoprotein (dfp) 48% 51% (recF/uvrF)3’endonuclease) (nfi)(recB/rorA) 53% 32% 30% (dat/dat1)(mutX)(mutY/mutB) 46% 46% 38% BIOSYNTHESIS OF SMALL MOLECULES/COFACTORS, PROSTHETIC GROUPS, CARRIERS BIOSYNTHESIS/Others XF1916 coenzyme F390 synthetase ACID AND BIOSYNTHESIS OF SMALL MOLECULES/FATTY ACID BIOSYNTHESIS PHOSPHATIDIC XF1044 (3r)-hydroxymyristoyl ACP dehydrase (fabZ)XF2269 3-alpha-hydroxysteroid dehydrogenase 49% 25% XF0173 3-oxoacyl-[ACP] reductaseXF0671 3-oxoacyl-[ACP] reductase (fabG) 34% XF0673 3-oxoacyl-[ACP] synthase II (fabF)XF1970 3-oxoacyl-[ACP] synthase IIIXF0319 acetoacetyl-CoA reductase (phbB)XF0203 acetyl-coenzyme A carboxylase carboxyl 66% 60% XF1467 42% acetyl-coenzyme A carboxylase carboxyl 65% XF0672 acyl carrier protein (acpP) 24% XF0771 acyl carrier protein (acpC)XF0572 beta-hydroxydecanoyl-ACP dehydratase XF1639 beta-ketoacyl-[ACP] synthase II (fabF/fabJ)XF1817 beta-ketoacyl-[ACP] synthase III (fabH) 34% XF0048 biotin carboxyl carrier protein of 72% XF0049 62% 40% biotin carboxylase subunit of XF1087 cardiolipin synthaseXF1209 cardiolipin synthase (cls/nov)XF2716 ketoreductaseXF0670 malonyl CoA-ACP transacylase (fabD)XF1049 phosphatidate cytidylyltransferase (cdsA/cds) 36% XF1365 phosphatidylserine decarboxylase (psd) 51% BIOSYNTHESIS OF SMALL MOLECULES/POLYAMINES 34% 44% BIOSYNTHESIS 33% XF0144 biosynthetic arginine decarboxylase (speA)XF1539 S-adenosyl methionine decarboxylase 45% XF0143 29% spermidine synthase (speE)MACROMOLECULE METABOLISM/DNA METABOLISM/Replication XF2680 DNA helicase (rep) ATP-dependent XF0882 helicase (yoaA) ATP-dependent 41% XF1229 helicase ATP-dependent XF0001 chromosomal replication initiator (dnaA)XF2552 43% DNA gyrase subunit A (gyrA)XF0005 53% DNA gyrase subunit B (gyrB)XF2556 43% DNA ligase (ligA/lig/dnaL/pdeC/lop)XF1103 DNA polymerase I (polA/resA)XF0136 DNA polymerase III holoenzyme chi subunit 46% 43% XF1807 57% DNA polymerase III subunit 60% XF0204 DNA polymerase III, alpha chain 52% XF0002 DNA polymerase III, beta chain (dnaN)XF0676 DNA polymerase III, delta subunit (holB)XF2178 DNA polymerase III, delta subunit (holA)XF2157 51% 35% DNA polymerase III, epsilon chain (dnaQ)XF0430 29% DNA primase (dnaG/dnaP/parB)XF2025 49% DNA primase (traC)XF0920 DNA topoisomerase I (topA)XF1776 DNA topoisomerase III (topB)XF0149 DNA/pantothenate metabolism 46% XF1935 glucose inhibited division protein (gidB)XF2106 glucose inhibited division protein A (gidA)XF1383 dependent (hrpA) helicase, ATP 41% 45% 65% XF2689 48% primosomal protein N’ (priA)XF0361 56% replicative DNA helicase (dnaB/groP/grpA)XF1127 TldD protein (tldD) 53% XF1353 topoisomerase IV subunit (parC)XF1286 50% topoisomerase IV subunit B (parE)MACROMOLECULE METABOLISM/DNA 44% DNA binding proteins METABOLISM/Structural 61% 64% XF2558 chromosome segregation protein (smc)XF0446 DNA-binding protein (bbh3)XF1998 DNA-binding protein (fis) 61% 27% XF1190 histone-like protein (hbs/hbsU)XF1943 histone-like proteinXF0482 single-stranded DNA binding protein (ssb)XF1392 single-stranded DNA binding protein (ssb) 49% XF1558 single-stranded DNA binding protein (ssb) 33% 56% XF1644 single-stranded DNA binding protein (ssb) 64% 36% XF1778 single-stranded DNA binding protein (ssb) 58% 54% 25% MACROMOLECULE METABOLISM/DNA METABOLISM/Recombination 54% XF0354 DNA helicase (recG) ATP-dependent XF1381 DNA helicaseXF2248 DNA repair protein RecO (recO)XF0003 DNA replication and repair RecF protein 55% XF1892 endonuclease V (deoxyinosine XF0425 35% exodeoxyribonuclease V alpha chain (recD)XF0423 exodeoxyribonuclease V beta chain 38% XF0422 exodeoxyribonuclease V gamma chain (recC)XF1425 29% integrase/recombinase (xerD/xprB)XF0743 54% alpha subunit (himA) integration host factor, XF2437 73% beta subunit (himD) integration host factor, XF1809 72% recombination protein (recR)XF2343 53% recombination protein N (recN)XF0123 recombination protein RecA (recA)XF1110 single-stranded DNA exonuclease (recJ)XF1483 site-specific recombinase (sss/xerC)XF2028 45% site-specific recombinase (rin) 54% 91% 38% METABOLISM/Repair MACROMOLECULE METABOLISM/DNA 53% XF2598 6-O-methylguanine-DNA methyltransferase 81% XF1262 7,8-dihydro-8-oxoguanine-triphosphatase XF1909 A/G-specific adenine glycosylase XF0050 DNA helicase II (uvrD/mutU/pdeB/rad/recL) 56% hydroxymethyltransferase (panB) 55% protein (pdxJ)protein (pdxA) 49% 50% pyrophosphorylase (nadC) 54% reductoisomerase (dxr)precursor (apbE) 46% reductase 33% 4-phosphate synthase (ribA) 52% 21% hydroxylase (ubiH/visB)(ubiG/pufX)synthase) (ispA)(ubiA/cyr) 34% 49% 54% (hemF) 52% (hemB)(hemL) 63% 65% 80% (ygcM)dehydratase (phhB) 34% 63% BIOSYNTHESIS OF SMALL MOLECULES/COFACTORS, PROSTHETIC GROUPS, CARRIERS BIOSYNTHESIS/Molybdopterin XF0466 molybdopterin biosynthesis protein (moeB)XF1545 molybdopterin biosynthesis protein 53% BIOSYNTHESIS OF SMALL MOLECULES/COFACTORS, PROSTHETIC GROUPS, CARRIERS BIOSYNTHESIS/Pantothenate 42% XF0229 3-methyl-2-oxobutanoate XF0231 aspartate 1-decarboxylase precursor (panD)XF0230 53% pantoate--beta-alanine ligase (panC)BIOSYNTHESIS OF SMALL MOLECULES/COFACTORS, PROSTHETIC GROUPS, CARRIERS BIOSYNTHESIS/Pyridoxine 46% XF0060 pyridoxal phosphate biosynthetic XF0839 pyridoxal phosphate biosynthetic XF1337 pyridoxamine 5’-phosphate oxidase (fprA)BIOSYNTHESIS OF SMALL MOLECULES/COFACTORS, 52% PROSTHETIC GROUPS, CARRIERS BIOSYNTHESIS/Pyridine nucleotides XF1924 L-aspartate oxidaseXF1961 NH3-dependent NAD synthetase (nadE/adgA) 47% XF1097 nicotinate phosphoribosyltransferase (pncB)XF1925 43% nicotinate-mononucleotide XF1923 quinolinate synthetase A (nadA)BIOSYNTHESIS OF SMALL MOLECULES/COFACTORS, PROSTHETIC GROUPS, CARRIERS BIOSYNTHESIS/Thiamin 40% XF1048 42% 1-deoxy-D-xylulose 5-phosphate XF0621 phosphomethylpyrimidine kinaseXF0378 thiamin-phosphate pyrophosphorylase (thiE)XF0594 41% thiamine biosynthesis lipoprotein ApbE XF0783 thiamine biosynthesis protein (thiG) 45% XF1888 thiamine biosynthesis protein (thiC/thiA)XF0956 thiamine-monophosphate kinase (thiL) 67% 57% BIOSYNTHESIS OF SMALL MOLECULES/COFACTORS, PROSTHETIC GROUPS, CARRIERS BIOSYNTHESIS/Riboflavin 44% XF1748 5-amino-6-(5-phosphoribosylamino)uracil XF0954 6,7-dimethyl-8-ribityllumazine synthase (ribH) 45% XF0953 GTP cyclohydrolase II/3,4-dihydroxy-2-butanone XF1992 riboflavin biosynthesis protein (ribA)XF2419 riboflavin biosynthesis protein (ribF)XF0952 riboflavin synthase alpha chain (ribE)XF0950 riboflavin-specific deaminase (ribD/ribG) 35% 43% BIOSYNTHESIS OF SMALL MOLECULES/COFACTORS, 51% 45% PROSTHETIC GROUPS, CARRIERS BIOSYNTHESIS/Thioredoxin, glutaredoxin, glutathione XF0984 gamma-glutamyltranspeptidase (ggt)XF1428 glutamate-cysteine ligase precursor (gsh1)XF2595 glutaredoxin (grxC) 57% XF2394 glutaredoxin-like protein 39% XF1956 glutathione synthetase (gshB/gsh-II)XF1199 thioredoxin (trxA)XF2174 thioredoxin (ybbN)XF2698 thioredoxin (trxA/tsnC/fipA) 53% BIOSYNTHESIS OF SMALL MOLECULES/COFACTORS, PROSTHETIC GROUPS, CARRIERS 54% BIOSYNTHESIS/Menaquinone, ubiquinone 53% XF0835 2-octaprenyl-6-methoxyphenol 49% XF2471 34% 3-demethylubiquinone-9 3-methyltransferase 31% XF0661 geranyltranstransferase (farnesyl-diphosphate XF0068 hydroxybenzoate octaprenyltransferase XF1391 octaprenyl-diphosphate synthase (ispB/cel)XF1538 49% ubiquinone biosynthesis protein (coq7)XF1833 ubiquinone biosynthesis protein (aarF)XF1487 ubiquinone/menaquinone transferase (ubiE) 29% 58% BIOSYNTHESIS OF SMALL MOLECULES/COFACTORS, 43% PROSTHETIC GROUPS, CARRIERS BIOSYNTHESIS/Heme, porphyrin XF0017 coproporphyrinogen III oxidase, aerobic XF2306 delta-aminolevulinic acid dehydratase XF0566 ferrochelatase (hemH)XF2302 glutamate-1-semialdehyde 2,1-aminomutase XF2648 glutamyl-tRNA reductase (hemA)XF1627 hydroxymethylbilane synthase (hemC)XF1797 porphyrin biosynthesis protein (hemY)XF1512 protoporphyrinogen oxidase (hemK)XF0832 52% siroheme synthase (cysG) 76% XF1332 20% 48% uroporphyrinogen decarboxylase (hemE)XF1799 uroporphyrinogen-III synthase (hemD) 45% 54% BIOSYNTHESIS OF SMALL MOLECULES/COFACTORS, PROSTHETIC GROUPS, CARRIERS BIOSYNTHESIS/Cobalamin 27% XF1886 45% phosphoglycerate mutase (pgmA)BIOSYNTHESIS OF SMALL MOLECULES/COFACTORS, PROSTHETIC GROUPS, CARRIERS BIOSYNTHESIS/Biopterin 32% XF0193 6-pyruvoyl tetrahydrobiopterin synthase XF1457 pteridine reductase 1 (ptr1/ltdH)XF2604 pterin-4-alpha-carbinolamine 37% cyclohydrolase/phosphoribosyl-ATP pyrophosphatase bifunctional enzyme (hisI/hisIE)carboxamide ribotide isomerase (hisA) 44% synthetase (purM/purG) 56% transformylase (purN) 59% protein (purH) 43% dehydrogenase (guaB)synthetase (prsA/prs) 59% subunit (purK)carboxylase, ATPase carboxylase, catalytic subunit (purE) 64% 50% succinocarboxamide synthase (purC) 66% synthetase (purL/purI) 60% 53% large chain (carB/pyrA) 50% chain (carA) 68% 68% alpha chain (nrdA)beta chain (nrdB) 44% 34% phosphoribosyltransferase (hpt)pyrophosphatase precursor 27% 39% aminotransferase (bioA) 47% hydroxymethyldihydropteridine pyrophosphokinase (folK)hydroxymethyldihydropteridine pyrophosphokinase (folK)dehydrogenase/methenyltetrahydrofolate cyclohydrolase (folD) 50% 35% synthase (folC/dedC) 58% 44% XF2213 phosphoribosyl-AMP XF2215 phosphoribosylformimino-5-aminoimidazole BIOSYNTHESIS OF SMALL MOLECULES/NUCLEOTIDES BIOSYNTHESIS/Purine ribonucleotides XF0587 5’-phosphoribosyl-5-aminoimidazole XF0585 5’-phosphoribosylglycinamide XF0275 adenylate kinase (adk)XF1553 adenylosuccinate lyase (purB)XF0455 adenylosuccinate synthetase (purA)XF1949 amidophosphoribosyltransferase (purF)XF1975 bifunctional purine biosynthesis 61% XF2429 59% glutamine amidotransferase (guaA) 57% XF1976 glycinamide ribonucleotide synthetase (purD) 64% XF0560 47% GMP synthaseXF1503 guanylate kinase (gmk/spoR)XF2430 68% inosine-5’-monophosphate XF0458 nucleoside diphosphate kinase (ndk)XF2644 phosphoribosyl pyrophosphate XF2671 52% phosphoribosylaminoimidazole 68% XF2672 phosphoribosylaminoimidazole XF0205 37% phosphoribosylaminoimidazole- XF1423 phosphoribosylformylglycinamidine BIOSYNTHESIS OF SMALL MOLECULES/NUCLEOTIDES BIOSYNTHESIS/Pyrimidine ribonucleotides XF2226 aspartate carbamoyltransferase (pyrB)XF1107 carbamoyl-phosphate synthase XF1106 52% carbamoyl-phosphate synthase small XF2439 cytidylate kinase (cmkA)XF0988 dihydroorotase (pyrC)XF2571 dihydroorotate dehydrogenase (pyrD)XF0153 orotate phosphoribosyl transferase (pyrE)XF0034 orotidine 5’-phosphate decarboxylase (pyrF) 51% 51% 41% BIOSYNTHESIS OF SMALL MOLECULES/NUCLEOTIDES BIOSYNTHESIS/2’-Deoxyribonucleotides 48% XF0762 deoxycytidine triphosphate deaminase (dcd) 30% XF1441 65% phosphohydrolase (orfU1)XF1196 ribonucleoside-diphosphate reductase XF1197 ribonucleoside-diphosphate reductase XF1448 thioredoxin reductase (trxB)XF0580 thymidylate kinase 45% BIOSYNTHESIS OF SMALL MOLECULES/NUCLEOTIDES BIOSYNTHESIS/Salvage of nucleosides and nucleotides XF2089 5’-nucleotidase 70% XF2150 diadenosine tetraphosphatase (apaH)XF0150 dUTPase (dut/dnaS/sof)XF1831 formyltetrahydrofolate deformylase (purU)XF2354 44% hypoxanthine-guanine 39% 47% XF2599 phosphodiesterase-nucleotide XF2353 purine nucleoside phosphorylaseXF2332 thymidylate synthase (thyA) 59% 42% BIOSYNTHESIS OF SMALL MOLECULES/SUGARS AND SUGAR NUCLEOTIDES BIOSYNTHESIS 45% XF1297 gluconolactonase precursorXF0608 mannosyltransferase (mtfA) 70% BIOSYNTHESIS OF SMALL MOLECULES/COFACTORS, PROSTHETIC GROUPS, CARRIERS BIOSYNTHESIS/Biotin XF1357 8-amino-7-oxononanoate synthase (bioF) 37% XF0189 adenosylmethionine-8-amino-7-oxononanoate 38% 42% XF1356 biotin biosynthesis protein (bioH/bioB)XF0064 biotin synthase (bioB)XF2099 biotin synthesis protein (bioC)XF0356 36% cytochrome P-450 hydroxylaseXF0377 cytochrome P450-like enzyme (bioI)XF2477 dethiobiotin synthetase (bioD)BIOSYNTHESIS OF SMALL MOLECULES/ 36% PROSTHETIC GROUPS, COFACTORS, 37% 37% CARRIERS BIOSYNTHESIS/Folic acid 60% 44% XF0228 2-amino-4-hydroxy-6- XF1456 2-amino-4-hydroxy-6- XF2431 bifunctional methylenetetrahydrofolate XF2331 dihydrofolate reductase type IIIXF0436 dihydroneopterin aldolase (folB)XF0091 dihydropteroate synthase (folP)XF1946 folylpolyglutamate synthase/dihydrofolate XF1983 43% GTP cyclohydrolase I (folE) 50% BIOSYNTHESIS OF SMALL MOLECULES/COFACTORS, 52% PROSTHETIC GROUPS, CARRIERS BIOSYNTHESIS/Lipoate XF1270 lipoate biosynthesis protein B (lipB)XF1269 lipoic acid synthetase (lipA/lip) 52% 55% 60% me not shown). (gltB/aspB)reductase(argM/astC/cstC) 53% N-succinyltransferase (dapD) 33% subunit (leuA) 48% subunit (leuD) 60% reductase (metF)homocysteine methyltransferase (metE)large subunit (ilvG) 56% 63% 79% dehydrogenase (asd) 37% dehydrogenase I (thrA/thrA1/thrA2) 56% decarboxylase/aspartate kinase (lysA) 40% aminotransferase (ilvE) 59% 33% 55% desuccinylase (dapE) 52% 1-carboxyvinyltransferase (aroE) 46% isomerase (trpF)aldolase (aroG) 43% 61% dehydratase/histidinol-phosphate phosphatase bifunctional enzyme (hisB) 50% XF0853 two-component system, sensor protein (phs)XF0973 37% two-component system, sensor protein (flhS) 35% XF1625 two-component system, sensor protein (algZ) 40% XF1849 two-component system, sensor protein (ntrB) 37% XF2535 two-component system, sensor protein (colS) 34% XF2546 two-component system, sensor protein (pilS) 37% XF2577 two-component system, sensor protein (actS) 25% XF2592 two-component system, sensor protein (phoR)38% BIOSYNTHESIS OF SMALL MOLECULES/AMINO ACIDS BIOSYNTHESIS/Glutamate family|nitrogen assimilation XF1001 acetylglutamate kinase (argB)XF1000 acetylornithine deacetylase (argE)XF1003 argininosuccinate lyase (asl)XF0999 argininosuccinate synthase (argG)XF1005 gamma-glutamyl phosphate reductase (proA) 51% XF1004 glutamate 5-kinase 28% 30% XF2710 glutamate synthase, alpha subunit 36% XF2709 35% glutamate synthase, beta subunit (gltD/aspB) 55% XF1842 glutamine synthetase (glnA)XF1002 N-acetyl-gamma-glutamyl-phosphate XF0998 ornithine carbamoyltransferase (argF)XF2712 pyrroline-5-carboxylate reductase (proC)XF1427 46% succinylornithine aminotransferase 36% 49% 64% BIOSYNTHESIS OF SMALL MOLECULES/AMINO ACIDS pyruvate family BIOSYNTHESIS/Aspartate family, XF0114 2,3,4,5-tetrahydropyridine-2-carboxylate XF1818 2-isopropylmalate synthase (leuA)XF2375 3-isopropylmalate dehydratase large XF2374 3-isopropylmalate dehydratase small 47% XF2372 3-isopropylmalate dehydrogenase (leuB)XF1121 5,10-methylenetetrahydrofolate 78% XF2272 5-methyltetrahydropteroyltriglutamate-- XF1821 acetolactate synthase isozyme II, XF1473 aminotransferase (nifS)XF2396 aminotransferase (aspC)XF0118 asparagine synthase B (asnB)XF1371 aspartate-B-semialdehyde XF2100 aspartyl/asparaginyl beta-hydroxylase (aspH) 28% XF2443 beta-alanine synthetaseXF2225 bifunctional aspartokinase/homoserine 47% 60% 45% XF1116 bifunctional diaminopimelate XF1999 branched-chain amino acid XF0864 cystathionine gamma-synthase (metB) 62% XF1481 diaminopimelate epimerase (dapF)XF1105 dihydrodipicolinate reductase (dapB)XF0099 57% dihydroxy-acid dehydratase (ilvD)XF0963 dihydroxydipicolinate synthase (dapA)XF2211 45% enolase-phosphatase (masA) 34% XF2224 homoserine kinase (thrB)XF0863 42% homoserine O-acetyltransferase (met2) 73% XF2465 homoserine O-acetyltransferaseXF1822 ketol-acid reductoisomerase (ilvC) 30% XF0116 succinyl-diaminopimelate 50% XF2223 threonine synthase (thrC) 34% 59% 33% BIOSYNTHESIS OF SMALL MOLECULES/AMINO ACIDS BIOSYNTHESIS/Glycine-serine family|sulfur metabolism XF0603 cystathionine beta-synthase (cysB)XF0128 cysteine synthaseXF0831 38% cysteine synthase (cysK)XF2206 D-3-phosphoglycerate dehydrogenase (serA)XF2326 62% 31% phosphoserine aminotransferase (serC)XF0946 serine hydroxymethyltransferase (glyA) 49% BIOSYNTHESIS OF SMALL MOLECULES/AMINO ACIDS 71% BIOSYNTHESIS/Aromatic amino acid family 51% XF1334 3-dehydroquinate synthase (aroB) 27% XF2324 3-phosphoshikimate XF0212 anthranilate phosphoribosyltransferase (trpD) 48% XF0210 anthranilate synthase component I (trpE) 47% XF0674 anthranilate synthase component I (trpE)XF1914 57% anthranilate synthase component I (trpE)XF0211 36% anthranilate synthase component II (trpG)XF1915 37% anthranilate synthase component II (trpG)XF0036 67% aromatic-amino-acid aminotranferase (tyrB)XF0047 43% 55% catabolic dehydroquinase (aroQ)XF1141 chorismate mutaseXF2338 chorismate mutaseXF1369 chorismate synthase (aroC)XF0213 indole-3-glycerol phosphate synthase (trpC)XF1374 65% 63% N-(5’-phosphoribosyl) anthranilate XF2325 P-protein (aroQ/pheA)XF0026 phospho-2-dehydro-3-deoxyheptonate 62% XF0624 shikimate 5-dehydrogenase (aroE) 25% XF1335 shikimate kinase (aroK) 29% XF1376 tryptophan synthase alpha chain (trpA)XF1375 tryptophan synthase beta chain (trpB) 43% 46% BIOSYNTHESIS OF SMALL MOLECULES/AMINO ACIDS 75% BIOSYNTHESIS/Histidine 65% XF2216 amidotransferase (hisH)XF2220 40% phosphoribosyltransferase (hisG) ATP XF2214 cyclase (hisF)XF2219 histidinol dehydrogenase (hisD)XF2218 43% histidinol-phosphate aminotransferase (hisC) 42% XF2217 imidazoleglycerolphosphate 43% 50% 61% (sucB)protein (sdhB)flavoprotein subunit (sdhA)membrane anchor subunit (sdhC) 53% anchor subunit (sdhD)alpha subunit (sucD) 69% 38% 70% 36% 71% (atpG/uncG/papC) 57% repressor (hrcA)pyrophosphohydrolase (spoT)regulator (phoU) 40% associated protein (phaF) 47% 20% (sspA/ssp/pog) 43% 46% (LuxR/UhpA family) (agmR/glpR)(LuxR/UhpA family) (gacA) 38% 44% protein (wrbA)sensor/regulatory proteinprotein (tctD)protein (popP/feuP/phoP)protein (pilH) 39% 28% protein (algR) 54% protein (glnG/ntrC/glnT) 45% protein (colR)protein (colR) 50% protein (pilR) 51% protein (actR) 47% protein (phoB) 51% 59% 58% 40% 56% XF1535 citrate synthase (gltA)XF1548 dihydrolipoamide dehydrogenase (lpd)XF1549 dihydrolipoamide S-succinyltransferase XF1554 58% fumarate hydratase (fumC)XF1855 fumarate hydratase (fumB)XF2596 isocitrate dehydrogenase (icd)XF2700 isocitrate dehydrogenase (icd)XF1211 61% malate dehydrogenase (mdh)XF0942 malate:quinone oxidoreductase (yojH)XF1550 oxoglutarate dehydrogenase (odhA)XF1073 58% succinate dehydrogenase iron-sulfur 49% 30% 57% 75% XF1072 succinate dehydrogenase, 54% 62% XF1070 succinate dehydrogenase, XF1071 succinate dehydrogenase, membrane XF2548 succinyl-CoA synthetase, XF2547 succinyl-CoA synthetase, beta subunit (sucC) 58% METABOLISM, INTERMEDIARY METABOLISM/ENERGY motive force interconversion CARBON/ATP-proton XF1149 synthase, A chain (atpB/uncB/papD) ATP XF1145 synthase, alpha chain (atpA/uncA) ATP XF1147 46% synthase, B chain (atpF/uncF) ATP XF1143 synthase, beta chain (atpD) ATP 74% XF1148 synthase, C chain (atpE/uncE) ATP XF1146 synthase, delta chain (atpH/uncH) ATP XF1142 45% synthase, epsilon chain (atpC) ATP XF1144 synthase, gamma chain ATP 37% 78% 56% FUNCTIONS INTERMEDIARY METABOLISM/REGULATORY 46% XF1241 aconitate hydratase 1 (acnA/acn)XF1316 3’-pyrophosphotranferase (relA) ATP:GTP XF0125 carbon storage regulator (csrA)XF2352 42% cold shock protein (scoF)XF2476 extragenic supressor (suhB/ssyA) ---% XF2342 heat-inducible transcriptional XF0122 84% LexA repressor (lexA)XF1182 lipase modulator (act) 44% XF1813 methanol dehydrogenase regulatory proteinXF1830 53% 69% nitrile hydratase activatorXF1843 nitrogen regulatory protein P-II (glnB)XF0352 pentaphosphate guanosine-3’- XF2145 87% phosphate regulon transcriptional 76% XF1275 53% poly(hydroxyalcanoate) granule 46% XF2691 RNA polymerase sigma-32 factor (rpoH)XF1408 RNA polymerase sigma-54 factor (rpoN)XF1350 80% RNA polymerase sigma-70 factor (rpoD)XF2239 64% RNA polymerase sigma-H factor (algU/algT)XF1407 56% 63% sigma-54 modulation proteinXF0911 stringent starvation protein A XF0912 stringent starvation protein B (sspB)XF2165 transcription-related protein (tex)XF0962 transcriptional regulator (gcvR)XF1749 44% transcriptional regulator (opdE) 42% XF1858 transcriptional regulator (exsB)XF2038 transcriptional regulator (paiB) 59% XF2228 transcriptional regulator (algH)XF2085 26% transcriptional regulator (AcrR family)XF1254 77% transcriptional regulator (AraC family) (araL) 34% XF0767 49% transcriptional regulator (ArsR family) (hlyU) 34% XF1540 23% 31% transcriptional regulator (Crp/Fnr family) (clp) 85% XF0821 45% transcriptional regulator (Fur family) (zur)XF2344 transcriptional regulator (Fur family) (fur)XF1463 38% transcriptional regulator (LacI family)XF0972 85% transcriptional regulator XF2608 32% transcriptional regulator XF0833 family) (cysB) transcriptional regulator (LysR 39% XF1132 family) (act) transcriptional regulator (LysR XF1730 33% family) (yafC) transcriptional regulator (LysR XF1752 35% family) transcriptional regulator (LysR XF1768 family) (ycjZ) transcriptional regulator (LysR XF0216 45% transcriptional regulator (MarR family) (prsX) 22% XF1354 80% transcriptional regulator (MarR family) (yybA) 28% XF1490 transcriptional regulator (MarR/EmrR family) 26% XF1996 transcriptional regulator (PbsX family)XF0061 transcriptional repressor (korB)XF2062 transcriptional repressor (korC)XF1920 35% operon transcriptional repressor (trpR) Trp XF1094 tryptophan repressor binding 36% XF1133 28% tryptophan repressor binding proteinXF1733 69% tryptophan repressor binding proteinXF1455 two-component system, hybrid 33% XF0322 31% two-component system, regulatory XF0389 two-component system, regulatory XF0450 two-component system, regulatory XF1113 two-component system, regulatory proteinXF1626 30% two-component system, regulatory XF1848 two-component system, regulatory XF2336 two-component system, regulatory XF2534 two-component system, regulatory XF2545 two-component system, regulatory XF2578 two-component system, regulatory XF2593 two-component system, regulatory XF0323 two-component system, sensor protein (tctE) 31% XF0390 two-component system, sensor protein (phoQ)36% genes. Gene numbers correspond to those in Fig. 1. Percentages represent % identities Percentages 1. Gene numbers correspond to those in Fig. genes. (cysQ/amtA)dehydrogenase (gpsA)dehydrogenase (glpD)NQO1 subunit (nuoF) 45% NQO10 subunit (nuoJ) 46% NQO11 subunit (nuoK)NQO12 subunit (nuoL) 54% NQO13 subunit (nuoM) 53% NQO14 subunit (nuoN) 45% 69% NQO2 subunit (nuoE)NQO3 subunit (nuoG) 42% 50% NQO4 subunit (nuoD) 43% NQO5 subunit (nuoC)NQO6 subunit (nuoB) 41% NQO7 subunit (nuoA) 38% NQO8 subunit (nuoH) 58% NQO9 subunit (nuoI) 63% 87% 53% 56% 60% membrane protein (cycK)protein (copper tolerance) (dsbD)protein/thioredoxin (dsbE/ccmG) 52% 32% subunit I (cyoB) 39% subunit II (cyoA)subunit III (cyoC)subunit IV (cyoD)subunit (etfA)subunit (etfB/etfS) 69% 56% ubiquinone oxidoreductase (etf-QO) 63% 46% 41% 51% 54% cytochrome B subunit (petB)cytochrome C1 subunit (petC)iron-sulfur subunit (petA) 56% 48% 52% dehydrogenase (gapA) 68% XF0187 sulfite synthesis pathway protein METABOLISM, INTERMEDIARY METABOLISM/ENERGY CARBON/Aerobic respiration XF0347 D-lactate dehydrogenase (dld1)XF1802 glycerol-3-phosphate XF2266 glycerol-3-phosphate XF0310 38% NADH-ubiquinone oxidoreductase, XF0314 NADH-ubiquinone oxidoreductase, XF0315 NADH-ubiquinone oxidoreductase, XF0316 NADH-ubiquinone oxidoreductase, XF0317 NADH-ubiquinone oxidoreductase, XF0318 NADH-ubiquinone oxidoreductase, XF0309 NADH-ubiquinone oxidoreductase, XF0311 NADH-ubiquinone oxidoreductase, XF0308 NADH-ubiquinone oxidoreductase, XF0307 NADH-ubiquinone oxidoreductase, XF0306 NADH-ubiquinone oxidoreductase, XF0305 NADH-ubiquinone oxidoreductase, XF0312 NADH-ubiquinone oxidoreductase, XF0313 NADH-ubiquinone oxidoreductase, METABOLISM, INTERMEDIARY METABOLISM/ENERGY CARBON/Anaerobic respiration and fermentation XF1746 alcohol dehydrogenase (yahK)XF2389 alcohol dehydrogenase (yahK)XF1136 NADP-alcohol dehydrogenaseXF1727 NADP-alcohol dehydrogenase (adh)XF1734 NADP-alcohol dehydrogenase 81% METABOLISM, INTERMEDIARY METABOLISM/ENERGY 78% CARBON/Electron transport 42% 56% XF2460 c-type cytochrome biogenesis 56% XF2459 c-type cytochrome biogenesis protein (cycJ)XF2462 39% c-type cytochrome biogenesis protein (cycL)XF0620 52% c-type cytochrome biogenesis XF2461 c-type cytochrome biogenesis XF1328 cytochrome B561 (yodB)XF1360 cytochrome C oxidase assembly factor (coxD) 41% XF1389 cytochrome O ubiquinol oxidase, XF1390 cytochrome O ubiquinol oxidase, XF1388 cytochrome O ubiquinol oxidase, 34% XF1387 cytochrome O ubiquinol oxidase, XF0253 electron transfer flavoprotein alpha XF0254 electron transfer flavoprotein beta XF1298 electron transfer flavoprotein XF0557 electron transfer protein azurin I (az1)XF0983 ferredoxinXF1964 ferredoxin (ykgJ)XF2601 49% ferredoxinXF0547 ferredoxin II (ydgM)XF0053 flavohemoprotein (fhp)XF2082 oxidoreductaseXF1990 thioredoxin (yneN)XF0909 ubiquinol cytochrome C oxidoreductase, XF0910 ubiquinol cytochrome C oxidoreductase, XF0908 47% ubiquinol cytochrome C oxidoreductase, 40% 54% 56% METABOLISM, INTERMEDIARY METABOLISM/ENERGY 70% CARBON/Glycolysis 30% 31% XF0274 6-phosphofructokinase (pfkA)XF1291 enolase (eno)XF0826 fructose-bisphosphate aldolaseXF0232 glucose-6-phosphate isomerase (pgi)XF0457 glyceraldehyde-3-phosphate XF0823 31% phosphoglycerate kinase (pgk) 79% XF1893 52% phosphoglyceromutase (gpmA/gpm)XF0824 pyruvate kinase type II (pykA)XF0303 triosephosphate isomerase (tpiA/tpi) 56% METABOLISM, INTERMEDIARY METABOLISM/ENERGY 60% CARBON/Oxidative branch, pentose pathway 63% 48% XF1063 50% 6-phosphogluconolactonase (pgl)XF1065 glucose-6-phosphate 1-dehydrogenase (zwf) 46% METABOLISM, INTERMEDIARY METABOLISM/ENERGY CARBON/Pyruvate dehydrogenase 35% XF0869 dihydrolipoamide acetyltranferase (pdhB)XF0868 dihydrolipoamide dehydrogenase (lpdA/lpd)XF0669 52% 57% pyruvate dehydrogenase (aceE) METABOLISM, INTERMEDIARY METABOLISM/ENERGY CARBON/TCA cycle XF0292 56% aconitate hydratase 2 (acnB) 72%

Xylella fastidiosa ferredoxin protein (bedB)phosphonomutase (prpB) 37% 62% uridylyltransferase (gtaB)aminotransferase (glmS) 82% phosphateaminotransferasedeacetylase (nagA) 54% 47% aldolase (eda/hga/kdgA) 39% 41% 3-epimerase (rpe/dod) 76% phosphomannomutase (xanA)mannose pyrophosphorylase (xanB) 84% 84% 5’-phosphosulfate reductase (cysH) 57% subunit (cysJ)protein (cysI) 40% 52% INTERMEDIARY METABOLISM/ DEGRADATION/Degradation INTERMEDIARY METABOLISM/ of small molecules XF2395 acetylxylan esterase (axeA)XF1250 arginine deaminase (rocF)XF1472 benzene 1,2-dioxygenase, XF0840 beta-galactosidase (bga)XF0439 beta-glucosidase (bglX)XF0846 beta-mannosidase precursor 34% XF1234 carboxyphosphonoenolpyruvate 45% XF2210 dioxygenaseXF1743 esterase (est)XF1610 fructokinase 71% XF1740 35% glucose dehydrogenase B (yliI)XF1064 41% glucose kinase (glk)XF1460 glucose kinase (glk)XF1965 haloalkane dehalogenase (dhaA)XF2677 L-ascorbate oxidase (aao)XF1253 lipase (lipP) 44% XF0781 lipase/esterase (estA)XF1825 NAD(P)H steroid dehydrogenase (cdh)XF1201 30% phosphoglycolate phosphatase (yfbT) 48% XF2470 46% phosphoglycolate phosphatase (cbbZC)XF2259 41% 35% polyvinylalcohol dehydrogenase 36% XF0366 35% 29% 35% ribokinase (rbsK) 37% XF0379 rubredoxin (rubA)XF1819 threonine dehydratase catabolic (tdcB)XF1181 25% triacylglycerol lipase precursor (lip)XF0610 22% UDP-glucose 4-epimerase (galE)XF2432 39% UTP-glucose-1-phosphate 46% 56% INTERMEDIARY INTERMEDIARY METABOLISM/CENTRAL sugars METABOLISM/Amino 27% 38% XF0141 54% glucosamine--fructose-6-phosphate XF1464 glucosamine--fructose-6- XF2355 N-acetyl-beta-glucosaminidase (exo)XF1465 N-acetylglucosamine-6-phosphate 45% INTERMEDIARY INTERMEDIARY METABOLISM/CENTRAL METABOLISM/Entner-Douderoff XF1061 2-keto-3-deoxy-6-phosphogluconate XF1062 6-phosphogluconate dehydratase (edd) INTERMEDIARY INTERMEDIARY METABOLISM/CENTRAL 58% METABOLISM/Gluconeogenesis XF0977 malate oxidoreductase (maeB)XF1259 phosphoenolpyruvate synthase (ppsA/pps) 64% INTERMEDIARY INTERMEDIARY METABOLISM/CENTRAL branch, pentose pathway METABOLISM/Non-oxidative 57% XF0208 D-ribulose-5-phosphate XF2015 ribose-5-phosphate isomerase A (rpiA)XF1936 transketolase 1 (tktA/tkt) INTERMEDIARY INTERMEDIARY METABOLISM/CENTRAL 57% interconversions METABOLISM/Nucleotide XF1288 CTP synthetase (pyrG)XF1058 uridylate kinase (pyrH) 63% INTERMEDIARY INTERMEDIARY METABOLISM/CENTRAL compounds METABOLISM/Phosphorus XF0657 alkaline phosphatase (phoA)XF0904 protein (ybeZ) ATP-binding XF2590 exopolyphosphatase (ppx) 65% XF2591 54% polyphosphate kinase (ppk) INTERMEDIARY INTERMEDIARY METABOLISM/CENTRAL multipurpose conversions METABOLISM/Pool, 32% XF2255 55% acetyl coenzyme A synthetase (acs)XF1037 42% adenosylhomocysteinase (ahcY) 33% XF0880 carbonic anhydrase (yadF)XF2095 carbonic anhydraseXF2249 61% deoxyxylulose-5-phosphate synthase (dxs)XF1889 ferredoxin-NADP reductase (fpr) 55% XF2268 65% glycerol kinase (glpK)XF0181 glycine cleavage H protein (gcvH)XF0183 glycine cleavage T protein (gcvT)XF1385 46% glycine decarboxylase (gcvP)XF2160 59% hydroxyacylglutathione hydrolase (gloB)XF2171 inorganic pyrophosphatase (ppa) 48% XF1399 32% lactoylglutathione lyase (gloA) 45% 55% XF0392 methionine adenosyltransferase (metK)XF0913 tropinone reductase 59% 57% 70% INTERMEDIARY INTERMEDIARY METABOLISM/CENTRAL 59% biosynthesis, conversions METABOLISM/Sugar-nucleotide 63% XF0609 GDP-mannose 4,6 dehydratase (gmd)XF2279 nucleotide sugar epimerase (wbnF)XF0260 phosphoglucomutase/ 50% XF1468 43% phosphomannomutase (mrsA)XF0259 51% phosphomannose isomerase-GDP- XF1606 UDP-glucose dehydrogenase (ugd) INTERMEDIARY INTERMEDIARY METABOLISM/CENTRAL metabolism METABOLISM/Sulfur 55% 63% XF1497 3’-phosphoadenosine XF1501 sulfurylase, large subunit (nodQ) ATP XF1500 sulfurylase, small subunit (cysD) ATP XF1499 NADPH-sulfite reductase, flavoprotein 55% XF1498 NADPH-sulfite reductase, iron-sulfur 67% Table 3 Putative identification of Table relative to the most relevant database hit (conservedrelative to the most relevant hypotheticals and % identities of genes with frameshift/stop codon in fra

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