The genome sequence of the plant pathogen Xylella fastidiosa

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The genome sequence of the plantpathogen Xylella fastidiosaThe Xylella fastidiosa Consortium of the Organization for Nucleotide Sequencing and Analysis*, Sao 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 wereport the complete genome sequence of X. fastidiosa clone 9a5c, which causes citrus variegated chlorosis—a serious disease oforange trees. The genome comprises a 52.7% GC-rich 2,679,305-base-pair (bp) circular chromosome and two plasmids of51,158 bp and 1,285 bp. We can assign putative functions to 47% of the 2,904 predicted coding regions. Efficient metabolicfunctions are predicted, with sugars as the principal energy and carbon source, supporting existence in the nutrient-poor xylemsap. The mechanisms associated with pathogenicity and virulence involve toxins, antibiotics and ion sequestration systems, aswell as bacterium–bacterium and bacterium–host interactions mediated by a range of proteins. Orthologues of some of theseproteins have only been identified in animal and human pathogens; their presence in X. fastidiosa indicates that the molecularbasis for bacterial pathogenicity is both conserved and independent of host. At least 83 genes are bacteriophage-derived andinclude virulence-associated genes from other bacteria, providing direct evidence of phage-mediated horizontal gene transfer.

Citrus variegated chlorosis (CVC), which was first recorded in Brazilin 1987, affects all commercial sweet orange varieties1. Symptomsinclude conspicuous variegations on older leaves, with chloroticareas on the upper side and corresponding light brown lesions, withgum-like material on the lower side. Affected fruits are small,hardened and of no commercial value. A strain of Xylella fastidiosawas first identified as the causal bacterium in 1993 (ref. 2) and foundto be transmitted by sharpshooter leafhoppers in 1996 (ref. 3). CVCcontrol is at present limited to removing infected shoots by pruning,the application of insecticides and the use of healthy plants for neworchards. In addition to CVC, other strains of X. fastidiosa cause arange of economically important plant diseases including Pierce’sdisease of grapevine, alfalfa dwarf, phony peach disease, periwinklewilt and leaf scorch of plum, and are also associated with diseases inmulberry, pear, almond, elm, sycamore, oak, maple, pecan andcoffee4. The triply cloned X. fastidiosa 9a5c, sequenced here, wasderived from the pathogenic culture 8.1b obtained in 1992 inBordeaux (France) from CVC-affected Valencia sweet orangetwigs collected in Macaubal (Sao Paulo, Brazil) on May 21, 1992(ref. 2). Strain 9a5c produces typical CVC symptoms on inoculationinto experimental citrus plants5, and into Nicotiana tabacum (S. A.Lopes, personal communication) and Catharantus roseus (P. Brant-Monteiro, personal communication)—two novel experimentalhosts.

General features of the genomeThe basic features of the genome are listed in Table 1 and a detailedmap is shown in Fig. 1. The conserved origin of replication of thelarge chromosome has been identified in a region between theputative 50S ribosomal protein L34 and gyrB genes containingdnaA, dnaN and recF6. The Escherichia coli DnaA box consensussequence TTATCCACA is found on both DNA strands close todnaA. In addition, there are typical 13-nucleotide (ACCACCAC-CACCA) and 9-nucleotide (two TTTCATTGG and two TTTTA-TATT) sequences in other intergenic sequences of this region. Thisregion is coincident with the calculated GC-skew signal inversion7.We have designated base 1 of the X. fastidiosa genome as the first Tofthe only TTTTAT sequence found between the ribosomal proteinL34 gene and dnaA.

The overall percentage of open reading frames (ORFs) for which aputative biological function could be assigned (47%) was slightlybelow that for other sequenced genomes such as Thermotogamaritima8 (54%), Deinococcus radiodurans9 (52.5%) and Neisseria

meningitidis10 (53.7%). This may reflect the lack of previouscomplete genome sequences from phytopathogenic bacteria. Plas-mid pXF1.3 contains only two ORFs, one of which encodes areplication-associated protein. Plasmid pXF51 contains 64 ORFs,of which 5 encode proteins involved in replication or plasmidstability and 20 encode proteins potentially involved in conjugativetransfer. One ORF encodes a protein similar to the virulence-associated protein D (VapD), found in many other bacterialpathogens11. Four regions of pXF51 present significant DNA simi-larity to parts of transposons found in plasmids from other bacteria,suggesting interspecific horizontal exchange of genetic material.

The principal paralogous families are summarized in Table 2. Thecomplete list of ORFs with assigned function is shown in Table 3.Seventy-five proteins present in the 21 completely sequencedgenomes in the COG database12 (as of 15th March 2000) werealso found in X. fastidiosa. Each of these sequences was used to

Table 1 General features of the Xylella fastidiosa 9a5c genome

Main chromosomeLength (bp) 2,679,305G+C ratio 52.7%Open reading frames (ORFs) 2,782Coding region (% of chromosome size) 88.0%Average ORF length (bp) 799ORFs with functional assignment 1,283ORFs with matches to conservedhypothetical proteins

310

ORFs without significant data base match 1,083Ribosomal RNA operons 2

(16SrRNA-Ala-TGC-tRNA-Ile-GAT-tRNA-23SrRNA-5SrRNA)

tRNAs 49 (46 different sequencescorresponding to all 20 amino acids)

tmRNA 1.............................................................................................................................................................................

Plasmid pXF51Length (bp) 51,158G+C ratio 49.6%Open reading frames (ORFs) 64Protein coding region (% of plasmid size) 86.9%ORFs with functional assignment 30ORFs with matches to conservedhypothetical proteins

8

ORFs without significant data base match 24.............................................................................................................................................................................

Plasmid pXF1.3Length (bp) 1,285G+C ratio 55.6%Open reading frames (ORFs) 2ORFs with functional assignment 1.............................................................................................................................................................................

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generate a phylogenetic tree of the 22 organisms. In 69% of suchtrees, X. fastidiosa was grouped with Haemophilus influenzae andE. coli, consistent with a phylogenetic analysis undertaken with the16S rRNA gene13.

One ORF, a cytosine methyltransferase (XF1774), is interruptedby a Group II intron. The intron was identified on the basis of thepresence of a reverse transcriptase-like gene (as in other Group IIintrons), conserved splice sites, conserved sequence in structure Vand conserved elements of secondary structure14. Group II intronsare rare in prokaryotes, but have been found in different evolutivelineages including E. coli, cyanobacteria and proteobacteria15.

Transcription, translation and repairThe basic transcriptional and translational machinery of X. fasti-diosa is similar to that of E. coli16. Recombinational repair, nucleo-tide and base-excision repair, and transcription-coupled repair arepresent with some noteworthy features. For example, no photolyasewas found, indicating exclusively dark repair. Although the maingenes of the SOS pathway, recA and lexA, are present, ORFscorresponding to the three DNA polymerases induced by SOS inE. coli (DNA polymerases II, IVand V)17 are missing, indicating thatthe mutational pathway itself may be distinct.

Energy metabolismEven though X. fastidiosa is, as its name suggests, a fastidiousorganism, energy production is apparently efficient. In additionto all the genes for the glycolytic pathway, all genes for thetricarboxylic acid cycle and oxidative and electron transportchains are present. ATP synthesis is driven by the resulting chemi-osmotic proton gradient and occurs by an F-type ATP synthase.Fructose, mannose and glycerol can be utilized in addition toglucose in the glycolytic pathway. There is a complete pathway forhydrolysis of cellulose to glucose, consisting of 1,4-b-cellobiosidase,endo-1,4-b-glucanase and b-glucosidase, suggesting that cellulosebreakdown may supplement the often low concentrations of mono-saccharides in the xylem18. Two lipases are encoded in the genome,but there is no b-oxidation pathway for the hydrolysis of fatty acids,presumably precluding their utilization as an alternative carbon andenergy source. Likewise, although enzymes required for the break-down of threonine, serine, glycine, alanine, aspartate and glutamateare present, pathways for the catabolism of the other naturallyoccurring amino acids are incomplete or absent.

The gluconeogenesis pathway appears to be incomplete. Phos-phoenolpyruvate carboxykinase and the gluconeogenic enzymefructose-1,6-bisphosphatase, which are required to bypass theirreversible step in glycolysis, are not present. The absence of thefirst is compensated by the presence of phosphoenolpyruvatesynthase and malate oxidoreductase, which together can generatephosphoenolpyruvate from malate. There appears, however, to beno known compensating pathway for the absence of fructose-1,6-bisphosphatase. It is possible that among the large number ofunidentified X. fastidiosa genes there are non-homologous genesthat compensate for steps in such critical pathways. Barring thispossibility, however, the absence of a functional gluconeogenesispathway implies a strict dependence on carbohydrates both as a

source of energy and anabolic precursors. The glyoxylate cycle isabsent and the pentose phosphate pathway is incomplete. In thelatter pathway, genes for neither 6-phosphogluconic dehydrogenasenor transaldolase were identified.

Small molecule metabolismX. fastidiosa exhibits extensive biosynthetic capabilities, pre-sumably an absolute requirement for a xylem-dwelling bacterium.Most of the genes found in E. coli necessary for the synthesis of allamino acids from chorismate, pyruvate, 3-phosphoglycerate, glu-tamate and oxaloacetic acid16 were identified. However, some genesin X. fastidiosa are bi-functional, such as phosphoribosyl-AMPcyclohydrolase/phosphoribosyl-ATP pyrophosphatase (XF2213),aspartokinase/homoserine dehydrogenase I (XF2225), imidazole-glycerolphosphate dehydratase/histidinol-phosphate phosphatase(XF2217) and a new diaminopimelate decarboxylase/aspartatekinase (XF1116) that would catalyse the first and the last steps oflysine biosynthesis. In addition, the gene for acetylglutamate kinase(XF1001) has an acetyltransferase domain at its carboxy-terminalend that would compensate for the missing acetyltransferase in thearginine biosynthesis pathway. Other missing genes include phos-phoserine phosphatase, cystathionine b-lyase, homoserine O-suc-cinyltransferase and 2,4,5-methyltetrahydrofolate-homocysteinemethyltransferase. The first two enzymes are also absent in theBacillus subtilis genome, the third is absent in Haemophilus influ-enzae and the fourth is missing in both genomes12. We thus presumethat alternative, unidentified enzymes complete the biosyntheticpathways in these organisms and in X. fastidiosa.

The pathways for the synthesis of purines, pyrimidines andnucleotides are all complete. X. fastidiosa is also apparently capableof both synthesizing and elongating fatty acids from acetate. Again,however, some E. coli enzymes were not found, such as holo acyl-carrier-protein synthase (also absent in Synechocystis sp., H. influenzaeand Mycoplasma genitalium) and enoyl-ACP reductase (NADPH)(FabI) (also absent from M. genitalium, Borrelia burgdorferi andTreponema pallidum)12.

X. fastidiosa appears to be capable of synthesizing an extensivevariety of enzyme cofactors and prosthetic groups, including biotin,folic acid, pantothenate and coenzyme A, ubiquinone, glutathione,thioredoxin, glutaredoxin, riboflavin, FMN, FAD, pyrimidinenucleotides, porphyrin, thiamin, pyridoxal 59-phosphate and lipo-ate. In a number of the synthetic pathways, one or more of theenzymes present in E. coli are absent, but this is also true for at leastone other sequenced Gram-negative bacterial genome in each case12.We therefore again infer that the missing enzymes are either notessential or replaced by unknown proteins with novel structures.

Transport-related proteinsA total of 140 genes encoding transport-related proteins wereidentified, representing 4.8% of all ORFs. For comparison, E. coli,B. subtilis and M. genitalium have around 10% of genes encodingtransport proteins, whereas Helicobacter pylori, Synechocystis sp. andMethanococcus jannaschii have 3.5–5.4% (ref. 19). Transport sys-tems are central components of the host–pathogen relationship(Fig. 2). There are a number of ion transporters and transporters forthe uptake of carbohydrates, amino acids, peptides, nitrate/nitrite,sulphate, phosphate and vitamin B12. Many different transport

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Table 2 Largest families of paralogous genes

Family(total number of families = 312)

Number of genes(total number of genes = 853)

.............................................................................................................................................................................

ATP-binding subunits of ABC transporters 23Reductases/dehydrogenases 12Two-component system, regulatory proteins 12Hypothetical proteins 10Transcriptional regulators 9Fimbrial proteins 9Two-component system, sensor proteins 9.............................................................................................................................................................................

Figure 1 Linear representation of the main chromosome and plasmids pXF51 andpXF1.3 of the Xylella fastidiosa genome. Genes are coloured according to theirbiological role. Arrows indicate the direction of transcription. Genes with frameshift andpoint mutations are indicated with an X. Ribosomal RNA genes, the tmRNA, the principalrepeats, prophages and the group II intron are indicated by coloured lines. Transfer RNAsare identified by a single letter identifying the amino acid. Pie chart represents thedistribution of the number of genes according to biological role. The numbers belowprotein-producing genes correspond to gene IDs.

Q

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families are represented and include both small and large mechano-sensitive conductance ion channels, a monovalent cation:protonantiporter (CAP-2) and a glycerol facilitator belonging to themajor intrinsic protein (MIP) family. In addition, 23 ABCtransport systems comprising 41 genes can be identified. X. fasti-diosa appears to possess a phosphotransferase system (PTS) thattypically mediates small carbohydrate uptake. There are both theenzyme I and HPr components of this system, as well as a genesupposedly involved in its regulation (pstK or hprK); however, thereis no PTS permease—an essential component of the phosphotrans-ferase complex. The functionality of the system therefore remains inquestion.

There are five outer membrane receptors, including siderophores,ferrichrome-iron and haemin receptors, which are all associatedwith iron transport. The energizing complexes, TonB–ExbB–ExbDand the paralogous TolA–TolR–TolQ, essential for the functioningof the outer membrane receptors, are also present. In all, 67 genesencode proteins involved in iron metabolism. We propose that in X.fastidiosa the uptake of iron and possibly of other transition metalions such as manganese causes a reduction in essential micro-nutrients in the plant xylem, contributing to the typical symptomsof leaf variegation.

The X. fastidiosa genome encodes a battery of proteins thatmediate drug inactivation and detoxification, alteration of potentialdrug targets, prevention of drug entry and active extrusion ofdrugs and toxins. These include ABC transporters and transportprocesses driven by a proton gradient. Of the latter, eight belong tothe hydrophobe/amphiphile efflux-1 (HAE1) family, which act asmultidrug resistance factors.

AdhesionX. fastidiosa is characteristically observed embedded in an extra-cellular translucent matrix in planta20. Clumps of bacteria formwithin the xylem vessels leading to their blockage and symptoms ofthe disease such as water-stress leaf curling. We deduce, from ouranalysis of the complete genome sequence, that the matrix iscomposed of extracellular polysaccharides (EPSs) synthesized byenzymes closely related to those of Xanthomonas campestris pvcampestris (Xcc) that produce what is commercially known asxanthan gum. In comparison with Xcc, however, we did not findgumI (encoding glycosyltransferase V, which incorporates theterminal mannose), gumL (encoding ketalase which adds pyruvateto the polymer) or gumG (encoding acetyltransferase which addsacetate), suggesting that Xylella gum may be less viscous than itsXanthomonas counterpart.

Positive regulation of the synthesis of extracelullar enzymes andEPS in Xanthomomas is effected by proteins coded by the rpf(regulation of pathogenicity factors) gene cluster21. Mutations inany of these genes in Xanthomomas results in failure to synthesizethe EPS. In consequence, the strain becomes non-pathogenic21.X. fastidiosa contains genes that encode RpfA, RpfB, RpfC and RpfF,suggesting that both bacteria may regulate the synthesis of patho-genic EPS factors through similar mechanisms.

Fimbria-like structures are readily apparent upon electron micro-scopical observation of X. fastidiosa within both its plant and insecthosts22. Because of the high velocity of xylem sap passing throughnarrow portions of the insect foregut, fimbria-mediated attachmentmay be essential for insect colonization. Indeed, in the insectmouthparts the bacteria are attached in ordered arrays, indicatingspecific and polarized adhesion23. In addition, fimbriae are thoughtto be involved in both plant–bacterium and bacterium–bacteriuminteractions during colonization of the xylem itself. We identified 26genes encoding proteins responsible for the biogenesis and functionof Type 4 fimbria filaments. This type of fimbria is found at the polesof a wide range of bacterial pathogens where they act to mediateadhesion and translocation along epithelial surfaces24. The genesinclude pilS and pilR homologues, which encode a two-component

system controlling transcription of fimbrial subunits, presumably inresponse to host cues, and pilG, H, I, J and chpA, which encode achemotactic system transducing environmental signals to the pilusmachinery.

In addition to the EPS and fimbriae, which are likely to havecentral roles in the clumping of bacteria and in adhesion to thexylem walls, we also identified outer membrane protein homo-logues for afimbrial adhesins. Although fimbrial adhesins are wellcharacterized as crucial virulence factors in both plant and humanpathogens25, afimbrial adhesins, which are directly associated withthe bacterial cell surface, have been hitherto associated only withhuman and animal pathogens, where they promote adherence toepithelial tissue. Of the three putative adhesins of this kind iden-tified in X. fastidiosa, two exhibit significant similarity to eachother (XF1981, XF1529) and to the hsf and hia gene products ofH. influenzae26. The third (XF1516) is similar to the uspA1 geneproduct of Moraxella catarrhalis27. All these proteins share thecommon C-terminal domain of the autotransporter family28.Direct experimentation will be required to establish whether theseadhesins promote binding to plant cell structures or components ofthe insect vector foregut, or both. Nevertheless, their presence in theX. fastidiosa genome adds to the increasing evidence for thegenerality of mechanisms of bacterial pathogenicity, irrespectiveof the host organism29.

We also identified three different haemagglutinin-like genes.Again, similar genes have not previously been identified in plantpathogens. These genes (XF2775, XF2196, XF0889) are the largest inthe genome and exhibit highest similarity to a Neisseria meningitidisputative secreted protein10.

Intervessel migrationMovement between individual xylem vessels is crucial for effectivecolonization by X. fastidiosa. For this to occur, degradation of the pitmembrane of the xylem vessel is required. Of the known pectolyticenzymes capable of this function, a polygalacturonase precursorand a cellulase were identified, although the former contains anauthentic frameshift. These genes exhibited highest similarity toorthologues in Ralstonia solanacearum—which causes wilt diseasein tomatoes—where the polygalacturonase genes are required forwild-type virulence.

ToxicityWe identified five haemolysin-like genes: haemolysin III (XF0175),which belongs to an uncharacterized protein family, and four others(XF0668, XF1011, XF2407, XF2759) which belong to the RTX toxinfamily that contains tandemly repeated glycine-rich nonapeptidemotifs at the C-terminal domain. One of these ORFs is closelyrelated to bacteriocin, an RTX toxin also found in the plantbacterium Rhizobium leguminosarum30. RTX or RTX-like proteinsare important virulence factors widely distributed among Gram-negative pathogenic bacteria31.

There are two Colicin-V-like precursor proteins. Colicin V is anantibacterial polypeptide toxin produced by E. coli, which actsagainst closely related sensitive bacteria32. The precursors consistof 102-amino-acid peptides (XF0262, XF0263) that have the typicalconserved leader 15-amino-acid motif, and have some similaritywith Colicin V from E. coli at the remaining C-terminal portion.The necessary apparatus for Colicin biosynthesis and secretion isalso present. Interestingly, in E. coli most of the genes necessary forbiogenesis and export of Colicin V are in a gene cluster present in aplasmid, whereas in X. fastidiosa these genes are dispersed in thechromosome.

We found four genes that may function in polyketide biogenesis:polyketide synthase (PKS), pteridine-dependent deoxygenase,daunorubicin C-13 ketoreductase and a NonF-related protein.These genes belong to the synthesis pathways of frenolicin, rapa-mycin, daunorubicin and nonactin, respectively. These pathways

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Figure 2 A comprehensive view of the biochemical processes involved in Xylella fastidiosapathogenicity and survival in the host xylem. The principal functional categories are shownin bold, and the bacterial genes and gene products related to that function are arrangedwithin the coloured section containing the bold heading. Transporters are indicated asfollows: cylinders, channels; ovals, secondary carriers, including the MFS family; paireddumbbells, secondary carriers for drug extrusion; triple dumbbells, ABC transporters;bulb-like icon, F-type ATP synthase; squares, other transporters. Icons with two arrows

represent symporters and antiporters (H+ or Na+ porters, unless noted otherwise).2,5DDOL, 2,5-dichloro-2,5-cyclohexadiene-1,4-dol; EPS, exopolysaccharides; MATE,multi-antimicrobial extrusion family of transporters multidrug efflux gene (XF2686); MFS,major facilitator superfamily of transporters; Pbp, b-lactamase-like penicillin-bindingprotein (XF1621); RND, resistance-nodulation-cell division superfamily of transporters;ROS, reactive oxygen species.

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include many more enzymes, which we did not find; however, someof the genes listed lie close to ORFs without significant databasematches, suggesting that at least one (as yet undiscovered) poly-ketide pathway may be functional.

ProphagesBacteriophages can mediate the evolution and transfer of virulencefactors and occasional acquisition of new traits by the bacterial host.Because as much as 7% of the X. fastidiosa genome sequencedcorresponds to double-stranded (ds) DNA phage sequences, mostlyfrom the Lambda group, we suspect that this route may have beenof particular importance for this bacterium. It is noteworthy thata very high percentage of phage-related sequences has also beendetected in a second vascular-restricted plant pathogen,Spiroplasma citri33. We identified four regions, with a high densityof ORFs homologous to phage sequences, that we considered to beprophages, in addition to isolated phage sequences dispersedthroughout the genome. Two of these prophages (each ,42 kbp,designated XfP1 and XfP2) are similar to each other, lie in oppositeorientations in distinct regions and appear to belong to the dsDNA,tailed-phage group. Both appear to contain most of the genesresponsible for particle assembly, although we know of no reportsof phage particle release from X. fastidiosa cultures. In prophageXfP1, we found two ORFs between tail genes V and W that aresimilar to ORF118 and vapA from the virulence-associated region ofthe animal pathogen Dichelobacter nodosus, which by homologyencode a killer and a suppressor protein34. Interestingly, in prophageXfP2, we found two other ORFs also between tail genes V and Wthat are similar to hypothetical ORFs of Ralstonia eutropha trans-poson Tn4371 (ref. 35). The other two identified prophages, XfP3and XfP4, are also similar in sequence to each other and to theH. influenzae cryptic prophage fflu (ref. 36). They both contain a14,317-bp exact repeat. Few particle-assembly genes were found inthese regions, suggesting that these prophages are defective. An ORFsimilar to hicB from H. influenzae, a component of the major pilusgene cluster in some isolates, was found in XfP4 (ref. 37).

The presence of virulence-associated genes from other organismswithin the prophage sequences is strong evidence for a direct role forbacteriophage-mediated horizontal gene transfer in the definitionof the bacterial phenotype.

Absence of avirulence genesPhytopathogenic bacteria generally have a limited host range, oftenconfined to members of a single species or genus. This specificity isdefined by the products of the so-called avirulence (avr) genespresent in the pathogen, which are injected directly into host cells,on infection, through a type III secretory system38–40. BLAST41

searches with all known avr and type III secretory system sequencesfailed to identify genes encoding proteins with significant simi-larities in the genome of X. fastidiosa. Although the variability of avrgenes amongst bacteria might account for this apparent lack, thehigh level of similarity of some components of the type III secretorysystem argues against this. We suspect that these genes are, in fact,not required because of the insect-mediated transmission andvascular restriction of the bacterium that obviates the necessityof host cell infection. Furthermore, if the differing host ranges ofX. fastidiosa are molecularly defined, this may be by a quite differentmechanism not involving avr proteins.

ConclusionsBefore the elucidation of its complete genome sequence, very littlewas known of the molecular mechanisms of X. fastidiosa pathogeni-city. Indeed, this bacterium was probably the least characterized of allorganisms that have been fully sequenced. Our complete geneticanalysis has determined not only the basic metabolic and replicativecharacteristics of the bacterium, but also a number of potential

pathogenicity mechanisms. Some of these have not previously beenpostulated to occur in phytopathogens, providing new insights intothe generality of these processes. Indeed, the availability of this firstcomplete plant pathogen genome sequence will now allow theinitiation of the detailed comparison of animal and plant pathogensat the whole-genome level. In addition, the information containedin the sequence should provide the basis for an accelerated andrational experimental dissection of the interactions between X.fastidiosa and its hosts that might lead to fresh insights intopotential approaches to the control of CVC. M

MethodsThe sequencing and analysis in this project were carried out by a network of 34 biologylaboratories and one bioinformatics centre. The network is called the Organization forNucleotide Sequencing and Analysis (ONSA)42, and is entirely located in the state of SaoPaulo, Brazil.

Sequencing and assemblyThe sequence was generated using a combination of ordered cosmid and shotgunstrategies43. A cosmid library was constructed, providing roughly 15-fold genome cover-age, containing 1,056 clones with average insert size of 40 kilobases (kb). High-densitycolony filters of the library were made, and a physical map of the genome was constructedusing a strategy of hybridization without replacement44. A total of 113 cosmid clones wasselected for sequencing on the basis of the hybridization map and end-sequence analysis.The cosmid sequences were assembled into 15 contigs covering 90% of the genome.Additionally, shotgun libraries with different insert sizes (0.8–2.0 kb and 2.0–4.5 kb) wereconstructed from nebulized or restricted genomic DNA cloned into plasmids, andsequenced to achieve a 3.74-fold coverage of high-quality sequence (29,140 reads). Most ofthe sequencing was performed with BigDye terminators on ABI Prism 377 DNAsequencers.

Cosmid and shotgun sequences were assembled into six contigs. We identified sequencegaps by linking information from forward and reverse reads, and closed either by primerwalking or insert subcloning. The remaining physical gaps were closed by combinatorialPCR and by lambda clones selected from a lDash library by end-sequencing. Thecollinearity between the genome and the obtained sequence was confirmed by digestion ofgenomic DNA with AscI, NotI, SfiI, SmiI and SrfI, followed by comparison of the digestionpattern with the electronic digestion of the generated sequence. In addition, sequencesfrom both ends of most cosmid clones and 236 l clones were used to confirm theorientation and integrity of the contigs. The sequence was assembled usingphred+phrap+consed45. All consensus bases have quality with Phred value of at least 20.There are no unexplained high quality discrepancies, each consensus base is confirmed byat least one read from each strand, and the overall error estimate is less than 1 in every10,000 bases.

ORF prediction and annotationORFs were determined using glimmer 2.0 (ref. 46) and the glimmer post-processorRBSfinder (S. L. Salzberg, personal communication). A few ORFs were found by handguided by BLAST41 results. Annotation was carried out in a cooperative way, mostly bycomparison with sequences in public databases, using BLAST41 and tRNAscan-SE (ref. 47)and was based on the functional categories for E. coli48. Only one tmRNA was located(K. Williams, personal communication). To help annotate transport proteins, we built acustom BLAST41 database using sequences from http://www-biology.ucsd.edu/,msaier/transport/toc.html and compared our ORFs with these sequences. Phylogenetic trees forconserved COGs12 were built using ClustalX49 for multiple alignment and Phylip50.Paralogous gene families (Table 2) were determined using BLASTX with the E-valuecut-off equal to e-5 and such that at least 60% of the query sequence and at least 30% of thesubject sequence were aligned.

Received 24 March; accepted 24 May 2000.

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Supplementary information is available on Nature’s World-Wide Web site(http://www.nature.com), or on the author’s World-Wide Web site(http://www.lbi.ic.unicamp.br/xf) or as paper copy from the London editorial office ofNature.

AcknowledgementsThe consortium is indebted to J. F. Perez, Scientific Director of Fundacao de Amparo aPesquisa do Estado de Sao Paulo (FAPESP), for his strategic vision in creating andnurturing this project as well as C. A. de Pian and Jucara Parra for their administrativecoordination. We thank our Steering Committee: S. Oliver, A. Goffeau, J. Sgouros, A. C.M. Paiva and J. L. Azevedo for their critical accompaniment of the work. We also thank R.Fulton and P. Minx for their timely contribution and advice. Project funding was fromFAPESP, the RHAE programme of the Conselho Nacional de Desenvolvimento Cientıficoe Tecnologico (CNPq) and Fundecitrus. For the full list of individuals who contributed tothe completion of this project see (http://www.lbi. ic.unicamp.br/xf).

Correspondence and requests for materials should be addressed to J.C.S. (e-mail:[email protected]). The sequence has been deposited in GenBank with accessionnumbers AE003849 (chromosome), AE003850 (pXF1.3) and AE003851 (pXF51).

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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. Bove10, 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.Franca19, 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. de Sa34,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 dePesquisa sobre oCancer, Rua Prof. Antonio Prudente,109 – 4o andar, 01509-010, Sao Paulo - SP, Brazil;2, Departamento de Bioquımica, Instituto de Quımica, Universidade de Sao Paulo, Av. Prof. Lineu Prestes, 748, 05508-900, Sao Paulo -SP, Brazil; 3, Centro de Biologia Molecular e Engenharia Genetica, Universidade Estadual de Campinas, Caixa Postal 6010,13083-970,Campinas – SP, Brazil; 4, Laboratorio de BiologiaMolecular, Departamento de Patologia, Faculdade de MedicinaVeterinaria e Zootecnia,Universidade de Sao Paulo, Av. Prof. Dr. Orlando Marques de Paiva, 87, 05508-000, Sao Paulo – SP, Brazil; 5, Disciplina de Oncologia,Departamento de Radiologia, Faculdade de Medicina, Universidade de Sao Paulo, Av. Dr. Arnaldo, 455, 01296-903, Sao Paulo – SP,Brazil; 6, Departamento de Tecnologia, Faculdadede Ciencias Agrarias e Veterinarias de Jaboticabal, UniversidadeEstadual Paulista, Via

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de Acesso Prof. Paulo D. Castellane s/n, Km 5,14884-900, Jaboticabal – SP, Brazil; 7, Departamento de Microbiologia, Imunologia eParasitologia, Escola Paulista de Medicina,UniversidadeFederal de Sao Paulo, Rua Botucatu, 862, 04023-062, Sao Paulo – SP, Brazil; 8,Departamento deMicrobiologia, Instituto deCienciasBiomedicas,UniversidadedeSaoPaulo,Av. Prof. LineuPrestes,1374, 05508-900,Sao Paulo – SP, Brazil; 9, Hemocentro, Faculdade de Ciencias Medicas, Universidade Estadual de Campinas,13083-97, Campinas – SP,Brazil; 10, Institut National de la Recherche Agronomique et Universite Victor Segalen Bordeaux 2, 71 Avenue Edouard Bourleaux,Laboratoire de Biologie Cellulaire et Moleculaire, 33883 Vilenave d’Ornon Cedex, France; 11, Departamento de Biologia, Instituto deBiociencias,UniversidadedeSaoPaulo,RuadoMatao, 277, 05508-900,SaoPaulo – SP,Brazil; 12, EscolaSuperiordeAgricultura Luiz deQueiroz, Universidade de Sao Paulo, Av. Padua Dias,11,13418-900, Piracicaba – SP, Brazil; 13, Departamento de Genetica, Instituto deBiociencias, Universidade Estadual Paulista, Distrito de Rubiao Junior,18618-000, Botucatu – SP, Brazil; 14, Centro de Genetica, BiologiaMolecular e Fitoquımica, Instituto Agronomico de Campinas, Av. Barao de Itapura,1481, Caixa Postal 28,13001-970, Campinas – SP,Brazil; 15, Departamento de Clınica Medica, Faculdade de Medicina de Ribeirao Preto, Universidade de Sao Paulo, Av. Bandeirantes,3900,14049-900, Ribeirao Preto – SP, Brazil; 16, Departamento de Biofısica, Escola Paulista de Medicina, Universidade Federal de SaoPaulo, Rua Botucatu, 862, 04023-062, Sao Paulo – SP, Brazil; 17, Centro de Citricultura Sylvio Moreira, Instituto Agronomico deCampinas, Caixa Postal 04,13490-970, Cordeiropolis – SP, Brazil; 18, Laboratorio de Bioquımica Fitopatologica e Laboratorio deImunologia, Instituto Biologico, Av. Cons. Rodrigues Alves,1252, 04014-002, Sao Paulo – SP, Brazil; 19, Departamento de BiotecnologiadePlantasMedicinais, UniversidadedeRibeirao Preto,Av.Costabile Romano, 2201,14096-380, Ribeirao Preto – SP,Brazil; 20,Centro deEnergia Nuclear na Agricultura, Universidade de Sao Paulo, Av. Centenario, 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 Nutricao Animal, Faculdade de Medicina Veterinaria e Zootecnia, Universidade Estadual Paulista,Fazenda Lageado, Caixa Postal 560,18600-000, Botucatu - SP, Brazil; 23, Departamento de Ciencias Farmaceuticas , Faculdade deCiencias Farmaceuticas de Ribeirao Preto, Universidade de Sao Paulo, Av. do Cafe s/n,14040-903, Ribeirao Preto – SP, Brazil; 24,Departamento de Biologia, Faculdade de Filosofia, Ciencias e Letras de Ribeirao Preto, Universidade de Sao Paulo, Av. Bandeirantes,3900,14040-901,Ribeirao Preto – SP,Brazil; 25,Centro deBiotecnologia, InstitutoButantan,Av. Vital Brasil,1500, 05503-900, Sao Paulo– SP, Brazil; 26, Laboratorio de Genetica e Cardiologia Molecular/LIM 13, Instituto do Coracao (InCor), Faculdade de Medicina,Universidade de Sao Paulo, Av. Dr. Eneas de Carvalho Aguiar, 44, 05403-000, Sao Paulo – SP, Brazil; 27, Instituto de Computacao,Universidade Estadual de Campinas, Caixa Postal 6176,13083-970, Campinas – SP, Brazil; 28, Departamento de Producao Vegetal,Faculdade de Ciencias Agronomicas, Universidade Estadual Paulista, Fazenda Lageado, Caixa Postal 237,18603-970, Botucatu – SP,Brazil; 29, Departamento de Biologia Aplicada a Agropecuaria, Faculdade de Ciencias Agrarias e Veterinarias de Jaboticabal,UniversidadeEstadual Paulista, Via deAcessoProf. PauloDonato Castellane,14884-900, Jaboticabal – SP, Brazil; 30, Hospital doCancer– A.C. Camargo, R. Antonio Prudente, 211, 01509-010, Sao Paulo – SP, Brazil; 31, Nucleo Integrado de Biotecnologia, Universidade deMogi dasCruzes,Av.Dr.CandidoXavierdeAlmeidaSouza, 200, 08780-911,Mogi dasCruzes – SP,Brazil; 32,Departamento deGeneticae Evolucao, Instituto de Biologia, Universidade Estadual de Campinas, Caixa Postal 6010,13083-970, Campinas– SP, Brazil; 33,Departamento de Botanica, Instituto de Biociencias, Universidade de Sao Paulo, Rua do Matao, 277, 05508-900, Sao Paulo - SP, Brazil;34, Departamento de Parasitologia, Microbiologia e Imunologia, Faculdade de Medicina de Ribeirao Preto, Universidade de Sao Paulo,Av. Bandeirantes, 3900,14049-900, Ribeirao Preto – SP, Brazil; 35, Departamento de Psiquiatria, Instituto de Psiquiatria, Faculdade deMedicina, Universidade de Sao Paulo, Rua Dr. Ovıdeo Pires de Campos s/n, Sala 4051 (3o. andar), 05403-010, Sao Paulo – SP, Brazil.† Present addresses: Novartis Seeds LTDA, Av. Prof. Vicente Rao, 90, 04706-900, Sao Paulo – SP, Brazil (J. A. Machado); Centro de Ciencias Agrarias e Ambientais,Pontifıcia Universidade Catolica do Parana, BR-376, Km 14, Caixa Postal 129, 83010-500, Sao Jose dos Pinhais – PR, Brazil (H. M. F. Madeira); Instituto de Pesquisa eDesenvolvimento, Universidade do Vale do Paraıba, Av. Shishimi Hifumi, 2911, 12244-000, Sao Jose dos Campos – SP, Brazil (F. G. Nobrega).

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© 2000 Macmillan Magazines Ltd

Page 9

articles

NATURE | VOL 406 | 13 JULY 2000 | www.nature.com 159

INTE

RMED

IARY

MET

ABOL

ISM

/ DEG

RADA

TION

/Deg

rada

tion

of s

mal

l mol

ecul

es

XF23

95ac

etyl

xyla

n es

tera

se (a

xeA)

34%

XF12

50ar

gini

ne d

eam

inas

e (ro

cF)

45%

XF14

72be

nzen

e 1,

2-di

oxyg

enas

e,fe

rredo

xin

prot

ein

(bed

B)37

%XF

0840

beta

-gal

acto

sida

se (b

ga)

71%

XF04

39be

ta-g

luco

sida

se (b

glX)

41%

XF08

46be

ta-m

anno

sida

se p

recu

rsor

35%

XF12

34ca

rbox

ypho

spho

noen

olpy

ruva

teph

osph

onom

utas

e (p

rpB)

62%

XF22

10di

oxyg

enas

e48

%XF

1743

este

rase

(est

)46

%XF

1610

fruct

okin

ase

36%

XF17

40gl

ucos

e de

hydr

ogen

ase

B (y

liI)

44%

XF10

64gl

ucos

e ki

nase

(glk

)41

%XF

1460

gluc

ose

kina

se (g

lk)

35%

XF19

65ha

loal

kane

deh

alog

enas

e (d

haA)

30%

XF26

77L-

asco

rbat

e ox

idas

e (a

ao)

29%

XF12

53lip

ase

(lipP

)46

%XF

0781

lipas

e/es

tera

se (e

stA)

25%

XF18

25N

AD(P

)H s

tero

id d

ehyd

roge

nase

(cdh

)35

%XF

1201

phos

phog

lyco

late

pho

spha

tase

(yfb

T)35

%XF

2470

phos

phog

lyco

late

pho

spha

tase

(cbb

ZC)

37%

XF22

59po

lyvi

nyla

lcoh

ol d

ehyd

roge

nase

22%

XF03

66rib

okin

ase

(rbsK

)38

%XF

0379

rubr

edox

in (r

ubA)

54%

XF18

19th

reon

ine

dehy

drat

ase

cata

bolic

(tdc

B)39

%XF

1181

triac

ylgl

ycer

ol li

pase

pre

curs

or (l

ip)

56%

XF06

10UD

P-gl

ucos

e 4-

epim

eras

e (g

alE)

27%

XF24

32UT

P-gl

ucos

e-1-

phos

phat

eur

idyl

yltra

nsfe

rase

(gta

B)82

%

INTE

RMED

IARY

MET

ABOL

ISM

/CEN

TRAL

INTE

RMED

IARY

MET

ABOL

ISM

/Am

ino

suga

rs

XF01

41gl

ucos

amin

e--fr

ucto

se-6

-pho

spha

team

inot

rans

fera

se (g

lmS)

54%

XF14

64gl

ucos

amin

e--fr

ucto

se-6

-ph

osph

atea

min

otra

nsfe

rase

47%

XF23

55N

-ace

tyl-b

eta-

gluc

osam

inid

ase

(exo

)45

%XF

1465

N-a

cety

lglu

cosa

min

e-6-

phos

phat

ede

acet

ylas

e (n

agA)

39%

INTE

RMED

IARY

MET

ABOL

ISM

/CEN

TRAL

INTE

RMED

IARY

MET

ABOL

ISM

/Ent

ner-D

oude

roff

XF10

612-

keto

-3-d

eoxy

-6-p

hosp

hogl

ucon

ate

aldo

lase

(eda

/hga

/kdg

A)41

%XF

1062

6-ph

osph

oglu

cona

te d

ehyd

rata

se (e

dd)

58%

INTE

RMED

IARY

MET

ABOL

ISM

/CEN

TRAL

INTE

RMED

IARY

MET

ABOL

ISM

/Glu

cone

ogen

esis

XF09

77m

alat

e ox

idor

educ

tase

(mae

B)57

%XF

1259

phos

phoe

nolp

yruv

ate

synt

hase

(pps

A/pp

s)64

%

INTE

RMED

IARY

MET

ABOL

ISM

/CEN

TRAL

INTE

RMED

IARY

MET

ABOL

ISM

/Non

-oxi

dativ

e br

anch

, pen

tose

pat

hway

XF02

08D-

ribul

ose-

5-ph

osph

ate

3-ep

imer

ase

(rpe/

dod)

76%

XF20

15rib

ose-

5-ph

osph

ate

isom

eras

e A

(rpiA

)57

%XF

1936

trans

keto

lase

1 (t

ktA/

tkt)

63%

INTE

RMED

IARY

MET

ABOL

ISM

/CEN

TRAL

INTE

RMED

IARY

MET

ABOL

ISM

/Nuc

leot

ide

inte

rcon

vers

ions

XF12

88CT

P sy

nthe

tase

(pyr

G)65

%XF

1058

urid

ylat

e ki

nase

(pyr

H)54

%

INTE

RMED

IARY

MET

ABOL

ISM

/CEN

TRAL

INTE

RMED

IARY

MET

ABOL

ISM

/Pho

spho

rus

com

poun

ds

XF06

57al

kalin

e ph

osph

atas

e (p

hoA)

32%

XF09

04AT

P-bi

ndin

g pr

otei

n (y

beZ)

55%

XF25

90ex

opol

ypho

spha

tase

(ppx

)42

%XF

2591

poly

phos

phat

e ki

nase

(ppk

)33

%

INTE

RMED

IARY

MET

ABOL

ISM

/CEN

TRAL

INTE

RMED

IARY

MET

ABOL

ISM

/Poo

l, m

ultip

urpo

se c

onve

rsio

ns

XF22

55ac

etyl

coe

nzym

e A

synt

heta

se (a

cs)

61%

XF10

37ad

enos

ylho

moc

yste

inas

e (a

hcY)

65%

XF08

80ca

rbon

ic a

nhyd

rase

(yad

F)46

%XF

2095

carb

onic

anh

ydra

se32

%XF

2249

deox

yxyl

ulos

e-5-

phos

phat

e sy

ntha

se (d

xs)

55%

XF18

89fe

rredo

xin-

NAD

P re

duct

ase

(fpr)

59%

XF22

68gl

ycer

ol k

inas

e (g

lpK)

59%

XF01

81gl

ycin

e cl

eava

ge H

pro

tein

(gcv

H)48

%XF

0183

glyc

ine

clea

vage

T p

rote

in (g

cvT)

55%

XF13

85gl

ycin

e de

carb

oxyl

ase

(gcv

P)57

%XF

2160

hydr

oxya

cylg

luta

thio

ne h

ydro

lase

(glo

B)45

%XF

2171

inor

gani

c py

roph

osph

atas

e (p

pa)

59%

XF13

99la

ctoy

lglu

tath

ione

lyas

e (g

loA)

63%

XF03

92m

ethi

onin

e ad

enos

yltra

nsfe

rase

(met

K)70

%XF

0913

tropi

none

redu

ctas

e43

%

INTE

RMED

IARY

MET

ABOL

ISM

/CEN

TRAL

INTE

RMED

IARY

MET

ABOL

ISM

/Sug

ar-n

ucle

otid

e bi

osyn

thes

is, c

onve

rsio

ns

XF06

09GD

P-m

anno

se 4

,6 d

ehyd

rata

se (g

md)

50%

XF22

79nu

cleo

tide

suga

r epi

mer

ase

(wbn

F)51

%XF

0260

phos

phog

luco

mut

ase/

phos

phom

anno

mut

ase

(xan

A)84

%XF

1468

phos

phom

anno

mut

ase

(mrs

A)55

%XF

0259

phos

phom

anno

se is

omer

ase-

GDP-

man

nose

pyr

opho

spho

ryla

se (x

anB)

84%

XF16

06UD

P-gl

ucos

e de

hydr

ogen

ase

(ugd

)63

%

INTE

RMED

IARY

MET

ABOL

ISM

/CEN

TRAL

INTE

RMED

IARY

MET

ABOL

ISM

/Sul

fur m

etab

olis

m

XF14

973’

-pho

spho

aden

osin

e5’

-pho

spho

sulfa

te re

duct

ase

(cys

H)57

%XF

1501

ATP

sulfu

ryla

se, l

arge

sub

unit

(nod

Q)55

%XF

1500

ATP

sulfu

ryla

se, s

mal

l sub

unit

(cys

D)67

%XF

1499

NAD

PH-s

ulfit

e re

duct

ase,

flav

opro

tein

subu

nit (

cysJ

)40

%XF

1498

NAD

PH-s

ulfit

e re

duct

ase,

iron

-sul

fur

prot

ein

(cys

I)52

%

XF01

87su

lfite

syn

thes

is p

athw

ay p

rote

in(c

ysQ/

amtA

)45

%

INTE

RMED

IARY

MET

ABOL

ISM

/EN

ERGY

MET

ABOL

ISM

,CA

RBON

/Aer

obic

resp

iratio

n

XF03

47D-

lact

ate

dehy

drog

enas

e (d

ld1)

38%

XF18

02gl

ycer

ol-3

-pho

spha

tede

hydr

ogen

ase

(gps

A)46

%XF

2266

glyc

erol

-3-p

hosp

hate

dehy

drog

enas

e (g

lpD)

54%

XF03

10N

ADH-

ubiq

uino

ne o

xido

redu

ctas

e,N

QO1

subu

nit (

nuoF

)53

%XF

0314

NAD

H-ub

iqui

none

oxi

dore

duct

ase,

NQO

10 s

ubun

it (n

uoJ)

45%

XF03

15N

ADH-

ubiq

uino

ne o

xido

redu

ctas

e,N

QO11

sub

unit

(nuo

K)69

%XF

0316

NAD

H-ub

iqui

none

oxi

dore

duct

ase,

NQO

12 s

ubun

it (n

uoL)

42%

XF03

17N

ADH-

ubiq

uino

ne o

xido

redu

ctas

e,N

QO13

sub

unit

(nuo

M)

50%

XF03

18N

ADH-

ubiq

uino

ne o

xido

redu

ctas

e,N

QO14

sub

unit

(nuo

N)

43%

XF03

09N

ADH-

ubiq

uino

ne o

xido

redu

ctas

e,N

QO2

subu

nit (

nuoE

)41

%XF

0311

NAD

H-ub

iqui

none

oxi

dore

duct

ase,

NQO

3 su

buni

t (nu

oG)

38%

XF03

08N

ADH-

ubiq

uino

ne o

xido

redu

ctas

e,N

QO4

subu

nit (

nuoD

)58

%XF

0307

NAD

H-ub

iqui

none

oxi

dore

duct

ase,

NQO

5 su

buni

t (nu

oC)

63%

XF03

06N

ADH-

ubiq

uino

ne o

xido

redu

ctas

e,N

QO6

subu

nit (

nuoB

)87

%XF

0305

NAD

H-ub

iqui

none

oxi

dore

duct

ase,

NQO

7 su

buni

t (nu

oA)

53%

XF03

12N

ADH-

ubiq

uino

ne o

xido

redu

ctas

e,N

QO8

subu

nit (

nuoH

)56

%XF

0313

NAD

H-ub

iqui

none

oxi

dore

duct

ase,

NQO

9 su

buni

t (nu

oI)

60%

INTE

RMED

IARY

MET

ABOL

ISM

/EN

ERGY

MET

ABOL

ISM

,CA

RBON

/Ana

erob

ic re

spira

tion

and

ferm

enta

tion

XF17

46al

coho

l deh

ydro

gena

se (y

ahK)

81%

XF23

89al

coho

l deh

ydro

gena

se (y

ahK)

78%

XF11

36N

ADP-

alco

hol d

ehyd

roge

nase

56%

XF17

27N

ADP-

alco

hol d

ehyd

roge

nase

(adh

)42

%XF

1734

NAD

P-al

coho

l deh

ydro

gena

se56

%

INTE

RMED

IARY

MET

ABOL

ISM

/EN

ERGY

MET

ABOL

ISM

,CA

RBON

/Ele

ctro

n tra

nspo

rt

XF24

60c-

type

cyt

ochr

ome

biog

enes

ism

embr

ane

prot

ein

(cyc

K)52

%XF

2459

c-ty

pe c

ytoc

hrom

e bi

ogen

esis

pro

tein

(cyc

J)39

%XF

2462

c-ty

pe c

ytoc

hrom

e bi

ogen

esis

pro

tein

(cyc

L)52

%XF

0620

c-ty

pe c

ytoc

hrom

e bi

ogen

esis

prot

ein

(cop

per t

oler

ance

) (ds

bD)

32%

XF24

61c-

type

cyt

ochr

ome

biog

enes

ispr

otei

n/th

iore

doxi

n (d

sbE/

ccm

G)39

%XF

1328

cyto

chro

me

B561

(yod

B)34

%XF

1360

cyto

chro

me

C ox

idas

e as

sem

bly

fact

or (c

oxD)

41%

XF13

89cy

toch

rom

e O

ubiq

uino

l oxi

dase

,su

buni

t I (c

yoB)

69%

XF13

90cy

toch

rom

e O

ubiq

uino

l oxi

dase

,su

buni

t II (

cyoA

)56

%XF

1388

cyto

chro

me

O ub

iqui

nol o

xida

se,

subu

nit I

II (c

yoC)

63%

XF13

87cy

toch

rom

e O

ubiq

uino

l oxi

dase

,su

buni

t IV

(cyo

D)41

%XF

0253

elec

tron

trans

fer f

lavo

prot

ein

alph

asu

buni

t (et

fA)

51%

XF02

54el

ectro

n tra

nsfe

r fla

vopr

otei

n be

tasu

buni

t (et

fB/e

tfS)

54%

XF12

98el

ectro

n tra

nsfe

r fla

vopr

otei

nub

iqui

none

oxi

dore

duct

ase

(etf-

QO)

46%

XF05

57el

ectro

n tra

nsfe

r pro

tein

azu

rin I

(az1

)49

%XF

0983

ferre

doxi

n56

%XF

1964

ferre

doxi

n (y

kgJ)

47%

XF26

01fe

rredo

xin

70%

XF05

47fe

rredo

xin

II (y

dgM

)54

%XF

0053

flavo

hem

opro

tein

(fhp

)40

%XF

2082

oxid

ored

ucta

se31

%XF

1990

thio

redo

xin

(yne

N)

30%

XF09

09ub

iqui

nol c

ytoc

hrom

e C

oxid

ored

ucta

se,

cyto

chro

me

B su

buni

t (pe

tB)

56%

XF09

10ub

iqui

nol c

ytoc

hrom

e C

oxid

ored

ucta

se,

cyto

chro

me

C1 s

ubun

it (p

etC)

48%

XF09

08ub

iqui

nol c

ytoc

hrom

e C

oxid

ored

ucta

se,

iron-

sulfu

r sub

unit

(pet

A)52

%

INTE

RMED

IARY

MET

ABOL

ISM

/EN

ERGY

MET

ABOL

ISM

,CA

RBON

/Gly

coly

sis

XF02

746-

phos

phof

ruct

okin

ase

(pfk

A)31

%XF

1291

enol

ase

(eno

)63

%XF

0826

fruct

ose-

bisp

hosp

hate

ald

olas

e52

%XF

0232

gluc

ose-

6-ph

osph

ate

isom

eras

e (p

gi)

79%

XF04

57gl

ycer

alde

hyde

-3-p

hosp

hate

dehy

drog

enas

e (g

apA)

68%

XF08

23ph

osph

ogly

cera

te k

inas

e (p

gk)

60%

XF18

93ph

osph

ogly

cero

mut

ase

(gpm

A/gp

m)

56%

XF08

24py

ruva

te k

inas

e ty

pe II

(pyk

A)50

%XF

0303

trios

epho

spha

te is

omer

ase

(tpiA

/tpi

)48

%

INTE

RMED

IARY

MET

ABOL

ISM

/EN

ERGY

MET

ABOL

ISM

,CA

RBON

/Oxi

dativ

e br

anch

, pen

tose

pat

hway

XF10

636-

phos

phog

luco

nola

cton

ase

(pgl

)35

%XF

1065

gluc

ose-

6-ph

osph

ate

1-de

hydr

ogen

ase

(zwf)

46%

INTE

RMED

IARY

MET

ABOL

ISM

/EN

ERGY

MET

ABOL

ISM

,CA

RBON

/Pyr

uvat

e de

hydr

ogen

ase

XF08

69di

hydr

olip

oam

ide

acet

yltra

nfer

ase

(pdh

B)52

%XF

0868

dihy

drol

ipoa

mid

e de

hydr

ogen

ase

(lpdA

/lpd)

57%

XF06

69py

ruva

te d

ehyd

roge

nase

(ace

E)56

%

INTE

RMED

IARY

MET

ABOL

ISM

/EN

ERGY

MET

ABOL

ISM

,CA

RBON

/TCA

cyc

le

XF02

92ac

onita

te h

ydra

tase

2 (a

cnB)

72%

XF15

35ci

trate

syn

thas

e (g

ltA)

61%

XF15

48di

hydr

olip

oam

ide

dehy

drog

enas

e (lp

d)58

%XF

1549

dihy

drol

ipoa

mid

e S-

succ

inyl

trans

fera

se(s

ucB)

53%

XF15

54fu

mar

ate

hydr

atas

e (fu

mC)

58%

XF18

55fu

mar

ate

hydr

atas

e (fu

mB)

30%

XF25

96is

ocitr

ate

dehy

drog

enas

e (ic

d) 4

9%XF

2700

isoc

itrat

e de

hydr

ogen

ase

(icd)

75%

XF12

11m

alat

e de

hydr

ogen

ase

(mdh

) 6

2%XF

0942

mal

ate:

quin

one

oxid

ored

ucta

se (y

ojH)

57%

XF15

50ox

oglu

tara

te d

ehyd

roge

nase

(odh

A) 5

4%XF

1073

succ

inat

e de

hydr

ogen

ase

iron-

sulfu

rpr

otei

n (s

dhB)

70%

XF10

72su

ccin

ate

dehy

drog

enas

e,fla

vopr

otei

n su

buni

t (sd

hA)

69%

XF10

70su

ccin

ate

dehy

drog

enas

e,m

embr

ane

anch

or s

ubun

it (s

dhC)

38%

XF10

71su

ccin

ate

dehy

drog

enas

e, m

embr

ane

anch

or s

ubun

it (s

dhD)

36%

XF25

48su

ccin

yl-C

oA s

ynth

etas

e,al

pha

subu

nit (

sucD

) 7

1%XF

2547

succ

inyl

-CoA

syn

thet

ase,

bet

a su

buni

t (su

cC)

58%

INTE

RMED

IARY

MET

ABOL

ISM

/EN

ERGY

MET

ABOL

ISM

,CA

RBON

/ATP

-pro

ton

mot

ive

forc

e in

terc

onve

rsio

n

XF11

49AT

P sy

ntha

se, A

cha

in (a

tpB/

uncB

/pap

D) 4

6%XF

1145

ATP

synt

hase

, alp

ha c

hain

(atp

A/un

cA)

74%

XF11

47AT

P sy

ntha

se, B

cha

in (a

tpF/

uncF

) 4

5%XF

1143

ATP

synt

hase

, bet

a ch

ain

(atp

D) 7

8%XF

1148

ATP

synt

hase

, C c

hain

(atp

E/un

cE)

56%

XF11

46AT

P sy

ntha

se, d

elta

cha

in (a

tpH/

uncH

) 3

7%XF

1142

ATP

synt

hase

, eps

ilon

chai

n (a

tpC)

46%

XF11

44AT

P sy

ntha

se, g

amm

a ch

ain

(atp

G/un

cG/p

apC)

57%

INTE

RMED

IARY

MET

ABOL

ISM

/REG

ULAT

ORY

FUN

CTIO

NS

XF12

41ac

onita

te h

ydra

tase

1 (a

cnA/

acn)

---%

XF13

16AT

P:GT

P 3’

-pyr

opho

spho

tranf

eras

e (re

lA)

42%

XF01

25ca

rbon

sto

rage

regu

lato

r (cs

rA)

84%

XF23

52co

ld s

hock

pro

tein

(sco

F) 6

9%XF

2476

extra

geni

c su

pres

sor (

suhB

/ssy

A) 4

4%XF

2342

heat

-indu

cibl

e tra

nscr

iptio

nal

repr

esso

r (hr

cA)

40%

XF01

22Le

xA re

pres

sor (

lexA

) 7

6%XF

1182

lipas

e m

odul

ator

(act

) 5

3%XF

1813

met

hano

l deh

ydro

gena

se re

gula

tory

pro

tein

53%

XF18

30ni

trile

hyd

rata

se a

ctiv

ator

46%

XF18

43ni

troge

n re

gula

tory

pro

tein

P-II

(gln

B) 8

7%XF

0352

pent

apho

spha

te g

uano

sine

-3’-

pyro

phos

phoh

ydro

lase

(spo

T) 4

7%XF

2145

phos

phat

e re

gulo

n tra

nscr

iptio

nal

regu

lato

r (ph

oU)

43%

XF12

75po

ly(h

ydro

xyal

cano

ate)

gra

nule

asso

ciat

ed p

rote

in (p

haF)

20%

XF26

91RN

A po

lym

eras

e si

gma-

32 fa

ctor

(rpo

H) 8

0%XF

1408

RNA

poly

mer

ase

sigm

a-54

fact

or (r

poN

) 6

4%XF

1350

RNA

poly

mer

ase

sigm

a-70

fact

or (r

poD)

63%

XF22

39RN

A po

lym

eras

e si

gma-

H fa

ctor

(alg

U/al

gT)

56%

XF14

07si

gma-

54 m

odul

atio

n pr

otei

n 4

4%XF

0911

strin

gent

sta

rvat

ion

prot

ein

A(s

spA/

ssp/

pog)

46%

XF09

12st

ringe

nt s

tarv

atio

n pr

otei

n B

(ssp

B) 4

2%XF

2165

trans

crip

tion-

rela

ted

prot

ein

(tex)

59%

XF09

62tra

nscr

iptio

nal r

egul

ator

(gcv

R) 2

6%XF

1749

trans

crip

tiona

l reg

ulat

or (o

pdE)

77%

XF18

58tra

nscr

iptio

nal r

egul

ator

(exs

B) 4

9%XF

2038

trans

crip

tiona

l reg

ulat

or (p

aiB)

31%

XF22

28tra

nscr

iptio

nal r

egul

ator

(alg

H) 4

5%XF

2085

trans

crip

tiona

l reg

ulat

or (A

crR

fam

ily)

23%

XF12

54tra

nscr

iptio

nal r

egul

ator

(Ara

C fa

mily

) (ar

aL)

34%

XF07

67tra

nscr

iptio

nal r

egul

ator

(Ars

R fa

mily

) (hl

yU)

34%

XF15

40tra

nscr

iptio

nal r

egul

ator

(Crp

/Fnr

fam

ily) (

clp)

85%

XF08

21tra

nscr

iptio

nal r

egul

ator

(Fur

fam

ily) (

zur)

38%

XF23

44tra

nscr

iptio

nal r

egul

ator

(Fur

fam

ily) (

fur)

85%

XF14

63tra

nscr

iptio

nal r

egul

ator

(Lac

I fam

ily)

32%

XF09

72tra

nscr

iptio

nal r

egul

ator

(Lux

R/Uh

pA fa

mily

) (ag

mR/

glpR

) 3

8%XF

2608

trans

crip

tiona

l reg

ulat

or(L

uxR/

UhpA

fam

ily) (

gacA

) 4

4%XF

0833

trans

crip

tiona

l reg

ulat

or (L

ysR

fam

ily) (

cysB

) 3

9%XF

1132

trans

crip

tiona

l reg

ulat

or (L

ysR

fam

ily) (

act)

33%

XF17

30tra

nscr

iptio

nal r

egul

ator

(Lys

R fa

mily

) (ya

fC)

35%

XF17

52tra

nscr

iptio

nal r

egul

ator

(Lys

R fa

mily

) 8

0%XF

1768

trans

crip

tiona

l reg

ulat

or (L

ysR

fam

ily) (

ycjZ

) 4

5%XF

0216

trans

crip

tiona

l reg

ulat

or (M

arR

fam

ily) (

prsX

) 22

%XF

1354

trans

crip

tiona

l reg

ulat

or (M

arR

fam

ily) (

yybA

) 28%

XF14

90tra

nscr

iptio

nal r

egul

ator

(Mar

R/Em

rR fa

mily

) 26

%XF

1996

trans

crip

tiona

l reg

ulat

or (P

bsX

fam

ily)

35%

XF00

61tra

nscr

iptio

nal r

epre

ssor

(kor

B) 2

8%XF

2062

trans

crip

tiona

l rep

ress

or (k

orC)

69%

XF19

20Tr

p op

eron

tran

scrip

tiona

l rep

ress

or (t

rpR)

36%

XF10

94try

ptop

han

repr

esso

r bin

ding

prot

ein

(wrb

A) 3

9%XF

1133

trypt

opha

n re

pres

sor b

indi

ng p

rote

in 3

3%XF

1733

trypt

opha

n re

pres

sor b

indi

ng p

rote

in 3

1%XF

1455

two-

com

pone

nt s

yste

m, h

ybrid

sens

or/r

egul

ator

y pr

otei

n 2

8%XF

0322

two-

com

pone

nt s

yste

m, r

egul

ator

ypr

otei

n (tc

tD)

45%

XF03

89tw

o-co

mpo

nent

sys

tem

, reg

ulat

ory

prot

ein

(pop

P/fe

uP/p

hoP)

54%

XF04

50tw

o-co

mpo

nent

sys

tem

, reg

ulat

ory

prot

ein

(pilH

) 5

0%XF

1113

two-

com

pone

nt s

yste

m, r

egul

ator

y pr

otei

n 3

0%XF

1626

two-

com

pone

nt s

yste

m, r

egul

ator

ypr

otei

n (a

lgR)

47%

XF18

48tw

o-co

mpo

nent

sys

tem

, reg

ulat

ory

prot

ein

(gln

G/nt

rC/g

lnT)

51%

XF23

36tw

o-co

mpo

nent

sys

tem

, reg

ulat

ory

prot

ein

(col

R)51

%XF

2534

two-

com

pone

nt s

yste

m, r

egul

ator

ypr

otei

n (c

olR)

59%

XF25

45tw

o-co

mpo

nent

sys

tem

, reg

ulat

ory

prot

ein

(pilR

)58

%XF

2578

two-

com

pone

nt s

yste

m, r

egul

ator

ypr

otei

n (a

ctR)

40%

XF25

93tw

o-co

mpo

nent

sys

tem

, reg

ulat

ory

prot

ein

(pho

B)56

%XF

0323

two-

com

pone

nt s

yste

m, s

enso

r pro

tein

(tct

E)31

%XF

0390

two-

com

pone

nt s

yste

m, s

enso

r pro

tein

(pho

Q)36

%

XF08

53tw

o-co

mpo

nent

sys

tem

, sen

sor p

rote

in (p

hs)

37%

XF09

73tw

o-co

mpo

nent

sys

tem

, sen

sor p

rote

in (f

lhS)

35%

XF16

25tw

o-co

mpo

nent

sys

tem

, sen

sor p

rote

in (a

lgZ)

40%

XF18

49tw

o-co

mpo

nent

sys

tem

, sen

sor p

rote

in (n

trB)

37%

XF25

35tw

o-co

mpo

nent

sys

tem

, sen

sor p

rote

in (c

olS)

34%

XF25

46tw

o-co

mpo

nent

sys

tem

, sen

sor p

rote

in (p

ilS)

37%

XF25

77tw

o-co

mpo

nent

sys

tem

, sen

sor p

rote

in (a

ctS)

25%

XF25

92tw

o-co

mpo

nent

sys

tem

, sen

sor p

rote

in (p

hoR)

38%

BIOS

YNTH

ESIS

OF

SMAL

L M

OLEC

ULES

/AM

INO

ACID

SBI

OSYN

THES

IS/G

luta

mat

e fa

mily

|nitr

ogen

ass

imila

tion

XF10

01ac

etyl

glut

amat

e ki

nase

(arg

B)30

%XF

1000

acet

ylor

nith

ine

deac

etyl

ase

(arg

E)28

%XF

1003

argi

nino

succ

inat

e ly

ase

(asl

)35

%XF

0999

argi

nino

succ

inat

e sy

ntha

se (a

rgG)

36%

XF10

05ga

mm

a-gl

utam

yl p

hosp

hate

redu

ctas

e (p

roA)

51%

XF10

04gl

utam

ate

5-ki

nase

46%

XF27

10gl

utam

ate

synt

hase

, alp

ha s

ubun

it(g

ltB/a

spB)

53%

XF27

09gl

utam

ate

synt

hase

, bet

a su

buni

t (gl

tD/a

spB)

55%

XF18

42gl

utam

ine

synt

heta

se (g

lnA)

64%

XF10

02N

-ace

tyl-g

amm

a-gl

utam

yl-p

hosp

hate

redu

ctas

e33

%XF

0998

orni

thin

e ca

rbam

oyltr

ansf

eras

e (a

rgF)

36%

XF27

12py

rrolin

e-5-

carb

oxyl

ate

redu

ctas

e (p

roC)

49%

XF14

27su

ccin

ylor

nith

ine

amin

otra

nsfe

rase

(arg

M/a

stC/

cstC

)48

%

BIOS

YNTH

ESIS

OF

SMAL

L M

OLEC

ULES

/AM

INO

ACID

SBI

OSYN

THES

IS/A

spar

tate

fam

ily, p

yruv

ate

fam

ily

XF01

142,

3,4,

5-te

trahy

drop

yrid

ine-

2-ca

rbox

ylat

eN

-suc

ciny

ltran

sfer

ase

(dap

D)60

%XF

1818

2-is

opro

pylm

alat

e sy

ntha

se (l

euA)

47%

XF23

753-

isop

ropy

lmal

ate

dehy

drat

ase

larg

esu

buni

t (le

uA)

63%

XF23

743-

isop

ropy

lmal

ate

dehy

drat

ase

smal

lsu

buni

t (le

uD)

79%

XF23

723-

isop

ropy

lmal

ate

dehy

drog

enas

e (le

uB)

78%

XF11

215,

10-m

ethy

lene

tetra

hydr

ofol

ate

redu

ctas

e (m

etF)

37%

XF22

725-

met

hylte

trahy

drop

tero

yltri

glut

amat

e--

hom

ocys

tein

e m

ethy

ltran

sfer

ase

(met

E)56

%XF

1821

acet

olac

tate

syn

thas

e is

ozym

e II,

larg

e su

buni

t (ilv

G)56

%XF

1473

amin

otra

nsfe

rase

(nifS

)47

%XF

2396

amin

otra

nsfe

rase

(asp

C)45

%XF

0118

aspa

ragi

ne s

ynth

ase

B (a

snB)

60%

XF13

71as

parta

te-B

-sem

iald

ehyd

ede

hydr

ogen

ase

(asd

)59

%XF

2100

aspa

rtyl/a

spar

agin

yl b

eta-

hydr

oxyl

ase

(asp

H) 2

8%XF

2443

beta

-ala

nine

syn

thet

ase

62%

XF22

25bi

func

tiona

l asp

arto

kina

se/h

omos

erin

ede

hydr

ogen

ase

I (th

rA/t

hrA1

/thr

A2)

40%

XF11

16bi

func

tiona

l dia

min

opim

elat

ede

carb

oxyl

ase/

aspa

rtate

kin

ase

(lysA

)33

%XF

1999

bran

ched

-cha

in a

min

o ac

idam

inot

rans

fera

se (i

lvE)

55%

XF08

64cy

stat

hion

ine

gam

ma-

synt

hase

(met

B)57

%XF

1481

diam

inop

imel

ate

epim

eras

e (d

apF)

45%

XF11

05di

hydr

odip

icol

inat

e re

duct

ase

(dap

B)34

%XF

0099

dihy

drox

y-ac

id d

ehyd

rata

se (i

lvD)

73%

XF09

63di

hydr

oxyd

ipic

olin

ate

synt

hase

(dap

A)42

%XF

2211

enol

ase-

phos

phat

ase

(mas

A)50

%XF

2224

hom

oser

ine

kina

se (t

hrB)

33%

XF08

63ho

mos

erin

e O-

acet

yltra

nsfe

rase

(met

2)30

%XF

2465

hom

oser

ine

O-ac

etyl

trans

fera

se34

%XF

1822

keto

l-aci

d re

duct

oiso

mer

ase

(ilvC

)59

%XF

0116

succ

inyl

-dia

min

opim

elat

ede

succ

inyl

ase

(dap

E)52

%XF

2223

thre

onin

e sy

ntha

se (t

hrC)

38%

BIOS

YNTH

ESIS

OF

SMAL

L M

OLEC

ULES

/AM

INO

ACID

SBI

OSYN

THES

IS/G

lyci

ne-s

erin

e fa

mily

|sul

fur m

etab

olis

m

XF06

03cy

stat

hion

ine

beta

-syn

thas

e (c

ysB)

31%

XF01

28cy

stei

ne s

ynth

ase

27%

XF08

31cy

stei

ne s

ynth

ase

(cys

K)51

%XF

2206

D-3-

phos

phog

lyce

rate

deh

ydro

gena

se (s

erA)

62%

XF23

26ph

osph

oser

ine

amin

otra

nsfe

rase

(ser

C)49

%XF

0946

serin

e hy

drox

ymet

hyltr

ansf

eras

e (g

lyA)

71%

BIOS

YNTH

ESIS

OF

SMAL

L M

OLEC

ULES

/AM

INO

ACID

SBI

OSYN

THES

IS/A

rom

atic

am

ino

acid

fam

ily

XF13

343-

dehy

droq

uina

te s

ynth

ase

(aro

B)47

%XF

2324

3-ph

osph

oshi

kim

ate

1-ca

rbox

yvin

yltra

nsfe

rase

(aro

E)46

%XF

0212

anth

rani

late

pho

spho

ribos

yltra

nsfe

rase

(trp

D)48

%XF

0210

anth

rani

late

syn

thas

e co

mpo

nent

I (tr

pE)

57%

XF06

74an

thra

nila

te s

ynth

ase

com

pone

nt I

(trpE

)36

%XF

1914

anth

rani

late

syn

thas

e co

mpo

nent

I (tr

pE)

37%

XF02

11an

thra

nila

te s

ynth

ase

com

pone

nt II

(trp

G)67

%XF

1915

anth

rani

late

syn

thas

e co

mpo

nent

II (t

rpG)

43%

XF00

36ar

omat

ic-a

min

o-ac

id a

min

otra

nfer

ase

(tyrB

)55

%XF

0047

cata

bolic

deh

ydro

quin

ase

(aro

Q)65

%XF

1141

chor

ism

ate

mut

ase

25%

XF23

38ch

oris

mat

e m

utas

e29

%XF

1369

chor

ism

ate

synt

hase

(aro

C)62

%XF

0213

indo

le-3

-gly

cero

l pho

spha

te s

ynth

ase

(trpC

)63

%XF

1374

N-(5

’-pho

spho

ribos

yl) a

nthr

anila

teis

omer

ase

(trpF

)43

%XF

2325

P-pr

otei

n (a

roQ/

pheA

)75

%XF

0026

phos

pho-

2-de

hydr

o-3-

deox

yhep

tona

teal

dola

se (a

roG)

61%

XF06

24sh

ikim

ate

5-de

hydr

ogen

ase

(aro

E)43

%XF

1335

shik

imat

e ki

nase

(aro

K)40

%XF

1376

trypt

opha

n sy

ntha

se a

lpha

cha

in (t

rpA)

46%

XF13

75try

ptop

han

synt

hase

bet

a ch

ain

(trpB

)65

%

BIOS

YNTH

ESIS

OF

SMAL

L M

OLEC

ULES

/AM

INO

ACID

SBI

OSYN

THES

IS/H

istid

ine

XF22

16am

idot

rans

fera

se (h

isH)

43%

XF22

20AT

P ph

osph

orib

osyl

trans

fera

se (h

isG)

43%

XF22

14cy

clas

e (h

isF)

61%

XF22

19hi

stid

inol

deh

ydro

gena

se (h

isD)

50%

XF22

18hi

stid

inol

-pho

spha

te a

min

otra

nsfe

rase

(his

C)42

%XF

2217

imid

azol

egly

cero

lpho

spha

tede

hydr

atas

e/hi

stid

inol

-pho

spha

te p

hosp

hata

sebi

func

tiona

l enz

yme

(his

B)50

%

XF22

13ph

osph

orib

osyl

-AM

Pcy

cloh

ydro

lase

/pho

spho

ribos

yl-A

TPpy

roph

osph

atas

e bi

func

tiona

len

zym

e (h

isI/h

isIE

)56

%XF

2215

phos

phor

ibos

ylfo

rmim

ino-

5-am

inoi

mid

azol

eca

rbox

amid

e rib

otid

e is

omer

ase

(his

A)44

%

BIOS

YNTH

ESIS

OF

SMAL

L M

OLEC

ULES

/NUC

LEOT

IDES

BIOS

YNTH

ESIS

/Pur

ine

ribon

ucle

otid

es

XF05

875’

-pho

spho

ribos

yl-5

-am

inoi

mid

azol

esy

nthe

tase

(pur

M/p

urG)

59%

XF05

855’

-pho

spho

ribos

ylgl

ycin

amid

etra

nsfo

rmyl

ase

(pur

N)

43%

XF02

75ad

enyl

ate

kina

se (a

dk)

47%

XF15

53ad

enyl

osuc

cina

te ly

ase

(pur

B)57

%XF

0455

aden

ylos

ucci

nate

syn

thet

ase

(pur

A)59

%XF

1949

amid

opho

spho

ribos

yltra

nsfe

rase

(pur

F)61

%XF

1975

bifu

nctio

nal p

urin

e bi

osyn

thes

ispr

otei

n (p

urH)

59%

XF24

29gl

utam

ine

amid

otra

nsfe

rase

(gua

A)68

%XF

1976

glyc

inam

ide

ribon

ucle

otid

e sy

nthe

tase

(pur

D)64

%XF

0560

GMP

synt

hase

37%

XF15

03gu

anyl

ate

kina

se (g

mk/

spoR

)52

%XF

2430

inos

ine-

5’-m

onop

hosp

hate

dehy

drog

enas

e (g

uaB)

64%

XF04

58nu

cleo

side

dip

hosp

hate

kin

ase

(ndk

)68

%XF

2644

phos

phor

ibos

yl p

yrop

hosp

hate

synt

heta

se (p

rsA/

prs)

60%

XF26

71ph

osph

orib

osyl

amin

oim

idaz

ole

carb

oxyl

ase,

ATP

ase

subu

nit (

purK

)50

%XF

2672

phos

phor

ibos

ylam

inoi

mid

azol

eca

rbox

ylas

e, c

atal

ytic

sub

unit

(pur

E)66

%XF

0205

phos

phor

ibos

ylam

inoi

mid

azol

e-su

ccin

ocar

boxa

mid

e sy

ntha

se (p

urC)

53%

XF14

23ph

osph

orib

osyl

form

ylgl

ycin

amid

ine

synt

heta

se (p

urL/

purI)

50%

BIOS

YNTH

ESIS

OF

SMAL

L M

OLEC

ULES

/NUC

LEOT

IDES

BIOS

YNTH

ESIS

/Pyr

imid

ine

ribon

ucle

otid

es

XF22

26as

parta

te c

arba

moy

ltran

sfer

ase

(pyr

B)52

%XF

1107

carb

amoy

l-pho

spha

te s

ynth

ase

larg

e ch

ain

(car

B/py

rA)

68%

XF11

06ca

rbam

oyl-p

hosp

hate

syn

thas

e sm

all

chai

n (c

arA)

68%

XF24

39cy

tidyl

ate

kina

se (c

mkA

)48

%XF

0988

dihy

droo

rota

se (p

yrC)

30%

XF25

71di

hydr

ooro

tate

deh

ydro

gena

se (p

yrD)

51%

XF01

53or

otat

e ph

osph

orib

osyl

tran

sfer

ase

(pyr

E)51

%XF

0034

orot

idin

e 5’

-pho

spha

te d

ecar

boxy

lase

(pyr

F)41

%

BIOS

YNTH

ESIS

OF

SMAL

L M

OLEC

ULES

/NUC

LEOT

IDES

BIOS

YNTH

ESIS

/2’-D

eoxy

ribon

ucle

otid

es

XF07

62de

oxyc

ytid

ine

triph

osph

ate

deam

inas

e (d

cd)

65%

XF14

41ph

osph

ohyd

rola

se (o

rfU1)

45%

XF11

96rib

onuc

leos

ide-

diph

osph

ate

redu

ctas

eal

pha

chai

n (n

rdA)

44%

XF11

97rib

onuc

leos

ide-

diph

osph

ate

redu

ctas

ebe

ta c

hain

(nrd

B)34

%XF

1448

thio

redo

xin

redu

ctas

e (tr

xB)

70%

XF05

80th

ymid

ylat

e ki

nase

39%

BIOS

YNTH

ESIS

OF

SMAL

L M

OLEC

ULES

/NUC

LEOT

IDES

BIOS

YNTH

ESIS

/Sal

vage

of n

ucle

osid

es a

nd n

ucle

otid

es

XF20

895’

-nuc

leot

idas

e42

%XF

2150

diad

enos

ine

tetra

phos

phat

ase

(apa

H)44

%XF

0150

dUTP

ase

(dut

/dna

S/so

f)59

%XF

1831

form

ylte

trahy

drof

olat

e de

form

ylas

e (p

urU)

47%

XF23

54hy

poxa

nthi

ne-g

uani

neph

osph

orib

osyl

trans

fera

se (h

pt)

27%

XF25

99ph

osph

odie

ster

ase-

nucl

eotid

epy

roph

osph

atas

e pr

ecur

sor

39%

XF23

53pu

rine

nucl

eosi

de p

hosp

hory

lase

45%

XF23

32th

ymid

ylat

e sy

ntha

se (t

hyA)

70%

BIOS

YNTH

ESIS

OF S

MAL

L MOL

ECUL

ES/S

UGAR

S AN

D SU

GAR

NUC

LEOT

IDES

BIO

SYN

THES

IS

XF12

97gl

ucon

olac

tona

se p

recu

rsor

37%

XF06

08m

anno

syltr

ansf

eras

e (m

tfA)

38%

BIOS

YNTH

ESIS

OF

SMAL

L M

OLEC

ULES

/COF

ACTO

RS,

PROS

THET

IC G

ROUP

S, C

ARRI

ERS

BIOS

YNTH

ESIS

/Bio

tin

XF13

578-

amin

o-7-

oxon

onan

oate

syn

thas

e (b

ioF)

42%

XF01

89ad

enos

ylm

ethi

onin

e-8-

amin

o-7-

oxon

onan

oate

amin

otra

nsfe

rase

(bio

A)47

%XF

1356

biot

in b

iosy

nthe

sis

prot

ein

(bio

H/bi

oB)

36%

XF00

64bi

otin

syn

thas

e (b

ioB)

60%

XF20

99bi

otin

syn

thes

is p

rote

in (b

ioC)

36%

XF03

56cy

toch

rom

e P-

450

hydr

oxyl

ase

37%

XF03

77cy

toch

rom

e P4

50-li

ke e

nzym

e (b

ioI)

37%

XF24

77de

thio

biot

in s

ynth

etas

e (b

ioD)

44%

BIOS

YNTH

ESIS

OF

SMAL

L M

OLEC

ULES

/CO

FACT

ORS,

PRO

STHE

TIC

GROU

PS,

CARR

IERS

BIO

SYN

THES

IS/F

olic

aci

d

XF02

282-

amin

o-4-

hydr

oxy-

6-hy

drox

ymet

hyld

ihyd

ropt

erid

ine

pyro

phos

phok

inas

e (fo

lK)

50%

XF14

562-

amin

o-4-

hydr

oxy-

6-hy

drox

ymet

hyld

ihyd

ropt

erid

ine

pyro

phos

phok

inas

e (fo

lK)

35%

XF24

31bi

func

tiona

l met

hyle

nete

trahy

drof

olat

ede

hydr

ogen

ase/

met

heny

ltetra

hydr

ofol

ate

cycl

ohyd

rola

se (f

olD)

58%

XF23

31di

hydr

ofol

ate

redu

ctas

e ty

pe II

I43

%XF

0436

dihy

dron

eopt

erin

ald

olas

e (fo

lB)

50%

XF00

91di

hydr

opte

roat

e sy

ntha

se (f

olP)

52%

XF19

46fo

lylp

olyg

luta

mat

e sy

ntha

se/d

ihyd

rofo

late

synt

hase

(fol

C/de

dC)

44%

XF19

83GT

P cy

cloh

ydro

lase

I (fo

lE)

52%

BIOS

YNTH

ESIS

OF

SMAL

L M

OLEC

ULES

/COF

ACTO

RS,

PROS

THET

IC G

ROUP

S, C

ARRI

ERS

BIOS

YNTH

ESIS

/Lip

oate

XF12

70lip

oate

bio

synt

hesi

s pr

otei

n B

(lipB

)55

%XF

1269

lipoi

c ac

id s

ynth

etas

e (li

pA/li

p)60

%

BIOS

YNTH

ESIS

OF

SMAL

L M

OLEC

ULES

/COF

ACTO

RS,

PROS

THET

IC G

ROUP

S, C

ARRI

ERS

BIOS

YNTH

ESIS

/Mol

ybdo

pter

in

XF04

66m

olyb

dopt

erin

bio

synt

hesi

s pr

otei

n (m

oeB)

53%

XF15

45m

olyb

dopt

erin

bio

synt

hesi

s pr

otei

n42

%

BIOS

YNTH

ESIS

OF

SMAL

L M

OLEC

ULES

/COF

ACTO

RS,

PROS

THET

IC G

ROUP

S, C

ARRI

ERS

BIOS

YNTH

ESIS

/Pan

toth

enat

e

XF02

293-

met

hyl-2

-oxo

buta

noat

ehy

drox

ymet

hyltr

ansf

eras

e (p

anB)

55%

XF02

31as

parta

te 1

-dec

arbo

xyla

se p

recu

rsor

(pan

D)53

%XF

0230

pant

oate

--bet

a-al

anin

e lig

ase

(pan

C)46

%

BIOS

YNTH

ESIS

OF

SMAL

L M

OLEC

ULES

/COF

ACTO

RS,

PROS

THET

IC G

ROUP

S, C

ARRI

ERS

BIOS

YNTH

ESIS

/Pyr

idox

ine

XF00

60py

ridox

al p

hosp

hate

bio

synt

hetic

prot

ein

(pdx

J)49

%XF

0839

pyrid

oxal

pho

spha

te b

iosy

nthe

ticpr

otei

n (p

dxA)

50%

XF13

37py

ridox

amin

e 5’

-pho

spha

te o

xida

se (f

prA)

52%

BIOS

YNTH

ESIS

OF

SMAL

L M

OLEC

ULES

/COF

ACTO

RS,

PROS

THET

IC G

ROUP

S, C

ARRI

ERS

BIOS

YNTH

ESIS

/Pyr

idin

enu

cleo

tides

XF19

24L-

aspa

rtate

oxi

dase

40%

XF19

61N

H3-d

epen

dent

NAD

syn

thet

ase

(nad

E/ad

gA)4

7%XF

1097

nico

tinat

e ph

osph

orib

osyl

trans

fera

se (p

ncB)

43%

XF19

25ni

cotin

ate-

mon

onuc

leot

ide

pyro

phos

phor

ylas

e (n

adC)

54%

XF19

23qu

inol

inat

e sy

nthe

tase

A (n

adA)

42%

BIOS

YNTH

ESIS

OF

SMAL

L M

OLEC

ULES

/COF

ACTO

RS,

PROS

THET

IC G

ROUP

S, C

ARRI

ERS

BIOS

YNTH

ESIS

/Thi

amin

XF10

481-

deox

y-D-

xylu

lose

5-p

hosp

hate

redu

ctoi

som

eras

e (d

xr)

46%

XF06

21ph

osph

omet

hylp

yrim

idin

e ki

nase

45%

XF03

78th

iam

in-p

hosp

hate

pyr

opho

spho

ryla

se (t

hiE)

41%

XF05

94th

iam

ine

bios

ynth

esis

lipo

prot

ein

ApbE

prec

urso

r (ap

bE)

33%

XF07

83th

iam

ine

bios

ynth

esis

pro

tein

(thi

G)57

%XF

1888

thia

min

e bi

osyn

thes

is p

rote

in (t

hiC/

thiA

)67

%XF

0956

thia

min

e-m

onop

hosp

hate

kin

ase

(thiL

)44

%

BIOS

YNTH

ESIS

OF

SMAL

L M

OLEC

ULES

/COF

ACTO

RS,

PROS

THET

IC G

ROUP

S, C

ARRI

ERS

BIOS

YNTH

ESIS

/Rib

ofla

vin

XF17

485-

amin

o-6-

(5-p

hosp

horib

osyl

amin

o)ur

acil

redu

ctas

e21

%XF

0954

6,7-

dim

ethy

l-8-ri

bity

llum

azin

e sy

ntha

se (r

ibH)

45%

XF09

53GT

P cy

cloh

ydro

lase

II/3

,4-d

ihyd

roxy

-2-b

utan

one

4-ph

osph

ate

synt

hase

(rib

A)52

%XF

1992

ribof

lavi

n bi

osyn

thes

is p

rote

in (r

ibA)

35%

XF24

19rib

ofla

vin

bios

ynth

esis

pro

tein

(rib

F)43

%XF

0952

ribof

lavi

n sy

ntha

se a

lpha

cha

in (r

ibE)

45%

XF09

50rib

ofla

vin-

spec

ific

deam

inas

e (ri

bD/r

ibG)

51%

BIOS

YNTH

ESIS

OF

SMAL

L M

OLEC

ULES

/COF

ACTO

RS,

PROS

THET

IC G

ROUP

S, C

ARRI

ERS

BIOS

YNTH

ESIS

/Thi

ored

oxin

,gl

utar

edox

in, g

luta

thio

ne

XF09

84ga

mm

a-gl

utam

yltra

nspe

ptid

ase

(ggt

)39

%XF

1428

glut

amat

e-cy

stei

ne li

gase

pre

curs

or (g

sh1)

57%

XF25

95gl

utar

edox

in (g

rxC)

53%

XF23

94gl

utar

edox

in-li

ke p

rote

in54

%XF

1956

glut

athi

one

synt

heta

se (g

shB/

gsh-

II)53

%XF

1199

thio

redo

xin

(trxA

)34

%XF

2174

thio

redo

xin

(ybb

N)

31%

XF26

98th

iore

doxi

n (tr

xA/t

snC/

fipA)

49%

BIOS

YNTH

ESIS

OF

SMAL

L M

OLEC

ULES

/COF

ACTO

RS,

PROS

THET

IC G

ROUP

S, C

ARRI

ERS

BIOS

YNTH

ESIS

/Men

aqui

none

, ubi

quin

one

XF08

352-

octa

pren

yl-6

-met

hoxy

phen

olhy

drox

ylas

e (u

biH/

visB

)34

%XF

2471

3-de

met

hylu

biqu

inon

e-9

3-m

ethy

ltran

sfer

ase

(ubi

G/pu

fX)

49%

XF06

61ge

rany

ltran

stra

nsfe

rase

(far

nesy

l-dip

hosp

hate

synt

hase

) (is

pA)

54%

XF00

68hy

drox

yben

zoat

e oc

tapr

enyl

trans

fera

se(u

biA/

cyr)

52%

XF13

91oc

tapr

enyl

-dip

hosp

hate

syn

thas

e (is

pB/c

el)

49%

XF15

38ub

iqui

none

bio

synt

hesi

s pr

otei

n (c

oq7)

29%

XF18

33ub

iqui

none

bio

synt

hesi

s pr

otei

n (a

arF)

43%

XF14

87ub

iqui

none

/men

aqui

none

tran

sfer

ase

(ubi

E)58

%

BIOS

YNTH

ESIS

OF

SMAL

L M

OLEC

ULES

/COF

ACTO

RS,

PROS

THET

IC G

ROUP

S, C

ARRI

ERS

BIOS

YNTH

ESIS

/Hem

e,po

rphy

rin

XF00

17co

prop

orph

yrin

ogen

III o

xida

se, a

erob

ic(h

emF)

63%

XF23

06de

lta-a

min

olev

ulin

ic a

cid

dehy

drat

ase

(hem

B)65

%XF

0566

ferro

chel

atas

e (h

emH)

48%

XF23

02gl

utam

ate-

1-se

mia

ldeh

yde

2,1-

amin

omut

ase

(hem

L)80

%XF

2648

glut

amyl

-tRN

A re

duct

ase

(hem

A)76

%XF

1627

hydr

oxym

ethy

lbila

ne s

ynth

ase

(hem

C)52

%XF

1797

porp

hyrin

bio

synt

hesi

s pr

otei

n (h

emY)

20%

XF15

12pr

otop

orph

yrin

ogen

oxi

dase

(hem

K)45

%XF

0832

siro

hem

e sy

ntha

se (c

ysG)

45%

XF13

32ur

opor

phyr

inog

en d

ecar

boxy

lase

(hem

E)54

%XF

1799

urop

orph

yrin

ogen

-III s

ynth

ase

(hem

D)27

%

BIOS

YNTH

ESIS

OF

SMAL

L M

OLEC

ULES

/COF

ACTO

RS,

PROS

THET

IC G

ROUP

S, C

ARRI

ERS

BIOS

YNTH

ESIS

/Cob

alam

in

XF18

86ph

osph

ogly

cera

te m

utas

e (p

gmA)

32%

BIOS

YNTH

ESIS

OF

SMAL

L M

OLEC

ULES

/COF

ACTO

RS,

PROS

THET

IC G

ROUP

S, C

ARRI

ERS

BIOS

YNTH

ESIS

/Bio

pter

in

XF01

936-

pyru

voyl

tetra

hydr

obio

pter

in s

ynth

ase

(ygc

M)

63%

XF14

57pt

erid

ine

redu

ctas

e 1

(ptr1

/ltdH

)37

%XF

2604

pter

in-4

-alp

ha-c

arbi

nola

min

ede

hydr

atas

e (p

hhB)

34%

BIOS

YNTH

ESIS

OF

SMAL

L M

OLEC

ULES

/COF

ACTO

RS,

PROS

THET

IC G

ROUP

S, C

ARRI

ERS

BIOS

YNTH

ESIS

/Oth

ers

XF19

16co

enzy

me

F390

syn

thet

ase

25%

BIOS

YNTH

ESIS

OF

SMAL

L M

OLEC

ULES

/FAT

TY A

CID

AND

PHOS

PHAT

IDIC

ACI

D BI

OSYN

THES

IS

XF10

44(3

r)-hy

drox

ymyr

isto

yl A

CP d

ehyd

rase

(fab

Z)49

%XF

2269

3-al

pha-

hydr

oxys

tero

id d

ehyd

roge

nase

34%

XF01

733-

oxoa

cyl-[

ACP]

redu

ctas

e42

%XF

0671

3-ox

oacy

l-[AC

P] re

duct

ase

(fabG

)66

%XF

0673

3-ox

oacy

l-[AC

P] s

ynth

ase

II (fa

bF)

60%

XF19

703-

oxoa

cyl-[

ACP]

syn

thas

e III

24%

XF03

19ac

etoa

cety

l-CoA

redu

ctas

e (p

hbB)

65%

XF02

03ac

etyl

-coe

nzym

e A

carb

oxyl

ase

carb

oxyl

trans

fera

se s

ubun

it al

pha

(acc

A)64

%XF

1467

acet

yl-c

oenz

yme

A ca

rbox

ylas

e ca

rbox

yltra

nsfe

rase

sub

unit

beta

(acc

D/de

dB/u

sg)

62%

XF06

72ac

yl c

arrie

r pro

tein

(acp

P)72

%XF

0771

acyl

car

rier p

rote

in (a

cpC)

40%

XF05

72be

ta-h

ydro

xyde

cano

yl-A

CP d

ehyd

rata

se(fa

bA)

63%

XF16

39be

ta-k

etoa

cyl-[

ACP]

syn

thas

e II

(fabF

/fab

J)34

%XF

1817

beta

-ket

oacy

l-[AC

P] s

ynth

ase

III (f

abH)

62%

XF00

48bi

otin

car

boxy

l car

rier p

rote

in o

fac

etyl

-CoA

car

boxi

lase

(acc

B/fa

bE)

53%

XF00

49bi

otin

car

boxy

lase

sub

unit

ofac

etyl

CoA

car

boxy

lase

(acc

C/fa

bG)

76%

XF10

87ca

rdio

lipin

syn

thas

e33

%XF

1209

card

iolip

in s

ynth

ase

(cls

/nov

)34

%XF

2716

keto

redu

ctas

e29

%XF

0670

mal

onyl

CoA

-ACP

tran

sacy

lase

(fab

D)51

%XF

1049

phos

phat

idat

e cy

tidyl

yltra

nsfe

rase

(cds

A/cd

s)36

%XF

1365

phos

phat

idyl

serin

e de

carb

oxyl

ase

(psd

)44

%

BIOS

YNTH

ESIS

OF

SMAL

L M

OLEC

ULES

/POL

YAM

INES

BIOS

YNTH

ESIS

XF01

44bi

osyn

thet

ic a

rgin

ine

deca

rbox

ylas

e (s

peA)

45%

XF15

39S-

aden

osyl

met

hion

ine

deca

rbox

ylas

epr

oenz

yme

(spe

D)66

%XF

0143

sper

mid

ine

synt

hase

(spe

E)41

%

MAC

ROM

OLEC

ULE

MET

ABOL

ISM

/DN

AM

ETAB

OLIS

M/R

eplic

atio

n

XF26

80AT

P-de

pend

ent D

NA

helic

ase

(rep)

43%

XF08

82AT

P-de

pend

ent h

elic

ase

(yoa

A)43

%XF

1229

ATP-

depe

nden

t hel

icas

e43

%XF

0001

chro

mos

omal

repl

icat

ion

initi

ator

(dna

A)53

%XF

2552

DNA

gyra

se s

ubun

it A

(gyr

A)57

%XF

0005

DNA

gyra

se s

ubun

it B

(gyr

B)60

%XF

2556

DNA

ligas

e (li

gA/li

g/dn

aL/p

deC/

lop)

46%

XF11

03DN

A po

lym

eras

e I (

polA

/res

A)52

%XF

0136

DNA

poly

mer

ase

III h

oloe

nzym

e ch

i sub

unit

(hol

C)34

%XF

1807

DNA

poly

mer

ase

III s

ubun

it(d

naX/

dnaZ

/dna

ZX)

40%

XF02

04DN

A po

lym

eras

e III

, alp

ha c

hain

(dna

E/po

lC)

48%

XF00

02DN

A po

lym

eras

e III

, bet

a ch

ain

(dna

N)

51%

XF06

76DN

A po

lym

eras

e III

, del

ta s

ubun

it (h

olB)

35%

XF21

78DN

A po

lym

eras

e III

, del

ta s

ubun

it (h

olA)

29%

XF21

57DN

A po

lym

eras

e III

, eps

ilon

chai

n (d

naQ)

49%

XF04

30DN

A pr

imas

e (d

naG/

dnaP

/par

B)46

%XF

2025

DNA

prim

ase

(traC

)56

%XF

0920

DNA

topo

isom

eras

e I (

topA

)41

%XF

1776

DNA

topo

isom

eras

e III

(top

B)48

%XF

0149

DNA/

pant

othe

nate

met

abol

ism

flavo

prot

ein

(dfp

)51

%XF

1935

gluc

ose

inhi

bite

d di

visi

on p

rote

in (g

idB)

45%

XF21

06gl

ucos

e in

hibi

ted

divi

sion

pro

tein

A (g

idA)

65%

XF13

83he

licas

e, A

TP d

epen

dent

(hrp

A)50

%XF

2689

prim

osom

al p

rote

in N

’ (pr

iA)

44%

XF03

61re

plic

ativ

e DN

A he

licas

e (d

naB/

groP

/grp

A)53

%XF

1127

TldD

pro

tein

(tld

D)61

%XF

1353

topo

isom

eras

e IV

sub

unit

(par

C)61

%XF

1286

topo

isom

eras

e IV

sub

unit

B (p

arE)

64%

MAC

ROM

OLEC

ULE

MET

ABOL

ISM

/DN

AM

ETAB

OLIS

M/S

truct

ural

DN

A bi

ndin

g pr

otei

ns

XF25

58ch

rom

osom

e se

greg

atio

n pr

otei

n (s

mc)

27%

XF04

46DN

A-bi

ndin

g pr

otei

n (b

bh3)

33%

XF19

98DN

A-bi

ndin

g pr

otei

n (fi

s)58

%XF

1190

hist

one-

like

prot

ein

(hbs

/hbs

U)64

%XF

1943

hist

one-

like

prot

ein

54%

XF04

82si

ngle

-stra

nded

DN

A bi

ndin

g pr

otei

n (s

sb)

49%

XF13

92si

ngle

-stra

nded

DN

A bi

ndin

g pr

otei

n (s

sb)

56%

XF15

58si

ngle

-stra

nded

DN

A bi

ndin

g pr

otei

n (s

sb)

36%

XF16

44si

ngle

-stra

nded

DN

A bi

ndin

g pr

otei

n (s

sb)

54%

XF17

78si

ngle

-stra

nded

DN

A bi

ndin

g pr

otei

n (s

sb)

25%

MAC

ROM

OLEC

ULE

MET

ABOL

ISM

/DN

AM

ETAB

OLIS

M/R

ecom

bina

tion

XF03

54AT

P-de

pend

ent D

NA

helic

ase

(recG

)55

%XF

1381

DNA

helic

ase

54%

XF22

48DN

A re

pair

prot

ein

RecO

(rec

O)35

%XF

0003

DNA

repl

icat

ion

and

repa

ir Re

cF p

rote

in(re

cF/u

vrF)

32%

XF18

92en

donu

clea

se V

(deo

xyin

osin

e3’

endo

nucl

ease

) (nf

i)53

%XF

0425

exod

eoxy

ribon

ucle

ase

V al

pha

chai

n (re

cD)

38%

XF04

23ex

odeo

xyrib

onuc

leas

e V

beta

cha

in(re

cB/r

orA)

30%

XF04

22ex

odeo

xyrib

onuc

leas

e V

gam

ma

chai

n (re

cC)

29%

XF14

25in

tegr

ase/

reco

mbi

nase

(xer

D/xp

rB)

53%

XF07

43in

tegr

atio

n ho

st fa

ctor

, alp

ha s

ubun

it (h

imA)

73%

XF24

37in

tegr

atio

n ho

st fa

ctor

, bet

a su

buni

t (hi

mD)

72%

XF18

09re

com

bina

tion

prot

ein

(recR

)54

%XF

2343

reco

mbi

natio

n pr

otei

n N

(rec

N)

38%

XF01

23re

com

bina

tion

prot

ein

RecA

(rec

A)91

%XF

1110

sing

le-s

trand

ed D

NA

exon

ucle

ase

(recJ

)45

%XF

1483

site

-spe

cific

reco

mbi

nase

(sss

/xer

C)53

%XF

2028

site

-spe

cific

reco

mbi

nase

(rin

)81

%

MAC

ROM

OLEC

ULE

MET

ABOL

ISM

/DN

A M

ETAB

OLIS

M/R

epai

r

XF25

986-

O-m

ethy

lgua

nine

-DN

A m

ethy

ltran

sfer

ase

(dat

/dat

1)46

%XF

1262

7,8-

dihy

dro-

8-ox

ogua

nine

-trip

hosp

hata

se(m

utX)

38%

XF19

09A/

G-sp

ecifi

c ad

enin

e gl

ycos

ylas

e(m

utY/

mut

B)46

%XF

0050

DNA

helic

ase

II (u

vrD/

mut

U/pd

eB/r

ad/r

ecL)

56%

XF07

60DN

A m

ism

atch

repa

ir pr

otei

n M

utL

(mut

L)42

%XF

0148

DNA

repa

ir pr

otei

n (ra

dC)

41%

XF13

78DN

A re

pair

prot

ein

(radA

/sm

s)61

%XF

1299

DNA

repa

ir sy

stem

spe

cific

for a

lkyl

ated

DNA

(alk

B)28

%XF

1326

DNA-

3-m

ethy

lade

nine

gly

cosi

dase

(mag

1)35

%XF

1806

DNA-

dam

age-

indu

cibl

e pr

otei

n (d

inD/

pcsA

)---

%XF

2081

DNA-

dam

age-

indu

cibl

e pr

otei

n (d

inJ)

57%

XF06

47en

donu

clea

se II

I (nt

h)67

%XF

2426

exci

nucl

ease

ABC

sub

unit

A (u

vrA)

70%

XF09

67ex

cinu

clea

se A

BC s

ubun

it B

(uvr

B)83

%XF

2311

exci

nucl

ease

ABC

sub

unit

C (u

vrC)

50%

XF01

64ex

odeo

xyrib

onuc

leas

e43

%XF

2022

exod

eoxy

ribon

ucle

ase

I (sb

cB/x

onA/

cpeA

)43

%XF

1933

exod

eoxy

ribon

ucle

ase

II I (

xthA

)46

%XF

0660

exod

eoxy

ribon

ucle

ase

smal

l sub

unit

(xse

B)39

%XF

0755

exod

eoxy

ribon

ucle

ase

VII l

arge

sub

unit

(xse

A)41

%XF

0071

form

amid

opyr

imid

ine

DNA

glyc

osyl

ase

(mut

M/f

pg)

51%

XF01

70fo

rmam

idop

yrim

idin

e DN

A gl

ycos

ylas

e(m

utM

/fpg

)51

%XF

1902

holli

day

junc

tion

bind

ing

prot

ein,

DNA

helic

ase

(ruvB

)69

%XF

1904

holli

day

junc

tion

bind

ing

prot

ein,

DNA

helic

ase

(ruvA

)42

%XF

1905

holli

day

junc

tion

reso

lvas

e,en

dode

oxyr

ibon

ucle

ase

(ruvC

)52

%XF

1716

mis

mat

ch re

pair

prot

ein

(mut

S)54

%XF

0045

trans

crip

tion-

repa

ir co

uplin

g fa

ctor

(mfd

)49

%XF

2692

urac

il-DN

A gl

ycos

ylas

e (u

ng)

55%

MAC

ROM

OLEC

ULE

MET

ABOL

ISM

/DN

AM

ETAB

OLIS

M/R

estri

ctio

n, m

odifi

catio

n

XF13

68ad

enin

e-sp

ecifi

c m

ethy

lase

46%

XF22

97DN

A m

ethy

lase

40%

XF06

41DN

A m

ethy

ltran

sfer

ase

(sfiI

M)

31%

XF17

74DN

A m

ethy

ltran

sfer

ase

(gen

e w

ith in

tron)

---%

XF09

24DN

A pr

oces

sing

cha

in A

(sm

f/dp

rA)

37%

XF09

35m

ethy

ltran

sfer

ase

37%

XF19

68m

ethy

ltran

sfer

ase

(kpn

IM)

33%

XF18

04si

te-s

peci

fic D

NA-

met

hyltr

ansf

eras

e (s

phIM

)39

%XF

2313

site

-spe

cific

DN

A-m

ethy

ltran

sfer

ase

41%

XF27

24ty

pe I

rest

rictio

n-m

odifi

catio

n sy

stem

(hsd

M)

25%

XF02

97ty

pe I

rest

rictio

n-m

odifi

catio

n sy

stem

DNA

met

hyla

se---

%XF

2723

type

I re

stric

tion-

mod

ifica

tion

syst

emDN

A m

ethy

lase

(hsd

M)

44%

XF27

28ty

pe I

rest

rictio

n-m

odifi

catio

n sy

stem

DNA

met

hyla

se61

%XF

2742

type

I re

stric

tion-

mod

ifica

tion

syst

emDN

A m

ethy

lase

(hsd

M)

53%

XF02

95ty

pe I

rest

rictio

n-m

odifi

catio

n sy

stem

endo

nucl

ease

---%

XF27

21ty

pe I

rest

rictio

n-m

odifi

catio

n sy

stem

endo

nucl

ease

(hsd

R1)

20%

XF27

25ty

pe I

rest

rictio

n-m

odifi

catio

n sy

stem

endo

nucl

ease

53%

XF27

39ty

pe I

rest

rictio

n-m

odifi

catio

n sy

stem

endo

nucl

ease

(hsd

R)42

%XF

0296

type

I re

stric

tion-

mod

ifica

tion

syst

emsp

ecifi

city

det

erm

inan

t27

%XF

2722

type

I re

stric

tion-

mod

ifica

tion

syst

emsp

ecifi

city

det

erm

inan

t21

%XF

2726

type

I re

stric

tion-

mod

ifica

tion

syst

emsp

ecifi

city

det

erm

inan

t (hs

dS)

24%

XF27

41ty

pe I

rest

rictio

n-m

odifi

catio

n sy

stem

spec

ifici

ty d

eter

min

ant (

hsdS

)24

%

MAC

ROM

OLEC

ULE

MET

ABOL

ISM

/RN

AM

ETAB

OLIS

M/R

ibos

omal

pro

tein

s

XF24

3830

S rib

osom

al p

rote

in S

1 (rp

sA/s

syF)

67%

XF11

5130

S rib

osom

al p

rote

in S

10 (r

psJ)

72%

XF11

7430

S rib

osom

al p

rote

in S

11 (r

psK)

86%

XF26

3130

S rib

osom

al p

rote

in S

12 (r

psL)

81%

XF11

7330

S rib

osom

al p

rote

in S

13 (r

psM

)85

%XF

1165

30S

ribos

omal

pro

tein

S14

(rps

N)

62%

XF02

3830

S rib

osom

al p

rote

in S

15 (r

psO/

secC

)62

%XF

0107

30S

ribos

omal

pro

tein

S16

(rps

P)65

%XF

1161

30S

ribos

omal

pro

tein

S17

(rps

Q)51

%XF

2560

30S

ribos

omal

pro

tein

S18

(rps

R)70

%XF

1156

30S

ribos

omal

pro

tein

S19

(rps

S)60

%XF

2580

30S

ribos

omal

pro

tein

S2

(rpsB

)60

%XF

2421

30S

ribos

omal

pro

tein

S20

(rps

T)54

%XF

0434

30S

ribos

omal

pro

tein

S21

(rps

U)67

%XF

1158

30S

ribos

omal

pro

tein

S3

(rpsC

)67

%XF

1175

30S

ribos

omal

pro

tein

S4

(rpsD

)84

%XF

1169

30S

ribos

omal

pro

tein

S5

(rpsE

/spc

)71

%XF

2561

30S

ribos

omal

pro

tein

S6

(rpsF

)67

%XF

2630

30S

ribos

omal

pro

tein

S7

(rpsG

/rps

7)60

%XF

1166

30S

ribos

omal

pro

tein

S8

(rpsH

/rps

8)56

%XF

1536

30S

ribos

omal

pro

tein

S9

(rpsI

/rps

9)68

%XF

2636

50S

ribos

omal

pro

tein

L1

(rplA

/rpl

1)64

%XF

2635

50S

ribos

omal

pro

tein

L10

(rpl

J)43

%XF

2637

50S

ribos

omal

pro

tein

L11

(rpl

K/re

lC)

69%

XF15

3750

S rib

osom

al p

rote

in L

13 (r

plM

)71

%XF

1162

50S

ribos

omal

pro

tein

L14

(rpl

N)

80%

XF11

7150

S rib

osom

al p

rote

in L

15 (r

plO)

48%

XF11

5950

S rib

osom

al p

rote

in L

16 (r

plP)

69%

XF11

7750

S rib

osom

al p

rote

in L

17 (r

plQ)

80%

XF11

6850

S rib

osom

al p

rote

in L

18 (r

plR)

53%

XF01

1050

S rib

osom

al p

rote

in L

19 (r

plS)

65%

XF11

5550

S rib

osom

al p

rote

in L

2 (rp

lB)

69%

XF07

4050

S rib

osom

al p

rote

in L

20 (r

plT)

72%

XF24

2450

S rib

osom

al p

rote

in L

21 (r

plU)

53%

XF11

5750

S rib

osom

al p

rote

in L

22 (r

plV)

63%

XF11

5450

S rib

osom

al p

rote

in L

23 (r

plW

)52

%XF

1163

50S

ribos

omal

pro

tein

L24

(rpl

X)48

%XF

2643

50S

ribos

omal

pro

tein

L25

(rpl

Y)48

%XF

2423

50S

ribos

omal

pro

tein

L27

(rpm

A)64

%XF

1206

50S

ribos

omal

pro

tein

L28

(rpm

B)71

%XF

1160

50S

ribos

omal

pro

tein

L29

(rpm

C)50

%XF

1152

50S

ribos

omal

pro

tein

L3

(rplC

/rpl

3)61

%XF

1170

50S

ribos

omal

pro

tein

L30

(rpm

D)47

%XF

1534

50S

ribos

omal

pro

tein

L31

(rpm

E)57

%XF

1816

50S

ribos

omal

pro

tein

L32

(rpm

F)75

%XF

1207

50S

ribos

omal

pro

tein

L33

(rpm

G)73

%XF

2782

50S

ribos

omal

pro

tein

L34

(rpm

H)76

%XF

0739

50S

ribos

omal

pro

tein

L35

(rpm

I)60

%XF

2440

50S

ribos

omal

pro

tein

L36

(rpm

J)65

%XF

1153

50S

ribos

omal

pro

tein

L4

(rplD

)54

%XF

1164

50S

ribos

omal

pro

tein

L5

(rplE

/rpl

5)63

%XF

1167

50S

ribos

omal

pro

tein

L6

(rplF

)52

%XF

2634

50S

ribos

omal

pro

tein

L7/

L12

(rplL

)67

%XF

2559

50S

ribos

omal

pro

tein

L9

(rplI)

52%

MAC

ROM

OLEC

ULE

MET

ABOL

ISM

/RN

AM

ETAB

OLIS

M/R

ibos

omes

- m

atur

atio

n an

d m

odifi

catio

n

XF01

0816

S rR

NA

proc

essi

ng p

rote

in (r

imM

)36

%XF

2607

ribon

ucle

ase

E (rn

e/am

s/hm

p1)

43%

XF11

25rib

onuc

leas

e G

(caf

A/rn

g)53

%XF

0939

ribos

omal

larg

e su

buni

t pse

udou

ridin

esy

ntha

se D

(rlu

D/sf

hB)

54%

XF22

01rib

osom

al p

rote

in L

11 m

ethy

ltran

sfer

ase

(prm

A)46

%XF

2532

ribos

omal

pro

tein

S6

mod

ifica

tion

prot

ein

(rim

K)---

%XF

1200

ribos

omal

sm

all s

ubun

it ps

eudo

urid

ine

synt

hase

(rsu

A)42

%XF

0236

ribos

omal

-bin

ding

fact

or A

(rbf

A)35

%XF

0441

ribos

omal

-pro

tein

-ala

nine

acet

yltra

nsfe

rase

(rim

I)38

%XF

2358

RNA

met

hyltr

ansf

eras

e (y

gcA)

38%

XF19

72tR

NA/

rRN

A m

ethy

lase

(yib

K)57

%XF

1985

tRN

A/rR

NA

met

hyltr

ansf

eras

e (y

jfH)

50%

MAC

ROM

OLEC

ULE

MET

ABOL

ISM

/RN

AM

ETAB

OLIS

M/A

min

oacy

l tRN

A sy

nthe

tase

s,tR

NA

mod

ifica

tion

XF01

24al

anyl

-tRN

A sy

nthe

tase

(ala

S/lo

vB)

56%

XF01

47ar

giny

l-tRN

A sy

nthe

tase

(arg

S)40

%XF

2563

aspa

ragi

nyl-t

RNA

synt

heta

se (a

snS/

tss)

66%

XF18

56as

party

l-tRN

A sy

nthe

tase

(asp

S)53

%XF

0995

cyst

einy

l-tRN

A sy

nthe

tase

(cys

S)46

%XF

1338

glut

amin

yl-tR

NA

synt

heta

se (g

lnS)

54%

XF08

22gl

utam

yl-tR

NA

synt

heta

se (g

ltX)

54%

XF19

60gl

ycyl

-tRN

A sy

nthe

tase

alp

ha c

hain

(gly

Q/gl

yS(A

))74

%XF

1959

glyc

yl-tR

NA

synt

heta

se b

eta

chai

n(g

lyS/

glyS

(B))

39%

XF22

22hi

stid

yl-tR

NA

synt

heta

se (h

isS)

36%

XF24

18is

oleu

cyl-t

RNA

synt

heta

se (i

leS/

ilvS)

54%

XF21

76le

ucyl

-tRN

A sy

nthe

tase

(leu

S)58

%XF

1112

lysy

l-tRN

A sy

nthe

tase

(lys

U)56

%XF

2555

lysy

l-tRN

A sy

nthe

tase

(yje

A/ge

nX)

47%

XF09

27m

ethi

onyl

-tRN

A fo

rmyl

trans

fera

se (f

mt)

56%

XF05

49m

ethi

onyl

-tRN

A sy

nthe

tase

(met

G)54

%XF

0742

phen

ylal

anyl

-tRN

A si

nthe

tase

bet

a ch

ain

(phe

T)42

%XF

0741

phen

ylal

anyl

-tRN

A sy

nthe

tase

alp

hach

ain

(phe

S)59

%XF

0445

prol

yl-tR

NA

synt

heta

se (p

roS/

drpA

)55

%XF

0751

ribon

ucle

ase

D (rn

d)31

%XF

2781

ribon

ucle

ase

P (rn

pA)

37%

XF13

14S-

aden

osyl

met

hion

ine:

tRN

Arib

osyl

trans

fera

se-is

omer

ase

(que

A)52

%XF

2286

sery

l-tRN

A sy

nthe

tase

(ser

S)59

%XF

0736

thre

onyl

-tRN

A sy

nthe

tase

(thr

S)59

%XF

0109

tRN

A (g

uani

ne-N

1-)-m

ethy

ltran

sfer

ase

(trm

D)51

%XF

1362

tRN

A ad

enyl

yltra

nsfe

rase

(cca

)52

%XF

0090

tRN

A de

lta(2

)-iso

pent

enyl

pyro

phos

phat

etra

nsfe

rase

(mia

A/trp

X)49

%XF

1440

tRN

A m

ethy

ltran

sfer

ase

(trm

U/as

uE)

55%

XF13

73tR

NA

pseu

dour

idin

e sy

ntha

se A

(truA

/his

T/as

uC/le

uK)

52%

XF02

37tR

NA

pseu

dour

idin

e sy

ntha

se B

(tru

B)42

%XF

2475

tRN

A/rR

NA

met

hyltr

ansf

eras

e41

%XF

0428

trypt

opha

nyl-t

RNA

synt

heta

se34

%XF

0169

tyro

syl-t

RNA

synt

heta

se (t

yrS)

53%

XF01

34va

lyl-t

RNA

synt

heta

se (v

alS)

51%

MAC

ROM

OLEC

ULE

MET

ABOL

ISM

/RN

A M

ETAB

OLIS

M/R

NA

synt

hesi

s, m

odifi

catio

n, D

NA

trans

crip

tion

XF01

92AT

P-de

pend

ent R

NA

helic

ase

(rhlE

)52

%XF

0252

ATP

-dep

ende

nt R

NA

helic

ase

(dea

D)55

%XF

2696

ATP-

depe

nden

t RN

A he

licas

e (rh

lB/m

mrA

)52

%XF

0234

N u

tiliza

tion

subs

tanc

e pr

otei

n A

(nus

A)56

%XF

0227

poly

nucl

eotid

e ad

enyl

trans

fera

se (p

cnB)

48%

XF26

06ps

eudo

urid

ylat

e sy

ntha

se (r

luC)

48%

XF11

76RN

A po

lym

eras

e al

pha

subu

nit (

rpoA

)87

%XF

2633

RNA

poly

mer

ase

beta

sub

unit

(rpoB

/gro

N/n

itB/r

if/ro

n)67

%XF

2632

RNA

poly

mer

ase

beta

’ sub

unit

(rpoC

/tab

B)71

%XF

1502

RNA

poly

mer

ase

omeg

a su

buni

t (rp

oZ)

43%

XF26

38tra

nscr

iptio

n an

titer

min

atio

n fa

ctor

(nus

G)60

%XF

0955

trans

crip

tion

term

inat

ion

fact

or (n

usB/

ssyB

)49

%XF

2699

trans

crip

tion

term

inat

ion

fact

or R

ho(rh

o/ni

tA/p

suA/

rnsC

/tsu

)72

%XF

1108

trans

crip

tiona

l elo

ngat

ion

fact

or (g

reA)

62%

MAC

ROM

OLEC

ULE

MET

ABOL

ISM

/RN

A M

ETAB

OLIS

M/R

NA

degr

adat

ion

XF12

57ol

igor

ibon

ucle

ase

(orn

)58

%XF

0239

poly

nucl

eotid

e ph

osph

oryl

ase

(pnp

)64

%XF

2615

ribon

ucle

ase

44%

XF21

58rib

onuc

leas

e H

(rnhA

/rnh

)60

%XF

1041

ribon

ucle

ase

HII (

rnhB

)55

%XF

2246

ribon

ucle

ase

III (r

nc)

50%

XF15

05rib

onuc

leas

e PH

(rph

)63

%XF

2146

ribon

ucle

ase

T (rn

t)47

%

MAC

ROM

OLEC

ULE

MET

ABOL

ISM

/PRO

TEIN

MET

ABOL

ISM

/Tra

nsla

tion

and

mod

ifica

tion

XF10

18ar

gini

ne-tR

NA-

prot

ein

trans

fera

se (a

te1)

25%

XF14

36di

sulfi

de o

xido

redu

ctas

e (d

sbA)

38%

XF18

34di

sulp

hide

isom

eras

e30

%XF

2629

elon

gatio

n fa

ctor

G (f

usA)

70%

XF22

03el

onga

tion

fact

or P

(yei

P)39

%XF

2473

elon

gatio

n fa

ctor

P (e

fp)

63%

XF25

79el

onga

tion

fact

or T

s (ts

f)50

%XF

2628

elon

gatio

n fa

ctor

Tu

(tufA

)82

%XF

2640

elon

gatio

n fa

ctor

Tu

(tufB

)82

%XF

2553

initi

atio

n fa

ctor

eIF

-2B,

alp

hasu

buni

t-rel

ated

50%

XF14

45in

itiat

ion

fact

or IF

-1 (i

nfA)

73%

XF02

35in

itiat

ion

fact

or IF

-2 (i

nfB)

49%

XF07

37in

itiat

ion

fact

or IF

-3 (i

nfC)

60%

XF08

57L-

isoa

spar

tate

O-m

ethy

ltran

sfer

ase

(pcm

)47

%XF

2417

lipop

rote

in s

igna

l pep

tidas

e (ls

pA)

45%

XF22

98lo

w m

olec

ular

wei

ght p

hosp

hoty

rosi

nepr

otei

n ph

osph

atas

e (s

tp1)

40%

XF05

76m

etal

lope

ptid

ase

37%

XF01

11m

ethi

onin

e am

inop

eptid

ase

(map

)60

%XF

2649

pept

ide

chai

n re

leas

e fa

ctor

1(p

rfA/s

ueB/

uar)

61%

XF11

11pe

ptid

e ch

ain

rele

ase

fact

or 2

(prfB

)66

%XF

0174

pept

ide

chai

n re

leas

e fa

ctor

3 (p

rfC)

62%

XF19

40pe

ptid

e m

ethi

onin

e su

lfoxi

de re

duct

ase

(msr

A/pm

s)59

%XF

2642

pept

idyl

tRN

A hy

drol

ase

(pth

)49

%XF

0644

pept

idyl

-pro

lyl c

is-tr

ans

isom

eras

e (m

ip)

38%

XF06

52pe

ptid

yl-p

roly

l cis

-tran

s is

omer

ase

(sly

D)43

%XF

0838

pept

idyl

-pro

lyl c

is-tr

ans

isom

eras

e (s

urA)

32%

XF11

91pe

ptid

yl-p

roly

l cis

-tran

s is

omer

ase

(ppi

D)25

%XF

1212

pept

idyl

-pro

lyl c

is-tr

ans

isom

eras

e (p

piB/

ppi)

60%

XF16

05pe

ptid

yl-p

roly

l cis

-tran

s is

omer

ase

36%

XF04

42ph

osph

atid

yltra

nsfe

rase

(ptr)

37%

XF09

26po

lype

ptid

e de

form

ylas

e (d

ef/f

ms)

55%

XF21

56pr

otei

n ph

osph

atas

e (y

loO)

35%

XF14

46pr

otei

n tra

nsfe

rase

(aat

)51

%XF

2585

prot

ein-

L-is

oasp

arta

teO-

met

hyltr

ansf

eras

e (p

cm)

34%

XF10

51rib

osom

e re

cycl

ing

fact

or (f

rr)58

%XF

2244

sign

al p

eptid

ase

I (le

pB)

40%

XF14

37th

iol:d

isul

fide

inte

rcha

nge

prot

ein

(dsb

A)39

%XF

0353

trans

latio

n in

itiat

ion

inhi

bito

r54

%

MAC

ROM

OLEC

ULE

MET

ABOL

ISM

/PRO

TEIN

MET

ABOL

ISM

/Cha

pero

nes

XF06

1610

kDa

chap

eron

in (g

roES

/htp

A)59

%XF

0615

60kD

a ch

aper

onin

(mop

A/gr

oEL)

77%

XF14

52ch

aper

one

(lolA

)32

%XF

2233

DnaJ

pro

tein

(dna

J)41

%XF

2339

DnaJ

pro

tein

(dna

J)59

%XF

2340

DnaK

pro

tein

(dna

K/gr

pF/g

roP/

seg)

72%

XF09

91Dn

aK s

upre

ssor

48%

XF09

78he

at s

hock

pro

tein

G (h

tpG)

58%

XF23

41he

at s

hock

pro

tein

Grp

E (g

rpE)

38%

XF11

86pe

ptid

yl-p

roly

l cis

-tran

s is

omer

ase

(tig)

32%

MAC

ROM

OLEC

ULE

MET

ABOL

ISM

/PRO

TEIN

MET

ABOL

ISM

/Pro

tein

deg

rada

tion

XF22

60al

anyl

dip

eptid

yl p

eptid

ase

30%

XF01

38am

inop

eptid

ase

A/I (

pepA

/xer

B/ca

rP)

47%

XF14

88am

inop

eptid

ase

N36

%XF

2009

amin

opep

tidas

e P

(pep

P)46

%XF

1188

ATP-

depe

nden

t Clp

pro

teas

e AT

Pbi

ndin

g su

buni

t Clp

x (c

lpX/

lopC

)73

%XF

1187

ATP-

depe

nden

t Clp

pro

teas

e pr

oteo

lytic

subu

nit (

clpP

/lopP

)73

%XF

0381

ATP-

depe

nden

t Clp

pro

teas

e su

buni

t(c

lpB/

htpM

)69

%XF

1443

ATP-

depe

nden

t Clp

pro

teas

e su

buni

t(c

lpA/

lopD

)61

%XF

1189

ATP-

depe

nden

t ser

ine

prot

eina

se L

a(lo

n/ca

pR/d

eg/m

uc/lo

pA)

64%

XF27

04ca

rbox

yl-te

rmin

al p

rote

ase

(ctp

A)41

%XF

1282

carb

oxyp

eptid

ase

rela

ted

prot

ein

33%

XF01

56cy

stei

ne p

rote

ase

(cpr

6)28

%XF

0015

dipe

ptid

yl-p

eptid

ase

28%

XF14

84he

at s

hock

pro

tein

(hsl

V/ht

pO)

65%

XF14

85he

at s

hock

pro

tein

(hsl

U/ht

pI)

66%

XF04

52in

tegr

al m

embr

ane

prot

ease

(hflK

/hflA

)33

%XF

0453

inte

gral

mem

bran

e pr

otei

nase

(hflC

)36

%XF

0280

leuc

ine

amin

opep

tidas

e (p

epA)

34%

XF04

35O-

sial

ogly

copr

otei

n en

dope

ptid

ase

(gcp

)63

%XF

0127

olig

opep

tidas

e A

(prlC

/opd

A/op

tA)

50%

XF14

79pe

ptid

ase

(ptrB

/tlp

)44

%XF

1944

pept

idyl

-dip

eptid

ase

(dcp

)53

%XF

2241

perip

lasm

ic p

rote

ase

(muc

D)47

%XF

0220

prol

ine

dipe

ptid

ase

(pep

Q)33

%XF

1510

prol

ine

imin

o-pe

ptid

ase

(pip

/xap

)81

%XF

2330

prot

eina

se (s

lpD)

22%

XF02

67se

rine

prot

ease

(psp

B)28

%XF

1026

serin

e pr

otea

se (p

spB)

27%

XF18

51se

rine

prot

ease

25%

XF18

23ta

il-sp

ecifi

c pr

otea

se (p

rc/t

sp)

39%

XF08

16zin

c pr

otea

se40

%

MAC

ROM

OLEC

ULE

MET

ABOL

ISM

/OTH

ER M

ACRO

MOL

ECUL

ESM

ETAB

OLIS

M/P

olys

acch

arid

es

XF27

14al

pha-

L-fu

cosi

dase

(fuc

A1)

36%

XF22

78do

licho

l-pho

spha

te m

anno

syltr

ansf

eras

e(d

pm1)

24%

XF08

87m

anno

syltr

ansf

eras

e (m

tfA)

31%

MAC

ROM

OLEC

ULE

MET

ABOL

ISM

/OTH

ER M

ACRO

MOL

ECUL

ESM

ETAB

OLIS

M/P

hosp

holip

ids

XF23

10CD

P-di

acyl

glyc

erol

-gly

cero

l-3-p

hosp

hate

3-

phos

phat

idyl

trans

fera

se (p

gsA)

49%

XF10

31gl

ycer

ol-3

-pho

spha

te a

cyltr

ansf

eras

e (p

lsB)

37%

CELL

STR

UCTU

RE/M

EMBR

ANE

COM

PON

ENTS

/Inne

rm

embr

ane

XF27

8060

kDa

inne

r-mem

bran

e pr

otei

n40

%XF

1640

anky

rin-li

ke p

rote

in (a

nk2)

26%

XF22

35bi

func

tiona

l pen

icill

in-b

indi

ngpr

otei

n 1C

pre

curs

or (p

bpC)

47%

XF00

82ch

aper

one

prot

ein

prec

urso

r (ec

pD)

40%

XF08

51D-

amin

o ac

id d

ehyd

roge

nase

sub

unit

(dad

A/da

dR)

54%

XF23

34di

acyl

glyc

erol

kin

ase

(dgk

A)54

%XF

0340

disu

lfide

bon

d fo

rmat

ion

prot

ein

B (d

sbB)

33%

XF24

33ep

imer

ase/

dehy

drat

ase

prot

ein

(cap

D)37

%XF

0256

gluc

ose-

1-ph

osph

ate

thym

idyl

yltra

nsfe

rase

(rfbA

)78

%XF

0375

inne

r mem

bran

e pr

otei

n (y

jdB)

36%

XF01

03m

embr

ane

prot

ein

25%

XF07

64m

embr

ane

prot

ein

36%

XF07

77m

embr

ane

prot

ein

(act

II-3)

22%

XF22

30pe

nici

llin-

bind

ing

prot

ein

6 pr

ecur

sor (

dacC

)47

%XF

0151

phos

phom

anno

mut

ase

(alg

C)45

%XF

1183

poly

sacc

harid

e bi

osyn

thet

ic p

rote

in(v

ipA/

tviB

)52

%XF

2333

prol

ipop

rote

in d

iacy

lgly

cery

l tra

nsfe

rase

(lgt/

umpA

)48

%XF

1310

rod

shap

e-de

term

inin

g pr

otei

n (m

reC)

37%

XF13

13ro

d sh

ape-

dete

rmin

ing

prot

ein

(mrd

B/ro

dA)

48%

XF19

79tra

nsm

embr

ane

prot

ein

(am

pE)

28%

XF11

40UD

P-N

-ace

tylg

luco

sam

ine

pyro

phos

phor

ylas

e (g

lmU)

49%

CELL

STR

UCTU

RE/M

EMBR

ANE

COM

PON

ENTS

/Out

erm

embr

ane

cons

titue

nts

XF23

92au

toly

tic ly

sozy

me

(lyc)

30%

XF08

47be

ta-h

exos

amin

idas

e pr

ecur

sor (

nahA

)37

%XF

2184

mem

bran

e-bo

und

lytic

trans

glyc

osyl

ase

(mltB

)36

%

XF10

46ou

ter m

embr

ane

antig

en (o

ma)

37%

XF03

84ou

ter m

embr

ane

hem

in re

cept

or (p

huR)

22%

XF03

43ou

ter m

embr

ane

prot

ein

(mop

B)31

%XF

0872

oute

r mem

bran

e pr

otei

n (o

mpW

)30

%XF

0873

oute

r mem

bran

e pr

otei

n43

%XF

1053

oute

r mem

bran

e pr

otei

n (o

mpP

1)28

%XF

1123

oute

r mem

bran

e pr

otei

n34

%XF

1739

oute

r mem

bran

e pr

otei

n (ro

mA)

43%

XF23

45ou

ter m

embr

ane

prot

ein

(sm

pA)

38%

XF10

24ou

ter m

embr

ane

prot

ein

H.8

prec

urso

r42

%XF

1811

oute

r mem

bran

e pr

otei

n Sl

p pr

ecur

sor (

slp)

31%

XF15

47pe

ptid

ogly

can-

asso

ciat

ed o

uter

mem

bran

elip

opro

tein

pre

curs

or (p

cp/lp

p)29

%XF

0033

PilE

pro

tein

(pilE

)37

%XF

0975

poly

phos

phat

e-se

lect

ive

porin

O (o

prO)

23%

XF03

21po

rin O

pre

curs

or (o

prO)

23%

XF00

28pr

e-pi

lin li

ke le

ader

seq

uenc

e (fi

mT)

37%

XF13

63so

lubl

e ly

tic m

urei

n tra

nsgl

ycos

ylas

epr

ecur

sor (

slt/

sltY

)25

%

CELL

STR

UCTU

RE/M

UREI

N S

ACCU

LUS,

PEP

TIDO

GLYC

AN

XF08

52al

anin

e ra

cem

ase

(alr)

45%

XF07

99D-

alan

ine-

-D-a

lani

ne li

gase

B (d

dlB/

ddl)

51%

XF08

55lip

opro

tein

(nlp

D/lp

pB)

39%

XF04

16lip

opro

tein

pre

curs

or (v

acJ)

36%

XF17

15m

onof

unct

iona

l bio

synt

hetic

pept

idog

lyca

n tra

nsgl

ycos

ylas

e (m

tgA)

50%

XF07

59N

-ace

tylm

uram

oyl-L

-ala

nine

am

idas

epr

ecur

sor (

amiC

)45

%XF

2646

oute

r mem

bran

e lip

opro

tein

pre

curs

or(lo

lB/h

emM

)29

%XF

1896

oute

r mem

bran

e pr

otei

n P6

pre

curs

or(p

al/o

mpP

6)37

%XF

1614

peni

cilli

n bi

ndin

g pr

otei

n (p

bp4)

39%

XF03

68pe

nici

llin-

bind

ing

prot

ein

1A (m

rcA/

ponA

)39

%XF

0884

peni

cilli

n-bi

ndin

g pr

otei

n 1B

(pon

B)41

%XF

1312

peni

cilli

n-bi

ndin

g pr

otei

n 2

(mrd

A/pb

p2)

38%

XF07

92pe

nici

llin-

bind

ing

prot

ein

3 (ft

sI/p

bpB)

43%

XF07

95ph

osph

o-N

-ace

tylm

uram

oyl-p

enta

pept

ide-

trans

fera

se (m

raY/

mur

X)59

%XF

2185

rare

lipo

prot

ein

A (rl

pA)

30%

XF13

09ro

d sh

ape-

dete

rmin

ing

prot

ein

(mre

B/en

vB/r

odY)

77%

XF13

11ro

d sh

ape-

dete

rmin

ing

prot

ein

(mre

D)32

%XF

0907

solu

ble

lytic

mur

ein

trans

glyc

osyl

ase

prec

urso

r (yj

bJ)

42%

XF07

97UD

P-N

-ace

tylg

luco

sam

ine-

-N-a

cety

lmur

amyl

-(p

enta

pept

ide)

pyr

opho

spho

ryl-u

ndec

apre

nol

(mur

G)47

%XF

0798

UDP-

N-a

cety

lmur

amat

e--a

lani

ne li

gase

(mur

C)53

%XF

0276

UDP-

N-a

cety

lmur

amat

e-L-

alan

ine

ligas

e(m

pl)

50%

XF11

18UD

P-N

-ace

tylm

uram

oyla

lani

ne--D

-glu

tam

ate

ligas

e (m

urD)

29%

XF07

93UD

P-N

-ace

tylm

uram

oyla

lany

l-D-g

luta

mat

e--

2,6-

diam

inop

imel

ate

ligas

e (m

urE)

43%

XF07

94UD

P-N

-ace

tylm

uram

oyla

lany

l-D-g

luta

myl

-2,6

diam

inop

imel

ate-

-D-a

lany

l-D-a

lany

llig

ase

(mur

F/m

ra)

41%

XF25

72UD

P-N

-ace

tylp

yruv

oylg

luco

sam

ine

redu

ctas

e (m

urB)

43%

XF10

50un

deca

pren

yl p

yrop

hosp

hate

syn

thet

ase

(upp

S/rth

)51

%

CELL

STR

UCTU

RE/S

URFA

CE P

OLYS

ACCH

ARID

ES,

LIPO

POLY

SACC

HARI

DES,

AN

D AN

TIGE

NS

XF12

892-

dehy

dro-

3-de

oxyp

hosp

hooc

tona

teal

dola

se (k

dsA)

44%

XF01

053-

deox

y-D-

man

no-o

ctul

oson

ic a

cid

trans

fera

se (k

dtA/

waa

A)44

%XF

2299

3-de

oxy-

man

no-o

ctul

oson

ate

cytid

ylyl

trans

fera

se (k

dsB)

50%

XF14

19ac

etyl

trans

fera

se (l

pxD/

firA/

omsA

)26

%XF

0918

acyl

-[ACP

]-UDP

-N-a

cety

lglu

cosa

min

e (lp

xA)

32%

XF19

94be

ta 1

,4 g

luco

syltr

ansf

eras

e29

%XF

0612

dolic

hol-p

hosp

hate

man

nosy

ltran

sfer

ase

(dm

t)24

%XF

1638

dolic

hyl-p

hosp

hate

man

nose

syn

thas

ere

late

d pr

otei

n34

%XF

0257

dTDP

-4-d

ehyd

rorh

amno

se 3

,5-e

pim

eras

e(rf

bD)

75%

XF02

58dT

DP-4

-ket

o-L-

rham

nose

redu

ctas

e (rf

bC)

54%

XF02

55dT

DP-g

luco

se 4

,6-d

ehyd

rata

se (r

fbB)

76%

XF06

11dT

DP-g

luco

se 4

-6-d

ehyd

rata

se (r

fbB)

63%

XF16

37gl

ycos

yl tr

ansf

eras

e (s

psQ)

29%

XF10

82lip

id A

4’-k

inas

e (lp

xK)

38%

XF01

04lip

id A

bio

synt

hesi

s la

uroy

l acy

ltran

sfer

ase

(htrB

/waa

M)

40%

XF13

48lip

id A

bio

synt

hesi

s la

uroy

l acy

ltran

sfer

ase

(htrB

/waa

M)

26%

XF10

42lip

id A

dis

acch

arid

e sy

ntha

se (l

pxB/

pgsB

)45

%XF

0879

lipop

olys

acch

arid

e bi

osyn

thes

is p

rote

in (r

fbU)

26%

XF24

34lip

opol

ysac

char

ide

core

bio

synt

hesi

s pr

otei

n37

%XF

0980

lipop

olys

acch

arid

e sy

nthe

sis

enzy

me

(kdt

B)56

%XF

0778

O-an

tigen

ace

tyla

se (o

afA)

26%

XF14

13po

lysi

alic

aci

d ca

psul

e ex

pres

sion

pro

tein

(kps

F)45

%XF

2154

sacc

harid

e bi

osyn

thes

is re

gula

tory

pro

tein

(ops

X)73

%XF

0176

suga

r tra

nsfe

rase

43%

XF10

45UD

P-3-

O-(R

-3-h

ydro

xym

yris

toyl

)-glu

cosa

min

eN

-acy

ltran

sfer

ase

(lpxD

/firA

/ssc

)41

%XF

1646

UDP-

3-O-

(R-3

-hyd

roxy

myr

isto

yl)-g

luco

sam

ine

N-a

cyltr

ansf

eras

e (lp

xD/f

irA)

28%

XF04

86UD

P-3-

O-[3

-hyd

roxy

myr

isto

yl] g

luco

sam

ine

N-

acyl

trans

fera

se (l

pxD)

31%

XF08

03UD

P-3-

O-[3

-hyd

roxy

myr

isto

yl] N

-ac

etyl

gluc

osam

ine

deac

etyl

ase

(lpxC

)59

%XF

1415

UDP-

N-a

cety

lglu

cosa

min

e 1-

carb

oxyv

inyl

trans

fera

se (m

urA/

mur

Z)62

%XF

1043

UDP-

N-a

cety

lglu

cosa

min

e ac

yltra

nsfe

rase

(lpxA

)44

%

CELL

STR

UCTU

RE/S

URFA

CE S

TRUC

TURE

S

XF00

77fim

bria

l adh

esin

pre

curs

or (m

rkD)

30%

XF00

78fim

bria

l adh

esin

pre

curs

or (m

rkD)

32%

XF00

80fim

bria

l adh

esin

pre

curs

or (f

imA/

pilA

)29

%XF

0369

fimbr

ial a

ssem

bly

mem

bran

e pr

otei

n (p

ilM)

61%

XF03

70fim

bria

l ass

embl

y m

embr

ane

prot

ein

(pilN

)44

%XF

0371

fimbr

ial a

ssem

bly

mem

bran

e pr

otei

n (p

ilO)

43%

XF03

72fim

bria

l ass

embl

y pr

otei

n (p

ilP)

38%

XF03

73fim

bria

l ass

embl

y pr

otei

n (p

ilQ)

34%

XF04

78fim

bria

l ass

embl

y pr

otei

n (p

ilY1)

33%

XF25

38fim

bria

l ass

embl

y pr

otei

n (p

ilC)

56%

XF25

39fim

bria

l pro

tein

48%

XF25

42fim

bria

l pro

tein

53%

XF00

83fim

bria

l sub

unit

prec

urso

r42

%XF

0487

fimbr

illin

37%

XF05

38fim

brill

in37

%XF

0539

fimbr

illin

(fim

A)38

%XF

1791

fimbr

illin

48%

XF00

81ou

ter m

embr

ane

ushe

r pro

tein

pre

curs

or(fi

mD)

36%

XF19

53pi

lus

biog

enes

is p

rote

in (p

ilJ)

46%

XF19

54pi

lus

biog

enes

is p

rote

in (p

ilI)

33%

XF25

44pi

lus

biog

enes

is p

rote

in (p

ilB)

55%

XF19

55pi

lus

prot

ein

(pilG

)82

%XF

0031

PilX

pro

tein

(pilX

)28

%XF

0032

PilY

1 ge

ne p

rodu

ct (p

ilY1)

32%

XF12

24Pi

lY1

gene

pro

duct

(pilY

1)30

%XF

2537

pre-

pilin

lead

er p

eptid

ase

(xps

O)76

%XF

0029

pre-

pilin

lead

er s

eque

nce

(pilV

)33

%XF

1632

twitc

hing

mot

ility

pro

tein

(pilU

)60

%XF

1633

twitc

hing

mot

ility

pro

tein

(pilT

)74

%XF

0677

type

4 fi

mbr

iae

asse

mbl

y pr

otei

n (p

ilZ)

62%

XF04

79ty

pe IV

pili

n (p

ilE)

35%

CELL

ULAR

PRO

CESS

ES/T

RAN

SPOR

T/Am

ino

acid

s, a

min

es

XF04

08am

ino

acid

tran

spor

ter (

yhdG

)43

%XF

2730

amin

o ac

id tr

ansp

orte

r (rh

tC)

28%

XF22

07ca

tioni

c am

ino

acid

tran

spor

ter

43%

XF22

08ca

tioni

c am

ino

acid

tran

spor

ter

41%

XF18

91di

-trip

eptid

e AB

C tra

nspo

rter m

embr

ane

prot

ein

(ycl

F)35

%XF

0656

glut

amat

e sy

mpo

rt pr

otei

n (g

ltT)

28%

XF19

37pr

oton

glu

tam

ate

sym

port

prot

ein

(gltP

)35

%

CELL

ULAR

PRO

CESS

ES/T

RAN

SPOR

T/An

ions

XF04

11AB

C tra

nspo

rter n

itrat

e pe

rmea

se (n

rtB)

26%

XF21

41AB

C tra

nspo

rter p

hosp

hate

bin

ding

pro

tein

(pho

X)67

%XF

2142

ABC

trans

porte

r pho

spha

te p

erm

ease

(pst

C/ph

oW)

50%

XF21

43AB

C tra

nspo

rter p

hosp

hate

per

mea

se(p

stA/

phoT

)53

%XF

1344

ABC

trans

porte

r sul

fate

bin

ding

pro

tein

(sbp

)64

%XF

1345

ABC

trans

porte

r sul

fate

per

mea

se(c

ysU/

cysT

)50

%XF

1346

ABC

trans

porte

r sul

fate

per

mea

se (c

ysW

)49

%XF

0412

nitra

te A

BC tr

ansp

orte

r ATP

-bin

ding

prot

ein

(nrtD

)46

%XF

2144

phos

phat

e AB

C tra

nspo

rter A

TP-b

indi

ngpr

otei

n (p

stB/

phoT

)65

%XF

1347

sulfa

te A

BC tr

ansp

orte

r ATP

-bin

ding

prot

ein

(cys

A)61

%

CELL

ULAR

PRO

CESS

ES/T

RAN

SPOR

T/Ca

rboh

ydra

tes,

org

anic

acid

s, a

lcoh

ols

XF24

46AB

C tra

nspo

rter s

ugar

per

mea

se40

%XF

2447

ABC

trans

porte

r sug

ar p

erm

ease

(lac

F)37

%XF

2448

ABC

trans

porte

r sug

ar-b

indi

ng p

rote

in (m

alE)

24%

XF00

87al

pha-

keto

glut

arat

e pe

rmea

se s

ympo

rter

(kgt

P/w

itA)

64%

XF09

76C4

-dic

arbo

xyla

te tr

ansp

ort p

rote

in (d

ctA)

66%

XF14

62gl

ucos

e/ga

lact

ose

trans

porte

r (gl

uP)

31%

XF16

09gl

ucos

e/ga

lact

ose

trans

porte

r (gl

uP)

48%

XF22

67gl

ycer

ol u

ptak

e fa

cilit

ator

pro

tein

(glp

F)39

%XF

1406

HPr k

inas

e/ph

osph

atas

e (p

tsK)

36%

XF03

20M

g++/

citra

te c

ompl

ex tr

ansp

orte

r(c

itN/c

itH)

60%

XF14

02ph

osph

otra

nsfe

rase

sys

tem

enz

yme

I (ph

bI)

40%

XF14

03ph

osph

otra

nsfe

rase

sys

tem

HPr

enz

yme

(phb

H)52

%XF

1067

suga

r ABC

tran

spor

ter A

TP-b

indi

ng p

rote

in53

%

CELL

ULAR

PRO

CESS

ES/T

RAN

SPOR

T/Ca

tions

XF23

28AB

C tra

nspo

rter s

odiu

m p

erm

ease

(nat

B)27

%XF

1844

amm

oniu

m tr

ansp

orte

r (am

tB)

57%

XF03

95ba

cter

iofe

rritin

(bfr)

61%

XF21

40ca

tion:

prot

on a

ntip

orte

r (yb

aL)

57%

XF21

34fe

rric

ente

roba

ctin

rece

ptor

(bfe

A)22

%XF

2137

ferri

c en

tero

bact

in re

cept

or (b

feA)

22%

XF09

32fe

rrous

iron

tran

spor

t pro

tein

47%

XF09

33fe

rrous

iron

tran

spor

t pro

tein

B (f

eoB)

52%

XF14

26io

n tra

nspo

rter

48%

XF09

00m

agne

sium

and

cob

alt t

rans

port

prot

ein

(cor

A)33

%XF

1015

man

gane

se tr

ansp

ort p

rote

in (m

ntH2

)64

%XF

1401

Mg+

+ tra

nspo

rter (

mgt

E)26

%XF

1398

Na+

/H+

exch

ange

pro

tein

24%

XF20

19N

a+:H

+ an

tipor

ter (

yjcE

)42

%XF

0324

perip

lasm

ic ir

on-b

indi

ng p

rote

in (a

fuA)

24%

XF09

01po

lar a

min

o ac

id tr

ansp

orte

r (yb

eX)

46%

XF19

03po

tass

ium

upt

ake

prot

ein

(kup

/trk

D)48

%XF

2329

sodi

um A

BC tr

ansp

orte

r ATP

-bin

ding

prot

ein

(nat

A)47

%XF

0599

TonB

-dep

ende

nt re

cept

or fo

r iro

ntra

nspo

rt (y

biL)

47%

XF14

96To

nB-d

epen

dent

rece

ptor

for i

ron

trans

port

(ync

D)23

%XF

0367

volta

ge-g

ated

pot

assi

um c

hann

el b

eta

subu

nit

50%

CELL

ULAR

PRO

CESS

ES/T

RAN

SPOR

T/Pr

otei

n, p

eptid

e se

cret

ion

XF24

55he

me

ABC

trans

porte

r ATP

-bin

ding

prot

ein

(ccm

A)41

%XF

2456

hem

e AB

C tra

nspo

rter m

embr

ane

prot

ein

(ccm

B)50

%XF

2457

hem

e AB

C tra

nspo

rter m

embr

ane

prot

ein

(ccm

C)48

%XF

2261

olig

opep

tide

trans

porte

r40

%XF

0806

prep

rote

in tr

ansl

ocas

e Se

cA s

ubun

it(s

ecA/

prlD

/azi/

pea)

60%

XF11

72pr

epro

tein

tran

sloc

ase

SecY

sub

unit

(sec

Y/pr

lA)

55%

XF26

39pr

epro

tein

tran

sloc

ase

subu

nit (

secE

)33

%XF

0224

prep

rote

in tr

ansl

ocas

e Ya

jC s

ubun

it (y

ajC)

36%

XF26

85pr

otea

se IV

(spp

A)40

%XF

0225

prot

ein-

expo

rt m

embr

ane

prot

ein

(sec

D)44

%XF

0226

prot

ein-

expo

rt m

embr

ane

prot

ein

(sec

F)38

%XF

0304

prot

ein-

expo

rt m

embr

ane

prot

ein

(sec

G)43

%XF

1801

prot

ein-

expo

rt pr

otei

n (s

ecB)

43%

XF05

62se

c-in

depe

nden

t pro

tein

tran

sloc

ase

(tatC

/mttB

)47

%XF

0073

sign

al re

cogn

ition

par

ticle

pro

tein

(ffh

)63

%

XF19

13ty

pe V

sec

reto

ry p

athw

ay p

rote

in (m

ttC)

46%

CELL

ULAR

PRO

CESS

ES/T

RAN

SPOR

T/Ot

her

XF08

75AB

C tra

nspo

rter A

TP-b

indi

ng p

rote

in (y

usC)

48%

XF09

44AB

C tra

nspo

rter A

TP-b

indi

ng p

rote

in (y

jjK)

69%

XF10

77AB

C tra

nspo

rter A

TP-b

indi

ng p

rote

in (y

cfV)

55%

XF10

81AB

C tra

nspo

rter A

TP-b

indi

ng p

rote

in (m

sbA)

41%

XF12

23AB

C tra

nspo

rter A

TP-b

indi

ng p

rote

in (y

adG)

54%

XF13

02AB

C tra

nspo

rter A

TP-b

indi

ng p

rote

in42

%XF

1409

ABC

trans

porte

r ATP

-bin

ding

pro

tein

60%

XF14

75AB

C tra

nspo

rter A

TP-b

indi

ng p

rote

in (y

nhD)

63%

XF16

02AB

C tra

nspo

rter A

TP-b

indi

ng p

rote

in31

%XF

2133

ABC

trans

porte

r ATP

-bin

ding

pro

tein

(yhe

S)45

%XF

2568

ABC

trans

porte

r ATP

-bin

ding

pro

tein

(rfb

E)45

%XF

2582

ABC

trans

porte

r ATP

-bin

ding

pro

tein

42%

XF26

17AB

C tra

nspo

rter A

TP-b

indi

ng p

rote

in (u

up)

49%

XF26

95AB

C tra

nspo

rter A

TP-b

indi

ng p

rote

in (f

tsE)

47%

XF14

74AB

C tra

nspo

rter m

embr

ane

prot

ein

(ynh

C)33

%XF

1476

ABC

trans

porte

r mem

bran

e pr

otei

n69

%XF

0874

ABC

trans

porte

r per

mea

se p

rote

in48

%XF

2567

ABC

trans

porte

r per

mea

se p

rote

in (r

fbD)

35%

XF16

04AB

C tra

nspo

rter v

itam

in B

12 u

ptak

epe

rmea

se (b

tuE)

44%

XF04

06ex

port

prot

ein

(ygj

T)54

%XF

0039

larg

e-co

nduc

tanc

e m

echa

nose

nsiti

vech

anne

l (m

scL)

52%

XF05

89pe

rmea

se28

%XF

2301

poly

sacc

harid

e ex

port

prot

ein

(mrp

)63

%XF

1258

smal

l con

duct

ance

mec

hano

sens

itive

ion

chan

nel (

yggB

)35

%XF

2251

solu

te:N

a+ s

ympo

rter (

ppa)

58%

XF02

81tra

nspo

rt pr

otei

n (y

ueF)

24%

XF06

51tra

nspo

rt pr

otei

n (y

xaH)

33%

XF17

28tra

nspo

rt pr

otei

n27

%

CELL

ULAR

PRO

CESS

ES/C

ELL

DIVI

SION

XF06

59ce

ll cy

cle

prot

ein

(mes

J)42

%XF

0286

cell

divi

sion

inhi

bito

r (su

lA)

39%

XF13

22ce

ll di

visi

on in

hibi

tor (

min

C)35

%XF

0093

cell

divi

sion

pro

tein

(hflB

/fts

H/m

rsC/

tolZ

)64

%XF

0094

cell

divi

sion

pro

tein

(fts

J/m

rsF)

52%

XF07

91ce

ll di

visi

on p

rote

in (f

tsL)

30%

XF07

96ce

ll di

visi

on p

rote

in (f

tsW

)44

%XF

0800

cell

divi

sion

pro

tein

(fts

Q)32

%XF

0801

cell

divi

sion

pro

tein

(fts

A/di

vA)

45%

XF08

02ce

ll di

visi

on p

rote

in (f

tsZ)

59%

XF14

50ce

ll di

visi

on p

rote

in (f

tsK)

50%

XF19

10ce

ll di

visi

on p

rote

in (f

tsY)

45%

XF25

57ce

ll di

visi

on p

rote

in (z

ipA)

27%

XF26

94ce

ll di

visi

on p

rote

in (f

tsX/

ftsS)

31%

XF13

20ce

ll di

visi

on to

polo

gica

l spe

cific

ity fa

ctor

(min

E)48

%XF

1657

cell

filam

enta

tion

prot

ein

(fic)

38%

XF22

81ch

rom

osom

e pa

rtitio

ning

pro

tein

43%

XF22

82ch

rom

osom

e pa

rtitio

ning

pro

tein

(par

A)49

%XF

1785

chro

mos

ome

parti

tioni

ng re

late

dpr

otei

n (s

oj)

27%

XF22

47GT

P bi

ndin

g pr

otei

n (e

ra)

51%

XF10

84pa

rtitio

n pr

otei

n (p

arA)

32%

XF13

21se

ptum

site

-det

erm

inin

g pr

otei

n (m

inD)

68%

CELL

ULAR

PRO

CESS

ES/C

HEM

OTAX

IS A

ND

MOB

ILIT

Y

XF19

52ch

emot

axis

-rela

ted

prot

ein

kina

se (c

hpA)

42%

MOB

ILE

GEN

ETIC

ELE

MEN

TS/P

HAGE

-REL

ATED

FUN

CTIO

NS

AND

PROP

HAGE

S

XF00

89ho

st fa

ctor

-I pr

otei

n (h

fq)

92%

XF07

19ph

age-

rela

ted

base

plat

e as

sem

bly

prot

ein

(gpV

)32

%XF

0723

phag

e-re

late

d ba

sepl

ate

asse

mbl

y pr

otei

n(g

pW)

40%

XF07

24ph

age-

rela

ted

base

plat

e as

sem

bly

prot

ein

(gpJ

)46

%XF

2488

phag

e-re

late

d ba

sepl

ate

asse

mbl

y pr

otei

n(g

pJ)

46%

XF24

89ph

age-

rela

ted

base

plat

e as

sem

bly

prot

ein

(gpW

)40

%XF

2492

phag

e-re

late

d ba

sepl

ate

asse

mbl

y pr

otei

n(g

pV)

32%

XF07

27ph

age-

rela

ted

cont

ract

ile ta

il sh

eath

prot

ein

(fIR2

)46

%XF

2485

phag

e-re

late

d co

ntra

ctile

tail

shea

thpr

otei

n (fI

R2)

46%

XF07

28ph

age-

rela

ted

cont

ract

ile ta

il tu

be p

rote

in(fI

IR2)

41%

XF06

83ph

age-

rela

ted

DNA

poly

mer

ase

(dpo

L)50

%XF

2525

phag

e-re

late

d DN

A po

lym

eras

e (d

poL)

49%

XF05

13ph

age-

rela

ted

endo

lysi

n (ly

cV)

46%

XF06

31ph

age-

rela

ted

inte

gras

e (in

t)28

%XF

0678

phag

e-re

late

d in

tegr

ase

(int)

27%

XF16

42ph

age-

rela

ted

inte

gras

e (in

t)28

%XF

1718

phag

e-re

late

d in

tegr

ase

(int)

91%

XF22

88ph

age-

rela

ted

inte

gras

e (in

t)26

%XF

2530

phag

e-re

late

d in

tegr

ase

(int)

28%

XF15

64ph

age-

rela

ted

lyso

zym

e (ly

cV)

43%

XF16

69ph

age-

rela

ted

lyso

zym

e (ly

cV)

43%

XF23

14ph

age-

rela

ted

lyso

zym

e (ly

cV)

42%

XF07

13ph

age-

rela

ted

porta

l pro

tein

(gp4

)25

%XF

2498

phag

e-re

late

d po

rtal p

rote

in (g

p4)

25%

XF04

85ph

age-

rela

ted

prot

ein

34%

XF06

80ph

age-

rela

ted

prot

ein

56%

XF06

82ph

age-

rela

ted

prot

ein

50%

XF06

84ph

age-

rela

ted

prot

ein

49%

XF06

85ph

age-

rela

ted

prot

ein

53%

XF06

86ph

age-

rela

ted

prot

ein

41%

XF07

04ph

age-

rela

ted

prot

ein

32%

XF07

05ph

age-

rela

ted

prot

ein

32%

XF07

07ph

age-

rela

ted

prot

ein

44%

XF07

10ph

age-

rela

ted

prot

ein

27%

XF15

55ph

age-

rela

ted

prot

ein

34%

XF15

70ph

age-

rela

ted

prot

ein

29%

XF15

73ph

age-

rela

ted

prot

ein

27%

XF16

45ph

age-

rela

ted

prot

ein

31%

XF16

63ph

age-

rela

ted

prot

ein

47%

XF16

75ph

age-

rela

ted

prot

ein

29%

XF16

78ph

age-

rela

ted

prot

ein

27%

XF17

63ph

age-

rela

ted

prot

ein

30%

XF17

86ph

age-

rela

ted

prot

ein

42%

XF18

64ph

age-

rela

ted

prot

ein

48%

XF18

69ph

age-

rela

ted

prot

ein

37%

XF18

70ph

age-

rela

ted

prot

ein

35%

XF18

75ph

age-

rela

ted

prot

ein

36%

XF18

76ph

age-

rela

ted

prot

ein

36%

XF21

27ph

age-

rela

ted

prot

ein

24%

XF21

32ph

age-

rela

ted

prot

ein

34%

XF22

90ph

age-

rela

ted

prot

ein

57%

XF22

91ph

age-

rela

ted

prot

ein

47%

XF22

92ph

age-

rela

ted

prot

ein

50%

XF22

94ph

age-

rela

ted

prot

ein

32%

XF22

95ph

age-

rela

ted

prot

ein

53%

XF24

79ph

age-

rela

ted

prot

ein

32%

XF24

82ph

age-

rela

ted

prot

ein

21%

XF24

84ph

age-

rela

ted

prot

ein

41%

XF25

01ph

age-

rela

ted

prot

ein

27%

XF25

04ph

age-

rela

ted

prot

ein

44%

XF25

05ph

age-

rela

ted

prot

ein

34%

XF25

11ph

age-

rela

ted

prot

ein

28%

XF25

22ph

age-

rela

ted

prot

ein

41%

XF25

23ph

age-

rela

ted

prot

ein

52%

XF25

24ph

age-

rela

ted

prot

ein

43%

XF25

26ph

age-

rela

ted

prot

ein

50%

XF25

27ph

age-

rela

ted

prot

ein

21%

XF25

28ph

age-

rela

ted

prot

ein

56%

XF05

00ph

age-

rela

ted

repr

esso

r pro

tein

(rac

R)50

%XF

0696

phag

e-re

late

d re

pres

sor p

rote

in (r

pcI)

29%

XF16

58ph

age-

rela

ted

repr

esso

r pro

tein

(CI)

24%

XF17

06ph

age-

rela

ted

tail

fiber

pro

tein

(gp3

7)25

%XF

0725

phag

e-re

late

d ta

il pr

otei

n (g

pI)

35%

XF07

30ph

age-

rela

ted

tail

prot

ein

(gpT

)21

%XF

0731

phag

e-re

late

d ta

il pr

otei

n (g

pU)

40%

XF07

32ph

age-

rela

ted

tail

prot

ein

(gpX

)41

%XF

0733

phag

e-re

late

d ta

il pr

otei

n (g

pD)

32%

XF24

80ph

age-

rela

ted

tail

prot

ein

(gpX

)41

%XF

2481

phag

e-re

late

d ta

il pr

otei

n (g

pU)

40%

XF24

87ph

age-

rela

ted

tail

prot

ein

(gpI

)35

%XF

0508

phag

e-re

late

d te

rmin

ase

larg

e su

buni

t (gp

2)25

%XF

0711

phag

e-re

late

d te

rmin

ase

larg

e su

buni

t (gp

2)28

%XF

2500

phag

e-re

late

d te

rmin

ase

larg

e su

buni

t (gp

2)28

%

MOB

ILE

GEN

ETIC

ELE

MEN

TS/P

LASM

ID-R

ELAT

ED F

UNCT

ION

S

XF20

45co

njug

al tr

ansf

er p

rote

in (t

rbN

)76

%XF

2046

conj

ugal

tran

sfer

pro

tein

(trb

L)45

%XF

2048

conj

ugal

tran

sfer

pro

tein

(trb

J)---

%XF

2049

conj

ugal

tran

sfer

pro

tein

(trb

I)53

%XF

2050

conj

ugal

tran

sfer

pro

tein

(trb

H)45

%XF

2051

conj

ugal

tran

sfer

pro

tein

(trb

G)65

%XF

2052

conj

ugal

tran

sfer

pro

tein

(trb

F)49

%XF

2053

conj

ugal

tran

sfer

pro

tein

(trb

E)---

%XF

2054

conj

ugal

tran

sfer

pro

tein

(trb

D)68

%XF

2055

conj

ugal

tran

sfer

pro

tein

(trb

C)52

%XF

2056

conj

ugal

tran

sfer

pro

tein

(trb

B)69

%XF

2058

conj

ugal

tran

sfer

pro

tein

(tra

F)59

%XF

2059

conj

ugal

tran

sfer

pro

tein

(tra

E)73

%XF

2060

conj

ugal

tran

sfer

pro

tein

(tra

D)43

%XF

1759

cons

erve

d pl

asm

id p

rote

in35

%XF

2066

cons

erve

d pl

asm

id p

rote

in (y

acB)

35%

XF21

61co

nser

ved

plas

mid

pro

tein

30%

XF20

61DN

A pr

imas

e (tr

aC)

44%

XF24

44ph

erom

one

shut

dow

n pr

otei

n (tr

aB)

31%

XF15

89pl

asm

id s

tabi

lizat

ion

prot

ein

50%

XF15

90pl

asm

id s

tabi

lizat

ion

prot

ein

62%

XF20

31pl

asm

id s

tabi

lizat

ion

prot

ein

(par

D)81

%XF

2032

plas

mid

sta

biliz

atio

n pr

otei

n (p

arE)

75%

XF15

74pl

asm

id-re

late

d pr

otei

n (tr

aN)

34%

XF16

79pl

asm

id-re

late

d pr

otei

n (tr

aN)

34%

XF19

45Vi

rK p

rote

in (v

irK)

35%

MOB

ILE

GEN

ETIC

ELE

MEN

TS/T

RAN

SPOS

ON- A

ND

INTR

ON-

RELA

TED

FUN

CTIO

NS

XF20

63DN

A-in

verta

se (r

in)

---%

XF19

30re

solv

ase

(tnpR

)---

%XF

1775

reve

rse

trans

crip

tase

---%

XF19

31tra

nspo

sase

(tnp

A)---

%XF

2303

trans

posa

se (t

npA)

71%

XF03

25tra

nspo

sase

OrfA

64%

XF05

35tra

nspo

sase

OrfA

64%

XF03

26tra

nspo

sase

OrfB

---%

XF05

36tra

nspo

sase

OrfB

35%

PATH

OGEN

ICIT

Y, V

IRUL

ENCE

, AN

D AD

APTA

TION

/TOX

INPR

ODUC

TION

AN

D DE

TOXI

FICA

TION

XF17

262,

5-di

chlo

ro-2

,5-c

yclo

hexa

dien

e-1,

4-di

olde

hydr

ogen

ase

(linC

)39

%XF

0243

acrif

lavi

n re

sist

ance

pro

tein

(yer

P)23

%XF

2386

acrif

lavi

n re

sist

ance

pro

tein

(yeg

N)

42%

XF23

85ac

rifla

vin

resi

stan

ce p

rote

in D

(yeg

N)

50%

XF24

07ba

cter

ioci

n27

%XF

0165

beta

-lact

amas

e in

duct

ion

sign

al tr

ansd

ucer

prot

ein

(am

pG)

38%

XF16

21be

ta-la

ctam

ase-

like

prot

ein

(pbp

)24

%XF

0010

biop

olym

er tr

ansp

ort E

xbB

prot

ein

(exb

B)81

%XF

0011

biop

olym

er tr

ansp

ort E

xbD1

pro

tein

(exb

D1)

78%

XF00

12bi

opol

ymer

tran

spor

t Exb

D2 p

rote

in (e

xbD2

)82

%XF

2232

cata

lase

/per

oxid

ase

(cpe

B)66

%XF

2083

catio

n ef

flux

syst

em p

rote

in (c

zcA)

24%

XF02

62co

licin

V p

recu

rsor

(cva

C)36

%XF

0263

colic

in V

pre

curs

or (c

vaC)

31%

XF19

48co

licin

V p

rodu

ctio

n pr

otei

n (c

vpA)

31%

XF12

20co

licin

V s

ecre

tion

ABC

trans

porte

rAT

P-bi

ndin

g pr

otei

n (c

vaB)

40%

XF12

16co

licin

V s

ecre

tion

prot

ein

(cva

A)25

%XF

2084

com

pone

nt o

f mul

tidru

g ef

flux

syst

em (m

exE)

28%

XF13

41co

pper

hom

eost

asis

pro

tein

(cut

C)47

%XF

0132

copp

er re

sist

ance

pro

tein

A p

recu

rsor

(cop

A)61

%XF

0133

copp

er re

sist

ance

pro

tein

B p

recu

rsor

(cop

B)38

%XF

1741

daun

orub

icin

C-1

3 ke

tore

duct

ase

(dnr

U)31

%XF

2148

dim

ethy

lade

nosi

ne tr

ansf

eras

e (k

sgA/

rsm

A)48

%XF

2416

drug

tole

ranc

e pr

otei

n (ly

tB)

64%

XF09

93dr

ug:p

roto

n an

tipor

ter (

tetV

)24

%XF

1765

drug

:pro

ton

antip

orte

r (m

mr)

33%

XF10

29gl

utar

yl-7

-ACA

acy

lase

pre

curs

or (g

aa)

60%

XF18

90gl

utat

hion

e pe

roxi

dase

-like

pro

tein

(gpo

)50

%XF

1210

glut

athi

one

S-tra

nsfe

rase

(gst

)38

%XF

0175

hem

olys

in II

I pro

tein

48%

XF23

98he

mol

ysin

sec

retio

n pr

otei

n D

(hly

D)39

%XF

0668

hem

olys

in-ty

pe c

alci

um b

indi

ng p

rote

in (f

rpC)

32%

XF10

11he

mol

ysin

-type

cal

cium

bin

ding

pro

tein

(frp

C)30

%XF

2759

hem

olys

in-ty

pe c

alci

um b

indi

ng p

rote

in (f

rpC)

35%

XF19

34He

tI pr

otei

n (h

etI)

35%

XF02

44m

embr

ane

fusi

on p

rote

in (m

exC)

25%

XF23

84m

embr

ane

fusi

on p

rote

in p

recu

rsor

(mtrC

)37

%XF

2686

mul

tidru

g ef

flux

prot

ein

(ydh

E)34

%XF

2094

mul

tidru

g-ef

flux

trans

porte

r (ac

rF/e

nvD)

50%

XF17

32N

AD(P

)H-d

epen

dent

2-c

yclo

hexe

n-1-

one

redu

ctas

e (n

cr)

40%

XF11

37N

onF-

rela

ted

prot

ein

(non

F)34

%

XF18

27or

gani

c hy

drop

erox

ide

resi

stan

cepr

otei

n (o

hr)

70%

XF25

86ou

ter m

embr

ane

expo

rt fa

ctor

(tolC

/mtc

B/m

ukA/

refI)

33%

XF25

50ou

ter m

embr

ane

hem

olys

in a

ctiv

ator

prot

ein

(hec

B)26

%XF

1532

oxid

ativ

e st

ress

tran

scrip

tiona

l reg

ulat

or(o

xyR)

81%

XF10

38pe

ptid

e sy

ntha

se23

%XF

2276

pept

ide

synt

hase

26%

XF06

19pe

ripla

smic

div

alen

t cat

ion

tole

ranc

epr

otei

n (c

utA/

cycY

/cut

A1)

37%

XF17

29ph

enyl

acet

alde

hyde

deh

ydro

gena

se61

%XF

1131

PmbA

pro

tein

(pm

bA/t

ldE)

45%

XF21

35po

lyke

tide

synt

hase

(PKS

) (frn

E)35

%XF

2093

prec

urso

r of d

rug

resi

stan

ce p

rote

in(a

crA/

mtc

A/lir

)42

%XF

0769

pter

idin

e-de

pend

ent d

eoxy

gena

se (r

apK)

34%

XF15

30su

buni

t C o

f alk

yl h

ydro

pero

xide

redu

ctas

e(a

hpC)

70%

XF15

31su

buni

t F o

f alk

yl h

ydro

pero

xide

redu

ctas

e(a

hpF)

77%

XF26

14su

pero

xide

dis

mut

ase

[MN

] (so

dA/s

od)

78%

XF19

21su

pero

xide

dis

mut

ase

[MN

] pre

curs

or(s

odA/

sodM

)57

%XF

2778

thio

phen

e an

d fu

ran

oxid

atio

n pr

otei

n(th

dF/t

rmE)

47%

XF18

98To

lA p

rote

in (t

olA)

21%

XF18

97To

lB p

rote

in p

recu

rsor

(tol

B)40

%XF

1900

TolQ

pro

tein

(tol

Q/fii

)48

%XF

1899

TolR

pro

tein

(tol

R)34

%XF

0009

TonB

pro

tein

(ton

B)72

%XF

1957

TonB

pro

tein

(ton

B)26

%XF

2287

TonB

pro

tein

(ton

B)29

%XF

2327

TonB

pro

tein

(ton

B)28

%XF

2605

TonB

pro

tein

(ton

B)36

%XF

2397

toxi

n se

cret

ion

ABC

trans

porte

r ATP

-bin

ding

prot

ein

(hly

B)61

%XF

1841

unde

capr

enol

kin

ase

(bac

A)38

%

PATH

OGEN

ICIT

Y, V

IRUL

ENCE

, AN

D AD

APTA

TION

/HOS

T CE

LLW

ALL

DEGR

ADAT

ION

XF12

671,

4-be

ta-c

ello

bios

idas

e (c

bhA)

46%

XF08

18en

do-1

,4-b

eta-

gluc

anas

e (e

ngXC

A)64

%XF

2708

endo

-1,4

-bet

a-gl

ucan

ase

(egl

)47

%XF

0810

extra

cellu

lar e

ndog

luca

nase

pre

curs

or(e

ngXC

A)33

%XF

0845

fam

ily 3

gly

cosi

de h

ydro

lase

(xyl

A)45

%XF

2466

poly

gala

ctur

onas

e pr

ecur

sor (

pglA

)---

%

PATH

OGEN

ICIT

Y, V

IRUL

ENCE

, AN

DAD

APTA

TION

/EXO

POLY

SACC

HARI

DES

XF23

70Gu

mB

prot

ein

(gum

B)67

%XF

2369

Gum

C pr

otei

n (g

umC)

62%

XF23

67Gu

mD

prot

ein

(gum

D)73

%XF

2366

Gum

E pr

otei

n (g

umE)

61%

XF23

65Gu

mF

prot

ein

(gum

F)44

%XF

2364

Gum

H pr

otei

n (g

umH)

64%

XF23

62Gu

mJ

prot

ein

(gum

J)65

%XF

2361

Gum

K pr

otei

n (g

umK)

69%

XF23

60Gu

mM

pro

tein

(gum

M)

69%

PATH

OGEN

ICIT

Y, V

IRUL

ENCE

, AN

D AD

APTA

TION

/SUR

FACE

PROT

EIN

S

XF08

89he

mag

glut

inin

-like

sec

rete

d pr

otei

n (p

spA)

25%

XF21

96he

mag

glut

inin

-like

sec

rete

d pr

otei

n (p

spA)

35%

XF27

75he

mag

glut

inin

-like

sec

rete

d pr

otei

n (p

spA)

35%

XF15

29su

rface

pro

tein

(hsf

)22

%XF

1981

surfa

ce p

rote

in (h

sf)

24%

XF15

16su

rface

-exp

osed

out

er m

embr

ane

prot

ein

(usp

A1)

28%

PATH

OGEN

ICIT

Y, V

IRUL

ENCE

, AN

DAD

APTA

TION

/ADA

PTAT

ION

, ATY

PICA

L CO

NDI

TION

S

XF04

32Br

kB p

rote

in (b

rk)

33%

XF08

66co

balt-

zinc-

cadm

ium

resi

stan

ce p

rote

in(c

zcD)

53%

XF02

85he

at s

hock

pro

tein

(htrA

/deg

P/pt

d)43

%XF

2625

heat

sho

ck p

rote

in (h

tpX)

53%

XF22

34lo

w m

olec

ular

wei

ght h

eat s

hock

pro

tein

(hsp

A)38

%XF

1379

luci

fera

se31

%XF

0837

orga

nic

solv

ent t

oler

ance

pre

curs

or(im

p/os

tA)

29%

XF16

23pe

ripla

smic

glu

can

bios

ynth

esis

pro

tein

(mdo

H)37

%XF

2682

perip

lasm

ic g

luca

n bi

osyn

thes

is p

rote

in(m

doG)

36%

XF07

85su

lfur d

epriv

atio

n re

spon

se re

gula

tor (

sac1

)22

%XF

0858

surv

ival

pro

tein

(sur

E)60

%XF

2622

tem

pera

ture

acc

limat

ion

prot

ein

B (ta

pB)

85%

XF04

18to

luen

e to

lera

nce

prot

ein

(ttg2

D)24

%XF

0419

tolu

ene

tole

ranc

e pr

otei

n (tt

g2C)

41%

XF04

20to

luen

e to

lera

nce

prot

ein

(ttg2

B)42

%XF

0421

tolu

ene

tole

ranc

e pr

otei

n (tt

g2A)

50%

PATH

OGEN

ICIT

Y, V

IRUL

ENCE

, AN

D AD

APTA

TION

/OTH

ER

XF02

90ac

onita

se (r

pfA)

79%

XF14

24ch

itina

se (c

hi)

43%

XF15

27ge

nera

l sec

reto

ry p

athw

ay p

rote

in D

prec

urso

r (xp

sD/p

efD)

68%

XF15

17ge

nera

l sec

reto

ry p

athw

ay p

rote

in E

(xps

E/pe

fE)

81%

XF15

18ge

nera

l sec

reto

ry p

athw

ay p

rote

in F

(xps

F)66

%XF

1519

gene

ral s

ecre

tory

pat

hway

pro

tein

Gpr

ecur

sor (

xpsG

/pef

G)78

%XF

1520

gene

ral s

ecre

tory

pat

hway

pro

tein

Hpr

ecur

sor (

xpsH

)67

%XF

1521

gene

ral s

ecre

tory

pat

hway

pro

tein

Ipr

ecur

sor (

xpsI

/pef

I)55

%XF

1522

gene

ral s

ecre

tory

pat

hway

pro

tein

Jpr

ecur

sor (

xpsJ

/pef

J)56

%XF

1523

gene

ral s

ecre

tory

pat

hway

pro

tein

K (p

efK)

60%

XF15

24ge

nera

l sec

reto

ry p

athw

ay p

rote

in L

(pef

L)60

%XF

1020

path

ogen

icity

-rela

ted

prot

ein

48%

XF07

20pr

otei

c ki

ller a

ctiv

e pr

otei

n (h

igB)

33%

XF07

21pr

otei

c ki

ller s

uppr

essi

on p

rote

in (h

igA)

40%

XF02

23qu

euin

e tR

NA-

ribos

yltra

nsfe

rase

(tgt

/vac

C)61

%XF

0287

regu

lato

r of p

atho

geni

city

fact

ors

(rpfB

)72

%XF

1114

regu

lato

r of p

atho

geni

city

fact

ors

(rpfC

)59

%XF

1115

regu

lato

r of p

atho

geni

city

fact

ors

(rpfF

)67

%XF

1987

VacB

pro

tein

(vac

B)46

%

XF05

91vi

rule

nce

fact

or48

%XF

2420

viru

lenc

e fa

ctor

(mvi

N)

39%

XF07

54vi

rule

nce

prot

ein

(acv

B)39

%XF

2679

viru

lenc

e pr

otei

n (a

cvB)

28%

XF07

49vi

rule

nce

regu

lato

r (xr

vA)

47%

XF14

93vi

rule

nce

regu

lato

r (xr

vA)

46%

XF05

06vi

rule

nce-

asso

ciat

ed p

rote

in E

(vap

E)31

%XF

2121

viru

lenc

e-as

soci

ated

pro

tein

E (v

apE)

32%

ORFS

WIT

H UN

DEFI

NED

CAT

EGOR

Y

XF21

49Ap

aG p

rote

in (a

paG/

corD

)45

%XF

1828

ATPa

se28

%XF

0961

bact

erio

ferri

tin c

omig

rato

ry p

rote

in (b

cp)

51%

XF11

20bi

func

tiona

l DGT

P-py

roph

osph

ohyd

rola

se/t

hiam

ine

phos

phat

esy

ntha

se (m

utT/

thiE

1)43

%XF

1796

bifu

nctio

nal t

rans

crip

tiona

l rep

ress

or o

fth

e bi

otin

ope

ron/

biot

in a

cety

l-CoA

-car

boxy

lase

synt

heta

se (b

irA/b

ioR/

dhbB

)40

%XF

1624

carb

oxyl

este

rase

(est

B)37

%XF

0063

com

pete

nce

prot

ein

F (c

omF)

37%

XF11

79co

mpe

tenc

e re

late

d pr

otei

n (c

omM

)52

%XF

1078

DNA

upta

ke p

rote

in (c

omA)

35%

XF22

43GT

P bi

ndin

g pr

otei

n (le

pA)

69%

XF12

13GT

P-bi

ndin

g el

onga

tion

fact

or p

rote

in (t

ypA)

69%

XF00

88GT

P-bi

ndin

g pr

otei

n (h

flX)

54%

XF04

65GT

P-bi

ndin

g pr

otei

n (y

fgK)

46%

XF14

30GT

P-bi

ndin

g pr

otei

n (y

ihA)

52%

XF24

22GT

P-bi

ndin

g pr

otei

n (y

hbZ)

55%

XF26

41GT

P-bi

ndin

g pr

otei

n68

%XF

1668

HicB

-rela

ted

prot

ein

38%

XF11

92in

tegr

al m

embr

ane

prot

ein

49%

XF19

27in

tegr

al m

embr

ane

prot

ein

---%

XF26

45is

open

teny

l mon

opho

spha

te k

inas

e (ip

k)50

%XF

0145

oxid

ored

ucta

se (y

dfG)

50%

XF17

44ox

idor

educ

tase

71%

XF17

23su

gar-p

hosp

hate

deh

ydro

gena

se (y

rpG)

55%

XF17

24su

gar-p

hosp

hate

deh

ydro

gena

se (y

rpG)

55%

pXF5

1 ge

nes:

INTE

RMED

IARY

MET

ABOL

ISM

/REG

ULAT

ORY

FUN

CTIO

NS

XFa0

001

trans

crip

tiona

l reg

ulat

or31

%XF

a005

7tra

nscr

iptio

nal r

egul

ator

(kor

A)40

%

MAC

ROM

OLEC

ULE

MET

ABOL

ISM

/DN

AM

ETAB

OLIS

M/R

eplic

atio

n

XFa0

061

sing

le-s

trand

bin

ding

pro

tein

(ssb

)54

%XF

a000

3to

pois

omer

ase

I (to

pA/s

upX)

35%

MAC

ROM

OLEC

ULE

MET

ABOL

ISM

/DN

AM

ETAB

OLIS

M/R

ecom

bina

tion

XFa0

019

site

-spe

cific

reco

mbi

nase

(rin

)91

%

MOB

ILE

GEN

ETIC

ELE

MEN

TS/P

LASM

ID-R

ELAT

ED F

UNCT

ION

S

XFa0

002

conj

ugal

tran

sfer

pro

tein

(tra

L/vi

rB1)

46%

XFa0

005

conj

ugal

tran

sfer

pro

tein

(trb

C/vi

rB2)

32%

XFa0

006

conj

ugal

tran

sfer

pro

tein

(tra

A/vi

rB3)

39%

XFa0

007

conj

ugal

tran

sfer

pro

tein

(tra

B/vi

rB4)

43%

XFa0

008

conj

ugal

tran

sfer

pro

tein

(tra

C/vi

rB5)

28%

XFa0

011

conj

ugal

tran

sfer

pro

tein

(tra

D/vi

rB6)

23%

XFa0

012

conj

ugal

tran

sfer

pro

tein

(tra

E/vi

rB8)

33%

XFa0

013

conj

ugal

tran

sfer

pro

tein

(tra

O/vi

rB9)

34%

XFa0

014

conj

ugal

tran

sfer

pro

tein

(tra

F/vi

rB10

)40

%XF

a001

5co

njug

al tr

ansf

er p

rote

in(tr

aG/v

irB11

)41

%XF

a001

6co

njug

al tr

ansf

er p

rote

in (t

raG/

virD

4)35

%XF

a003

6co

njug

al tr

ansf

er p

rote

in (t

rbN

)76

%XF

a003

7co

njug

al tr

ansf

er p

rote

in (t

rbL)

45%

XFa0

039

conj

ugal

tran

sfer

pro

tein

(trb

J)54

%XF

a004

0co

njug

al tr

ansf

er p

rote

in (t

rbI)

52%

XFa0

041

conj

ugal

tran

sfer

pro

tein

(trb

H)44

%XF

a004

2co

njug

al tr

ansf

er p

rote

in (t

rbG)

65%

XFa0

043

conj

ugal

tran

sfer

pro

tein

(trb

F)47

%XF

a004

4co

njug

al tr

ansf

er p

rote

in (t

rbE)

---%

XFa0

047

nick

ase

(taxC

)30

%XF

a002

7pl

asm

id m

aint

enan

ce p

rote

in (p

emK)

48%

XFa0

060

plas

mid

repl

icat

ion

prot

ein

(incC

)34

%XF

a005

9pl

asm

id re

plic

atio

n/pa

rtitio

n pr

otei

n32

%XF

a002

9pl

asm

id s

tabi

lizat

ion

prot

ein

(par

E)76

%

PATH

OGEN

ICIT

Y, V

IRUL

ENCE

, AN

D AD

APTA

TION

/OTH

ER

XFa0

052

viru

lenc

e-as

soci

ated

pro

tein

D (v

apD)

64%

pXF1

.3 g

enes

:

MOB

ILE

GEN

ETIC

ELE

MEN

TS/P

LASM

ID-R

ELAT

ED F

UNCT

ION

S

XFb0

001

repl

icat

ion

prot

ein

41%

Tabl

e 3

Puta

tive

iden

tific

atio

n of

Xyl

ella

fast

idio

sa g

enes

. Gen

e nu

mbe

rs c

orre

spon

d to

thos

e in

Fig

. 1. P

erce

ntag

es re

pres

ent %

iden

titie

sre

lativ

e to

the

mos

t rel

evan

t dat

abas

e hi

t (co

nser

ved

hypo

thet

ical

s an

d %

iden

titie

s of

gen

es w

ith fr

ames

hift/

stop

cod

on in

fram

e no

t sho

wn)

.

© 2000 Macmillan Magazines Ltd