Protein Clusters in Enterobacteria

Cluster	Description	COG	Pfam	Smart
0	IS1 protein InsB\|IS1 transposase. Transposase proteins are necessary for efficient DNA transposition. This family represents bacterial IS1 transposases; pfam03400\|Escherichia coli O157:H7 ortholog: z1632	COG1662(361)	PF03400(257), PF03811(1)
6	Transposase insD for insertion element IS2A/D/F/H/I/K\|Integrase core domain. Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022; pfam00665\|Escherichia coli K-12 ortholog: b4273; Escherichia coli O157:H7 ortholog: z1825	COG2801(163)	PF00665(185), PF02022(20)
16	putative transposase OrfB protein of insertion sequence IS629\|Transposase and inactivated derivatives [DNA replication, recombination, and repair]; COG2801\|Integrase core domain. Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022; pfam00665	COG2801(100)	PF00665(94), PF02022(29)
24	putative transposase\|Transposase IS66 family. Transposase proteins are necessary for efficient DNA transposition. This family includes IS66 from Agrobacterium tumefaciens; pfam03050	COG3436(18), COG1196(1), COG3883(1)\|COG3436(1)	PF03938(18)\|PF03050(18), PF03050(47)
152	putative IS orf\|Transposase. Transposase proteins are necessary for efficient DNA transposition. This family consists of various E. coli insertion elements and other bacterial transposases some of which are members of the IS3 family; pfam01527	COG2963(6), COG2390(2)	PF01527(35)
188	lysis protein S		PF04971(34)
213	hypothetical protein\|Domain of unknown function (DUF303). Distribution of this domain seems limited to prokaryotes and viruses; pfam03629	COG2801(6)	PF03629(15), PF08410(21)\|PF03629(21)
215	putative antirestriction protein\|Antirestriction protein. This family includes various protein that are involved in antirestriction. The ArdB protein efficiently inhibits restriction by members of the three known families of type I systems of E. coli; pfam03230		PF03230(26)
225	Hypothetical protein ydfU\|Protein of unknown function (DUF1277). This family contains a number of hypothetical proteins of unknown function approximately 350 residues long. These are of bacterial and viral origin; pfam06914\|Escherichia coli K-12 ortholog: b1560; Escherichia coli O157:H7 ortholog: z2100		PF06914(28)
282	glutamate decarboxylase beta\|Glutamate decarboxylase and related PLP-dependent proteins [Amino acid transport and metabolism]; COG0076\|Pyridoxal-dependent decarboxylase conserved domain; pfam00282	COG0076(29)	PF00282(29)
1030	hypothetical protein YeeT\|Protein of unknown function (DUF987). Family of bacterial proteins that are related to the hypothetical protein yeeT; pfam06174		PF06174(26)
1731	hypothetical metabolite transport protein YdjE\|Sugar (and other) transporter; pfam00083\|Major Facilitator Superfamily; pfam07690	COG0477(4)	PF00083(14), PF00083(11)\|PF07690(11)
1856	Probable lysozyme from lambdoid prophage Qin\|Endolysins and autolysins are found in viruses and bacteria, respectively; cd00737\|Escherichia coli K-12 ortholog: b1554; Escherichia coli O157:H7 ortholog: z1796	COG3772(4)	PF00959(1)
1976	L-sorbose 1-phosphate reductase\|Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; COG1063\|Alcohol dehydrogenase GroES-like domain. This is the catalytic domain of alcohol dehydrogenases. Many of them contain an inserted zinc binding domain. This domain has a GroES-like structure; pfam08240\|Zinc-binding dehydrogenase; pfam00107	COG1063(23)	PF00107(4), PF08240(20)\|PF00107(20)
2015	putative cation efflux system protein CusA\|Putative silver efflux pump [Inorganic ion transport and metabolism]; COG3696	COG3696(15)	PF00873(1)
2366	hypothetical protein YehI	COG3831(4)	PF05406(1)
2372	hypothetical protein YibH\|Multidrug resistance efflux pump [Defense mechanisms]; COG1566\|predicted membrane fusion protein of efflux pump; PRK10476	COG1566(19)	PF00529(5)
2510	hypothetical protein YjdA\|conserved protein with nucleoside triphosphate hydrolase domain; PRK09866\|HflX subfamily. A distinct conserved domain with a glycine-rich segment N-terminal of the GTPase domain characterizes the HflX subfamily. The E; cd01878\|Era (E. coli Ras-like protein)-like; cd00880	COG0699(1)	PF01926(10)
2743	putative copper efflux system protein CusB precursor\|copper/silver efflux system, membrane fusion protein; PRK09783\|periplasmic multidrug efflux lipoprotein precursor; PRK09578	COG0845(2)
2877	putative zinc-binding dehydrogenase\|Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; COG1063\|Alcohol dehydrogenase GroES-like domain. This is the catalytic domain of alcohol dehydrogenases. Many of them contain an inserted zinc binding domain. This domain has a GroES-like structure; pfam08240\|Zinc-binding dehydrogenase; pfam00107	COG1063(14)	PF08240(14)\|PF00107(14)
2948	beta-lactamase precursor\|Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]; COG1680\|beta-lactamase; PRK11289	COG1680(15)	PF00144(1)
2980	hypothetical protein YnjA\|Uncharacterized conserved protein [Function unknown]; COG2128	COG2128(15)	PF02627(1)
2981	hypothetical protein YdjX (hypothetical transmembrane protein)\|Uncharacterized conserved protein [Function unknown]; COG0398	COG0398(15)	PF09335(1)
2994	hypothetical protein\|UTRA domain. The UbiC transcription regulator-associated (UTRA) domain is a conserved ligand-binding domain that has a similar fold to pfam04345; pfam07702	COG2188(16)	PF07702(1), PF00392(16)\|PF07702(16)
3003	arsenate reductase\|Arsenate Reductase (ArsC) family, ArsC subfamily; arsenic reductases similar to that encoded by arsC on the R733 plasmid of Escherichia coli. E; cd03034	COG1393(5)	PF03960(1)
3018	hypothetical protein YcdJ\|alpha/beta hydrolase fold. This catalytic domain is found in a very wide range of enzymes; pfam00561	COG0596(5)	PF00561(14)
3037	hypothetical protein YnjF (probable CDP-alcohol phosphatidyltransferase\|Phosphatidylglycerophosphate synthase [Lipid metabolism]; COG0558	COG0558(13)	PF01066(1)
3039	hypothetical protein YdeP\|predicted oxidoreductase; PRK09939\|The MopB_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. These members belong to the molybdopterin_binding (MopB) superfamily of proteins; cd02767	COG0243(5)	PF01568(1)
3063	protein RtcB\|Uncharacterized conserved protein [Function unknown]; COG1690	COG1690(14)	PF0027(1), PF01139(1)
3073	hypothetical protein YoaC (putative cytoplasmic protein)\|Domain of unknown function (DUF1889). This domain is found in a set of hypothetical bacterial proteins; pfam08986		PF08986(15)
3084	pyruvate formate-lyase 2 activating enzyme\|pyruvate formate lyase II activase; PRK10076\|Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; COG0602	COG0602(5)\|COG1180(5), COG0602(10)	PF04055(1)
3094	aquaporin Z\|Major intrinsic protein (MIP) superfamily. Members of the MIP superfamily function as membrane channels that selectively transport water, small neutral molecules, and ions out of and between cells; cd00333	COG0580(4)	PF00230(1)
3100	cation transport protein ChaC	COG3703(15)	PF04752(1)
3107	hypothetical protein YpfH\|esterase YpfH; PRK11460	COG0400(5)	PF02230(1)
3109	TdcF protein\|YjgH belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase however there is no sequence similarity and no functional connection; cd02198	COG0251(4)	PF01042(1)
3122	putative shikimate 5-dehydrogenase\|quinate/shikimate dehydrogenase; PRK12749\|Shikimate dehydrogenase substrate binding domain. This domain is the substrate binding domain of shikimate dehydrogenase; pfam08501\|S-adenosyl-L-homocysteine hydrolase (AdoHycase) catalyzes the hydrolysis of S-adenosyl-L-homocysteine (AdoHyc) to form adenosine (Ado) and homocysteine (Hcy). The equilibrium lies far on the side of AdoHyc synthesis, but in nature the removal of Ado...; cl09931	COG0169(4)	PF08501(15)
3130	hypothetical amino acid transporter YbaT protein\|Gamma-aminobutyrate permease and related permeases [Amino acid transport and metabolism]; COG1113	COG1113(3), COG1113(11)\|COG0531(11)	PF03845(1)
3137	nickel transport ATP-binding protein NikE\|nickel transporter subunit; PRK10419\|The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; cd03257	COG1124(5)	PF00005(1)
3138	nickel transport ATP-binding protein NikD\|nickel transporter subunit; PRK10418\|The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane...; cd03257	COG0444(5)	PF08352(5), PF00005(1)
3139	nickel transport system permease protein NikC\|Binding-protein-dependent transport system inner membrane component. The alignments cover the most conserved region of the proteins, which is thought to be located in a cytoplasmic loop between two transmembrane domains. The members of this family have...; cl00427	COG1173(5)	PF00528(1)
3140	nickel transport system permease protein NikB\|Binding-protein-dependent transport system inner membrane component. The alignments cover the most conserved region of the proteins, which is thought to be located in a cytoplasmic loop between two transmembrane domains. The members of this family have...; cl00427\|ABC-type uncharacterized transport system, permease component [General function prediction only]; COG4174	COG4174(9), COG4174(5)\|COG0601(5)	PF00528(1)
3141	nickel-binding periplasmic protein precursor\|ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; COG0747	COG0747(15)	PF00496(1)
3142	putative amino-acid ABC transporter binding protein YhdW precursor\|Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic i; cd00134	COG0834(6)
3143	glycerol metabolism operon regulatory protein\|DNA-binding transcriptional regulator DhaR; PRK11388\|PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels; smart00091\|Sigma-54 interaction domain; pfam00158\|Bacterial regulatory protein, Fis family; pfam02954	COG3284(3)	PF00158(13)\|PF02954(13)	SM00091(12)
3150	hypothetical protein YbaA\|Uncharacterized conserved protein [Function unknown]; COG5507	COG5507(14)	PF07237(1)
3155	hypothetical ABC transporter ATP-binding protein YnjD\|ABC-type uncharacterized transport system, ATPase component [General function prediction only]; COG4136\|ABC Carbohydrate and Solute Transporters-like subgroup. This family is comprised of proteins involved in the transport of apparently unrelated solutes and proteins specific for di- and oligosaccharides and polyols; cd03259	COG4136(1)\|COG1130(1), COG4136(14)	PF00005(1)
3156	hypothetical oxidoreductase YdgB\|short chain dehydrogenase; PRK06483\|pteridine reductase; PRK09135	COG1028(5)	PF00106(1)
3166	D-erythro-7,8-dihydroneopterin triphosphate epimerase\|Dihydroneopterin aldolase (DHNA) and 7,8-dihydroneopterin triphosphate epimerase domain (DHNTPE); these enzymes have been designated folB and folX, respectively; cd00534	COG1539(5)	PF02152(1)
3167	hypothetical protein YpdB\|Response regulator of the LytR/AlgR family [Transcription / Signal transduction mechanisms]; COG3279\|Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; contains; cd00156\|LytTr DNA-binding domain. This domain is found in a variety of bacterial transcriptional regulators. The domain binds to a specific DNA sequence pattern (see ); pfam04397	COG3279(15)	PF04397(15)
3168	putative PTS system IIC component YpdG\|Phosphotransferase system, fructose-specific IIC component [Carbohydrate transport and metabolism]; COG1299	COG1299(14)	PF02378(1)
3169	putative PTS system IIB component YpdH\|PTS system, Fructose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. The sugar-specific...; cl00634	COG1445(5)	PF02379(1)
3178	hypothetical protein YiiS	COG3691(5)	PF04175(1)
3179	RNA 3'-terminal phosphate cyclase\|RNA 3'-terminal-phosphate cyclase; PRK04204\|RNA 3' phosphate cyclase domain - RNA phosphate cyclases are enzymes that catalyze the ATP-dependent conversion of 3'-phosphate at the end of RNA into 2', 3'-cyclic phosphodiester bond. The enzymes are conserved in eucaryotes, bacteria and archaea; cd00295	COG0430(5)	PF05189(1)
3182	hypothetical protein YfdE	COG1804(5)	PF02515(1)
3185	hypothetical protein YeaP\|FOG: GAF domain [Signal transduction mechanisms]; COG2203\|Diguanylate-cyclase (DGC) or GGDEF domain: Originally named after a conserved residue pattern, and initially described as domain of unknown function 1 (DUF1); cd01949	COG2203(13)	PF01590(1)
3199	hypothetical protein YfdV\|predicted transporter; PRK09903	COG0679(5)	PF03547(1)
3201	hypothetical amino-acid ABC transporter ATP-binding protein YhdZ\|ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; COG1126\|HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively. Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP...; cd03262	COG1126(14)	PF00005(1)
3202	hypothetical amino-acid ABC transporter permease protein YhdY\|Binding-protein-dependent transport system inner membrane component. The alignments cover the most conserved region of the proteins, which is thought to be located in a cytoplasmic loop between two transmembrane domains. The members of this family have...; cl00427	COG0765(5)
3203	hypothetical membrane protein YraQ\|Predicted permease. This family of integral membrane proteins are predicted to be permeases of unknown specificity; pfam03773	COG0701(4)	PF03773(14)
3205	hypothetical protein YggD\|predicted DNA-binding transcriptional regulator; PRK10022	COG3722(3)	PF05068(1)
3206	hypothetical protein YggC\|Pantothenate kinase (PanK) catalyzes the phosphorylation of pantothenic acid to form 4'-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway; cd02025	COG1072(5)
3209	hypothetical protein YfiL
3212	putative exported protein\|hypothetical protein; PRK10259		PF07338(1)
3214	putative malate/L-lactate dehydrogenase\|predicted dehydrogenase; PRK10098	COG2055(5)	PF02615(1)
3215	hypothetical protein\|Predicted membrane protein [Function unknown]; COG4763	COG4763(14)	PF01757(1)
3219	hypothetical protein YdaM\|PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels; cd00130\|Diguanylate-cyclase (DGC) or GGDEF domain: Originally named after a conserved residue pattern, and initially described as domain of unknown function 1 (DUF1); cd01949	COG3829(1), COG2202(1), COG2199(2)	PF08448(1)	SM00091(1)
3220	hypothetical protein YeiN\|Uncharacterized enzyme involved in pigment biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]; COG2313	COG2313(12)	PF04227(1)
3223	hypothetical protein YpdE\|predicted peptidase; PRK09961\|M42 glutamyl aminopeptidase. These peptidases are found in Archaea and Bacteria. The example in Lactococcus lactis, PepA, aids growth on milk; pfam05343	COG1363(5)	PF05343(14)
3243	hypothetical protein YijF precursor\|Uncharacterized protein conserved in bacteria [Function unknown]; COG3738	COG3738(13)	PF06940(1)
3244	probable adenine deaminase\|cryptic adenine deaminase; PRK10027\|N-acetylglucosamine-6-phosphate deacetylase, NagA, catalyzes the hydrolysis of the N-acetyl group of N-acetyl-glucosamine-6-phosphate (GlcNAc-6-P) to glucosamine 6-phosphate and acetate; cd00854	COG1001(5)	PF01979(1)
3245	DNA-damage-inducible protein D
3247	transcriptional regulator GadX\|DNA-binding transcriptional dual regulator; PRK09978\|Bacterial regulatory helix-turn-helix proteins, AraC family; pfam00165	COG2207(5)	PF00165(14)
3248	hypothetical membrane protein\|Outer membrane lipoprotein [Cell envelope biogenesis, outer membrane]; COG3133	COG3133(14)	PF05433(1)
3252	hypothetical protein YeiK (Inosine-uridine preferring nucleoside hydrolase)\|ribonucleoside hydrolase 1; PRK10443\|nuc_hydro_IU_UC_XIUA: inosine-uridine preferring, xanthosine-inosine-uridine-adenosine-preferring and, uridine-cytidine preferring nucleoside hydrolases; cd02651	COG1957(5)	PF01156(1)
3256	hypothetical protein YdjZ (hypothetical transmembrane protein, DedA family)\|Uncharacterized conserved protein [Function unknown]; COG0398	COG0398(15)	PF09335(1)
3257	ferredoxin-like protein YdiT\|Ferredoxin-like protein [Energy production and conversion]; COG2440	COG2440(13)
3258	hypothetical transport protein YdiN\|Major Facilitator Superfamily; pfam07690	COG0477(4)	PF07690(10)
3259	hypothetical protein YdiL\|Domain of unknown function (DUF1870). This domain is found in a set of hypothetical bacterial proteins; pfam08965		PF08965(14)
3260	7-alpha-hydroxysteroid dehydrogenase\|S-adenosyl-L-homocysteine hydrolase (AdoHycase) catalyzes the hydrolysis of S-adenosyl-L-homocysteine (AdoHyc) to form adenosine (Ado) and homocysteine (Hcy). The equilibrium lies far on the side of AdoHyc synthesis, but in nature the removal of Ado...; cl09931\|sorbitol-6-phosphate dehydrogenase; PRK12384	COG1028(4)	PF00106(1)
3261	uid operon repressor\|Transcriptional regulator [Transcription]; COG1309\|Bacterial regulatory proteins, tetR family; pfam00440	COG1309(15)	PF00440(15)
3262	putative HTH-type transcriptional regulator YddM\|Plasmid maintenance system antidote protein [General function prediction only]; COG3093	COG3093(15)	PF01381(1)
3263	hypothetical protein YneF\|Diguanylate-cyclase (DGC) or GGDEF domain: Originally named after a conserved residue pattern, and initially described as domain of unknown function 1 (DUF1); cd01949	COG2199(3)	PF00990(1)
3264	putative outer membrane protein YieC precursor\|The Maltoporin-like channels (LamB porin) form a trimeric structure which facilitate the diffusion of maltodextrins and other sugars across the outer membrane of Gram-negative bacteria; cd01346	COG4580(2)	PF02264(1)
3268	putative NADH dehydrogenase/NAD(P)H nitroreductase Ycdi\|Nitroreductase-like family 5. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase; cd02148	COG0778(4)	PF00881(1)
3270	hypothetical PKHD-type hydroxylase YbiX\|putative hydroxylase; PRK05467	COG3128(13)	PF03171(1)
3272	hypothetical protein YibI
3273	positive transcription regulator EvgA\|DNA-binding response regulator in two-component regulatory system with EvgS; PRK09958\|Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems...; cd00156\|Sigma-70, region 4. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix...; cl01055	COG2197(5)	PF00196(1)
3277	conserved hypothetical protein\|periplasmic copper-binding protein; PRK09838	COG5569(2)
3282	hypothetical protein YdhW
3285	putative PTS system enzyme I\|fused predicted dihydroxyacetone-specific PTS enzymes: HPr component/EI component; PRK11377\|Uncharacterized protein conserved in bacteria [Function unknown]; COG3412\|Histidine-containing phosphocarrier protein (HPr)-like proteins. HPr is a central component of the bacterial phosphoenolpyruvate sugar phosphotransferase system (PTS); cd00367\|PEP-utilising enzyme, N-terminal; pfam05524	COG3412(1)\|COG1080(1), COG3412(13)	PF05524(14)\|PF00391(14)
3286	transcriptional regulator cbl\|Bacterial regulatory helix-turn-helix protein, lysR family; cl09147\|Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and...; cl00115	COG0583(4)	PF03466(1)
3288	hypothetical protein YehD precursor\|P pilus assembly protein, pilin FimA [Cell motility and secretion / Intracellular trafficking and secretion]; COG3539	COG3539(13)	PF00419(1)
3289	malate:quinone oxidoreductase\|Predicted dehydrogenase [General function prediction only]; COG0579	COG0579(13)	PF06039(1)
3291	hypothetical protein YpdA\|Putative regulator of cell autolysis [Signal transduction mechanisms]; COG3275\|5TMR of 5TMR-LYT. This entry represents the transmembrane region of the 5TM-LYT (5TM Receptors of the LytS-YhcK type); pfam07694\|Histidine kinase. This family represents a region within bacterial histidine kinase enzymes; pfam06580\|Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; cd00075	COG3275(12)	PF06580(1), PF07694(11)\|PF06580(11)
3292	hypothetical transcriptional regulator YpdC\|helix_turn_helix, arabinose operon control protein; smart00342\|Bacterial regulatory helix-turn-helix proteins, AraC family; pfam00165	COG2207(3)	PF00165(11)	SM00342(11)
3301	putative outer membrane efflux protein\|Outer membrane efflux protein. The OEP family (Outer membrane efflux protein) form trimeric channels that allow export of a variety of substrates in Gram negative bacteria. Each member of this family is composed of two repeats; pfam02321	COG1538(3)	PF02321(14)
3302	hypothetical transport protein YijE\|Integral membrane protein DUF6. This family includes many hypothetical membrane proteins of unknown function. Many of the proteins contain two copies of the aligned region; pfam00892	COG0697(5)	PF00892(14)
3303	hypothetical protein YiiX precursor\|predicted peptidoglycan peptidase; PRK10030		PF06520(1)
3304	hypothetical protein YiiT\|Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents; cd00293	COG0589(5)	PF00582(1)
3305	hypothetical protein YidB	COG3753(4)	PF06078(1)
3308	hypothetical transcriptional regulator YhiW\|predicted DNA-binding transcriptional activator; PRK09940\|Bacterial regulatory helix-turn-helix proteins, AraC family; pfam00165	COG2207(4)	PF00165(13)
3309	hypothetical protein YhiE	COG2771(4)
3310	Hns-dependent expression protein HdeA\|stress-response and acid-resistance protein; PRK10208		PF06411(1)
3311	hypothetical transcriptional regulator YhiF\|Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]; COG2197\|helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon; smart00421	COG2197(4)\|COG2771(4), COG2197(9)	PF00196(1)	SM00421(13)
3312	outer membrane protein Slp precursor	COG3065(10)	PF03843(4)
3313	transcriptional regulatory protein RtcR\|Sigma54-dependent transcription regulator containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]; COG4650\|Sigma-54 interaction domain; pfam00158\|AAA-superfamily of ATPases associated with a wide variety of cellular activities, including membrane fusion, proteolysis, and DNA replication; cd00009	COG4650(1)\|COG1221(1), COG4650(12)	PF06956(12)\|PF00158(12), PF06956(1)\|PF00158(1)\|PF07728(1)
3315	hypothetical lipoprotein YqhH precursor\|predicted outer membrane lipoprotein; PRK09973	COG4238(4)
3316	hypothetical protein YqhG precursor
3317	hypothetical transcriptional regulator YgfI\|Bacterial regulatory helix-turn-helix protein, lysR family; pfam00126\|Transcriptional regulator [Transcription]; COG0583\|LysR substrate binding domain. The structure of this domain is known and is similar to the periplasmic binding proteins; pfam03466	COG0583(12)	PF00126(5), PF00126(8)\|PF03466(8)
3321	hypothetical protein YfdW\|formyl-coenzyme A transferase; PRK05398	COG1804(5)	PF02515(1)
3322	probable oxalyl-CoA decarboxylase\|putative oxalyl-CoA decarboxylase; PRK09259\|Thiamine pyrophosphate enzyme, N-terminal TPP binding domain; pfam02776\|Thiamine pyrophosphate enzyme, central domain. The central domain of TPP enzymes contains a 2-fold Rossman fold; pfam00205\|Thiamine pyrophosphate (TPP) family, BZL_OCoD_HPCL subfamily, TPP-binding module; composed of proteins similar to benzaldehyde lyase (BZL), oxalyl-CoA decarboxylase (OCoD) and 2-hydroxyphytanoyl-CoA lyase (2-HPCL); cd02004	COG0028(5)	PF02776(14)\|PF00205(14)
3325	hypothetical protein YegX\|Lyzozyme M1 (1,4-beta-N-acetylmuramidase) [Cell envelope biogenesis, outer membrane]; COG3757\|Glycosyl hydrolases family 25; smart00641	COG3757(14)	PF01183(1)	SM00641(14)
3326	hypothetical protein\|VWA subfamily: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF); cd01464	COG4245(4)	PF00092(1)
3327	hypothetical protein YegK
3328	putative electron transfer flavoprotein subunit YdiR\|The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase; cd01715	COG2025(3)	PF00766(12)
3329	hypothetical transcriptional regulator YdiP\|AraC-like ligand binding domain. This family represents the arabinose-binding and dimerisation domain of the bacterial gene regulatory protein AraC. The domain is found in conjunction with the helix-turn-helix (HTH) DNA-binding motif pfam00165; pfam02311\|AraC-type DNA-binding domain-containing proteins [Transcription]; COG2207	COG2207(10)	PF02311(11)\|PF07883(11), PF07883(1)
3330	hypothetical transport protein YdiM\|Major Facilitator Superfamily; pfam07690\|multidrug resistance protein D; PRK11652	COG0477(1), COG2271(1)\|COG0477(1), COG2271(3)	PF07690(12)
3331	hypothetical protein YdhQ	COG3468(4)
3333	hypothetical protein YmjA
3334	hypothetical transcriptional regulator YcjW\|Transcriptional regulators [Transcription]; COG1609\|helix_turn _helix lactose operon repressor; smart00354	COG1609(12)	PF00532(1)	SM00354(12)
3335	hypothetical protein YddB\|Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]; COG4771\|TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; cd01347,	COG4771(13)	PF07715(1), PF07715(1)\|PF00593(1)
3336	hypothetical transcriptional regulator YdeO\|predicted DNA-binding transcriptional activator; PRK09940\|Bacterial regulatory helix-turn-helix proteins, AraC family; pfam00165	COG2207(5)	PF00165(14)
3340	putative monooxygenase YcdM\|Alkanesulfonate monoxygenase is the monoxygenase of a two-component system that catalyzes the conversion of alkanesulfonates to the corresponding aldehyde and sulfite; cd01094\|Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and related flavin-dependent oxidoreductases [Energy production and conversion]; COG2141	COG2141(14)	PF00296(1)
3341	hypothetical isochorismatase family protein YcdL\|Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle; cd00431	COG1335(3)	PF00857(1)
3342	probable transport protein YcdG\|Xanthine/uracil permeases [Nucleotide transport and metabolism]; COG2233	COG2233(13)	PF00860(1)
3347	inhibitor of vertebrate lysozyme precursor		PF08816(1)
3348	phosphotriesterase-like protein\|Phosphotriesterase (PTE) catalyzes the hydrolysis of organophosphate nerve agents, including the chemical warfare agents VX, soman, and sarin as well as the insecticide paraoxon. PTE exists as a homodimer with one active site per monomer; cd00530	COG1735(5)	PF02126(1)
3349	putative electron transfer flavoprotein subunit YgcR\|The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase; cd01714	COG2086(4)	PF01012(1)
3350	putative electron transfer flavoprotein subunit YgcQ\|Electron transfer flavoprotein, alpha subunit [Energy production and conversion]; COG2025\|The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase; cd01715	COG2025(13)	PF00766(11)
3351	ferredoxin-like protein YgcO\|Ferredoxin-like protein [Energy production and conversion]; COG2440	COG2440(14)
3352	hypothetical protein YjcZ
3356	tryptophanase\|Tryptophanase [Amino acid transport and metabolism]; COG3033\|Beta-eliminating lyase; pfam01212	COG3033(12)	PF01212(12)
3360	hypothetical protein\|Protein of unknown function (DUF453). FldA is thought to be involved in the degradation of the polyaromatic hydrocarbon fluorene by Sphingomonas sp. LB126; pfam04303	COG2828(3)	PF04303(11)
3361	aconitate hydratase\|hypothetical protein; PRK11413\|Bacterial Aconitase-like catalytic domain. Aconitase (aconitate hydratase or citrate hydrolyase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle; cd01585	COG1048(4)	PF00694(1)
3362	putative electron transport protein YccM\|Polyferredoxin [Energy production and conversion]; COG0348\|Acetyl-CoA synthase (ACS), also known as acetyl-CoA decarbonylase, is found in acetogenic and methanogenic organisms and is responsible for the synthesis and breakdown of acetyl-CoA; cd01916	COG0348(13)	PF00037(1)
3364	cytochrome c-type protein TorY\|nitrate reductase, cytochrome c-type, periplasmic; PRK10617	COG3005(3)	PF03264(3)
3365	hypothetical protein YdhT
3366	hypothetical protein YdeH\|Diguanylate-cyclase (DGC) or GGDEF domain: Originally named after a conserved residue pattern, and initially described as domain of unknown function 1 (DUF1); cd01949	COG2199(3)	PF00990(1)
3367	hypothetical protein YdcH	COG2841(5)	PF04325(1)
3369	hypothetical sugar kinase YeiI\|predicted kinase; PRK09954\|helix_turn_helix ASNC type; AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli); smart00344\|YeiC-like sugar kinase. Found in eukaryotes and bacteria, YeiC-like kinase is part of the ribokinase/pfkB sugar kinase superfamily. Its oligomerization state is unknown at this time; cd01941	COG0524(5)	PF08279(1)	SM00344(10)
3370	hypothetical protein YphB (aldose 1-epimerase)\|Galactose mutarotase and related enzymes [Carbohydrate transport and metabolism]; COG2017	COG2017(14)	PF01263(1)
3371	hypothetical protein YphH\|Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]; COG1940\|ROK family; pfam00480	COG1940(14)	PF00480(14)
3377	tdcABC operon transcription activator\|DNA-binding transcriptional activator TdcR; PRK11424
3381	hypothetical protein YjdF	COG3647(4)
3385	evolved beta-galactosidase beta-subunit\|cryptic beta-D-galactosidase subunit beta; PRK10202	COG2731(4)	PF04074(1)
3386	ebg operon repressor\|DNA-binding transcriptional repressor; PRK10339	COG1609(5)	PF00532(1)	SM00354(13)
3387	hypothetical type II secretion protein GspM\|predicted secretion pathway M-type protein, membrane anchored; PRK09731	COG3149(2)	PF04612(2)
3391	hypothetical zinc-type alcohol dehydrogenase-like protein YphC\|Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; COG1063\|Alcohol dehydrogenase GroES-like domain. This is the catalytic domain of alcohol dehydrogenases. Many of them contain an inserted zinc binding domain. This domain has a GroES-like structure; pfam08240\|Zinc-binding dehydrogenase; pfam00107	COG1063(11)	PF08240(13)\|PF00107(13)
3392	putative membrane protein	COG2259(13)	PF07681(1)
3393	hypothetical protein YfbM\|Domain of unknown function (DUF1877). This domain is found in a set of hypothetical bacterial proteins; pfam08974		PF08974(13)
3394	hypothetical protein YfaP precursor\|Uncharacterized protein conserved in bacteria [Function unknown]; COG4676	COG4676(14)
3395	hypothetical protein YeiL\|DNA-binding transcriptional activator of stationary phase nitrogen survival; PRK10402\|effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sen; cd00038	COG0664(5)	PF00027(1)
3396	hypothetical protein YegI\|Uncharacterized protein with protein kinase and helix-hairpin-helix DNA-binding domains [General function prediction only]; COG4248\|Pol_IV_kappa, a member of the Y-family of DNA polymerases. Pol_Y's can transverse replication-blocking DNA lesions, such as cyclobutane pyrimidine dimers resulting from UV damage, at the cost of an elevated error rate; cd03586	COG4248(13)
3397	hypothetical zinc-type alcohol dehydrogenase-like protein YdjL\|Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; COG1063\|Alcohol dehydrogenase GroES-like domain. This is the catalytic domain of alcohol dehydrogenases. Many of them contain an inserted zinc binding domain. This domain has a GroES-like structure; pfam08240\|Zinc-binding dehydrogenase; pfam00107	COG1063(13)	PF08240(13)\|PF00107(13)
3398	hypothetical transcriptional regulator YdjF\|Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]; COG1349\|Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; cl00088\|SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to...; cl00339	COG1349(13)	PF08279(1)
3399	hypothetical protein YdjY precursor
3400	hypothetical protein YdiD\|short chain acyl-CoA synthetase; PRK06087	COG0318(2)
3401	putative electron transfer flavoprotein subunit YdiQ\|The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase; cd01714	COG2086(2)
3402	hypothetical zinc-type alcohol dehydrogenase-like protein YcjQ\|Threonine dehydrogenase and related Zn-dependent dehydrogenases [Amino acid transport and metabolism / General function prediction only]; COG1063\|Zinc-binding dehydrogenase; pfam00107	COG1063(11)	PF00107(12)
3403	hypothetical glycosyl hydrolase\|Trehalose and maltose hydrolases (possible phosphorylases) [Carbohydrate transport and metabolism]; COG1554\|Glycosyl hydrolase family 65, N-terminal domain. This family of glycosyl hydrolases contains vacuolar acid trehalase and maltose phosphorylase; pfam03636	COG1554(12)	PF03636(12)\|PF03632(12)\|PF03633(12)
3404	hypothetical protein YdcA precursor
3405	hypothetical binding-protein-dependent transport system inner membrane component\|ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]; COG1177	COG1177(13)	PF00528(1)
3409	hypothetical protein YbjH precursor
3413	hypothetical protein YhfY
3414	hypothetical protein YhfX\|Alanine racemase, N-terminal domain; pfam01168\|Predicted amino acid racemase [Amino acid transport and metabolism]; COG3457	COG3457(12)	PF01168(6)
3415	hypothetical protein YhfW\|putative mutase; PRK12383\|Phosphopentomutase N-terminal. This is the phosphopentomutase N-terminal domain, which is found together with metalloenzyme superfamily domains (pfam01676) in bacterial proteins; pfam08342\|Metalloenzyme superfamily. This family includes phosphopentomutase and 2,3-bisphosphoglycerate-independent phosphoglycerate mutase. This family is also related to pfam00245; pfam01676	COG1015(4)	PF08342(12)\|PF01676(12)
3416	hypothetical protein YhfU\|Uncharacterized conserved protein [Function unknown]; COG1315,	COG1315(1)
3419	hypothetical protein\|Uncharacterized conserved protein [Function unknown]; COG1556	COG1556(11)	PF02589(1)
3420	putative electron transport protein YkgF\|Uncharacterized conserved protein containing a ferredoxin-like domain [Energy production and conversion]; COG1139\|Uncharacterised ACR, YkgG family COG1556; pfam02589\|Acetyl-CoA synthase (ACS), also known as acetyl-CoA decarbonylase, is found in acetogenic and methanogenic organisms and is responsible for the synthesis and breakdown of acetyl-CoA; cd01916	COG1139(12)\|COG1556(12)	PF02589(12)
3421	hypothetical protein YkgE\|Cysteine-rich domain. This domain is usually found in two copies per protein. It contains up to four conserved cysteines; pfam02754	COG0247(3)	PF02754(12)
3423	hypothetical flavoprotein YgcU\|FAD/FMN-containing dehydrogenases [Energy production and conversion]; COG0277\|FAD binding domain. This family consists of various enzymes that use FAD as a co-factor, most of the enzymes are similar to oxygen oxidoreductase; pfam01565	COG0277(10)	PF01565(8)\|PF02913(8), PF02913(5)
3428	putative lipoprotein\|NlpC/P60 family. The function of this domain is unknown. It is found in several lipoproteins; cl03001	COG0791(3)	PF00877(1)
3429	hypothetical transcriptional regulator\|LysR substrate binding domain. The structure of this domain is known and is similar to the periplasmic binding proteins; pfam03466	COG0583(9)	PF03466(2), PF00126(9)\|PF03466(9)
3432	putative HTH-type transcriptional regulator YbaQ\|Plasmid maintenance system antidote protein [General function prediction only]; COG3093	COG3093(14)	PF01381(1)
3433	putative thiosulfate sulfurtransferase\|Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]; COG2897\|Thiosulfate sulfurtransferase (TST), N-terminal, inactive domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the 1st repeat, which does not contain the catalytically active Cys residue; cd01448	COG2897(11)		SM00450(7)
3434	hypothetical protein YnjB	COG4134(2)
3435	putative ferredoxin-like protein YdhY\|predicted 4Fe-4S ferridoxin-type protein; PRK09898	COG0437(3), COG1142(1)	PF00037(1)
3436	hypothetical protein YdhV (hypothetical aldehyde ferredoxin oxidoreductase)\|predicted oxidoreductase; PRK09849\|Aldehyde ferredoxin oxidoreductase, N-terminal domain. Aldehyde ferredoxin oxidoreductase (AOR) catalyses the reversible oxidation of aldehydes to their corresponding carboxylic acids with their accompanying reduction of the redox protein ferredoxin; pfam02730	COG2414(4)	PF02730(12)\|PF01314(12)
3439	glyceraldehyde 3-phosphate dehydrogenase C\|Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]; COG0057\|S-adenosyl-L-homocysteine hydrolase (AdoHycase) catalyzes the hydrolysis of S-adenosyl-L-homocysteine (AdoHyc) to form adenosine (Ado) and homocysteine (Hcy). The equilibrium lies far on the side of AdoHyc synthesis, but in nature the removal of Ado...; cl09931\|Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain. GAPDH is a tetrameric NAD-binding enzyme involved in glycolysis and glyconeogenesis. C-terminal domain is a mixed alpha/antiparallel beta fold; pfam02800	COG0057(11)	PF02800(11)
3440	putative peptidase YpdF\|predicted peptidase; PRK09795\|Creatinase/Prolidase N-terminal domain. This family includes the N-terminal non-catalytic domains from creatinase and prolidase. The exact function of this domain is uncertain; pfam01321\|Similar to Prolidase and Aminopeptidase P. The members of this subfamily presumably catalyse hydrolysis of Xaa-Pro dipeptides and/or release of any N-terminal amino acid, including proline, that is linked with proline; cd01092	COG0006(2)	PF01321(10)
3441	hypothetical transport protein YjjL\|Sugar phosphate permease [Carbohydrate transport and metabolism]; COG2271\|Major Facilitator Superfamily; pfam07690	COG2271(2)\|COG0477(2), COG2271(9)	PF07690(11)
3450	protein YcgK precursor\|Bacterial pre-peptidase C-terminal domain. This domain is normally found at the C-terminus of secreted bacterial peptidases. They are not present in the active peptidase; pfam04151		PF04151(10)
3457	hypothetical protein YidS precursor\|putative oxidoreductase; PRK11445	COG0644(4)
3459	putative purine permease YgfU\|Xanthine/uracil permeases [Nucleotide transport and metabolism]; COG2233	COG2233(13)	PF00860(1)
3460	xanthine dehydrogenase, FAD binding subunit\|FAD binding domain in molybdopterin dehydrogenase; pfam00941\|CO dehydrogenase flavoprotein C-terminal domain; pfam03450	COG1319(4)	PF00941(13)\|PF03450(13)
3461	xanthine dehydrogenase, molybdenum binding subunit\|Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; pfam01315	COG1529(4)	PF01315(13)\|PF02738(13)
3463	hypothetical ABC transporter permease protein YphD\|Ribose/xylose/arabinose/galactoside ABC-type transport systems, permease components [Carbohydrate transport and metabolism]; COG1172	COG1172(13)	PF02653(1)
3464	protein InaA\|hypothetical protein; PRK09902		PF06293(1)
3468	hypothetical oxidoreductase YdjG\|Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion]; COG0667	COG0667(13)	PF00248(1)
3469	beta-glucuronidase\|beta-D-glucuronidase; PRK10150\|Glycosyl hydrolases family 2, sugar binding domain. This family contains beta-galactosidase, beta-mannosidase and beta-glucuronidase activities and has a jelly-roll fold; pfam02837	COG3250(3)	PF00703(2)\|PF02836(2), PF02837(10)\|PF00703(10)\|PF02836(10)
3470	hypothetical outer membrane porin
3471	putative beta-phosphoglucomutase\|Predicted phosphatase/phosphohexomutase [General function prediction only]; COG0637	COG0637(12)	PF00702(1)
3472	probable zinc protease PqqL\|Predicted Zn-dependent peptidases [General function prediction only]; COG0612\|Insulinase (Peptidase family M16); pfam00675\|Peptidase M16 inactive domain. Peptidase M16 consists of two structurally related domains. One is the active peptidase, whereas the other is inactive. The two domains hold the substrate like a clamp; pfam05193	COG0612(12)	PF00675(12)\|PF05193(12)
3476	hypothetical protein YcdK\|YjgH belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase however there is no sequence similarity and no functional connection; cd02198	COG0251(3)	PF01042(1)
3477	chaperone protein HchA\|Type 1 glutamine amidotransferase (GATase1)-like domain found in Escherichia coli Hsp31 protein (EcHsp31). This group includes proteins similar to EcHsp31. EcHsp31 has chaperone activity; cd03148	COG0693(3)	PF01965(1)
3478	hypothetical protein
3480	hypothetical protein YbcH precursor
3485	hypothetical protein YhfS	COG1167(7)
3486	hypothetical protein Yjdi\|Uncharacterized conserved protein [Function unknown]; COG3592	COG3592(12)	PF06902(1)
3487	hypothetical protein YjdJ\|Predicted acetyltransferase [General function prediction only]; COG2388	COG2388(11)
3490	FimH protein precursor\|FimH, mannose binding. Members of this family adopt a secondary structure consisting of a beta sandwich, with nine strands arranged in two sheets in a Greek key topology; pfam09160\|Fimbrial protein; pfam00419		PF09160(1), PF09160(12)\|PF00419(12)
3492	putative periplasmic protein YaaX
3500	hypothetical ABC transporter permease protein YnjC\|ABC-type uncharacterized transport system, permease component [General function prediction only]; COG4135	COG4135(6)\|COG1177(6), COG4135(1), COG1177(3)\|COG4135(3)
3502	hypothetical protein YjhA precursor\|Oligogalacturonate-specific porin protein (KdgM). This family consists of several bacterial proteins which are homologous to the oligogalacturonate-specific porin protein KdgM from Erwinia chrysanthemi. The phytopathogenic Gram-negative bacteria...; pfam06178		PF06178(13)
3504	FimG protein precursor\|P pilus assembly protein, pilin FimA [Cell motility and secretion / Intracellular trafficking and secretion]; COG3539	COG3539(13)	PF00419(1)
3510	hypothetical sugar kinase YeiC\|YeiC-like sugar kinase. Found in eukaryotes and bacteria, YeiC-like kinase is part of the ribokinase/pfkB sugar kinase superfamily. Its oligomerization state is unknown at this time; cd01941	COG0524(3)	PF00294(1)
3511	hypothetical protein YddU (hypothetical sensor protein)\|cAMP phosphodiesterase; PRK11359\|PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels; cd00130\|Diguanylate-cyclase (DGC) or GGDEF domain: Originally named after a conserved residue pattern, and initially described as domain of unknown function 1 (DUF1); cd01949	COG2202(3), COG2202(2)\|COG2199(2), COG2203(1)	PF08448(1)
3514	hypothetical protein YphG\|Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, pl; cd00189		PF07719(1)
3522	hypothetical protein YegR
3525	glutamate--putrescine ligase\|Glutamine synthetase [Amino acid transport and metabolism]; COG0174\|Glutamine synthetase, catalytic domain; pfam00120\|identified by similarity to SP:P78061; match to protein family HMM PF00120	COG0174(12)	PF00120(12)
3529	hypothetical protein YjjM\|helix_turn_helix gluconate operon transcriptional repressor; smart00345\|Transcriptional regulators [Transcription]; COG1802\|FCD domain. This domain is the C-terminal ligand binding domain of many members of the GntR family; pfam07729	COG2188(2)\|COG1802(2), COG1802(11)	PF00392(1), PF07729(9), PF00392(3)\|PF07729(3)	SM00345(4)
3531	hypothetical protein YigE\|Predicted periplasmic protein [Function unknown]; COG3698	COG3698(11)
3535	putative glucosyl hydrolase precursor\|predicted glycosyl hydrolase; PRK10137
3536	hypothetical transporter YgjI\|Amino acid transporters [Amino acid transport and metabolism]; COG0531	COG0531(12)	PF00324(12)
3538	guanine deaminase\|Guanine deaminase (GDEase). Guanine deaminase is an aminohydrolase responsible for the conversion of guanine to xanthine and ammonia, the first step to utilize guanine as a nitrogen source; cd01303		PF07969(1)
3539	xanthine dehydrogenase iron-sulfur binding subunit\|[2Fe-2S] binding domain; pfam01799	COG2080(4)	PF01799(13)
3541	hypothetical membrane spanning protein\|Domain of unknown function (DUF477). The function of this presumed domain is unknown. It is found in both eukarya and eubacteria; pfam04536	COG1512(6)	PF04536(12)
3543	ABC transporter periplasmic binding protein YphF precursor\|ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]; COG1879	COG1879(10)\|COG4213(10), COG4213(2)\|COG1879(2)	PF00532(2)
3544	hypothetical protein YfaT precursor\|Protein of unknown function (DUF1175). This family consists of several hypothetical bacterial proteins of around 210 residues in length. The function of this family is unknown; pfam06672	COG3234(3)	PF06672(12)
3545	hypothetical protein YfaQ precursor\|Predicted secreted protein [Function unknown]; COG5445	COG5445(12)
3547	hypothetical protein YehQ	COG2801(3)	PF04434(1)
3549	hypothetical protein YdhS\|conserved protein with FAD/NAD(P)-binding domain; PRK09897\|Uncharacterized protein conserved in bacteria [Function unknown]; COG4529	COG4529(13)
3550	hypothetical protein YcgJ precursor\|Fels-1 Prophage Protein-like; pfam05666		PF05666(11)
3551	putative extracellular solute-binding protein YdcS precursor\|Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]; COG0687	COG0687(11)	PF01547(11)
3556	hypothetical membrane protein YliF\|Diguanylate-cyclase (DGC) or GGDEF domain: Originally named after a conserved residue pattern, and initially described as domain of unknown function 1 (DUF1); cd01949	COG2199(1)	PF00990(1)
3558	hypothetical protein YmgD precursor
3560	hypothetical protein YkiA
3563	hypothetical protein YhfT
3565	putative anti-terminator regulatory protein YgcP\|Glycerol-3-phosphate responsive antiterminator. Intracellular glycerol is usually converted to glycerol-3-phosphate in an ATP-requiring phosphorylation reaction catalysed by glycerol kinase (GlpK) glycerol-3-phosphate activates the antiterminator GlpP; pfam04309	COG1954(5)	PF04309(8)
3569	FimF protein precursor\|Fimbrial protein; cl01416	COG3539(3)	PF00419(1)
3577	hypothetical protein YddH\|Conserved protein/domain typically associated with flavoprotein oxygenases, DIM6/NTAB family [General function prediction only]; COG1853	COG1853(10)
3578	glutathione S-transferase\|GST_C family, Class Beta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therape; cd03188	COG0625(8)
3611	Outer-membrane protein yhbX precursor\|Predicted membrane-associated, metal-dependent hydrolase [General function prediction only]; COG2194\|Sulfatase; pfam00884\|Escherichia coli K-12 ortholog: b3173; Escherichia coli O157:H7 ortholog: z4535	COG2194(9)	PF00884(9)
3612	PTS system, N-acetylgalactosamine-specific IID component\|PTS system mannose/fructose/sorbose family IID component; cl01507		PF03613(1)
3613	hypothetical protein YgjJ precursor
3617	PemK-like protein\|toxin of the ChpA-ChpR toxin-antitoxin system, endoribonuclease; PRK09907	COG2337(3)	PF02452(1)
3619	hypothetical protein YehP\|pyruvate carboxylase subunit A; PRK08654\|VWA YIEM type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF); cd01462	COG3552(6)	PF05762(2)
3620	hypothetical protein YehL\|MoxR-like ATPases [General function prediction only]; COG0714\|ATPase family associated with various cellular activities (AAA). This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model; pfam07728	COG0714(11)	PF07728(11)
3623	hypothetical protein YeaI (putative membrane protein)	COG2199(2)	PF00990(1)
3626	hypothetical ABC transporter ATP-binding protein YddA\|ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only]; COG4178\|putative transporter; PRK12369\|Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome; cd03223	COG4178(10)	PF05992(1), PF06472(1)
3627	Hypothetical fimbrial-like protein ydeQ precursor\|FimH, mannose binding. Members of this family adopt a secondary structure consisting of a beta sandwich, with nine strands arranged in two sheets in a Greek key topology; pfam09160\|Fimbrial protein; pfam00419\|Escherichia coli K-12 ortholog: b1502; Escherichia coli O157:H7 ortholog: z2206		PF09160(11)\|PF00419(11)
3650	R-phenyllactate dehydratase activator\|Activator of 2-hydroxyglutaryl-CoA dehydratase (HSP70-class ATPase domain) [Lipid metabolism]; COG1924	COG1924(10)	PF01869(1)
3658	hypothetical oxidoreductase YdbC\|predicted oxidoreductase, NAD(P)-binding; PRK10376		PF00248(1)
3697	hypothetical protein YkgH
3704	hypothetical protein YihF\|Uncharacterized protein conserved in bacteria [Function unknown]; COG5339	COG5339(10)	PF06097(1)
3706	putative galactosamine-6-phosphate isomerase\|GlcN6P_deaminase: Glucosamine-6-phosphate (GlcN6P) deaminase subfamily; GlcN6P deaminase catalyzes the reversible conversion of GlcN6P to D-fructose-6-phosphate (Fru6P) and ammonium; cd01399	COG0363(1)	PF01182(1)
3707	PTS system, N-acetylgalactosamine-specific IIC component 1\|PTS system sorbose-specific iic component; cl01506		PF03609(1)
3708	hypothetical ATP-binding protein YghT\|Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor; cd01672\|Adenylate kinase and related kinases [Nucleotide transport and metabolism]; COG0563	COG0563(6)
3710	hypothetical protein YgfJ\|Uncharacterized MobA-related protein [General function prediction only]; COG2068	COG2068(10)
3711	hypothetical protein YqeC		PF02606(8)
3712	hypothetical protein YqeB\|Xanthine and CO dehydrogenases maturation factor, XdhC/CoxF family [Posttranslational modification, protein turnover, chaperones]; COG1975\|XdhC and CoxI family. This domain is often found in association with an NAD-binding region, related to TrkA-N (pfam02254; personal obs:C. Yeats). XdhC is believed to be involved in the attachment of molybdenum to Xanthine Dehydrogenase; pfam02625\|Predicted deacylase [General function prediction only]; COG3608	COG1975(1), COG1975(9)\|COG3608(9)	PF02625(10)
3713	carbamate kinase-like protein YqeA\|AAK_CK: Carbamate kinase (CK) catalyzes both the ATP-phosphorylation of carbamate and carbamoyl phosphate (CP) utilization with the production of ATP from ADP and CP; cd04235	COG0549(2)	PF00696(1)
3714	hypothetical protein YgeY (hypothetical metallopeptidase)\|Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase and related deacylases [Amino acid transport and metabolism]; COG0624\|peptidase; PRK13004	COG0624(10)	PF07687(1)
3716	hypothetical protein YfaA	COG4685(9)
3717	hypothetical protein YehM
3719	hypothetical protein
3720	binding-protein-dependent transport system inner membrane component\|ABC-type spermidine/putrescine transport system, permease component I [Amino acid transport and metabolism]; COG1176	COG1176(9)	PF00528(1)
3726	probable tonB-dependent receptor YbiL precursor\|predicted iron outer membrane transporter; PRK09840\|TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; cd01347	COG4774(1)	PF07715(1)
3727	hypothetical transcriptional regulator YcgE\|Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain; cd04763	COG0789(1)	PF00376(1)
3728	bacteriophage N4 adsorption protein B\|GSPII_E N-terminal domain. This domain is found at the N-terminus of members of the general secretory system II protein E; pfam05157		PF05157(10)
3746	hypothetical sugar kinase YgcE\|Sugar (pentulose and hexulose) kinases [Carbohydrate transport and metabolism]; COG1070\|FGGY family of carbohydrate kinases, N-terminal domain. This domain adopts a ribonuclease H-like fold and is structurally related to the C-terminal domain; pfam00370	COG1070(9)	PF00370(9)\|PF02782(9)
3747	hypothetical oxidoreductase YgcW\|2-deoxy-D-gluconate 3-dehydrogenase; PRK06935\|S-adenosyl-L-homocysteine hydrolase (AdoHycase) catalyzes the hydrolysis of S-adenosyl-L-homocysteine (AdoHyc) to form adenosine (Ado) and homocysteine (Hcy). The equilibrium lies far on the side of AdoHyc synthesis, but in nature the removal of Ado...; cl09931	COG1028(1)	PF00106(1)
3751	chaperone protein FimC precursor\|P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]; COG3121\|Gram-negative pili assembly chaperone, N-terminal domain. C2 domain-like beta-sandwich fold; pfam00345	COG3121(13)	PF00345(13)\|PF02753(13)
3752	fimbrin-like protein fimI precursor\|Fimbrial protein; pfam00419	COG3539(2)	PF00419(12)
3753	type-1 fimbrial major subunit\|Fimbrial protein; cl01416	COG3539(3)	PF00419(1)
3754	type 1 fimbriae regulatory protein FimE\|FimB and FimE and related proteins, DNA breaking-rejoining enzymes, integrase/recombinases, catalytic domain. This CD includes those proteins similar to E.coli FimE and FimB regulatory proteins and Proteus mirabilis MrpI; cd01197	COG0582(3)	PF00589(1)
3755	type 1 fimbriae regulatory protein FimB\|FimB and FimE and related proteins, DNA breaking-rejoining enzymes, integrase/recombinases, catalytic domain. This CD includes those proteins similar to E.coli FimE and FimB regulatory proteins and Proteus mirabilis MrpI; cd01197	COG0582(3)	PF00589(1)
3756	hypothetical protein YjiM\|Benzoyl-CoA reductase/2-hydroxyglutaryl-CoA dehydratase subunit, BcrC/BadD/HgdB [Amino acid transport and metabolism]; COG1775	COG1775(9)	PF06050(1)
3792	hypothetical protein YkgK\|helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon; smart00421	COG2771(1)	PF00196(1)	SM00421(10)
3793	RNA 2'-phosphotransferase\|RNA 2'-phosphotransferase-like protein; PRK00819	COG1859(6)	PF01885(1)
3796	sorbitol-6-phosphate 2-dehydrogenase\|S-adenosyl-L-homocysteine hydrolase (AdoHycase) catalyzes the hydrolysis of S-adenosyl-L-homocysteine (AdoHyc) to form adenosine (Ado) and homocysteine (Hcy). The equilibrium lies far on the side of AdoHyc synthesis, but in nature the removal of Ado...; cl09931\|3-ketoacyl-(acyl-carrier-protein) reductase; PRK05557	COG1028(4)
3799	hypothetical protein YiiE\|Ribbon-helix-helix protein, copG family. The structure of this protein repressor, which is the shortest reported to date and the first isolated from a plasmid, has a homodimeric ribbon-helix-helix arrangement; pfam01402		PF01402(11)
3800	hypothetical protein YhiM
3801	PTS system, N-acetylgalactosamine-specific IIB component 1\|PTS_IIB, PTS system, Mannose/sorbose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes; cd00001		PF03830(1)
3802	tRNA-binding protein YgjH\|tRNA-binding-domain-containing CsaA-like proteins. CsaA is a molecular chaperone with export related activities. CsaA has a putative tRNA binding activity. The functional unit of CsaA is a homodimer and this domain acts as a dimerization domain; cd02798	COG0073(3)	PF01588(1)
3803	hypothetical ATP-binding protein YghS\|Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor; cd01672
3804	hypothetical ATP-binding protein YghR\|Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor; cd01672
3805	hypothetical protein YghQ (putative polysaccharide biosynthesis protein)\|colanic acid exporter; PRK10459	COG2244(3)	PF01943(3)
3807	glc operon transcriptional activator\|DNA-binding transcriptional dual regulator, glycolate-binding; PRK09990\|Bacterial regulatory proteins, gntR family. This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector-binding/oligomerisation domain; pfam00392	COG2186(2)	PF00392(9)\|PF07729(9)
3808	malate synthase G\|Malate synthase G (MSG), monomeric enzyme present in some bacteria. In general, malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to malyl-CoA , which hydrolyzes to malate and CoA; cd00728	COG2225(2)	PF01274(1)
3810	possible hypoxanthine oxidase XdhD\|fused predicted xanthine/hypoxanthine oxidase: molybdopterin-binding subunit/Fe-S binding subunit; PRK09800\|[2Fe-2S] binding domain; pfam01799\|Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain; pfam01315	COG1529(1)	PF01799(9)\|PF01315(9)\|PF02738(9)
3811	hypothetical protein YgfM\|predicted oxidoreductase; PRK09799\|FAD binding domain in molybdopterin dehydrogenase; pfam00941\|CO dehydrogenase flavoprotein C-terminal domain; pfam03450	COG1319(1)	PF00941(9)\|PF03450(9)
3812	SsnA protein\|Cytosine deaminase and related metal-dependent hydrolases [Nucleotide transport and metabolism / General function prediction only]; COG0402\|TRZ/ATZ family contains enzymes from the atrazine degradation pathway and related hydrolases. Atrazine, a chlorinated herbizide, can be catabolized by a variety of different bacteria; cd01298	COG0402(9)	PF01979(1)
3813	hypothetical hydrolase YgeZ\|dihydropyrimidinase; PRK08323\|D-hydantoinases (D-HYD) also called dihydropyrimidases (DHPase) and related proteins; DHPases are a family of enzymes that catalyze the reversible hydrolytic ring opening of the amide bond in five- or six-membered cyclic diamides, like dihydropyrimidine o; cd01314	COG0044(1)	PF07969(1)
3814	hypothetical protein YgeW\|Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; pfam02729	COG0078(1)	PF02729(9)\|PF00185(9)
3815	hypothetical sigma-54-dependent transcriptional regulator YgeV\|GAF domain. Domain present in phytochromes and cGMP-specific phosphodiesterases; cl00853\|Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]; COG3829\|PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in...; cl02459\|AAA-superfamily of ATPases associated with a wide variety of cellular activities, including membrane fusion, proteolysis, and DNA replication; cd00009\|Bacterial regulatory protein, Fis family; cl01091	COG3829(9)	PF02954(1)
3818	hypothetical protein YfaL precursor (autotransporter domain)\|adhesin; PRK09752\|Pertactin-like passenger domains (virulence factors), C-terminal, subgroup 2, of autotransporter proteins of the type V secretion system of Gram-negative bacteria; cd01344\|Autotransporter beta-domain. Secretion of protein products occurs by a number of different pathways in bacteria. One of these pathways known as the type V pathway was first described for the IgA1 protease; pfam03797	COG3468(1)	PF03797(9)
3821	hypothetical protein\|Putative NADH-flavin reductase [General function prediction only]; COG2910	COG2910(6), COG2910(3)\|COG0702(3)
3826	hypothetical protein YliE\|EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2); cd01948		PF00563(1)
3827	bacteriophage N4 adsorption protein A precursor\|bacteriophage N4 receptor, outer membrane subunit; PRK09782\|Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, pl; cd00189	COG0457(1)
3830	hypothetical protein YahJ\|Bacterial cytosine deaminase and related metal-dependent hydrolases. Cytosine deaminases (CDs) catalyze the deamination of cytosine, producing uracil and ammonia. They play an important role in pyrimidine salvage; cd01293	COG0402(1)	PF07969(1)
3831	carbamate kinase-like protein YahI\|AAK_CK: Carbamate kinase (CK) catalyzes both the ATP-phosphorylation of carbamate and carbamoyl phosphate (CP) utilization with the production of ATP from ADP and CP; cd04235	COG0549(1)	PF00696(1)
3832	hypothetical protein YahE
3833	ankyrin-repeats protein\|ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example); cd00204		PF00023(1)
3834	hypothetical transcriptional regulator YahB\|predicted DNA-binding transcriptional regulator; PRK11074\|Bacterial regulatory helix-turn-helix protein, lysR family; pfam00126\|LysR substrate binding domain. The structure of this domain is known and is similar to the periplasmic binding proteins; pfam03466		PF00126(8)\|PF03466(8)
3835	hypothetical protein (EAL domain)\|helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon; smart00421\|EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2); cd01948	COG2200(1)	PF00563(1)	SM00421(8)
3836	hypothetical protein YagZ precursor
3837	hypothetical protein YagY precursor
3842	lipid A-core:surface polymer ligase WaaL\|Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; COG3307\|O-Antigen Polymerase. This group of bacterial proteins is involved in the synthesis of O-antigen, a lipopolysaccharide found in the outer membrane in gram-negative bacteria; pfam04932	COG3307(4)	PF04932(7)
3892	hypothetical lipoprotein YpdI precursor
3902	putative electron transport protein YgfS\|Fe-S-cluster-containing hydrogenase components 2 [Energy production and conversion]; COG1142	COG1142(9)	PF00037(1)
3903	hypothetical protein YgfK\|predicted oxidoreductase, Fe-S subunit; PRK09853\|Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]; COG0167\|Pyridine nucleotide-disulphide oxidoreductase. This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases. This domain is actually a small NADH binding domain within a larger FAD binding domain; pfam00070	COG0167(8)	PF00070(1)\|PF07992(1), PF00070(7)
3912	hypothetical membrane protein\|Protein of unknown function (DUF1097). This family consists of several bacterial putative membrane proteins; pfam06496		PF06496(8)