Citation
Mela, F. (2011, February 22). Genomic analysis of bacterial mycophagy.
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Table A1. Subset of C. fungivorans genes differentially expressed at T1 GENE_NAMEFUNCTIONFold Change T1Fold Change T2 Cluster ACf_2063acetolactate synthase large subunit9.8up6.9up Cluster ACf_2064NAD-dependent formate dehydrogenase gamma subunit3.4up2.2up Cluster ACf_2065NAD-dependent formate dehydrogenase beta subunit2.5up2.3up Cluster ACf_2066uncharacterized anaerobic dehydrogenase5.3up3.9up Cluster ACf_2067NAD-dependent formate dehydrogenase delta subunit3.7up1.4up Cluster ACf_2070Protein cbbY, plasmid35.2up3.9up Cluster ACf_2071hypothetical protein predicted by Glimmer/Critica23.5up2.8up Cluster ACf_2072Oxalate:formate antiporter9.9up3.3up Cluster ACf_2073fumarylacetoacetate hydrolase family protein6.8up6.3up Cluster ACf_20742-dehydropantoate 2-reductase7.2up3.5up Cluster ACf_2075Monocarboxylate transporter 29.4up4.5up Cluster ACf_2076Putative quinone oxidoreductase2.9up1.4up Cluster ACf_2079acetolactate synthase large subunit14.0up8.5up Cluster ACf_2080putative enzyme13.4up6.1up Cluster ACf_2081PAS4.3up2.7up Cluster ACf_2082putative enzyme2.4up2.2up Cluster ACf_2083Putative HTH-type transcriptional regulator yeaM2.2up1.9up Cluster BCf_35402-hydroxy-3-oxopropionate reductase4.9up5.4up Cluster BCf_3541hydroxypyruvate isomerase3.8up4.2up Cluster BCf_3542glyoxylate carboligase5.3up6.3up Cluster CCf_2982hypothetical protein2.6up18.3up135
GENE_NAMEFUNCTIONFold Change T1Fold Change T2 Cluster CCf_2983hypothetical protein2.7up6.6up Cluster CCf_2984hypothetical protein predicted by Glimmer/Critica13.1up4.7up Cluster CCf_2985formamidase32.8up4.8up Cluster CCf_2986aliphatic amidase55.8up9.3up Cluster CCf_2987ABC-type urea permease17.0up2.0up Cluster CCf_2988ABC-type urea permease22.4up4.1up Cluster CCf_2989ABC-type urea permease48.5up10.7up Cluster CCf_2990ABC-type urea permease22.6up3.2up Cluster CCf_2991ABC-type urea permease70.9up6.8up Cluster CCf_2992two-component hybrid sensor and regulator2.3up3.4up Cluster CCf_2993putative two-component response regulator protein2.3up2.0up Cluster DCf_4054uroporphyrin-III C-methyltransferase5.1up3.1up Cluster DCf_4055Nitrate transport protein nasD.9.5up3.5up Cluster DCf_4056Nitrate transport permease protein nrtB.16.3up6.1up Cluster DCf_4057Nitrate transport protein nrtA.20.8up5.5up Cluster ECf_223probable high affinity nitrate transporter transmembrane protein7.2up7.0up Cluster ECf_224nitrite reductase17.1up5.9up Cluster ECf_225nitrite reductase12.6up5.2up Cluster ECf_226nitrite reductase4.6up2.1up Cluster ECf_227nitrate reductase large subunit6.1up4.5up Cluster FCf_556glutamate synthase2.2up1.6do Cluster FCf_2775Allantoin permease (Allantoin transport protein).5.9up7.0up Cluster GCf_4241Acetyltransferase2.8up1.8up
136
GENE_NAMEFUNCTIONFold Change T1Fold Change T2 Cluster GCf_4242ammonium transporter9.8up1.9up Cluster GCf_4243Nitrogen regulatory protein P-II.5.7up2.5up Cluster HCf_2912ABC-type urea permease11.6up6.8up Cluster HCf_2913ABC-type urea permease6.1up8.0up Cluster HCf_2914ABC-type urea permease6.8up6.3up Cluster HCf_2915ABC-type urea permease6.8up6.3up Cluster HCf_2916ABC-type urea permease9.2up7.0up Cluster ICf_2786GumF protein3.7up15.8up Cluster ICf_2787phosphomannomutase3.3up12.3up Cluster ICf_2788mannose-6-phosphate isomerase / mannose-1-phosphate guanylyltransferase5.5up54.3up Cluster ICf_2789mannose-1-phosphate guanyltransferase8.3up74.6up Cluster ICf_2790GumM protein7.7up50.2up Cluster ICf_2791Hypothetical 55.0 kDa protein in cps region3.8up24.4up Cluster ICf_2792Polypeptide N-acetylgalactosaminyltransferase 15.4up34.8up Cluster ICf_2793cellulase2.5up15.1up Cluster ICf_2794O-acetyltransferase oatA (EC 2.3.1.-).5.3up28.7up Cluster ICf_2795GumH protein4.8up26.0up Cluster ICf_2796hypothetical protein predicted by Glimmer/Critica4.3up27.6up Cluster ICf_2797hypothetical protein4.5up33.8up Cluster ICf_2798lipopolysaccharide biosynthesis7.4up76.2up Cluster ICf_2799EPS I polysaccharide export outer membrane protein epsA precursor.5.1up56.5up Cluster ICf_2800hypothetical protein9.6up100.4up
137
GENE_NAMEFUNCTIONFold Change T1Fold Change T2 Cluster ICf_2801hypothetical protein predicted by Glimmer/Critica5.2up53.4up Cluster ICf_2802Putative colanic biosynthesis UDP-glucose lipid carrier transferase.3.9up16.7up Cluster ICf_2803hypothetical protein3.8up30.1up Cluster JCf_2051Putative polysaccharide export protein wza precursor.11.0up2.9up Cluster JCf_2052Probable low molecular weight protein-tyrosine-phosphatase amsI9.3up2.1up Cluster JCf_2053exopolysaccharide transport protein9.1up3.5up Cluster JCf_2054hypothetical protein predicted by Glimmer/Critica7.7up4.2up Cluster JCf_2055hypothetical protein predicted by Glimmer/Critica6.9up1.9up Cluster JCf_2056hypothetical protein4.6up1.7up Cluster JCf_2057Hypothetical 41.2 kDa protein in cps region5.0up1.2up Cluster JCf_2058hypothetical protein4.6up1.9up Cluster JCf_2059UTP--glucose-1-phosphate uridylyltransferase24.0up2.7up Cluster JCf_2060sugar transferase22.1up2.9up Cluster KCf_1128hypothetical protein predicted by Glimmer/Critica2.4up1.8up Cluster KCf_1129High molecular weight rubredoxin6.5up3.4up Cluster KCf_1130Abhydrolase domain-containing protein 12.6.7up3.9up Cluster KCf_1131fatty acid desaturase9.0up2.9up Cluster KCf_1132Putative polyketide synthase pksM.8.5up3.6up Cluster KCf_1133Acyl-CoA desaturase 14.7up2.1up Cluster KCf_1134Delta-9 acyl-lipid desaturase 2 (EC 1.14.19.-).3.4up2.0up Cluster KCf_1135probable peptide synthetase protein4.7up2.9up Cluster KCf_1136Possible Multidrug resistance protein B.4.5up3.5up
138
GENE_NAMEFUNCTIONFold Change T1Fold Change T2 Cluster KCf_1137hypothetical protein predicted by Glimmer/Critica7.4up3.9up Cluster KCf_1138vanillate O-demethylase oxygenase subunit6.8up2.1up Cluster KCf_1139fatty acid desaturase7.7up1.8up Cluster KCf_1140Protein fixC.6.9up1.6up Cluster KCf_11413-oxoacyl-acyl carrier protein synthase II7.8up2.3up Cluster KCf_1142hypothetical protein predicted by Glimmer/Critica7.4up1.1do Cluster LCf_2276hypothetical protein2.3up2.5up Cluster LCf_2277Hypothetical protein MJ0779.2.8up1.9up Cluster LCf_2278Hypothetical protein MJ0900.2.8up2.3up Cluster LCf_2279hypothetical protein predicted by Glimmer/Critica2.0up1.1do Cluster LCf_2280General secretion pathway protein D precursor.2.2up1.9up Cluster LCf_2281hypothetical protein predicted by Glimmer/Critica2.0up1.2up Cluster LCf_2282hypothetical protein predicted by Glimmer/Critica2.2up1.1up Cluster LCf_2283hypothetical protein predicted by Glimmer/Critica2.6up1.3up Cluster LCf_2284hypothetical protein predicted by Glimmer/Critica2.1up1.0up Cluster MCf_986Flagellar protein flhE precursor.3.3up15.5up Cluster MCf_991CDS2.5up8.5up Cluster MCf_992Flagellar basal-body rod protein flgC.2.4up7.9up Cluster MCf_994CDS2.9up9.5up Cluster MCf_996CDS3.3up11.8up Cluster MCf_997Flagellar L-ring protein precursor2.7up9.2up Cluster MCf_998CDS2.0up7.9up Cluster MCf_1000CDS2.2up10.4up
139
GENE_NAMEFUNCTIONFold Change T1Fold Change T2 Cluster MCf_1003CDS2.5up12.8up Cluster MCf_1004CDS3.4up18.4up Cluster MCf_1005CDS2.3up10.8up Cluster MCf_1006CDS2.1up8.1up Cluster MCf_1007Flagellar fliL protein.2.4up12.1up Cluster MCf_1010hypothetical protein predicted by Glimmer/Critica2.8up17.7up Cluster MCf_1013CDS2.4up10.3up Cluster MCf_1019CDS2.4up10.2up Cluster MCf_1029Transcriptional activator flhD.2.3up2.3up Cluster MCf_1030CDS2.0up1.3up Cluster MCf_1031CDS2.5up3.1up Cluster MCf_1033Probable transcriptional regulator ycf272.1up4.8up Cluster MCf_1034chemotaxis protein CheA2.4up3.5up Cluster MCf_1035Chemotaxis protein cheW.2.7up3.7up Cluster MCf_1036Hypothetical 14.4 kDa protein y4sN.2.1up1.8up Cluster NCf_1047Terminase, ATPase subunit (GpP).2.3up4.2up Cluster NCf_1048Presumed capsid scaffolding protein (GpO).2.3up4.2up Cluster NCf_1050Terminase, endonuclease subunit (GpM).2.2up3.1up Cluster NCf_1054hypothetical protein predicted by Glimmer/Critica2.1up3.4up Cluster NCf_1055Protein lysB.2.5up5.2up Cluster NCf_1058prophage PSPPH02, putative adenine modification methytransferase2.1up4.6up Cluster NCf_1062hypothetical protein2.5up5.6up
140
GENE_NAMEFUNCTIONFold Change T1Fold Change T2 Cluster NCf_1063Tail fiber assembly protein homolog from lambdoid prophage DLP12.2.3up4.8up Cluster NCf_1064Major tail sheath protein (Protein FI).2.1up3.7up Cluster NCf_1068Minor tail protein Gp26.2.4up5.1up Cluster NCf_1073hypothetical protein predicted by Glimmer/Critica2.1up3.7up Cluster NCf_1074hypothetical protein2.3up3.9up Cluster OCf_2102hypothetical protein2.2up4.1up Cluster OCf_2103hypothetical protein2.2up5.7up Cluster OCf_2110hypothetical protein predicted by Glimmer/Critica2.5up5.6up Cluster OCf_2111hypothetical protein predicted by Glimmer/Critica2.9up11.1up Cluster OCf_2112hypothetical protein predicted by Glimmer/Critica2.2up5.2up Cluster OCf_2115hypothetical protein2.4up4.7up Cluster PCf_2031Hypothetical protein3.59up5.39up Cluster PCf_2032IMP dehydrogenase/GMP reductase, DJ-1/PfpI family4.45up12.02up Cluster PCf_2033Hypothetical protein3.66up10.14up Cluster PCf_2034Hypothetical protein2.54up5.44up Cluster PCf_2035Prokaryotic type, Ku70/Ku80 beta-barrel domain; High confidence in function and specificity3.52up6.9up Cluster PCf_2036DNA ligase (EC 6.5.1.1) (Polydeoxyribonucleotide synthase [ATP]), ATP-dependent DNA ligase2.89up4.89up Cluster PCf_2037Haloacid dehalogenase-like hydrolase;Hypothetical protein2.75up2.38up Cluster PCf_2038Hypothetical protein3.39up1.12do Cluster PCf_2039CsbD-like;Conserved hypothetical protein2.98up1.24up Cluster QCf_3498Response regulator receiver;Hypothetical protein2.6up1.04up
141
GENE_NAMEFUNCTIONFold Change T1Fold Change T2 Cluster QCf_3499CheY-like, Response regulator receiver domain; Conserved hypothetical protein4.2up4.96up Cluster QCf_3500Transport-associated;Conserved hypothetical protein7.07up15.3up Cluster QCf_3501Hypothetical protein5.16up11.71up Cluster QCf_3502CsbD-like, CsbD-like;Conserved hypothetical protein3.45up6.98up plasmidpTer331_2hypothetical protein2.3up30.7up plasmidpTer331_3hypothetical protein predicted by Glimmer/Critica2.2up21.6up plasmidpTer331_9Transcriptional repressor protein korB.2.0up22.0up plasmidpTer331_10exported protein2.5up27.6up plasmidpTer331_12T-DNA border endonuclease virD22.1up30.9up plasmidpTer331_15conjugation protein2.1up22.9up plasmidpTer331_1612-oxophytodienoate reductase 32.4up12.4up plasmidpTer331_17Protein virD4.2.4up27.1up plasmidpTer331_18VirB11 protein.2.1up31.2up plasmidpTer331_20Protein virB9 precursor.2.3up28.3up plasmidpTer331_21Protein virB8.2.3up26.7up plasmidpTer331_22hypothetical protein predicted by Glimmer/Critica2.9up25.3up plasmidpTer331_23type IV secretion system protein VirB62.1up20.5up plasmidpTer331_25type IV secretion system protein VirB52.3up22.4up plasmidpTer331_26Protein virB4 precursor.2.1up23.0up plasmidpTer331_32hypothetical protein predicted by Glimmer/Critica2.5up19.5up plasmidpTer331_34hypothetical protein predicted by Glimmer/Critica2.2up21.5up plasmidpTer331_35hypothetical protein predicted by Glimmer/Critica2.5up13.9up
142
Table A2. Genes differentially expressed in A. niger at T1 ORF codeGI-numberBlastP resultsFold change T1Funcat2 category An12g07530145247106strong similarity to hypothetical protein B2J23.80 - Neurospora crassa2.9down01 metabolism An01g11390145230485strong similarity to Sequence 385 from patent WO0100842 - Corynebacterium glutamicum3.4down02 energy An01g08550145229937strong similarity to aminotriazole resistance protein ATR1 - Saccharomyces cerevisiae4.5down20 cellular transport, transport facilitation and transport routes An01g11380145230483strong similarity to Sequence 1 from patent EP0845532 - Pseudomonas sp.5.6down99 unclassified protein An15g05660145251163hypotetical protein2.1up99 unclassified protein An13g03910145248545strong similarity to dihydropyrimidinase PYD2 - Saccharomyces kluyveri2.3up01 metabolism An07g00370145236966strong similarity to allantoin transport protein DAL4 - Saccharomyces cerevisiae2.3up20 cellular transport, transport facilitation and transport routes An12g09920145247586weak similarity to PG123 patent WO9929870-A1 - Porphorymonas gingivalis2.4up99 unclassified protein An13g01520145248085hypothetical protein2.6up99 unclassified protein An07g08770145238608strong similarity to allantoate permease DAL5 - Saccharomyces cerevisiae2.7up20 cellular transport, transport facilitation and transport routes An02g11180145233749hypothetical protein3.1up99 unclassified protein An18g01740145254465strong similarity to aliphatic nitrilase - Rhodococcus rhodochrous3.8up32 cell rescue, defense and virulence An10g00730145256235strong similarity to aliphatic nitrilase - Rhodococcus rhodochrous K223.9up32 cell rescue, defense and virulence An09g01140145241572similarity to patent WO200073470-A2 glucanase ZmGnsN3 - Zea mays4.1up99 unclassified protein An16g01850145251970similarity to blastomyces yeast phase-specific protein 1 bys1 - Ajellomyces dermatitidis5.4up40 cell fate An16g01400145251880similarity to cutinase transcription factor 1 CTF1 alpha - Hematonectria haematococca8.7up11 transcription An12g10200145247636weak similarity to ice nucleation gene inaX - Xanthomonas campestris9.2up99 unclassified protein
143
ORF codeGI-numberBlastP resultsFold change T1Funcat2 category An01g14540145231158strong similarity to the hypothetical protein encoded by An13g01370 - Aspergillus niger9.3up11 transcription An02g01550145231639strong similarity to secreted serine protease 19 kDa CS antigen CS-Ag - Coccidioides immitis9.6up32 cell rescue, defense and virulence An01g06750145229579similarity to hypothetical acetyltransferase SCD72A.11 - Streptomyces coelicolor11.6up99 unclassified protein An01g14550145231160strong similarity to cyanide hydratase Cht - Gloeocercospora sorghi101.8up32 cell rescue, defense and virulence
144
Table A3. Genes differentially expressed in A. niger at T2 ORF codeGI-numberBlastP resultsFold change T2Funcat2 category An12g07750145247154putative GPI anchored protein2.1down99 unclassified protein An08g09420145240813cell wall galactomannoprotein2.1down99 unclassified protein An01g11390145230485strong similarity to Sequence 385 from patent WO0100842 - Corynebacterium glutamicum2.2down02 energy An04g01690145256851similarity to glycoprotein X precursor - equine herpesvirus 12.3down99 unclassified protein An16g06800145252938strong similarity to endoglucanase eglB - Aspergillus niger2.6down01 metabolism An16g05920145252774weak similarity to surface recognition protein PTH11 - Magnaporthe grisea3.0down43 cell type differentiation An01g12170145230720strong similarity to alcohol dehydrogenase B alcB - Aspergillus nidulans3.1down01 metabolism An09g06400145242762strong similarity to chitinase chiA - Aspergillus nidulans3.1down01 metabolism An06g00930145236545hypothetical protein3.5down99 unclassified protein An08g09680145240863strong similarity to 2,4 -dihydroxyacetophenone dioxygenase dad - Alcaligenes sp3.6down99 unclassified protein An16g05910145252772similarity to cholesterol 7alpha-hydroxylase CYP7 - Sus scrofa4.2down01 metabolism An01g11380145230483strong similarity to Sequence 1 from patent EP0845532 - Pseudomonas sp.4.4down99 unclassified protein An06g00900145236541hypothetical protein5.8down99 unclassified protein An06g00940145236547weak similarity to nucleobinding precursor NUCB1 - Homo sapiens9.0down99 unclassified protein An07g05900145238042strong similarity to fructosyl amino acid oxidase faoA - Aspergillus terreus2.0up01 metabolism An02g00560145231426strong similarity to uric acid-xanthine permease uapA - Aspergillus nidulans2.1up20 cellular transpot, transport facilitation and transport routes An03g05630145235587weak similarity to hypothetical protein An11g08750 - Aspergillus niger2.1up99 unclassified protein
145
ORF codeGI-numberBlastP resultsFold change T2Funcat2 category An01g05820145229395strong similarity to homoprotocatechuate operon enzyme hpcE - Escherichia coli2.1up01 metabolism An08g08010145240539similarity to hypothetical protein MmcH - Streptomyces lavendulae2.3up99 unclassified protein An03g01220145234751weak similarity to apyrase of patent GB2261878-A - Shigella flexneri2.3up99 unclassified protein An12g02660145246192hypothetical protein2.5up99 unclassified protein An08e08270trnaRacg2.7up99 unclassified protein An13g03910145248545strong similarity to dihydropyrimidinase PYD2 - Saccharomyces kluyveri3.0up01 metabolism An08g08000145240537strong similarity to maltose transport protein MAL31 - Saccharomyces cerevisiae3.2up20 cellular transpot, transport facilitation and transport routes An04g02760145257196strong similarity to starvation-sensing protein RspA - Escherichia coli3.2up01 metabolism An03g00580145234627strong similarity to the cytochrome P450 protein eln2 SEQ ID NO:1 of patent JP2000152788-A - Coprinus cinereus3.4up01 metabolism An08g03810145239703putative DNA-binding protein3.5up99 unclassified protein An07g04260145237722strong similarity to 3-hydroxy-3-methylglutaryl- coenzyme A synthase HMGS - Saccharomyces cerevisiae3.9up01 metabolism An01g00200145228325strong similarity to succinyl-CoA:3-ketoacid-CoA transferase SCOT - Homo sapiens4.0up01 metabolism An12g09940145247590strong similarity to stearoyl-CoA desaturase Ole1 - Ajellomyces capsulata4.0up01 metabolism An01g07940145229821weak similarity to protein Y38B5A.a - Caenorhabditis elegans4.0up99 unclassified protein An01g10790145230375strong similarity to hypothetical conidiation-specific protein con-10 - Neurospora crassa5.5up43 cell type differentiation An16g07700145253112similarity to dapA - Corynebacterium glutamicum5.8up01 metabolism An04g02220145257019strong similarity to L-serine dehydratase CHA1 - Saccharomyces cerevisiae6.3up01 metabolism
146
ORF codeGI-numberBlastP resultsFold change T2Funcat2 category An11g01330145243202similarity to hypothetical protein encoded by SMc00431 - Sinorhizobium meliloti7.7up99 unclassified protein An16g01400145251880similarity to cutinase transcription factor 1 CTF1 alpha - Hematonectria haematococca22.8up11 transcription An01g06750145229579similarity to hypothetical acetyltransferase SCD72A.11 - Streptomyces coelicolor112.3up99 unclassified protein
147
Table A 4. Collimonas-signature genes GeneD. E. *Gene function Colli20061116_71hypothetical protein Colli20061116_72hypothetical protein Colli20061116_74hypothetical protein Colli20061116_96hypothetical protein Colli20061116_103Probable D-methionine-binding lipoprotein metQ precursor Colli20061116_111hypothetical protein Colli20061116_142hypothetical protein Colli20061116_171hypothetical protein Colli20061116_172hypothetical protein Colli20061116_181Putative ski2-type helicase (EC 3.6.1.-). Colli20061116_183putative aminotransferase Colli20061116_186protein phosphatase 2C Colli20061116_1922;4-dienoyl-CoA reductase Colli20061116_197Glutamate receptor 3.4 precursor Colli20061116_199Glutathione S-transferase D2 Colli20061116_204hypothetical protein Colli20061116_208hypothetical protein predicted by Glimmer/Critica Colli20061116_209Transcriptional activator protein solR. Colli20061116_211hypothetical protein Colli20061116_2163-oxoadipate CoA-transferase subunit B Colli20061116_232peptidyl-dipeptidase Colli20061116_234Protein HI0882. Colli20061116_237hypothetical protein Colli20061116_239YESTranscriptional activator protein czcR. Colli20061116_238YEShypothetical protein Colli20061116_252SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member Colli20061116_265Protein PA3922 precursor. Colli20061116_267Niemann-Pick C1 protein precursor. Colli20061116_268Ycf48-like protein precursor. Colli20061116_270hypothetical protein Colli20061116_275Epoxide hydrolase 2 Colli20061116_276YESPesticin receptor precursor (IRPC).
148
GeneD. E. *Gene function Colli20061116_290ketoglutarate semialdehyde dehydrogenase Colli20061116_291dihydrodipicolinate synthetase Colli20061116_292Uxu operon transcriptional regulator. Colli20061116_294galactarate dehydratase Colli20061116_318carboxymethylenebutenolidase Colli20061116_46250S ribosomal protein L3. Colli20061116_46630S ribosomal protein S19. Colli20061116_47050S ribosomal protein L29. Colli20061116_498putative haloacid dehalogenase-like hydrolase Colli20061116_504Protein cyaY. Colli20061116_511Cell division protein ftsA. Colli20061116_513fimbrial assembly membrane protein Colli20061116_5163-dehydroquinate synthase Colli20061116_517putative phosphohydrolase Colli20061116_543putative thiolase Colli20061116_546UPF0126 membrane protein HI1240. Colli20061116_547Vitamin B12 transporter btuB precursor Colli20061116_550AMP nucleosidase Colli20061116_5532-nitropropane dioxygenase Colli20061116_557glutamate synthase Colli20061116_581hypothetical protein Colli20061116_597Possible multiple antibiotic resistance protein Colli20061116_602enoyl-CoA hydratase Colli20061116_606cytochrome c oxidase; subunit II Colli20061116_607cytochrome c oxidase; subunit I Colli20061116_620RNA polymerase sigma factor rpoD (Sigma-42). Colli20061116_630Inner membrane protein ytfF. Colli20061116_631Arabinose operon regulatory protein. Colli20061116_641D-aminopeptidase (EC 3.4.11.-). Colli20061116_646putative peptide transport system ATP-binding protein Colli20061116_653YESformate dehydrogenase A chain Colli20061116_659peptidyl-tRNA hydrolase Colli20061116_661ribose-phosphate pyrophosphokinase Colli20061116_684Ferric transport system permease protein fbpB.
149
GeneD. E. *Gene function Colli20061116_689phosphonoacetate hydrolase Colli20061116_690aldehyde dehydrogenase Colli20061116_691Uncharacterized protein L432. Colli20061116_700Spermidine/putrescine transport system permease protein potC. Colli20061116_702hypothetical protein Colli20061116_703protein of unknown function DUF502 Colli20061116_708hypothetical protein Colli20061116_709RNA polymerase sigma-E factor (Sigma-24). Colli20061116_736Leu/Ile/Val-binding protein precursor (LIV-BP). Colli20061116_742C4-dicarboxylate transport protein 2. Colli20061116_750indole-3-glycerol phosphate synthase Colli20061116_751anthranilate synthase component II Colli20061116_753anthranilate synthase component I Colli20061116_7542-phosphoglycolate phosphatase Colli20061116_757putative membrane-bound transglycolase Colli20061116_759putative enoyl-CoA hydratase Colli20061116_760Holliday junction ATP-dependent DNA helicase ruvA Colli20061116_761Holliday junction ATP-dependent DNA helicase ruvB Colli20061116_779twin-arginine translocation pathway signal Colli20061116_807Twitching motility protein. Colli20061116_812Hydrogen peroxide-inducible genes activator Colli20061116_813ATP-dependent DNA helicase RecG Colli20061116_814YESS-adenosylmethionine:tRNA ribosyltransferase-isomerase Colli20061116_816queuine tRNA-ribosyltransferase Colli20061116_830Biotin carboxyl carrier protein of acetyl-CoA carboxylase Colli20061116_894hypothetical protein Colli20061116_899Bacitracin resistance protein BacA Colli20061116_902rubredoxin reductase Colli20061116_912Hypothetical protein MJ0900. Colli20061116_922putative membrane protein Colli20061116_933Putative molybdopterin biosynthesis protein MJ0886. Colli20061116_935NAD-dependent formate dehydrogenase gamma subunit Colli20061116_936NAD-dependent formate dehydrogenase beta subunit Colli20061116_983GTP-binding signal recognition particle SRP54; G-domain
150
GeneD. E. *Gene function Colli20061116_1076RNA polymerase sigma factor rpoD (Sigma-70). Colli20061116_1077DNA primase Colli20061116_1082Carboxylate-amine ligase RSc3298 (EC 6.3.-.-). Colli20061116_1085Probable RNA polymerase sigma-D factor. Colli20061116_1087O-sialoglycoprotein endopeptidase Colli20061116_1088Putative ATP-dependent RNA helicase rhlE Colli20061116_1089tRNA synthetases class I domain protein Colli20061116_1090Putative HTH-type transcriptional regulator ydhB. Colli20061116_1091P25 protein (Brefeldin A resistance protein). Colli20061116_1093DNA polymerase III; alpha subunit Colli20061116_1092UPF0176 protein PSPTO_1734. Colli20061116_1099Maf-like protein NE0356. Colli20061116_1105UPF0082 protein MCA1220. Colli20061116_1147xylulokinase Colli20061116_1149maltose/maltodextrin transport ATP-binding protein Colli20061116_1152Maltose transport system permease protein malF. Colli20061116_1153Putative ABC transporter periplasmic-binding protein ycjN precursor. Colli20061116_1156YEShypothetical protein predicted by Glimmer/Critica Colli20061116_1164YEShypothetical protein Colli20061116_1180cadmium-translocating P-type ATPase Colli20061116_1181Sulfide:quinone oxidoreductase; mitochondrial precursor Colli20061116_1182Hydroxyacylglutathione hydrolase cytoplasmic Colli20061116_1184Hypothetical protein ybcJ. Colli20061116_1190spermidine N1-acetyltransferase Colli20061116_1207Hypothetical response regulatory protein VCA0850. Colli20061116_1219acyl-CoA dehydrogenase Colli20061116_122130S ribosomal protein S16. Colli20061116_1223tRNA (guanine-N1)-methyltransferase Colli20061116_1225Probable nudix hydrolase C6G9.05 (EC 3.6.1.-). Colli20061116_1233chorismate binding enzyme Colli20061116_1258Maltose transport system permease protein malG. Colli20061116_1261acyl-CoA dehydrogenase Colli20061116_1267putative acyl-CoA thiolase Colli20061116_1273Protein tolQ.
151
GeneD. E. *Gene function Colli20061116_1274Putative biopolymer transport exbD-like protein 1. Colli20061116_1275tetraacyldisaccharide 4'-kinase Colli20061116_1278adenylate kinase Colli20061116_1280patatin Colli20061116_128850S ribosomal protein L28. Colli20061116_1289DNA repair protein radC homolog. Colli20061116_1292Galactoside transport system permease protein mglC. Colli20061116_1293High-affinity branched-chain amino acid transport system permease protein livM Colli20061116_1326Cation transport protein chaC. Colli20061116_1341succinyl-diaminopimelate desuccinylase Colli20061116_1343Twitching motility protein. Colli20061116_13442;3;4;5-tetrahydropyridine-2;6-dicarboxylate N-succinyltransferase Colli20061116_1349putative membrane protein Colli20061116_1350DNA ligase Colli20061116_1353Glutathione-regulated potassium-efflux system protein kefB Colli20061116_1355Outer membrane pore protein E precursor. Colli20061116_1363ketoglutarate semialdehyde dehydrogenase Colli20061116_1380cyanophycin synthetase Colli20061116_1384YESprotein-P-II uridylyltransferase Colli20061116_1390undecaprenyl pyrophosphate synthetase Colli20061116_13921-deoxy-D-xylulose 5-phosphate reductoisomerase Colli20061116_1400ribonuclease HII Colli20061116_1431YEScytidine/deoxycytidylate deaminase; zinc-binding region Colli20061116_1442L-aspartate oxidase Colli20061116_1444Proline/betaine transporter Colli20061116_1445siderophore biosynthesis protein; putative Colli20061116_1449putative oxidoreductase Colli20061116_1451Putative HTH-type transcriptional regulator ywbI. Colli20061116_1466porphobilinogen deaminase Colli20061116_1469YESProtein hemY. Colli20061116_1480ATP-dependent RNA helicase hrpA homolog Colli20061116_1481deoxycytidine triphosphate deaminase Colli20061116_1487Glucans biosynthesis glucosyltransferase H Colli20061116_1490Probable macrolide-specific efflux protein macA precursor.
152
GeneD. E. *Gene function Colli20061116_1501glucose-6-phosphate 1-dehydrogenase Colli20061116_1503Outer membrane pore protein E precursor. Colli20061116_1509glucose-6-phosphate isomerase Colli20061116_15106-phosphogluconate dehydratase Colli20061116_1521putative membrane-bound lytic murein transglycosylase D precursor Colli20061116_1522hydroxyacylglutathione hydrolase Colli20061116_1539alpha;alpha-trehalose-phosphate synthase (UDP-forming) Colli20061116_1558Multidrug resistance outer membrane protein mdtQ precursor. Colli20061116_1562Translation initiation factor IF-3. Colli20061116_1563YES50S ribosomal protein L20. Colli20061116_1566phenylalanyl-tRNA synthetase; beta subunit Colli20061116_1567Integration host factor beta-subunit (IHF-beta). Colli20061116_1568HTH-type transcriptional regulator mlrA Colli20061116_1574Nodulation protein D. Colli20061116_1578Serine/threonine-protein kinase pkn1 Colli20061116_1580acyl carrier protein phosphodiesterase Colli20061116_15812-isopropylmalate synthase Colli20061116_1585Putative tartrate transporter. Colli20061116_1586hypothetical protein predicted by Glimmer/Critica Colli20061116_1598cystathionine gamma-lyase-like protein Colli20061116_1627hypothetical protein Colli20061116_1628Protein HI0441 (ORFJ). Colli20061116_1636Chaperone protein fimC precursor. Colli20061116_1642probable pyridoxal phosphate aminotransferase protein Colli20061116_1647putative serine/threonine dehydratase Colli20061116_1653NADH dehydrogenase I; D subunit Colli20061116_1662NADH-ubiquinone oxidoreductase; chain M Colli20061116_1663proton-translocating NADH-quinone oxidoreductase; chain N Colli20061116_1672Lipase 1 precursor Colli20061116_1703putative epoxide hydrolase protein Colli20061116_1704hypothetical protein Colli20061116_1705Putative metal-dependent hydrolase DR_0841 Colli20061116_1706Mechanosensory protein 2. Colli20061116_1707Egl nine homolog 3
153
GeneD. E. *Gene function Colli20061116_1708PKHD-type hydroxylase piuC Colli20061116_1709Probable tonB-dependent receptor bfrD precursor Colli20061116_1721Probable multidrug resistance protein Colli20061116_1722YESprobable multidrug resistance transmembrane protein Colli20061116_1726hypothetical protein Colli20061116_1727cytochrome c oxidase subunit II Colli20061116_1729YESProbable cytochrome c oxidase subunit 3 Colli20061116_1730cytochrome c oxidase subunit III Colli20061116_1739dihydrodipicolinate synthase Colli20061116_1740Lipoprotein 34 precursor. Colli20061116_1741YESCoenzyme PQQ synthesis protein B Colli20061116_1742hypothetical protein predicted by Glimmer/Critica Colli20061116_1746DNA mismatch repair protein mutS. Colli20061116_1759hypothetical protein Colli20061116_1788gamma-glutamyltranspeptidase Colli20061116_1811UPF0350 protein YPTB3173. Colli20061116_1815dihydrolipoamide dehydrogenase Colli20061116_1818Hypothetical protein yhcM. Colli20061116_1823exopolyphosphatase Colli20061116_1832Competence lipoprotein comL precursor. Colli20061116_1835probable transmembrane protein Colli20061116_1859Plasma membrane iron permease. Colli20061116_1869branched-chain amino acid transport system ATP-binding protein Colli20061116_1870hypothetical protein predicted by Glimmer/Critica Colli20061116_1884HAM1 protein homolog. Colli20061116_1885putative oxygen-independent coproporphyrinogen III oxidase Colli20061116_1902Protein icc homolog. Colli20061116_1916hypothetical protein Colli20061116_1922HTH-type transcriptional regulator glxA. Colli20061116_19293-isopropylmalate dehydratase small subunit Colli20061116_1931aspartate-semialdehyde dehydrogenase Colli20061116_1932Absent in melanoma 1 protein. Colli20061116_1933tRNA pseudouridine synthase A Colli20061116_1935tryptophan synthase beta chain
154
GeneD. E. *Gene function Colli20061116_1936tryptophan synthase; alpha chain Colli20061116_1939Transient receptor potential protein. Colli20061116_1944HTH-type protein slmA. Colli20061116_19623-oxoacyl-(acyl-carrier-protein) reductase; putative Colli20061116_1972nucleoside-diphosphate kinase Colli20061116_1978UPF0070 protein 1057. Colli20061116_1984putative inner membrane-anchored protein Colli20061116_1985ATP phosphoribosyltransferase regulatory subunit Colli20061116_1988hypothetical protein Y4HM precursor Colli20061116_1991Ribose transport system permease protein rbsC Colli20061116_2017Hypothetical protein RA0937. Colli20061116_2022Probable chromate transport protein. Colli20061116_2027hypothetical protein Colli20061116_2029ABC-type transport system ipermease component Colli20061116_2055YEShypothetical protein predicted by Glimmer/Critica Colli20061116_2062putative enoyl-CoA hydratase/isomerase family protein Colli20061116_2064YESNAD-dependent formate dehydrogenase gamma subunit Colli20061116_2065YESNAD-dependent formate dehydrogenase beta subunit Colli20061116_2085glycine dehydrogenase Colli20061116_2086glycine cleavage system T protein Colli20061116_2088serine O-acetyltransferase Colli20061116_2122hypothetical protein Colli20061116_2129YESTetR-family transcriptional regulator Colli20061116_2132Putative thiosulfate sulfurtransferase Colli20061116_2133hypothetical protein Colli20061116_2136lipoprotein; putative Colli20061116_21403-oxoadipate enol-lactone hydrolase / 4-carboxymuconolactone decarboxylase Colli20061116_21413-carboxy-cis;cis-muconate cycloisomerase Colli20061116_2143protocatechuate 3;4-dioxygenase; beta subunit Colli20061116_2144Acetate operon repressor. Colli20061116_21474-hydroxyphenylpyruvate dioxygenase Colli20061116_21494-hydroxyphenylpyruvate dioxygenase Colli20061116_2153Shikimate transporter. Colli20061116_2159hypothetical protein predicted by Glimmer/Critica
155
GeneD. E. *Gene function Colli20061116_2161putative oxidoreductase Colli20061116_2165ABC transporter; nucleotide binding/ATPase protein Colli20061116_2168Proline-rich protein 6. Colli20061116_2173hypothetical protein Colli20061116_2181Inner membrane ABC transporter permease protein yehW. Colli20061116_2184Hypothetical protein yehZ precursor. Colli20061116_2206malate dehydrogenase (acceptor) Colli20061116_2218NADH dehydrogenase Colli20061116_2223probable transporter lipoprotein transmembrane Colli20061116_2224Antibiotic efflux pump periplasmic linker protein arpA precursor. Colli20061116_2232GntR family regulatory protein Colli20061116_2238Leu/Ile/Val-binding protein precursor (LIV-BP). Colli20061116_2254aldehyde dehydrogenase Colli20061116_2261sensor histidine kinase Colli20061116_2265cytochrome o ubiquinol oxidase; subunit I Colli20061116_2274short chain dehydrogenase Colli20061116_2278YESHypothetical protein MJ0900. Colli20061116_2289Hypothetical protein yaiT precursor. Colli20061116_2301UPF0194 membrane protein ybhG precursor. Colli20061116_2309Membrane transporter of Superfamily (MFS) Colli20061116_2312C4-dicarboxylate transport sensor protein Colli20061116_2316peptidase; M24 family protein Colli20061116_2321Inner membrane protein yebS. Colli20061116_2322Paraquat-inducible protein A. Colli20061116_2332aldehyde dehydrogenase Colli20061116_2340cardiolipin synthase Colli20061116_2351Protein gvpE 1. Colli20061116_2357L-ornithine 5-monooxygenase Colli20061116_2372Molybdopterin-converting factor subunit 1 Colli20061116_2374threonine synthase Colli20061116_2378(p)ppGpp synthetase I (GTP pyrophosphokinase); SpoT/RelA Colli20061116_2382hypothetical protein predicted by Glimmer/Critica Colli20061116_2392YESGalactoside transport system permease protein mglC homolog. Colli20061116_2398aspartokinase
156
GeneD. E. *Gene function Colli20061116_2401DNA-3-methyladenine glycosylase Colli20061116_2402cysteinyl-tRNA synthetase Colli20061116_2404peptidyl-prolyl cis-trans isomerase B Colli20061116_2407serine O-acetyltransferase Colli20061116_2424Hypothetical protein yieF. Colli20061116_2425putative redox protein Colli20061116_2433Chemotaxis protein cheW. Colli20061116_2434sensor histidine kinase/response regulator Colli20061116_2435protein-glutamate methylesterase Colli20061116_2451urocanate hydratase Colli20061116_2456High-affinity branched-chain amino acid transport ATP-binding protein livG Colli20061116_2463putative peptidyl-prolyl cis-trans isomerase Colli20061116_2476Outer membrane usher protein fimD precursor. Colli20061116_2478malate synthase A Colli20061116_2479Probable HTH-type transcriptional regulator ltrA. Colli20061116_2484DNA repair protein radA homolog Colli20061116_2485alanine racemase Colli20061116_2488hypothetical protein Colli20061116_2496acyl-CoA thioesterase I precursor Colli20061116_2505Multidrug resistance protein mdtC Colli20061116_2508putative phytoene synthase Colli20061116_2509YESPhytoene dehydrogenase; chloroplast precursor Colli20061116_2510L-lactate dehydrogenase Colli20061116_2511Ankyrin-3 (ANK-3) (Ankyrin-G). Colli20061116_2512putative deoxyribonuclease Colli20061116_2513ribonuclease PH Colli20061116_2521glycosyl transferase; family 39 Colli20061116_2531Taurine transport system permease protein tauC. Colli20061116_2533YESProtein NMT1 homolog Colli20061116_2538Probable Multidrug resistance translocase Colli20061116_254530S ribosomal protein S18. Colli20061116_2554sensory transduction histidine kinases Colli20061116_2564carbamoyl-phosphate synthase; small subunit Colli20061116_2570Phosphate transport system protein phoU.
157
GeneD. E. *Gene function Colli20061116_2575polyphosphate kinase Colli20061116_25762;3-bisphosphoglycerate-dependent phosphoglycerate mutase Colli20061116_2590hypothetical protein Colli20061116_2613Putative HTH-type transcriptional regulator ydcN. Colli20061116_2644putative carboxy-terminal processing protease precursor Colli20061116_2652Probable multidrug resistance protein mdtA precursor Colli20061116_2654Toluene efflux pump outer membrane protein ttgF precursor. Colli20061116_2655transporter; putative Colli20061116_2662Hydrogen peroxide-inducible genes activator. Colli20061116_2670ABC-type sugar transport system; ATPase component Colli20061116_2671Predicted N-acetylglucosamine kinase Colli20061116_2675Hypothetical protein yddH. Colli20061116_26763-oxoacyl- Colli20061116_2680hypothetical protein Colli20061116_2682DNA polymerase III alpha subunit Colli20061116_2685hypothetical protein; INTERPRO suggestion: probable haloacid dehalogenase-like hydrolase Colli20061116_2713hypothetical protein predicted by Glimmer/Critica Colli20061116_2747seryl-tRNA synthetase Colli20061116_2762oxidoreductase; FAD-binding Colli20061116_2771Protein fecR. Colli20061116_2798YESlipopolysaccharide biosynthesis Colli20061116_2808Probable NADPH:quinone oxidoreductase 2 Colli20061116_2812Nitrilotriacetate monooxygenase component A Colli20061116_2817hypothetical protein Colli20061116_2827cytochrome d terminal oxidase; polypeptide subunit I Colli20061116_2838putative ABC transport protein; substrate-binding component Colli20061116_2845Multidrug resistance protein B. Colli20061116_2847ABC transporter ATP-binding protein Colli20061116_2851Hypothetical protein yraQ. Colli20061116_2866xanthine dehydrogenase Colli20061116_2874Hypothetical ABC transporter ATP-binding protein MJ0412. Colli20061116_2875Pyrimidine precursor biosynthesis enzyme THI13. Colli20061116_2884nitrilotriacetate monooxygenase Colli20061116_2888putative amidase
158
GeneD. E. *Gene function Colli20061116_2913YESHigh-affinity branched-chain amino acid transport system permease protein livH Colli20061116_2914YESHigh-affinity branched-chain amino acid transport system permease protein livM Colli20061116_2915YESHigh-affinity branched-chain amino acid transport ATP-binding protein livG Colli20061116_2917Urease accessory protein ureD. Colli20061116_2918urease; gamma subunit Colli20061116_2931putative holo- Colli20061116_2933DNA repair protein recO (Recombination protein O). Colli20061116_2935ribonuclease III Colli20061116_29443-oxoacyl- Colli20061116_29463-oxoacyl- Colli20061116_2968chorismate synthase Colli20061116_2996argininosuccinate lyase Colli20061116_2999High-affinity branched-chain amino acid transport system permease protein livM Colli20061116_3004putative lipoprotein Colli20061116_3007hypothetical protein predicted by Glimmer/Critica Colli20061116_3011YESHTH-type transcriptional repressor purR Colli20061116_3013putative ATP-binding protein of ribose ABC transport system Colli20061116_3015Protein pmbA. Colli20061116_3019probable carboxylesterase Colli20061116_3022copper-translocating P-type ATPase Colli20061116_3033amino-acid N-acetyltransferase (ArgA) Colli20061116_3034Probable Fe(2+)-trafficking protein. Colli20061116_3035putative zinc protease Colli20061116_3044N-acetylglucosamine-6-phosphate deacetylase Colli20061116_3084hypothetical protein Colli20061116_3090histidine ammonia-lyase Colli20061116_3094Transcriptional regulator modE. Colli20061116_3095aliphatic sulfonates ABC transporter; ATP-binding protein Colli20061116_3096Putative aliphatic sulfonates transport permease protein ssuC. Colli20061116_3100NADH-dependent FMN reductase Colli20061116_3101Thiosulfate-binding protein precursor. Colli20061116_3103Membrane protein mosC. Colli20061116_3111Histone deacetylase 1 (HD1). Colli20061116_3112hypothetical protein
159
GeneD. E. *Gene function Colli20061116_3118Protein nirF. Colli20061116_3119peptidylprolyl isomerase Colli20061116_31222-hydroxyacid dehydrogenase Colli20061116_3132putative lipoprotein Colli20061116_3133tRNA-processing ribonuclease BN Colli20061116_3179RecJ exonuclease Colli20061116_3190Heat shock 70 kDa protein (HSP70). Colli20061116_3193Co-chaperone protein hscB homolog. Colli20061116_3195Iron sulfur cluster assembly protein 1; mitochondrial precursor Colli20061116_3201UvrABC system protein B Colli20061116_3202aromatic-amino-acid transaminase Colli20061116_3222xylose isomerase Colli20061116_3230Probable HTH-type transcriptional regulator ltrA. Colli20061116_3247Inner membrane ABC transporter permease protein yddR. Colli20061116_3253HTH-type transcriptional regulator pecT Colli20061116_3265Putative HTH-type transcriptional regulator PH1519. Colli20061116_3266YEShypothetical protein Colli20061116_3267serine protease Colli20061116_3271Putative HTH-type transcriptional regulator ygiP. Colli20061116_3272Multidrug resistance protein mdtM. Colli20061116_3275hypothetical protein Colli20061116_3285homogentisate 1;2-dioxygenase Colli20061116_32864-hydroxybenzoate transporter. Colli20061116_3288Protein emrE Colli20061116_3291ATP-dependent DNA ligase Colli20061116_3293exonuclease Colli20061116_3294STE24 endopeptidase Colli20061116_3297argininosuccinate synthase Colli20061116_3298UPF0345 protein MCA1207. Colli20061116_3314Protein tldD homolog. Colli20061116_3316Hypothetical protein yhdP precursor. Colli20061116_3324riboflavin biosynthesis protein Colli20061116_3326lipoprotein signal peptidase Colli20061116_3333Cold shock-like protein cspA.
160
GeneD. E. *Gene function Colli20061116_3335pseudouridine synthase; Rsu Colli20061116_3340Virulence factor mviN homolog. Colli20061116_3343ABC transporter related Colli20061116_3344Hypothetical signaling protein CC0091. Colli20061116_3367Activator of 90 kDa heat shock protein ATPase homolog 1 Colli20061116_3379thermolabile hemolysin Colli20061116_3421Hypothetical transport protein yetK. Colli20061116_3423fumarate hydratase; class I Colli20061116_3464glucose-methanol-choline oxidoreductase Colli20061116_3472Fimbrial protein precursor Colli20061116_3473YESprotein of unknown function DUF193 Colli20061116_3475YESPesticin receptor precursor (IRPC) (IPR65). Colli20061116_3476putative oxidoreductase Colli20061116_3478Protein tolQ. Colli20061116_3479Biopolymer transport exbD1 protein. Colli20061116_3482Peptidoglycan-associated lipoprotein precursor. Colli20061116_3483Aspartyl/asparaginyl beta-hydroxylase Colli20061116_3484Hypothetical protein sll1773. Colli20061116_3487hypothetical protein Colli20061116_3488Adenine deaminase Colli20061116_3489Hypothetical protein yaiC. Colli20061116_3497Virulence sensor protein bvgS precursor Colli20061116_3503putative glutamate synthase Colli20061116_3504maleylacetoacetate isomerase Colli20061116_3505hypothetical protein Colli20061116_3506probable aminotransferase Colli20061116_3507N utilization substance protein B homolog Colli20061116_35086;7-dimethyl-8-ribityllumazine synthase Colli20061116_35093;4-dihydroxy-2-butanone 4-phosphate synthase Colli20061116_3510tRNA-dihydrouridine synthase A Colli20061116_3513omega-amino acid-pyruvate aminotransferase Colli20061116_3514GTP-binding protein typA/BipA Colli20061116_3515tRNA pseudouridine synthase B Colli20061116_3516Ribosome-binding factor A.
161
GeneD. E. *Gene function Colli20061116_3517Translation initiation factor IF-2. Colli20061116_3518Transcription elongation protein nusA. Colli20061116_3519UPF0090 protein Bcep18194_A4639. Colli20061116_3520putative ribosomal large subunit pseudouridine synthase B Colli20061116_3528hypothetical protein Colli20061116_3529Nodulation protein D 1. Colli20061116_3531N-carbamyl-L-amino acid amidohydrolase Colli20061116_3532chlorohydrolase family protein Colli20061116_3538pyruvate kinase Colli20061116_3540YES2-hydroxy-3-oxopropionate reductase Colli20061116_3557Segregation and condensation protein A. Colli20061116_3576DnaJ domain protein Colli20061116_3580hypothetical protein Colli20061116_3598cytosol aminopeptidase Colli20061116_3605hypothetical protein Colli20061116_3623Leucine-specific-binding protein precursor Colli20061116_3635dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex Colli20061116_3636pyruvate dehydrogenase E1 component Colli20061116_3644Putative auxin efflux carrier component 8 Colli20061116_3645Putative electron transport protein yjeS. Colli20061116_3647N-acetylmuramoyl-L-alanine amidase Colli20061116_3688CDK5RAP1-like protein. Colli20061116_3689YESPhoH-like protein. Colli20061116_3691hypothetical protein Colli20061116_3694Magnesium and cobalt efflux protein corC. Colli20061116_3700hypothetical protein Colli20061116_3707aminoglycoside phosphotransferase Colli20061116_3714aspartate 1-decarboxylase precursor Colli20061116_3720putative antibiotic resistance protein Colli20061116_3722p-hydroxybenzoic acid efflux pump subunit aaeA Colli20061116_3723High affinity sulfate transporter 2. Colli20061116_3728phosphodiesterase/alkaline phosphatase D Colli20061116_3732putative membrane protein Colli20061116_3737Leucine-; isoleucine-; valine-; threonine-; and alanine-binding protein precursor
162
GeneD. E. *Gene function Colli20061116_3738D-isomer specific 2-hydroxyacid dehydrogenase family protein Colli20061116_3742conserved hypothetical protein similar to putative glucosaminyltransferase Colli20061116_3744hypothetical protein Colli20061116_3745putative outer membrane protein Colli20061116_3779phosphatidylglycerophosphatase A Colli20061116_380410 kDa chaperonin (Protein Cpn10) (groES protein). Colli20061116_3807Probable D-methionine transport system permease protein metI. Colli20061116_3813Nucleolar GTP-binding protein 2. Colli20061116_3814Histone deacetylase 1 (HD1). Colli20061116_3822hypothetical protein predicted by Glimmer/Critica Colli20061116_3823cysteine synthase B Colli20061116_3832Probable global transcription activator SNF2L1 Colli20061116_3836chorismate mutase/prephenate dehydratase Colli20061116_3837phosphoserine aminotransferase Colli20061116_3841ubiquinone biosynthesis O-methyltransferase Colli20061116_3853Spermidine/putrescine transport system permease protein potC. Colli20061116_3864Outer membrane protein W precursor. Colli20061116_3865Hypothetical protein ywlC. Colli20061116_3866phosphoribosylaminoimidazole carboxylase; ATPase subunit Colli20061116_3867phosphoribosylaminoimidazole carboxylase catalytic subunit Colli20061116_3868phosphoribosylaminoimidazole-succinocarboxamide synthase Colli20061116_3874hypothetical protein Colli20061116_3884succinyl-CoA ligase; alpha subunit Colli20061116_3892HTH-type transcriptional activator ampR. Colli20061116_3898acyl-CoA dehydrogenase family protein Colli20061116_3910hypothetical protein Colli20061116_39203-methyl-2-oxobutanoate hydroxymethyltransferase Colli20061116_3924Phosphoserine phosphatase Colli20061116_3940Outer membrane lipoprotein omlA precursor. Colli20061116_3951YEShypothetical protein predicted by Glimmer/Critica Colli20061116_3959Protein piccolo Colli20061116_3965Nif-specific regulatory protein. Colli20061116_3970signal recognition particle protein Colli20061116_3973alkaline phosphatase precursor
163
GeneD. E. *Gene function Colli20061116_3976prolyl-tRNA synthetase Colli20061116_398150S ribosomal protein L27. Colli20061116_3991Cell division topological specificity factor. Colli20061116_4011pyrophosphatase; NUDIX family Colli20061116_4012hypothetical protein Colli20061116_4018Hybrid peroxiredoxin hyPrx5 Colli20061116_4020Cell division protein ftsA. Colli20061116_4024UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N- acetylglucosamine transferase Colli20061116_4038Phytochrome-like protein cph2 Colli20061116_4052putative ubiquinone biosynthesis protein Colli20061116_4053hypothetical protein Colli20061116_4054YESuroporphyrin-III C-methyltransferase Colli20061116_4066Hydrogen peroxide-inducible genes activator Colli20061116_4079Oligopeptide transport ATP-binding protein appF. Colli20061116_4082Inner membrane ABC transporter permease protein yddR. Colli20061116_4087Biotin synthesis protein bioC. Colli20061116_4100phenylalanine-4-hydroxylase Colli20061116_4138Putative general secretion pathway protein H precursor Colli20061116_4154Leucine-specific-binding protein precursor Colli20061116_4156Hypothetical protein TP0675. Colli20061116_4166probable UDP-sugar diphosphatase Colli20061116_4171hypothetical protein Colli20061116_4184aspartate aminotransferase Colli20061116_4185topB2; DNA topoisomerase III [EC:5.99.1.2] Colli20061116_4188hypothetical protein Colli20061116_4201Rod shape-determining protein mreB. Colli20061116_4219Leucine-responsive regulatory protein. Colli20061116_4220YESornithine aminotransferase Colli20061116_4221YESArginine deiminase Colli20061116_42225-methyltetrahydrofolate--homocysteine methyltransferase Colli20061116_4225Inner membrane protein yicO. Colli20061116_4236phosphoenolpyruvate-protein phosphotransferase Colli20061116_4255UPF0102 protein PSPTO_4420.
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GeneD. E. *Gene function Colli20061116_4265putative membrane protein Colli20061116_4266putative membrane protein Colli20061116_4267hypothetical protein Colli20061116_4278UPF0250 protein RSc0326. Colli20061116_4279probable class IV aminotransferase Colli20061116_4303hypothetical protein Colli20061116_4304Heat shock 70 kDa protein (HSP70). Colli20061116_4305Chloride channel protein; skeletal muscle Colli20061116_4307Inner membrane protein yphA. Colli20061116_4310Leucine-responsive regulatory protein. Colli20061116_4313succinyl-diaminopimelate desuccinylase Colli20061116_4320L-asparaginase Colli20061116_4329Transcriptional regulatory protein srrA Colli20061116_4336biotin carboxylase subunit of acetyl-CoA carboxylase Colli20061116_4349acetyl-CoA acetyltransferase Colli20061116_4350isocitrate dehydrogenase kinase/phosphatase Colli20061116_4351serine dehydratase-like Colli20061116_4352isovaleryl-CoA dehydrogenase Colli20061116_4353HTH-type transcriptional regulator cueR Colli20061116_4354YESHypothetical protein yqjP. Colli20061116_4355Arginine exporter protein argO. Colli20061116_4357thiol:disulfide interchange protein Colli20061116_4369Hypothetical protein ybdD. Colli20061116_4370Carbon starvation protein A. Colli20061116_4385Cytochrome c6 precursor Colli20061116_4392Antigen 43 precursor Colli20061116_4460Exu regulon transcriptional regulator. Colli20061116_4461Primosomal protein N' Colli20061116_4463HTH-type transcriptional regulator metR. Colli20061116_4464agmatinase Colli20061116_4467Probable sugar efflux transporter. Colli20061116_4468succinate-semialdehyde dehydrogenase Colli20061116_4481YESATP synthase F1; beta subunit Colli20061116_4482ATP synthase F1; gamma subunit
165
GeneD. E. *Gene function Colli20061116_4484ATP synthase delta chain Colli20061116_4485ATP synthase B chain Colli20061116_4486ATP synthase c chain Colli20061116_4488putative ATP synthase protein I Colli20061116_4490Probable chromosome partitioning protein parB. Colli20061116_4491Chromosome partitioning protein parA. Colli20061116_4494tRNA uridine 5-carboxymethylaminomethyl modification enzyme gidA Colli20061116_4496High-affinity branched-chain amino acid transport system permease protein livM Colli20061116_4497High-affinity branched-chain amino acid transport system permease protein livM Colli20061116_4498putative exported protein Colli20061116_4499ABC transporter ATP-binding protein Colli20061116_4500ABC transporter related Colli20061116_4501oxidoreductase; GMC family Colli20061116_4505Hypothetical protein yhjG. Colli20061116_4507proline dehydrogenase Colli20061116_4511gluconate kinase Colli20061116_4512Nodulation protein D 1. Colli20061116_4515phosphoenolpyruvate carboxykinase (GTP) Colli20061116_4517hypothetical protein predicted by Glimmer/Critica Colli20061116_4519glucose-methanol-choline oxidoreductase Colli20061116_4520cytochrome c; class I Colli20061116_4521asparaginase Colli20061116_4522peptidyl-dipeptidase Colli20061116_4523YESMajor outer membrane protein P.IB precursor Colli20061116_4526YESProtein HI0131 precursor. Colli20061116_4529putative two-component system sensor kinase Colli20061116_4538tRNA modification GTPase trmE. Colli20061116_4541Ribonuclease P protein component * Genes differentially expressed when C. fungivorans Ter331 was confronted with the fungus A. niger
166
Table A5. Gene clusters differentially expressed in C. fungivorans Ter331 during in vitro confrontation with A. niger. Present, x; absent, GENE NAMEFUNCTIONFold change T1
Fold change T2
Ter 6Ter1 0Ter1 4Ter9 1 Cluster ACf_2063acetolactate synthase large subunit9.8up6.9upx-xx Cluster ACf_2064NAD-dependent formate dehydrogenase gamma subunit3.4up2.2upxxxx Cluster ACf_2065NAD-dependent formate dehydrogenase beta subunit2.5up2.3upxxxx Cluster ACf_2066uncharacterized anaerobic dehydrogenase5.3up3.9upxxx- Cluster ACf_2067NAD-dependent formate dehydrogenase delta subunit3.7up1.4upxxx- Cluster ACf_2070Protein cbbY, plasmid35.2up3.9upx-x- Cluster ACf_2071hypothetical protein predicted by Glimmer/Critica23.5up2.8upNANANANA Cluster ACf_2072Oxalate:formate antiporter9.9up3.3upx-x- Cluster ACf_2073fumarylacetoacetate hydrolase family protein6.8up6.3upx-xx Cluster ACf_20742-dehydropantoate 2-reductase7.2up3.5upx-xx Cluster ACf_2075Monocarboxylate transporter 29.4up4.5upx-xx Cluster ACf_2076Putative quinone oxidoreductase2.9up1.4up--x- Cluster ACf_2079acetolactate synthase large subunit14up8.5upx-xx Cluster ACf_2080putative enzyme13.4up6.1upx-xx Cluster ACf_2081PAS4.3up2.7upxxxx Cluster ACf_2082putative enzyme2.4up2.2upx-xx Cluster ACf_2083Putative HTH-type transcriptional regulator yeaM2.2up1.9upxxxx Cluster BCf_35402-hydroxy-3-oxopropionate reductase4.9up5.4upxxxx Cluster BCf_3541hydroxypyruvate isomerase3.8up4.2upxxxx Cluster BCf_3542glyoxylate carboligase5.3up6.3upxxxx Cluster CCf_2982hypothetical protein2.6up18.3upxxxx Cluster CCf_2983hypothetical protein2.7up6.6upxxxx Cluster CCf_2984hypothetical protein predicted by Glimmer/Critica13.1up4.7upx-x- Cluster CCf_2985formamidase32.8up4.8upx-x- Cluster CCf_2986aliphatic amidase55.8up9.3upx-x- Cluster CCf_2987ABC-type urea permease17up2upxxx-
167
GENE NAMEFUNCTIONFold change T1
Fold change T2
Ter 6Ter1 0Ter1 4Ter9 1 Cluster CCf_2988ABC-type urea permease22.4up4.1upx-xx Cluster CCf_2989ABC-type urea permease48.5up10.7upx-x- Cluster CCf_2990ABC-type urea permease22.6up3.2upx-x- Cluster CCf_2991ABC-type urea permease70.9up6.8upx-x- Cluster CCf_2992two-component hybrid sensor and regulator2.3up3.4upx-x- Cluster CCf_2993putative two-component response regulator protein2.3up2upxxx- Cluster DCf_4054uroporphyrin-III C-methyltransferase5.1up3.1upxxxx Cluster DCf_4055Nitrate transport protein nasD.9.5up3.5upxxxx Cluster DCf_4056Nitrate transport permease protein nrtB.16.3up6.1upxxxx Cluster DCf_4057Nitrate transport protein nrtA.20.8up5.5upxxxx Cluster ECf_223probable high affinity nitrate transporter transmembrane protein7.2up7up-xxx Cluster ECf_224nitrite reductase17.1up5.9upxxxx Cluster ECf_225nitrite reductase12.6up5.2upxxxx Cluster ECf_226nitrite reductase4.6up2.1upxxxx Cluster ECf_227nitrate reductase large subunit6.1up4.5upxxxx Cluster FCf_556glutamate synthase2.2up1.6downxxxx Cluster FCf_2775Allantoin permease (Allantoin transport protein).5.9up7upxxxx Cluster GCf_4241Acetyltransferase2.8up1.8upxxxx Cluster GCf_4242ammonium transporter9.8up1.9upxxxx Cluster GCf_4243Nitrogen regulatory protein P-II.5.7up2.5upx-xx Cluster HCf_2912ABC-type urea permease11.6up6.8upxxxx Cluster HCf_2913ABC-type urea permease6.1up8upxxxx Cluster HCf_2914ABC-type urea permease6.8up6.3upxxxx Cluster HCf_2915ABC-type urea permease6.8up6.3upxxxx Cluster HCf_2916ABC-type urea permease9.2up7upxxx- Cluster ICf_2786GumF protein3.7up15.8up--x-
168
GENE NAMEFUNCTIONFold change T1
Fold change T2
Ter 6Ter1 0Ter1 4Ter9 1 Cluster ICf_2787phosphomannomutase3.3up12.3up-xx- Cluster ICf_2788mannose-6-phosphate isomerase / mannose-1-phosphate guanylyltransferase5.5up54.3upxxxx Cluster ICf_2789mannose-1-phosphate guanyltransferase8.3up74.6upxxxx Cluster ICf_2790GumM protein7.7up50.2upx-xx Cluster ICf_2791Hypothetical 55.0 kDa protein in cps region3.8up24.4upxxx- Cluster ICf_2792Polypeptide N-acetylgalactosaminyltransferase 15.4up34.8upx-xx Cluster ICf_2793cellulase2.5up15.1upxxxx Cluster ICf_2794O-acetyltransferase oatA (EC 2.3.1.-).5.3up28.7upx-x- Cluster ICf_2795GumH protein4.8up26upxxxx Cluster ICf_2796hypothetical protein predicted by Glimmer/Critica4.3up27.6upx-xx Cluster ICf_2797hypothetical protein4.5up33.8upxxxx Cluster ICf_2798lipopolysaccharide biosynthesis7.4up76.2upxxxx Cluster ICf_2799EPS I polysaccharide export outer membrane protein epsA precursor.5.1up56.5upxxxx Cluster ICf_2800hypothetical protein9.6up100.4upx-xx Cluster ICf_2801hypothetical protein predicted by Glimmer/Critica5.2up53.4upx-xx Cluster ICf_2802Putative colanic biosynthesis UDP-glucose lipid carrier transferase.3.9up16.7upxxxx Cluster ICf_2803hypothetical protein3.8up30.1upx-xx Cluster JCf_2051Putative polysaccharide export protein wza precursor.11up2.9upx-x- Cluster JCf_2052Probable low molecular weight protein-tyrosine-phosphatase amsI9.3up2.1upx-x- Cluster JCf_2053exopolysaccharide transport protein9.1up3.5upx-x- Cluster JCf_2054hypothetical protein predicted by Glimmer/Critica7.7up4.2upx-xx Cluster JCf_2055hypothetical protein predicted by Glimmer/Critica6.9up1.9upxxxx Cluster JCf_2056hypothetical protein4.6up1.7upx-x- Cluster JCf_2057Hypothetical 41.2 kDa protein in cps region5up1.2upx-x-
169
GENE NAMEFUNCTIONFold change T1
Fold change T2
Ter 6Ter1 0Ter1 4Ter9 1 Cluster JCf_2058hypothetical protein4.6up1.9upx-x- Cluster JCf_2059UTP--glucose-1-phosphate uridylyltransferase24up2.7upx-x- Cluster JCf_2060sugar transferase22.1up2.9upx-x- Cluster KCf_1128hypothetical protein predicted by Glimmer/Critica2.4up1.8upNANANANA Cluster KCf_1129High molecular weight rubredoxin6.5up3.4upNANANANA Cluster KCf_1130Abhydrolase domain-containing protein 12.6.7up3.9upxxxx Cluster KCf_1131fatty acid desaturase9up2.9upx-x- Cluster KCf_1132Putative polyketide synthase pksM.8.5up3.6upx-x- Cluster KCf_1133Acyl-CoA desaturase 14.7up2.1upx-x- Cluster KCf_1134Delta-9 acyl-lipid desaturase 2 (EC 1.14.19.-).3.4up2upNANANANA Cluster KCf_1135probable peptide synthetase protein4.7up2.9upx-x- Cluster KCf_1136Possible Multidrug resistance protein B.4.5up3.5up--x- Cluster KCf_1137hypothetical protein predicted by Glimmer/Critica7.4up3.9up--x- Cluster KCf_1138vanillate O-demethylase oxygenase subunit6.8up2.1up--x- Cluster KCf_1139fatty acid desaturase7.7up1.8up--x- Cluster KCf_1140monooxygenase6.9up1.6up--x- Cluster KCf_11413-oxoacyl-acyl carrier protein synthase II7.8up2.3up--x- Cluster KCf_1142hypothetical protein predicted by Glimmer/Critica7.4up1.1downNANANANA Cluster LCf_2276hypothetical protein2.3up2.5upx-xx Cluster LCf_2277Hypothetical protein MJ0779.2.8up1.9upx-xx Cluster LCf_2278Hypothetical protein MJ0900.2.8up2.3upxxxx Cluster LCf_2279hypothetical protein predicted by Glimmer/Critica2up1.1downx-xx Cluster LCf_2280General secretion pathway protein D precursor.2.2up1.9upxxxx Cluster LCf_2281hypothetical protein predicted by Glimmer/Critica2up1.2upx-xx Cluster LCf_2282hypothetical protein predicted by Glimmer/Critica2.2up1.1upx-xx Cluster LCf_2283hypothetical protein predicted by Glimmer/Critica2.6up1.3upx-xx Cluster LCf_2284hypothetical protein predicted by Glimmer/Critica2.1up1upx-xx
170
GENE NAMEFUNCTIONFold change T1
Fold change T2
Ter 6Ter1 0Ter1 4Ter9 1 Cluster MCf_986Flagellar protein flhE precursor.3.3up15.5up--x- Cluster MCf_991CDS2.5up8.5upxxx- Cluster MCf_992Flagellar basal-body rod protein flgC.2.4up7.9upxxx- Cluster MCf_994CDS2.9up9.5upxxx- Cluster MCf_996CDS3.3up11.8upxxx- Cluster MCf_997Flagellar L-ring protein precursor2.7up9.2upxxx- Cluster MCf_998CDS2up7.9upxxx- Cluster MCf_1000CDS2.2up10.4upxxx- Cluster MCf_1003CDS2.5up12.8upxxx- Cluster MCf_1004CDS3.4up18.4upxxx- Cluster MCf_1005CDS2.3up10.8upxxx- Cluster MCf_1006CDS2.1up8.1upxxx- Cluster MCf_1007Flagellar fliL protein2.4up12.1upx-x- Cluster MCf_1010hypothetical protein predicted by Glimmer/Critica2.8up17.7upNANANANA Cluster MCf_1013CDS2.4up10.3upxxx- Cluster MCf_1019CDS2.4up10.2upx-x- Cluster MCf_1029Transcriptional activator flhD.2.3up2.3upx-x- Cluster MCf_1030CDS2up1.3upxxx- Cluster MCf_1031CDS2.5up3.1upxxx- Cluster MCf_1033Probable transcriptional regulator ycf272.1up4.8up-xx- Cluster MCf_1034chemotaxis protein CheA2.4up3.5upxxx- Cluster MCf_1035Chemotaxis protein cheW.2.7up3.7upx-x- Cluster MCf_1036Hypothetical 14.4 kDa protein y4sN.2.1up1.8upxxx- Cluster NCf_1047Terminase, ATPase subunit (GpP).2.3up4.2up---- Cluster NCf_1048Presumed capsid scaffolding protein (GpO).2.3up4.2up---- Cluster NCf_1050Terminase, endonuclease subunit (GpM).2.2up3.1up---- Cluster NCf_1054hypothetical protein predicted by Glimmer/Critica2.1up3.4up----
