Environment and Gene Regulatory Influence Network (EGRIN) model for C. difficile 630

The Environment and Gene Regulatory Influence Network (EGRIN) model of C. difficile 630 was inferred using cMonkey2 and a compendium of 136 transcriptomes (retrieved from the Gene Expression Omnibus repository) with 4,070 sequence features including 35 rRNAs and 90 tRNAs . The C. difficile EGRIN model groups genes in subsets (406 modules in total), that are co-regulated in specific environments, and also identifies the associated, putative cis-acting gene regulatory elements (GREs), which represent potential TF binding locations. Transcriptome compendium included conditions: response to iron limitation, response to oxygen, in vivo vs in vitro growth, short term infection (0, 30, 60, 120 mins), response to commensals and host diet, transition from exponential to stationary phase, fur KO, codY KO, sporulation TF (and sigma factors) KOs.

Explore Regulatory Modules

Displaying 1 - 10 of 406

Candidate transcriptional regulators for each module were determined with a linear regression based approach (Inferelator) and by evaluating the statistical significance of the overlap (Hypergeometric) between modules and putative TF and alternative sigma factor regulons (CcpA, CodY, Fur, PrdR, SigB, SigD, SigE, SigF, SigG, SigH, SigK, Spo0A) compiled from available literature.

* Given that translation start was used to define the 3' end of putative promoters, some cis-regulatory motifs are likely to be ribosome binding sites (i.e., Shine-Dalgarno sequence). RBS is typically a six nucleotide sequence 5'-GGAGGA-3'.

Title	Gene Count	Motif 1 e-value	Motif 2 e-value	Residual	TF Influences
Module_320	20 CD630_30390 - Type: Gene Product:Putative ATPase \| Pathway: \| COG: Function unknown CD630_23380 - 4hbD Type: Gene Product:4-hydroxybutyrate dehydrogenase(4-hydroxybutanoate:NAD+ oxidoreductase) \| Pathway: \| COG: Energy production and conversion CD630_21170 - trxB Type: Gene Product:Thioredoxin reductase \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_23400 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_30380 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_30400 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_18230 - Type: Gene Product:Conserved hypothetical protein, UPF0246 family \| Pathway: \| COG: Replication, recombination and repair CD630_18220 - bcp Type: Gene Product:Putative thiol peroxidase \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_23390 - cat2 Type: Gene Product:4-hydroxybutyrate CoA transferase \| Pathway: \| COG: Energy production and conversion CD630_32150 - Type: Gene Product:ABC-type transport system, glycinebetaine/carnitine/choline ATP-binding protein \| Pathway: \| COG: Amino acid transport and metabolism CD630_34120 - uvrB Type: Gene Product:Excinuclease ABC subunit B \| Pathway: \| COG: Replication, recombination and repair CD630_34100 - uvrC Type: Gene Product:Excinuclease ABC subunit C \| Pathway: \| COG: Replication, recombination and repair CD630_34090 - hprK Type: Gene Product:PTS system, HPr kinase/phosphorylase \| Pathway: \| COG: Signal transduction mechanisms CD630_34110 - uvrA Type: Gene Product:Excinuclease ABC subunit A \| Pathway: \| COG: Replication, recombination and repair CD630_18240 - Type: Gene Product:P-type calcium transport ATPase \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_23410 - abfD Type: Gene Product:Gamma-aminobutyrate metabolismdehydratase/isomerase [includes: 4- hydroxybutyryl-coadehydratase; vinylacetyl-coa-delta-isomerase] \| Pathway: \| COG: Secondary metabolites biosynthesis, transport and catabolism CD630_34770 - Type: Gene Product:Putative dCMP deaminase \| Pathway: \| COG: Nucleotide transport and metabolism CD630_32160 - Type: Gene Product:ABC-type transport system, glycinebetaine/carnitine/choline permease \| Pathway: \| COG: Amino acid transport and metabolism CD630_r0150 - 5s_rRNA Type: Gene Product: \| Pathway: \| COG:	0.03	`NA`	0.36	Inferelator: 3 Hypergeometric: 0 TF Influences from Inferelator CD630_06110 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms CD630_10090 - Type: Gene Product:Transcriptional regulator, GntR family \| Pathway: \| COG: Transcription CD630_19100 - eutV Type: Gene Product:Two-component response regulator, Ethanolaminespecific \| Pathway: \| COG: Signal transduction mechanisms TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_342	18 CD630_05360 - cheW Type: Gene Product:Purine-binding chemotaxis protein CheW \| Pathway: \| COG: Cell motility, Signal transduction mechanisms CD630_32730 - feoA Type: Gene Product:Ferrous iron transport protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_23190 - rpe Type: Gene Product:Putative ribulose-phosphate 3-epimerase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_05350 - cheD Type: Gene Product:Probable chemoreceptor glutamine deamidase CheD \| Pathway: \| COG: Cell motility, Signal transduction mechanisms CD630_32720 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_05390 - cheA Type: Gene Product:Chemotaxis protein CheA \| Pathway: \| COG: Signal transduction mechanisms CD630_05420 - Type: Gene Product:Putative protein-glutamate methylesterase \| Pathway: \| COG: Signal transduction mechanisms CD630_05380 - Type: Gene Product:Putative methyl-accepting chemotaxis receptor,MCP family \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_32710 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_32740 - feoB Type: Gene Product:Ferrous iron transport protein B \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_05410 - cheR Type: Gene Product:Methyl-accepting chemotaxis proteinsmethyltransferase, MCP family \| Pathway: \| COG: Signal transduction mechanisms CD630_23200 - rpiB1 Type: Gene Product:Ribose-5-phosphate isomerase B1(Phosphoriboisomerase B) \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_23220 - tkt Type: Gene Product:Transketolase, N-terminal(Sedoheptulose-7-phosphate:D-glyceraldehyde-3-phosphateglycolaldehydetransferase) \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_05400 - cheW Type: Gene Product:Chemotaxis protein CheW \| Pathway: \| COG: Cell motility, Signal transduction mechanisms CD630_23210 - tkt Type: Gene Product:Transketolase, central and C-terminal(Sedoheptulose-7-phosphate:D-glyceraldehyde-3-phosphateglycolaldehydetransferase) \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_05340 - cheC Type: Gene Product:Chemotaxis protein CheY-P phosphatase CheC \| Pathway: \| COG: Cell motility, Signal transduction mechanisms CD630_05370 - Type: Gene Product:Putative CheY-like chemosensory protein \| Pathway: \| COG: Signal transduction mechanisms CD630_05330 - cheY Type: Gene Product:Chemotaxis protein CheY \| Pathway: \| COG: Signal transduction mechanisms	0.02	`NA`	0.45	Inferelator: 1 Hypergeometric: 1 TF Influences from Inferelator CD630_01710 - rex Type: Gene Product:Transcriptional regulator, Redox-sensingrepressor Rex \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test CD630_02660 - sigD Type: Gene Product:RNA polymerase sigma-28 factor for flagellaroperon \| Pathway: \| COG: Transcription
Module_89	27 CD630_26550 - murF Type: Gene Product:UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase (UDP-MurNAc-pentapeptide synthetase)(D-alanyl-D-alanine-adding enzyme) \| Pathway: Cell wall biogenesis \| COG: Cell wall/membrane/envelope biogenesis CD630_34380 - cobU Type: Gene Product:Bifunctional adenosylcobalamin biosynthesisprotein CobU [Adenosylcobinamide kinase;Adenosylcobinamide-phosphate guanylyltransferase] \| Pathway: \| COG: Coenzyme transport and metabolism CD630_26470 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_18150 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_26490 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_35880 - carB1 Type: Gene Product:Carbamoyl-phosphate synthase large chain 1 \| Pathway: Amino-acid biosynthesis \| COG: Nucleotide transport and metabolism CD630_18170 - Type: Gene Product:Putative acyltransferase \| Pathway: \| COG: Lipid transport and metabolism CD630_35400 - metG Type: Gene Product:Methionyl-tRNA synthetase (Methionine--tRNAligase) (MetRS) \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_34370 - cobS Type: Gene Product:Cobalamin synthase CobS (Cobalamin-5-phosphatesynthase) \| Pathway: Cofactor biosynthesis \| COG: Coenzyme transport and metabolism CD630_26520 - spoVE Type: Gene Product:Cell division/stage V sporulation protein \| Pathway: \| COG: Cell cycle control, cell division, chromosome partitioning CD630_35390 - Type: Gene Product:Putative deoxyribonuclease \| Pathway: \| COG: Replication, recombination and repair CD630_18140 - Type: Gene Product:Putative phosphoglycerate mutase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_35910 - carA Type: Gene Product:Carbamoyl-phosphate synthase small chain \| Pathway: Amino-acid biosynthesis \| COG: Nucleotide transport and metabolism CD630_36250 - Type: Gene Product:Putative signaling protein \| Pathway: \| COG: Signal transduction mechanisms CD630_26500 - Type: Gene Product:Putative cell division protein Fts-Q type \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_18160 - cmk Type: Gene Product:Cytidylate kinase (CK) (Cytidine monophosphatekinase) (CMP kinase) \| Pathway: \| COG: Nucleotide transport and metabolism CD630_26540 - mraY Type: Gene Product:Phospho-N-acetylmuramoyl-pentapeptide-transferase(UDP- MurNAc-pentapeptide phosphotransferase) \| Pathway: Cell wall biogenesis \| COG: Cell wall/membrane/envelope biogenesis CD630_35890 - carA Type: Gene Product:Carbamoyl-phosphate synthase small chain \| Pathway: Amino-acid biosynthesis \| COG: Nucleotide transport and metabolism CD630_34390 - cobT Type: Gene Product:Nicotinate-nucleotide--dimethylbenzimidazolephosphoribosyltransferase (NN:DBI PRT)(N(1)-alpha-phosphoribosyltransferase) \| Pathway: Nucleoside biosynthesis \| COG: Coenzyme transport and metabolism CD630_26480 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_24800 - Type: Gene Product:Putative hydrolase \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_18180 - ispH Type: Gene Product:4-hydroxy-3-methylbut-2-enyl diphosphatereductase \| Pathway: Isoprenoid biosynthesis \| COG: Lipid transport and metabolism CD630_34360 - cobC Type: Gene Product:Cobalamin biosynthesis phosphoglycerate mutaseCobC \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_35920 - pyrF Type: Gene Product:Orotidine 5'-phosphate decarboxylase (OMPdecarboxylase) (OMPDCase) (OMPdecase) \| Pathway: Pyrimidine metabolism \| COG: Nucleotide transport and metabolism CD630_26530 - murD Type: Gene Product:UDP-N-acetylmuramoylalanine--D-glutamate ligase(UDP-N- acetylmuramoyl-L-alanyl-D-glutamate synthetase)(D-glutamic acid- adding enzyme) \| Pathway: Cell wall biogenesis \| COG: Cell wall/membrane/envelope biogenesis CD630_26510 - murG Type: Gene Product:UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosaminetransferase \| Pathway: Cell wall biogenesis \| COG: Cell wall/membrane/envelope biogenesis CD630_35900 - carB2 Type: Gene Product:Carbamoyl-phosphate synthase large chain 2 \| Pathway: Amino-acid biosynthesis \| COG: Nucleotide transport and metabolism	8.7	`NA`	0.47	Inferelator: 1 Hypergeometric: 0 TF Influences from Inferelator CD630_17820 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_358	23 CD630_02500 - fliH Type: Gene Product:Flagellar assembly protein FliH \| Pathway: \| COG: Cell motility CD630_02490 - fliG Type: Gene Product:Flagellar motor switch protein FliG \| Pathway: \| COG: Cell motility CD630_02640 - flhF Type: Gene Product:Flagellar biosynthesis regulator FlhF(Flagella-associated GTP-binding protein) \| Pathway: \| COG: Cell motility CD630_02470 - fliE Type: Gene Product:Flagellar hook-basal body complex protein FliE \| Pathway: \| COG: Cell motility CD630_02600 - fliP Type: Gene Product:Flagellar biosynthesis protein FliP \| Pathway: \| COG: Cell motility CD630_02660 - sigD Type: Gene Product:RNA polymerase sigma-28 factor for flagellaroperon \| Pathway: \| COG: Transcription CD630_02520 - fliJ Type: Gene Product:Flagellar protein FliJ \| Pathway: \| COG: Cell motility CD630_02620 - flhB Type: Gene Product:Bifunctional flagellar biosynthesis proteinFliR/FlhB \| Pathway: \| COG: Cell motility CD630_02560 - motA Type: Gene Product:Flagellar motor rotation protein MotA \| Pathway: \| COG: Cell motility CD630_02540 - flgD Type: Gene Product:Basal-body rod modification protein FlgD \| Pathway: \| COG: Cell motility CD630_02580 - fliL Type: Gene Product:Flagellar basal body-associated protein FliL \| Pathway: \| COG: Cell motility CD630_02480 - fliF Type: Gene Product:Flagellar M-ring protein FliF \| Pathway: \| COG: Cell motility CD630_02650 - flhG Type: Gene Product:Flagellar number regulator FlhG \| Pathway: \| COG: Cell cycle control, cell division, chromosome partitioning CD630_02510 - fliI Type: Gene Product:ATP synthase subunit beta FliI \| Pathway: \| COG: Cell motility, Intracellular trafficking, secretion, and vesicular transport CD630_02550 - flgE Type: Gene Product:Flagellar hook protein FlgE (Distal rod protein) \| Pathway: \| COG: Cell motility CD630_02551 - FlbD Type: Gene Product:Flagellar protein FlbD \| Pathway: \| COG: Cell motility CD630_02530 - fliK Type: Gene Product:Flagellar hook-length control protein FliK \| Pathway: \| COG: Cell motility CD630_02460 - flgC Type: Gene Product:Flagellar basal-body rod protein FlgC \| Pathway: \| COG: Cell motility CD630_02670 - Type: Gene Product:Putative flagellar protein \| Pathway: \| COG: CD630_02570 - motB Type: Gene Product:Flagellar motor rotation protein MotB (Chemotaxisprotein MotB) \| Pathway: \| COG: Cell motility CD630_02630 - flhA Type: Gene Product:Flagellar biosynthesis protein FlhA \| Pathway: \| COG: Cell motility CD630_02610 - fliQ Type: Gene Product:Flagellar biosynthetic protein FliQ \| Pathway: \| COG: Cell motility CD630_02590 - fliZ Type: Gene Product:Flagellar protein FliZ \| Pathway: \| COG: Cell motility	`NA`	`NA`	0.39	Inferelator: 2 Hypergeometric: 1 TF Influences from Inferelator CD630_02660 - sigD Type: Gene Product:RNA polymerase sigma-28 factor for flagellaroperon \| Pathway: \| COG: Transcription CD630_22140 - SinR Type: Gene Product:Transcriptional regulator, HTH-type \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test CD630_02660 - sigD Type: Gene Product:RNA polymerase sigma-28 factor for flagellaroperon \| Pathway: \| COG: Transcription
Module_256	22 CD630_30270 - Type: Gene Product:PTS system, glucose-like IIA component \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_02210 - purG Type: Gene Product:Phosphoribosylformylglycinamidine cyclo-ligase \| Pathway: Purine metabolism \| COG: Nucleotide transport and metabolism CD630_26660 - ptsG-A Type: Gene Product:PTS system, glucose-specific IIA component \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_02190 - purC Type: Gene Product:Phosphoribosylaminoimidazole-succinocarboxamidesynthase \| Pathway: Purine metabolism \| COG: Nucleotide transport and metabolism CD630_02230 - purH Type: Gene Product:Bifunctional purine biosynthesis protein purH[Includes: Phosphoribosylaminoimidazolecarboxamideformyltransferase ; IMP cyclohydrolase] \| Pathway: Purine metabolism \| COG: Nucleotide transport and metabolism CD630_02250 - purL Type: Gene Product:Phosphoribosylformylglycinamidine synthase \| Pathway: Purine metabolism \| COG: Nucleotide transport and metabolism CD630_22120 - Type: Gene Product:Transcriptional regulator, MarR family \| Pathway: \| COG: Transcription CD630_03590 - Type: Gene Product:Putative RNA polymerase sigma factor Tn916-like,CTn1-Orf4 \| Pathway: \| COG: Function unknown CD630_30280 - Type: Gene Product:Putative phosphosugar isomerase \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_22100 - Type: Gene Product:ABC-type transport system, multidrug-familyATP-binding/permease \| Pathway: \| COG: Defense mechanisms CD630_05720 - Type: Gene Product:Putative sporulation protein \| Pathway: \| COG: Function unknown CD630_30300 - Type: Gene Product:PTS system, glucose-like IIBC component \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_26670 - ptsG-BC Type: Gene Product:PTS system, glucose-specific IIBC component \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_02200 - purF Type: Gene Product:Amidophosphoribosyltransferase \| Pathway: Purine metabolism \| COG: Nucleotide transport and metabolism CD630_02240 - purD Type: Gene Product:Phosphoribosylamine--glycine ligase \| Pathway: Purine metabolism \| COG: Nucleotide transport and metabolism CD630_02220 - purN Type: Gene Product:Phosphoribosylglycinamide formyltransferase \| Pathway: Purine metabolism \| COG: Nucleotide transport and metabolism CD630_02180 - purE Type: Gene Product:Phosphoribosylaminoimidazole carboxylasecatalytic subunit \| Pathway: Purine metabolism \| COG: Nucleotide transport and metabolism CD630_03580 - Type: Gene Product:Putative conjugative transposon proteinTn916-like, CTn1-Orf3 \| Pathway: \| COG: Function unknown CD630_30290 - malY Type: Gene Product:Bifunctional protein: cystathionine beta-lyase /repressor \| Pathway: \| COG: Amino acid transport and metabolism CD630_22110 - Type: Gene Product:ABC-type transport system, multidrug-familyATP-binding/permease \| Pathway: \| COG: Defense mechanisms CD630_05730 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_05710 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown	0.11	`NA`	0.53	Inferelator: 2 Hypergeometric: 1 TF Influences from Inferelator CD630_26650 - Type: Gene Product:Transcriptional regulator, AraC family \| Pathway: \| COG: Transcription CD630_31900 - Type: Gene Product:Transcriptional regulator, MerR family \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test CD630_12140 - spo0A Type: Gene Product:Stage 0 sporulation protein A \| Pathway: \| COG: Signal transduction mechanisms
Module_176	27 CD630_32450 - prdR Type: Gene Product:Transcriptional regulator, sigma-54-dependent \| Pathway: \| COG: Transcription CD630_31890 - Type: Gene Product:Putative NADPH-dependent FMN reductase \| Pathway: \| COG: Function unknown CD630_07970 - Type: Gene Product:Putative pyruvate carboxyltransferase \| Pathway: \| COG: Lipid transport and metabolism CD630_07420 - Type: Gene Product:Putative ethanolamine transporter \| Pathway: \| COG: Amino acid transport and metabolism CD630_23690 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_33290 - Type: Gene Product:Putative RNA polymerase sigma factor Tn916-like,CTn6-Orf5 \| Pathway: \| COG: Function unknown CD630_16120 - Type: Gene Product:Putative amidohydrolase \| Pathway: \| COG: Secondary metabolites biosynthesis, transport and catabolism CD630_32850 - pgi Type: Gene Product:Glucose-6-phosphate isomerase (GPI)(Phosphoglucose isomerase) (PGI) (Phosphohexose isomerase)(PHI) \| Pathway: Carbohydrate biosynthesis \| COG: Carbohydrate transport and metabolism CD630_34050 - Type: Gene Product:Putative iron-onlyhydrogenase,electron-transferring subunit HymA-like \| Pathway: \| COG: Energy production and conversion CD630_34030 - Type: Gene Product:Putative formate/nitrite transporter \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_34070 - Type: Gene Product:Putative iron-only hydrogenase, catalytic subunitHymC-like \| Pathway: \| COG: Energy production and conversion CD630_26830 - Type: Gene Product:Putative propanediol utilization protein \| Pathway: Polyol metabolism \| COG: Secondary metabolites biosynthesis, transport and catabolism CD630_31900 - Type: Gene Product:Transcriptional regulator, MerR family \| Pathway: \| COG: Transcription CD630_21810 - Type: Gene Product:Putative alpha/beta hydrolase \| Pathway: \| COG: Function unknown CD630_20460 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_13790 - Type: Gene Product:Transcriptional regulator, Phage-type \| Pathway: \| COG: Transcription CD630_27550 - ptsI Type: Gene Product:PTS system, EI component \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_03560 - xis Type: Gene Product:Excisionase Tn916-like, CTn1-Orf2 \| Pathway: \| COG: Function unknown CD630_32460 - Type: Gene Product:Putative surface protein \| Pathway: \| COG: Function unknown CD630_33280 - Type: Gene Product:Putative conjugative transposon proteinTn916-like, CTn6-Orf4 \| Pathway: \| COG: Function unknown CD630_25960 - Type: Gene Product:Putative pseudouridylate synthase, RluC/RluDfamily \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_25970 - lspA Type: Gene Product:Lipoprotein signal peptidase (Prolipoproteinsignal peptidase) (Signal peptidase II) (SPase II) \| Pathway: Protein modification \| COG: Cell wall/membrane/envelope biogenesis, Intracellular trafficking, secretion, and vesicular transport CD630_15111 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_31910 - Type: Gene Product:Putative oxidoreductase \| Pathway: \| COG: Energy production and conversion CD630_34060 - Type: Gene Product:Putative iron-onlyhydrogenase,electron-transferring subunit HymB-like \| Pathway: \| COG: Energy production and conversion CD630_34040 - cls Type: Gene Product:Cardiolipin synthetase (Cardiolipin synthase) (CLsynthase) \| Pathway: \| COG: Lipid transport and metabolism CD630_21100 - Type: Gene Product:Putative transaldolaseC-like \| Pathway: Carbohydrate degradation \| COG: Carbohydrate transport and metabolism	4e-31	`NA`	0.47	Inferelator: 3 Hypergeometric: 0 TF Influences from Inferelator CD630_17980 - Type: Gene Product:Transcriptional regulator, LysR family \| Pathway: \| COG: Transcription CD630_31900 - Type: Gene Product:Transcriptional regulator, MerR family \| Pathway: \| COG: Transcription CD630_35440 - Type: Gene Product:Transcriptional regulator, AsnC/Lrp family \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_25	29 CD630_12480 - rnc Type: Gene Product:ribonuclease III \| Pathway: \| COG: Transcription CD630_31140 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_12520 - ffh Type: Gene Product:Signal recognition particle protein \| Pathway: \| COG: Intracellular trafficking, secretion, and vesicular transport CD630_12560 - trmD Type: Gene Product:tRNA (guanine-N(1)-)-methyltransferase(M1G-methyltransferase) (tRNA [GM37] methyltransferase ) \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_12500 - smc Type: Gene Product:Structural maintenance chromosome protein SMC \| Pathway: \| COG: Cell cycle control, cell division, chromosome partitioning CD630_12460 - efp Type: Gene Product:Elongation factor P (EF-P) \| Pathway: Protein biosynthesis \| COG: Translation, ribosomal structure and biogenesis CD630_12540 - Type: Gene Product:Putative RNA-binding protein \| Pathway: \| COG: Function unknown CD630_31120 - Type: Gene Product:Putative peptidase, M20D family \| Pathway: \| COG: Amino acid transport and metabolism CD630_31960 - Type: Gene Product:Putative penicillin-binding protein \| Pathway: \| COG: Defense mechanisms CD630_20190 - Type: Gene Product:Transporter drug resistance, Major FacilitatorSuperfamily (MFS) \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_31940 - Type: Gene Product:Transcriptional regulator, AraC family \| Pathway: \| COG: Transcription CD630_08620 - Type: Gene Product:PTS system, lactose/cellobiose-family IICmembrane component \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_32620 - pstA Type: Gene Product:ABC-type transport system, phosphate-specificpermease \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_32600 - phoU Type: Gene Product:Phosphate uptake regulator, PhoU \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_12530 - rpsP Type: Gene Product:30S ribosomal protein S16 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_31980 - cme Type: Gene Product:Multidrug resistance protein Cme; Transporter,Major Facilitator Superfamily (MFS) \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_31130 - Type: Gene Product:Putative aminobenzoyl-glutamate utilizationprotein B \| Pathway: \| COG: Amino acid transport and metabolism CD630_12470 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_12660 - Type: Gene Product:ABC-type transport system, multidrug-familypermease \| Pathway: \| COG: Function unknown CD630_12511 - Type: Gene Product:Putative DNA-binding regulator \| Pathway: \| COG: Function unknown CD630_12510 - ftsY Type: Gene Product:signal recognition particle receptor \| Pathway: \| COG: Intracellular trafficking, secretion, and vesicular transport CD630_12550 - rimM Type: Gene Product:16S rRNA processing protein RimM \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_12570 - rplS Type: Gene Product:50S ribosomal protein L19 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_31970 - Type: Gene Product:Transcriptional regulator, MerR family \| Pathway: \| COG: Transcription CD630_12680 - Type: Gene Product:ABC-type transport system, multidrug-familyATP-binding protein \| Pathway: \| COG: Defense mechanisms CD630_32610 - pstB Type: Gene Product:ABC-type transport system, phosphate-specificATP-binding \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_31950 - Type: Gene Product:Putative UvrABC system protein A 2 (UvrA protein2) (Excinuclease ABC subunit A 2) \| Pathway: \| COG: Replication, recombination and repair CD630_32630 - pstC Type: Gene Product:ABC-type transport system, phosphate-specificpermease \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_20180 - Type: Gene Product:Transcriptional regulator, AraC family \| Pathway: \| COG: Transcription	0.000001	`NA`	0.56	Inferelator: 2 Hypergeometric: 0 TF Influences from Inferelator CD630_24120 - Type: Gene Product:Putative negative regulator of gluconeogenesis \| Pathway: \| COG: Transcription CD630_36390 - Type: Gene Product:Transcriptional regulator, LysR family \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_374	20 CD630_15500 - hisB Type: Gene Product:Imidazoleglycerol-phosphate dehydratase \| Pathway: Amino-acid biosynthesis \| COG: Amino acid transport and metabolism CD630_32690 - Type: Gene Product:Putative oligoendopeptidase F, M3B family \| Pathway: \| COG: Amino acid transport and metabolism CD630_10370 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_15530 - hisF Type: Gene Product:Imidazole glycerol phosphate synthase subunitHisF \| Pathway: Amino-acid biosynthesis \| COG: Amino acid transport and metabolism CD630_15480 - hisG Type: Gene Product:ATP phosphoribosyltransferase (ATP-PRTase)(ATP-PRT) \| Pathway: Amino-acid biosynthesis \| COG: Amino acid transport and metabolism CD630_10430 - sbcC Type: Gene Product:Nuclease SbcCD subunit C \| Pathway: \| COG: Replication, recombination and repair CD630_15520 - hisA Type: Gene Product:1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase \| Pathway: Amino-acid biosynthesis \| COG: Amino acid transport and metabolism CD630_32700 - Type: Gene Product:Putative magnesium transport ATPase, MgtC/SapBfamily \| Pathway: \| COG: Function unknown CD630_15470 - hisZ Type: Gene Product:ATP phosphoribosyltransferase regulatory subunit \| Pathway: \| COG: Amino acid transport and metabolism CD630_15490 - hisC Type: Gene Product:Histidinol-phosphate aminotransferase (Imidazoleacetol-phosphate transaminase) \| Pathway: Amino-acid biosynthesis \| COG: Amino acid transport and metabolism CD630_10410 - addA Type: Gene Product:ATP-dependent nuclease subunit A (ATP-dependenthelicase addA) \| Pathway: \| COG: Replication, recombination and repair CD630_21430 - Type: Gene Product:Transcriptional regulator, HTH-type \| Pathway: \| COG: Transcription CD630_10400 - addB Type: Gene Product:ATP-dependent nuclease subunit B (ATP-dependenthelicase addB), Superfamily 1 UvrD-family \| Pathway: \| COG: Replication, recombination and repair CD630_10380 - Type: Gene Product:Putative helicase, superfamily 1, UvrD-family \| Pathway: \| COG: Replication, recombination and repair CD630_10420 - sbcD Type: Gene Product:Nuclease SbcCD subunit D \| Pathway: \| COG: Replication, recombination and repair CD630_10390 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_15540 - hisI Type: Gene Product:Histidine biosynthesis bifunctional protein HisIE[Includes: Phosphoribosyl-AMP cyclohydrolase ;Phosphoribosyl-ATP pyrophosphatase] \| Pathway: Amino-acid biosynthesis \| COG: Amino acid transport and metabolism CD630_15510 - hisH Type: Gene Product:Imidazole glycerol phosphate synthase subunitHisH \| Pathway: Amino-acid biosynthesis \| COG: Amino acid transport and metabolism CD630_21440 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_20020 - Type: Gene Product:Transcriptional regulator, HTH-type \| Pathway: \| COG: Transcription	0.76	`NA`	0.57	Inferelator: 1 Hypergeometric: 1 TF Influences from Inferelator CD630_21430 - Type: Gene Product:Transcriptional regulator, HTH-type \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test CD630_12750 - codY Type: Gene Product:Transcriptional regulator, GTP-sensingpleiotropic repressor \| Pathway: \| COG: Transcription
Module_192	23 CD630_27610 - Type: Gene Product:Putative N-acetylmuramoyl-L-alanine amidase \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_36550 - purA Type: Gene Product:Adenylosuccinate synthetase (IMP--aspartateligase) (AdSS) (AMPSase) \| Pathway: Purine metabolism \| COG: Nucleotide transport and metabolism CD630_17330 - hemE Type: Gene Product:Uroporphyrinogen decarboxylase (URO-D) \| Pathway: \| COG: Coenzyme transport and metabolism CD630_13100 - rbfA Type: Gene Product:Ribosome-binding factor A \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_13060 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_13080 - Type: Gene Product:Ribosomal protein L7Ae/L30e/S12e/Gadd45 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_22750 - topB2 Type: Gene Product:DNA topoisomerase III \| Pathway: \| COG: Replication, recombination and repair CD630_07100 - Type: Gene Product:Conserved hypothetical protein, DUF523 family \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_28020 - tgt Type: Gene Product:Queuine tRNA-ribosyltransferase (tRNA-guaninetransglycosylase) (Guanine insertion enzyme) \| Pathway: tRNA modification \| COG: Translation, ribosomal structure and biogenesis CD630_28000 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_28040 - queA Type: Gene Product:S-adenosylmethionine:tRNAribosyltransferase-isomerase (Queuosine biosynthesisprotein QueA) \| Pathway: tRNA modification \| COG: Translation, ribosomal structure and biogenesis CD630_17320 - Type: Gene Product:Putative cobalamin-binding protein \| Pathway: \| COG: Function unknown CD630_13071 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Transcription CD630_13070 - nusA Type: Gene Product:Transcription elongation protein \| Pathway: \| COG: Transcription CD630_36560 - Type: Gene Product:Conserved hypothetical protein with a TonB box \| Pathway: \| COG: CD630_17340 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Energy production and conversion CD630_13090 - infB Type: Gene Product:Translation initiation factor IF-2 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_07090 - mutS2 Type: Gene Product:DNA mismatch repair protein \| Pathway: \| COG: Replication, recombination and repair CD630_26820 - pfo Type: Gene Product:Pyruvate-ferredoxin oxidoreductase \| Pathway: \| COG: Energy production and conversion CD630_28030 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_22740 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_28010 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Intracellular trafficking, secretion, and vesicular transport CD630_13050 - dnaF Type: Gene Product:DNA polymerase III PolC-type (PolIII) \| Pathway: \| COG: Replication, recombination and repair	0.00069	`NA`	0.47	Inferelator: 2 Hypergeometric: 0 TF Influences from Inferelator CD630_06480 - Type: Gene Product:Transcriptional regulator, GntR family \| Pathway: \| COG: Transcription CD630_06700 - Type: Gene Product:Transcriptional regulator, beta-lactamsrepressor \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_121	20 CD630_27720 - tuaG Type: Gene Product:Putative glycosyl transferase, family 2 \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_27730 - Type: Gene Product:Putative glycosyl transferase, family 2 \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_15570 - Type: Gene Product:Putative peptidylprolyl isomerase \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_27710 - rkpK Type: Gene Product:UDP-glucose 6-dehydrogenase \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_27750 - Type: Gene Product:Putative glycerophosphotransferase \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_15560 - Type: Gene Product:Putative polysaccharide deacetylase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_27760 - Type: Gene Product:Putative glycosyl transferase, family 2 \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_15590 - rsiV Type: Gene Product:Anti Sigma Factor, ECF family \| Pathway: \| COG: Function unknown CD630_27740 - Type: Gene Product:Putative glycosyl transferase, family 2 \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_27800 - pgm Type: Gene Product:Alpha-phosphoglucomutase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_15610 - Type: Gene Product:Putative dehydrogenase \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_27780 - Type: Gene Product:Putative glycosyl transferase \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_15580 - sigV Type: Gene Product:Extra-Cytoplasmic Function sigma factors, ECFfamily \| Pathway: \| COG: Transcription CD630_15600 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_27690 - Type: Gene Product:Putative polysaccharide biosynthesis protein \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_27700 - Type: Gene Product:Putative glycosyl transferase, group 1 \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_27820 - cwp7 Type: Gene Product:Cell wall binding protein \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_15620 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_27790 - manC Type: Gene Product:Putative mannose-1-phosphate guanylyltransferase \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_27770 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown	`NA`	`NA`	0.40	Inferelator: 3 Hypergeometric: 0 TF Influences from Inferelator CD630_10230 - Type: Gene Product:Putative transcriptional regulator, HTH \| Pathway: \| COG: Transcription CD630_11770 - fapR Type: Gene Product:Transcriptional regulator, DeoR family (Fattyacid and phospholipid biosynthesis regulator) \| Pathway: \| COG: Transcription CD630_16860 - Type: Gene Product:Transcriptional regulator, repressor-like \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`