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 111 - 120 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_62	9 CD630_06012 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_20060 - Type: Gene Product:Fragment of putative topoisomerase (C-terminalregion) \| Pathway: \| COG: Function unknown CD630_19901 - Type: Gene Product:Fragment of transcriptional regulator,beta-lactams repressor (Part 2) \| Pathway: \| COG: Transcription CD630_23052 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_20131 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_14220 - Type: Gene Product:Transcriptional regulator, MerR family \| Pathway: \| COG: Transcription CD630_20090 - Type: Gene Product:Fragment of putative topoisomerase (C-terminalregion) \| Pathway: \| COG: Replication, recombination and repair CD630_11230 - Type: Gene Product:Putative phosphoesterase \| Pathway: \| COG: Function unknown CD630_06620 - Type: Gene Product:Fragment of phage endolysin CwlH \| Pathway: \| COG:	`NA`	`NA`	0.46	Inferelator: 1 Hypergeometric: 0 TF Influences from Inferelator CD630_14220 - Type: Gene Product:Transcriptional regulator, MerR family \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_30	22 CD630_25270 - Type: Gene Product:Transcriptional regulator, TetR family \| Pathway: \| COG: Transcription CD630_34380 - cobU Type: Gene Product:Bifunctional adenosylcobalamin biosynthesisprotein CobU [Adenosylcobinamide kinase;Adenosylcobinamide-phosphate guanylyltransferase] \| Pathway: \| COG: Coenzyme transport and metabolism CD630_08870 - Type: Gene Product:Transcriptional regulator, GntR family \| Pathway: \| COG: Transcription CD630_11750 - ackA Type: Gene Product:Acetate kinase (Acetokinase) \| Pathway: Metabolic intermediate biosynthesis \| COG: Energy production and conversion CD630_07580 - pflA Type: Gene Product:Pyruvate formate-lyase activating enzyme \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_05200 - Type: Gene Product:Two-component sensor histidine kinase \| Pathway: \| COG: Signal transduction mechanisms CD630_15380 - Type: Gene Product:Putative signaling protein \| Pathway: \| COG: Signal transduction mechanisms CD630_14190 - Type: Gene Product:Putative diguanylate kinase signaling protein \| Pathway: \| COG: Signal transduction mechanisms CD630_05210 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms CD630_14210 - Type: Gene Product:Putative diguanylate kinase signaling protein \| Pathway: \| COG: Signal transduction mechanisms CD630_08410 - Type: Gene Product:5-aminoimidazole-4-carboxamide ribonucleotidetransformylase \| Pathway: \| COG: Nucleotide transport and metabolism CD630_08100 - Type: Gene Product:Putative flavodoxin/nitric oxide synthase \| Pathway: \| COG: Function unknown CD630_26630 - Type: Gene Product:Putative signaling protein \| Pathway: \| COG: Signal transduction mechanisms CD630_08360 - Type: Gene Product:Putative acetyltransferase \| Pathway: \| COG: Transcription CD630_25280 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_16540 - Type: Gene Product:Putative lipoate-protein ligase \| Pathway: Protein modification \| COG: Coenzyme transport and metabolism CD630_24920 - Type: Gene Product:Two-component sensor histidine kinase,sporulation-associated spo0A \| Pathway: \| COG: Signal transduction mechanisms CD630_07590 - plfB Type: Gene Product:Formate acetyltransferase (Pyruvateformate-lyase) \| Pathway: \| COG: Energy production and conversion CD630_08400 - Type: Gene Product:Putative isomerase/hydrolase \| Pathway: \| COG: Secondary metabolites biosynthesis, transport and catabolism CD630_15150 - Type: Gene Product:Putative diguanylate kinase signaling protein \| Pathway: \| COG: Signal transduction mechanisms CD630_14200 - dccA Type: Gene Product:Diguanylate cyclase protein \| Pathway: \| COG: Signal transduction mechanisms CD630_13920 - Type: Gene Product:Putative endoribonuclease \| Pathway: \| COG: Translation, ribosomal structure and biogenesis	0.000000000000032	`NA`	0.46	Inferelator: 3 Hypergeometric: 0 TF Influences from Inferelator CD630_10640 - ccpA Type: Gene Product:Transcriptional regulator, LacI family \| Pathway: \| COG: Transcription CD630_17820 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms CD630_25270 - Type: Gene Product:Transcriptional regulator, TetR family \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_47	20 CD630_23130 - Type: Gene Product:ABC-type transport system, molybdenum-likeATP-binding protein \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_08610 - Type: Gene Product:PTS system, lactose/cellobiose-family IIBcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_25450 - bcsA Type: Gene Product:Cellulose synthase catalytic subunit(UDP-forming) \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_23140 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_25440 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_08620 - Type: Gene Product:PTS system, lactose/cellobiose-family IICmembrane component \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_25460 - Type: Gene Product:Endoglucanase (cellulase) \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_23120 - Type: Gene Product:ABC-type transport system, molybdenum-likepermease \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_08640 - Type: Gene Product:Maltose-6'-phosphate glucosidase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_20180 - Type: Gene Product:Transcriptional regulator, AraC family \| Pathway: \| COG: Transcription CD630_25420 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_23110 - Type: Gene Product:ABC-type transport system, molybdenum-likeextracellular solute-binding protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_08630 - Type: Gene Product:PTS system, lactose/cellobiose-family IIAcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_25430 - Type: Gene Product:Putative membrane-bound 0-ACYL transferase, MBOATfamily \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis	0.05	`NA`	0.46	Inferelator: 2 Hypergeometric: 0 TF Influences from Inferelator CD630_20180 - Type: Gene Product:Transcriptional regulator, AraC family \| Pathway: \| COG: Transcription CD630_30940 - Type: Gene Product:Transcriptional regulator, sigma-54-dependent \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_159	24 CD630_04000 - etfB1 Type: Gene Product:Beta-subunit of electron transfer flavoprotein \| Pathway: \| COG: Energy production and conversion CD630_07280 - Type: Gene Product:Bifunctional carbon monoxidedehydrogenase/acetyl-CoA synthase, subunit alpha/beta \| Pathway: \| COG: Energy production and conversion CD630_03940 - ldhA Type: Gene Product:D-lactate dehydrogenase \| Pathway: \| COG: Energy production and conversion CD630_07180 - fhs Type: Gene Product:Formate--tetrahydrofolate ligase(Formyltetrahydrofolate synthetase) (FHS) (FTHFS) \| Pathway: One-carbon metabolism \| COG: Nucleotide transport and metabolism CD630_03960 - hadI Type: Gene Product:Activator of 2-hydroxyisocaproyl-CoA dehydratase \| Pathway: \| COG: Lipid transport and metabolism CD630_07200 - folD Type: Gene Product:Bifunctional protein folD [Includes:Methylenetetrahydrofolate dehydrogenase ;Methenyltetrahydrofolate cyclohydrolase] \| Pathway: One-carbon metabolism \| COG: Coenzyme transport and metabolism CD630_03980 - hadC Type: Gene Product:Subunit of oxygen-sensitive2-hydroxyisocaproyl-CoA dehydratase C \| Pathway: \| COG: Amino acid transport and metabolism CD630_23490 - grdC Type: Gene Product:Glycine reductase complex component C subunitbeta (Protein PC beta) \| Pathway: \| COG: Energy production and conversion CD630_20200 - clpB Type: Gene Product:Chaperone protein \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_07220 - metF Type: Gene Product:5,10-methylenetetrahydrofolate reductase \| Pathway: One-carbon metabolism \| COG: Amino acid transport and metabolism CD630_07260 - Type: Gene Product:Bifunctional carbon monoxidedehydrogenase/acetyl-CoA synthase, delta subunit \| Pathway: \| COG: Energy production and conversion CD630_07240 - Type: Gene Product:Bifunctional carbon monoxidedehydrogenase/acetyl-CoA synthase,nickel-inserting subunit \| Pathway: \| COG: Cell cycle control, cell division, chromosome partitioning CD630_04010 - etfA1 Type: Gene Product:Alpha-subunit of electron transfer flavoprotein \| Pathway: \| COG: Energy production and conversion CD630_07290 - gcvH Type: Gene Product:Glycine cleavage system H protein \| Pathway: \| COG: Amino acid transport and metabolism CD630_03950 - hadA Type: Gene Product:Isocaprenoyl-CoA:2-hydroxyisocaproateCoA-transferase \| Pathway: \| COG: Energy production and conversion CD630_03970 - hadB Type: Gene Product:Subunit of oxygen-sensitive2-hydroxyisocaproyl-CoA dehydratase B \| Pathway: \| COG: Amino acid transport and metabolism CD630_07190 - fchA Type: Gene Product:Methenyltetrahydrofolate cyclohydrolase(5,10-methenyltetrahydrofolate 5-hydrolase) \| Pathway: \| COG: Amino acid transport and metabolism CD630_03990 - acdB Type: Gene Product:Acyl-CoA dehydrogenase, short-chain specific \| Pathway: \| COG: Lipid transport and metabolism CD630_07210 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_20210 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_07250 - Type: Gene Product:Bifunctional carbon monoxidedehydrogenase/acetyl-CoA synthase, subunit delta \| Pathway: \| COG: Energy production and conversion CD630_07230 - Type: Gene Product:Bifunctional carbon monoxidedehydrogenase/acetyl-CoA synthase, dihydrolipoyldehydrogenase subunit \| Pathway: \| COG: Energy production and conversion CD630_07270 - Type: Gene Product:Bifunctional carbon monoxidedehydrogenase/acetyl-CoA synthase, methyltransferasesubunit \| Pathway: \| COG: Amino acid transport and metabolism CD630_23480 - grdD Type: Gene Product:Glycine reductase complex component C subunitalpha (Protein PC alpha) \| Pathway: \| COG: Function unknown	`NA`	`NA`	0.46	Inferelator: 1 Hypergeometric: 2 TF Influences from Inferelator CD630_16930 - Type: Gene Product:Putative dinitrogenase iron-molybdenum cofactor \| Pathway: \| COG: Function unknown TF Influences from Hypergeometric Test CD630_10640 - ccpA Type: Gene Product:Transcriptional regulator, LacI family \| Pathway: \| COG: Transcription CD630_31760 - glnF Type: Gene Product:RNA polymerase sigma-54 factor \| Pathway: \| COG: Transcription
Module_31	23 CD630_28640 - Type: Gene Product:Putative hydrolase \| Pathway: \| COG: Function unknown CD630_29650 - Type: Gene Product:Putative signaling protein \| Pathway: \| COG: Signal transduction mechanisms CD630_09790 - Type: Gene Product:Transcriptional regulator, beta-lactams repressorPhage-type \| Pathway: \| COG: Transcription CD630_22220 - Type: Gene Product:Putative extrachromosomal origin protein \| Pathway: \| COG: Function unknown CD630_27970 - Type: Gene Product:Putative calcium-binding adhesion protein \| Pathway: \| COG: Function unknown CD630_06560 - Type: Gene Product:Chloride ion channel protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_18920 - Type: Gene Product:Putative methyltransferase, type 11 family \| Pathway: \| COG: Secondary metabolites biosynthesis, transport and catabolism CD630_28730 - Type: Gene Product:Putative signaling protein \| Pathway: \| COG: Signal transduction mechanisms CD630_27640 - Type: Gene Product:Putative hydrolase, HAD superfamily, IIBsubfamily \| Pathway: \| COG: Function unknown CD630_28650 - Type: Gene Product:Putative bacterioferritin \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_25690 - Type: Gene Product:Putative glycoside hydrolase, family 38; Putativealpha-mannosidase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_17290 - Type: Gene Product:Putative sodium:phosphate symporter \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_06590 - tcdR Type: Gene Product:Alternative RNA polymerase sigma factors \| Pathway: \| COG: CD630_03420 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_15730 - Type: Gene Product:Transcriptional regulator, HTH-type \| Pathway: \| COG: Transcription CD630_12510 - ftsY Type: Gene Product:signal recognition particle receptor \| Pathway: \| COG: Intracellular trafficking, secretion, and vesicular transport CD630_34550 - Type: Gene Product:Putative carboxy-terminal protease \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_06570 - cdu2 Type: Gene Product:Na(+)/H(+) antiporter \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_22440 - Type: Gene Product:Putative diguanylate kinase signaling protein \| Pathway: \| COG: Signal transduction mechanisms CD630_06610 - tcdE Type: Gene Product:Holin-like pore-forming protein \| Pathway: \| COG: Function unknown CD630_28690 - Type: Gene Product:Transcriptional regulator, sigma-54-dependent \| Pathway: \| COG: Transcription CD630_15110 - cotB Type: Gene Product:Spore outer coat layer protein CotB \| Pathway: \| COG: Function unknown CD630_23760 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown	5.2e-21	`NA`	0.46	Inferelator: 2 Hypergeometric: 0 TF Influences from Inferelator CD630_26420 - sigG Type: Gene Product:RNA polymerase sigma-G factor \| Pathway: \| COG: Transcription CD630_34990 - spoVT Type: Gene Product:Stage V sporulation protein T \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_272	29 CD630_06890 - Type: Gene Product:Putative nucleotide phosphodiesterase \| Pathway: \| COG: Nucleotide transport and metabolism CD630_18260 - metA Type: Gene Product:Homoserine O-succinyltransferase \| Pathway: Amino-acid biosynthesis \| COG: Amino acid transport and metabolism CD630_14900 - metI Type: Gene Product:ABC-type transport system, methionine-specificpermease \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_29670 - dpaB Type: Gene Product:Dipicolinate synthase subunit B \| Pathway: \| COG: Coenzyme transport and metabolism CD630_35230 - ksgA Type: Gene Product:Dimethyladenosine transferase(S-adenosylmethionine-6-N', N'-adenosyl(rRNA)dimethyltransferase) \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_29720 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_29700 - Type: Gene Product:Putative thiolase \| Pathway: \| COG: Lipid transport and metabolism CD630_21420 - Type: Gene Product:Putative transporter \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_29690 - Type: Gene Product:Putative AMP-binding protein \| Pathway: \| COG: Lipid transport and metabolism, Secondary metabolites biosynthesis, transport and catabolism CD630_01300 - metK Type: Gene Product:S-adenosylmethionine synthetase \| Pathway: Amino-acid biosynthesis \| COG: Coenzyme transport and metabolism CD630_16530 - Type: Gene Product:Putative Probable D-methionine-bindinglipoprotein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_00510 - gltX Type: Gene Product:Glutamyl-tRNA synthetase \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_06350 - Type: Gene Product:Putative hydrolase \| Pathway: \| COG: Function unknown CD630_05580 - glsA Type: Gene Product:Glutaminase (L-glutamine amidohydrolase) \| Pathway: \| COG: Amino acid transport and metabolism CD630_30630 - Type: Gene Product:Putative peptidase, S41 family \| Pathway: \| COG: Function unknown CD630_15160 - Type: Gene Product:Transcriptional regulator, MerR family \| Pathway: \| COG: Transcription CD630_18250 - metY Type: Gene Product:O-acetylhomoserine sulfhydrylase \| Pathway: \| COG: Amino acid transport and metabolism CD630_02440 - Type: Gene Product:Putative CDP-glycerol:Poly(glycerophosphate)glycerophosphotransferase \| Pathway: \| COG: Function unknown CD630_14910 - metQ Type: Gene Product:ABC-type transport system, methionine-specificsubstrate-binding lipoprotein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_35220 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_21410 - Type: Gene Product:Serine-type D-Ala-D-Ala carboxypeptidase \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_29680 - dpaA Type: Gene Product:Dipicolinate synthase subunit A \| Pathway: \| COG: Function unknown CD630_16520 - Type: Gene Product:Putative tellurium resistance protein \| Pathway: \| COG: Signal transduction mechanisms CD630_29710 - bioY Type: Gene Product:Biotin synthase \| Pathway: \| COG: Function unknown CD630_35240 - Type: Gene Product:Putative DNA-binding protein \| Pathway: \| COG: Replication, recombination and repair CD630_14890 - metN Type: Gene Product:ABC-type transport system, methionine-specificATP-binding protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_06340 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_17660 - Type: Gene Product:Putative lipoprotein \| Pathway: \| COG: CD630_05590 - Type: Gene Product:Transcriptional regulator, ArsR family \| Pathway: \| COG: Transcription	0.00000077	0.07	0.46	Inferelator: 3 Hypergeometric: 0 TF Influences from Inferelator CD630_06290 - Type: Gene Product:Transcriptional regulator, Crp family \| Pathway: \| COG: Transcription CD630_26420 - sigG Type: Gene Product:RNA polymerase sigma-G factor \| Pathway: \| COG: Transcription CD630_34990 - spoVT Type: Gene Product:Stage V sporulation protein T \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_1	18 CD630_12170 - Type: Gene Product:Putative glycosyl transferase, family 2 \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_12230 - drm Type: Gene Product:Phosphopentomutase (Phosphodeoxyribomutase) \| Pathway: Metabolic intermediate biosynthesis \| COG: Carbohydrate transport and metabolism CD630_12200 - nudF Type: Gene Product:Putative hydrolase, NUDIX family \| Pathway: \| COG: Nucleotide transport and metabolism CD630_12250 - pdp Type: Gene Product:Pyrimidine-nucleoside phosphorylase \| Pathway: \| COG: Nucleotide transport and metabolism CD630_36590 - Type: Gene Product:Putative signal transduction phosphoesterase \| Pathway: \| COG: Signal transduction mechanisms CD630_12160 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_12240 - pupG Type: Gene Product:Purine nucleoside phosphorylase \| Pathway: Purine metabolism \| COG: Nucleotide transport and metabolism CD630_12180 - Type: Gene Product:Putative glycosyl transferase \| Pathway: \| COG: Function unknown CD630_12190 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_36570 - dnaB Type: Gene Product:Replicative DNA helicase \| Pathway: \| COG: Replication, recombination and repair CD630_12220 - Type: Gene Product:Putative phage integrase site-specificrecombinase XerD-like \| Pathway: \| COG: Replication, recombination and repair CD630_36610 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_12150 - Type: Gene Product:Putative pyrophosphokinase, DUF115 family \| Pathway: \| COG: Function unknown CD630_12210 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: CD630_36630 - rpsF Type: Gene Product:30S ribosomal protein S6 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_36620 - ssb Type: Gene Product:Single-stranded DNA-binding protein(Helix-destabilizing protein) \| Pathway: \| COG: Replication, recombination and repair CD630_36580 - rplI Type: Gene Product:50S ribosomal protein L9 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_36611 - rpsR Type: Gene Product:30S ribosomal protein S18 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis	`NA`	`NA`	0.46	Inferelator: 1 Hypergeometric: 1 TF Influences from Inferelator CD630_05590 - Type: Gene Product:Transcriptional regulator, ArsR 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_34	6 CD630_15461 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_18930 - Type: Gene Product:Putative oligonucleotide binding regulator \| Pathway: \| COG: Function unknown CD630_06020 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_33331 - Type: Gene Product:Putative conjugative transposon proteinTn916-like, CTn6-Orf10 \| Pathway: \| COG: Function unknown CD630_33340 - Type: Gene Product:Putative transcriptional regulator Tn916-like,CTn6-Orf11 \| Pathway: \| COG: Function unknown	`NA`	`NA`	0.46	Inferelator: 3 Hypergeometric: 0 TF Influences from Inferelator CD630_19640 - Type: Gene Product:Putative transcriptional regulator \| Pathway: \| COG: Transcription CD630_23080 - Type: Gene Product:Transcriptional regulator, HTH-type \| Pathway: \| COG: Transcription CD630_26030 - cdtR Type: Gene Product:Clostridium difficile binary toxin regulatorygene, LytTR family \| Pathway: \| COG: Signal transduction mechanisms TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_84	23 CD630_32410 - prdB Type: Gene Product:Proline reductase (selenocysteine) \| Pathway: \| COG: Function unknown CD630_11730 - Type: Gene Product:Putative FAD-linked oxidase \| Pathway: \| COG: Energy production and conversion CD630_11710 - etfB Type: Gene Product:Electron transfer flavoprotein subunit alpha \| Pathway: \| COG: Energy production and conversion CD630_18980 - Type: Gene Product:Putative phage-related cell wall hydrolase(endolysin) \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_01430 - secA1 Type: Gene Product:Protein translocase subunit SecA1 \| Pathway: \| COG: Intracellular trafficking, secretion, and vesicular transport CD630_03060 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_32380 - Type: Gene Product:Putative component of proline reductaseprdE-like \| Pathway: \| COG: Function unknown CD630_09020 - Type: Gene Product:Putative cation efflux protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_24440 - Type: Gene Product:Putative ribosome-associated sigma 54 modulationprotein \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_13280 - recA Type: Gene Product:Protein RecA (Recombinase A) \| Pathway: \| COG: Replication, recombination and repair CD630_32360 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_15900 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_19000 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_32400 - prdD Type: Gene Product:Proline reductase PrdD \| Pathway: \| COG: Function unknown CD630_01440 - prfB Type: Gene Product:Peptide chain release factor 2 (RF-2) \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_03070 - Type: Gene Product:Putative chaperone protein \| Pathway: \| COG: Function unknown CD630_11700 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_11720 - etfA Type: Gene Product:Electron transfer flavoprotein subunit alpha \| Pathway: \| COG: Energy production and conversion CD630_01420 - Type: Gene Product:Putative RNA-binding protein \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_32390 - prdE Type: Gene Product:Proline reductase PrdE \| Pathway: \| COG: Function unknown CD630_32370 - prdF Type: Gene Product:Proline racemase \| Pathway: \| COG: Amino acid transport and metabolism CD630_18970 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_13290 - Type: Gene Product:RNase Y \| Pathway: \| COG: Function unknown	0.00000000000016	`NA`	0.46	Inferelator: 2 Hypergeometric: 3 TF Influences from Inferelator CD630_11770 - fapR Type: Gene Product:Transcriptional regulator, DeoR family (Fattyacid and phospholipid biosynthesis regulator) \| Pathway: \| COG: Transcription CD630_20480 - Type: Gene Product:Transcriptional regulator, RpiR family \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test CD630_32450 - prdR Type: Gene Product:Transcriptional regulator, sigma-54-dependent \| Pathway: \| COG: Transcription CD630_10640 - ccpA Type: Gene Product:Transcriptional regulator, LacI family \| Pathway: \| COG: Transcription CD630_31760 - glnF Type: Gene Product:RNA polymerase sigma-54 factor \| Pathway: \| COG: Transcription
Module_393	26 CD630_00670 - rpoC Type: Gene Product:DNA-directed RNA polymerase subunit beta' \| Pathway: \| COG: Transcription CD630_26720 - appA Type: Gene Product:ABC-type transport system, oligopeptide-familysolute-binding protein \| Pathway: \| COG: Amino acid transport and metabolism CD630_26700 - appF Type: Gene Product:ABC-type transport system, ATP-binding protein \| Pathway: \| COG: Amino acid transport and metabolism CD630_28520 - dltB Type: Gene Product:D-alanyl transferase DltB, MBOAT family \| Pathway: Cell wall biogenesis \| COG: Cell wall/membrane/envelope biogenesis CD630_05480 - Type: Gene Product:Putative penicillin-binding peptidase BlaR1-like,M56 family \| Pathway: \| COG: Transcription, Signal transduction mechanisms CD630_28540 - dltD Type: Gene Product:D-alanine transferase \| Pathway: Cell wall biogenesis \| COG: Cell wall/membrane/envelope biogenesis CD630_35560 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_28510 - dltC Type: Gene Product:D-alanine--poly(phosphoribitol) ligase subunit 2(D-alanyl carrier protein) (DCP) \| Pathway: Cell wall biogenesis \| COG: Cell wall/membrane/envelope biogenesis CD630_35540 - dusB Type: Gene Product:tRNA-dihydrouridine synthase \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_35520 - lysS Type: Gene Product:Lysyl-tRNA synthetase (Lysine--tRNA ligase)(LysRS) \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_18100 - Type: Gene Product:Transcriptional regulator, beta-lactamsrepressor \| Pathway: \| COG: Transcription CD630_07040 - Type: Gene Product:Putative metal-dependent phosphohydrolase \| Pathway: \| COG: Function unknown CD630_26710 - appD Type: Gene Product:ABC-type transport system, ATP-binding protein \| Pathway: \| COG: Amino acid transport and metabolism, Inorganic ion transport and metabolism CD630_00660 - rpoB Type: Gene Product:DNA-directed RNA polymerase subunit beta \| Pathway: \| COG: Transcription CD630_35580 - birA Type: Gene Product:BirA bifunctional protein [Includes: biotinoperon repressor and biotin--[acetyl-CoA-carboxylase]synthetase \| Pathway: \| COG: Coenzyme transport and metabolism CD630_28530 - dltA Type: Gene Product:D-alanine--poly(phosphoribitol) ligase subunit 1 \| Pathway: Cell wall biogenesis \| COG: Secondary metabolites biosynthesis, transport and catabolism CD630_19630 - Type: Gene Product:Putative methyltransferase \| Pathway: \| COG: Secondary metabolites biosynthesis, transport and catabolism CD630_35570 - Type: Gene Product:Putative peptidase \| Pathway: \| COG: Amino acid transport and metabolism, Secondary metabolites biosynthesis, transport and catabolism CD630_35530 - greA Type: Gene Product:Transcription elongation factor greA (Transcriptcleavage factor GreA) \| Pathway: \| COG: Transcription CD630_35550 - coaX Type: Gene Product:Type III pantothenate kinase (Pantothenic acidkinase) (PanK-III) \| Pathway: Cofactor biosynthesis \| COG: Transcription CD630_02030 - Type: Gene Product:Putative UvrABC system protein A 1 (UvrA protein1) (Excinuclease ABC subunit A 1) \| Pathway: \| COG: Replication, recombination and repair CD630_07030 - Type: Gene Product:Putative peptidase, U32 family \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_07050 - Type: Gene Product:Putative hydrolase, NUDIX family \| Pathway: \| COG: Replication, recombination and repair CD630_36690 - Type: Gene Product:Putative lipoprotein \| Pathway: \| COG: Function unknown CD630_05470 - Type: Gene Product:Transcriptional regulator, beta-lactamsrepressor \| Pathway: \| COG: Transcription CD630_26740 - appC Type: Gene Product:ABC-type transport system, oligopeptide-familypermease protein \| Pathway: \| COG: Inorganic ion transport and metabolism	0.0000000000019	`NA`	0.46	Inferelator: 1 Hypergeometric: 1 TF Influences from Inferelator CD630_18100 - Type: Gene Product:Transcriptional regulator, beta-lactamsrepressor \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test CD630_32450 - prdR Type: Gene Product:Transcriptional regulator, sigma-54-dependent \| Pathway: \| COG: Transcription