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 321 - 330 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_299	20 CD630_28090 - Type: Gene Product:Conserved hypothetical protein, DUF1540 family \| Pathway: \| COG: Function unknown CD630_29150 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_29170 - Type: Gene Product:Putative scaffold protein \| Pathway: \| COG: Function unknown CD630_28970 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: Function unknown CD630_03110 - GerG Type: Gene Product:Germination regulator \| Pathway: \| COG: CD630_29000 - Type: Gene Product:Putative phage tail protein \| Pathway: \| COG: Function unknown CD630_29010 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: Function unknown CD630_29030 - Type: Gene Product:Putative phage tail protein \| Pathway: \| COG: Function unknown CD630_10633 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_29140 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: Function unknown CD630_29120 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: Function unknown CD630_28980 - Type: Gene Product:Putative phage tail fiber protein \| Pathway: \| COG: Function unknown CD630_29020 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: Function unknown CD630_29050 - Type: Gene Product:Putative phage tail tape measure protein \| Pathway: \| COG: Function unknown CD630_10632 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_28080 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_29040 - Type: Gene Product:Putative phage cell wall hydrolase \| Pathway: \| COG: Function unknown CD630_29090 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: Function unknown CD630_29060 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_29080 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: Function unknown	0	`NA`	0.57	Inferelator: 1 Hypergeometric: 1 TF Influences from Inferelator CD630_34990 - spoVT Type: Gene Product:Stage V sporulation protein T \| 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_187	27 CD630_14880 - Type: Gene Product:Transcriptional regulator, DeoR family \| Pathway: \| COG: Transcription CD630_26760 - thlA2 Type: Gene Product:Acetoacetyl-CoA thiolase 2 \| Pathway: \| COG: Lipid transport and metabolism CD630_02330 - fliW Type: Gene Product:Flagellar assembly factor FliW \| Pathway: \| COG: Signal transduction mechanisms CD630_02370 - fliD Type: Gene Product:Flagellar hook-associated protein 2 FliD (orHAP2) \| Pathway: \| COG: Cell motility CD630_02310 - flgK Type: Gene Product:Flagellar hook-associated protein FlgK (or HAP1) \| Pathway: \| COG: Cell motility CD630_19520 - Type: Gene Product:Transcriptional regulator, LysR family \| Pathway: \| COG: Transcription CD630_02350 - fliS1 Type: Gene Product:Flagellar protein FliS1 \| Pathway: \| COG: Cell motility CD630_02270 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_26790 - bdhA Type: Gene Product:3-hydroxybutyrate dehydrogenase \| Pathway: \| COG: Function unknown CD630_02780 - Type: Gene Product:Transcriptional regulator, hxlR family \| Pathway: \| COG: Transcription CD630_02280 - fliN Type: Gene Product:Flagellar motor switch protein FliN \| Pathway: \| COG: Cell motility CD630_02380 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_26770 - scoA Type: Gene Product:Succinyl CoA:3-oxoacid CoA-transferase subunit A \| Pathway: \| COG: Lipid transport and metabolism CD630_14870 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_13830 - Type: Gene Product:Transcriptional regulator, GntR family \| Pathway: \| COG: Transcription CD630_02320 - flgL Type: Gene Product:Flagellar hook-associated protein FlgL (or HAP3) \| Pathway: \| COG: Cell motility CD630_07370 - hisK Type: Gene Product:Histidinol-phosphatase (HolPase) \| Pathway: Amino-acid biosynthesis \| COG: Amino acid transport and metabolism CD630_19530 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_02300 - Type: Gene Product:Putative flagellar biosynthesis protein \| Pathway: \| COG: Function unknown CD630_02260 - Type: Gene Product:Putative lytic transglycosylase \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_02340 - csrA Type: Gene Product:Carbon storage regulator \| Pathway: \| COG: Signal transduction mechanisms CD630_02360 - fliS2 Type: Gene Product:Flagellar protein FliS2 \| Pathway: \| COG: Cell motility CD630_02790 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_26800 - Type: Gene Product:Putative permease \| Pathway: \| COG: Amino acid transport and metabolism, Carbohydrate transport and metabolism CD630_02290 - flgM Type: Gene Product:Anti-sigma factor repressor of sigma(D)-dependenttranscription \| Pathway: \| COG: CD630_26780 - scoB Type: Gene Product:Succinyl CoA:3-oxoacid CoA-transferase subunit B \| Pathway: \| COG: Lipid transport and metabolism CD630_02390 - fliC Type: Gene Product:Flagellin C \| Pathway: \| COG: Cell motility	0.01	0.04	0.57	Inferelator: 0 Hypergeometric: 1 TF Influences from Inferelator `No TF influences from Inferelator` TF Influences from Hypergeometric Test CD630_02660 - sigD Type: Gene Product:RNA polymerase sigma-28 factor for flagellaroperon \| Pathway: \| COG: Transcription
Module_318	21 CD630_29780 - Type: Gene Product:Putative CRISPR-associated Cas3 family helicase \| Pathway: \| COG: Replication, recombination and repair CD630_07150 - ptb Type: Gene Product:Phosphate butyryltransferase(Phosphotransbutyrylase) \| Pathway: \| COG: Energy production and conversion CD630_29790 - Type: Gene Product:Putative CRISPR-associated Cas5 family protein \| Pathway: \| COG: Replication, recombination and repair CD630_21150 - Type: Gene Product:Putative copper-transporting P-type ATPase \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_29820 - Type: Gene Product:Putative CRISPR-associated Cas6 family protein \| Pathway: \| COG: Replication, recombination and repair CD630_27500 - agrB Type: Gene Product:Accessory gene regulator \| Pathway: \| COG: Signal transduction mechanisms CD630_29770 - Type: Gene Product:Putative CRISPR-associated Cas4 family protein \| Pathway: \| COG: Replication, recombination and repair CD630_31720 - tpi Type: Gene Product:Triosephosphate isomerase (TIM) (Triose-phosphateisomerase) \| Pathway: Carbohydrate biosynthesis \| COG: Carbohydrate transport and metabolism CD630_31710 - gpmI Type: Gene Product:2,3-bisphosphoglycerate-independentphosphoglycerate mutase (Phosphoglyceromutase)(BPG-independent PGAM) (iPGM) \| Pathway: Carbohydrate degradation \| COG: Carbohydrate transport and metabolism CD630_29760 - Type: Gene Product:Putative CRISPR-associated Cas1 family protein \| Pathway: \| COG: Replication, recombination and repair CD630_27491 - agrD Type: Gene Product:Autoinducer prepeptide \| Pathway: \| COG: CD630_31730 - pgk Type: Gene Product:Phosphoglycerate kinase \| Pathway: Carbohydrate degradation \| COG: Carbohydrate transport and metabolism CD630_07140 - Type: Gene Product:Putative protein involved in protein-proteininteractions \| Pathway: \| COG: Function unknown CD630_29750 - Type: Gene Product:Putative CRISPR-associated Cas2 family protein \| Pathway: \| COG: Replication, recombination and repair CD630_07121 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_31740 - gapA Type: Gene Product:Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_07130 - Type: Gene Product:Putative radical SAM domain-containing protein \| Pathway: \| COG: Energy production and conversion CD630_29810 - Type: Gene Product:Putative CRISPR-associated protein, CXXC-CXXC \| Pathway: \| COG: Replication, recombination and repair CD630_20720 - Type: Gene Product:Putative transposase \| Pathway: \| COG: Replication, recombination and repair CD630_31750 - cggR Type: Gene Product:Transcriptional regulator, SorC family \| Pathway: \| COG: Transcription CD630_29800 - Type: Gene Product:Putative CRISPR-associated autoregulator DevRfamily protein protein \| Pathway: \| COG: Replication, recombination and repair	0	1.8	0.58	Inferelator: 1 Hypergeometric: 2 TF Influences from Inferelator CD630_31750 - cggR Type: Gene Product:Transcriptional regulator, SorC 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
Module_191	28 CD630_01620 - Type: Gene Product:Putative radical SAM-family protein \| Pathway: \| COG: Function unknown CD630_13000 - pepA Type: Gene Product:Leucine aminopeptidase \| Pathway: \| COG: Amino acid transport and metabolism CD630_04410 - Type: Gene Product:Transcriptional regulator, sigma-54-dependent \| Pathway: \| COG: Transcription CD630_01600 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms CD630_28310 - Type: Gene Product:Collagen binding protein \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_28350 - abgT Type: Gene Product:Aminobenzoyl-glutamate transport protein \| Pathway: \| COG: Coenzyme transport and metabolism CD630_02410 - Type: Gene Product:Phosphate-threonine kinase \| Pathway: \| COG: Amino acid transport and metabolism CD630_32830 - pflE Type: Gene Product:Pyruvate formate-lyase (activating enzyme) \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_36390 - Type: Gene Product:Transcriptional regulator, LysR family \| Pathway: \| COG: Transcription CD630_12980 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_02020 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_24310 - Type: Gene Product:Putative nitrite/sulphite reductase \| Pathway: \| COG: Energy production and conversion CD630_01632 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_01630 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_01631 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_02750 - splB Type: Gene Product:Spore photoproduct (thymine dimer) lyase, radicalS-adenosylmethionine superfamily \| Pathway: \| COG: Replication, recombination and repair CD630_01610 - Type: Gene Product:ABC-type transport system, multidrug-familyATP-binding protein \| Pathway: \| COG: Defense mechanisms CD630_01290 - Type: Gene Product:Conserved hypothetical protein, DUF1256 family \| Pathway: \| COG: Function unknown CD630_02420 - Type: Gene Product:Phosphothreonine N-acetylglucosamine catalysis \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_28340 - glyA Type: Gene Product:Serine hydroxymethyltransferase (Serinemethylase) (SHMT) \| Pathway: Amino-acid biosynthesis \| COG: Amino acid transport and metabolism CD630_28360 - Type: Gene Product:Putative peptidase, M20D family \| Pathway: \| COG: Amino acid transport and metabolism CD630_00181 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_05750 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_32820 - pflD Type: Gene Product:Pyruvate formate-lyase \| Pathway: \| COG: Energy production and conversion CD630_12990 - Type: Gene Product:Transcriptional regulator, MarR family \| Pathway: \| COG: Transcription CD630_32140 - Type: Gene Product:Transcriptional regulator, AraC family \| Pathway: \| COG: Transcription CD630_12970 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG:	0.0000000000000077	`NA`	0.58	Inferelator: 3 Hypergeometric: 0 TF Influences from Inferelator CD630_16930 - Type: Gene Product:Putative dinitrogenase iron-molybdenum cofactor \| Pathway: \| COG: Function unknown CD630_19100 - eutV Type: Gene Product:Two-component response regulator, Ethanolaminespecific \| Pathway: \| COG: Signal transduction mechanisms CD630_31750 - cggR Type: Gene Product:Transcriptional regulator, SorC family \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_241	32 CD630_14860 - Type: Gene Product:Putative ribosome recycling factor \| Pathway: \| COG: CD630_20000 - isp Type: Gene Product:Intracellular serine protease \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_20432 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_23030 - Type: Gene Product:Fragment of putative phage transcriptionalrepressor (N-terminal region) \| Pathway: \| COG: Transcription CD630_01721 - fdxA Type: Gene Product:Ferredoxin (4Fe-4S cluster-containing protein)(fdx-like) \| Pathway: \| COG: Energy production and conversion CD630_06920 - Type: Gene Product:Putative metallo-hydrolase/oxidoreductase \| Pathway: \| COG: Function unknown CD630_14370 - Type: Gene Product:Fragment of transcriptional regulator,sigma-54-dependent (N-terminal region) \| Pathway: \| COG: Transcription CD630_28450 - rbr Type: Gene Product:Rubrerythrin \| Pathway: \| COG: Energy production and conversion CD630_07540 - thiI Type: Gene Product:Thiamine biosynthesis protein ThiI \| Pathway: Cofactor biosynthesis \| COG: Coenzyme transport and metabolism CD630_21420 - Type: Gene Product:Putative transporter \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_07560 - Type: Gene Product:Nitroreductase \| Pathway: \| COG: Energy production and conversion CD630_22460 - cspC Type: Gene Product:Germination- specific protease \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_31840 - dpaL Type: Gene Product:Diaminopropionate ammonia-lyase \| Pathway: \| COG: Amino acid transport and metabolism CD630_34540 - Type: Gene Product:Putative nucleotide-binding protein \| Pathway: \| COG: Function unknown CD630_22470 - cspBA Type: Gene Product:Subtilisin-like serine germination relatedprotease \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_26810 - Type: Gene Product:Putative sporulation protein \| Pathway: \| COG: Secondary metabolites biosynthesis, transport and catabolism CD630_06000 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Transcription CD630_17291 - Type: Gene Product:Fragment of putative transcriptional regulator,AraC family (C-terminal region) \| Pathway: \| COG: Signal transduction mechanisms CD630_21710 - Type: Gene Product:Fragment of putative sodium:dicarboxylatesymporter (Part 2) \| Pathway: \| COG: Energy production and conversion, Energy production and conversion CD630_25410 - Type: Gene Product:Sodium:glutamate/aspartate symporter family \| Pathway: \| COG: Function unknown CD630_29521 - Type: Gene Product:Fragment of ABC-type transport system,ATP-binding protein (Part 11) \| Pathway: \| COG: Amino acid transport and metabolism, Function unknown, Amino acid transport and metabolism CD630_03150 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_07530 - iscS1 Type: Gene Product:Cysteine desulfurase \| Pathway: \| COG: Amino acid transport and metabolism CD630_14300 - pdaA Type: Gene Product:Exported N-acetylmuramic acid deacetylase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_05102 - Type: Gene Product:Fragment of putative conjugative transposonprotein Tn5397, CTn3-Orf5 (C-terminal region) \| Pathway: \| COG: CD630_07660 - srlEb Type: Gene Product:PTS system, sorbitol-specific IIB C-terminalcomponent (Glucitol) \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_01210 - Type: Gene Product:Putative thiosulfate sulfurtransferase \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_23620 - Type: Gene Product:Fragment of ABC-type transport system, permease(Part 2) \| Pathway: \| COG: Function unknown, Inorganic ion transport and metabolism CD630_22451 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_09030 - Type: Gene Product:Fragment of putative oxydoreductase (Part 1) \| Pathway: \| COG: Energy production and conversion, Energy production and conversion CD630_35800 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_20140 - ilvD Type: Gene Product:Dihydroxy-acid dehydratase \| Pathway: Amino-acid biosynthesis \| COG: Amino acid transport and metabolism	`NA`	`NA`	0.58	Inferelator: 1 Hypergeometric: 1 TF Influences from Inferelator CD630_34990 - spoVT Type: Gene Product:Stage V sporulation protein T \| 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_289	10 CD630_10790 - Type: Gene Product:Transcriptional regulator, LysR family \| Pathway: \| COG: Transcription CD630_13770 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_36220 - Type: Gene Product:Conserved hypothetical protein, PhnA family \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_06052 - Type: Gene Product: \| Pathway: \| COG: CD630_06080 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_19860 - miaB Type: Gene Product:(Dimethylallyl)adenosine tRNAmethylthiotransferase miaB (tRNA-i(6)A37methylthiotransferase) \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_21120 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_29730 - Type: Gene Product:Putative acetyltransferase \| Pathway: \| COG: Transcription CD630_13930 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Amino acid transport and metabolism, Carbohydrate transport and metabolism CD630_05860 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown	0.02	`NA`	0.58	Inferelator: 1 Hypergeometric: 0 TF Influences from Inferelator 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_227	24 CD630_03780 - Type: Gene Product:Putative conjugative transposon proteinTn916-like, CTn1-Orf23 \| Pathway: \| COG: Function unknown CD630_27340 - Type: Gene Product:Putative Na+/H+ antiporter, NhaC family \| Pathway: \| COG: Energy production and conversion CD630_19340 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_33701 - Type: Gene Product:Putative conjugative transposon proteinTn916-like, CTn7-Orf2 \| Pathway: \| COG: Function unknown CD630_33861 - Type: Gene Product:Putative conjugative transposon proteinTn916-like, CTn7-Orf23 \| Pathway: \| COG: Function unknown CD630_32950 - pilC Type: Gene Product:Type IV pilus secretion protein \| Pathway: \| COG: Intracellular trafficking, secretion, and vesicular transport CD630_28430 - Type: Gene Product:Putative zinc-binding dehydrogenase \| Pathway: \| COG: Energy production and conversion CD630_32970 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_32930 - pilMN Type: Gene Product:Type IV pilus assembly protein \| Pathway: \| COG: Function unknown CD630_32910 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_19330 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_33340 - Type: Gene Product:Putative transcriptional regulator Tn916-like,CTn6-Orf11 \| Pathway: \| COG: Function unknown CD630_33710 - Type: Gene Product:Putative conjugative transposon proteinTn916-like, CTn7-Orf3 \| Pathway: \| COG: Function unknown CD630_27330 - Type: Gene Product:Putative pyridoxal phosphate-dependenttransferase \| Pathway: \| COG: Amino acid transport and metabolism CD630_30240 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_28440 - Type: Gene Product:Transcriptional regulator, MarR family \| Pathway: \| COG: Transcription CD630_32940 - pilA Type: Gene Product:Type IV pilus protein PilA \| Pathway: \| COG: Intracellular trafficking, secretion, and vesicular transport CD630_32960 - pilB Type: Gene Product:Type IV pilus transporter system, ATP-binding \| Pathway: \| COG: Intracellular trafficking, secretion, and vesicular transport CD630_32920 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_05140 - cwpV Type: Gene Product:Cell surface protein \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_06220 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_33720 - Type: Gene Product:Putative conjugative transposon proteinTn916-like, CTn7-Orf4 \| Pathway: \| COG: CD630_33331 - Type: Gene Product:Putative conjugative transposon proteinTn916-like, CTn6-Orf10 \| Pathway: \| COG: Function unknown CD630_30230 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG:	0.00006	0.04	0.58	Inferelator: 2 Hypergeometric: 0 TF Influences from Inferelator CD630_23900 - Type: Gene Product:Transcriptional regulator, beta-lactamsrepressor \| Pathway: \| COG: Transcription CD630_30540 - 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_326	19 CD630_11040 - Type: Gene Product:Putative conjugative transposon proteinTn1549-like, CTn4-Orf19 \| Pathway: \| COG: Function unknown CD630_27610 - Type: Gene Product:Putative N-acetylmuramoyl-L-alanine amidase \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_21480 - Type: Gene Product:Putative serine/threonine protein kinase \| Pathway: \| COG: Signal transduction mechanisms CD630_18980 - Type: Gene Product:Putative phage-related cell wall hydrolase(endolysin) \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_01060 - cwlD Type: Gene Product:Germination-specific N-acetylmuramoyl-L-alanineamidase, Autolysin \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_22550 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_32290 - dapB2 Type: Gene Product:Dihydrodipicolinate reductase 2 (DHPR 2) \| Pathway: Amino-acid biosynthesis \| COG: Amino acid transport and metabolism CD630_16671 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_20640 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_04950 - Type: Gene Product:Fragment of putative regulatory protein (Part 1) \| Pathway: \| COG: Function unknown, Function unknown CD630_28150 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_18030 - cwp23 Type: Gene Product:Putative cell wall-binding protein \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_18970 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_07120 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_10360 - cwp17 Type: Gene Product:Putative N-acetylmuramoyl-L-alanine amidase,autolysin \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_27950 - cwp11 Type: Gene Product:Cell wall binding protein \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_32230 - dapA2 Type: Gene Product:Dihydrodipicolinate synthase 2 \| Pathway: Amino-acid biosynthesis \| COG: Amino acid transport and metabolism CD630_20980 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_28160 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG:	0.0000000048	`NA`	0.58	Inferelator: 4 Hypergeometric: 0 TF Influences from Inferelator CD630_06700 - Type: Gene Product:Transcriptional regulator, beta-lactamsrepressor \| Pathway: \| COG: Transcription CD630_06930 - Type: Gene Product:Transcriptional regulator, MerR family \| Pathway: \| COG: Transcription CD630_20480 - Type: Gene Product:Transcriptional regulator, RpiR family \| Pathway: \| COG: Transcription CD630_23900 - Type: Gene Product:Transcriptional regulator, beta-lactamsrepressor \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_22	25 CD630_36051 - Type: Gene Product:Ferredoxin \| Pathway: \| COG: Energy production and conversion CD630_18300 - kdpE Type: Gene Product:Two-component response regulator KdpE \| Pathway: \| COG: Signal transduction mechanisms CD630_19760 - mutL Type: Gene Product:DNA mismatch repair protein MutL \| Pathway: \| COG: Replication, recombination and repair CD630_17430 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms CD630_17440 - Type: Gene Product:Two-component sensor histidine kinase \| Pathway: \| COG: Signal transduction mechanisms CD630_25950 - pyrR Type: Gene Product:Bifunctional protein PyrR [Includes: Pyrimidineoperon regulatory protein; Uracil phosphoribosyltransferase(UPRTase)] \| Pathway: \| COG: Nucleotide transport and metabolism CD630_25940 - uraA Type: Gene Product:Putative uracil permease \| Pathway: \| COG: Nucleotide transport and metabolism CD630_16140 - Type: Gene Product:ABC-type transport system, ATP-binding protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_18290 - kdpD Type: Gene Product:Two-component sensor histidine kinase KdpD \| Pathway: \| COG: Signal transduction mechanisms CD630_27660 - LcpB Type: Gene Product:Surface-anchoring factors, LytR-CpsA-Psr-likeprotein \| Pathway: \| COG: Transcription CD630_24110 - Type: Gene Product:Putative positive regulator of gluconeogenesis;putative phosphotransferase \| Pathway: \| COG: Function unknown CD630_24350 - recO Type: Gene Product:DNA repair protein RecO (Recombination proteinO) \| Pathway: \| COG: Replication, recombination and repair CD630_36060 - Type: Gene Product:Putative hydrolase \| Pathway: \| COG: Function unknown CD630_19770 - mutS Type: Gene Product:DNA mismatch repair protein MutS \| Pathway: \| COG: Replication, recombination and repair CD630_19730 - Type: Gene Product:Putative pyridoxal phosphate-dependenttransferase; putative aluminium resistance \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_19750 - miaA Type: Gene Product:tRNA delta(2)-isopentenylpyrophosphatetransferase \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_36080 - Type: Gene Product:ABC-type transport system, ATP-binding protein \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_16130 - cotA Type: Gene Product:Spore outer coat layer protein CotA \| Pathway: \| COG: CD630_17450 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_16150 - Type: Gene Product:ABC-type transport system, permease \| Pathway: \| COG: Defense mechanisms CD630_24100 - ppdK Type: Gene Product:Pyruvate phosphate dikinase (ATP:pyruvate,phosphate phosphotransferase) \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_24450 - Type: Gene Product:Putative transmembrane signaling protein,TspO/MBR family \| Pathway: \| COG: Signal transduction mechanisms CD630_36070 - Type: Gene Product:Putative iron-sulfur assembly protein \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_24120 - Type: Gene Product:Putative negative regulator of gluconeogenesis \| Pathway: \| COG: Transcription CD630_24340 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown	0.000000000004	`NA`	0.58	Inferelator: 4 Hypergeometric: 0 TF Influences from Inferelator CD630_19100 - eutV Type: Gene Product:Two-component response regulator, Ethanolaminespecific \| Pathway: \| COG: Signal transduction mechanisms CD630_26380 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms CD630_26400 - nrdR Type: Gene Product:Transcriptional regulator, repressor NrdR family \| 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_38	22 CD630_11320 - Type: Gene Product:Putative heavy-metal transport/detoxificationprotein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_t0510 - tRNA-Thr Type: Gene Product: \| Pathway: \| COG: CD630_13140 - truB Type: Gene Product:tRNA pseudouridine synthase B \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_13160 - rpsO Type: Gene Product:30S ribosomal protein S15 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_11300 - Type: Gene Product:Putative lytic transglycosylase-like protein \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_04550 - Type: Gene Product:Putative helicase, UvrD family \| Pathway: \| COG: Replication, recombination and repair CD630_t0490 - tRNA-Val Type: Gene Product: \| Pathway: \| COG: CD630_t0720 - tRNA-Met Type: Gene Product: \| Pathway: \| COG: CD630_t0130 - tRNA-Arg Type: Gene Product: \| Pathway: \| COG: CD630_t0030 - tRNA-Asn Type: Gene Product: \| Pathway: \| COG: CD630_11290 - coaE Type: Gene Product:Dephospho-CoA kinase (Dephosphocoenzyme Akinase) \| Pathway: Cofactor biosynthesis \| COG: Coenzyme transport and metabolism CD630_t0400 - tRNA-Met Type: Gene Product: \| Pathway: \| COG: CD630_13150 - ribC Type: Gene Product:Riboflavin biosynthesis protein \| Pathway: Cofactor biosynthesis \| COG: Coenzyme transport and metabolism CD630_13151 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_t0540 - tRNA-Arg Type: Gene Product: \| Pathway: \| COG: CD630_t0770 - tRNA-Gly Type: Gene Product: \| Pathway: \| COG: CD630_t0670 - tRNA-Leu Type: Gene Product: \| Pathway: \| COG: CD630_t0480 - tRNA-Glu Type: Gene Product: \| Pathway: \| COG: CD630_t0280 - tRNA-Val Type: Gene Product: \| Pathway: \| COG: CD630_35511 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_11280 - polA Type: Gene Product:DNA polymerase I (POLI) \| Pathway: \| COG: Replication, recombination and repair CD630_t0090 - tRNA-Asp Type: Gene Product: \| Pathway: \| COG:	0	2.29995e-41	0.58	Inferelator: 1 Hypergeometric: 1 TF Influences from Inferelator CD630_26400 - nrdR Type: Gene Product:Transcriptional regulator, repressor NrdR 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