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 81 - 90 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_105	25 CD630_06730 - Type: Gene Product:Putative methyltransferase \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_19010 - Type: Gene Product:Transcriptional regulator, Phage-type \| Pathway: \| COG: Function unknown CD630_05220 - Type: Gene Product:Putative c-di-GMP regulatory protein \| Pathway: \| COG: Signal transduction mechanisms CD630_21500 - Type: Gene Product:Putative endonuclease/exonuclease/phosphatase \| Pathway: \| COG: Function unknown CD630_26150 - Type: Gene Product:Transcriptional regulator, TetR family \| Pathway: \| COG: Transcription CD630_23450 - Type: Gene Product:Transcriptional regulator, LysR family \| Pathway: \| COG: Transcription CD630_05130 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_22320 - asrB Type: Gene Product:Anaerobic sulfite reductase subunit B \| Pathway: \| COG: Energy production and conversion CD630_22300 - Type: Gene Product:Putative formate/nitrite transporter \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_17860 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_02040 - Type: Gene Product:Putative signaling protein \| Pathway: \| COG: Signal transduction mechanisms CD630_01632 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_01631 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_05230 - Type: Gene Product:Putative transcriptional regulator \| Pathway: \| COG: Function unknown CD630_26140 - Type: Gene Product:Conserved hypothetical protein, DegV family \| Pathway: \| COG: Function unknown CD630_22310 - asrC Type: Gene Product:Anaerobic sulfite reductase subunit C \| Pathway: \| COG: Energy production and conversion CD630_04560 - Type: Gene Product:ABC-type transport system, ATP-binding protein \| Pathway: \| COG: Replication, recombination and repair CD630_22330 - asrA Type: Gene Product:Anaerobic sulfite reductase subunit A (Anaerobicsulfite reductase iron-sulfur subunit) \| Pathway: \| COG: Energy production and conversion CD630_07070 - Type: Gene Product:Putative diguanylate kinase signaling protein \| Pathway: \| COG: Signal transduction mechanisms 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_30170 - Type: Gene Product:Putative glucose uptake protein \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_21800 - Type: Gene Product:Putative DEAD-like helicase \| Pathway: \| COG: Replication, recombination and repair	0	0.67	0.58	Inferelator: 3 Hypergeometric: 0 TF Influences from Inferelator CD630_02760 - Type: Gene Product:Transcriptional regulator, AraC family \| Pathway: \| COG: Transcription CD630_10640 - ccpA Type: Gene Product:Transcriptional regulator, LacI family \| Pathway: \| COG: Transcription CD630_27320 - Type: Gene Product:Transcriptional regulator, sigma-54-dependent \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
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_139	24 CD630_29340 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_18360 - pheA Type: Gene Product:Bifunctional P-protein, chorismatemutase/prephenate dehydratase \| Pathway: \| COG: Amino acid transport and metabolism CD630_18340 - aroA Type: Gene Product:3-phosphoshikimate 1-carboxyvinyltransferase \| Pathway: Metabolic intermediate biosynthesis \| 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_15510 - hisH Type: Gene Product:Imidazole glycerol phosphate synthase subunitHisH \| Pathway: Amino-acid biosynthesis \| COG: Amino acid transport and metabolism CD630_15530 - hisF Type: Gene Product:Imidazole glycerol phosphate synthase subunitHisF \| Pathway: Amino-acid biosynthesis \| COG: Amino acid transport and metabolism CD630_15470 - hisZ Type: Gene Product:ATP phosphoribosyltransferase regulatory subunit \| Pathway: \| COG: Amino acid transport and metabolism CD630_18390 - tyrC Type: Gene Product:Prephenate dehydrogenase \| Pathway: \| COG: Amino acid transport and metabolism CD630_29330 - Type: Gene Product:Hypothetical protein \| Pathway: \| COG: CD630_18330 - aroB Type: Gene Product:3-dehydroquinate synthase \| Pathway: Metabolic intermediate biosynthesis \| COG: Amino acid transport and metabolism CD630_29310 - Type: Gene Product:Putative phage endodeoxyribonuclease RusA-like \| Pathway: \| COG: Replication, recombination and repair CD630_18350 - aroC Type: Gene Product:Chorismate synthase(5-enolpyruvylshikimate-3-phosphate phospholyase) \| Pathway: Metabolic intermediate 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_18370 - aroE1 Type: Gene Product:Shikimate dehydrogenase 1 \| Pathway: Metabolic intermediate biosynthesis \| COG: Amino acid transport and metabolism CD630_29290 - Type: Gene Product:Putative phage 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_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_18380 - aroK Type: Gene Product:Shikimate kinase (SK) \| Pathway: Metabolic intermediate biosynthesis \| COG: Amino acid transport and metabolism CD630_15500 - hisB Type: Gene Product:Imidazoleglycerol-phosphate dehydratase \| Pathway: Amino-acid biosynthesis \| COG: Amino acid transport and metabolism CD630_29320 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_29300 - Type: Gene Product:Putative phage anti-repressor protein \| Pathway: \| COG: Transcription CD630_18320 - aroF Type: Gene Product:3-deoxy-D-arabino-heptulosonate 7-phosphatesynthase \| Pathway: \| COG: Amino acid transport and metabolism	`NA`	`NA`	0.58	Inferelator: 3 Hypergeometric: 1 TF Influences from Inferelator CD630_19960 - Type: Gene Product:Transcriptional regulator, AraC family \| Pathway: \| COG: Signal transduction mechanisms CD630_26150 - Type: Gene Product:Transcriptional regulator, TetR family \| Pathway: \| COG: Transcription CD630_32090 - Type: Gene Product:Transcriptional regulator, PadR family \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test CD630_12750 - codY Type: Gene Product:Transcriptional regulator, GTP-sensingpleiotropic repressor \| Pathway: \| COG: Transcription
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_291	31 CD630_21270 - Type: Gene Product:Putative exported protein \| Pathway: \| COG: CD630_25400 - Type: Gene Product:Coenzyme A disulfide reductase \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_05090 - Type: Gene Product:Transcriptional regulator, HTH-type Tn5397,CTn3-Orf9 \| Pathway: \| COG: Transcription CD630_05091 - Type: Gene Product:Putative conjugative transposon protein Tn5397,CTn3-Orf10 \| Pathway: \| COG: CD630_28880 - Type: Gene Product:ABC-type transport system, iron-family permease \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_19640 - Type: Gene Product:Putative transcriptional regulator \| Pathway: \| COG: Transcription CD630_10520 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_18410 - Type: Gene Product:Two-component sensor histidine kinase \| Pathway: \| COG: Signal transduction mechanisms CD630_21640 - ldh Type: Gene Product:L-lactate dehydrogenase (L-LDH) \| Pathway: Fermentation \| COG: Energy production and conversion CD630_18400 - Type: Gene Product:Putative diguanylate kinase signaling protein \| Pathway: \| COG: Signal transduction mechanisms CD630_04401 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_10480 - Type: Gene Product:Putative phosphodiesterase \| Pathway: \| COG: Function unknown CD630_25060 - LinCd Type: Gene Product:Transporter, Major Facilitator Superfamily (MFS) \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_09772 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_09771 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_03090 - Type: Gene Product:Putative hydrolase, HAD superfamily, subfamilyIB \| Pathway: \| COG: Amino acid transport and metabolism CD630_10500 - Type: Gene Product:ABC-type transport system, multidrug-familyATP-binding protein \| Pathway: \| COG: Defense mechanisms CD630_25040 - Type: Gene Product:Putative D-alanyl-D-alanine carboxypeptidase \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_33300 - Type: Gene Product:Transcriptional regulator, HTH-type Tn916-like,CTn6-Orf6 \| Pathway: \| COG: Transcription CD630_18310 - Type: Gene Product:Putative cation (Mg2+ and Co2+)transport-related, membrane protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_21340 - Type: Gene Product:Putative signaling protein \| Pathway: \| COG: Signal transduction mechanisms CD630_28890 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_10530 - Type: Gene Product:Putative aminoacyl-tRNA synthetase-associateddomain \| Pathway: \| COG: Function unknown CD630_10510 - Type: Gene Product:ABC-type transport system, multidrug-familypermease \| Pathway: \| COG: CD630_19630 - Type: Gene Product:Putative methyltransferase \| Pathway: \| COG: Secondary metabolites biosynthesis, transport and catabolism CD630_18420 - Type: Gene Product:Conserved hypothetical protein, DUF218 family \| Pathway: \| COG: Function unknown CD630_10490 - ppnK Type: Gene Product:Inorganic polyphosphate/ATP-NAD kinase(Poly(P)/ATP NAD kinase) \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_14990 - Type: Gene Product:Putative virulence factor, MviN family protein(Disrupted IStron) \| Pathway: Cell wall biogenesis \| COG: Signal transduction mechanisms, Signal transduction mechanisms CD630_31870 - tdcF Type: Gene Product:Putative regulatory endoribonuclease \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_25250 - recX Type: Gene Product:Regulatory protein RecX \| Pathway: \| COG: Function unknown CD630_25050 - Type: Gene Product:Transcriptional regulator, TetR family \| Pathway: \| COG: Transcription	2e-21	0.000016	0.57	Inferelator: 3 Hypergeometric: 0 TF Influences from Inferelator CD630_05090 - Type: Gene Product:Transcriptional regulator, HTH-type Tn5397,CTn3-Orf9 \| Pathway: \| COG: Transcription CD630_16920 - Type: Gene Product:Transcriptional regulator, ArsR family \| Pathway: \| COG: Transcription CD630_18400 - Type: Gene Product:Putative diguanylate kinase signaling protein \| Pathway: \| COG: Signal transduction mechanisms TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_96	6 CD630_12870 - fur Type: Gene Product:Transcriptional regulator, Fur family \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_31470 - Type: Gene Product:Putative DNA-methyltransferase \| Pathway: \| COG: Replication, recombination and repair CD630_36340 - Type: Gene Product:Transcriptional regulator, MerR family \| Pathway: \| COG: Transcription CD630_09740 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_29640 - Type: Gene Product:Putative tRNA-binding protein \| Pathway: \| COG: Function unknown CD630_05320 - Type: Gene Product:Putative transcriptional regulator \| Pathway: \| COG: Transcription	`NA`	`NA`	0.57	Inferelator: 2 Hypergeometric: 0 TF Influences from Inferelator CD630_05320 - Type: Gene Product:Putative transcriptional regulator \| Pathway: \| COG: Transcription CD630_12870 - fur Type: Gene Product:Transcriptional regulator, Fur family \| Pathway: \| COG: Inorganic ion transport and metabolism TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_113	11 CD630_21170 - trxB Type: Gene Product:Thioredoxin reductase \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_25400 - Type: Gene Product:Coenzyme A disulfide reductase \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_30360 - Type: Gene Product:Transporter, Major Facilitator Superfamily (MFS) \| Pathway: \| COG: Amino acid transport and metabolism CD630_08670 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_26691 - Type: Gene Product:Putative Na(+)/H(+) antiporter \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_17780 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_18990 - Type: Gene Product:Putative dCMP deaminase \| Pathway: \| COG: Nucleotide transport and metabolism CD630_09740 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_17770 - Type: Gene Product:Putative arsenate reductase \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_26120 - Type: Gene Product:Putative amino acid permease \| Pathway: \| COG: Amino acid transport and metabolism CD630_17452 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG:	4	`NA`	0.57	Inferelator: 3 Hypergeometric: 0 TF Influences from Inferelator CD630_16920 - Type: Gene Product:Transcriptional regulator, ArsR family \| Pathway: \| COG: Transcription 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 TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_130	28 CD630_00010 - dnaA Type: Gene Product:Chromosomal replication initiator protein \| Pathway: \| COG: Replication, recombination and repair CD630_00110 - sigB Type: Gene Product:RNA polymerase sigma-B factor \| Pathway: \| COG: Transcription CD630_00030 - Type: Gene Product:Putative RNA-binding mediating protein \| Pathway: \| COG: Function unknown CD630_00070 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_00050 - gyrB Type: Gene Product:DNA gyrase subunit B \| Pathway: \| COG: Replication, recombination and repair CD630_17460 - gltC Type: Gene Product:Sodium/glutamate symporter \| Pathway: \| COG: Amino acid transport and metabolism CD630_00090 - rsbV Type: Gene Product:Anti-anti-sigma factor \| Pathway: \| COG: Signal transduction mechanisms CD630_24910 - pmi Type: Gene Product:Mannose-6-phosphate isomerase (Phosphomannoseisomerase) (PMI) (Phosphohexomutase) \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_21070 - Type: Gene Product:Xanthine/uracil/thiamine/ascorbate permeasefamily protein \| Pathway: \| COG: Function unknown CD630_16900 - trxA Type: Gene Product:Thioredoxin \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_24820 - Type: Gene Product:Putative lipoprotein \| Pathway: \| COG: Function unknown CD630_18000 - terD Type: Gene Product:Tellurium resistance protein \| Pathway: \| COG: Signal transduction mechanisms CD630_26160 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_00040 - recF Type: Gene Product:DNA replication and repair protein RecF \| Pathway: \| COG: Replication, recombination and repair CD630_24830 - Type: Gene Product:Putative lipoprotein \| Pathway: \| COG: Coenzyme transport and metabolism CD630_00020 - dnaN Type: Gene Product:DNA polymerase III subunit beta \| Pathway: \| COG: Replication, recombination and repair CD630_32290 - dapB2 Type: Gene Product:Dihydrodipicolinate reductase 2 (DHPR 2) \| Pathway: Amino-acid biosynthesis \| COG: Amino acid transport and metabolism CD630_00060 - gyrA Type: Gene Product:DNA gyrase subunit A \| Pathway: \| COG: Replication, recombination and repair CD630_04030 - fba Type: Gene Product:Fructose-1,6-bisphosphate aldolase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_24900 - Type: Gene Product:Putative peptidase, M20A family \| Pathway: \| COG: Amino acid transport and metabolism CD630_17451 - feoA Type: Gene Product:Ferrous iron transport protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_01070 - aspC Type: Gene Product:Aspartate aminotransferase \| Pathway: \| COG: Amino acid transport and metabolism CD630_24411 - Type: Gene Product:PhoH-like protein \| Pathway: \| COG: Signal transduction mechanisms CD630_28290 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Amino acid transport and metabolism, Carbohydrate transport and metabolism CD630_24810 - ung Type: Gene Product:Uracil-DNA glycosylase (UDG) \| Pathway: \| COG: Replication, recombination and repair CD630_20590 - glnS Type: Gene Product:Glutaminyl-tRNA synthetase \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_13390 - aspB Type: Gene Product:Aspartate aminotransferase (AspAT) (TransaminaseA) \| Pathway: \| COG: Amino acid transport and metabolism CD630_16910 - trxB Type: Gene Product:Putative thioredoxin-disulfide reductase \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones	2.1e-32	6.4	0.57	Inferelator: 3 Hypergeometric: 0 TF Influences from Inferelator CD630_16920 - Type: Gene Product:Transcriptional regulator, ArsR family \| Pathway: \| COG: Transcription CD630_17820 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms CD630_22200 - Type: Gene Product:Putative cyclic nucleotides-binding protein \| Pathway: \| COG: Signal transduction mechanisms TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_313	20 CD630_29460 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_25320 - Type: Gene Product:Aminotransferase, alanine--glyoxylatetransaminase \| Pathway: \| COG: Amino acid transport and metabolism CD630_14310 - Type: Gene Product:Putative helicase, DinG family \| Pathway: \| COG: Replication, recombination and repair CD630_29470 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_29471 - Type: Gene Product:Hypothetical protein \| Pathway: \| COG: CD630_25300 - Type: Gene Product:Transcriptional regulator, AraC family \| Pathway: \| COG: Transcription CD630_00340 - Type: Gene Product:Putative xylose transporter, sodium:galactosidesymporter family \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_29430 - Type: Gene Product:Putative phage replication protein \| Pathway: \| COG: Replication, recombination and repair CD630_25310 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_29450 - Type: Gene Product:Putative bacteriophage resistance protein \| Pathway: \| COG: Function unknown CD630_25290 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_29440 - Type: Gene Product:Putative phage essential recombination functionprotein \| Pathway: \| COG: Replication, recombination and repair CD630_29520 - Type: Gene Product:Putative phage site-specific integrase \| Pathway: \| COG: Replication, recombination and repair CD630_29490 - Type: Gene Product:Transcriptional regulator, Phage-type \| Pathway: \| COG: Transcription CD630_29420 - Type: Gene Product:Putative phage resolvase/integrase \| Pathway: \| COG: CD630_29480 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: Transcription CD630_00330 - Type: Gene Product:Putative glycoside hydrolase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_14320 - Type: Gene Product:Putative ribonuclease \| Pathway: \| COG: Function unknown CD630_00320 - Type: Gene Product:Putative beta-glucosidase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_29500 - Type: Gene Product:Transcriptional regulator, HTH-type \| Pathway: \| COG: Transcription	0.06	`NA`	0.57	Inferelator: 1 Hypergeometric: 0 TF Influences from Inferelator CD630_25300 - Type: Gene Product:Transcriptional regulator, AraC family \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`