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 301 - 310 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_387	26 CD630_28760 - fhuG Type: Gene Product:ABC-type transport system, ferrichrome-specificpermease \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_28780 - fhuD Type: Gene Product:ABC-type transport system, ferrichrome-specificextracellular solute-binding protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_21060 - Type: Gene Product:Putative ATP-dependent RNA helicase \| Pathway: \| COG: Replication, recombination and repair CD630_28740 - Type: Gene Product:Putative drug/sodium antiporter, MATE family \| Pathway: \| COG: Defense mechanisms CD630_04790 - spaE Type: Gene Product:ABC-type transport system,lantibiotic/multidrug-family permease \| Pathway: \| COG: Function unknown CD630_21040 - Type: Gene Product:ABC-type transport system, permease \| Pathway: \| COG: Function unknown CD630_14410 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_04850 - Type: Gene Product:Two-component sensor histidine kinase \| Pathway: \| COG: Signal transduction mechanisms CD630_12330 - cwp26 Type: Gene Product:Putative cell surface protein \| Pathway: \| COG: Function unknown CD630_18020 - Type: Gene Product:Putative hydrolase, metallo-beta-lactamasesuperfamily \| Pathway: \| COG: Function unknown CD630_22430 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: CD630_04810 - spaR Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms CD630_21050 - Type: Gene Product:ABC-type transport system, multidrug-familyATP-binding protein \| Pathway: \| COG: Defense mechanisms CD630_28770 - fhuB Type: Gene Product:ABC-type transport system, ferrichrome-specificpermease \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_28750 - fhuC Type: Gene Product:ABC-type transport system, ferrichrome-specificATP-binding protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_12120 - bltD Type: Gene Product:Diamine N-acetyltransferase \| Pathway: \| COG: Transcription CD630_12140 - spo0A Type: Gene Product:Stage 0 sporulation protein A \| Pathway: \| COG: Signal transduction mechanisms CD630_04780 - spaF Type: Gene Product:ABC-type transport system,lantibiotic/multidrug-family ATP-binding protein \| Pathway: \| COG: Defense mechanisms CD630_28790 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_22420 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_12320 - Type: Gene Product:Putative lipoprotein \| Pathway: \| COG: Function unknown CD630_04800 - spaG Type: Gene Product:ABC-type transport system,lantibiotic/multidrug-family permease \| Pathway: \| COG: Function unknown CD630_12110 - Type: Gene Product:Putative N-acetyltransferase \| Pathway: \| COG: Transcription CD630_04860 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms CD630_04820 - spaK Type: Gene Product:Two-component sensor histidine kinase \| Pathway: \| COG: Signal transduction mechanisms CD630_18010 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown	0.0000000016	0.0000013	0.56	Inferelator: 3 Hypergeometric: 0 TF Influences from Inferelator CD630_06480 - Type: Gene Product:Transcriptional regulator, GntR family \| Pathway: \| COG: Transcription CD630_06580 - cdu1 Type: Gene Product:Transcriptional regulator, beta-lactamsrepressor \| Pathway: \| COG: Transcription CD630_20650 - Type: Gene Product:Transcriptional regulator, beta-lactamsrepressor \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_388	29 CD630_28130 - garR Type: Gene Product:Tartronate semialdehyde reductase \| Pathway: \| COG: Lipid transport and metabolism CD630_32120 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_20410 - Type: Gene Product:Transcriptional regulator, HTH-type \| Pathway: \| COG: Transcription CD630_33581 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_19710 - Type: Gene Product:Putative protein, Sir2 family; putativesilencing, chromosome stability or ageing; putative ADPribosyltransferase \| Pathway: \| COG: Function unknown CD630_10070 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Transcription CD630_32130 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_19660 - Type: Gene Product:Putative acyl-CoA thioesterase \| Pathway: \| COG: Function unknown CD630_15431 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_15430 - Type: Gene Product:putative FMN-dependent NADH-azoreductase \| Pathway: \| COG: Lipid transport and metabolism CD630_09240 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_19850 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_30060 - Type: Gene Product:Alcohol dehydrogenase \| Pathway: \| COG: Energy production and conversion CD630_10890 - rgbR Type: Gene Product:Two-component response regulator VirR-like \| Pathway: \| COG: Signal transduction mechanisms CD630_12810 - mnmA Type: Gene Product:tRNA-specific 2-thiouridylase MnmA \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_17730 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_33590 - Type: Gene Product:ABC-type transport system, ATP-binding protein \| Pathway: \| COG: Function unknown CD630_28120 - Type: Gene Product:Putative gluconate permease \| Pathway: \| COG: Amino acid transport and metabolism, Carbohydrate transport and metabolism CD630_32340 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_19650 - Type: Gene Product:Putative permease \| Pathway: \| COG: Function unknown CD630_32440 - prdA Type: Gene Product:D-proline reductase proprotein prdA \| Pathway: \| COG: Function unknown CD630_29400 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_10900 - rgbS Type: Gene Product:Fragment of two-component sensor histidine kinase(N-terminal region) \| Pathway: \| COG: Signal transduction mechanisms CD630_29390 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_18780 - Type: Gene Product:Putative sigma factor Tn1549-like, CTn5-Orf38 \| Pathway: \| COG: Function unknown CD630_22760 - Type: Gene Product:Sodium:alanine symporter \| Pathway: \| COG: Amino acid transport and metabolism CD630_29380 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_28110 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_32430 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown	8.8e-19	0	0.56	Inferelator: 1 Hypergeometric: 0 TF Influences from Inferelator 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_306	23 CD630_21700 - Type: Gene Product:Putative cNMP-binding regulatory protein \| Pathway: \| COG: Signal transduction mechanisms CD630_30880 - Type: Gene Product:Putative cellobiose-phosphate degrading protein \| Pathway: \| COG: Function unknown CD630_13660 - Type: Gene Product:Putative phage tail protein \| Pathway: \| COG: Function unknown CD630_21460 - Type: Gene Product:Conserved hypothetical protein, UPF0027 family \| Pathway: \| COG: Replication, recombination and repair CD630_13620 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_13640 - Type: Gene Product:Putative phage XkdM-like protein \| Pathway: \| COG: Function unknown CD630_13700 - Type: Gene Product:Putative phage XkdS-like protein \| Pathway: \| COG: Function unknown CD630_13720 - Type: Gene Product:Putative phage XkdT-like protein \| Pathway: \| COG: Function unknown CD630_13680 - Type: Gene Product:Putative phage cell wall XkdQ-like hydrolase \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_13740 - Type: Gene Product:Putative beta-lactamase-inhibitor protein II \| Pathway: \| COG: Cell cycle control, cell division, chromosome partitioning, Cytoskeleton CD630_21690 - Type: Gene Product:Putative iron-sulfur binding protein \| Pathway: \| COG: Energy production and conversion CD630_14170 - Type: Gene Product:Putative ATP-binding protein \| Pathway: \| COG: Amino acid transport and metabolism CD630_30890 - Type: Gene Product:PTS system, glucose-like IIBC component \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_13670 - Type: Gene Product:Putative phage XkdP-like protein \| Pathway: \| COG: Function unknown CD630_13651 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_13650 - Type: Gene Product:Putative phage XkdN-like protein \| Pathway: \| COG: Function unknown CD630_13630 - Type: Gene Product:Putative phage XkdK-like protein \| Pathway: \| COG: Function unknown CD630_13710 - Type: Gene Product:Putative baseplate assembly predicted J-like \| Pathway: \| COG: Function unknown CD630_13730 - Type: Gene Product:Putative phage tail fiber protein \| Pathway: \| COG: Function unknown CD630_13690 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_14140 - Type: Gene Product:Putative oxidoreductase, Fe-S subunit \| Pathway: \| COG: Function unknown CD630_21680 - hcp Type: Gene Product:Hydroxylamine reductase \| Pathway: \| COG: Energy production and conversion CD630_14160 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown	0.000022	0	0.56	Inferelator: 2 Hypergeometric: 0 TF Influences from Inferelator CD630_30540 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms CD630_32800 - Type: Gene Product:Sigma-54 dpendent regulator, PTS fructose family \| Pathway: \| COG: Signal transduction mechanisms TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_21	29 CD630_04650 - Type: Gene Product:Transcriptional regulator, RpiR family \| Pathway: \| COG: Transcription CD630_20690 - Type: Gene Product:Putative molybdopterin cofactor biosynthesisprotein \| Pathway: Cofactor biosynthesis \| COG: Coenzyme transport and metabolism CD630_01700 - Type: Gene Product:ABC-type transport system, ATP-binding protein \| Pathway: \| COG: Function unknown CD630_36730 - Type: Gene Product:Putative stage 0 sporulation protein, DNA-bindingprotein Spo0J-like \| Pathway: \| COG: Transcription CD630_25130 - Type: Gene Product:Putative translation inhibitor endoribonuclease \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_30350 - Type: Gene Product:Putative diaminopimelate epimerase, PhzF family \| Pathway: \| COG: Function unknown CD630_32890 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_26130 - Type: Gene Product:Putative peptidase, M24 family \| Pathway: \| COG: Amino acid transport and metabolism CD630_36710 - spo0J Type: Gene Product:Stage 0 sporulation protein J, site-specificDNA-binding protein \| Pathway: \| COG: Transcription CD630_34780 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_04690 - Type: Gene Product:PTS system, sucrose-specific IIABC component \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_20710 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_32870 - Type: Gene Product:Putative oxidoreductase, FAD dependent \| Pathway: \| COG: Function unknown CD630_04670 - Type: Gene Product:Putative hydrolase, HAD superfamily, subfamilyIIB \| Pathway: \| COG: Function unknown CD630_25140 - tdcB Type: Gene Product:Threonine dehydratase II \| Pathway: \| COG: Amino acid transport and metabolism CD630_04660 - Type: Gene Product:Transcriptional regulator, RpiR family \| Pathway: \| COG: Transcription CD630_36700 - Type: Gene Product:Putative cysteine desulfurase family protein \| Pathway: \| COG: Amino acid transport and metabolism CD630_01710 - rex Type: Gene Product:Transcriptional regulator, Redox-sensingrepressor Rex \| Pathway: \| COG: Transcription CD630_30340 - Type: Gene Product:Transcriptional regulator, TrmB family \| Pathway: \| COG: Transcription CD630_01880 - Type: Gene Product:Putative ketopantoate reductase \| Pathway: Cofactor biosynthesis \| COG: Coenzyme transport and metabolism CD630_32880 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_04680 - malL Type: Gene Product:oligo-1,6-glucosidase (Sucrase-isomaltase) \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_32860 - Type: Gene Product:Putative sodium:phosphate symporter \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_20700 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_36720 - soj Type: Gene Product:Transcriptional regulator, sporulation initiationinhibitor, chromosome partitioning protein \| Pathway: \| COG: Cell cycle control, cell division, chromosome partitioning CD630_32900 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_01690 - Type: Gene Product:Putative drug/sodium antiporter, MATE family \| Pathway: \| COG: Defense mechanisms CD630_32840 - HtrA Type: Gene Product:High temperature requirement A protease \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_08930 - Type: Gene Product:Putative iron-dependent hydrogenase \| Pathway: \| COG: Energy production and conversion	0.00000000067	0.00014	0.56	Inferelator: 2 Hypergeometric: 0 TF Influences from Inferelator CD630_01710 - rex Type: Gene Product:Transcriptional regulator, Redox-sensingrepressor Rex \| Pathway: \| COG: Transcription CD630_17820 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_149	20 CD630_09960 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_20630 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_16530 - Type: Gene Product:Putative Probable D-methionine-bindinglipoprotein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_14890 - metN Type: Gene Product:ABC-type transport system, methionine-specificATP-binding protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_14900 - metI Type: Gene Product:ABC-type transport system, methionine-specificpermease \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_20600 - Type: Gene Product:Putative lipid kinase \| Pathway: \| COG: Lipid transport and metabolism CD630_20610 - Type: Gene Product:Conserved hypothetical protein, DUF1121 family \| Pathway: \| COG: Function unknown CD630_28570 - Type: Gene Product:Putative hydrolase, HAD superfamily, IAsubfamily \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_17740 - Type: Gene Product:ABC-type transport system, aminoacid-familyextracellular solute-binding protein \| Pathway: \| COG: Amino acid transport and metabolism CD630_15820 - hisD Type: Gene Product:Histidinol dehydrogenase (HDH) \| Pathway: Amino-acid biosynthesis \| COG: Amino acid transport and metabolism CD630_28560 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Replication, recombination and repair CD630_14910 - metQ Type: Gene Product:ABC-type transport system, methionine-specificsubstrate-binding lipoprotein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_17750 - Type: Gene Product:ABC-type transport system, aminoacid-familypermease \| Pathway: \| COG: Amino acid transport and metabolism CD630_20620 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_28580 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_16520 - Type: Gene Product:Putative tellurium resistance protein \| Pathway: \| COG: Signal transduction mechanisms CD630_09950 - serA Type: Gene Product:Putative D-3-phosphoglycerate dehydrogenase \| Pathway: \| COG: Amino acid transport and metabolism CD630_23300 - xpt Type: Gene Product:Xanthine phosphoribosyltransferase (XPRTase) \| Pathway: Purine metabolism \| COG: Nucleotide transport and metabolism CD630_23290 - tal Type: Gene Product:Transaldolase \| Pathway: Carbohydrate degradation \| COG: Carbohydrate transport and metabolism CD630_17760 - Type: Gene Product:ABC-type transport system, aminoacid-familyATP-binding protein \| Pathway: \| COG: Amino acid transport and metabolism	0.0000000000000079	2.6	0.56	Inferelator: 1 Hypergeometric: 0 TF Influences from Inferelator CD630_06700 - Type: Gene Product:Transcriptional regulator, beta-lactamsrepressor \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_70	23 CD630_29550 - ntpB Type: Gene Product:V-type sodium ATPase subunit B \| Pathway: \| COG: Energy production and conversion CD630_29610 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_32530 - folC Type: Gene Product:Folylpolyglutamate synthase \| Pathway: \| COG: Coenzyme transport and metabolism CD630_33690 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_35440 - Type: Gene Product:Transcriptional regulator, AsnC/Lrp family \| Pathway: \| COG: Transcription CD630_29590 - ntpK Type: Gene Product:V-type sodium ATPase subunit K \| Pathway: \| COG: Energy production and conversion CD630_29980 - Type: Gene Product:ABC-type transport system, iron-family permease \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_09240 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_16450 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_29600 - ntpI Type: Gene Product:V-type sodium ATPase subunit I \| Pathway: \| COG: Energy production and conversion CD630_01480 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_29540 - ntpD Type: Gene Product:V-type sodium ATPase subunit D \| Pathway: \| COG: Energy production and conversion CD630_29560 - ntpA Type: Gene Product:V-type sodium ATPase subunit A \| Pathway: \| COG: Energy production and conversion CD630_29561 - ntpF Type: Gene Product:V-type sodium ATPase subunit F \| Pathway: \| COG: Energy production and conversion CD630_29580 - ntpE Type: Gene Product:V-type sodium ATPase subunit E \| Pathway: \| COG: Energy production and conversion CD630_29970 - Type: Gene Product:ABC-type transport system, iron-familyATP-binding protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_23010 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_29990 - Type: Gene Product:ABC-type transport system, iron-familyextracellular solute-binding protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_32800 - Type: Gene Product:Sigma-54 dpendent regulator, PTS fructose family \| Pathway: \| COG: Signal transduction mechanisms CD630_35430 - Type: Gene Product:Putative nicotinate phosphribosyltransferase \| Pathway: Cofactor biosynthesis \| COG: Coenzyme transport and metabolism CD630_16460 - Type: Gene Product:Putative peptidase, M19 family \| Pathway: \| COG: Amino acid transport and metabolism CD630_16440 - Type: Gene Product:Transcriptional regulator, RmlC-type \| Pathway: \| COG: Transcription CD630_20451 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG:	`NA`	`NA`	0.56	Inferelator: 2 Hypergeometric: 2 TF Influences from Inferelator CD630_16050 - Type: Gene Product:Putative transcriptional regulator \| Pathway: \| COG: Transcription CD630_20480 - Type: Gene Product:Transcriptional regulator, RpiR family \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test CD630_12750 - codY Type: Gene Product:Transcriptional regulator, GTP-sensingpleiotropic repressor \| Pathway: \| COG: Transcription CD630_32450 - prdR Type: Gene Product:Transcriptional regulator, sigma-54-dependent \| Pathway: \| COG: Transcription
Module_182	24 CD630_29550 - ntpB Type: Gene Product:V-type sodium ATPase subunit B \| Pathway: \| COG: Energy production and conversion CD630_10350 - cwp16 Type: Gene Product:Putative N-acetylmuramoyl-L-alanine amidase,autolysin \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_29610 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_07950 - Type: Gene Product:Conserved hypothetical protein, UPF0082 family \| Pathway: \| COG: Transcription CD630_28600 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_29570 - ntpC Type: Gene Product:V-type sodium ATPase subunit C \| Pathway: \| COG: Energy production and conversion CD630_28620 - Type: Gene Product:Putative peptidase, M19 family \| Pathway: \| COG: Amino acid transport and metabolism CD630_15820 - hisD Type: Gene Product:Histidinol dehydrogenase (HDH) \| Pathway: Amino-acid biosynthesis \| COG: Amino acid transport and metabolism CD630_07930 - Type: Gene Product:Putative membrane protein, DUF81 family \| Pathway: \| COG: Function unknown CD630_06630 - tcdA Type: Gene Product:Toxin A \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_07940 - nadE Type: Gene Product:NH3-dependent NAD(+) synthetase \| Pathway: Cofactor biosynthesis \| COG: Coenzyme transport and metabolism CD630_29590 - ntpK Type: Gene Product:V-type sodium ATPase subunit K \| Pathway: \| COG: Energy production and conversion CD630_29600 - ntpI Type: Gene Product:V-type sodium ATPase subunit I \| Pathway: \| COG: Energy production and conversion CD630_27620 - uppS Type: Gene Product:Putative undecaprenyl pyrophosphate synthetase \| Pathway: \| COG: Lipid transport and metabolism CD630_29540 - ntpD Type: Gene Product:V-type sodium ATPase subunit D \| Pathway: \| COG: Energy production and conversion CD630_10450 - Type: Gene Product:Putative sporulation integral membrane protein \| Pathway: \| COG: Function unknown CD630_29560 - ntpA Type: Gene Product:V-type sodium ATPase subunit A \| Pathway: \| COG: Energy production and conversion CD630_29561 - ntpF Type: Gene Product:V-type sodium ATPase subunit F \| Pathway: \| COG: Energy production and conversion CD630_07920 - Type: Gene Product:Putative membrane protein, DUF81 family \| Pathway: \| COG: Function unknown CD630_28610 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_28590 - Type: Gene Product:Putative D-aminoacylase \| Pathway: \| COG: Secondary metabolites biosynthesis, transport and catabolism CD630_29580 - ntpE Type: Gene Product:V-type sodium ATPase subunit E \| Pathway: \| COG: Energy production and conversion CD630_10610 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_27630 - Type: Gene Product:Putative lipoprotein \| Pathway: \| COG:	0.000000000023	0.06	0.56	Inferelator: 3 Hypergeometric: 2 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 CD630_26420 - sigG Type: Gene Product:RNA polymerase sigma-G factor \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test CD630_12750 - codY Type: Gene Product:Transcriptional regulator, GTP-sensingpleiotropic repressor \| Pathway: \| COG: Transcription CD630_32450 - prdR Type: Gene Product:Transcriptional regulator, sigma-54-dependent \| Pathway: \| COG: Transcription
Module_25	29 CD630_12480 - rnc Type: Gene Product:ribonuclease III \| Pathway: \| COG: Transcription CD630_31140 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_12520 - ffh Type: Gene Product:Signal recognition particle protein \| Pathway: \| COG: Intracellular trafficking, secretion, and vesicular transport CD630_12560 - trmD Type: Gene Product:tRNA (guanine-N(1)-)-methyltransferase(M1G-methyltransferase) (tRNA [GM37] methyltransferase ) \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_12500 - smc Type: Gene Product:Structural maintenance chromosome protein SMC \| Pathway: \| COG: Cell cycle control, cell division, chromosome partitioning CD630_12460 - efp Type: Gene Product:Elongation factor P (EF-P) \| Pathway: Protein biosynthesis \| COG: Translation, ribosomal structure and biogenesis CD630_12540 - Type: Gene Product:Putative RNA-binding protein \| Pathway: \| COG: Function unknown CD630_31120 - Type: Gene Product:Putative peptidase, M20D family \| Pathway: \| COG: Amino acid transport and metabolism CD630_31960 - Type: Gene Product:Putative penicillin-binding protein \| Pathway: \| COG: Defense mechanisms CD630_20190 - Type: Gene Product:Transporter drug resistance, Major FacilitatorSuperfamily (MFS) \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_31940 - Type: Gene Product:Transcriptional regulator, AraC family \| Pathway: \| COG: Transcription CD630_08620 - Type: Gene Product:PTS system, lactose/cellobiose-family IICmembrane component \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_32620 - pstA Type: Gene Product:ABC-type transport system, phosphate-specificpermease \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_32600 - phoU Type: Gene Product:Phosphate uptake regulator, PhoU \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_12530 - rpsP Type: Gene Product:30S ribosomal protein S16 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_31980 - cme Type: Gene Product:Multidrug resistance protein Cme; Transporter,Major Facilitator Superfamily (MFS) \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_31130 - Type: Gene Product:Putative aminobenzoyl-glutamate utilizationprotein B \| Pathway: \| COG: Amino acid transport and metabolism CD630_12470 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_12660 - Type: Gene Product:ABC-type transport system, multidrug-familypermease \| Pathway: \| COG: Function unknown CD630_12511 - Type: Gene Product:Putative DNA-binding regulator \| Pathway: \| COG: Function unknown CD630_12510 - ftsY Type: Gene Product:signal recognition particle receptor \| Pathway: \| COG: Intracellular trafficking, secretion, and vesicular transport CD630_12550 - rimM Type: Gene Product:16S rRNA processing protein RimM \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_12570 - rplS Type: Gene Product:50S ribosomal protein L19 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_31970 - Type: Gene Product:Transcriptional regulator, MerR family \| Pathway: \| COG: Transcription CD630_12680 - Type: Gene Product:ABC-type transport system, multidrug-familyATP-binding protein \| Pathway: \| COG: Defense mechanisms CD630_32610 - pstB Type: Gene Product:ABC-type transport system, phosphate-specificATP-binding \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_31950 - Type: Gene Product:Putative UvrABC system protein A 2 (UvrA protein2) (Excinuclease ABC subunit A 2) \| Pathway: \| COG: Replication, recombination and repair CD630_32630 - pstC Type: Gene Product:ABC-type transport system, phosphate-specificpermease \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_20180 - Type: Gene Product:Transcriptional regulator, AraC family \| Pathway: \| COG: Transcription	0.000001	`NA`	0.56	Inferelator: 2 Hypergeometric: 0 TF Influences from Inferelator CD630_24120 - Type: Gene Product:Putative negative regulator of gluconeogenesis \| Pathway: \| COG: Transcription CD630_36390 - Type: Gene Product:Transcriptional regulator, LysR family \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_92	27 CD630_05820 - Type: Gene Product:Putative pyruvate phosphate dikinase,PEP/pyruvate-binding \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_20040 - effR Type: Gene Product:Transcriptional regulator, MarR family \| Pathway: \| COG: Transcription CD630_28210 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_04550 - Type: Gene Product:Putative helicase, UvrD family \| Pathway: \| COG: Replication, recombination and repair CD630_08220 - Type: Gene Product:ABC-type transport system, multidrug-familyATP-binding protein \| Pathway: \| COG: Defense mechanisms CD630_17460 - gltC Type: Gene Product:Sodium/glutamate symporter \| Pathway: \| COG: Amino acid transport and metabolism CD630_10870 - zupT Type: Gene Product:Putative zinc/iron transporter, ZupT subfamiliy \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_08240 - Type: Gene Product:ABC-type transport system, multidrug-familypermease \| Pathway: \| COG: Function unknown CD630_30120 - Type: Gene Product:Putative alpha-mannosidase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_30160 - Type: Gene Product:Transcription antiterminator, PTS operonregulator \| Pathway: \| COG: Transcription CD630_30140 - Type: Gene Product:PTS system, mannose-specfic IIB component \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_34580 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_20030 - effD Type: Gene Product:Putative drug/sodium antiporter, MATE family \| Pathway: \| COG: Defense mechanisms CD630_05810 - Type: Gene Product:Transcriptional regulator, TetR family \| Pathway: \| COG: Transcription CD630_31430 - Type: Gene Product:Putative ThiJ/pfpI family protein \| Pathway: \| COG: Function unknown CD630_03540 - Type: Gene Product:Fragment of putative membrane protein (Part 1) \| Pathway: \| COG: CD630_28200 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_08230 - Type: Gene Product:ABC-type transport system, multidrug-familypermease \| Pathway: \| COG: Function unknown CD630_28220 - Type: Gene Product:Putative glutamate carboxypeptidase, M20 family \| Pathway: \| COG: Amino acid transport and metabolism CD630_04540 - Type: Gene Product:Transcriptional regulator, AraC family \| Pathway: \| COG: Transcription CD630_17451 - feoA Type: Gene Product:Ferrous iron transport protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_30130 - Type: Gene Product:PTS system, mannose-specfic IIC component \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_30150 - Type: Gene Product:PTS system, mannose-specfic IIA component \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_05920 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_10880 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_31440 - Type: Gene Product:Transcriptional regulator, DeoR family \| Pathway: \| COG: Transcription CD630_05910 - Type: Gene Product:Putative ATPase, P-type, heavy metaltranslocating \| Pathway: \| COG: Inorganic ion transport and metabolism	0	`NA`	0.56	Inferelator: 1 Hypergeometric: 0 TF Influences from Inferelator CD630_22150 - SinR Type: Gene Product:Transcriptional regulator, HTH-type \| Pathway: \| COG: Transcription 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`