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 331 - 340 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_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
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_119	25 CD630_33170 - fdhF Type: Gene Product:Formate dehydrogenase-H (selenocysteine) \| Pathway: \| COG: Energy production and conversion CD630_21230 - Type: Gene Product:Putative multiprotein-complex assembly TPRrepeat-containing protein \| Pathway: \| COG: Function unknown CD630_18220 - bcp Type: Gene Product:Putative thiol peroxidase \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_36670 - Type: Gene Product:Conserved hypothetical protein, TusA family \| Pathway: \| COG: Function unknown CD630_12350 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_11910 - fbp Type: Gene Product:Fructose-1,6-bisphosphatase \| Pathway: Carbohydrate biosynthesis \| COG: Carbohydrate transport and metabolism CD630_15760 - Type: Gene Product:Putative esterase, SGNH hydrolase-type \| Pathway: \| COG: Amino acid transport and metabolism CD630_28140 - Type: Gene Product:Transcriptional regulator, GntR family \| Pathway: \| COG: Transcription CD630_36680 - rstA Type: Gene Product:Regulator of sporulation and toxins \| Pathway: \| COG: Transcription CD630_21240 - Type: Gene Product:Putative malate transporter \| Pathway: \| COG: Function unknown CD630_14130 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Amino acid transport and metabolism, Carbohydrate transport and metabolism CD630_14110 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_33160 - fdhD Type: Gene Product:Formate dehydrogenase formation protein \| Pathway: \| COG: Energy production and conversion CD630_33140 - hydA Type: Gene Product:Iron hydrogenase \| Pathway: \| COG: Energy production and conversion CD630_18230 - Type: Gene Product:Conserved hypothetical protein, UPF0246 family \| Pathway: \| COG: Replication, recombination and repair CD630_19942 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_15770 - pgm Type: Gene Product:Alpha-phosphoglucomutase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_02950 - Type: Gene Product:Putative iron-sulfur-binding protein \| Pathway: \| COG: Energy production and conversion CD630_02960 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_11900 - Type: Gene Product:Putative acyl-CoA N-acyltransferase \| Pathway: \| COG: Transcription CD630_14120 - Type: Gene Product:Transcriptional regulator, sigma-54-dependent \| Pathway: \| COG: Transcription CD630_18240 - Type: Gene Product:P-type calcium transport ATPase \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_33150 - hydN2 Type: Gene Product:Putative oxidoreductase, Fe-S subunit \| Pathway: \| COG: Energy production and conversion CD630_33151 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_33130 - hydN1 Type: Gene Product:Putative oxidoreductase, Fe-S subunit \| Pathway: \| COG: Energy production and conversion	0.00000044	0.000016	0.58	Inferelator: 2 Hypergeometric: 0 TF Influences from Inferelator CD630_10090 - Type: Gene Product:Transcriptional regulator, GntR family \| Pathway: \| COG: Transcription CD630_19100 - eutV Type: Gene Product:Two-component response regulator, Ethanolaminespecific \| Pathway: \| COG: Signal transduction mechanisms TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_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_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_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_233	27 CD630_28760 - fhuG Type: Gene Product:ABC-type transport system, ferrichrome-specificpermease \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_18591 - Type: Gene Product:Transcriptional regulator, AbrB family;Tn1549-like, CTn5-Orf17 \| Pathway: \| COG: Transcription CD630_18590 - Type: Gene Product:DNA topoisomerase protein, type IA, Tn1549-like,CTn5-Orf16 \| Pathway: \| COG: Replication, recombination and repair CD630_18550 - Type: Gene Product:Putative conjugative transposon proteinTn1549-like, CTn5-Orf11 \| Pathway: \| COG: Function unknown CD630_06850 - infC Type: Gene Product:Translation initiation factor IF-3 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_18610 - Type: Gene Product:Putative conjugative transposon proteinTn1549-like, CTn5-Orf19 \| Pathway: \| COG: Secondary metabolites biosynthesis, transport and catabolism CD630_28740 - Type: Gene Product:Putative drug/sodium antiporter, MATE family \| Pathway: \| COG: Defense mechanisms CD630_18630 - Type: Gene Product:Putative single-strand DNA-binding proteinTn1549-like, CTn5-Orf22 \| Pathway: \| COG: Function unknown CD630_18571 - Type: Gene Product:Putative conjugative transposon proteinTn1549-like, CTn5-Orf14 \| Pathway: \| COG: Function unknown CD630_18570 - Type: Gene Product:Putative cell wall hydrolase Tn1549-like,CTn5-Orf13 \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_18530 - Type: Gene Product:Putative membrane protein Tn1549-like, CTn5-Orf9 \| Pathway: \| COG: Function unknown CD630_18510 - Type: Gene Product:Putative single-strand DNA-binding proteinTn1549-like, CTn5-Orf7 \| Pathway: \| COG: Function unknown CD630_28780 - fhuD Type: Gene Product:ABC-type transport system, ferrichrome-specificextracellular solute-binding protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_06870 - rplT Type: Gene Product:50S ribosomal protein L20 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_18580 - Type: Gene Product:Putative cell surface protein Tn1549-like,CTn5-Orf15 \| Pathway: \| COG: Function unknown CD630_25000 - argH Type: Gene Product:Argininosuccinate lyase (Arginosuccinase) (ASAL) \| Pathway: Amino-acid biosynthesis \| COG: Amino acid transport and metabolism CD630_28770 - fhuB Type: Gene Product:ABC-type transport system, ferrichrome-specificpermease \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_18600 - Type: Gene Product:Putative conjugative transposon protein DUF1016family, Tn1549-like, CTn5-Orf18 \| Pathway: \| COG: Function unknown CD630_28750 - fhuC Type: Gene Product:ABC-type transport system, ferrichrome-specificATP-binding protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_18540 - Type: Gene Product:Putative conjugative transposon proteinTn1549-like, CTn5-Orf10 \| Pathway: \| COG: Function unknown CD630_34530 - Type: Gene Product:N-acetylglucosamine-6-phosphate deacetylase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_18560 - Type: Gene Product:Putative hydrolase Tn1549-like, CTn5-Orf12 \| Pathway: \| COG: Intracellular trafficking, secretion, and vesicular transport CD630_06860 - rpmI Type: Gene Product:50S ribosomal protein L35 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_18620 - Type: Gene Product:Putative DNA/RNA helicase Tn1549-like,CTn5-Orf21 \| Pathway: \| COG: Replication, recombination and repair CD630_18520 - Type: Gene Product:Putative conjugative transposon proteinTn1549-like, CTn5-Orf8 \| Pathway: \| COG: Function unknown CD630_34520 - Type: Gene Product:Transcriptional regulator, GntR family \| Pathway: \| COG: Transcription CD630_34490 - Type: Gene Product:Putative phosphosugar isomerase; putativetagatose-6-phosphate ketose/aldose isomerase AgaS \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis	`NA`	`NA`	0.58	Inferelator: 1 Hypergeometric: 0 TF Influences from Inferelator CD630_07960 - Type: Gene Product:Transcriptional regulator, LacI family \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_46	23 CD630_04730 - Type: Gene Product:Transcriptional regulator, MarR family \| Pathway: \| COG: Transcription CD630_03470 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_03430 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_03450 - Type: Gene Product:Putative GTP pyrophosphokinase \| Pathway: \| COG: Function unknown CD630_11420 - rnfB Type: Gene Product:Electron transport complex protein \| Pathway: \| COG: Energy production and conversion CD630_17290 - Type: Gene Product:Putative sodium:phosphate symporter \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_11400 - rnfE Type: Gene Product:Electron transport complex protein \| Pathway: \| COG: Energy production and conversion CD630_10170 - Type: Gene Product:ABC-type transport system, multidrug-familyATP-binding protein/permease \| Pathway: \| COG: Defense mechanisms CD630_14700 - Type: Gene Product:Putative rhodanese-like domain-containingprotein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_21830 - csdA Type: Gene Product:ATP-dependent RNA helicase \| Pathway: \| COG: Replication, recombination and repair CD630_04740 - Type: Gene Product:Putative iron-sulfur protein \| Pathway: \| COG: Energy production and conversion CD630_10180 - Type: Gene Product:ABC-type transport system, multidrug-familyATP-binding protein/permease \| Pathway: \| COG: Defense mechanisms CD630_11390 - rnfG Type: Gene Product:Electron transport complex protein \| Pathway: \| COG: Energy production and conversion CD630_03460 - Type: Gene Product:Putative phosphoesterase \| Pathway: \| COG: Function unknown CD630_04720 - Type: Gene Product:Putative reductase \| Pathway: \| COG: Function unknown CD630_04700 - blaR Type: Gene Product:Beta-lactamase-inducing penicillin-bindingprotein \| Pathway: \| COG: Transcription, Signal transduction mechanisms CD630_14690 - cwp20 Type: Gene Product:Putative cell surface protein ; putativepenicillin-binding protein \| Pathway: \| COG: Defense mechanisms CD630_03440 - Type: Gene Product:Putative beta-lactamase-like protein \| Pathway: \| COG: Function unknown CD630_10160 - Type: Gene Product:Transcriptional regulator, MerR family \| Pathway: \| COG: Transcription CD630_11410 - rnfA Type: Gene Product:Electron transport complex protein \| Pathway: \| COG: Energy production and conversion CD630_15830 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_04710 - blaI Type: Gene Product:Transcriptional regulator, Penicillinaserepressor \| Pathway: \| COG: Transcription CD630_11380 - rnfD Type: Gene Product:Electron transport complex protein \| Pathway: \| COG: Energy production and conversion	0.000000000057	0.0000054	0.58	Inferelator: 4 Hypergeometric: 1 TF Influences from Inferelator CD630_11770 - fapR Type: Gene Product:Transcriptional regulator, DeoR family (Fattyacid and phospholipid biosynthesis regulator) \| 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 CD630_26650 - Type: Gene Product:Transcriptional regulator, AraC family \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test CD630_32450 - prdR Type: Gene Product:Transcriptional regulator, sigma-54-dependent \| Pathway: \| COG: Transcription
Module_143	22 CD630_36050 - Type: Gene Product:Putative phosphatase \| Pathway: \| COG: Function unknown CD630_31480 - Type: Gene Product:Hypothetical protein \| Pathway: \| COG: Function unknown CD630_14510 - folB Type: Gene Product:Dihydroneopterin aldolase \| Pathway: Cofactor biosynthesis \| COG: Coenzyme transport and metabolism CD630_14430 - Type: Gene Product:Putative Ca++-chelating serine protease, SCP-likeextracellular domain protein \| Pathway: \| COG: Secondary metabolites biosynthesis, transport and catabolism CD630_14470 - pabC Type: Gene Product:Aminodeoxychorismate lyase(4-amino-4-deoxychorismate lyase) (ADC lyase) (ADCL) \| Pathway: \| COG: Amino acid transport and metabolism CD630_14530 - aroF Type: Gene Product:Phospho-2-dehydro-3-deoxyheptonate aldolase \| Pathway: \| COG: Amino acid transport and metabolism CD630_14450 - pabA Type: Gene Product:Para-aminobenzoate/anthranilate synthaseglutamine amidotransferase component II [Includes:Para-aminobenzoate synthase glutamine amidotransferasecomponent II; Anthranilate synthase component II] \| Pathway: \| COG: Amino acid transport and metabolism CD630_34370 - cobS Type: Gene Product:Cobalamin synthase CobS (Cobalamin-5-phosphatesynthase) \| Pathway: Cofactor biosynthesis \| COG: Coenzyme transport and metabolism CD630_14490 - folE Type: Gene Product:GTP cyclohydrolase 1 (GTP cyclohydrolase I)(GTP-CH-I) \| Pathway: Cofactor biosynthesis \| COG: Coenzyme transport and metabolism CD630_36040 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Carbohydrate transport and metabolism, Cell wall/membrane/envelope biogenesis CD630_31490 - Type: Gene Product:DNA helicase \| Pathway: \| COG: Replication, recombination and repair CD630_34390 - cobT Type: Gene Product:Nicotinate-nucleotide--dimethylbenzimidazolephosphoribosyltransferase (NN:DBI PRT)(N(1)-alpha-phosphoribosyltransferase) \| Pathway: Nucleoside biosynthesis \| COG: Coenzyme transport and metabolism CD630_01500 - Type: Gene Product:Putative peptidase, M22 family \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_14500 - folP Type: Gene Product:Dihydropteroate synthase \| Pathway: Cofactor biosynthesis \| COG: Coenzyme transport and metabolism CD630_14520 - folK Type: Gene Product:2-amino-4-hydroxy-6-hydroxymethyldihydropteridinepyrophosphokinase \| Pathway: \| COG: Coenzyme transport and metabolism CD630_14440 - Type: Gene Product:Putative exported polysaccharide deacetylase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_14460 - pabB Type: Gene Product:Para-aminobenzoate synthase component I \| Pathway: \| COG: Amino acid transport and metabolism, Coenzyme transport and metabolism CD630_34360 - cobC Type: Gene Product:Cobalamin biosynthesis phosphoglycerate mutaseCobC \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_01980 - guaA Type: Gene Product:Glutamine amidotransferase \| Pathway: Purine metabolism \| COG: Nucleotide transport and metabolism CD630_36030 - Type: Gene Product:Putative phosphoesterase \| Pathway: \| COG: Function unknown CD630_14480 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_31500 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown	`NA`	`NA`	0.58	Inferelator: 2 Hypergeometric: 0 TF Influences from Inferelator CD630_04020 - Type: Gene Product:Transcriptional regulator, sigma-54-dependent \| 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_203	26 CD630_33980 - Type: Gene Product:Putative hydrolase, NUDIX family \| Pathway: \| COG: Replication, recombination and repair CD630_12880 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_01721 - fdxA Type: Gene Product:Ferredoxin (4Fe-4S cluster-containing protein)(fdx-like) \| Pathway: \| COG: Energy production and conversion CD630_03120 - Type: Gene Product:Transcriptional regulator, ArsR family \| Pathway: \| COG: Transcription CD630_14290 - Type: Gene Product:Putative acyl-CoA N-acyltransferase \| Pathway: \| COG: Function unknown CD630_34560 - Type: Gene Product:5-formyltetrahydrofolate cyclo-ligase \| Pathway: \| COG: Coenzyme transport and metabolism CD630_15660 - ilvB Type: Gene Product:Acetolactate synthase large subunit \| Pathway: Amino-acid biosynthesis \| COG: Amino acid transport and metabolism CD630_34010 - Type: Gene Product:putative phosphoesterase \| Pathway: \| COG: Replication, recombination and repair CD630_33960 - dnaE Type: Gene Product:DNA polymerase III DnaE subunit alpha \| Pathway: \| COG: Replication, recombination and repair CD630_08280 - Type: Gene Product:Putative oxidative stress glutamate synthase \| Pathway: \| COG: Amino acid transport and metabolism CD630_r0140 - 23s_rRNA Type: Gene Product: \| Pathway: \| COG: CD630_r0200 - 23s_rRNA Type: Gene Product: \| Pathway: \| COG: CD630_33990 - Type: Gene Product:Conserved hypothetical protein, UPF0052 family \| Pathway: \| COG: Function unknown CD630_36180 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_14281 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_12890 - Type: Gene Product:Ribonuclease J family protein \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_03130 - Type: Gene Product:Putative K/Mg/Cd/Cu/Zn/Na/Ca/Na/H-transportingP-type ATPase \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_28400 - serS1 Type: Gene Product:Seryl-tRNA synthetase 1 (Seryl-tRNA(Ser/Sec)synthetase 1) (Serine--tRNA ligase 1) (SerRS 1) \| Pathway: Aminoacyl-tRNA biosynthesis \| COG: Translation, ribosomal structure and biogenesis CD630_17470 - add Type: Gene Product:Adenosine deaminase (Adenosine aminohydrolase) \| Pathway: \| COG: Nucleotide transport and metabolism CD630_34000 - Type: Gene Product:Conserved hypothetical protein, UPF0042 family \| Pathway: \| COG: Function unknown CD630_34550 - Type: Gene Product:Putative carboxy-terminal protease \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_15650 - ilvC Type: Gene Product:Ketol-acid reductoisomerase \| Pathway: Amino-acid biosynthesis \| COG: Amino acid transport and metabolism CD630_24550 - Type: Gene Product:Putative CRISPR-associated protein \| Pathway: \| COG: Replication, recombination and repair CD630_33970 - whiA Type: Gene Product:Putative sporulation transcription regulatorwhiA \| Pathway: \| COG: Transcription CD630_34020 - murB Type: Gene Product:UDP-N-acetylenolpyruvoylglucosamine reductase \| Pathway: Cell wall biogenesis \| COG: Cell wall/membrane/envelope biogenesis CD630_17480 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown	0.00000000033	0.000097	0.58	Inferelator: 1 Hypergeometric: 0 TF Influences from Inferelator CD630_27220 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`