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 371 - 380 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_50	42 CD630_20350 - Type: Gene Product:Putative sporulation integral membrane protein \| Pathway: \| COG: Function unknown 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_24610 - dnaK Type: Gene Product:Chaperone protein dnaK (Heat shock protein 70)(Heat shock 70 kDa protein) (HSP70) \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_18550 - Type: Gene Product:Putative conjugative transposon proteinTn1549-like, CTn5-Orf11 \| Pathway: \| COG: Function unknown CD630_18620 - Type: Gene Product:Putative DNA/RNA helicase Tn1549-like,CTn5-Orf21 \| Pathway: \| COG: Replication, recombination and repair CD630_31480 - Type: Gene Product:Hypothetical protein \| Pathway: \| COG: Function unknown CD630_20390 - Type: Gene Product:Conserved hypothetical protein \| 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_10170 - Type: Gene Product:ABC-type transport system, multidrug-familyATP-binding protein/permease \| Pathway: \| COG: Defense mechanisms CD630_22660 - Type: Gene Product:Putative oxidoreductase, FAD dependent \| Pathway: \| COG: Energy production and conversion CD630_33100 - Type: Gene Product:Putative D-isomer specific 2-hydroxyaciddehydrogenase \| Pathway: \| COG: Amino acid transport and metabolism, Coenzyme transport and metabolism CD630_22620 - Type: Gene Product:Transporter, Major Facilitator Superfamily (MFS) \| Pathway: \| COG: Amino acid transport and metabolism CD630_10180 - Type: Gene Product:ABC-type transport system, multidrug-familyATP-binding protein/permease \| Pathway: \| COG: Defense mechanisms CD630_18600 - Type: Gene Product:Putative conjugative transposon protein DUF1016family, Tn1549-like, CTn5-Orf18 \| Pathway: \| COG: Function unknown CD630_18580 - Type: Gene Product:Putative cell surface protein Tn1549-like,CTn5-Orf15 \| Pathway: \| COG: Function unknown CD630_24600 - dnaJ Type: Gene Product:Chaperone protein DnaJ \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_33120 - Type: Gene Product:Transporter, Major Facilitator Superfamily (MFS) \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_20400 - Type: Gene Product:Transcriptional regulator, MerR family \| Pathway: \| COG: Transcription CD630_24640 - hemN Type: Gene Product:Oxygen-independent coproporphyrinogen-III oxidase(Coproporphyrinogenase) (Coprogen oxidase) \| Pathway: \| COG: Coenzyme transport and metabolism CD630_24620 - grpE Type: Gene Product:Protein grpE (HSP-70 cofactor) \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_20360 - Type: Gene Product:Putative peptidylarginine deiminase \| Pathway: \| COG: Amino acid transport and metabolism CD630_31490 - Type: Gene Product:DNA helicase \| Pathway: \| COG: Replication, recombination and repair CD630_18540 - Type: Gene Product:Putative conjugative transposon proteinTn1549-like, CTn5-Orf10 \| Pathway: \| COG: Function unknown CD630_19941 - Type: Gene Product:Transcriptional regulator, ArsR family \| Pathway: \| COG: Transcription CD630_19940 - Type: Gene Product:Putative membrane protein, DUF1648 family \| Pathway: \| COG: Function unknown CD630_18560 - Type: Gene Product:Putative hydrolase Tn1549-like, CTn5-Orf12 \| Pathway: \| COG: Intracellular trafficking, secretion, and vesicular transport CD630_18610 - Type: Gene Product:Putative conjugative transposon proteinTn1549-like, CTn5-Orf19 \| Pathway: \| COG: Secondary metabolites biosynthesis, transport and catabolism CD630_20380 - Type: Gene Product:Putative drug/sodium antiporter, MATE family \| Pathway: \| COG: Defense mechanisms CD630_18520 - Type: Gene Product:Putative conjugative transposon proteinTn1549-like, CTn5-Orf8 \| Pathway: \| COG: Function unknown CD630_36140 - Type: Gene Product:Conserved hypothetical protein, DUF1130 family \| Pathway: \| COG: Function unknown CD630_05650 - nth Type: Gene Product:Endonuclease III \| Pathway: \| COG: Replication, recombination and repair CD630_33110 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_22650 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_18630 - Type: Gene Product:Putative single-strand DNA-binding proteinTn1549-like, CTn5-Orf22 \| Pathway: \| COG: Function unknown CD630_20370 - Type: Gene Product:Putative acyl-CoA acyltransferase \| Pathway: \| COG: Function unknown CD630_31500 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown	0	0	0.61	Inferelator: 3 Hypergeometric: 0 TF Influences from Inferelator CD630_01710 - rex Type: Gene Product:Transcriptional regulator, Redox-sensingrepressor Rex \| Pathway: \| COG: Transcription 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 TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_199	10 CD630_04981 - Type: Gene Product:Putative conjugative transposon protein Tn5397,CTn3-Orf20.1 \| Pathway: \| COG: Function unknown CD630_25020 - Type: Gene Product:Putative pyridoxal phosphate-dependenttransferase \| Pathway: \| COG: Amino acid transport and metabolism CD630_22890 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms CD630_26040 - Type: Gene Product:Fragment of ADP-ribosyltransferase CdtAB (Part1) \| Pathway: \| COG: CD630_14920 - Type: Gene Product:Histidine kinase, negative regulator ofsporulation \| Pathway: \| COG: Signal transduction mechanisms CD630_18940 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_10120 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: CD630_22880 - Type: Gene Product:Two-component sensor histidine kinase \| Pathway: \| COG: Signal transduction mechanisms CD630_00511 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_06620 - Type: Gene Product:Fragment of phage endolysin CwlH \| Pathway: \| COG:	`NA`	`NA`	0.62	Inferelator: 2 Hypergeometric: 0 TF Influences from Inferelator CD630_11770 - fapR Type: Gene Product:Transcriptional regulator, DeoR family (Fattyacid and phospholipid biosynthesis regulator) \| Pathway: \| COG: Transcription CD630_29800 - Type: Gene Product:Putative CRISPR-associated autoregulator DevRfamily protein protein \| Pathway: \| COG: Replication, recombination and repair TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_122	25 CD630_18300 - kdpE Type: Gene Product:Two-component response regulator KdpE \| Pathway: \| COG: Signal transduction mechanisms CD630_t0010 - tRNA-Ala Type: Gene Product: \| Pathway: \| COG: CD630_17220 - Type: Gene Product:Putative transcriptional regulator \| Pathway: \| COG: CD630_07470 - Type: Gene Product:Putative lipoprotein \| Pathway: \| COG: Function unknown CD630_06420 - Type: Gene Product:Transcriptional regulator, HTH-type \| Pathway: \| COG: Transcription CD630_t0650 - tRNA-Ala Type: Gene Product: \| Pathway: \| COG: CD630_06400 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_07460 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: CD630_18290 - kdpD Type: Gene Product:Two-component sensor histidine kinase KdpD \| Pathway: \| COG: Signal transduction mechanisms CD630_08390 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_05880 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_06271 - Type: Gene Product:Putative ferredoxin \| Pathway: \| COG: Energy production and conversion CD630_07480 - Type: Gene Product:Putative diguanylate kinase signaling protein \| Pathway: \| COG: Signal transduction mechanisms CD630_32050 - Type: Gene Product:Putative nitroreductase \| Pathway: \| COG: Energy production and conversion CD630_08380 - Type: Gene Product:Putative DNA-binding protein \| Pathway: \| COG: CD630_t0690 - tRNA-Ala Type: Gene Product: \| Pathway: \| COG: CD630_06280 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_17210 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_17230 - Type: Gene Product:Putative acyltransferase \| Pathway: \| COG: Lipid transport and metabolism CD630_06410 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: CD630_05870 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_32060 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: CD630_25621 - rpmB Type: Gene Product:50S ribosomal protein L28 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_33722 - Type: Gene Product:Putative conjugative transposon proteinTn916-like, CTn7-Orf6 \| Pathway: \| COG: Function unknown CD630_12331 - Type: Gene Product:Fragment of phage protein \| Pathway: \| COG:	4.1e-20	0.0000000000035	0.62	Inferelator: 2 Hypergeometric: 0 TF Influences from Inferelator CD630_20480 - Type: Gene Product:Transcriptional regulator, RpiR family \| Pathway: \| COG: Transcription 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_59	27 CD630_33000 - engB Type: Gene Product:GTP-binding protein EngB; putative endoglucanase \| Pathway: \| COG: Function unknown CD630_06480 - Type: Gene Product:Transcriptional regulator, GntR family \| Pathway: \| COG: Transcription CD630_35490 - Type: Gene Product:DNA polymerase III, delta prime subunit \| Pathway: \| COG: Replication, recombination and repair CD630_10680 - Type: Gene Product:Putative polysaccharide biosynthesis/sporulationprotein \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_10710 - Type: Gene Product:Conserved hypothetical protein, UPF0291 proteinfamily \| Pathway: \| COG: Function unknown CD630_01570 - Type: Gene Product:Fragment of putative membrane protein (Part 2) \| Pathway: \| COG: Function unknown CD630_15450 - Type: Gene Product:Conserved hypothetical protein, DUF1836 family \| Pathway: \| COG: Function unknown CD630_35460 - Type: Gene Product:Putative tetrapyrrole methylase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_03060 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_36020 - Type: Gene Product:Putative ATPase \| Pathway: \| COG: Cell cycle control, cell division, chromosome partitioning CD630_35500 - tmk Type: Gene Product:Thymidylate kinase (dTMP kinase) \| Pathway: \| COG: Nucleotide transport and metabolism CD630_36000 - rolB Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms CD630_35480 - Type: Gene Product:Putative YaaT-like protein involved insporulation or related to DNA replication \| Pathway: \| COG: Function unknown CD630_33010 - lon Type: Gene Product:ATP-dependent protease La, S16 peptidase family \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_07370 - hisK Type: Gene Product:Histidinol-phosphatase (HolPase) \| Pathway: Amino-acid biosynthesis \| COG: Amino acid transport and metabolism CD630_10720 - Type: Gene Product:Putative aminopeptidase I, M18 family \| Pathway: \| COG: Amino acid transport and metabolism CD630_35990 - rolA Type: Gene Product:Two-component sensor histidine kinase \| Pathway: \| COG: Signal transduction mechanisms CD630_10700 - Type: Gene Product:Putative aminotransferase \| Pathway: \| COG: Transcription CD630_10690 - Type: Gene Product:Putative histidinol phosphatase/hydrolase, PHPfamily \| Pathway: Amino-acid biosynthesis \| COG: Amino acid transport and metabolism CD630_15460 - Type: Gene Product:Putative channel-forming hemolysin \| Pathway: \| COG: Function unknown CD630_19902 - cspC Type: Gene Product:Major cold shock protein CspC \| Pathway: \| COG: Transcription CD630_03070 - Type: Gene Product:Putative chaperone protein \| Pathway: \| COG: Function unknown CD630_35470 - Type: Gene Product:Putative methyltransferase \| Pathway: \| COG: Replication, recombination and repair CD630_35510 - Type: Gene Product:Putative arginine decarboxylase \| Pathway: \| COG: Amino acid transport and metabolism CD630_23100 - cspD Type: Gene Product:Cold shock protein D \| Pathway: \| COG: Transcription CD630_36010 - Type: Gene Product:D-alanyl-D-alanine carboxypeptidase, M15 family(DD-peptidase) (DD-carboxypeptidase) \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_03080 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown	0.0000000022	0.00022	0.62	Inferelator: 2 Hypergeometric: 0 TF Influences from Inferelator CD630_19100 - eutV Type: Gene Product:Two-component response regulator, Ethanolaminespecific \| Pathway: \| COG: Signal transduction mechanisms 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_170	31 CD630_28500 - Type: Gene Product:Transcriptional regulator, DeoR family \| Pathway: \| COG: Transcription CD630_20270 - Type: Gene Product:N-carbamoyl-L-amino acid hydrolase \| Pathway: \| COG: Amino acid transport and metabolism CD630_12950 - scpA Type: Gene Product:Segregation and condensation protein A \| Pathway: \| COG: Function unknown CD630_15950 - cysE Type: Gene Product:Serine acetyltransferase (SAT) \| Pathway: \| COG: Amino acid transport and metabolism CD630_28660 - Type: Gene Product:Putative modulator of DNA gyrase, peptidase U62 \| Pathway: \| COG: Function unknown CD630_12930 - Type: Gene Product:Transcriptional regulator, AraC family \| Pathway: \| COG: Transcription CD630_26130 - Type: Gene Product:Putative peptidase, M24 family \| Pathway: \| COG: Amino acid transport and metabolism CD630_24810 - ung Type: Gene Product:Uracil-DNA glycosylase (UDG) \| Pathway: \| COG: Replication, recombination and repair CD630_07910 - Type: Gene Product:Conserved hypothetical protein, UPF0029 family \| Pathway: \| COG: Function unknown CD630_19950 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_14720 - Type: Gene Product:ABC-type transport system, multidrug-familyATP-binding protein/permease \| Pathway: \| COG: Defense mechanisms CD630_19930 - Type: Gene Product:Putative decarboxylase \| Pathway: \| COG: Function unknown CD630_11910 - fbp Type: Gene Product:Fructose-1,6-bisphosphatase \| Pathway: Carbohydrate biosynthesis \| COG: Carbohydrate transport and metabolism CD630_33550 - Type: Gene Product:Putative nitroreductase \| Pathway: \| COG: Energy production and conversion CD630_01680 - Type: Gene Product:Putative cyclic nucleotide-binding protein \| Pathway: \| COG: Signal transduction mechanisms CD630_12960 - scpB Type: Gene Product:Segregation and condensation protein B \| Pathway: \| COG: Transcription CD630_12920 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_12940 - Type: Gene Product:Putative membrane-associated peptidase, M50family \| Pathway: \| COG: Function unknown CD630_24820 - Type: Gene Product:Putative lipoprotein \| Pathway: \| COG: Function unknown CD630_02750 - splB Type: Gene Product:Spore photoproduct (thymine dimer) lyase, radicalS-adenosylmethionine superfamily \| Pathway: \| COG: Replication, recombination and repair CD630_28680 - Type: Gene Product:Putative oxidoreductase \| Pathway: \| COG: Energy production and conversion CD630_28670 - Type: Gene Product:Putative regulatory protease, U62 family \| Pathway: \| COG: Function unknown CD630_00310 - Type: Gene Product:Transcriptional regulator, AraC family \| Pathway: \| COG: Transcription CD630_15940 - cysK Type: Gene Product:O-acetyl-serine thiol-lyase A(O-acetyl-sulfhydrylase)(OAS-TL) \| Pathway: \| COG: Amino acid transport and metabolism CD630_14730 - Type: Gene Product:ABC-type transport system, multidrug-familyATP-binding/permease \| Pathway: \| COG: Defense mechanisms CD630_19960 - Type: Gene Product:Transcriptional regulator, AraC family \| Pathway: \| COG: Signal transduction mechanisms CD630_26960 - Type: Gene Product:Putative pyridoxal phosphate-dependenttransferase \| Pathway: \| COG: Amino acid transport and metabolism CD630_11900 - Type: Gene Product:Putative acyl-CoA N-acyltransferase \| Pathway: \| COG: Transcription CD630_33560 - Type: Gene Product:Transcriptional regulator, hxlR family \| Pathway: \| COG: Transcription CD630_15310 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms CD630_24830 - Type: Gene Product:Putative lipoprotein \| Pathway: \| COG: Coenzyme transport and metabolism	9e-28	0.00000033	0.62	Inferelator: 1 Hypergeometric: 0 TF Influences from Inferelator CD630_16930 - Type: Gene Product:Putative dinitrogenase iron-molybdenum cofactor \| Pathway: \| COG: Function unknown TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_282	26 CD630_28500 - Type: Gene Product:Transcriptional regulator, DeoR family \| Pathway: \| COG: Transcription CD630_08870 - Type: Gene Product:Transcriptional regulator, GntR family \| Pathway: \| COG: Transcription CD630_36190 - Type: Gene Product:Putative acyl-CoA N-acyltransferase \| Pathway: \| COG: Transcription CD630_33190 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_t0660 - tRNA-Ala Type: Gene Product: \| Pathway: \| COG: CD630_32640 - Type: Gene Product:Fragment of conserved hypothetical protein(C-terminal region) \| Pathway: \| COG: Function unknown CD630_16020 - Type: Gene Product:PTS system, lactose/cellobiose-family IIBcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_15200 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: CD630_21030 - Type: Gene Product:ABC-type transport system, permease \| Pathway: \| COG: Function unknown CD630_14130 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Amino acid transport and metabolism, Carbohydrate transport and metabolism CD630_22160 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_19410 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_26960 - Type: Gene Product:Putative pyridoxal phosphate-dependenttransferase \| Pathway: \| COG: Amino acid transport and metabolism CD630_01670 - Type: Gene Product:Transcriptional regulator, sigma-54-dependent \| Pathway: \| COG: Transcription CD630_t0460 - tRNA-Ala Type: Gene Product: \| Pathway: \| COG: CD630_15190 - Type: Gene Product:Putative acyltransferase \| Pathway: \| COG: Function unknown CD630_08980 - Type: Gene Product:Conserved hypothetical protein, DUF1846-family \| Pathway: \| COG: Function unknown CD630_08970 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_16200 - Type: Gene Product:Transporter, Major Facilitator Superfamily (MFS) \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_35450 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_28790 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_28550 - Type: Gene Product:Putative NAD(P)-binding oxidoreductase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_14110 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_09880 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_14120 - Type: Gene Product:Transcriptional regulator, sigma-54-dependent \| Pathway: \| COG: Transcription CD630_19420 - trmB Type: Gene Product:tRNA (guanine-N(7)-)-methyltransferase(tRNA(m7G46)-methyltransferase) \| Pathway: tRNA modification \| COG: Energy production and conversion	0.0000016	0.02	0.62	Inferelator: 2 Hypergeometric: 0 TF Influences from Inferelator CD630_08870 - Type: Gene Product:Transcriptional regulator, GntR family \| Pathway: \| COG: Transcription CD630_14120 - Type: Gene Product:Transcriptional regulator, sigma-54-dependent \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_371	26 CD630_19400 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: CD630_19401 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: CD630_28490 - phnXW Type: Gene Product:Bifunctional phosphonoacetaldehydehydrolase/aminoethylphosphonate transaminase [Includes:Phosphonoacetaldehyde hydrolase ;2-aminoethylphosphonate--pyruvate transaminase] \| Pathway: \| COG: Amino acid transport and metabolism CD630_00130 - Type: Gene Product:Putative mechanosensitive ion channel protein \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_10521 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_19600 - Type: Gene Product:Two-component sensor histidine kinase \| Pathway: \| COG: Signal transduction mechanisms CD630_29530 - Type: Gene Product:ABC-type transport system, iron-familyextracellular solute-binding protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_29740 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_19620 - Type: Gene Product:ABC-type transport system, permease \| Pathway: \| COG: Defense mechanisms CD630_23861 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_01570 - Type: Gene Product:Fragment of putative membrane protein (Part 2) \| Pathway: \| COG: Function unknown CD630_19590 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms CD630_09080 - Type: Gene Product:Putative antirepressor protein \| Pathway: \| COG: Transcription CD630_02000 - Type: Gene Product:Fragment of transcriptional regulator, LysRfamily (C-terminal region) \| Pathway: \| COG: Transcription CD630_00120 - Type: Gene Product:Putative small-molecule-binding protein \| Pathway: \| COG: Transcription CD630_t0830 - tRNA-Thr Type: Gene Product: \| Pathway: \| COG: CD630_05780 - Type: Gene Product:Transporter, Major Facilitator Superfamily (MFS) \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_19610 - Type: Gene Product:ABC-type transport system, ATP-binding protein \| Pathway: \| COG: Defense mechanisms CD630_05790 - Type: Gene Product:Transcriptional regulator, TetR family \| Pathway: \| COG: Transcription CD630_r0090 - 5s_rRNA Type: Gene Product: \| Pathway: \| COG: CD630_09071 - Type: Gene Product:Transcriptional regulator, Phage-type \| Pathway: \| COG: Transcription CD630_01811 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_04341 - Type: Gene Product:Putative conjugative transposon proteinTn1549-like, CTn2-Orf30 \| Pathway: \| COG: CD630_t0800 - tRNA-Gly Type: Gene Product: \| Pathway: \| COG: CD630_09090 - Type: Gene Product:Putative phage protein \| Pathway: \| COG:	0.00000000000058	0.000000016	0.62	Inferelator: 2 Hypergeometric: 0 TF Influences from Inferelator CD630_19010 - Type: Gene Product:Transcriptional regulator, Phage-type \| Pathway: \| COG: Function unknown CD630_19590 - 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_66	24 CD630_32080 - Type: Gene Product:Transcriptional regulator, MarR family \| Pathway: \| COG: Transcription CD630_29870 - Type: Gene Product:Two-component sensor histidine kinase \| Pathway: \| COG: Signal transduction mechanisms CD630_15990 - thiD Type: Gene Product:Phosphomethylpyrimidine kinase \| Pathway: \| COG: Coenzyme transport and metabolism CD630_29840 - Type: Gene Product:ABC-type transport system, permease \| Pathway: \| COG: Defense mechanisms CD630_29860 - uppP2 Type: Gene Product:Undecaprenyl-diphosphatase 2 (Undecaprenylpyrophosphate phosphatase 2) (Bacitracin resistance protein2) \| Pathway: \| COG: Defense mechanisms CD630_14880 - Type: Gene Product:Transcriptional regulator, DeoR family \| Pathway: \| COG: Transcription CD630_16000 - thiM Type: Gene Product:Hydroxyethylthiazole kinase \| Pathway: Cofactor biosynthesis \| COG: Coenzyme transport and metabolism CD630_32660 - Type: Gene Product:Two-component sensor histidine kinase \| Pathway: \| COG: Signal transduction mechanisms CD630_22430 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: CD630_09040 - Type: Gene Product:Putative phage integrase \| Pathway: \| COG: Replication, recombination and repair CD630_32070 - Type: Gene Product:Putative multi antimicrobial extrusion protein,MatE family \| Pathway: \| COG: Defense mechanisms CD630_29880 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms CD630_21130 - Type: Gene Product:Two-component sensor histidine kinase \| Pathway: \| COG: Signal transduction mechanisms CD630_29850 - Type: Gene Product:ABC-type transport system, ATP-binding protein \| Pathway: \| COG: Defense mechanisms CD630_14870 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_14180 - Type: Gene Product:Putative drug/sodium antiporter, MATE family \| Pathway: \| COG: Defense mechanisms CD630_15420 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_15390 - Type: Gene Product:ABC-type transport system, ATP-binding protein \| Pathway: \| COG: Defense mechanisms CD630_16010 - thiE Type: Gene Product:Thiamine-phosphate pyrophosphorylase \| Pathway: Cofactor biosynthesis \| COG: Coenzyme transport and metabolism CD630_32650 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms CD630_32670 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms CD630_22420 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_21140 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms CD630_33600 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms	0.000000000027	0.04	0.62	Inferelator: 1 Hypergeometric: 0 TF Influences from Inferelator CD630_32080 - Type: Gene Product:Transcriptional regulator, MarR family \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_120	7 CD630_28860 - Type: Gene Product:Putative drug/sodium antiporter, MATE family \| Pathway: \| COG: Defense mechanisms CD630_32340 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_32330 - Type: Gene Product:Putative sigma-54 interacting protein \| Pathway: \| COG: Transcription CD630_20090 - Type: Gene Product:Fragment of putative topoisomerase (C-terminalregion) \| Pathway: \| COG: Replication, recombination and repair CD630_27000 - Type: Gene Product:Transcriptional regulator, sigma-54 dependent \| Pathway: \| COG: Transcription CD630_21030 - Type: Gene Product:ABC-type transport system, permease \| Pathway: \| COG: Function unknown CD630_28410 - Type: Gene Product:Putative amidohydrolase \| Pathway: \| COG: Carbohydrate transport and metabolism	`NA`	`NA`	0.63	Inferelator: 2 Hypergeometric: 0 TF Influences from Inferelator CD630_06290 - Type: Gene Product:Transcriptional regulator, Crp family \| Pathway: \| COG: Transcription CD630_20400 - Type: Gene Product:Transcriptional regulator, MerR family \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_349	29 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_18380 - aroK Type: Gene Product:Shikimate kinase (SK) \| Pathway: Metabolic intermediate biosynthesis \| COG: Amino acid transport and metabolism CD630_11890 - Type: Gene Product:Putative amino acid/polyamine transporter I \| Pathway: \| COG: Amino acid transport and metabolism CD630_13180 - pnp Type: Gene Product:Polyribonucleotide nucleotidyltransferase \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_11870 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_18390 - tyrC Type: Gene Product:Prephenate dehydrogenase \| Pathway: \| COG: Amino acid transport and metabolism CD630_22040 - Type: Gene Product:Putative esterase \| Pathway: \| COG: Function unknown CD630_35760 - Type: Gene Product:Transporter, Major Facilitator Superfamily (MFS) \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_35740 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_22060 - aldH Type: Gene Product:Aldehyde dehydrogenase (aldehyde:NAD+oxidoreductase) \| Pathway: \| COG: Energy production and conversion CD630_18330 - aroB Type: Gene Product:3-dehydroquinate synthase \| Pathway: Metabolic intermediate biosynthesis \| COG: Amino acid transport and metabolism CD630_11761 - rpmF Type: Gene Product:50S ribosomal protein L32 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_11760 - Type: Gene Product:Conserved hypothetical protein, DUF177 family \| Pathway: \| COG: Function unknown CD630_13170 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_18350 - aroC Type: Gene Product:Chorismate synthase(5-enolpyruvylshikimate-3-phosphate phospholyase) \| Pathway: Metabolic intermediate biosynthesis \| COG: Amino acid transport and metabolism CD630_11880 - Type: Gene Product:Putative gamma-glutamyl-gamma-aminobutyratehydrolase \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_18370 - aroE1 Type: Gene Product:Shikimate dehydrogenase 1 \| Pathway: Metabolic intermediate biosynthesis \| COG: Amino acid transport and metabolism CD630_01790 - gluD Type: Gene Product:NAD-specific glutamate dehydrogenase \| Pathway: \| COG: Amino acid transport and metabolism CD630_33930 - rumA Type: Gene Product:23S rRNA (uracil-5-)-methyltransferase RumA (23SrRNA(M-5-U1939)-methyltransferase) \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_17850 - argG Type: Gene Product:Argininosuccinate synthase (Citrulline--aspartateligase) \| Pathway: Amino-acid biosynthesis \| COG: Amino acid transport and metabolism CD630_35750 - Type: Gene Product:Putative sodium:solute symporter \| Pathway: \| COG: Amino acid transport and metabolism CD630_35730 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_13410 - exoA Type: Gene Product:Exodeoxyribonuclease \| Pathway: \| COG: Replication, recombination and repair CD630_35770 - mdeA Type: Gene Product:methionine gamma-lyase \| Pathway: \| COG: Amino acid transport and metabolism CD630_25030 - Type: Gene Product:Putative cation-transporting P-type ATPase \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_15230 - Type: Gene Product:Putative transporter \| Pathway: \| COG: Function unknown CD630_22050 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_18320 - aroF Type: Gene Product:3-deoxy-D-arabino-heptulosonate 7-phosphatesynthase \| Pathway: \| COG: Amino acid transport and metabolism	0.0000000079	`NA`	0.63	Inferelator: 1 Hypergeometric: 0 TF Influences from Inferelator CD630_16920 - Type: Gene Product:Transcriptional regulator, ArsR family \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`