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 141 - 150 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_63	17 CD630_09000 - opuCA Type: Gene Product:ABC-type transport system, glycinebetaine/carnitine/choline ATP-binding protein \| Pathway: \| COG: Amino acid transport and metabolism CD630_20920 - Type: Gene Product:Transcriptional regulator, sigma-54-dependent \| Pathway: \| COG: Transcription CD630_34780 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_09010 - opuCC Type: Gene Product:ABC-type transport system, glycinebetaine/carnitine/choline permease \| Pathway: \| COG: Amino acid transport and metabolism CD630_21580 - gabT Type: Gene Product:4-aminobutyrate aminotransferase \| Pathway: \| COG: Amino acid transport and metabolism CD630_32280 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_31700 - eno Type: Gene Product:Enolase (2-phosphoglycerate dehydratase)(2-phospho-D-glycerate hydro-lyase) \| Pathway: Carbohydrate degradation \| COG: Carbohydrate transport and metabolism CD630_36390 - Type: Gene Product:Transcriptional regulator, LysR family \| Pathway: \| COG: Transcription CD630_17110 - Type: Gene Product:Conserved hypothetical protein, UPF0145 family \| Pathway: \| COG: Function unknown CD630_29640 - Type: Gene Product:Putative tRNA-binding protein \| Pathway: \| COG: Function unknown CD630_20460 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_20760 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_23870 - Type: Gene Product:Alpha-hydroxy acid dehydrogenase, FMN-dependent \| Pathway: \| COG: Energy production and conversion CD630_20910 - Type: Gene Product:Putative xanthine/uracil permease \| Pathway: \| COG: Nucleotide transport and metabolism CD630_27670 - cwp19 Type: Gene Product:Cell surface protein \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_20980 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_08790 - Type: Gene Product:Putative carbohydrate kinase \| Pathway: \| COG: Carbohydrate transport and metabolism	0.0000054	`NA`	0.47	Inferelator: 1 Hypergeometric: 0 TF Influences from Inferelator CD630_05090 - Type: Gene Product:Transcriptional regulator, HTH-type Tn5397,CTn3-Orf9 \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_244	22 CD630_07950 - Type: Gene Product:Conserved hypothetical protein, UPF0082 family \| Pathway: \| COG: Transcription CD630_18170 - Type: Gene Product:Putative acyltransferase \| Pathway: \| COG: Lipid transport and metabolism CD630_18150 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_24490 - Type: Gene Product:Putative methyltransferase \| Pathway: \| COG: Function unknown CD630_06810 - Type: Gene Product:Transporter, Major Facilitator Superfamily (MFS) \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_06830 - Type: Gene Product:Transcriptional regulator, LacI family \| Pathway: \| COG: Transcription CD630_21020 - Type: Gene Product:Putative Na(+)/H(+) antiporter \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_06790 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_24500 - prmA Type: Gene Product:Ribosomal protein L11 methyltransferase (L11Mtase) \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_20200 - clpB Type: Gene Product:Chaperone protein \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_18140 - Type: Gene Product:Putative phosphoglycerate mutase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_20220 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_18160 - cmk Type: Gene Product:Cytidylate kinase (CK) (Cytidine monophosphatekinase) (CMP kinase) \| Pathway: \| COG: Nucleotide transport and metabolism CD630_24480 - Type: Gene Product:Putative MiaB-like tRNA modifying enzyme \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_23930 - Type: Gene Product:Putative glycosyl transferase, family 51 \| Pathway: Cell wall biogenesis \| 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_18180 - ispH Type: Gene Product:4-hydroxy-3-methylbut-2-enyl diphosphatereductase \| Pathway: Isoprenoid biosynthesis \| COG: Lipid transport and metabolism CD630_06820 - Type: Gene Product:Putative sodium:solute symporter \| Pathway: \| COG: Amino acid transport and metabolism CD630_06800 - Type: Gene Product:Conserved hypothetical protein, DUF1486 family \| Pathway: \| COG: Function unknown CD630_20210 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_24470 - Type: Gene Product:Putative histidine triad (HIT) protein \| Pathway: \| COG: Nucleotide transport and metabolism, Carbohydrate transport and metabolism CD630_23940 - polC Type: Gene Product:DNA polymerase III, epsilon subunit \| Pathway: \| COG: Replication, recombination and repair	0.00000052	`NA`	0.47	Inferelator: 2 Hypergeometric: 0 TF Influences from Inferelator CD630_01710 - rex Type: Gene Product:Transcriptional regulator, Redox-sensingrepressor Rex \| Pathway: \| COG: Transcription CD630_24630 - hrcA Type: Gene Product:Transcriptional regulator, Heat-induciblerepressor HrcA \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_308	27 CD630_32790 - Type: Gene Product:PTS system, mannose/fructose/sorbose IIBcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_02880 - Type: Gene Product:PTS system, mannose/fructose/sorbose IICcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_01660 - Type: Gene Product:Putative peptidase, M20D family \| Pathway: \| COG: Amino acid transport and metabolism CD630_02860 - Type: Gene Product:PTS system, mannose/fructose/sorbose IIAcomponent \| Pathway: \| COG: CD630_02840 - Type: Gene Product:PTS system, mannose/fructose/sorbose IIAcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_32760 - Type: Gene Product:PTS system, mannose/fructose/sorbose IIDcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_02900 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_22770 - Type: Gene Product:Class II aldolase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_04930 - Type: Gene Product:PTS system, mannose/fructose/sorbose IICcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_22800 - Type: Gene Product:PTS system, fructose/mannitol family IICcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_04910 - Type: Gene Product:PTS system, mannose/fructose/sorbose IIAcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_22820 - Type: Gene Product:PTS system, fructose/mannitol family IIAcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_22790 - Type: Gene Product:Putative sugar-phosphate dehydrogenase \| Pathway: \| COG: Amino acid transport and metabolism CD630_32780 - Type: Gene Product:PTS system, mannose/fructose/sorbose IIAcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_02890 - Type: Gene Product:PTS system, mannose/fructose/sorbose IIDcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_01650 - Type: Gene Product:Putative amino acid transporter \| Pathway: \| COG: Amino acid transport and metabolism CD630_02910 - Type: Gene Product:Putative peptidase, M20A family \| Pathway: \| COG: Amino acid transport and metabolism CD630_02850 - Type: Gene Product:PTS system, mannose/fructose/sorbose IIBcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_02870 - Type: Gene Product:PTS system, mannose/fructose/sorbose IIBcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_22810 - Type: Gene Product:PTS system, fructose/mannitol family IIBcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_32750 - Type: Gene Product:Putative phosphosugar isomerase \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_32770 - Type: Gene Product:PTS system, mannose/fructose/sorbose IICcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_04940 - Type: Gene Product:PTS system, mannose/fructose/sorbose IIDcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_22780 - araD Type: Gene Product:L-ribulose-5-phosphate 4-epimerase(Phosphoribulose isomerase) \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_04900 - Type: Gene Product:Putative sugar-phosphate dehydrogenase \| Pathway: \| COG: Amino acid transport and metabolism CD630_04920 - Type: Gene Product:PTS system, mannose/fructose/sorbose IIBcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_22830 - Type: Gene Product:Sigma-54-dependent regulator, PTS regulatorydomain \| Pathway: \| COG: Transcription	0.0000000013	`NA`	0.47	Inferelator: 2 Hypergeometric: 1 TF Influences from Inferelator CD630_16050 - Type: Gene Product:Putative transcriptional regulator \| Pathway: \| COG: Transcription CD630_22830 - Type: Gene Product:Sigma-54-dependent regulator, PTS regulatorydomain \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test CD630_31760 - glnF Type: Gene Product:RNA polymerase sigma-54 factor \| Pathway: \| COG: Transcription
Module_229	21 CD630_25120 - Type: Gene Product:PTS system, glucose-like IIA component \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_31380 - bglG Type: Gene Product:Transcription antiterminator, PTS operonregulator \| Pathway: \| COG: Transcription CD630_25080 - Type: Gene Product:Transcriptional regulator, AraC family \| Pathway: \| COG: Transcription CD630_01360 - Type: Gene Product:PTS system, lactose/cellobiose-family IIBcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_25110 - Type: Gene Product:Transcription antiterminator, PTS operonregulator \| Pathway: \| COG: Transcription CD630_01370 - Type: Gene Product:PTS system, lactose/cellobiose-family IICcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_01380 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_09241 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_15140 - panG Type: Gene Product:Putative ketopantoate reductase \| Pathway: \| COG: Coenzyme transport and metabolism CD630_25090 - Type: Gene Product:Putative glycoside hydrolase, family 4 \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_01410 - cutC Type: Gene Product:Copper homeostasis protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_15130 - panB Type: Gene Product:Ketopantoate hydroxymethyltransferase \| Pathway: Cofactor biosynthesis \| COG: Coenzyme transport and metabolism CD630_01390 - Type: Gene Product:N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase \| Pathway: \| COG: Amino acid transport and metabolism CD630_25070 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_15120 - panC Type: Gene Product:Pantothenate synthetase \| Pathway: Cofactor biosynthesis \| COG: Coenzyme transport and metabolism CD630_31370 - bglF Type: Gene Product:PTS system, beta-glucoside-specific IIABCcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_01350 - Type: Gene Product:PTS system, lactose/cellobiose-family IIAcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_25100 - Type: Gene Product:PTS system, glucose-like IIBC component \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_31360 - bglA Type: Gene Product:6-phospho-beta-glucosidase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_t0860 - tRNA-Glu Type: Gene Product: \| Pathway: \| COG: CD630_01400 - Type: Gene Product:Putative peptidase \| Pathway: \| COG: Amino acid transport and metabolism	9.7	`NA`	0.47	Inferelator: 2 Hypergeometric: 1 TF Influences from Inferelator CD630_10090 - Type: Gene Product:Transcriptional regulator, GntR family \| Pathway: \| COG: Transcription CD630_25080 - Type: Gene Product:Transcriptional regulator, AraC family \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test CD630_12750 - codY Type: Gene Product:Transcriptional regulator, GTP-sensingpleiotropic repressor \| Pathway: \| COG: Transcription
Module_181	23 CD630_36340 - Type: Gene Product:Transcriptional regulator, MerR family \| Pathway: \| COG: Transcription CD630_33741 - Type: Gene Product:Putative conjugative transposon proteinTn916-like, CTn7-Orf9 \| Pathway: \| COG: Function unknown CD630_33740 - Type: Gene Product:Putative conjugative transposon proteinTn916-like, CTn7-Orf8 \| Pathway: \| COG: Function unknown CD630_04532 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_33760 - Type: Gene Product:Putative transcriptional regulator Tn916-like,CTn7-Orf11 \| Pathway: \| COG: Transcription CD630_28330 - Type: Gene Product:Putative calcium-transporting ATPase \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_28370 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_36450 - licC Type: Gene Product:PTS system, lichenan-specific IIC component \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_34160 - Type: Gene Product:ABC-type transport system, sugar-family permease \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_34140 - Type: Gene Product:ABC-type transport system, sugar-familyextracellular solute-binding protein \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_36330 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_33730 - mgtA Type: Gene Product:Magnesium-transporting ATPase, P-type 1;Tn916-like, CTn7-Orf7 \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_33770 - mgtA Type: Gene Product:Magnesium-transporting ATPase, P-type 1;Tn916-like, CTn7-Orf12 \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_33750 - mgtC Type: Gene Product:Magnesium-transporting ATPase protein C;Tn916-like, CTn7-Orf10 \| Pathway: \| COG: Function unknown CD630_t0040 - tRNA-Leu Type: Gene Product: \| Pathway: \| COG: CD630_34170 - Type: Gene Product:ABC-type transport system, sugar-familyATP-binding protein \| Pathway: \| COG: Amino acid transport and metabolism CD630_33780 - Type: Gene Product:Putative conjugative transposon proteinTn916-like, CTn7-Orf13 \| Pathway: \| COG: Energy production and conversion CD630_34150 - Type: Gene Product:ABC-type transport system, sugar-family permease \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_34130 - Type: Gene Product:Putative nucleotide pyrophosphatase \| Pathway: \| COG: Function unknown CD630_36320 - Type: Gene Product:Putative isochorismatase (2,3 dihydro-2,3dihydroxybenzoate synthase) \| Pathway: \| COG: Secondary metabolites biosynthesis, transport and catabolism CD630_02010 - Type: Gene Product:Putative chromate transporter \| Pathway: \| COG: Inorganic ion transport and metabolism	0.14	`NA`	0.47	Inferelator: 1 Hypergeometric: 0 TF Influences from Inferelator CD630_02760 - Type: Gene Product:Transcriptional regulator, AraC family \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_263	27 CD630_30090 - Type: Gene Product:Putative pyridine nucleotide-disulphideoxidoreductase, class I \| Pathway: \| COG: Energy production and conversion CD630_24591 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_32020 - Type: Gene Product:Two-component sensor histidine kinase \| Pathway: \| COG: Signal transduction mechanisms CD630_30330 - trxA Type: Gene Product:Thioredoxin \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_22930 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_26590 - lgt Type: Gene Product:Prolipoprotein diacylglyceryl transferase \| Pathway: Protein modification \| COG: Cell wall/membrane/envelope biogenesis CD630_14700 - Type: Gene Product:Putative rhodanese-like domain-containingprotein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_16790 - Type: Gene Product:Putative flavodoxin \| Pathway: \| COG: Coenzyme transport and metabolism CD630_25920 - fbpA Type: Gene Product:Fibronectin-binding protein A \| Pathway: \| COG: Transcription CD630_28920 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_30100 - Type: Gene Product:Putative cytochrome C assembly protein \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_28900 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: Function unknown CD630_22920 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: CD630_32030 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms CD630_13930 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Amino acid transport and metabolism, Carbohydrate transport and metabolism CD630_22900 - Type: Gene Product:Transcriptional regulator, beta-lactamsrepressor \| Pathway: \| COG: Transcription CD630_16800 - Type: Gene Product:Putative FMN-binding protein \| Pathway: \| COG: Function unknown CD630_26580 - mraW Type: Gene Product:S-adenosyl-L-methionine-dependentmethyltransferase MraW \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_19490 - Type: Gene Product:Two-component sensor histidine kinase \| Pathway: \| COG: Signal transduction mechanisms CD630_28910 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_05140 - cwpV Type: Gene Product:Cell surface protein \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_30110 - Type: Gene Product:Transcriptional regulator, HxlR family DUF24 \| Pathway: \| COG: Transcription CD630_19580 - Type: Gene Product:Putative 4Fe-4S binding protein; putativeferredoxin; putative dehydrogenase; putative reductase \| Pathway: \| COG: Energy production and conversion CD630_14041 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_14040 - Type: Gene Product:Putative oligopeptide transporter \| Pathway: \| COG: Function unknown CD630_16810 - Type: Gene Product:Transcriptional regulator, TetR family \| Pathway: \| COG: Transcription CD630_22910 - Type: Gene Product:Transcriptional regulator, HTH-type \| Pathway: \| COG: Transcription	0.0000000000000062	`NA`	0.47	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`
Module_115	24 CD630_00670 - rpoC Type: Gene Product:DNA-directed RNA polymerase subunit beta' \| Pathway: \| COG: Transcription CD630_26720 - appA Type: Gene Product:ABC-type transport system, oligopeptide-familysolute-binding protein \| Pathway: \| COG: Amino acid transport and metabolism CD630_26700 - appF Type: Gene Product:ABC-type transport system, ATP-binding protein \| Pathway: \| COG: Amino acid transport and metabolism CD630_00590 - secE Type: Gene Product:Preprotein translocase SecE subunit \| Pathway: \| COG: Intracellular trafficking, secretion, and vesicular transport CD630_00610 - rplK Type: Gene Product:50S ribosomal protein L11 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00630 - rplJ Type: Gene Product:50S ribosomal protein L10 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00570 - sigH Type: Gene Product:RNA polymerase factor sigma-70 \| Pathway: \| COG: Transcription CD630_00530 - mrnC Type: Gene Product:Ribonuclease III \| Pathway: \| COG: Function unknown CD630_00550 - Type: Gene Product:Putative tRNA/rRNA methyltransferase, TrmHfamily, group3 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_23340 - mtlA Type: Gene Product:PTS system, mannitol-specific, IICB component \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_23320 - mtlF Type: Gene Product:PTS system, mannitol-specific, EIIA component \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_26710 - appD Type: Gene Product:ABC-type transport system, ATP-binding protein \| Pathway: \| COG: Amino acid transport and metabolism, Inorganic ion transport and metabolism CD630_00660 - rpoB Type: Gene Product:DNA-directed RNA polymerase subunit beta \| Pathway: \| COG: Transcription CD630_26730 - appB Type: Gene Product:ABC-type transport system, oligopeptide-familypermease protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_00620 - rplA Type: Gene Product:50S ribosomal protein L1 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00640 - rplL Type: Gene Product:50S ribosomal protein L7/L12 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00600 - nusG Type: Gene Product:transcription antitermination protein \| Pathway: \| COG: Transcription CD630_00581 - rpmG Type: Gene Product:50S ribosomal protein L33 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00580 - tuf1 Type: Gene Product:Elongation factor EFTu/EF1A \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00560 - Type: Gene Product:Putative ribonuclease \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00540 - thyX Type: Gene Product:Thymidylate synthase \| Pathway: Pyrimidine metabolism \| COG: Nucleotide transport and metabolism CD630_00520 - cysS Type: Gene Product:Cysteinyl-tRNA synthetase (Cysteine--tRNA ligase)(CysRS) \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_23310 - mtlD Type: Gene Product:Mannitol-1-phosphate 5-dehydrogenase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_26740 - appC Type: Gene Product:ABC-type transport system, oligopeptide-familypermease protein \| Pathway: \| COG: Inorganic ion transport and metabolism	`NA`	`NA`	0.47	Inferelator: 1 Hypergeometric: 1 TF Influences from Inferelator CD630_17980 - Type: Gene Product:Transcriptional regulator, LysR family \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test CD630_32450 - prdR Type: Gene Product:Transcriptional regulator, sigma-54-dependent \| Pathway: \| COG: Transcription
Module_169	25 CD630_30190 - Type: Gene Product:Putative transporter \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_00220 - fusA1 Type: Gene Product:Elongation factor G (EF-G) \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00260 - clpC Type: Gene Product:class III stress response-related ATPase, AAA+superfamily \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_26330 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Energy production and conversion CD630_00240 - mcsA Type: Gene Product:Activator of protein kinase McsB \| Pathway: \| COG: Function unknown CD630_17980 - Type: Gene Product:Transcriptional regulator, LysR family \| Pathway: \| COG: Transcription CD630_00470 - ispD Type: Gene Product:2-C-methyl-D-erythritol 4-phosphatecytidylyltransferase \| Pathway: Isoprenoid biosynthesis \| COG: Lipid transport and metabolism CD630_17960 - Type: Gene Product:Putative nitrite and sulfite reductase subunit \| Pathway: \| COG: Energy production and conversion CD630_36020 - Type: Gene Product:Putative ATPase \| Pathway: \| COG: Cell cycle control, cell division, chromosome partitioning CD630_26300 - gpsA Type: Gene Product:Glycerol-3-phosphate dehydrogenase (NAD(P)+)(NAD(P)H-dependent glycerol-3-phosphate dehydrogenase) \| Pathway: Membrane lipid metabolism \| COG: Energy production and conversion CD630_05600 - nfo Type: Gene Product:Endonuclease IV \| Pathway: \| COG: Replication, recombination and repair CD630_00290 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_30180 - Type: Gene Product:Putative redox-active protein \| Pathway: \| COG: Function unknown CD630_00230 - ctsR Type: Gene Product:Transcriptional regulator, CtsR family \| Pathway: \| COG: Transcription CD630_00480 - ispF Type: Gene Product:2-C-methyl-D-erythritol 2,4-cyclodiphosphatesynthase \| Pathway: Isoprenoid biosynthesis \| COG: Lipid transport and metabolism CD630_35990 - rolA Type: Gene Product:Two-component sensor histidine kinase \| Pathway: \| COG: Signal transduction mechanisms CD630_26310 - Type: Gene Product:Putative membrane protein, UPF0078 family \| Pathway: Lipid metabolism \| COG: Function unknown CD630_26320 - Type: Gene Product:Putative GTP-binding protein EngA \| Pathway: \| COG: Nucleotide transport and metabolism CD630_00250 - mcsB Type: Gene Product:Tyrosine kinase protein \| Pathway: \| COG: Amino acid transport and metabolism CD630_00270 - radA Type: Gene Product:DNA repair protein \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_00460 - Type: Gene Product:Putative lipoate-protein ligase \| Pathway: Protein modification \| COG: Coenzyme transport and metabolism CD630_36010 - Type: Gene Product:D-alanyl-D-alanine carboxypeptidase, M15 family(DD-peptidase) (DD-carboxypeptidase) \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_17970 - Type: Gene Product:Coenzyme A disulfide reductase (CoA-disulfidereductase) (CoADR) \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_36000 - rolB Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms CD630_00280 - disA Type: Gene Product:DNA integrity scanning protein disA \| Pathway: \| COG: Replication, recombination and repair	0.00000018	0.0000076	0.47	Inferelator: 2 Hypergeometric: 0 TF Influences from Inferelator CD630_19980 - Type: Gene Product:Transcriptional regulator, TetR family \| Pathway: \| COG: Transcription 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`
Module_281	27 CD630_20430 - Type: Gene Product:Putative hydrolase \| Pathway: \| COG: Function unknown CD630_09290 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: Function unknown CD630_29120 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: Function unknown CD630_09260 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_09340 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_09341 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_09300 - Type: Gene Product:Putative phage reductase \| Pathway: \| COG: Function unknown CD630_09301 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_09360 - Type: Gene Product:Putative phage endodeoxyribonuclease \| Pathway: \| COG: Replication, recombination and repair CD630_06110 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms CD630_09320 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_04950 - Type: Gene Product:Fragment of putative regulatory protein (Part 1) \| Pathway: \| COG: Function unknown, Function unknown CD630_18120 - Type: Gene Product:Fragment of putative two-component responseregulator (N-terminal region) \| Pathway: \| COG: CD630_09380 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: Function unknown CD630_09280 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_29130 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: Function unknown CD630_22190 - Type: Gene Product:Fragment of conjugative transposon protein(central region) \| Pathway: \| COG: Function unknown CD630_29150 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_09350 - Type: Gene Product:Putative S-adenosyl-L-methionine-dependentmethyltransferase \| Pathway: \| COG: Replication, recombination and repair CD630_09270 - Type: Gene Product:Putative phage DNA modification methylase \| Pathway: \| COG: Replication, recombination and repair CD630_06100 - Type: Gene Product:Two-component sensor histidine kinase \| Pathway: \| COG: Signal transduction mechanisms CD630_23051 - Type: Gene Product:Fragment of transposase (N-terminal region) \| Pathway: \| COG: Replication, recombination and repair CD630_09250 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_09370 - Type: Gene Product:Putative phage anti-repressor \| Pathway: \| COG: Transcription CD630_09330 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_09310 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_28390 - Type: Gene Product:Two-component sensor histidine kinase \| Pathway: \| COG: Signal transduction mechanisms	4.1	`NA`	0.47	Inferelator: 2 Hypergeometric: 0 TF Influences from Inferelator CD630_30540 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms 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_53	19 CD630_27470 - Type: Gene Product:Putative ubiquinone biosynthesis protein \| Pathway: \| COG: Coenzyme transport and metabolism CD630_27390 - aspS Type: Gene Product:Aspartyl-tRNA synthetase (Aspartate--tRNA ligase)(AspRS) \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_27460 - recJ Type: Gene Product:Single-stranded-DNA-specific exonuclease \| Pathway: \| COG: Replication, recombination and repair CD630_07700 - spoIIAA Type: Gene Product:Anti-sigma F factor antagonist \| Pathway: \| COG: Signal transduction mechanisms CD630_22960 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Transcription CD630_27440 - relA Type: Gene Product:GTP pyrophosphokinase (RelA/SpoT) \| Pathway: \| COG: Transcription, Signal transduction mechanisms CD630_07710 - spoIIAB Type: Gene Product:Anti-sigma F factor (Stage II sporulation proteinAB) \| Pathway: \| COG: Signal transduction mechanisms CD630_24790 - Type: Gene Product:Putative molybdenum cofactor biosynthesis \| Pathway: \| COG: Coenzyme transport and metabolism CD630_10440 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_27400 - hisS Type: Gene Product:Histidyl-tRNA synthetase (Histidine--tRNA ligase)(HisRS) \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_24910 - pmi Type: Gene Product:Mannose-6-phosphate isomerase (Phosphomannoseisomerase) (PMI) (Phosphohexomutase) \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_08030 - Type: Gene Product:Putative acyl-CoA dehydrogenase \| Pathway: \| COG: Lipid transport and metabolism CD630_09100 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: Function unknown CD630_24900 - Type: Gene Product:Putative peptidase, M20A family \| Pathway: \| COG: Amino acid transport and metabolism CD630_22970 - Type: Gene Product:Putative phage-related regulatory protein \| Pathway: \| COG: Transcription CD630_27430 - dtd Type: Gene Product:D-tyrosyl-tRNA(Tyr) deacylase \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_08050 - etfA Type: Gene Product:Electron transfer flavoprotein alpha-subunit \| Pathway: \| COG: Energy production and conversion CD630_07720 - sigF Type: Gene Product:RNA polymerase sigma-F factor \| Pathway: \| COG: Transcription CD630_27420 - Type: Gene Product:Putative hydrolase beta-lactamase-like \| Pathway: \| COG: Secondary metabolites biosynthesis, transport and catabolism	0.000023	0.03	0.47	Inferelator: 1 Hypergeometric: 0 TF Influences from Inferelator CD630_31900 - Type: Gene Product:Transcriptional regulator, MerR family \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`