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 11 - 20 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_124	25 CD630_10600 - Type: Gene Product:Putative pseudouridylate synthase \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_22480 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_19500 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_09390 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: Function unknown CD630_17260 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_10440 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_14580 - wrbA Type: Gene Product:Putative flavodoxin protein \| Pathway: \| COG: Function unknown CD630_23000 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_17980 - Type: Gene Product:Transcriptional regulator, LysR family \| Pathway: \| COG: Transcription CD630_14550 - sigA1 Type: Gene Product:RNA polymerase sigma factor SigA1 (sigma-43) \| Pathway: \| COG: Transcription CD630_17960 - Type: Gene Product:Putative nitrite and sulfite reductase subunit \| Pathway: \| COG: Energy production and conversion CD630_06370 - Type: Gene Product:Putative acetyltransferase \| Pathway: \| COG: Function unknown CD630_08800 - Type: Gene Product:Putative protease \| Pathway: \| COG: Function unknown CD630_15080 - Type: Gene Product:Putative iron-sulfur binding protein \| Pathway: \| COG: Energy production and conversion CD630_08820 - glgC Type: Gene Product:Glucose-1-phosphate adenylyltransferase \| Pathway: Glycan biosynthesis \| COG: Carbohydrate transport and metabolism CD630_22490 - Type: Gene Product:Putative ATPase \| Pathway: \| COG: Secondary metabolites biosynthesis, transport and catabolism CD630_14570 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_14540 - dnaG Type: Gene Product:DNA primase \| Pathway: \| COG: Replication, recombination and repair CD630_14560 - Type: Gene Product:Putative SAM-dependent methyltransferase \| Pathway: \| COG: Function unknown CD630_09400 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: Function unknown CD630_05103 - Type: Gene Product:Putative conjugative transposon protein Tn5397,CTn3-Orf4 \| Pathway: \| COG: CD630_17970 - Type: Gene Product:Coenzyme A disulfide reductase (CoA-disulfidereductase) (CoADR) \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_08810 - Type: Gene Product:Putative protein modulating protease activity \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_23960 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_29260 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: Function unknown	0.000067	`NA`	0.51	Inferelator: 2 Hypergeometric: 0 TF Influences from Inferelator CD630_20480 - Type: Gene Product:Transcriptional regulator, RpiR family \| Pathway: \| COG: Transcription CD630_20610 - Type: Gene Product:Conserved hypothetical protein, DUF1121 family \| Pathway: \| COG: Function unknown TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_167	28 CD630_19260 - eutR Type: Gene Product:Fragment of transcription regulator, AraC family(C-terminal region) \| Pathway: \| COG: Transcription CD630_21210 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_25980 - Type: Gene Product:Putative oligosaccharide deacetylase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_32570 - Type: Gene Product:Putative polysaccharide deacetylase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_05560 - Type: Gene Product:Putative sugar isomerase / endonuclease \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_05520 - prsW Type: Gene Product:Site-1 protease \| Pathway: \| COG: Function unknown CD630_05540 - sip2 Type: Gene Product:Signal peptidase type I \| Pathway: \| COG: Intracellular trafficking, secretion, and vesicular transport CD630_05500 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_32580 - Type: Gene Product:Iron hydrogenase \| Pathway: \| COG: Energy production and conversion CD630_34880 - gtaB Type: Gene Product:UTP--glucose-1-phosphate uridylyltransferase \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_23730 - Type: Gene Product:Putative CstA-like carbon starvation protein \| Pathway: \| COG: Signal transduction mechanisms CD630_07120 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_33120 - Type: Gene Product:Transporter, Major Facilitator Superfamily (MFS) \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_15750 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_27190 - Type: Gene Product:Putative polysaccharide deacetylase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_24580 - Type: Gene Product:Transporter, Major Facilitator Superfamily (MFS) \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_05570 - Type: Gene Product:Putative uridine kinase \| Pathway: \| COG: Nucleotide transport and metabolism CD630_25990 - Type: Gene Product:Putative transcriptional regulator \| Pathway: \| COG: Transcription CD630_05550 - sip2 Type: Gene Product:Signal peptidase type I \| Pathway: \| COG: Intracellular trafficking, secretion, and vesicular transport CD630_14300 - pdaA Type: Gene Product:Exported N-acetylmuramic acid deacetylase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_05510 - sleC Type: Gene Product:Spore exo-acting lytic transglycosylase \| Pathway: \| COG: Function unknown CD630_05530 - Type: Gene Product:Putative RNA methyltransferase \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_14630 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_30070 - Type: Gene Product:Putative L,D-transpeptidases \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_23052 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_15790 - Type: Gene Product:Two-component sensor histidine kinase,sporulation-associated spo0A \| Pathway: \| COG: Signal transduction mechanisms CD630_22520 - Type: Gene Product:Glutamate 2,3-aminomutase \| Pathway: \| COG: Amino acid transport and metabolism CD630_34890 - Type: Gene Product:Putative oligoendopeptidase F, peptidase M3Bfamily \| Pathway: \| COG: Amino acid transport and metabolism	0.00000029	`NA`	0.51	Inferelator: 5 Hypergeometric: 1 TF Influences from Inferelator CD630_06290 - Type: Gene Product:Transcriptional regulator, Crp family \| Pathway: \| COG: Transcription CD630_25990 - Type: Gene Product:Putative transcriptional regulator \| Pathway: \| COG: Transcription CD630_26420 - sigG Type: Gene Product:RNA polymerase sigma-G factor \| Pathway: \| COG: Transcription CD630_26430 - sigE Type: Gene Product:RNA polymerase sigma-E factor \| Pathway: \| COG: Transcription CD630_34990 - spoVT Type: Gene Product:Stage V sporulation protein T \| 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_44	21 CD630_16360 - terD Type: Gene Product:Tellurium resistance protein \| Pathway: \| COG: Signal transduction mechanisms CD630_25900 - dapF Type: Gene Product:Diaminopimelate epimerase (DAP epimerase) \| Pathway: Amino-acid biosynthesis \| COG: Amino acid transport and metabolism CD630_16370 - Type: Gene Product:Putative calcium-transporting ATPase \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_25780 - Type: Gene Product:Putative serine/threonine-protein kinase andphosphatase \| Pathway: \| COG: Signal transduction mechanisms CD630_16350 - terD Type: Gene Product:Tellurium resistance protein \| Pathway: \| COG: Signal transduction mechanisms CD630_25790 - Type: Gene Product:Putative phosphatase, 2C family \| Pathway: \| COG: Signal transduction mechanisms CD630_25810 - rsmB Type: Gene Product:Ribosomal RNA small subunit methyltransferase B(rRNA (cytosine-C(5)-)-methyltransferase) \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_16400 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_25830 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_16410 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_25740 - thiN Type: Gene Product:Thiamine pyrophosphokinase (TPK) (Thiaminediphospho kinase) \| Pathway: \| COG: Coenzyme transport and metabolism CD630_13580 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_16430 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_25770 - fabG Type: Gene Product:3-oxoacyl-[acyl-carrier-protein] reductase(3-ketoacyl- acyl carrier protein reductase) \| Pathway: \| COG: Function unknown CD630_16380 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_16420 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_25860 - priA Type: Gene Product:Primosomal protein N' (ATP-dependent helicasepriA) (Replication factor Y) \| Pathway: \| COG: Replication, recombination and repair CD630_16390 - Type: Gene Product:Putative tellurite associated resistance protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_16330 - Type: Gene Product:Putative serine protease \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_13570 - Type: Gene Product:Putative peptidyl-prolyl isomerase \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_25871 - rpoZ Type: Gene Product:DNA-directed RNA polymerase subunit omega (RNAPomega subunit) (Transcriptase subunit omega) (RNApolymerase omega subunit) \| Pathway: \| COG: Transcription	`NA`	`NA`	0.48	Inferelator: 4 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_16920 - Type: Gene Product:Transcriptional regulator, ArsR family \| Pathway: \| COG: Transcription CD630_16930 - Type: Gene Product:Putative dinitrogenase iron-molybdenum cofactor \| Pathway: \| COG: Function unknown CD630_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_342	18 CD630_05360 - cheW Type: Gene Product:Purine-binding chemotaxis protein CheW \| Pathway: \| COG: Cell motility, Signal transduction mechanisms CD630_32730 - feoA Type: Gene Product:Ferrous iron transport protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_23190 - rpe Type: Gene Product:Putative ribulose-phosphate 3-epimerase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_05350 - cheD Type: Gene Product:Probable chemoreceptor glutamine deamidase CheD \| Pathway: \| COG: Cell motility, Signal transduction mechanisms CD630_32720 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_05390 - cheA Type: Gene Product:Chemotaxis protein CheA \| Pathway: \| COG: Signal transduction mechanisms CD630_05420 - Type: Gene Product:Putative protein-glutamate methylesterase \| Pathway: \| COG: Signal transduction mechanisms CD630_05380 - Type: Gene Product:Putative methyl-accepting chemotaxis receptor,MCP family \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_32710 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_32740 - feoB Type: Gene Product:Ferrous iron transport protein B \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_05410 - cheR Type: Gene Product:Methyl-accepting chemotaxis proteinsmethyltransferase, MCP family \| Pathway: \| COG: Signal transduction mechanisms CD630_23200 - rpiB1 Type: Gene Product:Ribose-5-phosphate isomerase B1(Phosphoriboisomerase B) \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_23220 - tkt Type: Gene Product:Transketolase, N-terminal(Sedoheptulose-7-phosphate:D-glyceraldehyde-3-phosphateglycolaldehydetransferase) \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_05400 - cheW Type: Gene Product:Chemotaxis protein CheW \| Pathway: \| COG: Cell motility, Signal transduction mechanisms CD630_23210 - tkt Type: Gene Product:Transketolase, central and C-terminal(Sedoheptulose-7-phosphate:D-glyceraldehyde-3-phosphateglycolaldehydetransferase) \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_05340 - cheC Type: Gene Product:Chemotaxis protein CheY-P phosphatase CheC \| Pathway: \| COG: Cell motility, Signal transduction mechanisms CD630_05370 - Type: Gene Product:Putative CheY-like chemosensory protein \| Pathway: \| COG: Signal transduction mechanisms CD630_05330 - cheY Type: Gene Product:Chemotaxis protein CheY \| Pathway: \| COG: Signal transduction mechanisms	0.02	`NA`	0.45	Inferelator: 1 Hypergeometric: 1 TF Influences from Inferelator CD630_01710 - rex Type: Gene Product:Transcriptional regulator, Redox-sensingrepressor Rex \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test CD630_02660 - sigD Type: Gene Product:RNA polymerase sigma-28 factor for flagellaroperon \| Pathway: \| COG: Transcription
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_140	27 CD630_03340 - adhE Type: Gene Product:Aldehyde-alcohol dehydrogenase \| Pathway: \| COG: Energy production and conversion CD630_20430 - Type: Gene Product:Putative hydrolase \| Pathway: \| COG: Function unknown CD630_24180 - Type: Gene Product:PTS system, Sorbitol-like IIC component(Glucitol) \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_04570 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: CD630_31060 - Type: Gene Product:Transaldolase \| Pathway: Carbohydrate degradation \| COG: Carbohydrate transport and metabolism CD630_31100 - Type: Gene Product:6-phosphofructokinase \| Pathway: Carbohydrate degradation \| COG: Carbohydrate transport and metabolism CD630_23430 - cat1 Type: Gene Product:Succinyl-CoA:coenzyme A transferase \| Pathway: \| COG: Energy production and conversion CD630_15760 - Type: Gene Product:Putative esterase, SGNH hydrolase-type \| Pathway: \| COG: Amino acid transport and metabolism CD630_26270 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Signal transduction mechanisms CD630_21910 - Type: Gene Product:Putative phosphoesterase \| Pathway: Amino-acid biosynthesis \| COG: Amino acid transport and metabolism CD630_21870 - Type: Gene Product:Putative phage-related cell wall hydrolase \| Pathway: \| COG: Cell motility, Intracellular trafficking, secretion, and vesicular transport CD630_26260 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_34600 - tkt Type: Gene Product:Transketolase, thiamine diphosphate bindingsubunit \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_32050 - Type: Gene Product:Putative nitroreductase \| Pathway: \| COG: Energy production and conversion CD630_04580 - Type: Gene Product:Putative beta-lactamase \| Pathway: \| COG: Defense mechanisms CD630_25260 - glgB Type: Gene Product:1,4-alpha-glucan branching enzyme \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_23440 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_31070 - Type: Gene Product:Transcription antiterminator, PTS operonregulator \| Pathway: \| COG: Transcription CD630_15770 - pgm Type: Gene Product:Alpha-phosphoglucomutase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_31030 - Type: Gene Product:PTS system, glucose-like IIA component \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_15750 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_23420 - sucD Type: Gene Product:Succinate-semialdehyde dehydrogenase (NAD(P)+) \| Pathway: \| COG: Energy production and conversion CD630_04600 - Type: Gene Product:ABC-type transport system, permease \| Pathway: \| COG: Defense mechanisms CD630_32060 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: CD630_05450 - Type: Gene Product:Putative lipoprotein \| Pathway: \| COG: CD630_34590 - tkt Type: Gene Product:Transketolase, pyridine binding subunit \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_04590 - Type: Gene Product:ABC-type transport system, ATP-binding protein \| Pathway: \| COG: Defense mechanisms	2.4e-22	`NA`	0.52	Inferelator: 4 Hypergeometric: 1 TF Influences from Inferelator CD630_06110 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms CD630_10090 - Type: Gene Product:Transcriptional regulator, GntR family \| Pathway: \| COG: Transcription CD630_17980 - Type: Gene Product:Transcriptional regulator, LysR family \| Pathway: \| COG: Transcription CD630_23900 - Type: Gene Product:Transcriptional regulator, beta-lactamsrepressor \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test CD630_12750 - codY Type: Gene Product:Transcriptional regulator, GTP-sensingpleiotropic repressor \| Pathway: \| COG: Transcription
Module_60	29 CD630_21160 - bipA Type: Gene Product:GTP-binding protein BipA \| Pathway: \| COG: Signal transduction mechanisms CD630_12710 - Type: Gene Product:Putative restriction endonuclease \| Pathway: \| COG: Replication, recombination and repair CD630_13840 - Type: Gene Product:Putative lamB-like protein, UPF0271 family \| Pathway: \| COG: Amino acid transport and metabolism CD630_13860 - Type: Gene Product:Putative allophanate hydrolase subunit 1 \| Pathway: \| COG: Amino acid transport and metabolism CD630_19760 - mutL Type: Gene Product:DNA mismatch repair protein MutL \| Pathway: \| COG: Replication, recombination and repair CD630_12730 - Type: Gene Product:Putative DNA processing Smf single strand bindingprotein \| Pathway: \| COG: Replication, recombination and repair CD630_12770 - Type: Gene Product:Putative acetyltransferase \| Pathway: \| COG: Transcription CD630_19740 - hfq Type: Gene Product:Hfq RNA chaperone \| Pathway: \| COG: Signal transduction mechanisms CD630_12790 - iscS2 Type: Gene Product:Cysteine desulfurase \| Pathway: Cofactor biosynthesis \| COG: Amino acid transport and metabolism CD630_28270 - Type: Gene Product:Transcriptional regulator, MarR family \| Pathway: \| COG: Transcription CD630_28250 - Type: Gene Product:Putative flavodoxin \| Pathway: \| COG: Energy production and conversion CD630_14980 - sigA2 Type: Gene Product:RNA polymerase sigma factor SigA2 (sigma-43) \| Pathway: \| COG: Transcription CD630_12800 - Type: Gene Product:Putative NifU-like protein \| Pathway: \| COG: Energy production and conversion CD630_19720 - Type: Gene Product:Putative peptidase, M20A family \| Pathway: \| COG: Amino acid transport and metabolism CD630_15340 - ggt Type: Gene Product:Gamma-glutamyltranspeptidase \| Pathway: \| COG: Amino acid transport and metabolism CD630_14390 - Type: Gene Product:Putative transporter, LrgA family \| Pathway: \| COG: Function unknown CD630_26750 - Type: Gene Product:Transcriptional regulator, LysR family \| Pathway: \| COG: Transcription CD630_04352 - Type: Gene Product:Putative conjugative transposon proteinTn1549-like, CTn2-Orf33 \| Pathway: \| COG: CD630_13870 - Type: Gene Product:Putative allophanate hydrolase subunit 2 \| Pathway: \| COG: Amino acid transport and metabolism CD630_13850 - Type: Gene Product:Putative natural resistance-associated macrophageprotein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_19770 - mutS Type: Gene Product:DNA mismatch repair protein MutS \| Pathway: \| COG: Replication, recombination and repair CD630_22090 - Type: Gene Product:Putative GTP-binding protein, HflX type \| Pathway: \| COG: Function unknown CD630_19730 - Type: Gene Product:Putative pyridoxal phosphate-dependenttransferase; putative aluminium resistance \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_19750 - miaA Type: Gene Product:tRNA delta(2)-isopentenylpyrophosphatetransferase \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_28260 - Type: Gene Product:Putative aldolase \| Pathway: \| COG: Energy production and conversion CD630_14400 - Type: Gene Product:Putative transporter, LrgB family \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_27960 - cwp10 Type: Gene Product:Cell surface protein \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_28290 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Amino acid transport and metabolism, Carbohydrate transport and metabolism CD630_22610 - Type: Gene Product:Putative peptidase, M24 family \| Pathway: \| COG: Amino acid transport and metabolism	0.00000000052	`NA`	0.50	Inferelator: 1 Hypergeometric: 0 TF Influences from Inferelator 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_280	9 CD630_31470 - Type: Gene Product:Putative DNA-methyltransferase \| Pathway: \| COG: Replication, recombination and repair CD630_21341 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_13940 - Type: Gene Product:Putative NAD(P)-binding oxidoreductase,GFO/IDH/MOCA family \| Pathway: \| COG: Function unknown CD630_32330 - Type: Gene Product:Putative sigma-54 interacting protein \| Pathway: \| COG: Transcription CD630_17800 - Type: Gene Product:Putative methylase \| Pathway: \| COG: Replication, recombination and repair CD630_05850 - Type: Gene Product:Transcriptional regulator, GntR family \| Pathway: \| COG: Transcription CD630_21820 - Type: Gene Product:Fragment of conserved hypothetical protein(C-terminal region) \| Pathway: \| COG: Function unknown CD630_34500 - Type: Gene Product:Putative oxidoreductase with NAD(P)-bindingRossmann-fold domain \| Pathway: \| COG: Function unknown CD630_17780 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown	`NA`	`NA`	0.53	Inferelator: 2 Hypergeometric: 0 TF Influences from Inferelator CD630_16930 - Type: Gene Product:Putative dinitrogenase iron-molybdenum cofactor \| Pathway: \| COG: Function unknown 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_157	23 CD630_34280 - cbiE Type: Gene Product:Cobalt-precorrin-6Y C(5)-methyltransferase(Cobalt-precorrin-6 methyltransferase) (Cobalt-precorrin-6Ymethylase) \| Pathway: \| COG: Coenzyme transport and metabolism CD630_16180 - Type: Gene Product:ABC-type transport system, multidrug-familyATP-binding protein \| Pathway: \| COG: Defense mechanisms CD630_34180 - sirC Type: Gene Product:Precorrin-2 dehydrogenase \| Pathway: Porphyrin-containing compound metabolism \| COG: Coenzyme transport and metabolism CD630_34350 - cobQ Type: Gene Product:Cobyric acid synthase CobQ \| Pathway: Cofactor biosynthesis \| COG: Coenzyme transport and metabolism CD630_33550 - Type: Gene Product:Putative nitroreductase \| Pathway: \| COG: Energy production and conversion CD630_34230 - cbiJ Type: Gene Product:Cobalt-precorrin-6A reductase \| Pathway: \| COG: Coenzyme transport and metabolism CD630_34250 - cbiG Type: Gene Product:Cobalamin biosynthesis protein CbiG \| Pathway: \| COG: Coenzyme transport and metabolism CD630_29980 - Type: Gene Product:ABC-type transport system, iron-family permease \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_34330 - cbiB Type: Gene Product:Cobalamin biosynthesis protein CbiB, CobD/CbiBfamily \| Pathway: Cofactor biosynthesis \| COG: Coenzyme transport and metabolism CD630_34310 - Type: Gene Product:Putative cobalamin biosynthesis L-threoninePduX-like kinase \| Pathway: \| COG: Secondary metabolites biosynthesis, transport and catabolism CD630_04760 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_04750 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Replication, recombination and repair CD630_16190 - Type: Gene Product:ABC-type transport system, multidrug-familypermease \| Pathway: \| COG: Function unknown CD630_34260 - cbiF Type: Gene Product:Cobalt-precorrin-4 C(11)-methyltransferase(Cobalt-precorrin-3 methylase) \| Pathway: \| COG: Coenzyme transport and metabolism CD630_29970 - Type: Gene Product:ABC-type transport system, iron-familyATP-binding protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_34340 - cobB Type: Gene Product:Cobyrinic acid A,C-diamide synthase \| Pathway: Cofactor biosynthesis \| COG: Coenzyme transport and metabolism CD630_29990 - Type: Gene Product:ABC-type transport system, iron-familyextracellular solute-binding protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_34300 - cbiC Type: Gene Product:Cobalt-precorrin-8X methylmutase(Cobalt-precorrin isomerase) (HBA synthase) \| Pathway: \| COG: Coenzyme transport and metabolism CD630_16170 - Type: Gene Product:Transcriptional regulator, GntR family \| Pathway: \| COG: Transcription CD630_34240 - cbiH Type: Gene Product:Cobalt-precorrin-3B C(17)-methyltransferase(Cobalt-precorrin-3 methyltransferase) (Cobalt-precorrin-3methylase) \| Pathway: \| COG: Coenzyme transport and metabolism CD630_34320 - cobD Type: Gene Product:Threonine-phosphate decarboxylase(L-threonine-O-3-phosphate decarboxylase), CobD/CbiBfamily \| Pathway: \| COG: Amino acid transport and metabolism CD630_34220 - cbiK Type: Gene Product:Sirohydrochlorin cobaltochelatase \| Pathway: \| COG: Coenzyme transport and metabolism CD630_01810 - Type: Gene Product:Putative membrane-associated metalloprotease, M56family \| Pathway: \| COG: Transcription, Signal transduction mechanisms	0.14	`NA`	0.55	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_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_77	21 CD630_35330 - phnL Type: Gene Product:ABC-type transport system, phosphonate-specificATP-binding protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_04300 - Type: Gene Product:ABC-type transport system, cobalt-specificpermease Tn1549-like, CTn2-Orf25 \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_35320 - phnM Type: Gene Product:Putative carbon-phosphorus lyase complex subunit \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_35300 - Type: Gene Product:ABC-type transport system, iron-familyATP-binding protein \| Pathway: \| COG: Amino acid transport and metabolism CD630_04310 - Type: Gene Product:ABC-type transport system, cobalt-specificATP-binding protein Tn1549-like, CTn2-Orf26 \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_04230 - Type: Gene Product:Putative DNA/RNA helicase Tn1549-like,CTn2-Orf18 \| Pathway: \| COG: Replication, recombination and repair CD630_04290 - Type: Gene Product:Putative membrane protein Tn1549-like,CTn2-Orf24 \| Pathway: \| COG: Function unknown CD630_04250 - Type: Gene Product:Putative endonuclease relaxase Tn1549-like,CTn2-Orf20 \| Pathway: \| COG: Intracellular trafficking, secretion, and vesicular transport CD630_04260 - Type: Gene Product:Putative conjugative transposon proteinTn1549-like, CTn2-Orf21 \| Pathway: \| COG: Function unknown CD630_04320 - Type: Gene Product:ABC-type transport system, multidrug-familypermease Tn1549-like, CTn2-Orf27 \| Pathway: \| COG: Defense mechanisms CD630_35340 - phnK Type: Gene Product:ABC-type transport system, phosphonate-specificATP-binding protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_27020 - brnQ Type: Gene Product:Branched-chain amino acid transport system IIcarrier protein \| Pathway: \| COG: Amino acid transport and metabolism CD630_35280 - Type: Gene Product:ABC-type transport system, iron-familyextracellular solute-binding protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_04340 - Type: Gene Product:Putative drug/sodium antiporter, MATE family,Tn1549-like, CTn2-Orf29 \| Pathway: \| COG: Defense mechanisms CD630_35350 - phnJ Type: Gene Product:Putative phosphonate metabolism protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_35290 - Type: Gene Product:ABC-type transport system, iron-family permease \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_04240 - Type: Gene Product:Putative nucleic acid-binding proteinTn1549-like, CTn2-Orf19 \| Pathway: \| COG: Function unknown CD630_35310 - Type: Gene Product:Putative polymerase/histidinol phosphatase-like \| Pathway: \| COG: Function unknown CD630_35370 - phnH Type: Gene Product:Putative phosphonate metabolism protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_35380 - phnG Type: Gene Product:Putative phosphonate metabolism protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_35360 - phnI Type: Gene Product:Putative phosphonate metabolism protein \| Pathway: \| COG: Inorganic ion transport and metabolism	`NA`	`NA`	0.40	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`