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 51 - 60 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_243	21 CD630_24950 - selA Type: Gene Product:L-seryl-tRNA(Sec) selenium transferase(Selenocysteine synthase) (Sec synthase)(Selenocysteinyl-tRNA(Sec) synthase ) \| Pathway: Aminoacyl-tRNA biosynthesis \| COG: Amino acid transport and metabolism CD630_24980 - dacF Type: Gene Product:D-alanyl-D-alanine carboxypeptidase (putativesporulation-specific penicillin-binding protein) \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_24930 - selB Type: Gene Product:Selenocysteinyl-tRNA-specific translation factor \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_35140 - prs Type: Gene Product:Ribose-phosphate pyrophosphokinase \| Pathway: Metabolic intermediate biosynthesis \| COG: Nucleotide transport and metabolism CD630_01940 - groL Type: Gene Product:60 kDa chaperonin (Protein Cpn60) (GroELprotein) \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_25240 - nadD Type: Gene Product:Nicotinate-nucleotide adenylyltransferase \| Pathway: Cofactor biosynthesis \| COG: Coenzyme transport and metabolism CD630_24970 - comE Type: Gene Product:Competence protein ComEA \| Pathway: \| COG: Replication, recombination and repair CD630_25230 - Type: Gene Product:Putative hydrolase \| Pathway: \| COG: Coenzyme transport and metabolism CD630_24960 - selD Type: Gene Product:Selenide, water dikinase (Selenophosphatesynthetase) (Selenium donor protein) \| Pathway: \| COG: Amino acid transport and metabolism CD630_27290 - Type: Gene Product:Putative regulator of the sigma(E) factor \| Pathway: \| COG: Signal transduction mechanisms CD630_01930 - groS Type: Gene Product:10 kDa chaperonin (Protein Cpn10) (GroESprotein) \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_21770 - Type: Gene Product:ABC-type transport system,cystine/aminoacid-family extracellular solute-bindingprotein \| Pathway: \| COG: Amino acid transport and metabolism CD630_25220 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_21760 - Type: Gene Product:ABC-type transport system,cystine/aminoacid-family permease \| Pathway: \| COG: Amino acid transport and metabolism CD630_35150 - glmU Type: Gene Product:Bifunctional protein GlmU [Includes:UDP-N-acetylglucosamine pyrophosphorylase ;Glucosamine-1-phosphate N-acetyltransferase] \| Pathway: Nucleotide-sugar biosynthesis \| COG: Cell wall/membrane/envelope biogenesis CD630_27310 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: CD630_21720 - Type: Gene Product:ABC-type transport system,cystine/aminoacid-family ATP-binding protein \| Pathway: \| COG: Amino acid transport and metabolism CD630_21750 - Type: Gene Product:ABC-type transport system,cystine/aminoacid-family permease \| Pathway: \| COG: Amino acid transport and metabolism CD630_21740 - Type: Gene Product:ABC-type transport system,cystine/aminoacid-family extracellular solute-bindingprotein \| Pathway: \| COG: Amino acid transport and metabolism, Signal transduction mechanisms CD630_27300 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_21730 - Type: Gene Product:Putative peptidase, M20D family \| Pathway: \| COG: Amino acid transport and metabolism	1.2	`NA`	0.39	Inferelator: 1 Hypergeometric: 1 TF Influences from Inferelator CD630_27220 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms TF Influences from Hypergeometric Test CD630_32450 - prdR Type: Gene Product:Transcriptional regulator, sigma-54-dependent \| Pathway: \| COG: Transcription
Module_65	25 CD630_24710 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_04040 - Type: Gene Product:Conserved hypothetical protein, DUF1904 family \| Pathway: \| COG: Function unknown CD630_27200 - Type: Gene Product:Putative transporter \| Pathway: \| COG: Function unknown CD630_20290 - Type: Gene Product:Putative lipoprotein \| Pathway: \| COG: Function unknown CD630_32180 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_30220 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_16160 - Type: Gene Product:Putative diguanylate kinase signaling protein \| Pathway: \| COG: Signal transduction mechanisms CD630_05170 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_24720 - Type: Gene Product:Transcriptional regulator, ArsR family \| Pathway: \| COG: Function unknown CD630_35950 - Type: Gene Product:Aminopeptidase \| Pathway: \| COG: Amino acid transport and metabolism CD630_04050 - rluA Type: Gene Product:Ribosomal small subunit pseudouridine synthase A \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_13910 - Type: Gene Product:Putative hydrolase, CocE/NonD family \| Pathway: \| COG: Function unknown CD630_05180 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_04220 - Type: Gene Product:Putative conjugative transposon proteinTn1549-like, CTn2-Orf17 \| Pathway: \| COG: Function unknown CD630_28440 - Type: Gene Product:Transcriptional regulator, MarR family \| Pathway: \| COG: Transcription CD630_23080 - Type: Gene Product:Transcriptional regulator, HTH-type \| Pathway: \| COG: Transcription CD630_35180 - murC Type: Gene Product:UDP-N-acetylmuramate--L-alanine ligase(UDP-N-acetylmuramoyl-L-alanine synthetase) \| Pathway: Cell wall biogenesis \| COG: Cell wall/membrane/envelope biogenesis CD630_22560 - Type: Gene Product:Putative PTS system, EIIC component \| Pathway: \| COG: Function unknown CD630_01210 - Type: Gene Product:Putative thiosulfate sulfurtransferase \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_01560 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_31870 - tdcF Type: Gene Product:Putative regulatory endoribonuclease \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_23070 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_13770 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_04770 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_32220 - sdaB Type: Gene Product:L-serine dehydratase \| Pathway: \| COG: Amino acid transport and metabolism	0.00000000000036	0.0000005	0.39	Inferelator: 2 Hypergeometric: 0 TF Influences from Inferelator CD630_23900 - Type: Gene Product:Transcriptional regulator, beta-lactamsrepressor \| Pathway: \| COG: Transcription CD630_26030 - cdtR Type: Gene Product:Clostridium difficile binary toxin regulatorygene, LytTR family \| Pathway: \| COG: Signal transduction mechanisms TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_358	23 CD630_02500 - fliH Type: Gene Product:Flagellar assembly protein FliH \| Pathway: \| COG: Cell motility CD630_02490 - fliG Type: Gene Product:Flagellar motor switch protein FliG \| Pathway: \| COG: Cell motility CD630_02640 - flhF Type: Gene Product:Flagellar biosynthesis regulator FlhF(Flagella-associated GTP-binding protein) \| Pathway: \| COG: Cell motility CD630_02470 - fliE Type: Gene Product:Flagellar hook-basal body complex protein FliE \| Pathway: \| COG: Cell motility CD630_02600 - fliP Type: Gene Product:Flagellar biosynthesis protein FliP \| Pathway: \| COG: Cell motility CD630_02660 - sigD Type: Gene Product:RNA polymerase sigma-28 factor for flagellaroperon \| Pathway: \| COG: Transcription CD630_02520 - fliJ Type: Gene Product:Flagellar protein FliJ \| Pathway: \| COG: Cell motility CD630_02620 - flhB Type: Gene Product:Bifunctional flagellar biosynthesis proteinFliR/FlhB \| Pathway: \| COG: Cell motility CD630_02560 - motA Type: Gene Product:Flagellar motor rotation protein MotA \| Pathway: \| COG: Cell motility CD630_02540 - flgD Type: Gene Product:Basal-body rod modification protein FlgD \| Pathway: \| COG: Cell motility CD630_02580 - fliL Type: Gene Product:Flagellar basal body-associated protein FliL \| Pathway: \| COG: Cell motility CD630_02480 - fliF Type: Gene Product:Flagellar M-ring protein FliF \| Pathway: \| COG: Cell motility CD630_02650 - flhG Type: Gene Product:Flagellar number regulator FlhG \| Pathway: \| COG: Cell cycle control, cell division, chromosome partitioning CD630_02510 - fliI Type: Gene Product:ATP synthase subunit beta FliI \| Pathway: \| COG: Cell motility, Intracellular trafficking, secretion, and vesicular transport CD630_02550 - flgE Type: Gene Product:Flagellar hook protein FlgE (Distal rod protein) \| Pathway: \| COG: Cell motility CD630_02551 - FlbD Type: Gene Product:Flagellar protein FlbD \| Pathway: \| COG: Cell motility CD630_02530 - fliK Type: Gene Product:Flagellar hook-length control protein FliK \| Pathway: \| COG: Cell motility CD630_02460 - flgC Type: Gene Product:Flagellar basal-body rod protein FlgC \| Pathway: \| COG: Cell motility CD630_02670 - Type: Gene Product:Putative flagellar protein \| Pathway: \| COG: CD630_02570 - motB Type: Gene Product:Flagellar motor rotation protein MotB (Chemotaxisprotein MotB) \| Pathway: \| COG: Cell motility CD630_02630 - flhA Type: Gene Product:Flagellar biosynthesis protein FlhA \| Pathway: \| COG: Cell motility CD630_02610 - fliQ Type: Gene Product:Flagellar biosynthetic protein FliQ \| Pathway: \| COG: Cell motility CD630_02590 - fliZ Type: Gene Product:Flagellar protein FliZ \| Pathway: \| COG: Cell motility	`NA`	`NA`	0.39	Inferelator: 2 Hypergeometric: 1 TF Influences from Inferelator CD630_02660 - sigD Type: Gene Product:RNA polymerase sigma-28 factor for flagellaroperon \| Pathway: \| COG: Transcription CD630_22140 - SinR Type: Gene Product:Transcriptional regulator, HTH-type \| 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_82	31 CD630_21210 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_30370 - Type: Gene Product:Transcriptional regulator, CarD family \| Pathway: \| COG: Transcription CD630_14960 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_24590 - Type: Gene Product:Putative glucokinase, ROK family \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_28330 - Type: Gene Product:Putative calcium-transporting ATPase \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_34630 - alr2 Type: Gene Product:Alanine racemase 2 \| Pathway: Amino-acid biosynthesis \| COG: Cell wall/membrane/envelope biogenesis CD630_26290 - spoIVA Type: Gene Product:Stage IV sporulation protein A \| Pathway: \| COG: Function unknown CD630_35190 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_35210 - Type: Gene Product:Putative peptidase T, M20B family \| Pathway: \| COG: Amino acid transport and metabolism CD630_06670 - cdd4 Type: Gene Product:ABC-type transport system,lantibiotic/multidrug-family ATP-binding protein \| Pathway: \| COG: Defense mechanisms CD630_14330 - cotE Type: Gene Product:Spore coat protein CotE; peroxiredoxin/chitinase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_34620 - Type: Gene Product:Putative antitoxin EndoAI \| Pathway: \| COG: Transcription CD630_01060 - cwlD Type: Gene Product:Germination-specific N-acetylmuramoyl-L-alanineamidase, Autolysin \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_14030 - Type: Gene Product:Putative synthetase \| Pathway: \| COG: Secondary metabolites biosynthesis, transport and catabolism CD630_24090 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_05460 - Type: Gene Product:Putative membrane protein, DUF975 family \| Pathway: \| COG: Function unknown CD630_34660 - acpS Type: Gene Product:Holo-[acyl-carrier-protein] synthase \| Pathway: \| COG: Lipid transport and metabolism CD630_26560 - spoVD Type: Gene Product:Stage V sporulation protein D(Sporulation-specific penicillin-binding protein) \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_10670 - CdeC Type: Gene Product:Clostridium difficile exosporium cycteine-richprotein \| Pathway: \| COG: CD630_35220 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_21410 - Type: Gene Product:Serine-type D-Ala-D-Ala carboxypeptidase \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_35200 - Type: Gene Product:Putative cation efflux protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_24430 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_34640 - GerS Type: Gene Product:Lipoprotein regulator, germination \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_34570 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_15110 - cotB Type: Gene Product:Spore outer coat layer protein CotB \| Pathway: \| COG: Function unknown CD630_24450 - Type: Gene Product:Putative transmembrane signaling protein,TspO/MBR family \| Pathway: \| COG: Signal transduction mechanisms CD630_34610 - EndoA Type: Gene Product:Endoribonuclease toxin \| Pathway: \| COG: Signal transduction mechanisms CD630_18030 - cwp23 Type: Gene Product:Putative cell wall-binding protein \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_34650 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_26570 - Type: Gene Product:Putative lipoprotein \| Pathway: \| COG:	0.0000000013	`NA`	0.39	Inferelator: 1 Hypergeometric: 2 TF Influences from Inferelator 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 CD630_26430 - sigE Type: Gene Product:RNA polymerase sigma-E factor \| Pathway: \| COG: Transcription
Module_3	24 CD630_33640 - Type: Gene Product:ABC-type transport system, multidrug-familyATP-binding protein \| Pathway: \| COG: Function unknown CD630_33620 - Type: Gene Product:ABC-type transport system, multidrug-familypermease \| Pathway: \| COG: Function unknown CD630_13000 - pepA Type: Gene Product:Leucine aminopeptidase \| Pathway: \| COG: Amino acid transport and metabolism CD630_31610 - Type: Gene Product:ABC-type transport system, multidrug-familypermease \| Pathway: \| COG: Function unknown CD630_33581 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_30780 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_30820 - Type: Gene Product:PTS system, lactose/cellobiose-family IIBcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_30750 - tagABC Type: Gene Product:PTS system, tagatose-specific IIABC component \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_20320 - argB Type: Gene Product:Acetylglutamate kinase \| Pathway: Amino-acid biosynthesis \| COG: Amino acid transport and metabolism CD630_31620 - Type: Gene Product:ABC-type transport system, multidrug-familyATP-binding protein \| Pathway: \| COG: Defense mechanisms CD630_30770 - Type: Gene Product:Transcriptional regulator, RpiR family \| Pathway: \| COG: Transcription CD630_33590 - Type: Gene Product:ABC-type transport system, ATP-binding protein \| Pathway: \| COG: Function unknown CD630_20340 - argC Type: Gene Product:N-acetyl-gamma-glutamyl-phosphate reductase \| Pathway: Amino-acid biosynthesis \| COG: Amino acid transport and metabolism CD630_31600 - Type: Gene Product:ABC-type transport system, multidrug-familypermease \| Pathway: \| COG: Function unknown CD630_20330 - argJ Type: Gene Product:Arginine biosynthesis bifunctional protein ArgJ[Includes: Glutamate N-acetyltransferase ; Amino-acidacetyltransferase] \| Pathway: Amino-acid biosynthesis \| COG: Amino acid transport and metabolism CD630_33630 - Type: Gene Product:ABC-type transport system, multidrug-familypermease \| Pathway: \| COG: Function unknown CD630_30810 - Type: Gene Product:PTS system, lactose/cellobiose-family IICcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_30830 - Type: Gene Product:Transcription antiterminator, PTS operonregulator \| Pathway: \| COG: Transcription CD630_30790 - bglA Type: Gene Product:6-phospho-beta-glucosidase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_20310 - argM Type: Gene Product:Succinylornithine transaminase (ACOAT) \| Pathway: Amino-acid biosynthesis \| COG: Amino acid transport and metabolism CD630_12990 - Type: Gene Product:Transcriptional regulator, MarR family \| Pathway: \| COG: Transcription CD630_30740 - Type: Gene Product:tagatose-bisphosphate aldolase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_20300 - argF Type: Gene Product:Ornithine carbamoyltransferase (OTCase) \| Pathway: \| COG: Amino acid transport and metabolism CD630_30760 - tagK Type: Gene Product:Tagatose-6-phosphate kinase \| Pathway: Carbohydrate metabolism \| COG: Carbohydrate transport and metabolism	0.01	0.64	0.39	Inferelator: 3 Hypergeometric: 0 TF Influences from Inferelator CD630_02760 - Type: Gene Product:Transcriptional regulator, AraC family \| Pathway: \| COG: Transcription CD630_30940 - Type: Gene Product:Transcriptional regulator, sigma-54-dependent \| Pathway: \| COG: Transcription CD630_36390 - Type: Gene Product:Transcriptional regulator, LysR family \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_121	20 CD630_27720 - tuaG Type: Gene Product:Putative glycosyl transferase, family 2 \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_27730 - Type: Gene Product:Putative glycosyl transferase, family 2 \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_15570 - Type: Gene Product:Putative peptidylprolyl isomerase \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_27710 - rkpK Type: Gene Product:UDP-glucose 6-dehydrogenase \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_27750 - Type: Gene Product:Putative glycerophosphotransferase \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_15560 - Type: Gene Product:Putative polysaccharide deacetylase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_27760 - Type: Gene Product:Putative glycosyl transferase, family 2 \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_15590 - rsiV Type: Gene Product:Anti Sigma Factor, ECF family \| Pathway: \| COG: Function unknown CD630_27740 - Type: Gene Product:Putative glycosyl transferase, family 2 \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_27800 - pgm Type: Gene Product:Alpha-phosphoglucomutase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_15610 - Type: Gene Product:Putative dehydrogenase \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_27780 - Type: Gene Product:Putative glycosyl transferase \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_15580 - sigV Type: Gene Product:Extra-Cytoplasmic Function sigma factors, ECFfamily \| Pathway: \| COG: Transcription CD630_15600 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_27690 - Type: Gene Product:Putative polysaccharide biosynthesis protein \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_27700 - Type: Gene Product:Putative glycosyl transferase, group 1 \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_27820 - cwp7 Type: Gene Product:Cell wall binding protein \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_15620 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_27790 - manC Type: Gene Product:Putative mannose-1-phosphate guanylyltransferase \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_27770 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown	`NA`	`NA`	0.40	Inferelator: 3 Hypergeometric: 0 TF Influences from Inferelator CD630_10230 - Type: Gene Product:Putative transcriptional regulator, HTH \| Pathway: \| COG: Transcription CD630_11770 - fapR Type: Gene Product:Transcriptional regulator, DeoR family (Fattyacid and phospholipid biosynthesis regulator) \| Pathway: \| COG: Transcription CD630_16860 - Type: Gene Product:Transcriptional regulator, repressor-like \| Pathway: \| COG: Transcription 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`
Module_165	5 CD630_11140 - Type: Gene Product:Putative conjugative transposon proteinTn1549-like, CTn4-Orf5 \| Pathway: \| COG: CD630_07660 - srlEb Type: Gene Product:PTS system, sorbitol-specific IIB C-terminalcomponent (Glucitol) \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_03150 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_07650 - srlEa Type: Gene Product:PTS system, sorbitol-specific IIB N-terminalcomponent (Glucitol) \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_33410 - Type: Gene Product:Fragment of putative conjugative transposonprotein Tn916-like, CTn6-Orf18 (N-terminal region) \| Pathway: \| COG: Function unknown	`NA`	`NA`	0.40	Inferelator: 1 Hypergeometric: 0 TF Influences from Inferelator CD630_07630 - srlM Type: Gene Product:Sorbitol operon activator protein (Glucitol) \| Pathway: \| COG: Function unknown TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_372	7 CD630_33690 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_13820 - glpK2 Type: Gene Product:Glycerol kinase 1 (ATP:glycerol3-phosphotransferase 1) (Glycerokinase 1) (GK 1) \| Pathway: Polyol metabolism \| COG: Energy production and conversion CD630_22850 - Type: Gene Product:Transcriptional regulator, GntR family \| Pathway: \| COG: Transcription CD630_19050 - Type: Gene Product:Site-specific recombinase, resolvase family \| Pathway: \| COG: Replication, recombination and repair CD630_24190 - Type: Gene Product:Transcriptional regulator, AraC family \| Pathway: \| COG: Transcription CD630_01600 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms CD630_14930 - Type: Gene Product:Putative 3-methyladenine DNA glycosylase \| Pathway: \| COG: Replication, recombination and repair	5.8	`NA`	0.40	Inferelator: 2 Hypergeometric: 0 TF Influences from Inferelator CD630_18830 - Type: Gene Product:Transcriptional regulator, AraC family \| Pathway: \| COG: Transcription CD630_20230 - Type: Gene Product:Transcriptional regulator, GntR family \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_129	24 CD630_29630 - ldtcd1 Type: Gene Product:L,D-transpeptidases \| Pathway: \| COG: Function unknown CD630_11420 - rnfB Type: Gene Product:Electron transport complex protein \| Pathway: \| COG: Energy production and conversion CD630_03510 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_11400 - rnfE Type: Gene Product:Electron transport complex protein \| Pathway: \| COG: Energy production and conversion CD630_23510 - grdB Type: Gene Product:Glycine reductase complex component B gammasubunit (selenocysteine) \| Pathway: \| COG: Function unknown CD630_14090 - Type: Gene Product:Putative competence-damage inducible protein,CinA family \| Pathway: \| COG: Coenzyme transport and metabolism CD630_25590 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Replication, recombination and repair CD630_27680 - Type: Gene Product:Putative cell-wall hydrolase \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_25610 - Type: Gene Product:Putative phosphatase \| Pathway: \| COG: Function unknown CD630_23490 - grdC Type: Gene Product:Glycine reductase complex component C subunitbeta (Protein PC beta) \| Pathway: \| COG: Energy production and conversion CD630_16920 - Type: Gene Product:Transcriptional regulator, ArsR family \| Pathway: \| COG: Transcription CD630_11390 - rnfG Type: Gene Product:Electron transport complex protein \| Pathway: \| COG: Energy production and conversion CD630_03500 - Type: Gene Product:Putative hydrolase, HAD superfamily \| Pathway: \| COG: Function unknown CD630_25570 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_29620 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_11370 - rnfC Type: Gene Product:Electron transport complex protein \| Pathway: \| COG: Energy production and conversion CD630_11410 - rnfA Type: Gene Product:Electron transport complex protein \| Pathway: \| COG: Energy production and conversion CD630_25580 - coaD Type: Gene Product:Phosphopantetheine adenylyltransferase(Pantetheine-phosphate adenylyltransferase) \| Pathway: Cofactor biosynthesis \| COG: Coenzyme transport and metabolism CD630_16930 - Type: Gene Product:Putative dinitrogenase iron-molybdenum cofactor \| Pathway: \| COG: Function unknown CD630_14100 - Type: Gene Product:Putative hydrolase, HAD superfamily, subfamilyIIB \| Pathway: \| COG: Function unknown CD630_25600 - recG Type: Gene Product:ATP-dependent DNA helicase RecG \| Pathway: \| COG: Replication, recombination and repair CD630_23480 - grdD Type: Gene Product:Glycine reductase complex component C subunitalpha (Protein PC alpha) \| Pathway: \| COG: Function unknown CD630_11380 - rnfD Type: Gene Product:Electron transport complex protein \| Pathway: \| COG: Energy production and conversion	0.06	`NA`	0.40	Inferelator: 1 Hypergeometric: 1 TF Influences from Inferelator CD630_16930 - Type: Gene Product:Putative dinitrogenase iron-molybdenum cofactor \| Pathway: \| COG: Function unknown TF Influences from Hypergeometric Test CD630_32450 - prdR Type: Gene Product:Transcriptional regulator, sigma-54-dependent \| Pathway: \| COG: Transcription