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 61 - 70 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'.

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Title Gene Count Motif 1 e-value Motif 2 e-value Residual Expression TF Influences
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

  1. 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_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

  1. CD630_16930 - Type: Gene
    Product:Putative dinitrogenase iron-molybdenum cofactor | Pathway: | COG: Function unknown

TF Influences from Hypergeometric Test

  1. CD630_32450 - prdR Type: Gene
    Product:Transcriptional regulator, sigma-54-dependent | Pathway: | COG: Transcription
Module_321 21
  • CD630_05822 - Type: Gene
    Product:Fragment of putative signaling protein precursor(N-terminal region) | Pathway: | COG: Signal transduction mechanisms
  • CD630_09640 - Type: Gene
    Product:Putative phage baseplate assembly protein | Pathway: | COG: Function unknown
  • CD630_28960 - Type: Gene
    Product:Putative phage protein | Pathway: | COG: Function unknown
  • CD630_09690 - Type: Gene
    Product:Putative phage protein | Pathway: | COG:
  • CD630_28990 - Type: Gene
    Product:Putative phage protein | Pathway: | COG: Function unknown
  • CD630_09590 - Type: Gene
    Product:Putative phage tail tape measure protein | Pathway: | COG: Function unknown
  • CD630_09700 - Type: Gene
    Product:Putative phage protein | Pathway: | COG: Function unknown
  • CD630_09670 - Type: Gene
    Product:Putative phage protein | Pathway: | COG: Function unknown
  • CD630_29030 - Type: Gene
    Product:Putative phage tail protein | Pathway: | COG: Function unknown
  • CD630_09600 - Type: Gene
    Product:Putative phage cell wall hydrolase | Pathway: | COG: Function unknown
  • CD630_09710 - Type: Gene
    Product:Putative phage holin protein | Pathway: | COG: Function unknown
  • CD630_29070 - Type: Gene
    Product:Putative phage lipoprotein | Pathway: | COG: Function unknown
  • CD630_09720 - Type: Gene
    Product:Putative phage-related cell wall hydrolase(endolysin) | Pathway: | COG: Cell wall/membrane/envelope biogenesis
  • CD630_09630 - Type: Gene
    Product:Putative phage protein | Pathway: | COG: Function unknown
  • CD630_09730 - Type: Gene
    Product:Putative phage protein | Pathway: | COG:
  • CD630_29050 - Type: Gene
    Product:Putative phage tail tape measure protein | Pathway: | COG: Function unknown
  • CD630_29010 - Type: Gene
    Product:Putative phage protein | Pathway: | COG: Function unknown
  • CD630_29040 - Type: Gene
    Product:Putative phage cell wall hydrolase | Pathway: | COG: Function unknown
  • CD630_19981 - Type: Gene
    Product:Fragment of conserved hypothetical protein(C-terminal region) | Pathway: | COG:
  • CD630_09660 - Type: Gene
    Product:Putative phage tail fiber protein | Pathway: | COG: Function unknown
  • CD630_09680 - Type: Gene
    Product:Putative phage protein | Pathway: | COG: Function unknown
NA NA 0.41 Inferelator: 2
Hypergeometric: 0

TF Influences from Inferelator

  1. CD630_04500 - Type: Gene
    Product:Putative transcriptional regulator | Pathway: | COG: Transcription
  2. CD630_30540 - Type: Gene
    Product:Two-component response regulator | Pathway: | COG: Signal transduction mechanisms

TF Influences from Hypergeometric Test

No TF Influences from the hypergeometric test
Module_51 25
  • CD630_35860 - Type: Gene
    Product:Two-component sensor histidine kinase | Pathway: | COG: Signal transduction mechanisms
  • CD630_25340 - Type: Gene
    Product:ABC-type transport system, ATP-binding protein | Pathway: | COG: Defense mechanisms
  • CD630_24030 - dut Type: Gene
    Product:Deoxyuridine 5'-triphosphate nucleotidohydrolase(dUTPase) (dUTP pyrophosphatase) | Pathway: Pyrimidine metabolism | COG: Nucleotide transport and metabolism
  • CD630_13100 - rbfA Type: Gene
    Product:Ribosome-binding factor A | Pathway: | COG: Translation, ribosomal structure and biogenesis
  • CD630_13060 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_15280 - Type: Gene
    Product:ABC-type transport system, ATP-binding protein | Pathway: | COG: Defense mechanisms
  • CD630_21890 - pgmB Type: Gene
    Product:Beta-phosphoglucomutase (beta-D-Glucose1,6-phosphomutase) | Pathway: | COG: Carbohydrate transport and metabolism
  • CD630_13080 - Type: Gene
    Product:Ribosomal protein L7Ae/L30e/S12e/Gadd45 | Pathway: | COG: Translation, ribosomal structure and biogenesis
  • CD630_21870 - Type: Gene
    Product:Putative phage-related cell wall hydrolase | Pathway: | COG: Cell motility, Intracellular trafficking, secretion, and vesicular transport
  • CD630_33260 - Type: Gene
    Product:Integrase, lambdoid phage family Tn916-like,CTn6-Orf1 | Pathway: | COG: Replication, recombination and repair
  • CD630_35870 - Type: Gene
    Product:Two-component response regulator, CheY family | Pathway: | COG: Signal transduction mechanisms
  • CD630_35850 - Type: Gene
    Product:ABC-type transport system, ATP-binding protein | Pathway: | COG: Defense mechanisms
  • CD630_25350 - Type: Gene
    Product:Two-component sensor histidine kinase | Pathway: | COG: Signal transduction mechanisms
  • CD630_25330 - Type: Gene
    Product:ABC-type transport system, permease | Pathway: | COG: Defense mechanisms
  • CD630_14970 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_13071 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Transcription
  • CD630_13070 - nusA Type: Gene
    Product:Transcription elongation protein | Pathway: | COG: Transcription
  • CD630_13050 - dnaF Type: Gene
    Product:DNA polymerase III PolC-type (PolIII) | Pathway: | COG: Replication, recombination and repair
  • CD630_13090 - infB Type: Gene
    Product:Translation initiation factor IF-2 | Pathway: | COG: Translation, ribosomal structure and biogenesis
  • CD630_21880 - mapA Type: Gene
    Product:Maltose phosphorylase/glycosyl hydrolase/vacuolaracid trehalase | Pathway: | COG: Carbohydrate transport and metabolism
  • CD630_15290 - Type: Gene
    Product:ABC-type transport system, permease | Pathway: | COG: Function unknown
  • CD630_15270 - Type: Gene
    Product:ABC-type transport system, permease | Pathway: | COG: Defense mechanisms
  • CD630_35840 - Type: Gene
    Product:ABC-type transport system, permease | Pathway: | COG: Defense mechanisms
  • CD630_25360 - Type: Gene
    Product:Two-component response regulator | Pathway: | COG: Signal transduction mechanisms
  • CD630_33270 - Type: Gene
    Product:Putative conjugative transposon proteinTn916-like, CTn6-Orf2 | Pathway: | COG: Function unknown
0.000000021 NA 0.41 Inferelator: 1
Hypergeometric: 0

TF Influences from Inferelator

  1. 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_4 13
  • CD630_34180 - sirC Type: Gene
    Product:Precorrin-2 dehydrogenase | Pathway: Porphyrin-containing compound metabolism | 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_34190 - hemB Type: Gene
    Product:Delta-aminolevulinic acid dehydratase(porphobilinogen synthase) | Pathway: | COG: Coenzyme transport and metabolism
  • CD630_11800 - fabK Type: Gene
    Product:Enoyl-(Acyl-carrier-protein) reductase II | Pathway: | COG: Lipid transport and metabolism
  • CD630_34270 - cbiT Type: Gene
    Product:Cobalt-precorrin-6Y C(15)-methyltransferase | Pathway: | COG: Coenzyme transport and metabolism
  • CD630_34290 - cbiD Type: Gene
    Product:Cobalt-precorrin-6A synthase [deacetylating] | Pathway: Cofactor biosynthesis | COG: Coenzyme transport and metabolism
  • CD630_34210 - hemC Type: Gene
    Product:Porphobilinogen deaminase (PBG)(Hydroxymethylbilane synthase) (HMBS) (Pre-uroporphyrinogensynthase) | Pathway: Porphyrin-containing compound metabolism | COG: Coenzyme transport and metabolism
  • CD630_34330 - cbiB Type: Gene
    Product:Cobalamin biosynthesis protein CbiB, CobD/CbiBfamily | Pathway: Cofactor biosynthesis | COG: Coenzyme transport and metabolism
  • CD630_34200 - cobA + hemD Type: Gene
    Product:Bifunctional uroporphyrinogen-IIImethyltransferase/uroporphyrinogen-III synthase | Pathway: | 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_11241 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG:
  • CD630_11820 - fabG Type: Gene
    Product:3-oxoacyl-[acyl-carrier protein] reductase(3-ketoacyl-acyl carrier protein reductase) | Pathway: Lipid metabolism | COG: Function unknown
  • CD630_11790 - fabH Type: Gene
    Product:3-oxoacyl-[acyl-carrier-protein] synthase 3 | Pathway: Lipid metabolism | COG: Lipid transport and metabolism
8.9 NA 0.41 Inferelator: 2
Hypergeometric: 0

TF Influences from Inferelator

  1. CD630_10090 - Type: Gene
    Product:Transcriptional regulator, GntR family | Pathway: | COG: Transcription
  2. CD630_11770 - fapR Type: Gene
    Product:Transcriptional regulator, DeoR family (Fattyacid and phospholipid biosynthesis regulator) | Pathway: | COG: Transcription

TF Influences from Hypergeometric Test

No TF Influences from the hypergeometric test
Module_213 20
  • CD630_11040 - Type: Gene
    Product:Putative conjugative transposon proteinTn1549-like, CTn4-Orf19 | Pathway: | COG: Function unknown
  • CD630_25730 - Type: Gene
    Product:Putative hydrolase, HAD superfamily, subfamilyIA | Pathway: | COG: Function unknown
  • CD630_28560 - Type: Gene
    Product:Putative membrane protein | Pathway: | COG: Replication, recombination and repair
  • CD630_19690 - Type: Gene
    Product:Putative oligonucleotide binding regulator | Pathway: | COG: Function unknown
  • CD630_25720 - Type: Gene
    Product:Putative nitroreductase | Pathway: | COG: Energy production and conversion
  • CD630_27840 - cwp6 Type: Gene
    Product:Putative N-acetylmuramoyl-L-alanine amidase,autolysin | Pathway: | COG: Cell wall/membrane/envelope biogenesis
  • CD630_34050 - Type: Gene
    Product:Putative iron-onlyhydrogenase,electron-transferring subunit HymA-like | Pathway: | COG: Energy production and conversion
  • CD630_19670 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG:
  • CD630_08130 - Type: Gene
    Product:Putative PTS system, IIB component | Pathway: | COG:
  • CD630_18950 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_28570 - Type: Gene
    Product:Putative hydrolase, HAD superfamily, IAsubfamily | Pathway: | COG: Translation, ribosomal structure and biogenesis
  • CD630_34060 - Type: Gene
    Product:Putative iron-onlyhydrogenase,electron-transferring subunit HymB-like | Pathway: | COG: Energy production and conversion
  • CD630_33240 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_08120 - Type: Gene
    Product:Putative universal stress protein A (UspA) | Pathway: | COG: Signal transduction mechanisms
  • CD630_18960 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_28580 - Type: Gene
    Product:Putative membrane protein | Pathway: | COG: Inorganic ion transport and metabolism
  • CD630_19680 - Type: Gene
    Product:Putative membrane protein | Pathway: | COG: Function unknown
  • CD630_19700 - Type: Gene
    Product:Putative enzyme, cyclase family | Pathway: | COG: Amino acid transport and metabolism
  • CD630_35160 - spoVG Type: Gene
    Product:Regulator required for spore cortex synthesis | Pathway: | COG: Cell wall/membrane/envelope biogenesis
  • CD630_34070 - Type: Gene
    Product:Putative iron-only hydrogenase, catalytic subunitHymC-like | Pathway: | COG: Energy production and conversion
0.00000000059 NA 0.41 Inferelator: 2
Hypergeometric: 0

TF Influences from Inferelator

  1. CD630_18100 - Type: Gene
    Product:Transcriptional regulator, beta-lactamsrepressor | Pathway: | COG: Transcription
  2. CD630_35440 - Type: Gene
    Product:Transcriptional regulator, AsnC/Lrp family | Pathway: | COG: Transcription

TF Influences from Hypergeometric Test

No TF Influences from the hypergeometric test
Module_154 21
  • CD630_30610 - Type: Gene
    Product:PTS system, alpha-glucoside-specific IIBCcomponent | Pathway: | COG: Carbohydrate transport and metabolism
  • CD630_30600 - Type: Gene
    Product:Phospho-alpha-glucosidase | Pathway: | COG: Carbohydrate transport and metabolism
  • CD630_35270 - Type: Gene
    Product:ABC-type transport system, iron-familyATP-binding protein | Pathway: | COG: Amino acid transport and metabolism
  • CD630_31290 - Type: Gene
    Product:Glycosyl hydrolase/phosphorylase | Pathway: | COG: Carbohydrate transport and metabolism
  • CD630_30570 - Type: Gene
    Product:Transporter, Major Facilitator Superfamily (MFS) | Pathway: | COG: Carbohydrate transport and metabolism
  • CD630_30840 - garK Type: Gene
    Product:Glycerate kinase | Pathway: | COG: Carbohydrate transport and metabolism
  • CD630_30860 - mngA Type: Gene
    Product:PTS system, 2-O-a-mannosyl-D-glycerate-specificIIABC component | Pathway: | COG: Carbohydrate transport and metabolism
  • CD630_30850 - mngB Type: Gene
    Product:Alpha-mannosidase | Pathway: | COG: Carbohydrate transport and metabolism
  • CD630_31300 - bglA Type: Gene
    Product:6-phospho-beta-glucosidase | Pathway: | COG: Carbohydrate transport and metabolism
  • CD630_30580 - Type: Gene
    Product:PTS system, alpha-glucoside-specific IIAcomponent | Pathway: | COG: Carbohydrate transport and metabolism
  • CD630_31270 - Type: Gene
    Product:PTS system, beta-glucoside-like IIBC component | Pathway: | COG: Carbohydrate transport and metabolism
  • CD630_31000 - Type: Gene
    Product:Putative C4-dicarboxylate anaerobic carrier, DcuCfamily | Pathway: | COG: Function unknown
  • CD630_30590 - Type: Gene
    Product:Putative membrane protein | Pathway: | COG:
  • CD630_06130 - Type: Gene
    Product:ABC-type transport system, ATP-binding protein | Pathway: | COG: Defense mechanisms
  • CD630_35250 - Type: Gene
    Product:ABC-type transport system, iron-familyextracellular solute-binding protein | Pathway: | COG: Inorganic ion transport and metabolism
  • CD630_06120 - Type: Gene
    Product:ABC-type transport system, permease | Pathway: | COG: Defense mechanisms
  • CD630_31280 - pgmB Type: Gene
    Product:Beta-phosphoglucomutase (beta-D-Glucose1,6-phosphomutase) | Pathway: | COG: Carbohydrate transport and metabolism
  • CD630_30870 - Type: Gene
    Product:Transcriptional regulator, RpiR family | Pathway: | COG: Transcription
  • CD630_35260 - Type: Gene
    Product:ABC-type transport system, iron-family permease | Pathway: | COG: Inorganic ion transport and metabolism
  • CD630_34510 - Type: Gene
    Product:Putative carbohydrate/purine kinase; putativetagatose-6-phosphate kinase LacC | Pathway: Carbohydrate metabolism | COG: Carbohydrate transport and metabolism
  • CD630_30990 - Type: Gene
    Product:Putative amidohydrolase, M20D family | Pathway: | COG: Amino acid transport and metabolism
0.00017 NA 0.41 Inferelator: 3
Hypergeometric: 0

TF Influences from Inferelator

  1. CD630_02760 - Type: Gene
    Product:Transcriptional regulator, AraC family | Pathway: | COG: Transcription
  2. CD630_32800 - Type: Gene
    Product:Sigma-54 dpendent regulator, PTS fructose family | Pathway: | COG: Signal transduction mechanisms
  3. CD630_33530 - Type: Gene
    Product:Transcriptional regulator, GntR family | Pathway: | COG: Transcription

TF Influences from Hypergeometric Test

No TF Influences from the hypergeometric test
Module_382 17
  • CD630_00890 - rplO Type: Gene
    Product:50S ribosomal protein L15 | Pathway: | COG: Translation, ribosomal structure and biogenesis
  • CD630_00840 - rplE Type: Gene
    Product:50S ribosomal protein L5 | Pathway: | COG: Translation, ribosomal structure and biogenesis
  • CD630_00760 - rplB Type: Gene
    Product:50S ribosomal protein L2 | Pathway: | COG: Translation, ribosomal structure and biogenesis
  • CD630_00730 - rplC Type: Gene
    Product:50S ribosomal protein L3 | Pathway: | COG: Translation, ribosomal structure and biogenesis
  • CD630_00970 - rpsD Type: Gene
    Product:30S ribosomal protein S4 | Pathway: | COG: Translation, ribosomal structure and biogenesis
  • CD630_01020 - cbiQ Type: Gene
    Product:ABC-type transport system, cobalt-specificpermease | Pathway: | COG: Inorganic ion transport and metabolism
  • CD630_00680 - rpsL Type: Gene
    Product:30S ribosomal protein S12 | Pathway: | COG: Translation, ribosomal structure and biogenesis
  • CD630_00690 - rpsG Type: Gene
    Product:30S ribosomal protein S7 | Pathway: | COG: Translation, ribosomal structure and biogenesis
  • CD630_00960 - rpsK Type: Gene
    Product:30S ribosomal protein S11 | Pathway: | COG: Translation, ribosomal structure and biogenesis
  • CD630_00850 - rpsH Type: Gene
    Product:30S ribosomal protein S8 | Pathway: | COG: Translation, ribosomal structure and biogenesis
  • CD630_01000 - cbiO1 Type: Gene
    Product:ABC-type transport system, cobalt-specificATP-binding protein | Pathway: | COG: Inorganic ion transport and metabolism
  • CD630_00800 - rplP Type: Gene
    Product:50S ribosomal protein L16 | Pathway: | COG: Translation, ribosomal structure and biogenesis
  • CD630_00720 - rpsJ Type: Gene
    Product:30S ribosomal protein S10 | Pathway: | COG: Translation, ribosomal structure and biogenesis
  • CD630_01030 - truA1 Type: Gene
    Product:tRNA pseudouridine synthase A 1 | Pathway: | COG: Translation, ribosomal structure and biogenesis
  • CD630_00910 - adk Type: Gene
    Product:Adenylate kinase | Pathway: Purine metabolism | COG: Nucleotide transport and metabolism
  • CD630_t0860 - tRNA-Glu Type: Gene
    Product: | Pathway: | COG:
  • CD630_01010 - cbiO2 Type: Gene
    Product:ABC-type transport system, cobalt-specificATP-binding protein | Pathway: | COG: Inorganic ion transport and metabolism
NA NA 0.41 Inferelator: 2
Hypergeometric: 0

TF Influences from Inferelator

  1. CD630_11770 - fapR Type: Gene
    Product:Transcriptional regulator, DeoR family (Fattyacid and phospholipid biosynthesis regulator) | Pathway: | COG: Transcription
  2. CD630_23830 - Type: Gene
    Product:Transcriptional regulator, sigma-54-dependent | Pathway: | COG: Transcription

TF Influences from Hypergeometric Test

No TF Influences from the hypergeometric test
Module_257 7
  • CD630_17410 - Type: Gene
    Product:Selenoprotein B,glycine/betaine/sarcosine/D-proline reductase family(sarcosine reductase) | Pathway: | COG: Function unknown
  • CD630_08580 - Type: Gene
    Product:Fragment of transcriptional regulator,sigma-54-dependent (Part 1), PRD domain | Pathway: | COG: Signal transduction mechanisms, Signal transduction mechanisms
  • CD630_31001 - Type: Gene
    Product:Fragment of artefact | Pathway: | COG:
  • CD630_27000 - Type: Gene
    Product:Transcriptional regulator, sigma-54 dependent | Pathway: | COG: Transcription
  • CD630_05990 - Type: Gene
    Product:Fragment of transcriptional regulator, AraCfamily (C-terminal region) | Pathway: | COG: Transcription
  • CD630_05460 - Type: Gene
    Product:Putative membrane protein, DUF975 family | Pathway: | COG: Function unknown
  • CD630_23950 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
NA NA 0.42 Inferelator: 1
Hypergeometric: 0

TF Influences from Inferelator

  1. CD630_26400 - nrdR Type: Gene
    Product:Transcriptional regulator, repressor NrdR family | Pathway: | COG: Transcription

TF Influences from Hypergeometric Test

No TF Influences from the hypergeometric test
Module_179 26
  • CD630_01080 - nrdD Type: Gene
    Product:Anaerobic ribonucleoside triphosphate reductase | Pathway: | COG: Nucleotide transport and metabolism
  • CD630_11650 - Type: Gene
    Product:Putative ribosome-associated protein | Pathway: | COG: Translation, ribosomal structure and biogenesis
  • CD630_r0050 - 23s_rRNA Type: Gene
    Product: | Pathway: | COG:
  • CD630_r0280 - 23s_rRNA Type: Gene
    Product: | Pathway: | COG:
  • CD630_11630 - rpmA Type: Gene
    Product:50S ribosomal protein L27 | Pathway: | COG: Translation, ribosomal structure and biogenesis
  • CD630_11610 - rplU Type: Gene
    Product:50S ribosomal protein L21 | Pathway: | COG: Translation, ribosomal structure and biogenesis
  • CD630_06770 - sigT Type: Gene
    Product:Extra-Cytoplasmic Function sigma factors, ECFfamily | Pathway: | COG: Transcription
  • CD630_11590 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_11640 - obgE Type: Gene
    Product:Spo0B-associated GTP-binding protein | Pathway: | COG: Energy production and conversion
  • CD630_24400 - Type: Gene
    Product:Putative metal-dependent hydrolase | Pathway: | COG: Nucleotide transport and metabolism
  • CD630_r0230 - 23s_rRNA Type: Gene
    Product: | Pathway: | COG:
  • CD630_t0810 - tRNA-Leu Type: Gene
    Product: | Pathway: | COG:
  • CD630_01090 - nrdG Type: Gene
    Product:Anaerobic ribonucleoside-triphosphatereductase-activating protein | Pathway: | COG: Posttranslational modification, protein turnover, chaperones
  • CD630_31760 - glnF Type: Gene
    Product:RNA polymerase sigma-54 factor | Pathway: | COG: Transcription
  • CD630_11600 - rng Type: Gene
    Product:Ribonuclease G (RNase G) (Cytoplasmic axialfilament protein) | Pathway: | COG: Translation, ribosomal structure and biogenesis
  • CD630_11620 - Type: Gene
    Product:Putative ribosome-associated protein | Pathway: | COG: Function unknown
  • CD630_24390 - Type: Gene
    Product:Putative diacylglycerol kinase | Pathway: | COG: Cell wall/membrane/envelope biogenesis
  • CD630_11580 - Type: Gene
    Product:Putative radical SAM-superfamily protein | Pathway: | COG: Energy production and conversion
  • CD630_06760 - rsiT Type: Gene
    Product:Anti Sigma factors, ECF family | Pathway: | COG: Function unknown
  • CD630_01070 - aspC Type: Gene
    Product:Aspartate aminotransferase | Pathway: | COG: Amino acid transport and metabolism
  • CD630_24360 - Type: Gene
    Product:Putative divalent cation transporter, MgtEfamily | Pathway: | COG: Inorganic ion transport and metabolism
  • CD630_r0150 - 5s_rRNA Type: Gene
    Product: | Pathway: | COG:
0.000000026 0.00000027 0.42 Inferelator: 4
Hypergeometric: 0

TF Influences from Inferelator

  1. CD630_06480 - Type: Gene
    Product:Transcriptional regulator, GntR family | Pathway: | COG: Transcription
  2. CD630_16920 - Type: Gene
    Product:Transcriptional regulator, ArsR family | Pathway: | COG: Transcription
  3. CD630_23900 - Type: Gene
    Product:Transcriptional regulator, beta-lactamsrepressor | Pathway: | COG: Transcription
  4. CD630_30540 - Type: Gene
    Product:Two-component response regulator | Pathway: | COG: Signal transduction mechanisms

TF Influences from Hypergeometric Test

No TF Influences from the hypergeometric test