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 111 - 120 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_152 16
  • CD630_01870 - pyrE Type: Gene
    Product:Orotate phosphoribosyltransferase (OPRT)(OPRTase) | Pathway: Pyrimidine metabolism | COG: Nucleotide transport and metabolism
  • CD630_02710 - fliN Type: Gene
    Product:Flagellar motor switch phosphatase FliN | Pathway: | COG: Cell motility
  • CD630_30270 - Type: Gene
    Product:PTS system, glucose-like IIA component | Pathway: | COG: Carbohydrate transport and metabolism
  • CD630_01860 - pyrD Type: Gene
    Product:Dihydroorotate dehydrogenase catalytic subunit | Pathway: Pyrimidine metabolism | COG: Nucleotide transport and metabolism
  • CD630_01840 - pyrB Type: Gene
    Product:Aspartate carbamoyltransferase (Aspartatetranscarbamylase) (ATCase) | Pathway: Pyrimidine metabolism | COG: Nucleotide transport and metabolism
  • CD630_02730 - htpG Type: Gene
    Product:Heat shock protein 90 (Heat shock proteinHtpG)(High temperature protein G) | Pathway: | COG: Posttranslational modification, protein turnover, chaperones
  • CD630_32440 - prdA Type: Gene
    Product:D-proline reductase proprotein prdA | Pathway: | COG: Function unknown
  • CD630_30290 - malY Type: Gene
    Product:Bifunctional protein: cystathionine beta-lyase /repressor | Pathway: | COG: Amino acid transport and metabolism
  • CD630_02680 - flgG1 Type: Gene
    Product:Flagellar hook-basal body complex protein FlgG1 | Pathway: | COG: Cell motility
  • CD630_30280 - Type: Gene
    Product:Putative phosphosugar isomerase | Pathway: | COG: Cell wall/membrane/envelope biogenesis
  • CD630_02690 - flgG Type: Gene
    Product:Flagellar basal body rod protein FlgG | Pathway: | COG: Cell motility
  • CD630_02700 - fliM Type: Gene
    Product:Flagellar motor switch protein FliM | Pathway: | COG: Cell motility
  • CD630_30300 - Type: Gene
    Product:PTS system, glucose-like IIBC component | Pathway: | COG: Carbohydrate transport and metabolism
  • CD630_01850 - pyrK Type: Gene
    Product:Dihydroorotate dehydrogenase electron transfersubunit | Pathway: | COG: Energy production and conversion
  • CD630_32430 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_02720 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
0.2 0.61 0.46 Inferelator: 2
Hypergeometric: 1

TF Influences from Inferelator

  1. CD630_05590 - Type: Gene
    Product:Transcriptional regulator, ArsR family | Pathway: | COG: Transcription
  2. CD630_26650 - Type: Gene
    Product:Transcriptional regulator, AraC family | Pathway: | COG: Transcription

TF Influences from Hypergeometric Test

  1. CD630_02660 - sigD Type: Gene
    Product:RNA polymerase sigma-28 factor for flagellaroperon | Pathway: | COG: Transcription
Module_283 10
  • CD630_13970 - Type: Gene
    Product:Conserved hypothetical protein, UPF0066 family | Pathway: | COG: Function unknown
  • CD630_16510 - Type: Gene
    Product:Putative signaling protein | Pathway: | COG: Signal transduction mechanisms
  • CD630_27110 - Type: Gene
    Product:Transcriptional regulator, LysR family | Pathway: | COG: Transcription
  • CD630_27360 - Type: Gene
    Product:Transcriptional regulator, LysR family | Pathway: | COG: Transcription
  • CD630_21220 - Type: Gene
    Product:Putative cations transporter | Pathway: | COG: Inorganic ion transport and metabolism
  • CD630_13980 - Type: Gene
    Product:Putative peptidase, M20D family | Pathway: | COG: Amino acid transport and metabolism
  • CD630_09970 - Type: Gene
    Product:Two-component sensor histidine kinase | Pathway: | COG: Signal transduction mechanisms
  • CD630_22940 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG:
  • CD630_18782 - Type: Gene
    Product:Putative conjugative transposon proteinTn1549-like, CTn5-Orf39 | Pathway: | COG: Function unknown
  • CD630_16600 - Type: Gene
    Product:Conserved hypothetical protein, DUF 1255 family | Pathway: | COG: Function unknown
0.85 NA 0.46 Inferelator: 2
Hypergeometric: 0

TF Influences from Inferelator

  1. CD630_06290 - Type: Gene
    Product:Transcriptional regulator, Crp family | Pathway: | COG: Transcription
  2. CD630_14070 - Type: Gene
    Product:Transcriptional regulator, GntR family | Pathway: | COG: Transcription

TF Influences from Hypergeometric Test

No TF Influences from the hypergeometric test
Module_204 24
  • CD630_20160 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG:
  • CD630_03100 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_20750 - pbuX Type: Gene
    Product:Putative xanthine permease | Pathway: | COG: Nucleotide transport and metabolism
  • CD630_23450 - Type: Gene
    Product:Transcriptional regulator, LysR family | Pathway: | COG: Transcription
  • CD630_25940 - uraA Type: Gene
    Product:Putative uracil permease | Pathway: | COG: Nucleotide transport and metabolism
  • CD630_21260 - Type: Gene
    Product:Putative membrane protein | Pathway: | COG: Function unknown
  • CD630_22730 - Type: Gene
    Product:Putative sporulation integral membrane protein | Pathway: | COG: Function unknown
  • CD630_22170 - aroD Type: Gene
    Product:Dehydroquinate dehydratase (3-dehydroquinatedehydratase) (Dehydroquinase) (DHQase) | Pathway: Metabolic intermediate biosynthesis | COG: Amino acid transport and metabolism
  • CD630_10060 - Type: Gene
    Product:Putative acyl-CoA N-acyltransferase | Pathway: | COG: Function unknown
  • CD630_27030 - Type: Gene
    Product:Putative pentapeptide repeat-containing protein | Pathway: | COG: Function unknown
  • CD630_01990 - Type: Gene
    Product:Putative membrane-associated nucleotidase | Pathway: | COG: Nucleotide transport and metabolism
  • CD630_33200 - cprR Type: Gene
    Product:Two-component response regulator, cationicantimicrobial peptide resistance | Pathway: | COG: Signal transduction mechanisms
  • CD630_16590 - Type: Gene
    Product:Cation-transporting ATPase | Pathway: | COG: Inorganic ion transport and metabolism
  • CD630_r0020 - 23s_rRNA Type: Gene
    Product: | Pathway: | COG:
  • CD630_27190 - Type: Gene
    Product:Putative polysaccharide deacetylase | Pathway: | COG: Carbohydrate transport and metabolism
  • CD630_10020 - Type: Gene
    Product:Putative nucleotide/oligonucleotide bindingprotein | Pathway: | COG: Function unknown
  • CD630_30080 - Type: Gene
    Product:Fragment of conserved hypothetical protein(N-terminal region) | Pathway: | COG: Function unknown
  • CD630_25950 - pyrR Type: Gene
    Product:Bifunctional protein PyrR [Includes: Pyrimidineoperon regulatory protein; Uracil phosphoribosyltransferase(UPRTase)] | Pathway: | COG: Nucleotide transport and metabolism
  • CD630_20680 - Type: Gene
    Product:ABC drug efflux pump | Pathway: | COG: Function unknown
  • CD630_27040 - Type: Gene
    Product:Putative permease | Pathway: | COG: Function unknown
  • CD630_05630 - Type: Gene
    Product:Putative iron-sulfur cluster-binding protein | Pathway: | COG: Energy production and conversion
  • CD630_22500 - Type: Gene
    Product:Putative membrane protein | Pathway: | COG: Inorganic ion transport and metabolism
  • CD630_02170 - Type: Gene
    Product:Putative nitroreductase | Pathway: | COG: Energy production and conversion
  • CD630_33600 - Type: Gene
    Product:Two-component response regulator | Pathway: | COG: Signal transduction mechanisms
NA NA 0.46 Inferelator: 2
Hypergeometric: 0

TF Influences from Inferelator

  1. CD630_10640 - ccpA Type: Gene
    Product:Transcriptional regulator, LacI family | Pathway: | COG: Transcription
  2. CD630_33600 - 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_41 23
  • CD630_35940 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Energy production and conversion
  • CD630_28520 - dltB Type: Gene
    Product:D-alanyl transferase DltB, MBOAT family | Pathway: Cell wall biogenesis | COG: Cell wall/membrane/envelope biogenesis
  • CD630_28540 - dltD Type: Gene
    Product:D-alanine transferase | Pathway: Cell wall biogenesis | COG: Cell wall/membrane/envelope biogenesis
  • CD630_22260 - sat Type: Gene
    Product:Streptogramin A acetyltransferase (Virginiamycinacetyltransferase D) (Vat(D)) | Pathway: | COG: Function unknown
  • CD630_26030 - cdtR Type: Gene
    Product:Clostridium difficile binary toxin regulatorygene, LytTR family | Pathway: | COG: Signal transduction mechanisms
  • CD630_16250 - vanS Type: Gene
    Product:Two-component sensor histidine kinase | Pathway: | COG: Signal transduction mechanisms
  • CD630_01300 - metK Type: Gene
    Product:S-adenosylmethionine synthetase | Pathway: Amino-acid biosynthesis | COG: Coenzyme transport and metabolism
  • CD630_17840 - truA2 Type: Gene
    Product:Pseudouridylate synthase (tRNA pseudouridinesynthase A) | Pathway: | COG: Translation, ribosomal structure and biogenesis
  • CD630_27151 - mldC Type: Gene
    Product:Midcell localizing division proteins | Pathway: | COG:
  • CD630_27170 - mldA Type: Gene
    Product:Midcell localizing division proteins | Pathway: | COG: Function unknown
  • CD630_35930 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_17820 - Type: Gene
    Product:Two-component response regulator | Pathway: | COG: Signal transduction mechanisms
  • CD630_28510 - dltC Type: Gene
    Product:D-alanine--poly(phosphoribitol) ligase subunit 2(D-alanyl carrier protein) (DCP) | Pathway: Cell wall biogenesis | COG: Cell wall/membrane/envelope biogenesis
  • CD630_28530 - dltA Type: Gene
    Product:D-alanine--poly(phosphoribitol) ligase subunit 1 | Pathway: Cell wall biogenesis | COG: Secondary metabolites biosynthesis, transport and catabolism
  • CD630_16220 - Type: Gene
    Product:Putative lipoprotein | Pathway: | COG: Function unknown
  • CD630_17790 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Replication, recombination and repair
  • CD630_23350 - guaB Type: Gene
    Product:Inositol-5'-monophosphate dehydrogenase (IMPdehydrogenase) (IMPDH) (IMPD) | Pathway: | COG: Nucleotide transport and metabolism
  • CD630_16240 - vanR Type: Gene
    Product:Two-component response regulator | Pathway: | COG: Signal transduction mechanisms
  • CD630_27160 - mldB Type: Gene
    Product:Midcell localizing division proteins | Pathway: | COG: Function unknown
  • CD630_06680 - Type: Gene
    Product:Two-component response regulator | Pathway: | COG: Signal transduction mechanisms
  • CD630_01980 - guaA Type: Gene
    Product:Glutamine amidotransferase | Pathway: Purine metabolism | COG: Nucleotide transport and metabolism
  • CD630_17830 - Type: Gene
    Product:Two-component sensor histidine kinase | Pathway: | COG: Signal transduction mechanisms
  • CD630_17810 - Type: Gene
    Product:Putative lipoprotein | Pathway: | COG: Function unknown
0.0000000032 NA 0.46 Inferelator: 1
Hypergeometric: 0

TF Influences from Inferelator

  1. CD630_01710 - rex Type: Gene
    Product:Transcriptional regulator, Redox-sensingrepressor Rex | Pathway: | COG: Transcription

TF Influences from Hypergeometric Test

No TF Influences from the hypergeometric test
Module_74 20
  • CD630_09540 - Type: Gene
    Product:Putative phage protein | Pathway: | COG: Function unknown
  • CD630_09550 - Type: Gene
    Product:Putative phage protein | Pathway: | COG: Function unknown
  • CD630_29200 - Type: Gene
    Product:Putative phage head protein | Pathway: | COG: Signal transduction mechanisms
  • CD630_29240 - Type: Gene
    Product:Putative phage protein | Pathway: | COG:
  • CD630_09470 - Type: Gene
    Product:Putative phage scaffold protein | Pathway: | COG: Function unknown
  • CD630_29100 - Type: Gene
    Product:Putative phage protein | Pathway: | COG: Function unknown
  • CD630_29101 - Type: Gene
    Product:Putative phage protein | Pathway: | COG:
  • CD630_09531 - Type: Gene
    Product:Putative phage protein | Pathway: | COG:
  • CD630_09530 - Type: Gene
    Product:Putative phage protein | Pathway: | COG: Function unknown
  • CD630_09490 - Type: Gene
    Product:Putative phage protein | Pathway: | COG:
  • CD630_29220 - Type: Gene
    Product:Putative phage terminase large subunit | Pathway: | COG: Replication, recombination and repair
  • CD630_29110 - Type: Gene
    Product:Putative phage protein | Pathway: | COG: Function unknown
  • CD630_09520 - Type: Gene
    Product:Putative phage protein | Pathway: | COG: Function unknown
  • CD630_29130 - Type: Gene
    Product:Putative phage protein | Pathway: | COG: Function unknown
  • CD630_09560 - Type: Gene
    Product:Putative XkdN-like phage protein | Pathway: | COG: Function unknown
  • CD630_09561 - Type: Gene
    Product:Putative phage protein | Pathway: | COG:
  • CD630_09500 - Type: Gene
    Product:Putative phage protein | Pathway: | COG: Function unknown
  • CD630_09480 - Type: Gene
    Product:Putative phage major capsid protein | Pathway: | COG: Function unknown
  • CD630_10921 - Type: Gene
    Product:Putative conjugative transposon proteinTn1549-like, CTn4-Orf32 | Pathway: | COG: Function unknown
  • CD630_09510 - Type: Gene
    Product:Putative phage protein | Pathway: | COG: Function unknown
0.0002 2.5 0.46 Inferelator: 2
Hypergeometric: 0

TF Influences from Inferelator

  1. CD630_06580 - cdu1 Type: Gene
    Product:Transcriptional regulator, beta-lactamsrepressor | Pathway: | COG: Transcription
  2. CD630_22140 - SinR Type: Gene
    Product:Transcriptional regulator, HTH-type | Pathway: | COG: Transcription

TF Influences from Hypergeometric Test

No TF Influences from the hypergeometric test
Module_11 22
  • CD630_11480 - Type: Gene
    Product:Putative penicillin-binding protein with aN-terminal TonB-box | Pathway: | COG: Cell wall/membrane/envelope biogenesis
  • CD630_11510 - minE Type: Gene
    Product:Cell division topological specificity factor | Pathway: | COG: Cell cycle control, cell division, chromosome partitioning
  • CD630_01720 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Energy production and conversion
  • CD630_13350 - Type: Gene
    Product:Transcriptional regulator, MarR family | Pathway: | COG: Transcription
  • CD630_11440 - radC Type: Gene
    Product:DNA repair protein RadC homolog | Pathway: | COG: Replication, recombination and repair
  • CD630_32990 - Type: Gene
    Product:Transporter, Major Facilitator Superfamily (MFS) | Pathway: | COG: Inorganic ion transport and metabolism
  • CD630_11530 - mgsA Type: Gene
    Product:Methylglyoxal synthase (MGS) | Pathway: | COG: Carbohydrate 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_28280 - Type: Gene
    Product:Putative pyridoxal phosphate-dependenttransferase | Pathway: | COG: Amino acid transport and metabolism
  • CD630_33260 - Type: Gene
    Product:Integrase, lambdoid phage family Tn916-like,CTn6-Orf1 | Pathway: | COG: Replication, recombination and repair
  • CD630_11500 - minD Type: Gene
    Product:Septum site-determining protein MinD (Celldivision inhibitor MinD) | Pathway: | COG: Cell cycle control, cell division, chromosome partitioning
  • CD630_11490 - minC Type: Gene
    Product:Cell division regulator (septum placement) | Pathway: | COG: Cell cycle control, cell division, chromosome partitioning
  • CD630_02770 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_11470 - Type: Gene
    Product:Putative permease | Pathway: | COG: Cell wall/membrane/envelope biogenesis
  • CD630_11520 - mrdB Type: Gene
    Product:Rod shape-determining protein MrdB | Pathway: | COG: Cell cycle control, cell division, chromosome partitioning
  • CD630_11450 - mreB2 Type: Gene
    Product:Rod shape-determining protein MreB | Pathway: | COG: Cell cycle control, cell division, chromosome partitioning
  • CD630_28260 - Type: Gene
    Product:Putative aldolase | Pathway: | COG: Energy production and conversion
  • CD630_11430 - Type: Gene
    Product:Putative Maf-like protein | Pathway: | COG: Cell cycle control, cell division, chromosome partitioning
  • CD630_27040 - Type: Gene
    Product:Putative permease | Pathway: | COG: Function unknown
  • CD630_05103 - Type: Gene
    Product:Putative conjugative transposon protein Tn5397,CTn3-Orf4 | Pathway: | COG:
  • CD630_33270 - Type: Gene
    Product:Putative conjugative transposon proteinTn916-like, CTn6-Orf2 | Pathway: | COG: Function unknown
NA NA 0.46 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_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_393 26
  • CD630_00670 - rpoC Type: Gene
    Product:DNA-directed RNA polymerase subunit beta' | Pathway: | COG: Transcription
  • CD630_26720 - appA Type: Gene
    Product:ABC-type transport system, oligopeptide-familysolute-binding protein | Pathway: | COG: Amino acid transport and metabolism
  • CD630_26700 - appF Type: Gene
    Product:ABC-type transport system, ATP-binding protein | Pathway: | COG: Amino acid transport and metabolism
  • CD630_28520 - dltB Type: Gene
    Product:D-alanyl transferase DltB, MBOAT family | Pathway: Cell wall biogenesis | COG: Cell wall/membrane/envelope biogenesis
  • CD630_05480 - Type: Gene
    Product:Putative penicillin-binding peptidase BlaR1-like,M56 family | Pathway: | COG: Transcription, Signal transduction mechanisms
  • CD630_28540 - dltD Type: Gene
    Product:D-alanine transferase | Pathway: Cell wall biogenesis | COG: Cell wall/membrane/envelope biogenesis
  • CD630_35560 - Type: Gene
    Product:Putative membrane protein | Pathway: | COG: Function unknown
  • CD630_28510 - dltC Type: Gene
    Product:D-alanine--poly(phosphoribitol) ligase subunit 2(D-alanyl carrier protein) (DCP) | Pathway: Cell wall biogenesis | COG: Cell wall/membrane/envelope biogenesis
  • CD630_35540 - dusB Type: Gene
    Product:tRNA-dihydrouridine synthase | Pathway: | COG: Translation, ribosomal structure and biogenesis
  • CD630_35520 - lysS Type: Gene
    Product:Lysyl-tRNA synthetase (Lysine--tRNA ligase)(LysRS) | Pathway: | COG: Translation, ribosomal structure and biogenesis
  • CD630_18100 - Type: Gene
    Product:Transcriptional regulator, beta-lactamsrepressor | Pathway: | COG: Transcription
  • CD630_07040 - Type: Gene
    Product:Putative metal-dependent phosphohydrolase | Pathway: | COG: Function unknown
  • CD630_26710 - appD Type: Gene
    Product:ABC-type transport system, ATP-binding protein | Pathway: | COG: Amino acid transport and metabolism, Inorganic ion transport and metabolism
  • CD630_00660 - rpoB Type: Gene
    Product:DNA-directed RNA polymerase subunit beta | Pathway: | COG: Transcription
  • CD630_35580 - birA Type: Gene
    Product:BirA bifunctional protein [Includes: biotinoperon repressor and biotin--[acetyl-CoA-carboxylase]synthetase | Pathway: | COG: Coenzyme transport and metabolism
  • CD630_28530 - dltA Type: Gene
    Product:D-alanine--poly(phosphoribitol) ligase subunit 1 | Pathway: Cell wall biogenesis | COG: Secondary metabolites biosynthesis, transport and catabolism
  • CD630_19630 - Type: Gene
    Product:Putative methyltransferase | Pathway: | COG: Secondary metabolites biosynthesis, transport and catabolism
  • CD630_35570 - Type: Gene
    Product:Putative peptidase | Pathway: | COG: Amino acid transport and metabolism, Secondary metabolites biosynthesis, transport and catabolism
  • CD630_35530 - greA Type: Gene
    Product:Transcription elongation factor greA (Transcriptcleavage factor GreA) | Pathway: | COG: Transcription
  • CD630_35550 - coaX Type: Gene
    Product:Type III pantothenate kinase (Pantothenic acidkinase) (PanK-III) | Pathway: Cofactor biosynthesis | COG: Transcription
  • CD630_02030 - Type: Gene
    Product:Putative UvrABC system protein A 1 (UvrA protein1) (Excinuclease ABC subunit A 1) | Pathway: | COG: Replication, recombination and repair
  • CD630_07030 - Type: Gene
    Product:Putative peptidase, U32 family | Pathway: | COG: Posttranslational modification, protein turnover, chaperones
  • CD630_07050 - Type: Gene
    Product:Putative hydrolase, NUDIX family | Pathway: | COG: Replication, recombination and repair
  • CD630_36690 - Type: Gene
    Product:Putative lipoprotein | Pathway: | COG: Function unknown
  • CD630_05470 - Type: Gene
    Product:Transcriptional regulator, beta-lactamsrepressor | Pathway: | COG: Transcription
  • CD630_26740 - appC Type: Gene
    Product:ABC-type transport system, oligopeptide-familypermease protein | Pathway: | COG: Inorganic ion transport and metabolism
0.0000000000019 NA 0.46 Inferelator: 1
Hypergeometric: 1

TF Influences from Inferelator

  1. CD630_18100 - Type: Gene
    Product:Transcriptional regulator, beta-lactamsrepressor | Pathway: | COG: Transcription

TF Influences from Hypergeometric Test

  1. CD630_32450 - prdR Type: Gene
    Product:Transcriptional regulator, sigma-54-dependent | Pathway: | COG: Transcription
Module_272 29
  • CD630_06890 - Type: Gene
    Product:Putative nucleotide phosphodiesterase | Pathway: | COG: Nucleotide transport and metabolism
  • CD630_18260 - metA Type: Gene
    Product:Homoserine O-succinyltransferase | Pathway: Amino-acid biosynthesis | COG: Amino acid transport and metabolism
  • CD630_14900 - metI Type: Gene
    Product:ABC-type transport system, methionine-specificpermease | Pathway: | COG: Inorganic ion transport and metabolism
  • CD630_29670 - dpaB Type: Gene
    Product:Dipicolinate synthase subunit B | Pathway: | COG: Coenzyme transport and metabolism
  • CD630_35230 - ksgA Type: Gene
    Product:Dimethyladenosine transferase(S-adenosylmethionine-6-N', N'-adenosyl(rRNA)dimethyltransferase) | Pathway: | COG: Translation, ribosomal structure and biogenesis
  • CD630_29720 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG:
  • CD630_29700 - Type: Gene
    Product:Putative thiolase | Pathway: | COG: Lipid transport and metabolism
  • CD630_21420 - Type: Gene
    Product:Putative transporter | Pathway: | COG: Inorganic ion transport and metabolism
  • CD630_29690 - Type: Gene
    Product:Putative AMP-binding protein | Pathway: | COG: Lipid transport and metabolism, Secondary metabolites biosynthesis, transport and catabolism
  • CD630_01300 - metK Type: Gene
    Product:S-adenosylmethionine synthetase | Pathway: Amino-acid biosynthesis | COG: Coenzyme transport and metabolism
  • CD630_16530 - Type: Gene
    Product:Putative Probable D-methionine-bindinglipoprotein | Pathway: | COG: Inorganic ion transport and metabolism
  • CD630_00510 - gltX Type: Gene
    Product:Glutamyl-tRNA synthetase | Pathway: | COG: Translation, ribosomal structure and biogenesis
  • CD630_06350 - Type: Gene
    Product:Putative hydrolase | Pathway: | COG: Function unknown
  • CD630_05580 - glsA Type: Gene
    Product:Glutaminase (L-glutamine amidohydrolase) | Pathway: | COG: Amino acid transport and metabolism
  • CD630_30630 - Type: Gene
    Product:Putative peptidase, S41 family | Pathway: | COG: Function unknown
  • CD630_15160 - Type: Gene
    Product:Transcriptional regulator, MerR family | Pathway: | COG: Transcription
  • CD630_18250 - metY Type: Gene
    Product:O-acetylhomoserine sulfhydrylase | Pathway: | COG: Amino acid transport and metabolism
  • CD630_02440 - Type: Gene
    Product:Putative CDP-glycerol:Poly(glycerophosphate)glycerophosphotransferase | Pathway: | COG: Function unknown
  • CD630_14910 - metQ Type: Gene
    Product:ABC-type transport system, methionine-specificsubstrate-binding lipoprotein | Pathway: | COG: Inorganic ion transport and metabolism
  • 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_29680 - dpaA Type: Gene
    Product:Dipicolinate synthase subunit A | Pathway: | COG: Function unknown
  • CD630_16520 - Type: Gene
    Product:Putative tellurium resistance protein | Pathway: | COG: Signal transduction mechanisms
  • CD630_29710 - bioY Type: Gene
    Product:Biotin synthase | Pathway: | COG: Function unknown
  • CD630_35240 - Type: Gene
    Product:Putative DNA-binding protein | Pathway: | COG: Replication, recombination and repair
  • CD630_14890 - metN Type: Gene
    Product:ABC-type transport system, methionine-specificATP-binding protein | Pathway: | COG: Inorganic ion transport and metabolism
  • CD630_06340 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_17660 - Type: Gene
    Product:Putative lipoprotein | Pathway: | COG:
  • CD630_05590 - Type: Gene
    Product:Transcriptional regulator, ArsR family | Pathway: | COG: Transcription
0.00000077 0.07 0.46 Inferelator: 3
Hypergeometric: 0

TF Influences from Inferelator

  1. CD630_06290 - Type: Gene
    Product:Transcriptional regulator, Crp family | Pathway: | COG: Transcription
  2. CD630_26420 - sigG Type: Gene
    Product:RNA polymerase sigma-G factor | Pathway: | COG: Transcription
  3. CD630_34990 - spoVT Type: Gene
    Product:Stage V sporulation protein T | Pathway: | COG: Transcription

TF Influences from Hypergeometric Test

No TF Influences from the hypergeometric test
Module_361 8
  • CD630_06380 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_05800 - gapN Type: Gene
    Product:Glyceraldehyde-3-phosphate dehydrogenase(NADP(+)) (GADPH) | Pathway: | COG: Energy production and conversion
  • CD630_06910 - Type: Gene
    Product:Putative short chain dehydrogenase/reductase, SDRfamily | Pathway: | COG: Function unknown
  • CD630_27120 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_06370 - Type: Gene
    Product:Putative acetyltransferase | Pathway: | COG: Function unknown
  • CD630_05620 - Type: Gene
    Product:Putative RusA-like endodeoxyribonuclease | Pathway: | COG: Function unknown
  • CD630_10640 - ccpA Type: Gene
    Product:Transcriptional regulator, LacI family | Pathway: | COG: Transcription
  • CD630_17920 - Type: Gene
    Product:Putative L-threonine 3-dehydrogenase | Pathway: | COG: Carbohydrate transport and metabolism, Cell wall/membrane/envelope biogenesis
6.4 NA 0.46 Inferelator: 2
Hypergeometric: 0

TF Influences from Inferelator

  1. CD630_10640 - ccpA Type: Gene
    Product:Transcriptional regulator, LacI family | Pathway: | COG: Transcription
  2. CD630_24120 - Type: Gene
    Product:Putative negative regulator of gluconeogenesis | Pathway: | COG: Transcription

TF Influences from Hypergeometric Test

No TF Influences from the hypergeometric test
Module_30 22
  • CD630_25270 - Type: Gene
    Product:Transcriptional regulator, TetR family | Pathway: | COG: Transcription
  • CD630_34380 - cobU Type: Gene
    Product:Bifunctional adenosylcobalamin biosynthesisprotein CobU [Adenosylcobinamide kinase;Adenosylcobinamide-phosphate guanylyltransferase] | Pathway: | COG: Coenzyme transport and metabolism
  • CD630_08870 - Type: Gene
    Product:Transcriptional regulator, GntR family | Pathway: | COG: Transcription
  • CD630_11750 - ackA Type: Gene
    Product:Acetate kinase (Acetokinase) | Pathway: Metabolic intermediate biosynthesis | COG: Energy production and conversion
  • CD630_07580 - pflA Type: Gene
    Product:Pyruvate formate-lyase activating enzyme | Pathway: | COG: Posttranslational modification, protein turnover, chaperones
  • CD630_05200 - Type: Gene
    Product:Two-component sensor histidine kinase | Pathway: | COG: Signal transduction mechanisms
  • CD630_15380 - Type: Gene
    Product:Putative signaling protein | Pathway: | COG: Signal transduction mechanisms
  • CD630_14190 - Type: Gene
    Product:Putative diguanylate kinase signaling protein | Pathway: | COG: Signal transduction mechanisms
  • CD630_05210 - Type: Gene
    Product:Two-component response regulator | Pathway: | COG: Signal transduction mechanisms
  • CD630_14210 - Type: Gene
    Product:Putative diguanylate kinase signaling protein | Pathway: | COG: Signal transduction mechanisms
  • CD630_08410 - Type: Gene
    Product:5-aminoimidazole-4-carboxamide ribonucleotidetransformylase | Pathway: | COG: Nucleotide transport and metabolism
  • CD630_08100 - Type: Gene
    Product:Putative flavodoxin/nitric oxide synthase | Pathway: | COG: Function unknown
  • CD630_26630 - Type: Gene
    Product:Putative signaling protein | Pathway: | COG: Signal transduction mechanisms
  • CD630_08360 - Type: Gene
    Product:Putative acetyltransferase | Pathway: | COG: Transcription
  • CD630_25280 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_16540 - Type: Gene
    Product:Putative lipoate-protein ligase | Pathway: Protein modification | COG: Coenzyme transport and metabolism
  • CD630_24920 - Type: Gene
    Product:Two-component sensor histidine kinase,sporulation-associated spo0A | Pathway: | COG: Signal transduction mechanisms
  • CD630_07590 - plfB Type: Gene
    Product:Formate acetyltransferase (Pyruvateformate-lyase) | Pathway: | COG: Energy production and conversion
  • CD630_08400 - Type: Gene
    Product:Putative isomerase/hydrolase | Pathway: | COG: Secondary metabolites biosynthesis, transport and catabolism
  • CD630_15150 - Type: Gene
    Product:Putative diguanylate kinase signaling protein | Pathway: | COG: Signal transduction mechanisms
  • CD630_14200 - dccA Type: Gene
    Product:Diguanylate cyclase protein | Pathway: | COG: Signal transduction mechanisms
  • CD630_13920 - Type: Gene
    Product:Putative endoribonuclease | Pathway: | COG: Translation, ribosomal structure and biogenesis
0.000000000000032 NA 0.46 Inferelator: 3
Hypergeometric: 0

TF Influences from Inferelator

  1. CD630_10640 - ccpA Type: Gene
    Product:Transcriptional regulator, LacI family | Pathway: | COG: Transcription
  2. CD630_17820 - Type: Gene
    Product:Two-component response regulator | Pathway: | COG: Signal transduction mechanisms
  3. CD630_25270 - Type: Gene
    Product:Transcriptional regulator, TetR family | Pathway: | COG: Transcription

TF Influences from Hypergeometric Test

No TF Influences from the hypergeometric test