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 151 - 160 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_176 27
  • CD630_32450 - prdR Type: Gene
    Product:Transcriptional regulator, sigma-54-dependent | Pathway: | COG: Transcription
  • CD630_31890 - Type: Gene
    Product:Putative NADPH-dependent FMN reductase | Pathway: | COG: Function unknown
  • CD630_07970 - Type: Gene
    Product:Putative pyruvate carboxyltransferase | Pathway: | COG: Lipid transport and metabolism
  • CD630_07420 - Type: Gene
    Product:Putative ethanolamine transporter | Pathway: | COG: Amino acid transport and metabolism
  • CD630_23690 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_33290 - Type: Gene
    Product:Putative RNA polymerase sigma factor Tn916-like,CTn6-Orf5 | Pathway: | COG: Function unknown
  • CD630_16120 - Type: Gene
    Product:Putative amidohydrolase | Pathway: | COG: Secondary metabolites biosynthesis, transport and catabolism
  • CD630_32850 - pgi Type: Gene
    Product:Glucose-6-phosphate isomerase (GPI)(Phosphoglucose isomerase) (PGI) (Phosphohexose isomerase)(PHI) | Pathway: Carbohydrate biosynthesis | COG: Carbohydrate transport and metabolism
  • CD630_34050 - Type: Gene
    Product:Putative iron-onlyhydrogenase,electron-transferring subunit HymA-like | Pathway: | COG: Energy production and conversion
  • CD630_34030 - Type: Gene
    Product:Putative formate/nitrite transporter | Pathway: | COG: Inorganic ion transport and metabolism
  • CD630_34070 - Type: Gene
    Product:Putative iron-only hydrogenase, catalytic subunitHymC-like | Pathway: | COG: Energy production and conversion
  • CD630_26830 - Type: Gene
    Product:Putative propanediol utilization protein | Pathway: Polyol metabolism | COG: Secondary metabolites biosynthesis, transport and catabolism
  • CD630_31900 - Type: Gene
    Product:Transcriptional regulator, MerR family | Pathway: | COG: Transcription
  • CD630_21810 - Type: Gene
    Product:Putative alpha/beta hydrolase | Pathway: | COG: Function unknown
  • CD630_20460 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG:
  • CD630_13790 - Type: Gene
    Product:Transcriptional regulator, Phage-type | Pathway: | COG: Transcription
  • CD630_27550 - ptsI Type: Gene
    Product:PTS system, EI component | Pathway: | COG: Carbohydrate transport and metabolism
  • CD630_03560 - xis Type: Gene
    Product:Excisionase Tn916-like, CTn1-Orf2 | Pathway: | COG: Function unknown
  • CD630_32460 - Type: Gene
    Product:Putative surface protein | Pathway: | COG: Function unknown
  • CD630_33280 - Type: Gene
    Product:Putative conjugative transposon proteinTn916-like, CTn6-Orf4 | Pathway: | COG: Function unknown
  • CD630_25960 - Type: Gene
    Product:Putative pseudouridylate synthase, RluC/RluDfamily | Pathway: | COG: Translation, ribosomal structure and biogenesis
  • CD630_25970 - lspA Type: Gene
    Product:Lipoprotein signal peptidase (Prolipoproteinsignal peptidase) (Signal peptidase II) (SPase II) | Pathway: Protein modification | COG: Cell wall/membrane/envelope biogenesis, Intracellular trafficking, secretion, and vesicular transport
  • CD630_15111 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG:
  • CD630_31910 - Type: Gene
    Product:Putative oxidoreductase | Pathway: | COG: Energy production and conversion
  • CD630_34060 - Type: Gene
    Product:Putative iron-onlyhydrogenase,electron-transferring subunit HymB-like | Pathway: | COG: Energy production and conversion
  • CD630_34040 - cls Type: Gene
    Product:Cardiolipin synthetase (Cardiolipin synthase) (CLsynthase) | Pathway: | COG: Lipid transport and metabolism
  • CD630_21100 - Type: Gene
    Product:Putative transaldolaseC-like | Pathway: Carbohydrate degradation | COG: Carbohydrate transport and metabolism
4e-31 NA 0.47 Inferelator: 3
Hypergeometric: 0

TF Influences from Inferelator

  1. CD630_17980 - Type: Gene
    Product:Transcriptional regulator, LysR family | Pathway: | COG: Transcription
  2. CD630_31900 - Type: Gene
    Product:Transcriptional regulator, MerR family | Pathway: | COG: Transcription
  3. 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_305 18
  • CD630_04160 - Type: Gene
    Product:Putative conjugative transposon proteinTn1549-like, CTn2-Orf10 | Pathway: | COG: Function unknown
  • CD630_04080 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_04081 - Type: Gene
    Product:Putative conjugative transposon proteinTn1549-like, CTn2-Orf2 | Pathway: | COG: Function unknown
  • CD630_04170 - Type: Gene
    Product:Putative conjugative transposon proteinTn1549-like, CTn2-Orf11 | Pathway: | COG: Function unknown
  • CD630_04190 - Type: Gene
    Product:Putative conjugative transposon proteinTn1549-like, CTn2-Orf13 | Pathway: | COG: Function unknown
  • CD630_04150 - Type: Gene
    Product:Putative membrane protein Tn1549-like, CTn2-Orf9 | Pathway: | COG: Function unknown
  • CD630_04130 - Type: Gene
    Product:Putative single-strand DNA-binding proteinTn1549-like, CTn2-Orf7 | Pathway: | COG: Function unknown
  • CD630_04180 - Type: Gene
    Product:Putative conjugative transposon proteinTn1549-like, CTn2-Orf12 | Pathway: | COG: Intracellular trafficking, secretion, and vesicular transport
  • CD630_04060 - Type: Gene
    Product:Putative tRNA (Uracil-5-)-methyltransferase | Pathway: | COG: Translation, ribosomal structure and biogenesis
  • CD630_04090 - Type: Gene
    Product:Putative replication initiation proteinTn1549-like, CTn2-Orf2 | Pathway: | COG: Replication, recombination and repair
  • CD630_04140 - Type: Gene
    Product:Putative conjugative transposon proteinTn1549-like, CTn2-Orf8 | Pathway: | COG: Function unknown
  • CD630_04110 - Type: Gene
    Product:Putative conjugative transposon proteinTn1549-like, CTn2-Orf4 | Pathway: | COG: Function unknown
  • CD630_04100 - Type: Gene
    Product:Putative conjugative transposon proteinTn1549-like, CTn2-Orf3 | Pathway: | COG: Replication, recombination and repair
  • CD630_04121 - Type: Gene
    Product:Putative conjugative transposon proteinTn1549-like, CTn2-Orf6 | Pathway: | COG:
  • CD630_04120 - Type: Gene
    Product:Putative conjugative transfer proteinTn1549-like, CTn2-Orf5 | Pathway: | COG: Intracellular trafficking, secretion, and vesicular transport
  • CD630_04191 - Type: Gene
    Product:Putative conjugative transposon proteinTn1549-like, CTn2-Orf14 | Pathway: | COG: Function unknown
  • CD630_04200 - Type: Gene
    Product:Putative cell surface protein Tn1549-like,CTn2-Orf15 | Pathway: | COG: Function unknown
  • CD630_04210 - Type: Gene
    Product:DNA topoisomerase protein, type IA, Tn1549-like,CTn2-Orf16 | Pathway: | COG: Replication, recombination and repair
NA NA 0.48 Inferelator: 2
Hypergeometric: 0

TF Influences from Inferelator

  1. CD630_01710 - rex Type: Gene
    Product:Transcriptional regulator, Redox-sensingrepressor Rex | Pathway: | COG: Transcription
  2. 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_345 18
  • CD630_29340 - Type: Gene
    Product:Putative phage protein | Pathway: | COG:
  • CD630_12690 - Type: Gene
    Product:Two-component response regulator | Pathway: | COG: Signal transduction mechanisms
  • CD630_15910 - kdpA Type: Gene
    Product:Potassium-translocating ATPase A chain | Pathway: | COG: Inorganic ion transport and metabolism
  • CD630_12700 - Type: Gene
    Product:Two-component sensor histidine kinase | Pathway: | COG: Signal transduction mechanisms
  • CD630_15930 - kdpC Type: Gene
    Product:Potassium-transporting ATPase C chain | Pathway: | COG: Inorganic ion transport and metabolism
  • CD630_12740 - topA Type: Gene
    Product:DNA topoisomerase I | Pathway: | COG: Replication, recombination and repair
  • CD630_12720 - Type: Gene
    Product:Putative magnesium chelatase | Pathway: | COG: Posttranslational modification, protein turnover, chaperones
  • CD630_36320 - Type: Gene
    Product:Putative isochorismatase (2,3 dihydro-2,3dihydroxybenzoate synthase) | Pathway: | COG: Secondary metabolites biosynthesis, transport and catabolism
  • CD630_12760 - Type: Gene
    Product:Putative replication-associated recombinationprotein A RarA | Pathway: | COG: Replication, recombination and repair
  • CD630_29330 - Type: Gene
    Product:Hypothetical protein | Pathway: | COG:
  • CD630_29290 - Type: Gene
    Product:Putative phage protein | Pathway: | COG: Function unknown
  • CD630_12750 - codY Type: Gene
    Product:Transcriptional regulator, GTP-sensingpleiotropic repressor | Pathway: | COG: Transcription
  • CD630_29320 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG:
  • CD630_36330 - Type: Gene
    Product:Putative membrane protein | Pathway: | COG: Function unknown
  • CD630_29300 - Type: Gene
    Product:Putative phage anti-repressor protein | Pathway: | COG: Transcription
  • CD630_12670 - Type: Gene
    Product:ABC-type transport system, multidrug-familypermease | Pathway: | COG: Function unknown
  • CD630_12780 - iscR Type: Gene
    Product:Transcriptional regulator, Rrf2 family | Pathway: | COG: Transcription
  • CD630_29310 - Type: Gene
    Product:Putative phage endodeoxyribonuclease RusA-like | Pathway: | COG: Replication, recombination and repair
NA NA 0.48 Inferelator: 1
Hypergeometric: 0

TF Influences from Inferelator

  1. 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_322 20
  • CD630_27720 - tuaG Type: Gene
    Product:Putative glycosyl transferase, family 2 | Pathway: | COG: Cell wall/membrane/envelope biogenesis
  • CD630_25730 - Type: Gene
    Product:Putative hydrolase, HAD superfamily, subfamilyIA | Pathway: | COG: Function unknown
  • CD630_27600 - Type: Gene
    Product:Putative signaling protein | Pathway: | COG: Signal transduction mechanisms
  • CD630_27710 - rkpK Type: Gene
    Product:UDP-glucose 6-dehydrogenase | Pathway: | COG: Cell wall/membrane/envelope biogenesis
  • CD630_25720 - Type: Gene
    Product:Putative nitroreductase | Pathway: | COG: Energy production and conversion
  • CD630_03910 - asnB Type: Gene
    Product:Asparagine synthetase [glutamine-hydrolyzing] | Pathway: | COG: Amino acid transport and metabolism
  • CD630_27650 - LcpA Type: Gene
    Product:Surface-anchoring factors, LytR-CpsA-Psr-likeprotein | Pathway: | COG: Transcription
  • CD630_27740 - Type: Gene
    Product:Putative glycosyl transferase, family 2 | Pathway: | COG: Cell wall/membrane/envelope biogenesis
  • CD630_13960 - Type: Gene
    Product:Putative amino acid amidase | Pathway: | COG: Amino acid transport and metabolism
  • CD630_27800 - pgm Type: Gene
    Product:Alpha-phosphoglucomutase | Pathway: | COG: Carbohydrate transport and metabolism
  • CD630_27750 - Type: Gene
    Product:Putative glycerophosphotransferase | Pathway: | COG: Cell wall/membrane/envelope biogenesis
  • CD630_27810 - mviN Type: Gene
    Product:Cell well glycopolymers exporter, flipase-type | Pathway: Cell wall biogenesis | COG: Signal transduction mechanisms
  • CD630_27730 - Type: Gene
    Product:Putative glycosyl transferase, family 2 | Pathway: | COG: Cell wall/membrane/envelope biogenesis
  • CD630_17510 - cwp13 Type: Gene
    Product:Cell surface protein | Pathway: | COG: Posttranslational modification, protein turnover, chaperones
  • CD630_27670 - cwp19 Type: Gene
    Product:Cell surface protein | Pathway: | COG: Cell wall/membrane/envelope biogenesis
  • CD630_27690 - Type: Gene
    Product:Putative polysaccharide biosynthesis protein | Pathway: | COG: Cell wall/membrane/envelope biogenesis
  • CD630_01730 - Type: Gene
    Product:Putative lipoprotein | Pathway: | COG: Cell wall/membrane/envelope biogenesis
  • CD630_27760 - Type: Gene
    Product:Putative glycosyl transferase, family 2 | Pathway: | COG: Cell wall/membrane/envelope biogenesis
  • 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
0.06 NA 0.48 Inferelator: 1
Hypergeometric: 0

TF Influences from Inferelator

  1. 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_136 25
  • CD630_13660 - Type: Gene
    Product:Putative phage tail protein | Pathway: | COG: Function unknown
  • CD630_12440 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_13620 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG:
  • CD630_13640 - Type: Gene
    Product:Putative phage XkdM-like protein | Pathway: | COG: Function unknown
  • CD630_13700 - Type: Gene
    Product:Putative phage XkdS-like protein | Pathway: | COG: Function unknown
  • CD630_12420 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG:
  • CD630_13720 - Type: Gene
    Product:Putative phage XkdT-like protein | Pathway: | COG: Function unknown
  • CD630_13680 - Type: Gene
    Product:Putative phage cell wall XkdQ-like hydrolase | Pathway: | COG: Cell wall/membrane/envelope biogenesis
  • CD630_14150 - Type: Gene
    Product:Putative membrane protein | Pathway: | COG: Function unknown
  • CD630_13760 - Type: Gene
    Product:Putative phage protein | Pathway: | COG:
  • CD630_13740 - Type: Gene
    Product:Putative beta-lactamase-inhibitor protein II | Pathway: | COG: Cell cycle control, cell division, chromosome partitioning, Cytoskeleton
  • CD630_25710 - Type: Gene
    Product:Two-component response regulator | Pathway: | COG: Signal transduction mechanisms
  • CD630_30410 - pepI Type: Gene
    Product:Proline iminopeptidase (Proline aminopeptidase)(PIP), peptidase S33 family | Pathway: | COG: Amino acid transport and metabolism
  • CD630_14170 - Type: Gene
    Product:Putative ATP-binding protein | Pathway: | COG: Amino acid transport and metabolism
  • CD630_13670 - Type: Gene
    Product:Putative phage XkdP-like protein | Pathway: | COG: Function unknown
  • CD630_13651 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG:
  • CD630_13650 - Type: Gene
    Product:Putative phage XkdN-like protein | Pathway: | COG: Function unknown
  • CD630_13630 - Type: Gene
    Product:Putative phage XkdK-like protein | Pathway: | COG: Function unknown
  • CD630_12430 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG:
  • CD630_13710 - Type: Gene
    Product:Putative baseplate assembly predicted J-like | Pathway: | COG: Function unknown
  • CD630_13730 - Type: Gene
    Product:Putative phage tail fiber protein | Pathway: | COG: Function unknown
  • CD630_13690 - Type: Gene
    Product:Putative phage protein | Pathway: | COG:
  • CD630_25700 - Type: Gene
    Product:Two-component sensor histidine kinase | Pathway: | COG: Signal transduction mechanisms
  • CD630_14140 - Type: Gene
    Product:Putative oxidoreductase, Fe-S subunit | Pathway: | COG: Function unknown
  • CD630_14160 - Type: Gene
    Product:Putative membrane protein | Pathway: | COG: Function unknown
0.000016 NA 0.48 Inferelator: 1
Hypergeometric: 0

TF Influences from Inferelator

  1. 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_163 25
  • CD630_18840 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG:
  • CD630_27540 - Type: Gene
    Product:Putative diguanylate kinase signaling protein | Pathway: | COG: Signal transduction mechanisms
  • CD630_21991 - Type: Gene
    Product:Putative 4Fe-4S ferredoxin iron-sulfur bindingdomain-containing protein | Pathway: | COG: Energy production and conversion
  • CD630_21990 - Type: Gene
    Product:Putative ferredoxin/flavodoxin oxidoreductase,alpha subunit | Pathway: | COG: Energy production and conversion
  • CD630_22000 - hisC Type: Gene
    Product:Histidinol-phosphate aminotransferase | Pathway: Amino-acid biosynthesis | COG: Amino acid transport and metabolism
  • CD630_06190 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG:
  • CD630_21440 - Type: Gene
    Product:Putative membrane protein | Pathway: | COG: Function unknown
  • CD630_23740 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG:
  • CD630_22660 - Type: Gene
    Product:Putative oxidoreductase, FAD dependent | Pathway: | COG: Energy production and conversion
  • CD630_35420 - spmA Type: Gene
    Product:Spore maturation protein A | Pathway: | COG: Function unknown
  • CD630_21970 - Type: Gene
    Product:Putative ferredoxin/flavodoxin oxidoreductase,gamma subunit | Pathway: | COG: Energy production and conversion
  • CD630_23130 - Type: Gene
    Product:ABC-type transport system, molybdenum-likeATP-binding protein | Pathway: | COG: Carbohydrate transport and metabolism
  • CD630_32520 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_27530 - Type: Gene
    Product:Putative signaling protein | Pathway: | COG: Signal transduction mechanisms
  • CD630_21430 - Type: Gene
    Product:Transcriptional regulator, HTH-type | Pathway: | COG: Transcription
  • CD630_21980 - Type: Gene
    Product:Putative ferredoxin/flavodoxin oxidoreductase,beta subunit | Pathway: | COG: Energy production and conversion
  • CD630_23110 - Type: Gene
    Product:ABC-type transport system, molybdenum-likeextracellular solute-binding protein | Pathway: | COG: Inorganic ion transport and metabolism
  • CD630_06200 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_23750 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_23120 - Type: Gene
    Product:ABC-type transport system, molybdenum-likepermease | Pathway: | COG: Inorganic ion transport and metabolism
  • CD630_23140 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_35410 - spmB Type: Gene
    Product:Spore maturation protein B | Pathway: | COG: Function unknown
  • CD630_22650 - Type: Gene
    Product:Putative membrane protein | Pathway: | COG: Function unknown
  • CD630_21960 - Type: Gene
    Product:Putative succinyl-CoA synthetase-like ATP-bindingprotein | Pathway: | COG: Energy production and conversion
  • CD630_32510 - Type: Gene
    Product:Putative dehydrogenase | Pathway: | COG: Function unknown
0.000000000047 0.03 0.48 Inferelator: 2
Hypergeometric: 2

TF Influences from Inferelator

  1. CD630_25990 - Type: Gene
    Product:Putative transcriptional regulator | Pathway: | COG: Transcription
  2. CD630_26430 - sigE Type: Gene
    Product:RNA polymerase sigma-E factor | Pathway: | COG: Transcription

TF Influences from Hypergeometric Test

  1. CD630_12140 - spo0A Type: Gene
    Product:Stage 0 sporulation protein A | Pathway: | COG: Signal transduction mechanisms
  2. CD630_26430 - sigE Type: Gene
    Product:RNA polymerase sigma-E factor | Pathway: | COG: Transcription
Module_57 26
  • CD630_17640 - Type: Gene
    Product:Putative phenylalanyl-tRNA synthetase beta chain | Pathway: | COG: Function unknown
  • CD630_28050 - ruvB Type: Gene
    Product:Holliday junction ATP-dependent DNA helicaseRuvB | Pathway: | COG: Replication, recombination and repair
  • CD630_28070 - ruvC Type: Gene
    Product:Crossover junction endodeoxyribonuclease RuvC(Holliday junction nuclease RuvC) (Holliday junctionresolvase RuvC) | Pathway: | COG: Replication, recombination and repair
  • CD630_13310 - sip3 Type: Gene
    Product:Signal peptidase I, S26A family | Pathway: | COG: Intracellular trafficking, secretion, and vesicular transport
  • CD630_27870 - cwp84 Type: Gene
    Product:Cell surface protein | Pathway: | COG: Posttranslational modification, protein turnover, chaperones
  • CD630_13330 - Type: Gene
    Product:Putative phage tyrosine recombinase | Pathway: | COG: Replication, recombination and repair
  • CD630_13270 - pgsA Type: Gene
    Product:CDP-diacylglycerol--glycerol-3-phosphate3-phosphatidyltransferase | Pathway: | COG: Lipid transport and metabolism
  • CD630_25960 - Type: Gene
    Product:Putative pseudouridylate synthase, RluC/RluDfamily | Pathway: | COG: Translation, ribosomal structure and biogenesis
  • CD630_35810 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_17630 - Type: Gene
    Product:Putative membrane protein | Pathway: | COG: Function unknown
  • CD630_22620 - Type: Gene
    Product:Transporter, Major Facilitator Superfamily (MFS) | Pathway: | COG: Amino acid transport and metabolism
  • CD630_06170 - Type: Gene
    Product:Putative membrane protein | Pathway: | COG: Function unknown
  • CD630_28060 - ruvA Type: Gene
    Product:Holliday junction ATP-dependent DNA helicaseRuvA | Pathway: | COG: Replication, recombination and repair
  • CD630_35830 - Type: Gene
    Product:Transcriptional regulator, MerR family | Pathway: | COG: Transcription
  • CD630_17650 - Type: Gene
    Product:Putative hydrolase, NUDIX family | Pathway: | COG: Replication, recombination and repair
  • CD630_27880 - Type: Gene
    Product:Putative membrane protein, GtrA family | Pathway: | COG: Function unknown
  • CD630_31640 - rnr Type: Gene
    Product:Ribonuclease R | Pathway: | COG: Transcription
  • CD630_13340 - purB Type: Gene
    Product:Adenylosuccinate lyase | Pathway: Purine metabolism | COG: Nucleotide transport and metabolism
  • CD630_19510 - Type: Gene
    Product:putative Acyl-CoA N-acyltransferase | Pathway: | COG: Translation, ribosomal structure and biogenesis
  • CD630_13260 - rimO Type: Gene
    Product:Ribosomal protein S12 methylthiotransferase | Pathway: | COG: Translation, ribosomal structure and biogenesis
  • CD630_29830 - Type: Gene
    Product:Putative Helix-Turn-Helix DNA-binding protein | Pathway: | COG: Transcription
  • CD630_13240 - ftsK Type: Gene
    Product:DNA FtsK/SpoIIIE translocase | Pathway: | COG: Cell cycle control, cell division, chromosome partitioning
  • CD630_13320 - uppP1 Type: Gene
    Product:Undecaprenyl-diphosphatase 1 (Undecaprenylpyrophosphate phosphatase 1) (Bacitracin resistance protein1) | Pathway: | COG: Defense mechanisms
  • CD630_25970 - lspA Type: Gene
    Product:Lipoprotein signal peptidase (Prolipoproteinsignal peptidase) (Signal peptidase II) (SPase II) | Pathway: Protein modification | COG: Cell wall/membrane/envelope biogenesis, Intracellular trafficking, secretion, and vesicular transport
  • CD630_35820 - Type: Gene
    Product:Putative pseudouridine synthase RsuA-like | Pathway: | COG: Translation, ribosomal structure and biogenesis
  • CD630_21250 - Type: Gene
    Product:Putative acetyltransferase | Pathway: | COG: Function unknown
9e-17 0 0.48 Inferelator: 2
Hypergeometric: 0

TF Influences from Inferelator

  1. CD630_08870 - Type: Gene
    Product:Transcriptional regulator, GntR family | Pathway: | COG: Transcription
  2. CD630_20480 - Type: Gene
    Product:Transcriptional regulator, RpiR family | Pathway: | COG: Transcription

TF Influences from Hypergeometric Test

No TF Influences from the hypergeometric test
Module_379 28
  • CD630_35230 - ksgA Type: Gene
    Product:Dimethyladenosine transferase(S-adenosylmethionine-6-N', N'-adenosyl(rRNA)dimethyltransferase) | Pathway: | COG: Translation, ribosomal structure and biogenesis
  • CD630_01470 - Type: Gene
    Product:Putative transporter | Pathway: | COG: Function unknown
  • CD630_16550 - Type: Gene
    Product:Putative Na+/H+ antiporter NhaC-like | Pathway: | COG: Energy production and conversion
  • CD630_09000 - opuCA Type: Gene
    Product:ABC-type transport system, glycinebetaine/carnitine/choline ATP-binding protein | Pathway: | COG: Amino acid transport and metabolism
  • CD630_35440 - Type: Gene
    Product:Transcriptional regulator, AsnC/Lrp family | Pathway: | COG: Transcription
  • CD630_21770 - Type: Gene
    Product:ABC-type transport system,cystine/aminoacid-family extracellular solute-bindingprotein | Pathway: | COG: Amino acid transport and metabolism
  • CD630_22020 - Type: Gene
    Product:Putative Na+/solute symporter, SSS family | Pathway: | COG: Amino acid transport and metabolism
  • CD630_15780 - Type: Gene
    Product:Putative membrane-associated ribonuclease BN-like(Rbn) | Pathway: | COG: Function unknown
  • CD630_05580 - glsA Type: Gene
    Product:Glutaminase (L-glutamine amidohydrolase) | Pathway: | COG: Amino acid transport and metabolism
  • CD630_16290 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_25160 - ansB Type: Gene
    Product:L-asparaginase | 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_21490 - Type: Gene
    Product:Putative vancomycin resistance protein, vanWfamily | Pathway: | COG: Defense mechanisms
  • CD630_36210 - 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
  • CD630_21450 - Type: Gene
    Product:DNA mismatch repair protein | Pathway: | COG: Replication, recombination and repair
  • CD630_00210 - pycA Type: Gene
    Product:Pyruvate carboxylase | Pathway: | COG: Energy production and conversion
  • CD630_20480 - Type: Gene
    Product:Transcriptional regulator, RpiR family | Pathway: | COG: Transcription
  • CD630_35240 - Type: Gene
    Product:Putative DNA-binding protein | Pathway: | COG: Replication, recombination and repair
  • CD630_09010 - opuCC Type: Gene
    Product:ABC-type transport system, glycinebetaine/carnitine/choline permease | Pathway: | COG: Amino acid transport and metabolism
  • CD630_35620 - murI Type: Gene
    Product:Glutamate racemase | Pathway: Cell wall biogenesis | COG: Cell wall/membrane/envelope biogenesis
  • CD630_35430 - Type: Gene
    Product:Putative nicotinate phosphribosyltransferase | Pathway: Cofactor biosynthesis | COG: Coenzyme transport and metabolism
  • CD630_21760 - Type: Gene
    Product:ABC-type transport system,cystine/aminoacid-family permease | Pathway: | COG: Amino acid transport and metabolism
  • CD630_22030 - Type: Gene
    Product:Transcriptional regulator, TetR family | Pathway: | COG: Transcription
  • CD630_21330 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_21720 - Type: Gene
    Product:ABC-type transport system,cystine/aminoacid-family ATP-binding protein | Pathway: | COG: Amino acid transport and metabolism
  • CD630_05590 - Type: Gene
    Product:Transcriptional regulator, ArsR family | Pathway: | COG: Transcription
  • 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
0.000000014 NA 0.48 Inferelator: 1
Hypergeometric: 1

TF Influences from Inferelator

  1. CD630_24300 - Type: Gene
    Product:Transcriptional regulator, IclR family | Pathway: | COG: Transcription

TF Influences from Hypergeometric Test

  1. CD630_32450 - prdR Type: Gene
    Product:Transcriptional regulator, sigma-54-dependent | Pathway: | COG: Transcription
Module_90 4
  • CD630_22510 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_19930 - Type: Gene
    Product:Putative decarboxylase | Pathway: | COG: Function unknown
  • CD630_31080 - Type: Gene
    Product:Putative membrane protein | Pathway: | COG: Function unknown
  • CD630_31090 - Type: Gene
    Product:Putative pentose-5-phosphate 3-epimerase | Pathway: | COG: Carbohydrate transport and metabolism
NA NA 0.48 Inferelator: 2
Hypergeometric: 0

TF Influences from Inferelator

  1. CD630_20480 - Type: Gene
    Product:Transcriptional regulator, RpiR family | 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_44 21
  • CD630_16360 - terD Type: Gene
    Product:Tellurium resistance protein | Pathway: | COG: Signal transduction mechanisms
  • CD630_25900 - dapF Type: Gene
    Product:Diaminopimelate epimerase (DAP epimerase) | Pathway: Amino-acid biosynthesis | COG: Amino acid transport and metabolism
  • CD630_16370 - Type: Gene
    Product:Putative calcium-transporting ATPase | Pathway: | COG: Inorganic ion transport and metabolism
  • CD630_25780 - Type: Gene
    Product:Putative serine/threonine-protein kinase andphosphatase | Pathway: | COG: Signal transduction mechanisms
  • CD630_16350 - terD Type: Gene
    Product:Tellurium resistance protein | Pathway: | COG: Signal transduction mechanisms
  • CD630_25790 - Type: Gene
    Product:Putative phosphatase, 2C family | Pathway: | COG: Signal transduction mechanisms
  • CD630_25810 - rsmB Type: Gene
    Product:Ribosomal RNA small subunit methyltransferase B(rRNA (cytosine-C(5)-)-methyltransferase) | Pathway: | COG: Translation, ribosomal structure and biogenesis
  • CD630_16400 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Carbohydrate transport and metabolism
  • CD630_25830 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_16410 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_25740 - thiN Type: Gene
    Product:Thiamine pyrophosphokinase (TPK) (Thiaminediphospho kinase) | Pathway: | COG: Coenzyme transport and metabolism
  • CD630_13580 - Type: Gene
    Product:Putative membrane protein | Pathway: | COG: Function unknown
  • CD630_16430 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_25770 - fabG Type: Gene
    Product:3-oxoacyl-[acyl-carrier-protein] reductase(3-ketoacyl- acyl carrier protein reductase) | Pathway: | COG: Function unknown
  • CD630_16380 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_16420 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_25860 - priA Type: Gene
    Product:Primosomal protein N' (ATP-dependent helicasepriA) (Replication factor Y) | Pathway: | COG: Replication, recombination and repair
  • CD630_16390 - Type: Gene
    Product:Putative tellurite associated resistance protein | Pathway: | COG: Inorganic ion transport and metabolism
  • CD630_16330 - Type: Gene
    Product:Putative serine protease | Pathway: | COG: Posttranslational modification, protein turnover, chaperones
  • CD630_13570 - Type: Gene
    Product:Putative peptidyl-prolyl isomerase | Pathway: | COG: Posttranslational modification, protein turnover, chaperones
  • CD630_25871 - rpoZ Type: Gene
    Product:DNA-directed RNA polymerase subunit omega (RNAPomega subunit) (Transcriptase subunit omega) (RNApolymerase omega subunit) | Pathway: | COG: Transcription
NA NA 0.48 Inferelator: 4
Hypergeometric: 0

TF Influences from Inferelator

  1. CD630_11770 - fapR Type: Gene
    Product:Transcriptional regulator, DeoR family (Fattyacid and phospholipid biosynthesis regulator) | Pathway: | COG: Transcription
  2. CD630_16920 - Type: Gene
    Product:Transcriptional regulator, ArsR family | Pathway: | COG: Transcription
  3. CD630_16930 - Type: Gene
    Product:Putative dinitrogenase iron-molybdenum cofactor | Pathway: | COG: Function unknown
  4. 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