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 351 - 360 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_117 27
  • CD630_01920 - cls Type: Gene
    Product:Cardiolipin synthetase 1 | Pathway: | COG: Lipid transport and metabolism
  • CD630_22870 - Type: Gene
    Product:Putative transporter | Pathway: | COG: Amino acid transport and metabolism
  • CD630_30440 - Type: Gene
    Product:Transcriptional regulator, RpiR family | Pathway: | COG: Transcription
  • CD630_12630 - Type: Gene
    Product:Putative FMN-dependent dehydrogenase | Pathway: | COG: Energy production and conversion
  • CD630_24750 - Type: Gene
    Product:Putative membrane protein | Pathway: | COG: Function unknown
  • CD630_12610 - Type: Gene
    Product:Putative ribonucleotide-diphosphate reductase | Pathway: | COG: Nucleotide transport and metabolism
  • CD630_24770 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_25220 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_10130 - Type: Gene
    Product:Two-component response regulator | Pathway: | COG: Signal transduction mechanisms
  • CD630_24780 - Type: Gene
    Product:Putative DNA uptake transporter | Pathway: | COG: Cell wall/membrane/envelope biogenesis
  • CD630_25710 - Type: Gene
    Product:Two-component response regulator | Pathway: | COG: Signal transduction mechanisms
  • CD630_34120 - uvrB Type: Gene
    Product:Excinuclease ABC subunit B | Pathway: | COG: Replication, recombination and repair
  • CD630_34100 - uvrC Type: Gene
    Product:Excinuclease ABC subunit C | Pathway: | COG: Replication, recombination and repair
  • CD630_30450 - Type: Gene
    Product:Putative ATPase, BadF/BadG/BcrA/BcrD type | Pathway: | COG: Carbohydrate transport and metabolism
  • CD630_34090 - hprK Type: Gene
    Product:PTS system, HPr kinase/phosphorylase | Pathway: | COG: Signal transduction mechanisms
  • CD630_32170 - Type: Gene
    Product:ABC-type transport system, ATP-binding protein | Pathway: | COG: Replication, recombination and repair
  • CD630_22860 - Type: Gene
    Product:Putative transporter | Pathway: | COG: Amino acid transport and metabolism
  • CD630_12620 - rnhB Type: Gene
    Product:Ribonuclease HII (RNase HII) | Pathway: | COG: Replication, recombination and repair
  • CD630_24740 - Type: Gene
    Product:Putative DNA polymerase III, delta subunit | Pathway: | COG: Replication, recombination and repair
  • CD630_25240 - nadD Type: Gene
    Product:Nicotinate-nucleotide adenylyltransferase | Pathway: Cofactor biosynthesis | COG: Coenzyme transport and metabolism
  • CD630_01910 - Type: Gene
    Product:Putative DNA glycosylase | Pathway: | COG: Replication, recombination and repair
  • CD630_24760 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_10140 - Type: Gene
    Product:Two-component sensor histidine kinase | Pathway: | COG: Signal transduction mechanisms
  • CD630_12640 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG:
  • CD630_25700 - Type: Gene
    Product:Two-component sensor histidine kinase | Pathway: | COG: Signal transduction mechanisms
  • CD630_34110 - uvrA Type: Gene
    Product:Excinuclease ABC subunit A | Pathway: | COG: Replication, recombination and repair
  • CD630_25230 - Type: Gene
    Product:Putative hydrolase | Pathway: | COG: Coenzyme transport and metabolism
0.04 NA 0.59 Inferelator: 1
Hypergeometric: 0

TF Influences from Inferelator

  1. CD630_23900 - Type: Gene
    Product:Transcriptional regulator, beta-lactamsrepressor | Pathway: | COG: Transcription

TF Influences from Hypergeometric Test

No TF Influences from the hypergeometric test
Module_55 24
  • CD630_11890 - Type: Gene
    Product:Putative amino acid/polyamine transporter I | Pathway: | COG: Amino acid transport and metabolism
  • CD630_00150 - tadA Type: Gene
    Product:tRNA specific adenosine deaminase | Pathway: | COG: Nucleotide transport and metabolism, Translation, ribosomal structure and biogenesis
  • CD630_05300 - Type: Gene
    Product:Putative membrane protein | Pathway: | COG: Function unknown
  • CD630_21520 - Type: Gene
    Product:Putative glutamyl-aminopeptidase, M42 family | Pathway: | COG: Amino acid transport and metabolism
  • CD630_00450 - Type: Gene
    Product:Putative sugar-phosphate aldolase | Pathway: | COG: Carbohydrate transport and metabolism
  • CD630_15550 - Type: Gene
    Product:Putative amino acid permease | Pathway: | COG: Amino acid transport and metabolism
  • CD630_30040 - kdgT2 Type: Gene
    Product:2-keto-3-deoxygluconate permease 2 | Pathway: | COG: Inorganic ion transport and metabolism
  • CD630_11870 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_30020 - uxaA Type: Gene
    Product:D-galactate dehydratase/Altronate hydrolase | Pathway: | COG: Carbohydrate transport and metabolism
  • CD630_30000 - dapA1 Type: Gene
    Product:Dihydrodipicolinate synthase 1 | Pathway: | COG: Amino acid transport and metabolism
  • CD630_05280 - Type: Gene
    Product:Putative amidohydrolase | Pathway: | COG: Amino acid transport and metabolism
  • CD630_06210 - Type: Gene
    Product:Putative membrane protein | Pathway: | COG:
  • CD630_22241 - Type: Gene
    Product:Putative extrachromosomal origin protein | Pathway: | COG:
  • CD630_20050 - Type: Gene
    Product:Fragment of conserved hypothetical protein(C-terminal region) | Pathway: | COG: Function unknown
  • CD630_11880 - Type: Gene
    Product:Putative gamma-glutamyl-gamma-aminobutyratehydrolase | Pathway: | COG: Translation, ribosomal structure and biogenesis
  • CD630_06180 - Type: Gene
    Product:Transcriptional regulator, LytR family | Pathway: | COG: Transcription, Signal transduction mechanisms
  • CD630_11190 - Type: Gene
    Product:Putative lipoprotein | Pathway: | COG:
  • CD630_18781 - Type: Gene
    Product:Fragment of conserved hypothetical protein(N-terminal region) | Pathway: | COG: Replication, recombination and repair
  • CD630_22560 - Type: Gene
    Product:Putative PTS system, EIIC component | Pathway: | COG: Function unknown
  • CD630_02970 - bioB Type: Gene
    Product:Biotin synthase | Pathway: Cofactor biosynthesis | COG: Coenzyme transport and metabolism
  • CD630_30010 - Type: Gene
    Product:Putative hydrolase/isomerase/hydratase | Pathway: | COG: Secondary metabolites biosynthesis, transport and catabolism
  • CD630_30030 - Type: Gene
    Product:Putative N-terminus region of carbohydratehydrolase, SAF domain | Pathway: | COG: Carbohydrate transport and metabolism
  • CD630_05290 - Type: Gene
    Product:Putative membrane protein | Pathway: | COG: Function unknown
  • CD630_06220 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
0.0000000000000037 NA 0.60 Inferelator: 0
Hypergeometric: 1

TF Influences from Inferelator

No TF influences from Inferelator

TF Influences from Hypergeometric Test

  1. CD630_32450 - prdR Type: Gene
    Product:Transcriptional regulator, sigma-54-dependent | Pathway: | COG: Transcription
Module_335 13
  • CD630_33430 - Type: Gene
    Product:Putative replication initiation factorTn916-like, CTn6-Orf21 | Pathway: | COG: Replication, recombination and repair
  • CD630_33480 - Type: Gene
    Product:Hypothetical protein | Pathway: | COG: Function unknown
  • CD630_33421 - Type: Gene
    Product:Putative conjugative transposon proteinTn916-like, CTn6-Orf20 | Pathway: | COG: Function unknown
  • CD630_33460 - Type: Gene
    Product:Putative conjugative transposon protein DUF961family Tn916-like, CTn6-Orf24 | Pathway: | COG: Function unknown
  • CD630_18260 - metA Type: Gene
    Product:Homoserine O-succinyltransferase | Pathway: Amino-acid biosynthesis | COG: Amino acid transport and metabolism
  • CD630_33440 - Type: Gene
    Product:Putative cell-division FtsK/SpoIIIE-familyprotein Tn916-like, CTn6-Orf22 | Pathway: | COG: Cell cycle control, cell division, chromosome partitioning
  • CD630_10910 - int Type: Gene
    Product:Integrase Tn1549-like, CTn4-Orf34 | Pathway: | COG: Replication, recombination and repair
  • CD630_33450 - Type: Gene
    Product:Putative conjugative transposon proteinTn916-like, CTn6-Orf23 | Pathway: | COG: Function unknown
  • CD630_33470 - Type: Gene
    Product:Putative membrane protein | Pathway: | COG:
  • CD630_10940 - Type: Gene
    Product:Putative RNA polymerase sigma factor Tn1549-like,CTn4-Orf31 | Pathway: | COG: Function unknown
  • CD630_10920 - xis Type: Gene
    Product:Excisionase Tn1549-like, CTn4-Orf33 | Pathway: | COG: Function unknown
  • CD630_10921 - Type: Gene
    Product:Putative conjugative transposon proteinTn1549-like, CTn4-Orf32 | Pathway: | COG: Function unknown
  • CD630_18250 - metY Type: Gene
    Product:O-acetylhomoserine sulfhydrylase | Pathway: | COG: Amino acid transport and metabolism
0.000000000091 0.00023 0.60 Inferelator: 2
Hypergeometric: 0

TF Influences from Inferelator

  1. CD630_13790 - Type: Gene
    Product:Transcriptional regulator, Phage-type | Pathway: | COG: Transcription
  2. CD630_22850 - Type: Gene
    Product:Transcriptional regulator, GntR family | Pathway: | COG: Transcription

TF Influences from Hypergeometric Test

No TF Influences from the hypergeometric test
Module_73 29
  • CD630_31200 - Type: Gene
    Product:Transcriptional regulator, AbrB family | Pathway: | COG: Transcription
  • CD630_19350 - spoVS Type: Gene
    Product:Stage V sporulation protein S | Pathway: | COG: Function unknown
  • CD630_16950 - Type: Gene
    Product:Putative symporter protein | Pathway: | COG: Inorganic ion transport and metabolism
  • CD630_18190 - Type: Gene
    Product:Putative membrane protein | Pathway: | COG: Function unknown
  • CD630_26310 - Type: Gene
    Product:Putative membrane protein, UPF0078 family | Pathway: Lipid metabolism | COG: Function unknown
  • CD630_03530 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_13370 - Type: Gene
    Product:Transcriptional regulator, RpiR family | Pathway: | COG: Transcription
  • CD630_15060 - Type: Gene
    Product:Putative drug/sodium antiporter, MATE family | Pathway: | COG: Defense mechanisms
  • CD630_21620 - Type: Gene
    Product:Putative GCN5-related N-acetyltransferase-likeprotein | Pathway: | COG: Function unknown
  • CD630_09860 - rpsA Type: Gene
    Product:30S ribosomal protein S1 | Pathway: | COG: Translation, ribosomal structure and biogenesis
  • CD630_31190 - Type: Gene
    Product:Putative UDP-glycosyltransferase, MGT subfamily | Pathway: | COG: Energy production and conversion, Carbohydrate transport and metabolism
  • CD630_21110 - Type: Gene
    Product:Transcriptional regulator, DeoR family | Pathway: | COG: Transcription
  • CD630_27660 - LcpB Type: Gene
    Product:Surface-anchoring factors, LytR-CpsA-Psr-likeprotein | Pathway: | COG: Transcription
  • CD630_15200 - Type: Gene
    Product:Putative membrane protein | Pathway: | COG:
  • CD630_07380 - Type: Gene
    Product:Putative exported protein | Pathway: | COG: Function unknown
  • CD630_21950 - ftnA Type: Gene
    Product:Ferritin | Pathway: | COG: Inorganic ion transport and metabolism
  • CD630_05830 - Type: Gene
    Product:Putative diguanylate kinase signaling protein | Pathway: | COG: Signal transduction mechanisms
  • CD630_17300 - Type: Gene
    Product:Putative ATP-binding protein | Pathway: | COG: Cell cycle control, cell division, chromosome partitioning
  • CD630_03541 - Type: Gene
    Product:Fragment of putative membrane protein | Pathway: | COG: Function unknown
  • CD630_26300 - gpsA Type: Gene
    Product:Glycerol-3-phosphate dehydrogenase (NAD(P)+)(NAD(P)H-dependent glycerol-3-phosphate dehydrogenase) | Pathway: Membrane lipid metabolism | COG: Energy production and conversion
  • CD630_21610 - Type: Gene
    Product:Putative membrane protein | Pathway: | COG:
  • CD630_03520 - Type: Gene
    Product:Transcriptional regulator, RmlC-type | Pathway: | COG: Transcription
  • CD630_21630 - Type: Gene
    Product:Putative alanyl-tRNA synthetase | Pathway: | COG: Function unknown
  • CD630_15190 - Type: Gene
    Product:Putative acyltransferase | Pathway: | COG: Function unknown
  • CD630_26320 - Type: Gene
    Product:Putative GTP-binding protein EngA | Pathway: | COG: Nucleotide transport and metabolism
  • CD630_16940 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_05840 - Type: Gene
    Product:Putative diguanylate kinase signaling protein | Pathway: | COG: Signal transduction mechanisms
  • CD630_05610 - Type: Gene
    Product:Putative aldo/keto reductase ; putativeferredoxin | Pathway: | COG: Energy production and conversion
  • CD630_13390 - aspB Type: Gene
    Product:Aspartate aminotransferase (AspAT) (TransaminaseA) | Pathway: | COG: Amino acid transport and metabolism
0.00000000000089 NA 0.60 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_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_9 25
  • CD630_25540 - tlpA Type: Gene
    Product:Transposase-like protein A | Pathway: | COG:
  • CD630_20650 - Type: Gene
    Product:Transcriptional regulator, beta-lactamsrepressor | Pathway: | COG: Transcription
  • CD630_22340 - Type: Gene
    Product:Transcriptional regulator, Crp family | Pathway: | COG: Signal transduction mechanisms
  • CD630_15550 - Type: Gene
    Product:Putative amino acid permease | Pathway: | COG: Amino acid transport and metabolism
  • CD630_22360 - Type: Gene
    Product:Putative glucokinase, ROK family | Pathway: | COG: Carbohydrate transport and metabolism, Transcription
  • CD630_15710 - tlpA Type: Gene
    Product:Transposase-like protein A | Pathway: | COG:
  • CD630_05170 - Type: Gene
    Product:Putative membrane protein | Pathway: | COG: Function unknown
  • CD630_22410 - nanE Type: Gene
    Product:N-acetylmannosamine-6-phosphate 2-epimerase(ManNAc-6-P epimerase) | Pathway: Amino-sugar metabolism | COG: Carbohydrate transport and metabolism
  • CD630_32280 - Type: Gene
    Product:Putative membrane protein | Pathway: | COG: Posttranslational modification, protein turnover, chaperones
  • CD630_16610 - tlpB Type: Gene
    Product:Transposase-like protein B | Pathway: | COG: Replication, recombination and repair
  • CD630_22380 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Carbohydrate transport and metabolism
  • CD630_21280 - ispG Type: Gene
    Product:4-hydroxy-3-methylbut-2-en-1-yl diphosphatesynthase | Pathway: Isoprenoid biosynthesis | COG: Lipid transport and metabolism
  • CD630_21300 - dxr Type: Gene
    Product:1-deoxy-D-xylulose 5-phosphate reductoisomerase | Pathway: Isoprenoid biosynthesis | COG: Lipid transport and metabolism
  • CD630_25531 - tlpB Type: Gene
    Product:Transposase-like protein B | Pathway: | COG: Replication, recombination and repair
  • CD630_05180 - Type: Gene
    Product:Putative membrane protein | Pathway: | COG: Function unknown
  • CD630_20660 - Type: Gene
    Product:Putative integrase | Pathway: | COG: Replication, recombination and repair
  • CD630_22350 - Type: Gene
    Product:Transcriptional regulator, RpiR family | Pathway: | COG: Transcription
  • CD630_22370 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_05100 - Type: Gene
    Product:Putative RNA polymerase sigma factor Tn5397,CTn3-Orf7 | Pathway: | COG: Function unknown
  • CD630_05101 - Type: Gene
    Product:Putative conjugative transposon protein Tn5397,CTn3-Orf8 | Pathway: | COG: Function unknown
  • CD630_15720 - tlpB Type: Gene
    Product:Transposase-like protein B | Pathway: | COG: Replication, recombination and repair
  • CD630_22400 - nanA Type: Gene
    Product:Acetylneuraminate lyase | Pathway: Amino-sugar metabolism | COG: Amino acid transport and metabolism, Cell wall/membrane/envelope biogenesis
  • CD630_22390 - Type: Gene
    Product:Putative Na+/solute symporter, SSS family | Pathway: | COG: Amino acid transport and metabolism
  • CD630_16601 - tlpA Type: Gene
    Product:Transposase-like protein A | Pathway: | COG:
  • CD630_21290 - Type: Gene
    Product:Putative membrane-associated peptidase, M50family | Pathway: | COG: Cell wall/membrane/envelope biogenesis
0.00000000000021 0.000000031 0.60 Inferelator: 2
Hypergeometric: 0

TF Influences from Inferelator

  1. CD630_22340 - Type: Gene
    Product:Transcriptional regulator, Crp family | Pathway: | COG: Signal transduction mechanisms
  2. CD630_22350 - Type: Gene
    Product:Transcriptional regulator, RpiR family | Pathway: | COG: Transcription

TF Influences from Hypergeometric Test

No TF Influences from the hypergeometric test
Module_266 21
  • CD630_17280 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_26660 - ptsG-A Type: Gene
    Product:PTS system, glucose-specific IIA component | Pathway: | COG: Carbohydrate transport and metabolism
  • CD630_29350 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_17270 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG:
  • CD630_23360 - Type: Gene
    Product:Putative toxic anion resistance protein | Pathway: | COG: Inorganic ion transport and metabolism
  • CD630_26670 - ptsG-BC Type: Gene
    Product:PTS system, glucose-specific IIBC component | Pathway: | COG: Carbohydrate transport and metabolism
  • CD630_23370 - Type: Gene
    Product:Putative membrane protein | Pathway: | COG: Function unknown
  • CD630_11190 - Type: Gene
    Product:Putative lipoprotein | Pathway: | COG:
  • CD630_20580 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_11240 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG:
  • CD630_03400 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_20570 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_30310 - Type: Gene
    Product:Transcription antiterminator, PTS operonregulator | Pathway: | COG: Transcription
  • CD630_29360 - Type: Gene
    Product:Putative phage protein | Pathway: | COG: Function unknown
  • CD630_22952 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG:
  • CD630_29370 - Type: Gene
    Product:Putative phage protein | Pathway: | COG:
0.01 NA 0.60 Inferelator: 3
Hypergeometric: 0

TF Influences from Inferelator

  1. CD630_10090 - Type: Gene
    Product:Transcriptional regulator, GntR family | Pathway: | COG: Transcription
  2. CD630_23900 - Type: Gene
    Product:Transcriptional regulator, beta-lactamsrepressor | Pathway: | COG: Transcription
  3. CD630_26650 - Type: Gene
    Product:Transcriptional regulator, AraC family | Pathway: | COG: Transcription

TF Influences from Hypergeometric Test

No TF Influences from the hypergeometric test
Module_316 21
  • CD630_31730 - pgk Type: Gene
    Product:Phosphoglycerate kinase | Pathway: Carbohydrate degradation | COG: Carbohydrate transport and metabolism
  • CD630_33950 - pfkA Type: Gene
    Product:6-phosphofructokinase (Phosphofructokinase)(Phosphohexokinase) | Pathway: Carbohydrate degradation | COG: Carbohydrate transport and metabolism
  • CD630_26400 - nrdR Type: Gene
    Product:Transcriptional regulator, repressor NrdR family | Pathway: | COG: Transcription
  • CD630_26410 - Type: Gene
    Product:Putative sporulation protein | Pathway: | COG: Function unknown
  • CD630_27500 - agrB Type: Gene
    Product:Accessory gene regulator | Pathway: | COG: Signal transduction mechanisms
  • CD630_31720 - tpi Type: Gene
    Product:Triosephosphate isomerase (TIM) (Triose-phosphateisomerase) | Pathway: Carbohydrate biosynthesis | COG: Carbohydrate transport and metabolism
  • CD630_33940 - pyk Type: Gene
    Product:Pyruvate kinase (PK) | Pathway: Carbohydrate degradation | COG: Carbohydrate transport and metabolism
  • CD630_31710 - gpmI Type: Gene
    Product:2,3-bisphosphoglycerate-independentphosphoglycerate mutase (Phosphoglyceromutase)(BPG-independent PGAM) (iPGM) | Pathway: Carbohydrate degradation | COG: Carbohydrate transport and metabolism
  • CD630_27491 - agrD Type: Gene
    Product:Autoinducer prepeptide | Pathway: | COG:
  • CD630_10670 - CdeC Type: Gene
    Product:Clostridium difficile exosporium cycteine-richprotein | Pathway: | COG:
  • CD630_26380 - Type: Gene
    Product:Two-component response regulator | Pathway: | COG: Signal transduction mechanisms
  • CD630_26350 - Type: Gene
    Product:Putative membrane protein | Pathway: | COG: Function unknown
  • CD630_26390 - Type: Gene
    Product:Putative laccase protein | Pathway: | COG: Function unknown
  • CD630_26370 - Type: Gene
    Product:Two-component sensor histidine kinase | Pathway: | COG: Signal transduction mechanisms
  • CD630_31740 - gapA Type: Gene
    Product:Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) | Pathway: | COG: Carbohydrate transport and metabolism
  • CD630_26440 - spoIIGA Type: Gene
    Product:Sporulation sigma-E factor processing peptidase | Pathway: | COG: Function unknown
  • CD630_26360 - Type: Gene
    Product:Putative membrane protein | Pathway: | COG: Function unknown
  • CD630_26420 - sigG Type: Gene
    Product:RNA polymerase sigma-G factor | Pathway: | COG: Transcription
  • CD630_26340 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_31750 - cggR Type: Gene
    Product:Transcriptional regulator, SorC family | Pathway: | COG: Transcription
  • CD630_26430 - sigE Type: Gene
    Product:RNA polymerase sigma-E factor | Pathway: | COG: Transcription
0.19 NA 0.60 Inferelator: 3
Hypergeometric: 2

TF Influences from Inferelator

  1. CD630_19100 - eutV Type: Gene
    Product:Two-component response regulator, Ethanolaminespecific | Pathway: | COG: Signal transduction mechanisms
  2. CD630_26400 - nrdR Type: Gene
    Product:Transcriptional regulator, repressor NrdR family | Pathway: | COG: Transcription
  3. CD630_31750 - cggR Type: Gene
    Product:Transcriptional regulator, SorC family | Pathway: | COG: Transcription

TF Influences from Hypergeometric Test

  1. CD630_32450 - prdR Type: Gene
    Product:Transcriptional regulator, sigma-54-dependent | Pathway: | COG: Transcription
  2. CD630_12140 - spo0A Type: Gene
    Product:Stage 0 sporulation protein A | Pathway: | COG: Signal transduction mechanisms
Module_406 21
  • CD630_33310 - Type: Gene
    Product:Putative conjugative transposon proteinTn916-like, CTn6-Orf7 | Pathway: | COG: Function unknown
  • CD630_14860 - Type: Gene
    Product:Putative ribosome recycling factor | Pathway: | COG:
  • CD630_09420 - Type: Gene
    Product:Putative phage protein | Pathway: | COG:
  • CD630_33930 - rumA Type: Gene
    Product:23S rRNA (uracil-5-)-methyltransferase RumA (23SrRNA(M-5-U1939)-methyltransferase) | Pathway: | COG: Translation, ribosomal structure and biogenesis
  • CD630_09410 - Type: Gene
    Product:Putative phage protein | Pathway: | COG: Function unknown
  • CD630_29190 - Type: Gene
    Product:Putative phage protein | Pathway: | COG:
  • CD630_31990 - Type: Gene
    Product:ABC-type transport system, multidrug-familypermease | Pathway: | COG: Function unknown
  • CD630_34540 - Type: Gene
    Product:Putative nucleotide-binding protein | Pathway: | COG: Function unknown
  • CD630_14850 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_30800 - Type: Gene
    Product:PTS system, lactose/cellobiose-family IIAcomponent | Pathway: | COG: Carbohydrate transport and metabolism
  • CD630_14281 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG:
  • CD630_14280 - Type: Gene
    Product:Transcriptional regulator, hxlR family | Pathway: | COG: Transcription
  • CD630_29230 - Type: Gene
    Product:Putative phage protein | Pathway: | COG: Function unknown
  • CD630_23040 - Type: Gene
    Product:Transcriptional regulator, beta-lactams repressorPhage-type | Pathway: | COG: Transcription
  • CD630_14290 - Type: Gene
    Product:Putative acyl-CoA N-acyltransferase | Pathway: | COG: Function unknown
  • CD630_31020 - Type: Gene
    Product:Putative peptidase, M20 family, peptidase Vrelated | Pathway: | COG: Amino acid transport and metabolism
  • CD630_29210 - Type: Gene
    Product:Putative phage portal protein | Pathway: | COG: Function unknown
  • CD630_25170 - Type: Gene
    Product:Transcriptional regulator, beta-lactamsrepressor | Pathway: | COG: Transcription
  • CD630_31010 - Type: Gene
    Product:PTS system, glucose-like IIBC component | Pathway: | COG: Carbohydrate transport and metabolism
  • CD630_09461 - Type: Gene
    Product:Putative phage protein | Pathway: | COG:
  • CD630_09460 - Type: Gene
    Product:Putative phage minor head protein | Pathway: | COG: Signal transduction mechanisms
0.00000000042 0.000000035 0.60 Inferelator: 1
Hypergeometric: 0

TF Influences from Inferelator

  1. 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_128 26
  • CD630_13120 - tlpB Type: Gene
    Product:Transposase-like protein B | Pathway: | COG: Replication, recombination and repair
  • CD630_25540 - tlpA Type: Gene
    Product:Transposase-like protein A | Pathway: | COG:
  • CD630_11550 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_15720 - tlpB Type: Gene
    Product:Transposase-like protein B | Pathway: | COG: Replication, recombination and repair
  • CD630_06810 - Type: Gene
    Product:Transporter, Major Facilitator Superfamily (MFS) | Pathway: | COG: Carbohydrate transport and metabolism
  • CD630_06052 - Type: Gene
    Product: | Pathway: | COG:
  • CD630_35210 - Type: Gene
    Product:Putative peptidase T, M20B family | Pathway: | COG: Amino acid transport and metabolism
  • CD630_15000 - tlpB Type: Gene
    Product:Transposase-like protein B | Pathway: | COG: Replication, recombination and repair
  • CD630_07080 - pepD Type: Gene
    Product:Peptidase D, aminoacyl-histidine dipeptidase | Pathway: | COG: Amino acid transport and metabolism
  • CD630_17190 - tlpB Type: Gene
    Product:Transposase-like protein B | Pathway: | COG: Replication, recombination and repair
  • CD630_07100 - Type: Gene
    Product:Conserved hypothetical protein, DUF523 family | Pathway: | COG: Translation, ribosomal structure and biogenesis
  • CD630_06790 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_16610 - tlpB Type: Gene
    Product:Transposase-like protein B | Pathway: | COG: Replication, recombination and repair
  • CD630_20440 - Type: Gene
    Product:Putative membrane protein | Pathway: | COG:
  • CD630_18210 - tlpB Type: Gene
    Product:Transposase-like protein B | Pathway: | COG: Replication, recombination and repair
  • CD630_25531 - tlpB Type: Gene
    Product:Transposase-like protein B | Pathway: | COG: Replication, recombination and repair
  • CD630_33670 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG:
  • CD630_11540 - cdPadR1 Type: Gene
    Product:Transcriptional regulator, PadR family | Pathway: | COG: Transcription
  • CD630_08980 - Type: Gene
    Product:Conserved hypothetical protein, DUF1846-family | Pathway: | COG: Function unknown
  • CD630_06800 - Type: Gene
    Product:Conserved hypothetical protein, DUF1486 family | Pathway: | COG: Function unknown
  • CD630_15710 - tlpA Type: Gene
    Product:Transposase-like protein A | Pathway: | COG:
  • CD630_07090 - mutS2 Type: Gene
    Product:DNA mismatch repair protein | Pathway: | COG: Replication, recombination and repair
  • CD630_06380 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_08170 - tlpB Type: Gene
    Product:Transposase-like protein B | Pathway: | COG: Replication, recombination and repair
  • CD630_16601 - tlpA Type: Gene
    Product:Transposase-like protein A | Pathway: | COG:
  • CD630_20450 - Type: Gene
    Product:Transcriptional regulator, HTH-type | Pathway: | COG: Transcription
4.3e-29 1.6e-21 0.60 Inferelator: 1
Hypergeometric: 0

TF Influences from Inferelator

  1. CD630_06830 - Type: Gene
    Product:Transcriptional regulator, LacI family | Pathway: | COG: Transcription

TF Influences from Hypergeometric Test

No TF Influences from the hypergeometric test
Module_258 28
  • CD630_01080 - nrdD Type: Gene
    Product:Anaerobic ribonucleoside triphosphate reductase | Pathway: | COG: Nucleotide transport and metabolism
  • CD630_24300 - Type: Gene
    Product:Transcriptional regulator, IclR family | Pathway: | COG: Transcription
  • CD630_18200 - ade Type: Gene
    Product:Adenine deaminase (Disrupted IStron) | Pathway: | COG: Nucleotide transport and metabolism, Nucleotide transport and metabolism
  • CD630_14990 - Type: Gene
    Product:Putative virulence factor, MviN family protein(Disrupted IStron) | Pathway: Cell wall biogenesis | COG: Signal transduction mechanisms, Signal transduction mechanisms
  • CD630_07420 - Type: Gene
    Product:Putative ethanolamine transporter | Pathway: | COG: Amino acid transport and metabolism
  • CD630_29900 - ssuB2 Type: Gene
    Product:ABC-type transport system, sulfonate-familyATP-binding protein | Pathway: | COG: Inorganic ion transport and metabolism
  • CD630_29920 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_26010 - Type: Gene
    Product:Two-component response regulator | Pathway: | COG: Signal transduction mechanisms
  • CD630_07400 - Type: Gene
    Product:Putative pyridoxal phosphate-dependentaminotransferase | Pathway: | COG: Amino acid transport and metabolism
  • CD630_27590 - Type: Gene
    Product:Transcriptional regulator, Rrf2 family | Pathway: | COG: Transcription
  • CD630_07160 - cooS Type: Gene
    Product:Bifunctional carbon monoxidedehydrogenase/acetyl-CoA synthase (CODH) | Pathway: | COG: Energy production and conversion
  • CD630_27570 - Type: Gene
    Product:Putative acyl transferase/phospholipase | Pathway: | COG: Function unknown
  • CD630_26750 - Type: Gene
    Product:Transcriptional regulator, LysR family | Pathway: | COG: Transcription
  • CD630_06880 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_27600 - Type: Gene
    Product:Putative signaling protein | Pathway: | COG: Signal transduction mechanisms
  • CD630_01090 - nrdG Type: Gene
    Product:Anaerobic ribonucleoside-triphosphatereductase-activating protein | Pathway: | COG: Posttranslational modification, protein turnover, chaperones
  • CD630_04400 - cwp27 Type: Gene
    Product:Putative cell wall binding protein | Pathway: | COG: Function unknown
  • CD630_29910 - ssuC2 Type: Gene
    Product:ABC-type transport system, sulfonate-familypermease | Pathway: | COG: Inorganic ion transport and metabolism
  • CD630_26000 - cstA Type: Gene
    Product:Carbon starvation protein, CstA | Pathway: | COG: Signal transduction mechanisms
  • CD630_29830 - Type: Gene
    Product:Putative Helix-Turn-Helix DNA-binding protein | Pathway: | COG: Transcription
  • CD630_26020 - Type: Gene
    Product:Two-component sensor histidine kinase | Pathway: | COG: Signal transduction mechanisms
  • CD630_07410 - glpK1 Type: Gene
    Product:Glycerol kinase (GK) | Pathway: Polyol metabolism | COG: Energy production and conversion
  • CD630_25910 - ltaE Type: Gene
    Product:Low specificity L-threonine aldolase | Pathway: | COG: Amino acid transport and metabolism
  • CD630_27580 - Type: Gene
    Product:Putative N6 adenine-specific DNAmethyltransferase, N12 class | Pathway: | COG: Defense mechanisms
  • CD630_29890 - ssuA2 Type: Gene
    Product:ABC-type transport system, sulfonate-familyextracellular solute-binding protein | Pathway: | COG: Inorganic ion transport and metabolism
  • CD630_07170 - Type: Gene
    Product:Bifunctional carbon monoxidedehydrogenase/acetyl-CoA synthase, accessory protein | Pathway: | COG: Cell cycle control, cell division, chromosome partitioning
  • CD630_09940 - Type: Gene
    Product:Putative serine-pyruvate aminotransferase | Pathway: | COG: Amino acid transport and metabolism
  • CD630_27560 - ptsH Type: Gene
    Product:PTS system, HPr protein | Pathway: | COG: Carbohydrate transport and metabolism
0.0000000038 NA 0.60 Inferelator: 2
Hypergeometric: 0

TF Influences from Inferelator

  1. CD630_16920 - Type: Gene
    Product:Transcriptional regulator, ArsR family | Pathway: | COG: Transcription
  2. CD630_23900 - Type: Gene
    Product:Transcriptional regulator, beta-lactamsrepressor | Pathway: | COG: Transcription

TF Influences from Hypergeometric Test

No TF Influences from the hypergeometric test