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 291 - 300 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_362 20
  • CD630_10960 - Type: Gene
    Product:ABC-type transport system, multidrug-familypermease Tn1549-like, CTn4-Orf29 | Pathway: | COG: Function unknown
  • CD630_10970 - Type: Gene
    Product:ABC-type transport system, multidrug-familyATP-binding protein Tn1549-like, CTn4-Orf28 | Pathway: | COG: Defense mechanisms
  • CD630_10950 - Type: Gene
    Product:ABC-type transport system, multidrug-familypermease Tn1549-like, CTn4-Orf30 | Pathway: | COG: Inorganic ion transport and metabolism
  • CD630_10991 - Type: Gene
    Product:Putative conjugative transposon proteinTn1549-like, CTn4-Orf25 | Pathway: | COG: Function unknown
  • CD630_10990 - Type: Gene
    Product:Two-component response regulator, Tn1549-like,CTn4-Orf26 | Pathway: | COG: Signal transduction mechanisms
  • CD630_03650 - Type: Gene
    Product:ABC-type transport system, multidrug-familypermease Tn916-like, CTn1-Orf10 | Pathway: | COG: Inorganic ion transport and metabolism
  • CD630_03760 - Type: Gene
    Product:Putative antirestriction protein Tn916-like,CTn1-Orf21 | Pathway: | COG: Function unknown
  • CD630_11180 - Type: Gene
    Product:Putative conjugative transposon proteinTn1549-like, CTn4-Orf1 | Pathway: | COG: Function unknown
  • CD630_03670 - Type: Gene
    Product:Two-component sensor histidine kinase,Tn916-like, CTn1-Orf12 | Pathway: | COG: Signal transduction mechanisms
  • CD630_03660 - Type: Gene
    Product:ABC-type transport system, multidrug-familyATP-binding protein Tn916-like, CTn1-Orf11 | Pathway: | COG: Defense mechanisms
  • CD630_03740 - Type: Gene
    Product:Putative ATPase Tn916-like, CTn1-Orf19 | Pathway: | COG: Function unknown
  • CD630_10980 - Type: Gene
    Product:Two-component sensor histidine kinase,Tn1549-like, CTn4-Orf27 | Pathway: | COG: Signal transduction mechanisms
  • CD630_11150 - Type: Gene
    Product:Putative conjugative transfer proteinTn1549-like, CTn4-Orf4 | Pathway: | COG: Intracellular trafficking, secretion, and vesicular transport
  • CD630_03770 - Type: Gene
    Product:Putative antirestriction protein Tn916-like,CTn1-Orf22 | Pathway: | COG: Function unknown
  • CD630_03700 - Type: Gene
    Product:Transcriptional regulator, HTH-type Tn916-like,CTn1-Orf15 | Pathway: | COG: Transcription
  • CD630_03680 - Type: Gene
    Product:Two-component response regulator, Tn916-like,CTn1-Orf13 | Pathway: | COG: Signal transduction mechanisms
  • CD630_03710 - Type: Gene
    Product:Putative conjugative transposon proteinTn916-like, CTn1-Orf16 | Pathway: | COG: Function unknown
  • CD630_11170 - Type: Gene
    Product:Putative conjugative transposon proteinTn1549-like, CTn4-Orf2 | Pathway: | COG: Function unknown
  • CD630_03730 - Type: Gene
    Product:Putative membrane protein Tn916-like, CTn1-Orf18 | Pathway: | COG: Function unknown
  • CD630_11160 - Type: Gene
    Product:Putative conjugative transposon proteinTn1549-like, CTn4-Orf3 | Pathway: | COG: Function unknown
5.4 NA 0.55 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_380 29
  • CD630_33980 - Type: Gene
    Product:Putative hydrolase, NUDIX family | Pathway: | COG: Replication, recombination and repair
  • CD630_36710 - spo0J Type: Gene
    Product:Stage 0 sporulation protein J, site-specificDNA-binding protein | Pathway: | COG: Transcription
  • CD630_36730 - Type: Gene
    Product:Putative stage 0 sporulation protein, DNA-bindingprotein Spo0J-like | Pathway: | COG: Transcription
  • CD630_17350 - Type: Gene
    Product:Putative hydrolase | Pathway: | COG: Function unknown
  • CD630_17370 - Type: Gene
    Product:Putative divalent ion symporter | Pathway: | COG: Amino acid transport and metabolism, Carbohydrate transport and metabolism
  • CD630_05340 - cheC Type: Gene
    Product:Chemotaxis protein CheY-P phosphatase CheC | Pathway: | COG: Cell motility, Signal transduction mechanisms
  • CD630_08260 - Type: Gene
    Product:Putative ferric-uptake regulator | Pathway: | COG: Transcription
  • CD630_17390 - Type: Gene
    Product:Two-component response regulator, sigma-54dependent regulator | Pathway: | COG: Signal transduction mechanisms
  • CD630_05360 - cheW Type: Gene
    Product:Purine-binding chemotaxis protein CheW | Pathway: | COG: Cell motility, Signal transduction mechanisms
  • CD630_34010 - Type: Gene
    Product:putative phosphoesterase | Pathway: | COG: Replication, recombination and repair
  • CD630_33960 - dnaE Type: Gene
    Product:DNA polymerase III DnaE subunit alpha | Pathway: | COG: Replication, recombination and repair
  • CD630_05380 - Type: Gene
    Product:Putative methyl-accepting chemotaxis receptor,MCP family | Pathway: | COG: Inorganic ion transport and metabolism
  • CD630_25630 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_05420 - Type: Gene
    Product:Putative protein-glutamate methylesterase | Pathway: | COG: Signal transduction mechanisms
  • CD630_36720 - soj Type: Gene
    Product:Transcriptional regulator, sporulation initiationinhibitor, chromosome partitioning protein | Pathway: | COG: Cell cycle control, cell division, chromosome partitioning
  • CD630_05330 - cheY Type: Gene
    Product:Chemotaxis protein CheY | Pathway: | COG: Signal transduction mechanisms
  • CD630_36700 - Type: Gene
    Product:Putative cysteine desulfurase family protein | Pathway: | COG: Amino acid transport and metabolism
  • CD630_33990 - Type: Gene
    Product:Conserved hypothetical protein, UPF0052 family | Pathway: | COG: Function unknown
  • CD630_25640 - Type: Gene
    Product:Transcriptional regulator, MerR family | Pathway: | COG: Transcription
  • CD630_17360 - Type: Gene
    Product:Transcriptional regulator, HTH-type | Pathway: | COG: Transcription
  • CD630_17380 - Type: Gene
    Product:Two-component sensor histidine kinase | Pathway: | COG: Signal transduction mechanisms
  • CD630_05350 - cheD Type: Gene
    Product:Probable chemoreceptor glutamine deamidase CheD | Pathway: | COG: Cell motility, Signal transduction mechanisms
  • CD630_34000 - Type: Gene
    Product:Conserved hypothetical protein, UPF0042 family | Pathway: | COG: Function unknown
  • CD630_05370 - Type: Gene
    Product:Putative CheY-like chemosensory protein | Pathway: | COG: Signal transduction mechanisms
  • CD630_08270 - rbo Type: Gene
    Product:Rubredoxin oxidoreductase (desulfoferrodoxin) | Pathway: | COG: Energy production and conversion
  • CD630_33970 - whiA Type: Gene
    Product:Putative sporulation transcription regulatorwhiA | Pathway: | COG: Transcription
  • CD630_05390 - cheA Type: Gene
    Product:Chemotaxis protein CheA | Pathway: | COG: Signal transduction mechanisms
  • CD630_05410 - cheR Type: Gene
    Product:Methyl-accepting chemotaxis proteinsmethyltransferase, MCP family | Pathway: | COG: Signal transduction mechanisms
  • CD630_34020 - murB Type: Gene
    Product:UDP-N-acetylenolpyruvoylglucosamine reductase | Pathway: Cell wall biogenesis | COG: Cell wall/membrane/envelope biogenesis
0 NA 0.55 Inferelator: 2
Hypergeometric: 1

TF Influences from Inferelator

  1. CD630_08260 - Type: Gene
    Product:Putative ferric-uptake regulator | Pathway: | COG: Transcription
  2. CD630_17980 - Type: Gene
    Product:Transcriptional regulator, LysR 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_332 21
  • CD630_06660 - cdd3 Type: Gene
    Product:ABC-type transport system,lantibiotic/multidrug-family permease | Pathway: | COG: Function unknown
  • CD630_31910 - Type: Gene
    Product:Putative oxidoreductase | Pathway: | COG: Energy production and conversion
  • CD630_01230 - murA Type: Gene
    Product:UDP-N-acetylglucosamine1-carboxyvinyltransferase | Pathway: Cell wall biogenesis | COG: Cell wall/membrane/envelope biogenesis
  • CD630_01420 - Type: Gene
    Product:Putative RNA-binding protein | Pathway: | COG: Translation, ribosomal structure and biogenesis
  • CD630_06650 - cdd2 Type: Gene
    Product:ABC-type transport system,lantibiotic/multidrug-family permease | Pathway: | COG: Function unknown
  • CD630_06690 - Type: Gene
    Product:Two-component sensor histidine kinase | Pathway: | COG: Signal transduction mechanisms
  • CD630_01220 - Type: Gene
    Product:Putative exported protein | Pathway: | COG: Function unknown
  • CD630_00220 - fusA1 Type: Gene
    Product:Elongation factor G (EF-G) | Pathway: | COG: Translation, ribosomal structure and biogenesis
  • CD630_31890 - Type: Gene
    Product:Putative NADPH-dependent FMN reductase | Pathway: | COG: Function unknown
  • CD630_24440 - Type: Gene
    Product:Putative ribosome-associated sigma 54 modulationprotein | Pathway: | COG: Translation, ribosomal structure and biogenesis
  • CD630_01430 - secA1 Type: Gene
    Product:Protein translocase subunit SecA1 | Pathway: | COG: Intracellular trafficking, secretion, and vesicular transport
  • CD630_24370 - era Type: Gene
    Product:GTP-binding protein Era | Pathway: | COG: Cell wall/membrane/envelope biogenesis
  • CD630_31900 - Type: Gene
    Product:Transcriptional regulator, MerR family | Pathway: | COG: Transcription
  • CD630_21100 - Type: Gene
    Product:Putative transaldolaseC-like | Pathway: Carbohydrate degradation | COG: Carbohydrate transport and metabolism
  • CD630_01440 - prfB Type: Gene
    Product:Peptide chain release factor 2 (RF-2) | Pathway: | COG: Translation, ribosomal structure and biogenesis
  • CD630_22150 - SinR Type: Gene
    Product:Transcriptional regulator, HTH-type | Pathway: | COG: Transcription
  • CD630_22140 - SinR Type: Gene
    Product:Transcriptional regulator, HTH-type | Pathway: | COG: Transcription
  • CD630_21580 - gabT Type: Gene
    Product:4-aminobutyrate aminotransferase | Pathway: | COG: Amino acid transport and metabolism
  • CD630_24380 - cdd Type: Gene
    Product:Cytidine deaminase (Cytidine aminohydrolase)(CDA) | Pathway: | COG: Nucleotide transport and metabolism
  • CD630_24350 - recO Type: Gene
    Product:DNA repair protein RecO (Recombination proteinO) | Pathway: | COG: Replication, recombination and repair
  • CD630_24340 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
0.000000000052 5.8 0.55 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_348 34
  • CD630_13780 - Type: Gene
    Product:Transcriptional regulator, Phage-type | Pathway: | COG: Transcription
  • CD630_31540 - Type: Gene
    Product:Transcriptional regulator, Phage-type | Pathway: | COG: Transcription
  • CD630_31560 - Type: Gene
    Product:phage integrase | Pathway: | COG: Replication, recombination and repair
  • CD630_08890 - speH Type: Gene
    Product:S-adenosylmethionine decarboxylase proenzyme | Pathway: Amine and polyamine biosynthesis | COG: Amino acid transport and metabolism
  • CD630_13940 - Type: Gene
    Product:Putative NAD(P)-binding oxidoreductase,GFO/IDH/MOCA family | Pathway: | COG: Function unknown
  • CD630_05480 - Type: Gene
    Product:Putative penicillin-binding peptidase BlaR1-like,M56 family | Pathway: | COG: Transcription, Signal transduction mechanisms
  • CD630_17220 - Type: Gene
    Product:Putative transcriptional regulator | Pathway: | COG:
  • CD630_15060 - Type: Gene
    Product:Putative drug/sodium antiporter, MATE family | Pathway: | COG: Defense mechanisms
  • CD630_11260 - Type: Gene
    Product:Transcriptional regulator, AraC family | Pathway: | COG: Transcription
  • CD630_16210 - Type: Gene
    Product:Putative mechanosensitive ion channel protein,MscS family | Pathway: | COG: Cell wall/membrane/envelope biogenesis
  • CD630_03330 - ppaC Type: Gene
    Product:Putative inorganic pyrophosphatase | Pathway: | COG: Energy production and conversion
  • CD630_15040 - Type: Gene
    Product:ABC-type transport system, multidrug-familyATP-binding protein | Pathway: | COG: Defense mechanisms
  • CD630_23470 - Type: Gene
    Product:Putative Xaa-Pro dipeptidase | Pathway: | COG: Amino acid transport and metabolism
  • CD630_14620 - Type: Gene
    Product:Transcriptional regulator, GntR family | Pathway: | COG: Transcription
  • CD630_24780 - Type: Gene
    Product:Putative DNA uptake transporter | Pathway: | COG: Cell wall/membrane/envelope biogenesis
  • CD630_05930 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_20420 - Type: Gene
    Product:Transcriptional regulator, TetR family | Pathway: | COG: Transcription
  • CD630_15050 - Type: Gene
    Product:ABC-type transport system, multidrug-familypermease | Pathway: | COG:
  • CD630_08900 - speE Type: Gene
    Product:Spermidine synthase | Pathway: Amine and polyamine biosynthesis | COG: Amino acid transport and metabolism
  • CD630_31550 - Type: Gene
    Product:Putative Fic/Doc-related protein | Pathway: | COG: Function unknown
  • CD630_20280 - Type: Gene
    Product:Putative aspartate racemase RacX | Pathway: | COG: Amino acid transport and metabolism
  • CD630_08880 - speA Type: Gene
    Product:Arginine decarboxylase | Pathway: | COG: Amino acid transport and metabolism
  • CD630_05490 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG:
  • CD630_17210 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_17230 - Type: Gene
    Product:Putative acyltransferase | Pathway: | COG: Lipid transport and metabolism
  • CD630_16590 - Type: Gene
    Product:Cation-transporting ATPase | Pathway: | COG: Inorganic ion transport and metabolism
  • CD630_15030 - Type: Gene
    Product:Transcriptional regulator, GntR family | Pathway: | COG: Transcription
  • CD630_15690 - Type: Gene
    Product:Transcriptional regulator, MarR family | Pathway: | COG: Transcription
  • CD630_17930 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_05470 - Type: Gene
    Product:Transcriptional regulator, beta-lactamsrepressor | Pathway: | COG: Transcription
  • CD630_17660 - Type: Gene
    Product:Putative lipoprotein | Pathway: | COG:
  • CD630_08910 - speB Type: Gene
    Product:Agmatinase (Agmatine ureohydrolase) (AUH) | Pathway: | COG: Amino acid transport and metabolism
  • CD630_07110 - argS Type: Gene
    Product:Arginyl-tRNA synthetase (Arginine--tRNA ligase)(ArgRS) | Pathway: | COG: Translation, ribosomal structure and biogenesis
0.00000039 NA 0.55 Inferelator: 2
Hypergeometric: 0

TF Influences from Inferelator

  1. CD630_06110 - Type: Gene
    Product:Two-component response regulator | Pathway: | COG: Signal transduction mechanisms
  2. CD630_19100 - eutV Type: Gene
    Product:Two-component response regulator, Ethanolaminespecific | Pathway: | COG: Signal transduction mechanisms

TF Influences from Hypergeometric Test

No TF Influences from the hypergeometric test
Module_401 21
  • CD630_06880 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_32470 - prdC Type: Gene
    Product:Putative electron transfer protein | Pathway: | COG: Energy production and conversion
  • CD630_19340 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_30180 - Type: Gene
    Product:Putative redox-active protein | Pathway: | COG: Function unknown
  • CD630_19330 - Type: Gene
    Product:Putative membrane protein | Pathway: | COG: Function unknown
  • CD630_30190 - Type: Gene
    Product:Putative transporter | Pathway: | COG: Inorganic ion transport and metabolism
  • CD630_26210 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_22070 - Type: Gene
    Product:Putative flavodoxin | Pathway: | COG: Function unknown
  • CD630_15111 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG:
  • CD630_06820 - Type: Gene
    Product:Putative sodium:solute symporter | Pathway: | COG: Amino acid transport and metabolism
  • CD630_12890 - Type: Gene
    Product:Ribonuclease J family protein | Pathway: | COG: Posttranslational modification, protein turnover, chaperones
  • CD630_00650 - Type: Gene
    Product:Putative NADP-dependent deshydrogenase | Pathway: | COG: Function unknown
  • CD630_16671 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG:
  • CD630_22090 - Type: Gene
    Product:Putative GTP-binding protein, HflX type | Pathway: | COG: Function unknown
  • CD630_08040 - etfB Type: Gene
    Product:Electron transfer flavoprotein beta-subunit,core | Pathway: | COG: Energy production and conversion
  • CD630_04030 - fba Type: Gene
    Product:Fructose-1,6-bisphosphate aldolase | Pathway: | COG: Carbohydrate transport and metabolism
  • CD630_08020 - Type: Gene
    Product:Putative CoA-transferase, family III | Pathway: | COG: Energy production and conversion
  • CD630_22080 - Type: Gene
    Product:Transcriptional regulator, MarR family | Pathway: | COG: Transcription
  • CD630_27680 - Type: Gene
    Product:Putative cell-wall hydrolase | Pathway: | COG: Cell wall/membrane/envelope biogenesis
  • CD630_06830 - Type: Gene
    Product:Transcriptional regulator, LacI family | Pathway: | COG: Transcription
  • CD630_26620 - Type: Gene
    Product:Putative GTP-binding protein | Pathway: | COG: Translation, ribosomal structure and biogenesis
0.00000000016 NA 0.55 Inferelator: 2
Hypergeometric: 0

TF Influences from Inferelator

  1. CD630_17820 - Type: Gene
    Product:Two-component response regulator | Pathway: | COG: Signal transduction mechanisms
  2. CD630_19310 - lexA Type: Gene
    Product:Transcriptional regulator, LexA repressor | Pathway: | COG: Transcription

TF Influences from Hypergeometric Test

No TF Influences from the hypergeometric test
Module_116 6
  • CD630_06740 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG:
  • CD630_13380 - Type: Gene
    Product:Putative 6-phospho-beta-glucosidase | Pathway: | COG: Carbohydrate transport and metabolism
  • CD630_07141 - Type: Gene
    Product:Fragment of sugar O-acetyltransferase (C-terminalregion) | Pathway: | COG: Function unknown
  • CD630_13370 - Type: Gene
    Product:Transcriptional regulator, RpiR family | Pathway: | COG: Transcription
  • CD630_06050 - Type: Gene
    Product:Fragment of conserved hypothetical protein(N-terminal region) | Pathway: | COG: Function unknown
NA NA 0.55 Inferelator: 1
Hypergeometric: 0

TF Influences from Inferelator

  1. CD630_13370 - Type: Gene
    Product:Transcriptional regulator, RpiR family | Pathway: | COG: Transcription

TF Influences from Hypergeometric Test

No TF Influences from the hypergeometric test
Module_353 24
  • CD630_21050 - Type: Gene
    Product:ABC-type transport system, multidrug-familyATP-binding protein | Pathway: | COG: Defense mechanisms
  • CD630_20410 - Type: Gene
    Product:Transcriptional regulator, HTH-type | Pathway: | COG: Transcription
  • CD630_21060 - Type: Gene
    Product:Putative ATP-dependent RNA helicase | Pathway: | COG: Replication, recombination and repair
  • CD630_31990 - Type: Gene
    Product:ABC-type transport system, multidrug-familypermease | Pathway: | COG: Function unknown
  • CD630_21040 - Type: Gene
    Product:ABC-type transport system, permease | Pathway: | COG: Function unknown
  • CD630_22240 - Type: Gene
    Product:Putative extrachromosomal origin protein | Pathway: | COG: Function unknown
  • CD630_27030 - Type: Gene
    Product:Putative pentapeptide repeat-containing protein | Pathway: | COG: Function unknown
  • CD630_09200 - Type: Gene
    Product:Putative phage protein | Pathway: | COG:
  • CD630_09220 - Type: Gene
    Product:Putative phage protein | Pathway: | COG:
  • CD630_09150 - Type: Gene
    Product:Putative phage protein | Pathway: | COG:
  • CD630_08060 - Type: Gene
    Product:Transcriptional regulator, sigma-54-dependent | Pathway: | COG: Transcription
  • CD630_09110 - Type: Gene
    Product:Transcriptional regulator, Phage-type | Pathway: | COG:
  • CD630_09130 - Type: Gene
    Product:Putative phage protein | Pathway: | COG:
  • CD630_32010 - Type: Gene
    Product:ABC-type transport system, multidrug-familyATP-binding protein | Pathway: | COG: Defense mechanisms
  • CD630_19270 - Type: Gene
    Product:Fragment of ABC-type transport system,ATP-binding protein (Part 2) | Pathway: | COG: Inorganic ion transport and metabolism
  • CD630_32000 - Type: Gene
    Product:ABC-type transport system, multidrug-familypermease | Pathway: | COG: Function unknown
  • CD630_22230 - Type: Gene
    Product:Putative extrachromosomal origin protein | Pathway: | COG: Function unknown
  • CD630_28181 - Type: Gene
    Product:Fragment of dihydrofolate reductase familyprotein | Pathway: | COG:
  • CD630_05060 - Type: Gene
    Product:Reverse transcriptase/maturase/endonuclease,Group II intron | Pathway: | COG: Replication, recombination and repair
  • CD630_09230 - Type: Gene
    Product:Putative phage protein | Pathway: | COG:
  • CD630_25930 - Type: Gene
    Product:ABC-type transport system,pristinamycin/multidrug-family ATP-binding protein | Pathway: | COG: Function unknown
  • CD630_09160 - Type: Gene
    Product:Putative phage protein involved in bacteriophageresistance | Pathway: | COG: Function unknown
  • CD630_09210 - Type: Gene
    Product:Putative phage protein | Pathway: | COG:
  • CD630_09140 - Type: Gene
    Product:Putative phage protein | Pathway: | COG:
0.00000000012 NA 0.55 Inferelator: 2
Hypergeometric: 0

TF Influences from Inferelator

  1. CD630_14550 - sigA1 Type: Gene
    Product:RNA polymerase sigma factor SigA1 (sigma-43) | 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_149 20
  • CD630_09960 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_20630 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG:
  • CD630_16530 - Type: Gene
    Product:Putative Probable D-methionine-bindinglipoprotein | Pathway: | COG: Inorganic ion transport and metabolism
  • CD630_14890 - metN Type: Gene
    Product:ABC-type transport system, methionine-specificATP-binding protein | Pathway: | COG: Inorganic ion transport and metabolism
  • CD630_14900 - metI Type: Gene
    Product:ABC-type transport system, methionine-specificpermease | Pathway: | COG: Inorganic ion transport and metabolism
  • CD630_20600 - Type: Gene
    Product:Putative lipid kinase | Pathway: | COG: Lipid transport and metabolism
  • CD630_20610 - Type: Gene
    Product:Conserved hypothetical protein, DUF1121 family | Pathway: | COG: Function unknown
  • CD630_28570 - Type: Gene
    Product:Putative hydrolase, HAD superfamily, IAsubfamily | Pathway: | COG: Translation, ribosomal structure and biogenesis
  • CD630_17740 - Type: Gene
    Product:ABC-type transport system, aminoacid-familyextracellular solute-binding protein | Pathway: | COG: Amino acid transport and metabolism
  • CD630_15820 - hisD Type: Gene
    Product:Histidinol dehydrogenase (HDH) | Pathway: Amino-acid biosynthesis | COG: Amino acid transport and metabolism
  • CD630_28560 - Type: Gene
    Product:Putative membrane protein | Pathway: | COG: Replication, recombination and repair
  • CD630_14910 - metQ Type: Gene
    Product:ABC-type transport system, methionine-specificsubstrate-binding lipoprotein | Pathway: | COG: Inorganic ion transport and metabolism
  • CD630_17750 - Type: Gene
    Product:ABC-type transport system, aminoacid-familypermease | Pathway: | COG: Amino acid transport and metabolism
  • CD630_20620 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_28580 - Type: Gene
    Product:Putative membrane protein | Pathway: | COG: Inorganic ion transport and metabolism
  • CD630_16520 - Type: Gene
    Product:Putative tellurium resistance protein | Pathway: | COG: Signal transduction mechanisms
  • CD630_09950 - serA Type: Gene
    Product:Putative D-3-phosphoglycerate dehydrogenase | Pathway: | COG: Amino acid transport and metabolism
  • CD630_23300 - xpt Type: Gene
    Product:Xanthine phosphoribosyltransferase (XPRTase) | Pathway: Purine metabolism | COG: Nucleotide transport and metabolism
  • CD630_23290 - tal Type: Gene
    Product:Transaldolase | Pathway: Carbohydrate degradation | COG: Carbohydrate transport and metabolism
  • CD630_17760 - Type: Gene
    Product:ABC-type transport system, aminoacid-familyATP-binding protein | Pathway: | COG: Amino acid transport and metabolism
0.0000000000000079 2.6 0.56 Inferelator: 1
Hypergeometric: 0

TF Influences from Inferelator

  1. CD630_06700 - Type: Gene
    Product:Transcriptional regulator, beta-lactamsrepressor | Pathway: | COG: Transcription

TF Influences from Hypergeometric Test

No TF Influences from the hypergeometric test
Module_21 29
  • CD630_04650 - Type: Gene
    Product:Transcriptional regulator, RpiR family | Pathway: | COG: Transcription
  • CD630_20690 - Type: Gene
    Product:Putative molybdopterin cofactor biosynthesisprotein | Pathway: Cofactor biosynthesis | COG: Coenzyme transport and metabolism
  • CD630_01700 - Type: Gene
    Product:ABC-type transport system, ATP-binding protein | Pathway: | COG: Function unknown
  • CD630_36730 - Type: Gene
    Product:Putative stage 0 sporulation protein, DNA-bindingprotein Spo0J-like | Pathway: | COG: Transcription
  • CD630_25130 - Type: Gene
    Product:Putative translation inhibitor endoribonuclease | Pathway: | COG: Translation, ribosomal structure and biogenesis
  • CD630_30350 - Type: Gene
    Product:Putative diaminopimelate epimerase, PhzF family | Pathway: | COG: Function unknown
  • CD630_32890 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_26130 - Type: Gene
    Product:Putative peptidase, M24 family | Pathway: | COG: Amino acid transport and metabolism
  • CD630_36710 - spo0J Type: Gene
    Product:Stage 0 sporulation protein J, site-specificDNA-binding protein | Pathway: | COG: Transcription
  • CD630_34780 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Posttranslational modification, protein turnover, chaperones
  • CD630_04690 - Type: Gene
    Product:PTS system, sucrose-specific IIABC component | Pathway: | COG: Carbohydrate transport and metabolism
  • CD630_20710 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_32870 - Type: Gene
    Product:Putative oxidoreductase, FAD dependent | Pathway: | COG: Function unknown
  • CD630_04670 - Type: Gene
    Product:Putative hydrolase, HAD superfamily, subfamilyIIB | Pathway: | COG: Function unknown
  • CD630_25140 - tdcB Type: Gene
    Product:Threonine dehydratase II | Pathway: | COG: Amino acid transport and metabolism
  • CD630_04660 - Type: Gene
    Product:Transcriptional regulator, RpiR family | Pathway: | COG: Transcription
  • CD630_36700 - Type: Gene
    Product:Putative cysteine desulfurase family protein | Pathway: | COG: Amino acid transport and metabolism
  • CD630_01710 - rex Type: Gene
    Product:Transcriptional regulator, Redox-sensingrepressor Rex | Pathway: | COG: Transcription
  • CD630_30340 - Type: Gene
    Product:Transcriptional regulator, TrmB family | Pathway: | COG: Transcription
  • CD630_01880 - Type: Gene
    Product:Putative ketopantoate reductase | Pathway: Cofactor biosynthesis | COG: Coenzyme transport and metabolism
  • CD630_32880 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG:
  • CD630_04680 - malL Type: Gene
    Product:oligo-1,6-glucosidase (Sucrase-isomaltase) | Pathway: | COG: Carbohydrate transport and metabolism
  • CD630_32860 - Type: Gene
    Product:Putative sodium:phosphate symporter | Pathway: | COG: Inorganic ion transport and metabolism
  • CD630_20700 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Posttranslational modification, protein turnover, chaperones
  • CD630_36720 - soj Type: Gene
    Product:Transcriptional regulator, sporulation initiationinhibitor, chromosome partitioning protein | Pathway: | COG: Cell cycle control, cell division, chromosome partitioning
  • CD630_32900 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_01690 - Type: Gene
    Product:Putative drug/sodium antiporter, MATE family | Pathway: | COG: Defense mechanisms
  • CD630_32840 - HtrA Type: Gene
    Product:High temperature requirement A protease | Pathway: | COG: Posttranslational modification, protein turnover, chaperones
  • CD630_08930 - Type: Gene
    Product:Putative iron-dependent hydrogenase | Pathway: | COG: Energy production and conversion
0.00000000067 0.00014 0.56 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_338 24
  • CD630_32260 - dapB1 Type: Gene
    Product:Dihydrodipicolinate reductase 1 (DHPR 1) | Pathway: Amino-acid biosynthesis | COG: Amino acid transport and metabolism
  • CD630_32240 - asd Type: Gene
    Product:Aspartate-semialdehyde dehydrogenase | Pathway: Amino-acid biosynthesis | COG: Amino acid transport and metabolism
  • CD630_36470 - licA Type: Gene
    Product:PTS system, lichenan-specific IIA component | Pathway: | COG: Carbohydrate transport and metabolism
  • CD630_06940 - Type: Gene
    Product:Transcriptional regulator, TetR family | Pathway: | COG: Transcription
  • CD630_21080 - Type: Gene
    Product:Putative drug/sodium antiporter, MATE family | Pathway: | COG: Defense mechanisms
  • CD630_02940 - Type: Gene
    Product:ABC-type transport system,bacitracin/multidrug-family permease | Pathway: | COG: Function unknown
  • CD630_15020 - deoC Type: Gene
    Product:Deoxyribose-phosphate aldolase(Phosphodeoxyriboaldolase) (Deoxyriboaldolase) (DERA) | Pathway: Carbohydrate degradation | COG: Nucleotide transport and metabolism
  • CD630_15740 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG: Function unknown
  • CD630_32720 - Type: Gene
    Product:Putative membrane 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_32250 - dapA3 Type: Gene
    Product:Dihydrodipicolinate synthase 3 | Pathway: Amino-acid biosynthesis | COG: Amino acid transport and metabolism
  • CD630_14390 - Type: Gene
    Product:Putative transporter, LrgA family | Pathway: | COG: Function unknown
  • CD630_32270 - dapH Type: Gene
    Product:2,3,4,5-tetrahydropyridine-2,6-dicarboxylateN-acetyltransferase | Pathway: Amino-acid biosynthesis | COG: Amino acid transport and metabolism
  • CD630_31660 - Type: Gene
    Product:Transcriptional regulator, hxlR family | Pathway: | COG: Transcription
  • CD630_36480 - licB Type: Gene
    Product:PTS system, lichenan-specific IIB component | Pathway: | COG: Carbohydrate transport and metabolism
  • CD630_06930 - Type: Gene
    Product:Transcriptional regulator, MerR family | Pathway: | COG: Transcription
  • CD630_14420 - Type: Gene
    Product:Putative MORN repeat-containing protein | Pathway: | COG: Function unknown
  • CD630_21090 - Type: Gene
    Product:Putative anion:Na+ symporter | Pathway: | COG: Function unknown
  • CD630_14400 - Type: Gene
    Product:Putative transporter, LrgB family | Pathway: | COG: Cell wall/membrane/envelope biogenesis
  • CD630_02930 - Type: Gene
    Product:ABC-type transport system,bacitracin/multidrug-family ATP-binding protein | Pathway: | COG: Defense mechanisms
  • CD630_30010 - Type: Gene
    Product:Putative hydrolase/isomerase/hydratase | Pathway: | COG: Secondary metabolites biosynthesis, transport and catabolism
  • CD630_32710 - Type: Gene
    Product:Conserved hypothetical protein | Pathway: | COG:
  • CD630_31930 - Type: Gene
    Product:Putative phage-related protein | Pathway: | COG: Function unknown
0.00000000000012 0.36 0.56 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