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 281 - 290 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'.

Title	Gene Count	Motif 1 e-value	Motif 2 e-value	Residual	TF Influences
Module_200	23 CD630_21700 - Type: Gene Product:Putative cNMP-binding regulatory protein \| Pathway: \| COG: Signal transduction mechanisms CD630_26600 - Type: Gene Product:Putative peptidase, M16 family \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_28660 - Type: Gene Product:Putative modulator of DNA gyrase, peptidase U62 \| Pathway: \| COG: Function unknown CD630_16310 - sodA Type: Gene Product:Spore coat protein, superoxide dismutase \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_23470 - Type: Gene Product:Putative Xaa-Pro dipeptidase \| Pathway: \| COG: Amino acid transport and metabolism CD630_23000 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_28680 - Type: Gene Product:Putative oxidoreductase \| Pathway: \| COG: Energy production and conversion CD630_17090 - mobA Type: Gene Product:Molybdopterin-guanine dinucleotide biosynthesisprotein A \| Pathway: \| COG: Coenzyme transport and metabolism CD630_21690 - Type: Gene Product:Putative iron-sulfur binding protein \| Pathway: \| COG: Energy production and conversion CD630_35780 - Type: Gene Product:Resolvase \| Pathway: \| COG: Replication, recombination and repair CD630_26610 - Type: Gene Product:Putative peptidase, M16 family \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_28670 - Type: Gene Product:Putative regulatory protease, U62 family \| Pathway: \| COG: Function unknown CD630_17100 - Type: Gene Product:Putative NAD(P)-binding protein \| Pathway: \| COG: Function unknown CD630_07820 - Type: Gene Product:Putative sporulation protein YunB \| Pathway: \| COG: Function unknown CD630_16300 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_16320 - asnB Type: Gene Product:Asparagine synthetase \| Pathway: \| COG: Amino acid transport and metabolism CD630_19840 - Type: Gene Product:Putative hydrolase, NUDIX family \| Pathway: \| COG: Replication, recombination and repair CD630_17080 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_23010 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_21680 - hcp Type: Gene Product:Hydroxylamine reductase \| Pathway: \| COG: Energy production and conversion CD630_07390 - Type: Gene Product:Putative exported protein \| Pathway: \| COG: CD630_35790 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_32040 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Intracellular trafficking, secretion, and vesicular transport	0.000000000021	0.0001	0.54	Inferelator: 4 Hypergeometric: 0 TF Influences from Inferelator CD630_12390 - Type: Gene Product:Transcriptional regulator, beta-lactams repressorPhage-type \| Pathway: \| COG: Transcription CD630_16860 - Type: Gene Product:Transcriptional regulator, repressor-like \| Pathway: \| COG: Transcription CD630_33530 - Type: Gene Product:Transcriptional regulator, GntR family \| Pathway: \| COG: Transcription 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_85	23 CD630_03230 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_31540 - Type: Gene Product:Transcriptional regulator, Phage-type \| Pathway: \| COG: Transcription CD630_03200 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms CD630_08890 - speH Type: Gene Product:S-adenosylmethionine decarboxylase proenzyme \| Pathway: Amine and polyamine biosynthesis \| COG: Amino acid transport and metabolism CD630_03220 - Type: Gene Product:Putative ATPase \| Pathway: \| COG: Function unknown CD630_03380 - Type: Gene Product:Two-component sensor histidine kinase \| Pathway: \| COG: Signal transduction mechanisms CD630_03160 - Type: Gene Product:ABC-type transport system, permease \| Pathway: \| COG: Function unknown CD630_08680 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_08710 - modC Type: Gene Product:ABC-type transport system, molybdenum-specificATP-binding protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_03190 - Type: Gene Product:Two-component sensor histidine kinase \| Pathway: \| COG: Signal transduction mechanisms CD630_03210 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown 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_03350 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_08880 - speA Type: Gene Product:Arginine decarboxylase \| Pathway: \| COG: Amino acid transport and metabolism CD630_03390 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms CD630_03170 - Type: Gene Product:ABC-type transport system, permease \| Pathway: \| COG: Function unknown CD630_08700 - modB Type: Gene Product:ABC-type transport system, molybdenum-specificpermease \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_08690 - modA Type: Gene Product:ABC-type transport system, molybdenum-specificextracellular solute-binding protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_08720 - maa Type: Gene Product:maltose O-acetyltransferase \| Pathway: \| COG: Amino acid transport and metabolism CD630_03180 - Type: Gene Product:ABC-type transport system,bacitracin/multidrug-family ATP-binding protein \| Pathway: \| COG: Defense mechanisms CD630_03360 - Type: Gene Product:ABC-type transport system, ATP-binding protein \| Pathway: \| COG: Defense mechanisms CD630_08910 - speB Type: Gene Product:Agmatinase (Agmatine ureohydrolase) (AUH) \| Pathway: \| COG: Amino acid transport and metabolism	0.18	0.03	0.55	Inferelator: 3 Hypergeometric: 0 TF Influences from Inferelator CD630_03200 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms CD630_30940 - Type: Gene Product:Transcriptional regulator, sigma-54-dependent \| Pathway: \| COG: Transcription CD630_33600 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_328	27 CD630_08370 - Type: Gene Product:Nitroreductase \| Pathway: \| COG: Function unknown CD630_30720 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_27930 - slpA Type: Gene Product:Precursor of the S-layer proteins \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_09820 - ubiA Type: Gene Product:Putative UbiA prenyltransferase \| Pathway: \| COG: Coenzyme transport and metabolism CD630_02740 - Type: Gene Product:Putative iron-containing alcohol dehydrogenase \| Pathway: \| COG: Energy production and conversion CD630_08340 - icd Type: Gene Product:Isocitrate dehydrogenase NAD-dependent \| Pathway: \| COG: Amino acid transport and metabolism CD630_20670 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_20630 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_09840 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_08320 - aksA Type: Gene Product:Trans-homoaconitate synthase \| Pathway: \| COG: Amino acid transport and metabolism CD630_22710 - Type: Gene Product:Transcription antiterminator, PTS operonregulator \| Pathway: \| COG: Transcription CD630_14590 - Type: Gene Product:Putative FMN-binding protein \| Pathway: \| COG: Nucleotide transport and metabolism CD630_27010 - Type: Gene Product:Putative lipoprotein \| Pathway: \| COG: Function unknown CD630_30410 - pepI Type: Gene Product:Proline iminopeptidase (Proline aminopeptidase)(PIP), peptidase S33 family \| Pathway: \| COG: Amino acid transport and metabolism CD630_30730 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_33030 - chrA Type: Gene Product:Chromate transport protein ChrA \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_09810 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: CD630_09850 - Type: Gene Product:Putative drug/sodium antiporter, MATE family \| Pathway: \| COG: Defense mechanisms CD630_01770 - cfa Type: Gene Product:Cyclopropane-fatty-acyl-phospholipid synthase \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_09830 - Type: Gene Product:Putative hydrolase, HAD superfamily, subfamilyIB \| Pathway: \| COG: Amino acid transport and metabolism CD630_08350 - Type: Gene Product:Transcriptional regulator, MarR family \| Pathway: \| COG: Transcription CD630_20620 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_27940 - cwp12 Type: Gene Product:Cell wall binding protein \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_08330 - acnB Type: Gene Product:Aconitate hydratase (Citrate hydro-lyase) \| Pathway: \| COG: Energy production and conversion CD630_28420 - Type: Gene Product:Nitrilase (carbon-nitrogen hydrolase) \| Pathway: \| COG: Function unknown CD630_22720 - Type: Gene Product:Putative protein-tyrosine phosphatase \| Pathway: \| COG: Signal transduction mechanisms CD630_34040 - cls Type: Gene Product:Cardiolipin synthetase (Cardiolipin synthase) (CLsynthase) \| Pathway: \| COG: Lipid transport and metabolism	0.00000000000016	0.26	0.55	Inferelator: 3 Hypergeometric: 1 TF Influences from Inferelator CD630_16920 - Type: Gene Product:Transcriptional regulator, ArsR family \| Pathway: \| COG: Transcription CD630_17820 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms CD630_22200 - Type: Gene Product:Putative cyclic nucleotides-binding protein \| Pathway: \| COG: Signal transduction mechanisms TF Influences from Hypergeometric Test CD630_10640 - ccpA Type: Gene Product:Transcriptional regulator, LacI family \| Pathway: \| COG: Transcription
Module_102	26 CD630_26450 - Type: Gene Product:ABC-type transport system, sugar-familyextracellular solute-binding protein \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_05560 - Type: Gene Product:Putative sugar isomerase / endonuclease \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_32950 - pilC Type: Gene Product:Type IV pilus secretion protein \| Pathway: \| COG: Intracellular trafficking, secretion, and vesicular transport CD630_05520 - prsW Type: Gene Product:Site-1 protease \| Pathway: \| COG: Function unknown CD630_05540 - sip2 Type: Gene Product:Signal peptidase type I \| Pathway: \| COG: Intracellular trafficking, secretion, and vesicular transport CD630_32970 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_32930 - pilMN Type: Gene Product:Type IV pilus assembly protein \| Pathway: \| COG: Function unknown CD630_32910 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_33320 - Type: Gene Product:Transcriptional regulator, TetR family;Tn916-like, CTn6-Orf8 \| Pathway: \| COG: Transcription CD630_05570 - Type: Gene Product:Putative uridine kinase \| Pathway: \| COG: Nucleotide transport and metabolism CD630_32940 - pilA Type: Gene Product:Type IV pilus protein PilA \| Pathway: \| COG: Intracellular trafficking, secretion, and vesicular transport CD630_05550 - sip2 Type: Gene Product:Signal peptidase type I \| Pathway: \| COG: Intracellular trafficking, secretion, and vesicular transport CD630_32960 - pilB Type: Gene Product:Type IV pilus transporter system, ATP-binding \| Pathway: \| COG: Intracellular trafficking, secretion, and vesicular transport CD630_05530 - Type: Gene Product:Putative RNA methyltransferase \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_32920 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_33330 - Type: Gene Product:Putative conjugative transposon proteinTn916-like, CTn6-Orf9 \| Pathway: \| COG: Transcription	`NA`	`NA`	0.55	Inferelator: 1 Hypergeometric: 0 TF Influences from Inferelator 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_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 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 CD630_08260 - Type: Gene Product:Putative ferric-uptake regulator \| Pathway: \| COG: Transcription CD630_17980 - Type: Gene Product:Transcriptional regulator, LysR family \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test 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 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 CD630_06110 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms 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_93	25 CD630_31200 - Type: Gene Product:Transcriptional regulator, AbrB family \| Pathway: \| COG: Transcription CD630_31201 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_24160 - Type: Gene Product:Transcription antiterminator, PTS operonregulator \| Pathway: \| COG: Transcription CD630_24140 - Type: Gene Product:PTS system, Sorbitol-like IIA component(Glucitol) \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_r0130 - 16s_rRNA Type: Gene Product: \| Pathway: \| COG: CD630_24850 - Type: Gene Product:Putative Xaa-Pro aminopeptidase, M24 family \| Pathway: \| COG: Amino acid transport and metabolism CD630_12130 - spoIVB Type: Gene Product:Stage IV sporulation protein B, peptidase S55family \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_31190 - Type: Gene Product:Putative UDP-glycosyltransferase, MGT subfamily \| Pathway: \| COG: Energy production and conversion, Carbohydrate transport and metabolism CD630_r0250 - 23s_rRNA Type: Gene Product: \| Pathway: \| COG: CD630_25560 - Type: Gene Product:PTS system, fructose/mannitol-family IIABcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_17940 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_24150 - Type: Gene Product:Putative sorbitol-like operon activator protein(Glucitol) \| Pathway: \| COG: CD630_24130 - Type: Gene Product:Putative NAD(P)-binding protein \| Pathway: \| COG: Amino acid transport and metabolism CD630_36160 - Type: Gene Product:Na(+)/H(+) antiporter \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_31210 - Type: Gene Product:Putative flavodoxin/nitric oxide synthase \| Pathway: \| COG: Energy production and conversion CD630_31230 - Type: Gene Product:Putative nitroreductase \| Pathway: \| COG: Energy production and conversion CD630_21340 - Type: Gene Product:Putative signaling protein \| Pathway: \| COG: Signal transduction mechanisms CD630_24840 - Type: Gene Product:Putative pyridoxal phosphate-dependenttransferase \| Pathway: \| COG: Amino acid transport and metabolism CD630_25550 - Type: Gene Product:PTS system, fructose/mannitol-family IIBcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_02671 - Type: Gene Product:Putative flagellar protein \| Pathway: \| COG: CD630_30390 - Type: Gene Product:Putative ATPase \| Pathway: \| COG: Function unknown CD630_14710 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_17950 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_31220 - Type: Gene Product:Transcriptional regulator, ArsR family \| Pathway: \| COG: Transcription CD630_36150 - Type: Gene Product:Transcriptional regulator, MerR family \| Pathway: \| COG: Transcription	0.00000044	1.4	0.55	Inferelator: 3 Hypergeometric: 0 TF Influences from Inferelator CD630_02760 - Type: Gene Product:Transcriptional regulator, AraC family \| Pathway: \| COG: Transcription CD630_22140 - SinR Type: Gene Product:Transcriptional regulator, HTH-type \| Pathway: \| COG: Transcription 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_157	23 CD630_34280 - cbiE Type: Gene Product:Cobalt-precorrin-6Y C(5)-methyltransferase(Cobalt-precorrin-6 methyltransferase) (Cobalt-precorrin-6Ymethylase) \| Pathway: \| COG: Coenzyme transport and metabolism CD630_16180 - Type: Gene Product:ABC-type transport system, multidrug-familyATP-binding protein \| Pathway: \| COG: Defense mechanisms CD630_34180 - sirC Type: Gene Product:Precorrin-2 dehydrogenase \| Pathway: Porphyrin-containing compound metabolism \| COG: Coenzyme transport and metabolism CD630_34350 - cobQ Type: Gene Product:Cobyric acid synthase CobQ \| Pathway: Cofactor biosynthesis \| COG: Coenzyme transport and metabolism CD630_33550 - Type: Gene Product:Putative nitroreductase \| Pathway: \| COG: Energy production and conversion CD630_34230 - cbiJ Type: Gene Product:Cobalt-precorrin-6A reductase \| Pathway: \| COG: Coenzyme transport and metabolism CD630_34250 - cbiG Type: Gene Product:Cobalamin biosynthesis protein CbiG \| Pathway: \| COG: Coenzyme transport and metabolism CD630_29980 - Type: Gene Product:ABC-type transport system, iron-family permease \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_34330 - cbiB Type: Gene Product:Cobalamin biosynthesis protein CbiB, CobD/CbiBfamily \| Pathway: Cofactor biosynthesis \| COG: Coenzyme transport and metabolism CD630_34310 - Type: Gene Product:Putative cobalamin biosynthesis L-threoninePduX-like kinase \| Pathway: \| COG: Secondary metabolites biosynthesis, transport and catabolism CD630_04760 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_04750 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Replication, recombination and repair CD630_16190 - Type: Gene Product:ABC-type transport system, multidrug-familypermease \| Pathway: \| COG: Function unknown CD630_34260 - cbiF Type: Gene Product:Cobalt-precorrin-4 C(11)-methyltransferase(Cobalt-precorrin-3 methylase) \| Pathway: \| COG: Coenzyme transport and metabolism CD630_29970 - Type: Gene Product:ABC-type transport system, iron-familyATP-binding protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_34340 - cobB Type: Gene Product:Cobyrinic acid A,C-diamide synthase \| Pathway: Cofactor biosynthesis \| COG: Coenzyme transport and metabolism CD630_29990 - Type: Gene Product:ABC-type transport system, iron-familyextracellular solute-binding protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_34300 - cbiC Type: Gene Product:Cobalt-precorrin-8X methylmutase(Cobalt-precorrin isomerase) (HBA synthase) \| Pathway: \| COG: Coenzyme transport and metabolism CD630_16170 - Type: Gene Product:Transcriptional regulator, GntR family \| Pathway: \| COG: Transcription CD630_34240 - cbiH Type: Gene Product:Cobalt-precorrin-3B C(17)-methyltransferase(Cobalt-precorrin-3 methyltransferase) (Cobalt-precorrin-3methylase) \| Pathway: \| COG: Coenzyme transport and metabolism CD630_34320 - cobD Type: Gene Product:Threonine-phosphate decarboxylase(L-threonine-O-3-phosphate decarboxylase), CobD/CbiBfamily \| Pathway: \| COG: Amino acid transport and metabolism CD630_34220 - cbiK Type: Gene Product:Sirohydrochlorin cobaltochelatase \| Pathway: \| COG: Coenzyme transport and metabolism CD630_01810 - Type: Gene Product:Putative membrane-associated metalloprotease, M56family \| Pathway: \| COG: Transcription, Signal transduction mechanisms	0.14	`NA`	0.55	Inferelator: 2 Hypergeometric: 0 TF Influences from Inferelator CD630_11770 - fapR Type: Gene Product:Transcriptional regulator, DeoR family (Fattyacid and phospholipid biosynthesis regulator) \| Pathway: \| COG: Transcription 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`