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 121 - 130 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_162	20 CD630_09430 - Type: Gene Product:Putative phage DNA-binding protein \| Pathway: \| COG: Function unknown CD630_36260 - Type: Gene Product:Putative 4-hydroxy-2-oxoglutarate aldolase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_36300 - Type: Gene Product:PTS system, fructose/mannitol-family IIBcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_28970 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: Function unknown CD630_36310 - Type: Gene Product:Transcription antiterminator, PTS operonregulator \| Pathway: \| COG: Transcription CD630_29020 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: Function unknown CD630_36290 - Type: Gene Product:PTS system, fructose/mannitol-family IICcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_28960 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: Function unknown CD630_36430 - Type: Gene Product:Dihydroorotase \| Pathway: \| COG: Function unknown CD630_36420 - Type: Gene Product:Putative selenocysteine synthase \| Pathway: \| COG: Amino acid transport and metabolism CD630_09440 - Type: Gene Product:Putative phage terminase, large subunit \| Pathway: \| COG: Replication, recombination and repair CD630_29070 - Type: Gene Product:Putative phage lipoprotein \| Pathway: \| COG: Function unknown CD630_28990 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: Function unknown CD630_36280 - Type: Gene Product:Putative phosphosugar isomerase \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_09450 - Type: Gene Product:Putative phage portal protein \| Pathway: \| COG: Function unknown CD630_36440 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_36410 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_36270 - dapA4 Type: Gene Product:Dihydrodipicolinate synthase 4 (DHDPS) \| Pathway: Amino-acid biosynthesis \| COG: Amino acid transport and metabolism CD630_29000 - Type: Gene Product:Putative phage tail protein \| Pathway: \| COG: Function unknown CD630_29060 - Type: Gene Product:Putative phage protein \| Pathway: \| COG:	0.02	`NA`	0.37	Inferelator: 2 Hypergeometric: 0 TF Influences from Inferelator CD630_02760 - Type: Gene Product:Transcriptional regulator, AraC family \| Pathway: \| COG: Transcription CD630_36390 - Type: Gene Product:Transcriptional regulator, LysR family \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_82	31 CD630_21210 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_30370 - Type: Gene Product:Transcriptional regulator, CarD family \| Pathway: \| COG: Transcription CD630_14960 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_24590 - Type: Gene Product:Putative glucokinase, ROK family \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_28330 - Type: Gene Product:Putative calcium-transporting ATPase \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_34630 - alr2 Type: Gene Product:Alanine racemase 2 \| Pathway: Amino-acid biosynthesis \| COG: Cell wall/membrane/envelope biogenesis CD630_26290 - spoIVA Type: Gene Product:Stage IV sporulation protein A \| Pathway: \| COG: Function unknown CD630_35190 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_35210 - Type: Gene Product:Putative peptidase T, M20B family \| Pathway: \| COG: Amino acid transport and metabolism CD630_06670 - cdd4 Type: Gene Product:ABC-type transport system,lantibiotic/multidrug-family ATP-binding protein \| Pathway: \| COG: Defense mechanisms CD630_14330 - cotE Type: Gene Product:Spore coat protein CotE; peroxiredoxin/chitinase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_34620 - Type: Gene Product:Putative antitoxin EndoAI \| Pathway: \| COG: Transcription CD630_01060 - cwlD Type: Gene Product:Germination-specific N-acetylmuramoyl-L-alanineamidase, Autolysin \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_14030 - Type: Gene Product:Putative synthetase \| Pathway: \| COG: Secondary metabolites biosynthesis, transport and catabolism CD630_24090 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_05460 - Type: Gene Product:Putative membrane protein, DUF975 family \| Pathway: \| COG: Function unknown CD630_34660 - acpS Type: Gene Product:Holo-[acyl-carrier-protein] synthase \| Pathway: \| COG: Lipid transport and metabolism CD630_26560 - spoVD Type: Gene Product:Stage V sporulation protein D(Sporulation-specific penicillin-binding protein) \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_10670 - CdeC Type: Gene Product:Clostridium difficile exosporium cycteine-richprotein \| Pathway: \| COG: CD630_35220 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_21410 - Type: Gene Product:Serine-type D-Ala-D-Ala carboxypeptidase \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_35200 - Type: Gene Product:Putative cation efflux protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_24430 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_34640 - GerS Type: Gene Product:Lipoprotein regulator, germination \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_34570 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_15110 - cotB Type: Gene Product:Spore outer coat layer protein CotB \| Pathway: \| COG: Function unknown CD630_24450 - Type: Gene Product:Putative transmembrane signaling protein,TspO/MBR family \| Pathway: \| COG: Signal transduction mechanisms CD630_34610 - EndoA Type: Gene Product:Endoribonuclease toxin \| Pathway: \| COG: Signal transduction mechanisms CD630_18030 - cwp23 Type: Gene Product:Putative cell wall-binding protein \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_34650 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_26570 - Type: Gene Product:Putative lipoprotein \| Pathway: \| COG:	0.0000000013	`NA`	0.39	Inferelator: 1 Hypergeometric: 2 TF Influences from Inferelator CD630_34990 - spoVT Type: Gene Product:Stage V sporulation protein T \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test CD630_12140 - spo0A Type: Gene Product:Stage 0 sporulation protein A \| Pathway: \| COG: Signal transduction mechanisms CD630_26430 - sigE Type: Gene Product:RNA polymerase sigma-E factor \| Pathway: \| COG: Transcription
Module_2	22 CD630_31460 - Type: Gene Product:Fragment of putative sortase B (Part 1) \| Pathway: \| COG: Intracellular trafficking, secretion, and vesicular transport CD630_30620 - Type: Gene Product:Transcriptional regulator, RpiR family \| Pathway: \| COG: Transcription CD630_30530 - Type: Gene Product:Two-component sensor histidine kinase \| Pathway: \| COG: Signal transduction mechanisms CD630_04020 - Type: Gene Product:Transcriptional regulator, sigma-54-dependent \| Pathway: \| COG: Transcription CD630_08990 - dinB Type: Gene Product:DNA polymerase IV (Pol IV) \| Pathway: \| COG: Replication, recombination and repair CD630_30940 - Type: Gene Product:Transcriptional regulator, sigma-54-dependent \| Pathway: \| COG: Transcription CD630_28410 - Type: Gene Product:Putative amidohydrolase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_16210 - Type: Gene Product:Putative mechanosensitive ion channel protein,MscS family \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_06290 - Type: Gene Product:Transcriptional regulator, Crp family \| Pathway: \| COG: Transcription CD630_09490 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_16630 - guaD Type: Gene Product:Guanine deaminase (Guanase) (Guanine aminase)(Guanine aminohydrolase) (GAH) \| Pathway: \| COG: Nucleotide transport and metabolism CD630_09060 - Type: Gene Product:Putative phage DNA-binding protein \| Pathway: \| COG: CD630_19650 - Type: Gene Product:Putative permease \| Pathway: \| COG: Function unknown CD630_15320 - Type: Gene Product:ABC-type transport system, ATP-binding protein \| Pathway: \| COG: Defense mechanisms CD630_30540 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms CD630_21260 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_29110 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: Function unknown CD630_08310 - Type: Gene Product:Putative ATP-dependent RNA helicase \| Pathway: \| COG: Replication, recombination and repair CD630_10800 - Type: Gene Product:Putative lipoprotein \| Pathway: \| COG: CD630_05790 - Type: Gene Product:Transcriptional regulator, TetR family \| Pathway: \| COG: Transcription CD630_31871 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_15330 - Type: Gene Product:ABC-type transport system, permease \| Pathway: \| COG: Defense mechanisms	0.0000000000000014	`NA`	0.63	Inferelator: 2 Hypergeometric: 0 TF Influences from Inferelator CD630_30540 - 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 TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_212	15 CD630_00840 - rplE Type: Gene Product:50S ribosomal protein L5 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00760 - rplB Type: Gene Product:50S ribosomal protein L2 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00880 - rpsE Type: Gene Product:30S ribosomal protein S5 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00881 - rpmD Type: Gene Product:50S ribosomal protein L30 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00680 - rpsL Type: Gene Product:30S ribosomal protein S12 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00941 - rpmJ Type: Gene Product:50S ribosomal protein L36 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00690 - rpsG Type: Gene Product:30S ribosomal protein S7 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00990 - rplQ Type: Gene Product:50S ribosomal protein L17 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00850 - rpsH Type: Gene Product:30S ribosomal protein S8 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00960 - rpsK Type: Gene Product:30S ribosomal protein S11 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00841 - rpsZ Type: Gene Product:30S ribosomal protein S14 type Z \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00710 - tuf Type: Gene Product:Elongation factor EFTu/EF1A (EF-Tu) \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00970 - rpsD Type: Gene Product:30S ribosomal protein S4 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00800 - rplP Type: Gene Product:50S ribosomal protein L16 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00801 - rpmC Type: Gene Product:50S ribosomal protein L29 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis	`NA`	`NA`	0.28	Inferelator: 0 Hypergeometric: 0 TF Influences from Inferelator `No TF influences from Inferelator` TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_331	21 CD630_16250 - vanS Type: Gene Product:Two-component sensor histidine kinase \| Pathway: \| COG: Signal transduction mechanisms CD630_02740 - Type: Gene Product:Putative iron-containing alcohol dehydrogenase \| Pathway: \| COG: Energy production and conversion CD630_06460 - Type: Gene Product:ABC-type transport system,lantibiotic/multidrug-family permease \| Pathway: \| COG: Function unknown CD630_16240 - vanR Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms CD630_08300 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_33250 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Energy production and conversion CD630_06440 - Type: Gene Product:Two-component sensor histidine kinase \| Pathway: \| COG: Signal transduction mechanisms CD630_22730 - Type: Gene Product:Putative sporulation integral membrane protein \| Pathway: \| COG: Function unknown CD630_r0080 - 23s_rRNA Type: Gene Product: \| Pathway: \| COG: CD630_29660 - adhE Type: Gene Product:Aldehyde-alcohol dehydrogenase \| Pathway: \| COG: Energy production and conversion CD630_30060 - Type: Gene Product:Alcohol dehydrogenase \| Pathway: \| COG: Energy production and conversion CD630_19580 - Type: Gene Product:Putative 4Fe-4S binding protein; putativeferredoxin; putative dehydrogenase; putative reductase \| Pathway: \| COG: Energy production and conversion CD630_08940 - Type: Gene Product:Putative iron-dependent hydrogenase \| Pathway: \| COG: Energy production and conversion CD630_16670 - Type: Gene Product:Putative maltose O-acetyltransferase \| Pathway: \| COG: Amino acid transport and metabolism CD630_23760 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_06430 - 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_16540 - Type: Gene Product:Putative lipoate-protein ligase \| Pathway: Protein modification \| COG: Coenzyme transport and metabolism CD630_00300 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_32500 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_20171 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG:	0.0000000013	`NA`	0.64	Inferelator: 2 Hypergeometric: 1 TF Influences from Inferelator CD630_16240 - vanR Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms CD630_17980 - Type: Gene Product:Transcriptional regulator, LysR family \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test CD630_32450 - prdR Type: Gene Product:Transcriptional regulator, sigma-54-dependent \| Pathway: \| COG: Transcription
Module_18	20 CD630_06890 - Type: Gene Product:Putative nucleotide phosphodiesterase \| Pathway: \| COG: Nucleotide transport and metabolism CD630_19870 - cwp28 Type: Gene Product:Putative cell wall binding protein \| Pathway: \| COG: Function unknown CD630_03910 - asnB Type: Gene Product:Asparagine synthetase [glutamine-hydrolyzing] \| Pathway: \| COG: Amino acid transport and metabolism CD630_32300 - bclA2 Type: Gene Product:Exosporium glycoprotein \| Pathway: \| COG: Function unknown CD630_15951 - Type: Gene Product:Ferredoxin \| Pathway: \| COG: Energy production and conversion CD630_07960 - Type: Gene Product:Transcriptional regulator, LacI family \| Pathway: \| COG: Transcription CD630_19060 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_24411 - Type: Gene Product:PhoH-like protein \| Pathway: \| COG: Signal transduction mechanisms CD630_32310 - hpt Type: Gene Product:Hypoxanthine phosphoribosyltransferase \| Pathway: Purine metabolism \| COG: Nucleotide transport and metabolism CD630_31590 - Type: Gene Product:Putative FemA-like peptidoglycan biosynthesisprotein \| Pathway: \| COG: Function unknown CD630_21520 - Type: Gene Product:Putative glutamyl-aminopeptidase, M42 family \| Pathway: \| COG: Amino acid transport and metabolism CD630_25370 - Type: Gene Product:Putative membrane-associated5'-nucleotidase/phosphoesterase \| Pathway: \| COG: Nucleotide transport and metabolism CD630_12590 - brnQ-1 Type: Gene Product:Branched chain amino acid transport systemcarrier protein \| Pathway: \| COG: Amino acid transport and metabolism CD630_19040 - Type: Gene Product:ABC-type transport system, permease \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_27990 - cwp8 Type: Gene Product:Cell wall binding protein \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis	0.00000000000017	`NA`	0.63	Inferelator: 2 Hypergeometric: 0 TF Influences from Inferelator CD630_12390 - Type: Gene Product:Transcriptional regulator, beta-lactams repressorPhage-type \| Pathway: \| COG: Transcription CD630_26400 - nrdR Type: Gene Product:Transcriptional regulator, repressor NrdR family \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_19	31 CD630_33170 - fdhF Type: Gene Product:Formate dehydrogenase-H (selenocysteine) \| Pathway: \| COG: Energy production and conversion CD630_24160 - Type: Gene Product:Transcription antiterminator, PTS operonregulator \| Pathway: \| COG: Transcription CD630_00380 - acoC Type: Gene Product:Acetoin dehydrogenase E2 component(dihydrolipoamide acetyltransferase) \| Pathway: \| COG: Energy production and conversion CD630_28210 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_07830 - spoIVB Type: Gene Product:Stage IV sporulation protein SpoIVB, S55peptidase family \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_27080 - aroE2 Type: Gene Product:Shikimate dehydrogenase 2 \| Pathway: Metabolic intermediate biosynthesis \| COG: Amino acid transport and metabolism CD630_00360 - acoA Type: Gene Product:Acetoin dehydrogenase E1 component (TPP-dependentalpha subunit) \| Pathway: \| COG: Energy production and conversion CD630_24140 - Type: Gene Product:PTS system, Sorbitol-like IIA component(Glucitol) \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_27070 - Type: Gene Product:Transporter, Major Facilitator Superfamily (MFS) \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_07990 - Type: Gene Product:Putative beta-alanine CoA-transferase, familyIII \| Pathway: \| COG: Energy production and conversion CD630_16450 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_22800 - Type: Gene Product:PTS system, fructose/mannitol family IICcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_00390 - acoL Type: Gene Product:Acetoin dehydrogenase E3 component(dihydrolipoamide dehydrogenase) \| Pathway: \| COG: Energy production and conversion CD630_22820 - Type: Gene Product:PTS system, fructose/mannitol family IIAcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_27090 - Type: Gene Product:Putative oxidoreductase \| Pathway: \| COG: Energy production and conversion CD630_33160 - fdhD Type: Gene Product:Formate dehydrogenase formation protein \| Pathway: \| COG: Energy production and conversion CD630_33140 - hydA Type: Gene Product:Iron hydrogenase \| Pathway: \| COG: Energy production and conversion CD630_00350 - Type: Gene Product:Transcriptional regulator \| Pathway: \| COG: Transcription CD630_07840 - Type: Gene Product:Putative N-acetylmuramoyl-L-alanine amidase \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_00370 - acoB Type: Gene Product:Acetoin dehydrogenase E1 component (TPP-dependentbeta subunit) \| Pathway: \| COG: Energy production and conversion CD630_28200 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_24150 - Type: Gene Product:Putative sorbitol-like operon activator protein(Glucitol) \| Pathway: \| COG: CD630_07980 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_16460 - Type: Gene Product:Putative peptidase, M19 family \| Pathway: \| COG: Amino acid transport and metabolism CD630_24130 - Type: Gene Product:Putative NAD(P)-binding protein \| Pathway: \| COG: Amino acid transport and metabolism CD630_27100 - Type: Gene Product:Putative sugar phosphate epimerase/isomerase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_28220 - Type: Gene Product:Putative glutamate carboxypeptidase, M20 family \| Pathway: \| COG: Amino acid transport and metabolism CD630_33150 - hydN2 Type: Gene Product:Putative oxidoreductase, Fe-S subunit \| Pathway: \| COG: Energy production and conversion CD630_33151 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_33130 - hydN1 Type: Gene Product:Putative oxidoreductase, Fe-S subunit \| Pathway: \| COG: Energy production and conversion CD630_22830 - Type: Gene Product:Sigma-54-dependent regulator, PTS regulatorydomain \| Pathway: \| COG: Transcription	0.31	`NA`	0.53	Inferelator: 3 Hypergeometric: 0 TF Influences from Inferelator CD630_02760 - Type: Gene Product:Transcriptional regulator, AraC family \| Pathway: \| COG: Transcription CD630_05790 - Type: Gene Product:Transcriptional regulator, TetR family \| Pathway: \| COG: Transcription CD630_22830 - Type: Gene Product:Sigma-54-dependent regulator, PTS regulatorydomain \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_229	21 CD630_25120 - Type: Gene Product:PTS system, glucose-like IIA component \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_31380 - bglG Type: Gene Product:Transcription antiterminator, PTS operonregulator \| Pathway: \| COG: Transcription CD630_25080 - Type: Gene Product:Transcriptional regulator, AraC family \| Pathway: \| COG: Transcription CD630_01360 - Type: Gene Product:PTS system, lactose/cellobiose-family IIBcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_25110 - Type: Gene Product:Transcription antiterminator, PTS operonregulator \| Pathway: \| COG: Transcription CD630_01370 - Type: Gene Product:PTS system, lactose/cellobiose-family IICcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_01380 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_09241 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_15140 - panG Type: Gene Product:Putative ketopantoate reductase \| Pathway: \| COG: Coenzyme transport and metabolism CD630_25090 - Type: Gene Product:Putative glycoside hydrolase, family 4 \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_01410 - cutC Type: Gene Product:Copper homeostasis protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_15130 - panB Type: Gene Product:Ketopantoate hydroxymethyltransferase \| Pathway: Cofactor biosynthesis \| COG: Coenzyme transport and metabolism CD630_01390 - Type: Gene Product:N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase \| Pathway: \| COG: Amino acid transport and metabolism CD630_25070 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_15120 - panC Type: Gene Product:Pantothenate synthetase \| Pathway: Cofactor biosynthesis \| COG: Coenzyme transport and metabolism CD630_31370 - bglF Type: Gene Product:PTS system, beta-glucoside-specific IIABCcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_01350 - Type: Gene Product:PTS system, lactose/cellobiose-family IIAcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_25100 - Type: Gene Product:PTS system, glucose-like IIBC component \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_31360 - bglA Type: Gene Product:6-phospho-beta-glucosidase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_t0860 - tRNA-Glu Type: Gene Product: \| Pathway: \| COG: CD630_01400 - Type: Gene Product:Putative peptidase \| Pathway: \| COG: Amino acid transport and metabolism	9.7	`NA`	0.47	Inferelator: 2 Hypergeometric: 1 TF Influences from Inferelator CD630_10090 - Type: Gene Product:Transcriptional regulator, GntR family \| Pathway: \| COG: Transcription CD630_25080 - Type: Gene Product:Transcriptional regulator, AraC family \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test CD630_12750 - codY Type: Gene Product:Transcriptional regulator, GTP-sensingpleiotropic repressor \| Pathway: \| COG: Transcription
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_115	24 CD630_00670 - rpoC Type: Gene Product:DNA-directed RNA polymerase subunit beta' \| Pathway: \| COG: Transcription CD630_26720 - appA Type: Gene Product:ABC-type transport system, oligopeptide-familysolute-binding protein \| Pathway: \| COG: Amino acid transport and metabolism CD630_26700 - appF Type: Gene Product:ABC-type transport system, ATP-binding protein \| Pathway: \| COG: Amino acid transport and metabolism CD630_00590 - secE Type: Gene Product:Preprotein translocase SecE subunit \| Pathway: \| COG: Intracellular trafficking, secretion, and vesicular transport CD630_00610 - rplK Type: Gene Product:50S ribosomal protein L11 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00630 - rplJ Type: Gene Product:50S ribosomal protein L10 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00570 - sigH Type: Gene Product:RNA polymerase factor sigma-70 \| Pathway: \| COG: Transcription CD630_00530 - mrnC Type: Gene Product:Ribonuclease III \| Pathway: \| COG: Function unknown CD630_00550 - Type: Gene Product:Putative tRNA/rRNA methyltransferase, TrmHfamily, group3 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_23340 - mtlA Type: Gene Product:PTS system, mannitol-specific, IICB component \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_23320 - mtlF Type: Gene Product:PTS system, mannitol-specific, EIIA component \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_26710 - appD Type: Gene Product:ABC-type transport system, ATP-binding protein \| Pathway: \| COG: Amino acid transport and metabolism, Inorganic ion transport and metabolism CD630_00660 - rpoB Type: Gene Product:DNA-directed RNA polymerase subunit beta \| Pathway: \| COG: Transcription CD630_26730 - appB Type: Gene Product:ABC-type transport system, oligopeptide-familypermease protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_00620 - rplA Type: Gene Product:50S ribosomal protein L1 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00640 - rplL Type: Gene Product:50S ribosomal protein L7/L12 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00600 - nusG Type: Gene Product:transcription antitermination protein \| Pathway: \| COG: Transcription CD630_00581 - rpmG Type: Gene Product:50S ribosomal protein L33 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00580 - tuf1 Type: Gene Product:Elongation factor EFTu/EF1A \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00560 - Type: Gene Product:Putative ribonuclease \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00540 - thyX Type: Gene Product:Thymidylate synthase \| Pathway: Pyrimidine metabolism \| COG: Nucleotide transport and metabolism CD630_00520 - cysS Type: Gene Product:Cysteinyl-tRNA synthetase (Cysteine--tRNA ligase)(CysRS) \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_23310 - mtlD Type: Gene Product:Mannitol-1-phosphate 5-dehydrogenase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_26740 - appC Type: Gene Product:ABC-type transport system, oligopeptide-familypermease protein \| Pathway: \| COG: Inorganic ion transport and metabolism	`NA`	`NA`	0.47	Inferelator: 1 Hypergeometric: 1 TF Influences from Inferelator CD630_17980 - Type: Gene Product:Transcriptional regulator, LysR family \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test CD630_32450 - prdR Type: Gene Product:Transcriptional regulator, sigma-54-dependent \| Pathway: \| COG: Transcription