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 211 - 220 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_97	29 CD630_33020 - chrA Type: Gene Product:Chromate transport protein ChrA \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_35960 - Type: Gene Product:putative homocysteine S-methyltransferase \| Pathway: \| COG: Amino acid transport and metabolism CD630_35980 - luxS Type: Gene Product:S-ribosylhomocysteine lyase (Autoinducer-2production protein luxS) (AI-2 synthesis protein) \| Pathway: \| COG: Signal transduction mechanisms CD630_13410 - exoA Type: Gene Product:Exodeoxyribonuclease \| Pathway: \| COG: Replication, recombination and repair CD630_00150 - tadA Type: Gene Product:tRNA specific adenosine deaminase \| Pathway: \| COG: Nucleotide transport and metabolism, Translation, ribosomal structure and biogenesis CD630_05220 - Type: Gene Product:Putative c-di-GMP regulatory protein \| Pathway: \| COG: Signal transduction mechanisms 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_11850 - Type: Gene Product:Putative diguanylate kinase signaling protein \| Pathway: \| COG: Signal transduction mechanisms CD630_15680 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_32300 - bclA2 Type: Gene Product:Exosporium glycoprotein \| Pathway: \| COG: Function unknown CD630_08280 - Type: Gene Product:Putative oxidative stress glutamate synthase \| Pathway: \| COG: Amino acid transport and metabolism CD630_15340 - ggt Type: Gene Product:Gamma-glutamyltranspeptidase \| Pathway: \| COG: Amino acid transport and metabolism CD630_35970 - Type: Gene Product:Putative S-adenosyl-L-methionine dependentmethionine synthase \| Pathway: \| COG: Function unknown CD630_32320 - CdsB Type: Gene Product:Cysteine desulfidase \| Pathway: \| COG: Function unknown CD630_12910 - dacF Type: Gene Product:D-alanyl-D-alanine carboxypeptidase \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_12900 - Type: Gene Product:Putative small acid-soluble spore protein SASP \| Pathway: \| COG: CD630_06950 - Type: Gene Product:Putative exported metalloendopeptidase \| Pathway: \| COG: Amino acid transport and metabolism CD630_32310 - hpt Type: Gene Product:Hypoxanthine phosphoribosyltransferase \| Pathway: Purine metabolism \| COG: Nucleotide transport and metabolism CD630_21090 - Type: Gene Product:Putative anion:Na+ symporter \| Pathway: \| COG: Function unknown CD630_05230 - Type: Gene Product:Putative transcriptional regulator \| Pathway: \| COG: Function unknown CD630_08250 - rbr Type: Gene Product:Rubrerythrin \| Pathway: \| COG: Energy production and conversion CD630_28870 - Type: Gene Product:Putative diguanylate kinase signaling protein \| Pathway: \| COG: Signal transduction mechanisms CD630_07070 - Type: Gene Product:Putative diguanylate kinase signaling protein \| Pathway: \| COG: Signal transduction mechanisms CD630_25150 - Type: Gene Product:Putative L-aspartate-beta-decarboxylase \| Pathway: \| COG: Amino acid transport and metabolism CD630_22610 - Type: Gene Product:Putative peptidase, M24 family \| Pathway: \| COG: Amino acid transport and metabolism	1.5e-18	`NA`	0.51	Inferelator: 4 Hypergeometric: 0 TF Influences from Inferelator CD630_12390 - Type: Gene Product:Transcriptional regulator, beta-lactams repressorPhage-type \| Pathway: \| COG: Transcription CD630_16930 - Type: Gene Product:Putative dinitrogenase iron-molybdenum cofactor \| Pathway: \| COG: Function unknown CD630_19100 - eutV Type: Gene Product:Two-component response regulator, Ethanolaminespecific \| Pathway: \| COG: Signal transduction mechanisms 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_377	23 CD630_20690 - Type: Gene Product:Putative molybdopterin cofactor biosynthesisprotein \| Pathway: Cofactor biosynthesis \| COG: Coenzyme transport and metabolism CD630_10500 - Type: Gene Product:ABC-type transport system, multidrug-familyATP-binding protein \| Pathway: \| COG: Defense mechanisms CD630_10520 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_14510 - folB Type: Gene Product:Dihydroneopterin aldolase \| Pathway: Cofactor biosynthesis \| COG: Coenzyme transport and metabolism CD630_14430 - Type: Gene Product:Putative Ca++-chelating serine protease, SCP-likeextracellular domain protein \| Pathway: \| COG: Secondary metabolites biosynthesis, transport and catabolism CD630_20710 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_02940 - Type: Gene Product:ABC-type transport system,bacitracin/multidrug-family permease \| Pathway: \| COG: Function unknown CD630_14470 - pabC Type: Gene Product:Aminodeoxychorismate lyase(4-amino-4-deoxychorismate lyase) (ADC lyase) (ADCL) \| Pathway: \| COG: Amino acid transport and metabolism CD630_14530 - aroF Type: Gene Product:Phospho-2-dehydro-3-deoxyheptonate aldolase \| Pathway: \| COG: Amino acid transport and metabolism CD630_14450 - pabA Type: Gene Product:Para-aminobenzoate/anthranilate synthaseglutamine amidotransferase component II [Includes:Para-aminobenzoate synthase glutamine amidotransferasecomponent II; Anthranilate synthase component II] \| Pathway: \| COG: Amino acid transport and metabolism CD630_10480 - Type: Gene Product:Putative phosphodiesterase \| Pathway: \| COG: Function unknown CD630_14490 - folE Type: Gene Product:GTP cyclohydrolase 1 (GTP cyclohydrolase I)(GTP-CH-I) \| Pathway: Cofactor biosynthesis \| COG: Coenzyme transport and metabolism CD630_10530 - Type: Gene Product:Putative aminoacyl-tRNA synthetase-associateddomain \| Pathway: \| COG: Function unknown CD630_10510 - Type: Gene Product:ABC-type transport system, multidrug-familypermease \| Pathway: \| COG: CD630_14500 - folP Type: Gene Product:Dihydropteroate synthase \| Pathway: Cofactor biosynthesis \| COG: Coenzyme transport and metabolism CD630_20700 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_14520 - folK Type: Gene Product:2-amino-4-hydroxy-6-hydroxymethyldihydropteridinepyrophosphokinase \| Pathway: \| COG: Coenzyme transport and metabolism CD630_14440 - Type: Gene Product:Putative exported polysaccharide deacetylase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_14460 - pabB Type: Gene Product:Para-aminobenzoate synthase component I \| Pathway: \| COG: Amino acid transport and metabolism, Coenzyme transport and metabolism CD630_02930 - Type: Gene Product:ABC-type transport system,bacitracin/multidrug-family ATP-binding protein \| Pathway: \| COG: Defense mechanisms CD630_10490 - ppnK Type: Gene Product:Inorganic polyphosphate/ATP-NAD kinase(Poly(P)/ATP NAD kinase) \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_14480 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_34770 - Type: Gene Product:Putative dCMP deaminase \| Pathway: \| COG: Nucleotide transport and metabolism	0.00042	0.04	0.51	Inferelator: 3 Hypergeometric: 0 TF Influences from Inferelator CD630_16920 - Type: Gene Product:Transcriptional regulator, ArsR family \| Pathway: \| COG: Transcription CD630_16930 - Type: Gene Product:Putative dinitrogenase iron-molybdenum cofactor \| Pathway: \| COG: Function unknown 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_330	18 CD630_15660 - ilvB Type: Gene Product:Acetolactate synthase large subunit \| Pathway: Amino-acid biosynthesis \| COG: Amino acid transport and metabolism CD630_14760 - Type: Gene Product:Putative signaling protein \| Pathway: \| COG: Signal transduction mechanisms CD630_28490 - phnXW Type: Gene Product:Bifunctional phosphonoacetaldehydehydrolase/aminoethylphosphonate transaminase [Includes:Phosphonoacetaldehyde hydrolase ;2-aminoethylphosphonate--pyruvate transaminase] \| Pathway: \| COG: Amino acid transport and metabolism CD630_28800 - celC Type: Gene Product:PTS system, cellobiose-specific IIA component \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_15650 - ilvC Type: Gene Product:Ketol-acid reductoisomerase \| Pathway: Amino-acid biosynthesis \| COG: Amino acid transport and metabolism CD630_28810 - celG Type: Gene Product:Putative cellobiose-phosphate degrading protein \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_28840 - celA Type: Gene Product:PTS system, cellobiose-specific IIB component \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_05660 - Type: Gene Product:Putative tRNA/rRNA methyltransferase \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_19350 - spoVS Type: Gene Product:Stage V sporulation protein S \| Pathway: \| COG: Function unknown CD630_05670 - Type: Gene Product:Conserved hypothetical protein, DegV family \| Pathway: \| COG: Function unknown CD630_24800 - Type: Gene Product:Putative hydrolase \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_08110 - Type: Gene Product:Putative cyclic di-GMP regulatory protein \| Pathway: \| COG: Signal transduction mechanisms CD630_12650 - Type: Gene Product:Transcriptional regulator, CarD family \| Pathway: \| COG: Transcription CD630_18930 - Type: Gene Product:Putative oligonucleotide binding regulator \| Pathway: \| COG: Function unknown CD630_28830 - celB Type: Gene Product:PTS system, cellobiose-specific IIC component \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_08070 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_28820 - celF Type: Gene Product:Cellobiose-6-phosphate hydrolase, family 4 \| Pathway: \| COG: Carbohydrate transport and metabolism	0	`NA`	0.51	Inferelator: 1 Hypergeometric: 0 TF Influences from Inferelator 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_148	24 CD630_18710 - Type: Gene Product:Putative oxidoreductase Tn1549-like, CTn5-Orf30 \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_02070 - Type: Gene Product:PTS system, fructose-like IIC component \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_13900 - Type: Gene Product:Conserved hypothetical protein, DUF819 family \| Pathway: \| COG: Function unknown CD630_35490 - Type: Gene Product:DNA polymerase III, delta prime subunit \| Pathway: \| COG: Replication, recombination and repair CD630_02050 - Type: Gene Product:Transcription antiterminator, PTS operonregulator \| Pathway: \| COG: Transcription CD630_02090 - Type: Gene Product:Putative tagatose 6-phosphate kinase \| Pathway: \| COG: Function unknown CD630_13890 - Type: Gene Product:Putative chloromuconate cycloisomerase \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_35460 - Type: Gene Product:Putative tetrapyrrole methylase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_35500 - tmk Type: Gene Product:Thymidylate kinase (dTMP kinase) \| Pathway: \| COG: Nucleotide transport and metabolism CD630_31530 - Type: Gene Product:Transcriptional regulator, Phage-type \| Pathway: \| COG: Transcription CD630_18720 - Type: Gene Product:Putative iron-sulfur binding protein Tn1549-like,CTn5-Orf32 \| Pathway: \| COG: Energy production and conversion CD630_18740 - vexP2 Type: Gene Product:ABC-type transport system, ATP-binding proteinTn1549-like, CTn5-Orf34 \| Pathway: \| COG: Defense mechanisms CD630_18700 - Type: Gene Product:Putative conjugative transposon proteinTn1549-like, CTn5-Orf29 \| Pathway: \| COG: Function unknown CD630_35480 - Type: Gene Product:Putative YaaT-like protein involved insporulation or related to DNA replication \| Pathway: \| COG: Function unknown CD630_13380 - Type: Gene Product:Putative 6-phospho-beta-glucosidase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_02080 - Type: Gene Product:PTS system, fructose-like IIB component \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_35510 - Type: Gene Product:Putative arginine decarboxylase \| Pathway: \| COG: Amino acid transport and metabolism CD630_18760 - vncR Type: Gene Product:Two-component response regulator; Tn1549-like,CTn5-Orf36 \| Pathway: \| COG: Signal transduction mechanisms CD630_02060 - Type: Gene Product:PTS system, fructose-like IIA component \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_31510 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: Function unknown CD630_35470 - Type: Gene Product:Putative methyltransferase \| Pathway: \| COG: Replication, recombination and repair CD630_31521 - Type: Gene Product:Transcriptional regulator, Phage-type \| Pathway: \| COG: Transcription CD630_31520 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_18690 - Type: Gene Product:Putative endonuclease relaxase Tn1549-like,CTn5-Orf28 \| Pathway: \| COG: Intracellular trafficking, secretion, and vesicular transport	0.000024	5.8	0.51	Inferelator: 1 Hypergeometric: 1 TF Influences from Inferelator CD630_34990 - spoVT Type: Gene Product:Stage V sporulation protein T \| 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_363	22 CD630_24630 - hrcA Type: Gene Product:Transcriptional regulator, Heat-induciblerepressor HrcA \| Pathway: \| COG: Transcription CD630_20120 - hydD Type: Gene Product:Putative hydrolase \| Pathway: \| COG: Function unknown CD630_20730 - xdhA Type: Gene Product:Xanthine dehydrogenase, molybdenum bindingsubunit \| Pathway: \| COG: Energy production and conversion CD630_08220 - Type: Gene Product:ABC-type transport system, multidrug-familyATP-binding protein \| Pathway: \| COG: Defense mechanisms CD630_15020 - deoC Type: Gene Product:Deoxyribose-phosphate aldolase(Phosphodeoxyriboaldolase) (Deoxyriboaldolase) (DERA) \| Pathway: Carbohydrate degradation \| COG: Nucleotide transport and metabolism CD630_08240 - Type: Gene Product:ABC-type transport system, multidrug-familypermease \| Pathway: \| COG: Function unknown CD630_16370 - Type: Gene Product:Putative calcium-transporting ATPase \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_16350 - terD Type: Gene Product:Tellurium resistance protein \| Pathway: \| COG: Signal transduction mechanisms CD630_01320 - Type: Gene Product:Putative DNA helicase, RecD/TraA type \| Pathway: \| COG: Replication, recombination and repair CD630_25490 - Type: Gene Product:ABC-type transport system, sugar-family permease \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_16410 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_16430 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_25470 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_20130 - hydR Type: Gene Product:Transcriptional regulator, TetR family \| Pathway: \| COG: Transcription CD630_08230 - Type: Gene Product:ABC-type transport system, multidrug-familypermease \| Pathway: \| COG: Function unknown CD630_20740 - Type: Gene Product:Putative FAD-binding subunit of xanthinedehydrogenase \| Pathway: \| COG: Energy production and conversion CD630_16400 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_01330 - Type: Gene Product:Putative phosphoribosyl transferase \| Pathway: \| COG: Function unknown CD630_16380 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_25480 - Type: Gene Product:ABC-type transport system, sugar-family permease \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_16420 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_25500 - Type: Gene Product:ABC-type transport system, sugar-familyextracellular solute-binding protein \| Pathway: \| COG: Carbohydrate transport and metabolism	0.00025	2.4	0.51	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_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_395	18 CD630_05760 - virS Type: Gene Product:Sensor histidine kinase \| Pathway: \| COG: Signal transduction mechanisms CD630_07760 - Type: Gene Product:Transcriptional regulator, LacI family \| Pathway: \| COG: Transcription CD630_06010 - ogt1 Type: Gene Product:Methylated-DNA-[protein]-cysteineS-methyltransferase 1 \| Pathway: \| COG: Replication, recombination and repair CD630_27650 - LcpA Type: Gene Product:Surface-anchoring factors, LytR-CpsA-Psr-likeprotein \| Pathway: \| COG: Transcription CD630_13420 - Type: Gene Product:Putative ribonuclease \| Pathway: \| COG: Replication, recombination and repair CD630_20760 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_33670 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_06640 - tcdC Type: Gene Product:Negative regulator of toxin gene expression \| Pathway: \| COG: Function unknown CD630_09790 - Type: Gene Product:Transcriptional regulator, beta-lactams repressorPhage-type \| Pathway: \| COG: Transcription CD630_20650 - Type: Gene Product:Transcriptional regulator, beta-lactamsrepressor \| Pathway: \| COG: Transcription CD630_01810 - Type: Gene Product:Putative membrane-associated metalloprotease, M56family \| Pathway: \| COG: Transcription, Signal transduction mechanisms CD630_08290 - Type: Gene Product:Putative metallo-beta-lactamase superfamilyprotein \| Pathway: \| COG: Function unknown CD630_34080 - Type: Gene Product:Putative DNA mismatch repair ATPase MutS \| Pathway: \| COG: Replication, recombination and repair CD630_12490 - Type: Gene Product:Putative radical SAM-superfamily protein \| Pathway: \| COG: Chromatin structure and dynamics, Transcription CD630_26030 - cdtR Type: Gene Product:Clostridium difficile binary toxin regulatorygene, LytTR family \| Pathway: \| COG: Signal transduction mechanisms CD630_01830 - Type: Gene Product:Putative cell wall hydrolase \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_00300 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_01780 - Type: Gene Product:Putative ATPase \| Pathway: \| COG: Function unknown	0.00051	`NA`	0.51	Inferelator: 2 Hypergeometric: 0 TF Influences from Inferelator CD630_18100 - Type: Gene Product:Transcriptional regulator, beta-lactamsrepressor \| Pathway: \| COG: Transcription CD630_35440 - Type: Gene Product:Transcriptional regulator, AsnC/Lrp family \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_167	28 CD630_19260 - eutR Type: Gene Product:Fragment of transcription regulator, AraC family(C-terminal region) \| Pathway: \| COG: Transcription CD630_21210 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_25980 - Type: Gene Product:Putative oligosaccharide deacetylase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_32570 - Type: Gene Product:Putative polysaccharide deacetylase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_05560 - Type: Gene Product:Putative sugar isomerase / endonuclease \| Pathway: \| COG: Carbohydrate transport and metabolism 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_05500 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_32580 - Type: Gene Product:Iron hydrogenase \| Pathway: \| COG: Energy production and conversion CD630_34880 - gtaB Type: Gene Product:UTP--glucose-1-phosphate uridylyltransferase \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_23730 - Type: Gene Product:Putative CstA-like carbon starvation protein \| Pathway: \| COG: Signal transduction mechanisms CD630_07120 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_33120 - Type: Gene Product:Transporter, Major Facilitator Superfamily (MFS) \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_15750 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_27190 - Type: Gene Product:Putative polysaccharide deacetylase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_24580 - Type: Gene Product:Transporter, Major Facilitator Superfamily (MFS) \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_05570 - Type: Gene Product:Putative uridine kinase \| Pathway: \| COG: Nucleotide transport and metabolism CD630_25990 - Type: Gene Product:Putative transcriptional regulator \| Pathway: \| COG: Transcription CD630_05550 - sip2 Type: Gene Product:Signal peptidase type I \| Pathway: \| COG: Intracellular trafficking, secretion, and vesicular transport CD630_14300 - pdaA Type: Gene Product:Exported N-acetylmuramic acid deacetylase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_05510 - sleC Type: Gene Product:Spore exo-acting lytic transglycosylase \| Pathway: \| COG: Function unknown CD630_05530 - Type: Gene Product:Putative RNA methyltransferase \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_14630 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_30070 - Type: Gene Product:Putative L,D-transpeptidases \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_23052 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_15790 - Type: Gene Product:Two-component sensor histidine kinase,sporulation-associated spo0A \| Pathway: \| COG: Signal transduction mechanisms CD630_22520 - Type: Gene Product:Glutamate 2,3-aminomutase \| Pathway: \| COG: Amino acid transport and metabolism CD630_34890 - Type: Gene Product:Putative oligoendopeptidase F, peptidase M3Bfamily \| Pathway: \| COG: Amino acid transport and metabolism	0.00000029	`NA`	0.51	Inferelator: 5 Hypergeometric: 1 TF Influences from Inferelator CD630_06290 - Type: Gene Product:Transcriptional regulator, Crp family \| Pathway: \| COG: Transcription CD630_25990 - Type: Gene Product:Putative transcriptional regulator \| Pathway: \| COG: Transcription CD630_26420 - sigG Type: Gene Product:RNA polymerase sigma-G factor \| Pathway: \| COG: Transcription CD630_26430 - sigE Type: Gene Product:RNA polymerase sigma-E factor \| Pathway: \| COG: Transcription 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
Module_39	22 CD630_36360 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: CD630_36361 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_04790 - spaE Type: Gene Product:ABC-type transport system,lantibiotic/multidrug-family permease \| Pathway: \| COG: Function unknown CD630_22990 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_11261 - Type: Gene Product:Transcriptional regulator, HTH-type \| Pathway: \| COG: Transcription CD630_27130 - ldtcd2 Type: Gene Product:L,D-transpeptidases \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_04850 - Type: Gene Product:Two-component sensor histidine kinase \| Pathway: \| COG: Signal transduction mechanisms CD630_27150 - gtaB Type: Gene Product:UTP--glucose-1-phosphate uridylyltransferase \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_04620 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms CD630_04810 - spaR Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms CD630_04640 - Type: Gene Product:Putative beta-lactamase-like hydrolase \| Pathway: \| COG: Function unknown CD630_36350 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_36370 - Type: Gene Product:Putative NADPH-dependent FMN reductase \| Pathway: \| COG: Function unknown CD630_11270 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_04780 - spaF Type: Gene Product:ABC-type transport system,lantibiotic/multidrug-family ATP-binding protein \| Pathway: \| COG: Defense mechanisms CD630_36380 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_27140 - galE Type: Gene Product:UDP-glucose 4-epimerase \| Pathway: Carbohydrate metabolism \| COG: Cell wall/membrane/envelope biogenesis CD630_04630 - Type: Gene Product:Transcriptional regulator, TetR family \| Pathway: \| COG: Transcription CD630_04800 - spaG Type: Gene Product:ABC-type transport system,lantibiotic/multidrug-family permease \| Pathway: \| COG: Function unknown CD630_04860 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms CD630_04820 - spaK Type: Gene Product:Two-component sensor histidine kinase \| Pathway: \| COG: Signal transduction mechanisms CD630_04610 - Type: Gene Product:Two-component sensor histidine kinase \| Pathway: \| COG: Signal transduction mechanisms	0.5	`NA`	0.51	Inferelator: 2 Hypergeometric: 2 TF Influences from Inferelator CD630_01710 - rex Type: Gene Product:Transcriptional regulator, Redox-sensingrepressor Rex \| Pathway: \| COG: Transcription CD630_02760 - Type: Gene Product:Transcriptional regulator, AraC family \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test CD630_07720 - sigF Type: Gene Product:RNA polymerase sigma-F factor \| Pathway: \| COG: Transcription CD630_26430 - sigE Type: Gene Product:RNA polymerase sigma-E factor \| Pathway: \| COG: Transcription
Module_24	20 CD630_19840 - Type: Gene Product:Putative hydrolase, NUDIX family \| Pathway: \| COG: Replication, recombination and repair CD630_30850 - mngB Type: Gene Product:Alpha-mannosidase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_05820 - Type: Gene Product:Putative pyruvate phosphate dikinase,PEP/pyruvate-binding \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_30320 - Type: Gene Product:Putative pyridoxal phosphate-dependenttransferase \| Pathway: \| COG: Amino acid transport and metabolism CD630_03020 - rbsC Type: Gene Product:ABC-type transport system, ribose-specificpermease \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_02990 - rbsK Type: Gene Product:Ribokinase, pfkB family \| Pathway: Carbohydrate metabolism \| COG: Carbohydrate transport and metabolism CD630_31650 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Replication, recombination and repair CD630_31670 - Type: Gene Product:Putative phosphatidylethanolamine-bindingregulatory protein \| Pathway: \| COG: Function unknown CD630_03030 - argE Type: Gene Product:Acetylornithine deacetylase ArgE \| Pathway: \| COG: Amino acid transport and metabolism CD630_03000 - rbsB Type: Gene Product:ABC-type transport system, ribose-specificextracellular solute-binding protein \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_05890 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_30870 - Type: Gene Product:Transcriptional regulator, RpiR family \| Pathway: \| COG: Transcription CD630_t0450 - tRNA-Val Type: Gene Product: \| Pathway: \| COG: CD630_30860 - mngA Type: Gene Product:PTS system, 2-O-a-mannosyl-D-glycerate-specificIIABC component \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_03010 - rbsA Type: Gene Product:ABC-type transport system, ribose-specificATP-binding protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_05810 - Type: Gene Product:Transcriptional regulator, TetR family \| Pathway: \| COG: Transcription CD630_03040 - Type: Gene Product:Conserved hypothetical protein, DUF1355 family \| Pathway: \| COG: Function unknown CD630_05900 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_23861 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_02980 - rbsR Type: Gene Product:Transcriptional regulator, LacI family \| Pathway: \| COG: Transcription	0.000009	`NA`	0.51	Inferelator: 2 Hypergeometric: 0 TF Influences from Inferelator CD630_02980 - rbsR Type: Gene Product:Transcriptional regulator, LacI family \| Pathway: \| COG: Transcription CD630_30870 - Type: Gene Product:Transcriptional regulator, RpiR family \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test `No TF Influences from the hypergeometric test`
Module_314	26 CD630_03510 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_11261 - Type: Gene Product:Transcriptional regulator, HTH-type \| Pathway: \| COG: Transcription CD630_15280 - Type: Gene Product:ABC-type transport system, ATP-binding protein \| Pathway: \| COG: Defense mechanisms CD630_07060 - Type: Gene Product:Putative nitroreductase \| Pathway: \| COG: Energy production and conversion CD630_02920 - Type: Gene Product:Transcriptional regulator, HTH-type \| Pathway: \| COG: Transcription CD630_31410 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: CD630_31390 - Type: Gene Product:Transcriptional regulator, Phage-type \| Pathway: \| COG: Transcription CD630_08140 - Type: Gene Product:Transcriptional regulator, GntR family \| Pathway: \| COG: Transcription CD630_r0060 - 5s_rRNA Type: Gene Product: \| Pathway: \| COG: CD630_03500 - Type: Gene Product:Putative hydrolase, HAD superfamily \| Pathway: \| COG: Function unknown CD630_07430 - Type: Gene Product:Transcriptional regulator, DeoR family \| Pathway: \| COG: Transcription CD630_20520 - Type: Gene Product:Putative lipoprotein \| Pathway: \| COG: Function unknown CD630_11270 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_15290 - Type: Gene Product:ABC-type transport system, permease \| Pathway: \| COG: Function unknown CD630_31400 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: CD630_15270 - Type: Gene Product:ABC-type transport system, permease \| Pathway: \| COG: Defense mechanisms CD630_08150 - Type: Gene Product:Transporter, Major Facilitator Superfamily (MFS) \| Pathway: \| COG: Carbohydrate transport and metabolism	0.000038	`NA`	0.52	Inferelator: 1 Hypergeometric: 0 TF Influences from Inferelator 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`