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 11 - 20 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_307	20 CD630_26190 - Type: Gene Product:Putative cell-division initiation protein DivIVA \| Pathway: \| COG: Cell cycle control, cell division, chromosome partitioning CD630_14950 - proC Type: Gene Product:Pyrroline-5-carboxylate reductase \| Pathway: Amino-acid biosynthesis \| COG: Amino acid transport and metabolism CD630_26200 - Type: Gene Product:Putative RNA-binding cell division protein \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_17700 - ogt2 Type: Gene Product:Methylated-DNA-[protein]-cysteineS-methyltransferase 2 \| Pathway: \| COG: Replication, recombination and repair CD630_14940 - Type: Gene Product:Transcriptional regulator, HTH-type \| Pathway: \| COG: Transcription CD630_22590 - Type: Gene Product:Conserved hypothetical protein with RmlC-likejelly roll fold \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_23800 - iorB Type: Gene Product:Indole pyruvate ferredoxin/flavodoxinoxidoreductase \| Pathway: \| COG: Energy production and conversion CD630_22580 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_15370 - aspB Type: Gene Product:Putative glutamate synthase \| Pathway: \| COG: Amino acid transport and metabolism CD630_23790 - buk Type: Gene Product:Butyrate kinase (Branched-chain carboxylic acidkinase) (BK) \| Pathway: \| COG: Energy production and conversion CD630_36650 - Type: Gene Product:Conserved hypothetical protein, DUF951 family \| Pathway: \| COG: Function unknown CD630_23810 - iorA Type: Gene Product:Indole pyruvate ferredoxin/flavodoxinoxidoreductase \| Pathway: \| COG: Energy production and conversion CD630_15360 - Type: Gene Product:Ferredoxin--NADP(+) reductase subunit alpha \| Pathway: \| COG: Energy production and conversion CD630_26220 - sepF Type: Gene Product:Cell division protein SepF \| Pathway: \| COG: Function unknown CD630_23820 - Type: Gene Product:Putative pyridoxal phosphate-dependenttransferase \| Pathway: \| COG: Amino acid transport and metabolism CD630_17710 - Type: Gene Product:Putative monooxygenase \| Pathway: \| COG: Function unknown CD630_36660 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_26240 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_36640 - Type: Gene Product:Putative aminotransferase \| Pathway: \| COG: Transcription CD630_26230 - Type: Gene Product:Putative pyridoxal 5'-phosphate-dependent enzyme \| Pathway: \| COG: Nucleotide transport and metabolism	0.00000000078	`NA`	0.33	Inferelator: 2 Hypergeometric: 1 TF Influences from Inferelator CD630_17980 - Type: Gene Product:Transcriptional regulator, LysR family \| Pathway: \| COG: Transcription CD630_19310 - lexA Type: Gene Product:Transcriptional regulator, LexA repressor \| Pathway: \| COG: Transcription TF Influences from Hypergeometric Test CD630_32450 - prdR Type: Gene Product:Transcriptional regulator, sigma-54-dependent \| Pathway: \| COG: Transcription
Module_136	25 CD630_13660 - Type: Gene Product:Putative phage tail protein \| Pathway: \| COG: Function unknown CD630_12440 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_13620 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_13640 - Type: Gene Product:Putative phage XkdM-like protein \| Pathway: \| COG: Function unknown CD630_13700 - Type: Gene Product:Putative phage XkdS-like protein \| Pathway: \| COG: Function unknown CD630_12420 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_13720 - Type: Gene Product:Putative phage XkdT-like protein \| Pathway: \| COG: Function unknown CD630_13680 - Type: Gene Product:Putative phage cell wall XkdQ-like hydrolase \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_14150 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_13760 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_13740 - Type: Gene Product:Putative beta-lactamase-inhibitor protein II \| Pathway: \| COG: Cell cycle control, cell division, chromosome partitioning, Cytoskeleton CD630_25710 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms CD630_30410 - pepI Type: Gene Product:Proline iminopeptidase (Proline aminopeptidase)(PIP), peptidase S33 family \| Pathway: \| COG: Amino acid transport and metabolism CD630_14170 - Type: Gene Product:Putative ATP-binding protein \| Pathway: \| COG: Amino acid transport and metabolism CD630_13670 - Type: Gene Product:Putative phage XkdP-like protein \| Pathway: \| COG: Function unknown CD630_13651 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_13650 - Type: Gene Product:Putative phage XkdN-like protein \| Pathway: \| COG: Function unknown CD630_13630 - Type: Gene Product:Putative phage XkdK-like protein \| Pathway: \| COG: Function unknown CD630_12430 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_13710 - Type: Gene Product:Putative baseplate assembly predicted J-like \| Pathway: \| COG: Function unknown CD630_13730 - Type: Gene Product:Putative phage tail fiber protein \| Pathway: \| COG: Function unknown CD630_13690 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_25700 - Type: Gene Product:Two-component sensor histidine kinase \| Pathway: \| COG: Signal transduction mechanisms CD630_14140 - Type: Gene Product:Putative oxidoreductase, Fe-S subunit \| Pathway: \| COG: Function unknown CD630_14160 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown	0.000016	`NA`	0.48	Inferelator: 1 Hypergeometric: 0 TF Influences from Inferelator 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_56	21 CD630_09180 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: Function unknown CD630_09260 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_09380 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: Function unknown CD630_09190 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_09340 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_09270 - Type: Gene Product:Putative phage DNA modification methylase \| Pathway: \| COG: Replication, recombination and repair CD630_09350 - Type: Gene Product:Putative S-adenosyl-L-methionine-dependentmethyltransferase \| Pathway: \| COG: Replication, recombination and repair CD630_09290 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: Function unknown CD630_09170 - Type: Gene Product:Putative phage recombination protein Bet \| Pathway: \| COG: Replication, recombination and repair CD630_09300 - Type: Gene Product:Putative phage reductase \| Pathway: \| COG: Function unknown CD630_09280 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_09250 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_09360 - Type: Gene Product:Putative phage endodeoxyribonuclease \| Pathway: \| COG: Replication, recombination and repair CD630_09370 - Type: Gene Product:Putative phage anti-repressor \| Pathway: \| COG: Transcription CD630_09210 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_09301 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_09120 - Type: Gene Product:Putative phage DNA-binding protein \| Pathway: \| COG: CD630_09330 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_09220 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_09320 - Type: Gene Product:Putative phage protein \| Pathway: \| COG: CD630_09310 - Type: Gene Product:Putative phage protein \| Pathway: \| COG:	`NA`	`NA`	0.39	Inferelator: 2 Hypergeometric: 0 TF Influences from Inferelator 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_402	17 CD630_00600 - nusG Type: Gene Product:transcription antitermination protein \| Pathway: \| COG: Transcription CD630_00530 - mrnC Type: Gene Product:Ribonuclease III \| Pathway: \| COG: Function unknown CD630_21370 - frr Type: Gene Product:Ribosome-recycling factor \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00540 - thyX Type: Gene Product:Thymidylate synthase \| Pathway: Pyrimidine metabolism \| COG: Nucleotide transport and metabolism CD630_00640 - rplL Type: Gene Product:50S ribosomal protein L7/L12 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00620 - rplA Type: Gene Product:50S ribosomal protein L1 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_21380 - pyrH Type: Gene Product:Uridylate kinase (UK) (Uridine monophosphatekinase) (UMP kinase) (UMPK) \| 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_21390 - tsf Type: Gene Product:Elongation factor Ts (EF-Ts) \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00590 - secE Type: Gene Product:Preprotein translocase SecE subunit \| Pathway: \| COG: Intracellular trafficking, secretion, and vesicular transport 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_00630 - rplJ Type: Gene Product:50S ribosomal protein L10 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00560 - Type: Gene Product:Putative ribonuclease \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00550 - Type: Gene Product:Putative tRNA/rRNA methyltransferase, TrmHfamily, group3 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00610 - rplK Type: Gene Product:50S ribosomal protein L11 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_00570 - sigH Type: Gene Product:RNA polymerase factor sigma-70 \| Pathway: \| COG: Transcription	`NA`	`NA`	0.32	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_323	22 CD630_19170 - eutE Type: Gene Product:Ethanolamine acetaldehyde oxydoreductase \| Pathway: \| COG: Energy production and conversion CD630_30920 - Type: Gene Product:Putative amino acid permease \| Pathway: \| COG: Amino acid transport and metabolism CD630_19480 - Type: Gene Product:ABC-type transport system, permease \| Pathway: \| COG: Defense mechanisms CD630_31020 - Type: Gene Product:Putative peptidase, M20 family, peptidase Vrelated \| Pathway: \| COG: Amino acid transport and metabolism CD630_32110 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_06500 - Type: Gene Product:Putative peptidase, S9 family \| Pathway: \| COG: Amino acid transport and metabolism CD630_19470 - Type: Gene Product:ABC-type transport system, ATP-binding protein \| Pathway: \| COG: Defense mechanisms CD630_19230 - Type: Gene Product:Ethanolamine carboxysome structural protein, BMCfamily \| Pathway: \| COG: Amino acid transport and metabolism CD630_19250 - eutQ Type: Gene Product:Ethanolamine utilization protein, Cupin barrelsfamily \| Pathway: \| COG: Amino acid transport and metabolism CD630_20010 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_30930 - Type: Gene Product:Putative gamma-glutamyl-gamma-aminobutyratehydrolase \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_06490 - Type: Gene Product:Putative peptidase, S9 family \| Pathway: \| COG: Amino acid transport and metabolism CD630_32100 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_31150 - bglA Type: Gene Product:6-phospho-beta-glucosidase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_32090 - Type: Gene Product:Transcriptional regulator, PadR family \| Pathway: \| COG: Transcription CD630_31010 - Type: Gene Product:PTS system, glucose-like IIBC component \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_06510 - Type: Gene Product:Putative permease \| Pathway: \| COG: Function unknown CD630_19190 - eutT Type: Gene Product:Ethanolamine corrinoid cobalaminadenosyltransferase \| Pathway: \| COG: Amino acid transport and metabolism CD630_32201 - Type: Gene Product:Small acid-soluble spore protein \| Pathway: \| COG: Function unknown CD630_32200 - Type: Gene Product:Putative methyltransferase \| Pathway: \| COG: Secondary metabolites biosynthesis, transport and catabolism CD630_19200 - eutD Type: Gene Product:Putative phosphotransacetylase \| Pathway: Polyol metabolism \| COG: Secondary metabolites biosynthesis, transport and catabolism CD630_19240 - eutH Type: Gene Product:Ethanolamine transport protein \| Pathway: \| COG: Amino acid transport and metabolism	0.01	`NA`	0.43	Inferelator: 0 Hypergeometric: 1 TF Influences from Inferelator `No TF influences from Inferelator` TF Influences from Hypergeometric Test CD630_32450 - prdR Type: Gene Product:Transcriptional regulator, sigma-54-dependent \| Pathway: \| COG: Transcription
Module_243	21 CD630_24950 - selA Type: Gene Product:L-seryl-tRNA(Sec) selenium transferase(Selenocysteine synthase) (Sec synthase)(Selenocysteinyl-tRNA(Sec) synthase ) \| Pathway: Aminoacyl-tRNA biosynthesis \| COG: Amino acid transport and metabolism CD630_24980 - dacF Type: Gene Product:D-alanyl-D-alanine carboxypeptidase (putativesporulation-specific penicillin-binding protein) \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_24930 - selB Type: Gene Product:Selenocysteinyl-tRNA-specific translation factor \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_35140 - prs Type: Gene Product:Ribose-phosphate pyrophosphokinase \| Pathway: Metabolic intermediate biosynthesis \| COG: Nucleotide transport and metabolism CD630_01940 - groL Type: Gene Product:60 kDa chaperonin (Protein Cpn60) (GroELprotein) \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_25240 - nadD Type: Gene Product:Nicotinate-nucleotide adenylyltransferase \| Pathway: Cofactor biosynthesis \| COG: Coenzyme transport and metabolism CD630_24970 - comE Type: Gene Product:Competence protein ComEA \| Pathway: \| COG: Replication, recombination and repair CD630_25230 - Type: Gene Product:Putative hydrolase \| Pathway: \| COG: Coenzyme transport and metabolism CD630_24960 - selD Type: Gene Product:Selenide, water dikinase (Selenophosphatesynthetase) (Selenium donor protein) \| Pathway: \| COG: Amino acid transport and metabolism CD630_27290 - Type: Gene Product:Putative regulator of the sigma(E) factor \| Pathway: \| COG: Signal transduction mechanisms CD630_01930 - groS Type: Gene Product:10 kDa chaperonin (Protein Cpn10) (GroESprotein) \| Pathway: \| COG: Posttranslational modification, protein turnover, chaperones CD630_21770 - Type: Gene Product:ABC-type transport system,cystine/aminoacid-family extracellular solute-bindingprotein \| Pathway: \| COG: Amino acid transport and metabolism CD630_25220 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_21760 - Type: Gene Product:ABC-type transport system,cystine/aminoacid-family permease \| Pathway: \| COG: Amino acid transport and metabolism CD630_35150 - glmU Type: Gene Product:Bifunctional protein GlmU [Includes:UDP-N-acetylglucosamine pyrophosphorylase ;Glucosamine-1-phosphate N-acetyltransferase] \| Pathway: Nucleotide-sugar biosynthesis \| COG: Cell wall/membrane/envelope biogenesis CD630_27310 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: CD630_21720 - Type: Gene Product:ABC-type transport system,cystine/aminoacid-family ATP-binding protein \| Pathway: \| COG: Amino acid transport and metabolism CD630_21750 - Type: Gene Product:ABC-type transport system,cystine/aminoacid-family permease \| Pathway: \| COG: Amino acid transport and metabolism CD630_21740 - Type: Gene Product:ABC-type transport system,cystine/aminoacid-family extracellular solute-bindingprotein \| Pathway: \| COG: Amino acid transport and metabolism, Signal transduction mechanisms CD630_27300 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_21730 - Type: Gene Product:Putative peptidase, M20D family \| Pathway: \| COG: Amino acid transport and metabolism	1.2	`NA`	0.39	Inferelator: 1 Hypergeometric: 1 TF Influences from Inferelator CD630_27220 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms TF Influences from Hypergeometric Test CD630_32450 - prdR Type: Gene Product:Transcriptional regulator, sigma-54-dependent \| Pathway: \| COG: Transcription
Module_73	29 CD630_31200 - Type: Gene Product:Transcriptional regulator, AbrB family \| Pathway: \| COG: Transcription CD630_19350 - spoVS Type: Gene Product:Stage V sporulation protein S \| Pathway: \| COG: Function unknown CD630_16950 - Type: Gene Product:Putative symporter protein \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_18190 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_26310 - Type: Gene Product:Putative membrane protein, UPF0078 family \| Pathway: Lipid metabolism \| COG: Function unknown CD630_03530 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_13370 - Type: Gene Product:Transcriptional regulator, RpiR family \| Pathway: \| COG: Transcription CD630_15060 - Type: Gene Product:Putative drug/sodium antiporter, MATE family \| Pathway: \| COG: Defense mechanisms CD630_21620 - Type: Gene Product:Putative GCN5-related N-acetyltransferase-likeprotein \| Pathway: \| COG: Function unknown CD630_09860 - rpsA Type: Gene Product:30S ribosomal protein S1 \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_31190 - Type: Gene Product:Putative UDP-glycosyltransferase, MGT subfamily \| Pathway: \| COG: Energy production and conversion, Carbohydrate transport and metabolism CD630_21110 - Type: Gene Product:Transcriptional regulator, DeoR family \| Pathway: \| COG: Transcription CD630_27660 - LcpB Type: Gene Product:Surface-anchoring factors, LytR-CpsA-Psr-likeprotein \| Pathway: \| COG: Transcription CD630_15200 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: CD630_07380 - Type: Gene Product:Putative exported protein \| Pathway: \| COG: Function unknown CD630_21950 - ftnA Type: Gene Product:Ferritin \| Pathway: \| COG: Inorganic ion transport and metabolism CD630_05830 - Type: Gene Product:Putative diguanylate kinase signaling protein \| Pathway: \| COG: Signal transduction mechanisms CD630_17300 - Type: Gene Product:Putative ATP-binding protein \| Pathway: \| COG: Cell cycle control, cell division, chromosome partitioning CD630_03541 - Type: Gene Product:Fragment of putative membrane protein \| Pathway: \| COG: Function unknown CD630_26300 - gpsA Type: Gene Product:Glycerol-3-phosphate dehydrogenase (NAD(P)+)(NAD(P)H-dependent glycerol-3-phosphate dehydrogenase) \| Pathway: Membrane lipid metabolism \| COG: Energy production and conversion CD630_21610 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: CD630_03520 - Type: Gene Product:Transcriptional regulator, RmlC-type \| Pathway: \| COG: Transcription CD630_21630 - Type: Gene Product:Putative alanyl-tRNA synthetase \| Pathway: \| COG: Function unknown CD630_15190 - Type: Gene Product:Putative acyltransferase \| Pathway: \| COG: Function unknown CD630_26320 - Type: Gene Product:Putative GTP-binding protein EngA \| Pathway: \| COG: Nucleotide transport and metabolism CD630_16940 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_05840 - Type: Gene Product:Putative diguanylate kinase signaling protein \| Pathway: \| COG: Signal transduction mechanisms CD630_05610 - Type: Gene Product:Putative aldo/keto reductase ; putativeferredoxin \| Pathway: \| COG: Energy production and conversion CD630_13390 - aspB Type: Gene Product:Aspartate aminotransferase (AspAT) (TransaminaseA) \| Pathway: \| COG: Amino acid transport and metabolism	0.00000000000089	`NA`	0.60	Inferelator: 2 Hypergeometric: 0 TF Influences from Inferelator CD630_01710 - rex Type: Gene Product:Transcriptional regulator, Redox-sensingrepressor Rex \| 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`
Module_180	9 CD630_14980 - sigA2 Type: Gene Product:RNA polymerase sigma factor SigA2 (sigma-43) \| Pathway: \| COG: Transcription CD630_00511 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_29521 - Type: Gene Product:Fragment of ABC-type transport system,ATP-binding protein (Part 11) \| Pathway: \| COG: Amino acid transport and metabolism, Function unknown, Amino acid transport and metabolism CD630_01280 - fabZ Type: Gene Product:(3R)-hydroxymyristoyl-[acyl-carrier-protein]dehydratase \| Pathway: \| COG: Lipid transport and metabolism CD630_10640 - ccpA Type: Gene Product:Transcriptional regulator, LacI family \| Pathway: \| COG: Transcription CD630_08080 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: CD630_21800 - Type: Gene Product:Putative DEAD-like helicase \| Pathway: \| COG: Replication, recombination and repair CD630_25620 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_01270 - mreB1 Type: Gene Product:Rod shape-determining protein MreB \| Pathway: \| COG: Cell cycle control, cell division, chromosome partitioning	0.03	`NA`	0.36	Inferelator: 1 Hypergeometric: 0 TF Influences from Inferelator 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_89	27 CD630_26550 - murF Type: Gene Product:UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase (UDP-MurNAc-pentapeptide synthetase)(D-alanyl-D-alanine-adding enzyme) \| Pathway: Cell wall biogenesis \| COG: Cell wall/membrane/envelope biogenesis CD630_34380 - cobU Type: Gene Product:Bifunctional adenosylcobalamin biosynthesisprotein CobU [Adenosylcobinamide kinase;Adenosylcobinamide-phosphate guanylyltransferase] \| Pathway: \| COG: Coenzyme transport and metabolism CD630_26470 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_18150 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_26490 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_35880 - carB1 Type: Gene Product:Carbamoyl-phosphate synthase large chain 1 \| Pathway: Amino-acid biosynthesis \| COG: Nucleotide transport and metabolism CD630_18170 - Type: Gene Product:Putative acyltransferase \| Pathway: \| COG: Lipid transport and metabolism CD630_35400 - metG Type: Gene Product:Methionyl-tRNA synthetase (Methionine--tRNAligase) (MetRS) \| Pathway: \| COG: Translation, ribosomal structure and biogenesis CD630_34370 - cobS Type: Gene Product:Cobalamin synthase CobS (Cobalamin-5-phosphatesynthase) \| Pathway: Cofactor biosynthesis \| COG: Coenzyme transport and metabolism CD630_26520 - spoVE Type: Gene Product:Cell division/stage V sporulation protein \| Pathway: \| COG: Cell cycle control, cell division, chromosome partitioning CD630_35390 - Type: Gene Product:Putative deoxyribonuclease \| Pathway: \| COG: Replication, recombination and repair CD630_18140 - Type: Gene Product:Putative phosphoglycerate mutase \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_35910 - carA Type: Gene Product:Carbamoyl-phosphate synthase small chain \| Pathway: Amino-acid biosynthesis \| COG: Nucleotide transport and metabolism CD630_36250 - Type: Gene Product:Putative signaling protein \| Pathway: \| COG: Signal transduction mechanisms CD630_26500 - Type: Gene Product:Putative cell division protein Fts-Q type \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_18160 - cmk Type: Gene Product:Cytidylate kinase (CK) (Cytidine monophosphatekinase) (CMP kinase) \| Pathway: \| COG: Nucleotide transport and metabolism CD630_26540 - mraY Type: Gene Product:Phospho-N-acetylmuramoyl-pentapeptide-transferase(UDP- MurNAc-pentapeptide phosphotransferase) \| Pathway: Cell wall biogenesis \| COG: Cell wall/membrane/envelope biogenesis CD630_35890 - carA Type: Gene Product:Carbamoyl-phosphate synthase small chain \| Pathway: Amino-acid biosynthesis \| COG: Nucleotide transport and metabolism CD630_34390 - cobT Type: Gene Product:Nicotinate-nucleotide--dimethylbenzimidazolephosphoribosyltransferase (NN:DBI PRT)(N(1)-alpha-phosphoribosyltransferase) \| Pathway: Nucleoside biosynthesis \| COG: Coenzyme transport and metabolism CD630_26480 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_24800 - Type: Gene Product:Putative hydrolase \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_18180 - ispH Type: Gene Product:4-hydroxy-3-methylbut-2-enyl diphosphatereductase \| Pathway: Isoprenoid biosynthesis \| COG: Lipid transport and metabolism CD630_34360 - cobC Type: Gene Product:Cobalamin biosynthesis phosphoglycerate mutaseCobC \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_35920 - pyrF Type: Gene Product:Orotidine 5'-phosphate decarboxylase (OMPdecarboxylase) (OMPDCase) (OMPdecase) \| Pathway: Pyrimidine metabolism \| COG: Nucleotide transport and metabolism CD630_26530 - murD Type: Gene Product:UDP-N-acetylmuramoylalanine--D-glutamate ligase(UDP-N- acetylmuramoyl-L-alanyl-D-glutamate synthetase)(D-glutamic acid- adding enzyme) \| Pathway: Cell wall biogenesis \| COG: Cell wall/membrane/envelope biogenesis CD630_26510 - murG Type: Gene Product:UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosaminetransferase \| Pathway: Cell wall biogenesis \| COG: Cell wall/membrane/envelope biogenesis CD630_35900 - carB2 Type: Gene Product:Carbamoyl-phosphate synthase large chain 2 \| Pathway: Amino-acid biosynthesis \| COG: Nucleotide transport and metabolism	8.7	`NA`	0.47	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_276	23 CD630_32020 - Type: Gene Product:Two-component sensor histidine kinase \| Pathway: \| COG: Signal transduction mechanisms CD630_02880 - Type: Gene Product:PTS system, mannose/fructose/sorbose IICcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_16890 - Type: Gene Product:Two-component sensor histidine kinase \| Pathway: \| COG: Signal transduction mechanisms CD630_06390 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_02860 - Type: Gene Product:PTS system, mannose/fructose/sorbose IIAcomponent \| Pathway: \| COG: CD630_02840 - Type: Gene Product:PTS system, mannose/fructose/sorbose IIAcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_02900 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_31920 - cwp21 Type: Gene Product:Putative cell surface peptidase, M4 family \| Pathway: \| COG: Cell wall/membrane/envelope biogenesis CD630_33610 - Type: Gene Product:Putative drug/sodium antiporter, MATE family \| Pathway: \| COG: Defense mechanisms CD630_32030 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms CD630_16860 - Type: Gene Product:Transcriptional regulator, repressor-like \| Pathway: \| COG: Transcription CD630_28100 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Replication, recombination and repair CD630_36600 - Type: Gene Product:Putative membrane protein \| Pathway: \| COG: Function unknown CD630_31700 - eno Type: Gene Product:Enolase (2-phosphoglycerate dehydratase)(2-phospho-D-glycerate hydro-lyase) \| Pathway: Carbohydrate degradation \| COG: Carbohydrate transport and metabolism CD630_24190 - Type: Gene Product:Transcriptional regulator, AraC family \| Pathway: \| COG: Transcription CD630_02890 - Type: Gene Product:PTS system, mannose/fructose/sorbose IIDcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_16880 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms CD630_02910 - Type: Gene Product:Putative peptidase, M20A family \| Pathway: \| COG: Amino acid transport and metabolism CD630_05750 - Type: Gene Product:Conserved hypothetical protein \| Pathway: \| COG: Function unknown CD630_02850 - Type: Gene Product:PTS system, mannose/fructose/sorbose IIBcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_02870 - Type: Gene Product:PTS system, mannose/fructose/sorbose IIBcomponent \| Pathway: \| COG: Carbohydrate transport and metabolism CD630_16850 - Type: Gene Product:Putative binding protein \| Pathway: \| COG: Replication, recombination and repair CD630_16870 - Type: Gene Product:Putative lipoprotein \| Pathway: \| COG:	0.00000036	`NA`	0.52	Inferelator: 3 Hypergeometric: 1 TF Influences from Inferelator CD630_06700 - Type: Gene Product:Transcriptional regulator, beta-lactamsrepressor \| Pathway: \| COG: Transcription CD630_16860 - Type: Gene Product:Transcriptional regulator, repressor-like \| Pathway: \| COG: Transcription CD630_17820 - Type: Gene Product:Two-component response regulator \| Pathway: \| COG: Signal transduction mechanisms TF Influences from Hypergeometric Test CD630_31760 - glnF Type: Gene Product:RNA polymerase sigma-54 factor \| Pathway: \| COG: Transcription