List of Transcription Factors
The classification of factors below is based on the existence of the Pfam motifs (Sanger Center, UK). Since these motifs do not always correspond to DNA-binding domains, a factor can belong to multiple families.

Helix turn helix family
AsnC_trans_reg AsnC family
DUF24 HxlR-like helix-turn-helix
DUF387 Putative transcriptional regulators (YpuH-like)
GerE Bacterial regulatory proteins, luxR family
HTH_1 Bacterial regulatory helix-turn-helix protein, lysR family
HTH_3 Helix-turn-helix
HTH_5 Bacterial regulatory protein, arsR family
HTH_6 Helix-turn-helix domain, rpiR family
HTH_8 Bacterial regulatory protein, Fis family
HTH_10 HTH DNA binding domain
HTH_11 Helix-turn-helix
HTH_AraC Bacterial regulatory helix-turn-helix proteins, AraC family
HTH_Mga M protein trans-acting positive regulator (MGA) HTH domain
HTH_psq helix-turn-helix, Psq domain
LexA_DNA_bind LexA DNA binding domain
MarR MarR family
ROK ROK family
Crp Bacterial regulatory proteins, crp family
DeoR Bacterial regulatory proteins, deoR family
GntR Bacterial regulatory proteins, gntR family
HTH_DeoR DeoR-like helix-turn-helix domain
HTH_IclR IclR helix-turn-helix domain
Arg_repressor Arginine repressor, DNA binding domain
LacI Bacterial regulatory proteins, lacI family
MerR MerR family regulatory protein
TetR_N Bacterial regulatory proteins, tetR family
PadR Transcriptional regulator PadR-like family
Mga Mga helix-turn-helix domain
FUR Ferric uptake regulator family
Rrf2 Transcriptional regulator
HTH_CodY CodY helix-turn-helix domain
Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain
Put_DNA-bind_N Putative DNA-binding protein N-terminus
Fe_dep_repress Iron dependent repressor, N-terminal Domain
Trans_reg_C Transcriptional regulatory protein, C terminal domain
TrmB Sugar-specific transcriptional regulator TrmB
Other family
Bac_DNA_binding Bacterial DNA-binding protein
CtsR Firmicute transcriptional repressor of class III stress genes (CtsR)
G3P_antiterm Glycerol-3-phosphate responsive antiterminator
HrcA HrcA protein C terminal domain
LytR_cpsA_psr Cell envelope-related transcriptional attenuator
MecA Negative regulator of genetic competence (MecA)
FMN_bind_2 Putative FMN-binding domain
CAT_RBD CAT RNA binding domain
PRD PRD domain
Ribosomal_S30AE Sigma 54 modulation protein / S30EA ribosomal protein
SpoVT_AbrB SpoVT / AbrB like domain
Sugar-bind Putative sugar-binding domain
TrpBP Tryptophan RNA-binding attenuator protein
Response_reg Response regulator receiver domain
LysR_substrate LysR substrate binding domain
SinI Anti-repressor SinI
GAF GAF domain
MerR-DNA-bind MerR, DNA binding
Spo0A_C Sporulation initiation factor Spo0A C terminal
YcbB YcbB domain
LytTR LytTr DNA-binding domain
HutP HutP
ComK ComK protein
PucR Purine catabolism regulatory protein-like family
PuR_N Bacterial purine repressor, N-terminal
Sigma54_activat Sigma-54 interaction domain
tRNA tRNA
Ribosomal_L20 Ribosomal protein L20
Sigma factors
Sigma54_DBD Sigma-54, DNA binding domain
sigma70 Sigma-70 factor family
Not assigned
ND Not assigned to Pfam domains


Helix turn helix family

 Domain: AsnC_trans_reg
ORF SubtiList Other
family		 Description Num. of
regulated operons
AlaR BG12361
regulation of the alaRT operon0
AzlB BG11914
negative regulation of the azlBCD operon1
LrpA BG12122
negative regulation of glyA transcription and KinB-dependent sporulation1
LrpB BG12123
negative regulation of glyA transcription and KinB-dependent sporulation1
LrpC BG12056
transcriptional regulator (Lrp/AsnC family)1
YwrC BG12522HTH_Mgaunknown; similar to transcriptional regulator (Lrp/AsnC family)0


 Domain: DUF24
ORF SubtiList Other
family		 Description Num. of
regulated operons
HxlR BG11184
positive regulator of hxlAB expression1
YdeP BG12143
unknown; similar to cinnamoyl ester hydrolase0
YdzF BG12809
unknown; similar to cinnamoyl ester hydrolase0
YkvN BG13316
unknown; similar to unknown proteins from B. subtilis0
YodB BG13531
unknown; similar to unknown proteins1
YtcD BG13831
unknown; similar to unknown proteins0
YvaP BG14071
unknown; similar to unknown proteins0
YybR BG10013
unknown; similar to ester hydrolase0


 Domain: DUF387
ORF SubtiList Other
family		 Description Num. of
regulated operons
YpuH BG10525
unknown; similar to unknown proteins0


 Domain: GerE
ORF SubtiList Other
family		 Description Num. of
regulated operons
ComA BG10381Response_regpositive regulation of late competence genes and surfactin production (comS, srfA, rapA, rapC-phrC)7
DegU BG10393Response_regessential for degradative enzyme (sacB and degQ) expression and competence regulation (positive regulation of comK expression)13
GerE BG10355
required for the expression of late spore coat genes (germination)20
YdfI BG12156Response_reg, HTH_10unknown; similar to two-component response regulator [YdfH]1
YfiK BG12216Response_reg, HTH_10unknown; similar to two-component response regulator [YfiJ]0
YhcZ BG13006Response_regunknown; similar to two-component response regulator [YhcY]0
YocG BG13520Response_regunknown; similar to two-component response regulator [YocF]1
YvfU BG12446Response_regunknown; similar to two-component response regulator [YvfT]0
YvqC BG14133Response_regunknown; similar to two-component response regulator [YvqE]0
YxjL BG11895Response_regunknown; similar to two-component response regulator [YxjM]0


 Domain: HTH_1
ORF SubtiList Other
family		 Description Num. of
regulated operons
AlsR BG10470LysR_substrateregulation of the alpha-acetolactate operon (alsSD)2
CcpC BG13297LysR_substratecarbon catabolite and anaerobic repression of citB and citZ3
CitR BG10853LysR_substratenegative regulation of the citrate synthase I gene (citA)1
GltC BG10810LysR_substratepositive regulation of the glutamate synthase operon (gltAB)2
GltR BG11942LysR_substratenegative regulation of the glutamate synthase operon (gltAB)2
YcgK BG12009LysR_substrateunknown; similar to transcriptional regulator (LysR family)0
YclA BG12022LysR_substrateunknown; similar to transcriptional regulator (LysR family)0
YoaU BG13491LysR_substrateunknown; similar to transcriptional regulator (LysR family)0
YofA BG13552LysR_substrateunknown; similar to transcriptional regulator (LysR family)1
YraN BG12278LysR_substrateunknown; similar to transcriptional regulator (LysR family)0
YrdQ BG12288LysR_substrateunknown; similar to transcriptional regulator (LysR family)0
YtlI BG13877LysR_substrateunknown; similar to transcriptional regulator (LysR family)1
YusT BG14032LysR_substrateunknown; similar to transcriptional regulator (LysR family)0
YvbU BG14087LysR_substrateunknown; similar to transcriptional regulator (LysR family)0
YwbI BG10570LysR_substrateunknown; similar to transcriptional regulator (LysR family)0
YwfK BG10635LysR_substrateunknown; similar to transcriptional regulator (LysR family)2
YwqM BG12517LysR_substrateunknown; similar to transcriptional regulator (LysR family)0
YxjO BG11898LysR_substrateunknown; similar to transcriptional regulator (LysR family)0
YybE BG10026LysR_substrateunknown; similar to transcriptional regulator (LysR family)0


 Domain: HTH_3
ORF SubtiList Other
family		 Description Num. of
regulated operons
AnsR BG10299
negative regulation of the ansAB operon2
SinR BG10754SinIregulation of post-exponential-phase responses genes (positive regulation of comK; negative regulation of aprE, kinB, sigD, spo0A, spoIIA, spoIIE, spoIIG)5
Slr BG11858SinIpositive regulation of competence development and sporulation genes0
Xre BG10994
negative regulation of the defective prophage PBSX genes2
YazB BG12701
unknown; similar to unknown proteins0
YdcN BG12101
unknown; similar to transcriptional regulator (phage-related) (Xre family)0
YobD BG13497
unknown; similar to transcriptional regulator (phage-related) (Xre family)0
YonR BG13628
unknown; similar to transcriptional regulator (phage-related) (Xre family)0
YopO BG13648
unknown; 0
YopS BG13652
unknown; similar to unknown proteins from B. subtilis0
YozG BG13754
unknown; similar to transcriptional regulator0
YqaE BG11256
unknown; similar to transcriptional regulator (phage-related) (Xre family)0
YqaF BG11257
unknown; 0
YqaG BG11258
unknown; 0
YvaN BG14069
unknown; similar to immunity repressor protein4
YvaO BG14070
unknown; similar to immunity repressor protein0
YvzC BG14159LacIunknown; similar to unknown proteins0


 Domain: HTH_5
ORF SubtiList Other
family		 Description Num. of
regulated operons
ArsR BG11301
arsenic resistance operon repressor (arsR-yqcK-arsBC)1
YczG BG12781
unknown; similar to transcriptional regulator (ArsR family)0
YdeT BG12147
unknown; similar to transcriptional regulator (ArsR family)0
YdfF BG12153
unknown; similar to unknown proteins0
YdgJ BG12177MarRunknown; similar to transcriptional regulator (MarR family)0
YozA BG13748
unknown; similar to transcriptional regulator (ArsR family)0
YvbA BG14078HTH_11unknown; similar to transcriptional regulator (ArsR family)2


 Domain: HTH_6
ORF SubtiList Other
family		 Description Num. of
regulated operons
YbbH BG11569
unknown; similar to unknown proteins0
YfiA BG11847
unknown; similar to unknown proteins1


 Domain: HTH_8
ORF SubtiList Other
family		 Description Num. of
regulated operons
AcoR BG11790Sigma54_activat, GAFpositive regulation of the acetoin dehydrogenase operon (acoABCL)1
BkdR BG11721Sigma54_activatinvolved in the control of isoleucine and valine utilization as sole nitrogen sources (bkd operon)1
RocR BG10723Sigma54_activatpositive regulation of arginine utilization operons (rocABC, rocDEF, rocG) (arginine and ornithine utilization)4


 Domain: HTH_10
ORF SubtiList Other
family		 Description Num. of
regulated operons
YdfI BG12156Response_reg, GerEunknown; similar to two-component response regulator [YdfH]1
YfiK BG12216Response_reg, GerEunknown; similar to two-component response regulator [YfiJ]0


 Domain: HTH_11
ORF SubtiList Other
family		 Description Num. of
regulated operons
BirA BG11206
negative regulation of the biotin operon (bioWAFDBI)1
CitT BG12577Response_reginvolved in the response to the environmental Mg-citrate complex (positive regulation of citM)1
CodY BG10968HTH_CodYnegative regulation of srfA and comK genes (in the presence of casamino-acids), dpp operon (rich medium), gabP gene and hut operon (in the presence of amino acids), ure operon (exponential growth)15
DctR BG12074Response_reg, Crpinvolved in C4-dicarboxylate transport1
GlcR BG12503DeoR, HTH_DeoRnegative regulation of the phosphotransferase system0
IolR BG11364DeoR, HTH_DeoRnegative regulation of the myo-inositol catabolism operon (iolABCDEFGHIJ/iolRS)3
LicR BG11346Mga, PRDpositive regulation of the lichenan operon (licBCAH) (lichenan degradation product utilization)1
ManR BG13175PRD, HTH_DeoRpositive regulation of the mannose operon (manPA-yjdF)0
YcnK BG12047HTH_DeoRunknown; similar to transcriptional regulator (DeoR family)0
YcxD BG10175GntRunknown; similar to transcriptional regulator (GntR family) / aminotransferase (MocR-like)0
YqzB BG13768HTH_DeoRunknown; similar to unknown proteins2
YrxA BG10865
unknown; similar to transcriptional regulator2
YulB BG12384DeoR, HTH_DeoRunknown; similar to transcriptional regulator (DeoR family)0
YvbA BG14078HTH_5unknown; similar to transcriptional regulator (ArsR family)2
YvnA BG14122MarRunknown; similar to unknown proteins from B. subtilis0


 Domain: HTH_AraC
ORF SubtiList Other
family		 Description Num. of
regulated operons
AdaA BG10166
adaptative response to DNA alkylation; positive regulation of the adaAB operon2
YbbB BG10834
unknown; similar to transcriptional regulator (AraC/XylS family)0
YbfI BG12738
unknown; similar to transcriptional regulator (AraC/XylS family)0
YbfP BG12744
unknown; similar to transcriptional regulator (AraC/XylS family)0
YdeC BG12130
unknown; similar to transcriptional regulator (AraC/XylS family)0
YdeE BG12132
unknown; similar to transcriptional regulator (AraC/XylS family)0
YesN BG12848Response_regunknown; similar to two-component response regulator [YesM]0
YesS BG12853
unknown; similar to transcriptional regulator (AraC/XylS family)0
YfiF BG11853
unknown; similar to transcriptional regulator (AraC/XylS family)0
YisR BG11064
unknown; similar to transcriptional regulator (AraC/XylS family)0
YobQ BG13508
unknown; similar to transcriptional regulator (AraC/XylS family)0
YtdP BG13838
unknown; similar to transcriptional regulator (AraC/XylS family)0


 Domain: HTH_Mga
ORF SubtiList Other
family		 Description Num. of
regulated operons
YwrC BG12522AsnC_trans_regunknown; similar to transcriptional regulator (Lrp/AsnC family)0


 Domain: HTH_psq
ORF SubtiList Other
family		 Description Num. of
regulated operons
YccF BG12756
unknown; 0


 Domain: LexA_DNA_bind
ORF SubtiList Other
family		 Description Num. of
regulated operons
LexA BG10678
negative regulation of the SOS regulon (DNA-damage inducible genes)34


 Domain: MarR
ORF SubtiList Other
family		 Description Num. of
regulated operons
Hpr BG10659
negative regulation of sporulation and extracellular proteases genes (aprE, nprE, sin)8
YbfA BG12732
unknown; 0
YcgE BG12003
unknown; similar to transcriptional regulator0
YdcH BG12095
unknown; similar to unknown proteins from B. subtilis0
YdgG BG12174
unknown; similar to transcriptional regulator (MarR family)0
YdgJ BG12177HTH_5unknown; similar to transcriptional regulator (MarR family)0
YetL BG12868
unknown; similar to transcriptional regulator (MarR family)0
YfiV BG12898
unknown; similar to transcriptional regulator (MarR family)0
YhbI BG13003
unknown; similar to transcriptional regulator (MarR family)0
YhjH BG13074
unknown; similar to unknown proteins0
YkmA BG13239
unknown; similar to unknown proteins1
YkoM BG13258
unknown; similar to transcriptional regulator (MarR family)0
YkvE BG13310
unknown; similar to transcriptional regulator (MarR family)0
YpoP BG11626
unknown; similar to transcriptional regulator (MarR family)0
YsmB BG12332
unknown; similar to transcriptional regulator (MarR family)0
YusO BG14027
unknown; similar to transcriptional regulator (MarR family)0
YvmB BG11018
unknown; similar to unknown proteins0
YvnA BG14122HTH_11unknown; similar to unknown proteins from B. subtilis0
YwaE BG10556
unknown; similar to transcriptional regulator (MarR family)0
YwhA BG12455
unknown; similar to transcriptional regulator (MarR family)0
YwoH BG12495TrmBunknown; similar to transcriptional regulator (MarR family)0
YxaD BG11106
unknown; similar to transcriptional regulator (MarR family)0
YybA BG10030
unknown; similar to transcriptional regulator (MarR family)0


 Domain: ROK
ORF SubtiList Other
family		 Description Num. of
regulated operons
GlcK BG11685
glucose kinase0
XylR BG11986
negative regulation of the xylose operon (xylAB)2
YdhR BG12195
unknown; similar to fructokinase0


 Domain: Crp
ORF SubtiList Other
family		 Description Num. of
regulated operons
DctR BG12074Response_reg, HTH_11involved in C4-dicarboxylate transport1
FNR BG11343
regulation of anaerobic genes (narK-fnr, narGHJI, lctEP, alsSD)4


 Domain: DeoR
ORF SubtiList Other
family		 Description Num. of
regulated operons
FruR BG12589HTH_DeoRnegative regulation of the fructose operon (fruRBA)1
GlcR BG12503HTH_DeoR, HTH_11negative regulation of the phosphotransferase system0
IolR BG11364HTH_DeoR, HTH_11negative regulation of the myo-inositol catabolism operon (iolABCDEFGHIJ/iolRS)3
YulB BG12384HTH_DeoR, HTH_11unknown; similar to transcriptional regulator (DeoR family)0


 Domain: GntR
ORF SubtiList Other
family		 Description Num. of
regulated operons
AraR BG11913
negative regulation of the L-arabinose metabolic operon (araABDLMNPQ-abfA) and of the araE/araR genes5
GabR BG12042
positive regulation of gabTD and negative autoregulation2
GntR BG10648
negative regulation of the gluconate operon (gntRKPZ) (gluconate utilization)1
TreR BG11011
negative regulation of the trehalose operon (trePAR)1
YbgA BG12747
unknown; similar to transcriptional regulator (GntR family)0
YcbG BG11162
unknown; similar to transcriptional regulator (GntR family)0
YcxD BG10175HTH_11unknown; similar to transcriptional regulator (GntR family) / aminotransferase (MocR-like)0
YdeF BG12133
unknown; similar to transcriptional regulator (GntR family) / aminotransferase (MocR-like)0
YdeL BG12139
unknown; similar to transcriptional regulator (GntR family) / aminotransferase (MocR-like)0
YdfD BG12151
unknown; similar to transcriptional regulator (GntR family) / aminotransferase (MocR-like)0
YdhC BG12180
unknown; similar to transcriptional regulator (GntR family)0
YdhQ BG12194
unknown; similar to transcriptional regulator (GntR family)0
YhcF BG11584
unknown; similar to transcriptional regulator (GntR family)0
YhdI BG13015
unknown; similar to transcriptional regulator (GntR family) / aminotransferase (MocR-like)0
YisV BG13101
unknown; similar to transcriptional regulator (GntR family) / aminotransferase (MocR-like)0
YmfC BG13423
unknown; similar to transcriptional regulator (GntR family)0
YtrA BG13911
unknown; similar to transcriptional regulator (GntR family)1
YurK BG13997
unknown; similar to transcriptional regulator (GntR family)0
YvoA BG14124HTH_DeoRunknown; similar to transcriptional regulator (GntR family)0
YydK BG11484
unknown; similar to transcriptional regulator (GntR family)0


 Domain: HTH_DeoR
ORF SubtiList Other
family		 Description Num. of
regulated operons
FruR BG12589DeoRnegative regulation of the fructose operon (fruRBA)1
GlcR BG12503DeoR, HTH_11negative regulation of the phosphotransferase system0
IolR BG11364DeoR, HTH_11negative regulation of the myo-inositol catabolism operon (iolABCDEFGHIJ/iolRS)3
ManR BG13175PRD, HTH_11positive regulation of the mannose operon (manPA-yjdF)0
YcnK BG12047HTH_11unknown; similar to transcriptional regulator (DeoR family)0
YqzB BG13768HTH_11unknown; similar to unknown proteins2
YtzE BG13939
unknown; similar to transcriptional regulator (DeoR family)0
YulB BG12384DeoR, HTH_11unknown; similar to transcriptional regulator (DeoR family)0
YvoA BG14124GntRunknown; similar to transcriptional regulator (GntR family)0


 Domain: HTH_IclR
ORF SubtiList Other
family		 Description Num. of
regulated operons
KipR BG11214
regulator of the kip operon1


 Domain: Arg_repressor
ORF SubtiList Other
family		 Description Num. of
regulated operons
AhrC BG10309
negative regulation of arginine biosynthesis and positive regulation of arginine catabolism (roc operons)3


 Domain: LacI
ORF SubtiList Other
family		 Description Num. of
regulated operons
CcpA BG10376
carbon catabolite control protein involved in glucose regulation of several genes; mediates carbon catabolite repression (CCR)44
CcpB BG10045
mediates catabolite repression by glucose, mannitol, and sucrose of gluconate (gnt) and xylose (xyl) operons, in parallel to CcpA2
DegA BG10847
stimulates degradation of glutamine phosphoribosylpyrophosphate amidotransferase (PurF)0
ExuR BG13211
repression of the hexuronate utilization operon (uxaC-yjmBCD-uxuA-yjmf-exuTR-uxaBA)1
KdgR BG11398
negative regulation of the pectin utilization operon (kdgRKAT)1
LacR BG12435
negative regulation of the beta-galactosidase gene (lacA)1
MsmR BG12626
transcriptional regulator (LacI family)0
RbsR BG10876
negative regulation of the ribose operon (rbsRKDACB)0
YhjM BG13079
unknown; similar to transcriptional regulator (LacI family)1
YkvZ BG13327
unknown; similar to transcriptional regulator (LacI family)0
YvdE BG12414
unknown; similar to transcriptional regulator (LacI family)0
YvzC BG14159HTH_3unknown; similar to unknown proteins0


 Domain: MerR
ORF SubtiList Other
family		 Description Num. of
regulated operons
BltR BG10904
regulation of the bltD operon1
BmrR BG10304
positive regulation of the bmrUR operon1
GlnR BG10424
negative regulation of the glutamine synthetase gene (glnA)4
Mta BG12482MerR-DNA-bindpositive regulation of multidrug-efflux transporter genes (bmr and blt)4
TnrA BG11805
global nitrogen regulation (positive regulation of nrgAB, nasBCDEF, gabP, ureABC, guaD; negative regulation of glnRA, gltAB)26
YdfL BG12159
unknown; similar to multidrug-efflux transporter regulator0
YfmP BG12967
unknown; similar to transcriptional regulator (MerR family)0
YhdQ BG13023
unknown; similar to transcriptional regulator (MerR family)0
YraB BG13777
unknown; similar to transcriptional regulator (MerR family)0
YyaN BG10038
unknown; similar to transcriptional regulator (MerR family)0


 Domain: TetR_N
ORF SubtiList Other
family		 Description Num. of
regulated operons
LmrA BG12612
negative regulation of the lincomycin operon (lmrBA)2
PksA BG12647
regulation of the polyketide synthase operon (pks)0
YcnC BG12039
unknown; similar to transcriptional regulator (TetR/AcrR family)0
YdeS BG12146
unknown; similar to transcriptional regulator (TetR/AcrR family)0
YdgC BG12170
unknown; similar to unknown proteins0
YerO BG12841
unknown; similar to transcriptional regulator (TetR/AcrR family)0
YezE BG14194
unknown; similar to transcriptional regulator (TetR family)0
YfiR BG12894
unknown; similar to transcriptional regulator (TetR/AcrR family)0
YhgD BG10432
unknown; similar to transcriptional regulator (TetR/AcrR family)0
YrhI BG12298
unknown; similar to transcriptional regulator (TetR/AcrR family)1
YsiA BG12330
unknown; similar to transcriptional regulator (TetR/AcrR family)5
YttP BG13927
unknown; similar to unknown proteins0
YuxN BG11072
unknown; similar to unknown proteins from B. subtilis0
YvaF BG14062
unknown; 0
YvdT BG12428
unknown; similar to transcriptional regulator (TetR/AcrR family)0
YvkB BG14113
unknown; similar to transcriptional regulator (TetR/AcrR family)0
YwcC BG10579
unknown; similar to unknown proteins0
YxaF BG11108
unknown; similar to transcriptional regulator0
YxbF BG11356
unknown; similar to unknown proteins0


 Domain: PadR
ORF SubtiList Other
family		 Description Num. of
regulated operons
PadR BG12220
repression of padC expression0


 Domain: Mga
ORF SubtiList Other
family		 Description Num. of
regulated operons
LicR BG11346PRD, HTH_11positive regulation of the lichenan operon (licBCAH) (lichenan degradation product utilization)1


 Domain: FUR
ORF SubtiList Other
family		 Description Num. of
regulated operons
Fur BG11766
negative regulation of siderophore biosynthesis and transcription of ferri-siderophore uptake genes23
PerR BG12227
negative regulation of the peroxide regulon (mrgA, katA, ahpCF)9
Zur BG11668
zinc-specific repression of operons implicated in zinc uptake (yciC, ycdHI-yceA)3


 Domain: Rrf2
ORF SubtiList Other
family		 Description Num. of
regulated operons
YhdE BG13011
unknown; similar to unknown proteins3
YrzC BG13813
unknown; similar to unknown proteins8
YwgB BG12454
unknown; similar to unknown proteins0


 Domain: HTH_CodY
ORF SubtiList Other
family		 Description Num. of
regulated operons
CodY BG10968HTH_11negative regulation of srfA and comK genes (in the presence of casamino-acids), dpp operon (rich medium), gabP gene and hut operon (in the presence of amino acids), ure operon (exponential growth)15


 Domain: Bac_DnaA_C
ORF SubtiList Other
family		 Description Num. of
regulated operons
DnaA BG10065
initiation of chromosome replication (DNA synthesis)2


 Domain: Put_DNA-bind_N
ORF SubtiList Other
family		 Description Num. of
regulated operons
YdiH BG12205
unknown; similar to DNA-binding protein4


 Domain: Fe_dep_repress
ORF SubtiList Other
family		 Description Num. of
regulated operons
MntR BG11702
regulation of manganese transport (repression of mntH in high Mn(II) conditions, activation of mntABCD under low Mn(II) conditions)2


 Domain: Trans_reg_C
ORF SubtiList Other
family		 Description Num. of
regulated operons
CssR BG14131Response_reginvolved in the control of cellular responses to protein secretion stress3
PhoP BG10363Response_reginvolved in phosphate regulation (phoA, phoB, phoD, resABCDE, tagAB, tagDEF, tuaA-H)19
ResD BG10534Response_regactivation role in global regulation of aerobic and anaerobic respiration (resA, ctaA, qcrABC, fnr, lctEP)13
YbdJ BG12723Response_regunknown; similar to two-component response regulator [YbdK]0
YcbL BG11167Response_regunknown; similar to two-component response regulator [YcbM]0
YclJ BG12031Response_regunknown; similar to two-component response regulator [YclK]0
YkoG BG13252Response_regunknown; similar to two-component response regulator [YkoH]0
YrkP BG11782Response_regunknown; similar to two-component response regulator [YrkQ]0
YtsA BG12340Response_regunknown; similar to two-component response regulator [YtsB]0
YvcP BG12405Response_regunknown; similar to two-component response regulator [YvcQ]0
YvrH BG12452Response_regunknown; similar to two-component response regulator [YvrG]7
YxdJ BG11126Response_regunknown; similar to two-component response regulator [YxdK]0
YycF BG10001Response_regunknown; similar to two-component response regulator [YycG]4


 Domain: TrmB
ORF SubtiList Other
family		 Description Num. of
regulated operons
YwoH BG12495MarRunknown; similar to transcriptional regulator (MarR family)0

Other family

 Domain: Bac_DNA_binding
ORF SubtiList Other
family		 Description Num. of
regulated operons
Hbs BG10276
involved in DNA repair, homologous recombination, and presecretory protein translocation1


 Domain: CtsR
ORF SubtiList Other
family		 Description Num. of
regulated operons
CtsR BG10145
negative regulation of class III stress genes (clpC, clpP, clpE)6


 Domain: G3P_antiterm
ORF SubtiList Other
family		 Description Num. of
regulated operons
GlpP BG10185
control of mRNA stability of glpD3


 Domain: HrcA
ORF SubtiList Other
family		 Description Num. of
regulated operons
HrcA BG10662
negative regulation of class I heat-shock genes (dnaK, groESL)2


 Domain: LytR_cpsA_psr
ORF SubtiList Other
family		 Description Num. of
regulated operons
LytR BG10404
attenuator role for lytABC and lytR expression2
YvhJ BG12449
unknown; similar to transcriptional regulator0
YwtF BG12537
unknown; similar to transcriptional regulator0


 Domain: MecA
ORF SubtiList Other
family		 Description Num. of
regulated operons
MecA BG10680
negative regulator of competence0
YpbH BG11434
unknown; similar to negative regulation of competence MecA homolog0


 Domain: FMN_bind_2
ORF SubtiList Other
family		 Description Num. of
regulated operons
PaiB BG10696
negative regulation of sporulation and degradative enzyme genes1


 Domain: CAT_RBD
ORF SubtiList Other
family		 Description Num. of
regulated operons
GlcT BG12593PRDessential for the expression of the ptsGHI operon1
LicT BG10474PRDrequired for substrate-dependent induction and catabolite repression of bglPH2
SacT BG10593PRDpositive regulation of sacA and sacP3
SacY BG10559PRDpositive regulation of levansucrase and sucrase synthesis (sucrase regulation)3


 Domain: PRD
ORF SubtiList Other
family		 Description Num. of
regulated operons
GlcT BG12593CAT_RBDessential for the expression of the ptsGHI operon1
LevR BG10677Sigma54_activatpositive regulation of the levanase operon (levDEFG/sacC)1
LicR BG11346Mga, HTH_11positive regulation of the lichenan operon (licBCAH) (lichenan degradation product utilization)1
LicT BG10474CAT_RBDrequired for substrate-dependent induction and catabolite repression of bglPH2
ManR BG13175HTH_DeoR, HTH_11positive regulation of the mannose operon (manPA-yjdF)0
MtlR BG12049
positive regulation of the mannitol operon (mtlAD)0
SacT BG10593CAT_RBDpositive regulation of sacA and sacP3
SacY BG10559CAT_RBDpositive regulation of levansucrase and sucrase synthesis (sucrase regulation)3


 Domain: Ribosomal_S30AE
ORF SubtiList Other
family		 Description Num. of
regulated operons
YvyD BG10740
unknown; similar to sigma-54 modulating factor of gram-negative bacteria0


 Domain: SpoVT_AbrB
ORF SubtiList Other
family		 Description Num. of
regulated operons
Abh BG10988
regulation of transition state genes0
AbrB BG10100
regulation of transition state genes (negative regulation of abrB, aprE, ftsAZ, kinC, motAB, nprE, pbpE, rbs, spo0H, spoVG, spo0E, tycA, sbo-alb, yqxM-sipW-tasA; positive regulation of comK, hpr)33
SpoVT BG10119
positive and negative regulation of sigma-G-dependent genes17


 Domain: Sugar-bind
ORF SubtiList Other
family		 Description Num. of
regulated operons
CggR BG14085
repression of gapA expression1
DeoR BG10982
negative regulation of the dra-nupC-pdp operon (deoxyribonucleoside)1


 Domain: TrpBP
ORF SubtiList Other
family		 Description Num. of
regulated operons
MtrB BG10278
regulation of tryptophan biosynthesis (required for transcription (and translation) attenuation in the trp operon); repression of the folate operon4


 Domain: Response_reg
ORF SubtiList Other
family		 Description Num. of
regulated operons
CheB BG10255
chemotaxis receptor demethylation0
CheV BG10823
modulation of CheA activity in response to attractants (chemotaxis)0
CheY BG10258
modulation of flagellar switch bias (chemotaxis)0
CitT BG12577HTH_11involved in the response to the environmental Mg-citrate complex (positive regulation of citM)1
ComA BG10381GerEpositive regulation of late competence genes and surfactin production (comS, srfA, rapA, rapC-phrC)7
CssR BG14131Trans_reg_Cinvolved in the control of cellular responses to protein secretion stress3
DctR BG12074Crp, HTH_11involved in C4-dicarboxylate transport1
DegU BG10393GerEessential for degradative enzyme (sacB and degQ) expression and competence regulation (positive regulation of comK expression)13
LytT BG11953LytTRinvolved in controlling the rate of autolysis0
PhoP BG10363Trans_reg_Cinvolved in phosphate regulation (phoA, phoB, phoD, resABCDE, tagAB, tagDEF, tuaA-H)19
ResD BG10534Trans_reg_Cactivation role in global regulation of aerobic and anaerobic respiration (resA, ctaA, qcrABC, fnr, lctEP)13
Spo0A BG10765Spo0A_Ccentral role in the initiation of sporulation (negative regulation of abrB, kinA, kinC, spo0A; positive regulation of spoIIA, spoIIE, spoIIG) (stage 0 sporulation)16
Spo0F BG10411
initiation of sporulation (stage 0 sporulation)0
YbdJ BG12723Trans_reg_Cunknown; similar to two-component response regulator [YbdK]0
YcbB BG10872YcbBunknown; similar to two-component response regulator [YcbA]0
YcbL BG11167Trans_reg_Cunknown; similar to two-component response regulator [YcbM]0
YccH BG11998LytTRunknown; similar to two-component response regulator [YccG]0
YclJ BG12031Trans_reg_Cunknown; similar to two-component response regulator [YclK]0
YdfI BG12156HTH_10, GerEunknown; similar to two-component response regulator [YdfH]1
YesN BG12848HTH_AraCunknown; similar to two-component response regulator [YesM]0
YfiK BG12216HTH_10, GerEunknown; similar to two-component response regulator [YfiJ]0
YhcZ BG13006GerEunknown; similar to two-component response regulator [YhcY]0
YkoG BG13252Trans_reg_Cunknown; similar to two-component response regulator [YkoH]0
YneI BG11250
unknown; similar to two-component response regulator (CheY homolog)0
YocG BG13520GerEunknown; similar to two-component response regulator [YocF]1
YrkP BG11782Trans_reg_Cunknown; similar to two-component response regulator [YrkQ]0
YtsA BG12340Trans_reg_Cunknown; similar to two-component response regulator [YtsB]0
YufM BG12348
unknown; similar to two-component response regulator [YufL]3
YvcP BG12405Trans_reg_Cunknown; similar to two-component response regulator [YvcQ]0
YvfU BG12446GerEunknown; similar to two-component response regulator [YvfT]0
YvqC BG14133GerEunknown; similar to two-component response regulator [YvqE]0
YvrH BG12452Trans_reg_Cunknown; similar to two-component response regulator [YvrG]7
YxdJ BG11126Trans_reg_Cunknown; similar to two-component response regulator [YxdK]0
YxjL BG11895GerEunknown; similar to two-component response regulator [YxjM]0
YycF BG10001Trans_reg_Cunknown; similar to two-component response regulator [YycG]4


 Domain: LysR_substrate
ORF SubtiList Other
family		 Description Num. of
regulated operons
AlsR BG10470HTH_1regulation of the alpha-acetolactate operon (alsSD)2
CcpC BG13297HTH_1carbon catabolite and anaerobic repression of citB and citZ3
CitR BG10853HTH_1negative regulation of the citrate synthase I gene (citA)1
GltC BG10810HTH_1positive regulation of the glutamate synthase operon (gltAB)2
GltR BG11942HTH_1negative regulation of the glutamate synthase operon (gltAB)2
YcgK BG12009HTH_1unknown; similar to transcriptional regulator (LysR family)0
YclA BG12022HTH_1unknown; similar to transcriptional regulator (LysR family)0
YoaU BG13491HTH_1unknown; similar to transcriptional regulator (LysR family)0
YofA BG13552HTH_1unknown; similar to transcriptional regulator (LysR family)1
YraN BG12278HTH_1unknown; similar to transcriptional regulator (LysR family)0
YrdQ BG12288HTH_1unknown; similar to transcriptional regulator (LysR family)0
YtlI BG13877HTH_1unknown; similar to transcriptional regulator (LysR family)1
YusT BG14032HTH_1unknown; similar to transcriptional regulator (LysR family)0
YvbU BG14087HTH_1unknown; similar to transcriptional regulator (LysR family)0
YwbI BG10570HTH_1unknown; similar to transcriptional regulator (LysR family)0
YwfK BG10635HTH_1unknown; similar to transcriptional regulator (LysR family)2
YwqM BG12517HTH_1unknown; similar to transcriptional regulator (LysR family)0
YxjO BG11898HTH_1unknown; similar to transcriptional regulator (LysR family)0
YybE BG10026HTH_1unknown; similar to transcriptional regulator (LysR family)0


 Domain: SinI
ORF SubtiList Other
family		 Description Num. of
regulated operons
SinR BG10754HTH_3regulation of post-exponential-phase responses genes (positive regulation of comK; negative regulation of aprE, kinB, sigD, spo0A, spoIIA, spoIIE, spoIIG)5
Slr BG11858HTH_3positive regulation of competence development and sporulation genes0


 Domain: GAF
ORF SubtiList Other
family		 Description Num. of
regulated operons
AcoR BG11790Sigma54_activat, HTH_8positive regulation of the acetoin dehydrogenase operon (acoABCL)1


 Domain: MerR-DNA-bind
ORF SubtiList Other
family		 Description Num. of
regulated operons
Mta BG12482MerRpositive regulation of multidrug-efflux transporter genes (bmr and blt)4


 Domain: Spo0A_C
ORF SubtiList Other
family		 Description Num. of
regulated operons
Spo0A BG10765Response_regcentral role in the initiation of sporulation (negative regulation of abrB, kinA, kinC, spo0A; positive regulation of spoIIA, spoIIE, spoIIG) (stage 0 sporulation)16


 Domain: YcbB
ORF SubtiList Other
family		 Description Num. of
regulated operons
YcbB BG10872Response_regunknown; similar to two-component response regulator [YcbA]0


 Domain: LytTR
ORF SubtiList Other
family		 Description Num. of
regulated operons
LytT BG11953Response_reginvolved in controlling the rate of autolysis0
YccH BG11998Response_regunknown; similar to two-component response regulator [YccG]0


 Domain: HutP
ORF SubtiList Other
family		 Description Num. of
regulated operons
HutP BG10666
positive regulation of the histidine utilization operon (hutPHUIGM)1


 Domain: ComK
ORF SubtiList Other
family		 Description Num. of
regulated operons
ComK BG11059
final autoregulatory control switch prior to competence development; activation of the expression of late competence genes involved in DNA-binding and uptake and in recombination27


 Domain: PucR
ORF SubtiList Other
family		 Description Num. of
regulated operons
PucR BG13983
regulation of puc genes (purine degradation)7


 Domain: PuR_N
ORF SubtiList Other
family		 Description Num. of
regulated operons
PurR BG10110
negative regulation of the purine operons (purEKBCLQFMNHD, purA)10


 Domain: Sigma54_activat
ORF SubtiList Other
family		 Description Num. of
regulated operons
AcoR BG11790HTH_8, GAFpositive regulation of the acetoin dehydrogenase operon (acoABCL)1
BkdR BG11721HTH_8involved in the control of isoleucine and valine utilization as sole nitrogen sources (bkd operon)1
LevR BG10677PRDpositive regulation of the levanase operon (levDEFG/sacC)1
RocR BG10723HTH_8positive regulation of arginine utilization operons (rocABC, rocDEF, rocG) (arginine and ornithine utilization)4
YplP BG11619
unknown; similar to transcriptional regulator (sigma-L-dependent)0


 Domain: tRNA
ORF SubtiList Other
family		 Description Num. of
regulated operons
TrnB-Gly1 BG00078
introduces alpha-1,6-linkages in starch and glycogen (glycogen biosynthesis)1
TrnB-Phe BG00088
introduces alpha-1,6-linkages in starch and glycogen (glycogen biosynthesis)1
TrnD-Cys BG00061
unknown; similar to unknown proteins from B. subtilis1
TrnD-Gly BG00060
unknown; similar to unknown proteins from B. subtilis1
TrnD-Phe BG00054
unknown; similar to unknown proteins from B. subtilis1
TrnD-Ser BG00049
unknown; similar to unknown proteins from B. subtilis1
TrnD-Trp BG00057
unknown; similar to unknown proteins from B. subtilis2
TrnD-Tyr BG00056
unknown; similar to unknown proteins from B. subtilis2
TrnI-Gly BG00040
unknown; similar to polysaccharide deacetylase1
TrnI-Thr BG00039
unknown; similar to polysaccharide deacetylase2
TrnJ-Gly BG00024
transfer RNA-Gly1
TrnS-Leu2 BG00070
unknown; similar to unknown proteins2
TrnSL-Tyr1 BG00111
unknown; similar to unknown proteins2
TrnSL-Val2 BG00118
unknown; similar to unknown proteins1


 Domain: Ribosomal_L20
ORF SubtiList Other
family		 Description Num. of
regulated operons
RplT BG11971
ribosomal protein L201

Sigma factors

 Domain: Sigma54_DBD
ORF SubtiList Other
family		 Description Num. of
regulated operons
SigL BG10748
involved in utilization of arginine and ornithine and transport of fructose6


 Domain: sigma70
ORF SubtiList Other
family		 Description Num. of
regulated operons
SigA BG10314
RNA polymerase major sigma-43 factor (sigma-A)323
SigB BG10735
general stress sigma factor (class II genes)66
SigD BG10751
regulon includes genes involved in flagellar synthesis, motility, chemotaxis, autolysis30
SigE BG10235
early mother cell-specific gene expression83
SigF BG10298
early forespore-specific gene expression30
SigG BG10236
late forespore-specific gene expression61
SigH BG10159
expression of vegetative and early stationary-phase genes24
SigI BG13269
RNA polymerase sigma factor1
SigK BG10459
late mother cell-specific gene expression (stage IV sporulation)58
SigM BG13019
RNA polymerase ECF(extracytoplasmic function)-type sigma factor (sigma-M)7
SigV BG11974
RNA polymerase ECF(extracytoplasmic function)-type sigma factor (sigma-V)0
SigW BG11573
probably activates a large stationary-phase regulon that functions in detoxification, production of antimicrobial compounds or both (pbpE-racX, yteI, yuaG, yknXYZ, ydjP, yfhM)34
SigX BG10536
may participate in the regulation of peptidoglycan synthesis and turnover15
SigY BG11975
RNA polymerase ECF(extracytoplasmic function)-type sigma factor (sigma-Y)2
SigZ BG11976
RNA polymerase ECF(extracytoplasmic function)-type sigma factor (sigma-Z)0
YlaC BG13340
unknown; similar to RNA polymerase ECF-type sigma factor1
YvrI BG14147
unknown; 0

Not assigned

 Domain: ND
ORF SubtiList Other
family		 Description Num. of
regulated operons
ArfM BG11345
activation of anaerobic respiratory and fermentative loci (nasDE, hmp, lctE, alsSD)7
ComZ BG13221
late competence gene1
GutR BG10178
positive regulation of the sorbitol dehydrogenase gene (gutB)1
HtrA BG12608
probably involved in processing, maturation, or secretion of extracellular enzymes1
Ipi BG10852
intracellular proteinase inhibitor BsuPI1
Med BG13126
positive regulator of comK1
NhaX BG13043
putative regulatory gene for nhaC0
PaiA BG10695
negative regulation of sporulation, septation and degradative enzyme genes (aprE, nprE, phoA, sacB)1
PyrR BG10712
attenuation (antitermination) of the pyrimidine operon (pyrPBCADFE) in the presence of UMP (pyrimidine biosynthesis)3
Rho BG10416
transcriptional terminator Rho1
Rok BG13307
repressor of comK10
RsfA BG10638
involved in the prespore-specific regulation of sigma-F-dependent genes6
SacV BG12670
regulation of the levansucrase gene (sacB)0
SenS BG10747
positive regulation of extracellular enzyme genes (amyE, aprE, nprE)2
SplA BG10202
negative regulation of the spore photoproduct lyase operon (splAB)1
SpoIIID BG10408
regulation of genes controlled by mother cell-specific sigma factors E and K (stage III sporulation)31
YjbD BG13133
unknown; similar to unknown proteins5
TenA BG10791
positive regulation of extracellular enzyme genes (aprE, nprE, phoA, sacB)4
TenI BG10792
positive regulation of extracellular enzyme genes1
Xpf BG10998
required for expression of the PBSX late operon1
YacF BG10143
unknown; similar to transcriptional regulator (nitrogen regulation protein)0
YbaL BG11494
unknown; similar to ATP-binding Mrp-like protein1
YcbA BG10871
unknown; similar to two-component sensor histidine kinase [YcbB]1
YceK BG12775
unknown; similar to transcriptional regulator (ArsR family)0
YdeB BG12129
unknown; similar to transcriptional regulator0
YezC BG12874
unknown; similar to transcriptional regulator (Lrp/AsnC family)0
YfhP BG12890
unknown; similar to unknown proteins2
YhcB BG11580
unknown; similar to trp repressor binding protein0
YjdI BG13181
unknown; similar to transcription regulation0
YlbO BG13367
unknown; similar to unknown proteins from B. subtilis6
YlpC BG13400
unknown; similar to unknown proteins5
YqfL BG11659
unknown; similar to unknown proteins1
YrhM BG12302
unknown; similar to anti-sigma factor0
YvfI BG12434
unknown; similar to transcriptional regulator (GntR family)0