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.

Sigma factors

Family ORF Synonym Other family Description #Binding sites

Sigma70

SigA RpoD CrsA   RNA polymerase major sigma-43 factor (sigma-A) 136
SigB RpoF   RNA polymerase sigma-37 factor (sigma-B) 16
SigD FlaB   RNA polymerase sigma-28 factor (sigma-D) 16
SigE SpoIIGB   RNA polymerase sporulation-specific sigma-29 factor (sigma-E) 34
SigF SpoIIAC   RNA polymerase sporulation-specific sigma factor (sigma-F) 10
SigG SpoIIIG   RNA polymerase sporulation-specific sigma factor (sigma-G) 19
SigK     RNA polymerase sporulation-specific sigma factor (sigma-K) 24
SigH Spo0H   RNA polymerase sigma-30 factor (sigma-H) 14
YkoZ     similar to RNA polymerase sigma factor  

Family ORF Synonym Other family Description #Binding sites

Sigma54_factors

SigL     RNA polymerase sigma-54 factor (sigma-L) 4

Family ORF Synonym Other family Description #Binding sites

Sigma70_ECF

SigV     RNA polymerase ECF-type sigma factor (sigma-V)  
SigW YbbL   RNA polymerase ECF-type sigma factor (sigma-W) 21
SigX YpuM   RNA polymerase ECF-type sigma factor (sigma-X) 8
SigY YxlB   RNA polymerase ECF-type sigma factor (sigma-Y)  
SigZ     RNA polymerase ECF-type sigma factor (sigma-Z)  
YlaC     similar to RNA polymerase ECF-type sigma factor  
YhdM SigM   similar to RNA polymerase ECF-type sigma factor 1
Xpf Pcf YkxE   RNA polymerase PBSX sigma factor-like  



Helix turn helix family

Family ORF Synonym Other family Description #Binding sites

MarR

YkvE     similar to transcriptional regulator (MarR family)  
YpoP     similar to transcriptional regulator (MarR family)  
YkoM     similar to transcriptional regulator (MarR family)  
YhbI     similar to transcriptional regulator (MarR family)  
YxaD     similar to transcriptional regulator (MarR family)  
YdgG     similar to transcriptional regulator (MarR family)  
YdgJ     similar to transcriptional regulator (MarR family)  
YfiV     similar to transcriptional regulator (MarR family)  
YusO     similar to transcriptional regulator (MarR family)  
YwoH     similar to transcriptional regulator (MarR family)  
YetL     similar to transcriptional regulator (MarR family)  
YybA     similar to transcriptional regulator (MarR family)  
YwhA     similar to transcriptional regulator (MarR family)  
YwaE Ipa-10R   similar to transcriptional regulator (MarR family)  
YsmB     similar to transcriptional regulator (MarR family)  
YkmA     similar to hypothetical proteins  
YcgE     ycgE  
Hpr CatA ScoC   transcriptional regulator 10
YdcH     similar to hypothetical proteins from B. subtilis  
YbfA     ybfA  
YvnA     similar to hypothetical proteins from B. subtilis  
YhjH     similar to hypothetical proteins  
YvmB YzhA   similar to hypothetical proteins  

Family ORF Synonym Other family Description #Binding sites

LacI

CcpA GraR AlsA   transcriptional regulator (Lacl family) 34
MsmR     transcriptional regulator (LacI family)  
YhjM     similar to transcriptional regulator (LacI family)  
RbsR     transcriptional regulator (LacI family)  
YkvZ     similar to transcriptional regulator (LacI family)  
DegA     transcriptional regulator (LacI family)  
YvdE     similar to transcriptional regulator (LacI family)  
YyaG CcpB   similar to transcriptional regulator (LacI family) 2
KdgR     transcriptional regulator (LacI family) 2
YjmH ExuR   similar to transcriptional regulator (LacI family) 1
LacR YvfJ   transcriptional regulator (LacI family) 1

Family ORF Synonym Other family Description #Binding sites

GntR

AraR AraC YvbS   transcriptional regulator (LacI family) 8
YbgA     similar to transcriptional regulator (GntR family)  
YydK     similar to transcriptional regulator (GntR family)  
YvoA     similar to transcriptional regulator (GntR family)  
YhcF     similar to transcriptional regulator (GntR family)  
YurK     similar to transcriptional regulator (GntR family)  
YmfC     similar to transcriptional regulator (GntR family)  
YdeF     similar to transcriptional regulator (GntR family) / aminotransferase (MocR-like)  
YdeL     similar to transcriptional regulator (GntR family) / aminotransferase (MocR-like)  
YcnF     similar to transcriptional regulator (GntR family) / aminotransferase (MocR-like)  
YisV     similar to transcriptional regulator (GntR family) / aminotransferase (MocR-like)  
YdfD     similar to transcriptional regulator (GntR family) / aminotransferase (MocR-like)  
YcxD     similar to transcriptional regulator (GntR family) / aminotransferase (MocR-like)  
YhdI     similar to transcriptional regulator (GntR family) / aminotransferase (MocR-like)  
TreR YfxA   transcriptional regulator (GntR family) 2
YdhC     similar to transcriptional regulator (GntR family)  
YtrA     similar to transcriptional regulator (GntR family)  
GntR     transcriptional regulator (GntR family) 1
YcbG     similar to transcriptional regulator (GntR family)  
YdhQ     similar to transcriptional regulator (GntR family)  
YvfI     similar to transcriptional regulator (GntR family)  

Family ORF Synonym Other family Description #Binding sites

LysR (HTH_1)

YrdQ     similar to transcriptional regulator (LysR family)  
YwbI Ipa-24D   similar to transcriptional regulator (LysR family)  
YybE     similar to transcriptional regulator (LysR family)  
YwqM     similar to transcriptional regulator (LysR family)  
GltR YrdL   transcriptional regulator (LysR family) 4
YkuM     similar to transcriptional regulator (LysR family)  
YusT     similar to transcriptional regulator (LysR family)  
YofA     similar to transcriptional regulator (LysR family)  
AlsR     transcriptional regulator (LysR family) 1
YvbU     similar to transcriptional regulator (LysR family)  
YwfK Ipa-89D   similar to transcriptional regulator (LysR family)  
CitR     transcriptional regulator (LysR family) 1
YtlI     similar to transcriptional regulator (LysR family)  
YcgK     similar to transcriptional regulator (LysR family)  
YclA     similar to transcriptional regulator (LysR family)  
YoaU     similar to transcriptional regulator (LysR family)  
YraN     similar to transcriptional regulator (LysR family)  
GltC     transcriptional regulator (LysR family) 3
YxjO     similar to transcriptional regulator (LysR family)  
YusF     yusF  

Family ORF Synonym Other family Description #Binding sites

ArsR (HTH_5)

YozA     similar to transcriptional regulator (ArsR family)  
YqcJ ArsR   similar to transcriptional regulator (ArsR family) 1
YvbA     similar to transcriptional regulator (ArsR family)  
YdeT     similar to transcriptional regulator (ArsR family)  
YceK     similar to transcriptional regulator (ArsR family)  
YczG     similar to transcriptional regulator (ArsR family)  
YdfF     ydfF  

Family ORF Synonym Other family Description #Binding sites

DeoR

IolR     transcriptional regulator (DeoR family) 4
YulB     similar to transcriptional regulator (DeoR family)  
FruR     transcriptional regulator (DeoR family) 1
GlcR YwpI   transcriptional regulator (DeoR family)  
YtzE     similar to transcriptional regulator (DeoR family)  
YcnK     similar to transcriptional regulator (DeoR family)  
SpoIIID     transcriptional regulator 14

Family ORF Synonym Other family Description #Binding sites

AraC (HTH_2)

YisR YuxC YucF   similar to transcriptional regulator (AraC/XylS family)  
YtdP     similar to transcriptional regulator (AraC/XylS family)  
YdeC     similar to transcriptional regulator (AraC/XylS family)  
YbfI     similar to transcriptional regulator (AraC/XylS family)  
YobQ     similar to transcriptional regulator (AraC/XylS family)  
YesS     similar to transcriptional regulator (AraC/XylS family)  
YfiF     similar to transcriptional regulator (AraC/XylS family)  
YbbB YzbC   similar to transcriptional regulator (AraC/XylS family)  
AdaA     methylphosphotriester-DNA alkyltransferase and transcriptional regulator (AraC/XylS family) 2
YdeE     similar to transcriptional regulator (AraC/XylS family)  
YbfP     similar to transcriptional regulator (AraC/XylS family)  
YesN   response_reg similar to two-component response regulator [YesM]  

Family ORF Synonym Other family Description #Binding sites

GerE

ComA SrfB ComAA response_reg two-component response regulator 7
YocG   response_reg similar to two-component response regulator [YocF]  
YvqC   response_reg similar to two-component response regulator [YvqE]  
YfiK   response_reg similar to two-component response regulator [YfiJ]  
YhcZ   response_reg similar to two-component response regulator [YhcY]  
DegU SacU Iep response_reg two-component response regulator 16
YdfI   response_reg similar to two-component response regulator [YdfH]  
YvfU   response_reg similar to two-component response regulator [YvfT]  
YxjL   response_reg similar to two-component response regulator [YxjM]  
GerE     transcriptional regulator 23

Family ORF Synonym Other family Description #Binding sites

Crp

YdbG   response_reg similar to two-component response regulator [YdbF] 1
Fnr     transcriptional regulator (FNR/CRP family) 2

Family ORF Synonym Other family Description #Binding sites

Xre (HTH_3)

YqaE     similar to transcriptional regulator (phage-related) (Xre family)  
YonR     similar to transcriptional regulator (phage-related) (Xre family)  
YdcN     similar to transcriptional regulator (phage-related) (Xre family)  
YobD     similar to transcriptional regulator (phage-related) (Xre family)  
AnsR     transcriptional regulator (Xre family) 1
Xre     transcriptional regulator 4
Slr YveJ   transcriptional regulator  
SinR Sin FlaD   transcriptional regulator 6
YvaN     similar to hypothetical proteins  
YvaO     similar to hypothetical proteins  
YopS     similar to hypothetical proteins from B. subtilis  
YotL     similar to hypothetical proteins from B. subtilis  
YqaF     yqaF  
YozG     similar to transcriptional regulator  
YazB     yazB  
YvzC     yvzC  
YopO     yopO  

Family ORF Synonym Other family Description #Binding sites

MerR

GlnR     transcriptional regulator 6
YraB     similar to transcriptional regulator (MerR family)  
TnrA ScgR   transcriptional regulator 11
YyaN     similar to transcriptional regulator (MerR family)  
YfmP     similar to transcriptional regulator (MerR family)  
BmrR     transcriptional regulator 1
BltR Bmr2R BmtR   transcriptional regulator 1
Mta YwnD   transcriptional regulator 4
YdfL     similar to multidrug-efflux transporter regulator  
YhdQ     similar to transcriptional regulator (MerR family)  

Family ORF Synonym Other family Description #Binding sites

TetR

YdeS     similar to transcriptional regulator (TetR/AcrR family)  
YhgD YixD   similar to transcriptional regulator (TetR/AcrR family)  
YsiA     similar to transcriptional regulator (TetR/AcrR family)  
YrhI     similar to transcriptional regulator (TetR/AcrR family)  
YvdT     similar to transcriptional regulator (TetR/AcrR family)  
YuxN     similar to hypothetical proteins from B. subtilis  
YerO     similar to transcriptional regulator (TetR/AcrR family)  
YcnC     similar to transcriptional regulator (TetR/AcrR family)  
YxaF     similar to hypothetical proteins  
LmrA Lin-2 YccB   transcriptional regulator 1
PksA     transcriptional regulator  
YvkB     similar to transcriptional regulator (TetR/AcrR family)  
YvaF     yvaF  
YttP     yttP  
YobS     yobS  
YwcC Ipa-33D   alternate gene name: ipa-33d  
YxbF YxaT   alternate gene name: yxaT  
YfiR     similar to hypothetical proteins  
YdgC     similar to hypothetical proteins  

Family ORF Synonym Other family Description #Binding sites

AsnC_trans_reg

AzlB YrdG   transcriptional regulator (Lrp/AsnC family) 1
YwrC     similar to transcriptional regulator (Lrp/AsnC family)  
LrpA YddO   transcriptional regulator (Lrp/AsnC family) 1
LrpB YddP   transcriptional regulator (Lrp/AsnC family) 1
LrpC YdaI   transcriptional regulator (Lrp/AsnC family) 1
YezC     similar to transcriptional regulator (Lrp/AsnC family)  
YugG     similar to transcriptional regulator (Lrp/AsnC family)  

Family ORF Synonym Other family Description #Binding sites

LexA_DNA_bind

LexA DinR   transcriptional regulator 8

Family ORF Synonym Other family Description #Binding sites

HTH_6

YbbH     similar to hypothetical proteins  
YfiA     similar to hypothetical proteins  



Other family

Family ORF Synonym Other family Description #Binding sites

trans_reg_C

YycF   response_reg similar to two-component response regulator [YycG]  
YbdJ   response_reg similar to two-component response regulator [YbdK]  
YcbL   response_reg similar to two-component response regulator [YcbM]  
YvcP   response_reg similar to two-component response regulator [YvcQ]  
YxdJ   response_reg similar to two-component response regulator [YxdK]  
ResD YpxD response_reg two-component response regulator 9
YrkP   response_reg similar to two-component response regulator [YrkQ]  
PhoP   response_reg two-component response regulator 15
YtsA   response_reg similar to two-component response regulator [YtsB]  
YkoG   response_reg similar to two-component response regulator [YkoH]  
YvqA   response_reg similar to two-component response regulator [YvqB]  
YclJ   response_reg similar to two-component response regulator [YclK]  
YvrH   response_reg similar to two-component response regulator [YvrG]  

Family ORF Synonym Other family Description #Binding sites

response_reg

YesN   AraC (HTH_2) similar to two-component response regulator [YesM]  
ComA SrfB ComAA GerE two-component response regulator 7
YocG   GerE similar to two-component response regulator [YocF]  
YvqC   GerE similar to two-component response regulator [YvqE]  
YfiK   GerE similar to two-component response regulator [YfiJ]  
YhcZ   GerE similar to two-component response regulator [YhcY]  
DegU SacU Iep GerE two-component response regulator 16
YdfI   GerE similar to two-component response regulator [YdfH]  
YvfU   GerE similar to two-component response regulator [YvfT]  
YxjL   GerE similar to two-component response regulator [YxjM]  
YdbG   Crp similar to two-component response regulator [YdbF] 1
YycF   trans_reg_C similar to two-component response regulator [YycG]  
YbdJ   trans_reg_C similar to two-component response regulator [YbdK]  
YcbL   trans_reg_C similar to two-component response regulator [YcbM]  
YvcP   trans_reg_C similar to two-component response regulator [YvcQ]  
YxdJ   trans_reg_C similar to two-component response regulator [YxdK]  
ResD YpxD trans_reg_C two-component response regulator 9
YrkP   trans_reg_C similar to two-component response regulator [YrkQ]  
PhoP   trans_reg_C two-component response regulator 15
YtsA   trans_reg_C similar to two-component response regulator [YtsB]  
YkoG   trans_reg_C similar to two-component response regulator [YkoH]  
YvqA   trans_reg_C similar to two-component response regulator [YvqB]  
YclJ   trans_reg_C similar to two-component response regulator [YclK]  
YvrH   trans_reg_C similar to two-component response regulator [YvrG]  
LytT     two-component response regulator  
CitT YflQ   two-component response regulator  
YufM     similar to two-component response regulator [YufL]  
YccH     similar to two-component response regulator [YccG]  
Spo0A Spo0C Spo0G SpoIIL Sof-1   two-component response regulator 23
YcbB YzgB   similar to two-component response regulator [YcbA]  
CheB CheL   methyl-accepting chemotaxis proteins (MCP)-glutamate methylesterase and two-component response regulator-like  
YneI YoxH   similar to two-component response regulator (CheY homolog)  
CheY CheB   two-component response regulator  
Spo0F     two-component response regulator  
CheV     modulation of CheA activity in response to attractants (chemotaxis)  

Family ORF Synonym Other family Description #Binding sites

Fur

YqfV Zur   similar to transcriptional regulator (Fur family) 2
YqkL Fur   similar to transcriptional regulator (Fur family) 3
YgaG     similar to transcriptional regulator (Fur family)  

Family ORF Synonym Other family Description #Binding sites

Sigma54-related factors

YqiR BkdR   similar to transcriptional regulator (sigma-L-dependent) 1
YplP     similar to transcriptional regulator (sigma-L-dependent)  
AcoR YfjG YzcB   transcriptional regulator 2
RocR     transcriptional regulator (NtrC/NifA family) 5
GlcT YkwA Bgl_antitermin transcriptional antiterminator (BglG family) 1

Family ORF Synonym Other family Description #Binding sites

Bgl_antitermin

GlcT YkwA Sigma54-related factors transcriptional antiterminator (BglG family) 1
LicR CelR   transcriptional regulator (antiterminator) 1
YjdC     similar to transcriptional antiterminator (BglG family)  
LicT     transcriptional antiterminator (BglG family) 2
SacT Ipa-47D   transcriptional antiterminator 1
SacY Ipa-13R SacS   transcriptional antiterminator 1
YdaA     similar to transcriptional antiterminator (BglG family)  
LevR     transcriptional regulator (NifA/NtrC family) 3

Family ORF Synonym Other family Description #Binding sites

CSD

CspB     major cold-shock protein  
CspC     cold-shock protein  
CspD     cold-shock protein  

Family ORF Synonym Other family Description #Binding sites

IclR

YcsO KipR   similar to transcriptional regulator (IclR family) 1

Family ORF Synonym Other family Description #Binding sites

GreA_GreB

GreA     transcription elongation factor  

Family ORF Synonym Other family Description #Binding sites

Fe_dep_repress

YqhN     similar to transcriptional regulator 2

Family ORF Synonym Other family Description #Binding sites

HrcA

HrcA YqxE YqeS   transcriptional regulator 2

Family ORF Synonym Other family Description #Binding sites

Arg_repressor

AhrC     transcriptional regulator 5



No family assigned

Family ORF Synonym Other family Description #Binding sites

 

PyrR     transcriptional attenuator and uracil phosphoribosyltransferase activity (minor)  
PurR YabI   transcriptional regulator 4
RibC     riboflavin kinase 1
XylR     transcriptional regulator 1
YacF     similar to transcriptional regulator (nitrogen regulation protein)  
PaiA     transcriptional regulator 1
ComQ     transcriptional regulator 1
YppQ     similar to transcriptional regulator (PilB family)  
BirA     transcriptional regulator and biotin acetyl-CoA-carboxylase synthetase 1
NrgB     nitrogen-regulated PII-like protein  
SacX Ipa-14R SacS   negative regulatory protein of SacY  
CodY     transcriptional regulator 8
DeoR YxxC   transcriptional regulator 2
TenI     transcriptional regulator 1
GutR     transcriptional regulator 1
SpoVT YabL   transcriptional regulator 16
Abh YlxT YzaA   transcriptional regulator  
AbrB CpsX   transcriptional regulator 21
LytR     membrane-bound protein 2
YvhJ     similar to transcriptional regulator  
YwtF     -  
ComK     competence transcription factor (CTF) 11
CtsR YacG   transcriptional regulator 10
GlpP     transcription antiterminator 4
HutP HutP1   transcriptional regulator 1
MtrB     tryptophan operon RNA-binding attenuation protein (TRAP) 1
PaiB YumE   transcriptional regulator 1
YpuN RsiX   similar to negative regulator of sigma-X activity  
SacV YdzC   transcriptional regulator  
SenS     transcriptional regulator 2
SplA YkxI   transcriptional regulator  
TenA     transcriptional regulator 4
YjdI     similar to transcription regulation  
YrhM     similar to anti-sigma factor  
FlgM     anti-sigma factor repressor of sigma-D-dependent transcription  
Med YjaW   positive regulator of comK 1
RsbX     serine phosphatase (dephosphorylation of RsbS)  
Spo0E     negative sporulation regulatory phosphatase