NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|496546009|ref|WP_009252084|]
View 

MULTISPECIES: RNA polymerase sporulation sigma factor SigE [Clostridia]

Protein Classification

RNA polymerase sporulation sigma factor SigE( domain architecture ID 18823932)

RNA polymerase sporulation sigma factor SigE is responsible for the expression of sporulation specific genes

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
SigE COG5811
Sporulation sigma factor SigE (mother cell-specific, SpoIIGB) [Cell cycle control, cell ...
 23-244 1.15e-147

Sporulation sigma factor SigE (mother cell-specific, SpoIIGB) [Cell cycle control, cell division, chromosome partitioning, Transcription];


:

Pssm-ID: 444513 [Multi-domain]  Cd Length: 232  Bit Score: 411.11  E-value: 1.15e-147
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009  23 LLSGQGDIHYIGGAEVLPPPLESEKENEIISDLgTEYEDEAKNILIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIK 102
Cdd:COG5811   12 LGLKKKEVYYIGGSEALPPPLTREEEAELLEKL-EEGDESVRSTLIERNLRLVVYIARKFENTGIGIEDLISIGTIGLIK 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009 103 SINTFKPDKNIKLATYASRCIENEILMYLRRNNKTRLEVSIDEPLNVDWDGNELLLSDILGTDEDVIYRDIENEVERKLL 182
Cdd:COG5811   91 AVNTFNPDKKIKLATYASRCIENEILMYLRRNNKTKSEVSFDEPLNVDWDGNELLLSDILGTENDIIYKNIEEEVDRELL 170

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 496546009 183 LKAINKLTDREKTIINLRFGLNtpDGQEMTQKEVATLLGISQSYISRLEKKIMKRLKREMVK 244
Cdd:COG5811  171 KKALKKLSERERKIMELRFGLN--GGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKEINK 230
 
Name Accession Description Interval E-value
SigE COG5811
Sporulation sigma factor SigE (mother cell-specific, SpoIIGB) [Cell cycle control, cell ...
 23-244 1.15e-147

Sporulation sigma factor SigE (mother cell-specific, SpoIIGB) [Cell cycle control, cell division, chromosome partitioning, Transcription];


Pssm-ID: 444513 [Multi-domain]  Cd Length: 232  Bit Score: 411.11  E-value: 1.15e-147
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009  23 LLSGQGDIHYIGGAEVLPPPLESEKENEIISDLgTEYEDEAKNILIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIK 102
Cdd:COG5811   12 LGLKKKEVYYIGGSEALPPPLTREEEAELLEKL-EEGDESVRSTLIERNLRLVVYIARKFENTGIGIEDLISIGTIGLIK 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009 103 SINTFKPDKNIKLATYASRCIENEILMYLRRNNKTRLEVSIDEPLNVDWDGNELLLSDILGTDEDVIYRDIENEVERKLL 182
Cdd:COG5811   91 AVNTFNPDKKIKLATYASRCIENEILMYLRRNNKTKSEVSFDEPLNVDWDGNELLLSDILGTENDIIYKNIEEEVDRELL 170

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 496546009 183 LKAINKLTDREKTIINLRFGLNtpDGQEMTQKEVATLLGISQSYISRLEKKIMKRLKREMVK 244
Cdd:COG5811  171 KKALKKLSERERKIMELRFGLN--GGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKEINK 230
PRK08301 PRK08301
RNA polymerase sporulation sigma factor SigE;
27-244 3.12e-141

RNA polymerase sporulation sigma factor SigE;


Pssm-ID: 236228 [Multi-domain]  Cd Length: 234  Bit Score: 394.99  E-value: 3.12e-141
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009  27 QGDIHYIGGAEVLPPPLESEKENEIISDLGTEyEDEAKNILIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKSINT 106
Cdd:PRK08301  18 TDEIYYIGGSEALPPPLSKEEEEYLLNKLPKG-DEAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNT 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009 107 FKPDKNIKLATYASRCIENEILMYLRRNNKTRLEVSIDEPLNVDWDGNELLLSDILGTDEDVIYRDIENEVERKLLLKAI 186
Cdd:PRK08301  97 FNPEKKIKLATYASRCIENEILMYLRRNNKVKAEVSFDEPLNIDWDGNELLLSDVLGTDNDIIYKDIEDEVDRKLLKKAL 176

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 496546009 187 NKLTDREKTIINLRFGLNtpDGQEMTQKEVATLLGISQSYISRLEKKIMKRLKREMVK 244
Cdd:PRK08301 177 KKLSDREKQIMELRFGLN--GGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKEINK 232
spore_sigmaE TIGR02835
RNA polymerase sigma-E factor; Members of this family comprise the Firmicutes lineage ...
 13-244 5.10e-117

RNA polymerase sigma-E factor; Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active. [Transcription, Transcription factors, Cellular processes, Sporulation and germination]


Pssm-ID: 131882 [Multi-domain]  Cd Length: 234  Bit Score: 333.71  E-value: 5.10e-117
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009   13 FKMIRREPSFLLSGQGDIHYIGGAEVLPPPLESEKENEIISDLgTEYEDEAKNILIEHNLRLVVYIAKKFDNTGVGVEDL 92
Cdd:TIGR02835   4 TRVLRKLLAKLLIRPREIYYIGGSEALPPPLTGEEEEALLQKL-TQGDESAKSTLIERNLRLVVYIARKFENTGIGIEDL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009   93 ISIGTIGLIKSINTFKPDKNIKLATYASRCIENEILMYLRRNNKTRLEVSIDEPLNVDWDGNELLLSDILGTDEDVIYRD 172
Cdd:TIGR02835  83 VSIGTIGLIKAVNTFNPSKKIKLATYASRCIENEILMYLRRNNKTRSEVSFDEPLNVDWDGNELLLSDVLGTDSDIVYKY 162

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 496546009  173 IENEVERKLLLKAINKLTDREKTIINLRFGLNtpDGQEMTQKEVATLLGISQSYISRLEKKIMKRLKREMVK 244
Cdd:TIGR02835 163 LEEEVDRELLRKALAKLNDREKKIMELRFGLV--GGTEKTQKEVADMLGISQSYISRLEKRILKRLKKEINR 232
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 67-137 1.41e-18

Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime. The aromatic residues of the recognition helix, found at the C-terminus of this domain are though to mediate strand separation, thereby allowing transcription initiation.


Pssm-ID: 427998 [Multi-domain]  Cd Length: 71  Bit Score: 77.24  E-value: 1.41e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 496546009   67 LIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKSINTFKPDKNIKLATYASRCIENEILMYLRRNNKT 137
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRRT 71
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 179-239 1.12e-11

Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP).


Pssm-ID: 100119 [Multi-domain]  Cd Length: 55  Bit Score: 58.27  E-value: 1.12e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 496546009 179 RKLLLKAINKLTDREKTIINLRFGlntpdgQEMTQKEVATLLGISQSYISRLEKKIMKRLK 239
Cdd:cd06171    1 RERLEEALDKLPEREREVILLRFG------EGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
209-232 6.02e-04

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 37.11  E-value: 6.02e-04
                           10        20
                   ....*....|....*....|....
gi 496546009   209 QEMTQKEVATLLGISQSYISRLEK 232
Cdd:smart00530   9 KGLTQEELAEKLGVSRSTLSRIEN 32
 
Name Accession Description Interval E-value
SigE COG5811
Sporulation sigma factor SigE (mother cell-specific, SpoIIGB) [Cell cycle control, cell ...
 23-244 1.15e-147

Sporulation sigma factor SigE (mother cell-specific, SpoIIGB) [Cell cycle control, cell division, chromosome partitioning, Transcription];


Pssm-ID: 444513 [Multi-domain]  Cd Length: 232  Bit Score: 411.11  E-value: 1.15e-147
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009  23 LLSGQGDIHYIGGAEVLPPPLESEKENEIISDLgTEYEDEAKNILIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIK 102
Cdd:COG5811   12 LGLKKKEVYYIGGSEALPPPLTREEEAELLEKL-EEGDESVRSTLIERNLRLVVYIARKFENTGIGIEDLISIGTIGLIK 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009 103 SINTFKPDKNIKLATYASRCIENEILMYLRRNNKTRLEVSIDEPLNVDWDGNELLLSDILGTDEDVIYRDIENEVERKLL 182
Cdd:COG5811   91 AVNTFNPDKKIKLATYASRCIENEILMYLRRNNKTKSEVSFDEPLNVDWDGNELLLSDILGTENDIIYKNIEEEVDRELL 170

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 496546009 183 LKAINKLTDREKTIINLRFGLNtpDGQEMTQKEVATLLGISQSYISRLEKKIMKRLKREMVK 244
Cdd:COG5811  171 KKALKKLSERERKIMELRFGLN--GGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKEINK 230
PRK08301 PRK08301
RNA polymerase sporulation sigma factor SigE;
27-244 3.12e-141

RNA polymerase sporulation sigma factor SigE;


Pssm-ID: 236228 [Multi-domain]  Cd Length: 234  Bit Score: 394.99  E-value: 3.12e-141
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009  27 QGDIHYIGGAEVLPPPLESEKENEIISDLGTEyEDEAKNILIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKSINT 106
Cdd:PRK08301  18 TDEIYYIGGSEALPPPLSKEEEEYLLNKLPKG-DEAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNT 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009 107 FKPDKNIKLATYASRCIENEILMYLRRNNKTRLEVSIDEPLNVDWDGNELLLSDILGTDEDVIYRDIENEVERKLLLKAI 186
Cdd:PRK08301  97 FNPEKKIKLATYASRCIENEILMYLRRNNKVKAEVSFDEPLNIDWDGNELLLSDVLGTDNDIIYKDIEDEVDRKLLKKAL 176

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 496546009 187 NKLTDREKTIINLRFGLNtpDGQEMTQKEVATLLGISQSYISRLEKKIMKRLKREMVK 244
Cdd:PRK08301 177 KKLSDREKQIMELRFGLN--GGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKEINK 232
spore_sigmaE TIGR02835
RNA polymerase sigma-E factor; Members of this family comprise the Firmicutes lineage ...
 13-244 5.10e-117

RNA polymerase sigma-E factor; Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active. [Transcription, Transcription factors, Cellular processes, Sporulation and germination]


Pssm-ID: 131882 [Multi-domain]  Cd Length: 234  Bit Score: 333.71  E-value: 5.10e-117
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009   13 FKMIRREPSFLLSGQGDIHYIGGAEVLPPPLESEKENEIISDLgTEYEDEAKNILIEHNLRLVVYIAKKFDNTGVGVEDL 92
Cdd:TIGR02835   4 TRVLRKLLAKLLIRPREIYYIGGSEALPPPLTGEEEEALLQKL-TQGDESAKSTLIERNLRLVVYIARKFENTGIGIEDL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009   93 ISIGTIGLIKSINTFKPDKNIKLATYASRCIENEILMYLRRNNKTRLEVSIDEPLNVDWDGNELLLSDILGTDEDVIYRD 172
Cdd:TIGR02835  83 VSIGTIGLIKAVNTFNPSKKIKLATYASRCIENEILMYLRRNNKTRSEVSFDEPLNVDWDGNELLLSDVLGTDSDIVYKY 162

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 496546009  173 IENEVERKLLLKAINKLTDREKTIINLRFGLNtpDGQEMTQKEVATLLGISQSYISRLEKKIMKRLKREMVK 244
Cdd:TIGR02835 163 LEEEVDRELLRKALAKLNDREKKIMELRFGLV--GGTEKTQKEVADMLGISQSYISRLEKRILKRLKKEINR 232
SigK COG5814
Sporulation sigma factor SigK (mother cell-specific, SpoIIIC/SpoIVCB) [Cell cycle control, ...
 32-245 1.15e-91

Sporulation sigma factor SigK (mother cell-specific, SpoIIIC/SpoIVCB) [Cell cycle control, cell division, chromosome partitioning, Transcription];


Pssm-ID: 444516 [Multi-domain]  Cd Length: 234  Bit Score: 269.40  E-value: 1.15e-91
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009  32 YIGGaEVLPPPLESEKENEIISDLgTEYEDEAKNILIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKSINTFKPDK 111
Cdd:COG5814   22 YINN-NAFPQPLSEEEEAKYLERM-AEGDEEARNILIEHNLRLVAHIVKKFENTGEDTEDLISIGTIGLIKAINTFDPDK 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009 112 NIKLATYASRCIENEILMYLRRNNKTRLEVSIDEPLNVDWDGNELLLSDILGTDEDVIYRDIENEVERKLLLKAINKLTD 191
Cdd:COG5814  100 GTKLATYAARCIENEILMHLRSTKKTRKEVSLQDPIGTDKEGNEITLIDILGTDEDDVVDQVELKLEKEKLYEKLKKLSE 179

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 496546009 192 REKTIINLRFGLntPDGQEMTQKEVATLLGISQSYISRLEKKIMKRLKREMVKE 245
Cdd:COG5814  180 REREVIELRYGL--LNGEEKTQREIAKKLGISRSYVSRIEKRALMKLFKEFYKE 231
PRK05803 PRK05803
RNA polymerase sporulation sigma factor SigK;
39-245 4.40e-87

RNA polymerase sporulation sigma factor SigK;


Pssm-ID: 180266 [Multi-domain]  Cd Length: 233  Bit Score: 257.95  E-value: 4.40e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009  39 LPPPLESEKENEIISDLgTEYEDEAKNILIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKSINTFKPDKNIKLATY 118
Cdd:PRK05803  27 FPQPLSEEEERKYLELM-KEGDEEARNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATY 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009 119 ASRCIENEILMYLRRNNKTRLEVSIDEPLNVDWDGNELLLSDILGTDEDVIYRDIENEVERKLLLKAINKLTDREKTIIN 198
Cdd:PRK05803 106 AARCIENEILMHLRNLKKTKKEVSLQDPIGVDKEGNEISLIDILGSEEDDVIEQVELKMEVEKLYKKIDILDEREKEVIE 185

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 496546009 199 LRFGLNtpDGQEMTQKEVATLLGISQSYISRLEKKIMKRLKREMVKE 245
Cdd:PRK05803 186 MRYGLG--NGKEKTQREIAKALGISRSYVSRIEKRALKKLFKELYRA 230
spore_sigmaK TIGR02846
RNA polymerase sigma-K factor; The sporulation-specific transcription factor sigma-K (also ...
 13-242 2.20e-81

RNA polymerase sigma-K factor; The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K. [Transcription, Transcription factors, Cellular processes, Sporulation and germination]


Pssm-ID: 131893 [Multi-domain]  Cd Length: 227  Bit Score: 243.09  E-value: 2.20e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009   13 FKMIRREPSFLLSgqgdihYIGGAEVLPPPLeSEKENEIISDLGTEYEDEAKNILIEHNLRLVVYIAKKFDNTGVGVEDL 92
Cdd:TIGR02846   6 LTLIVKSLLFLVG------YVTNNGSFPQPL-SEEEEKKYLDRLKEGDEEARNVLIERNLRLVAHIVKKFSNTGEDVDDL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009   93 ISIGTIGLIKSINTFKPDKNIKLATYASRCIENEILMYLRRNNKTRLEVSIDEPLNVDWDGNELLLSDILGTDEDVIYRD 172
Cdd:TIGR02846  79 ISIGTIGLIKAIDSFDPDKGTRLATYAARCIENEILMHLRALKKTKGEVSLQDPIGVDKEGNEISLIDILGSDGDSVIEQ 158

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009  173 IENEVERKLLLKAINKLTDREKTIINLRFGLNtpDGQEMTQKEVATLLGISQSYISRLEKKIMKRLKREM 242
Cdd:TIGR02846 159 VELNLEIKKLYKKLSVLDGREREVIEMRYGLG--DGRRKTQREIAKILGISRSYVSRIEKRALMKLYKEL 226
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 62-242 4.68e-38

DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA polymerase specialized sigma subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 440804 [Multi-domain]  Cd Length: 236  Bit Score: 132.64  E-value: 4.68e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009  62 EAKNILIEHNLRLVVYIAKKFDNTGV-GVEDLISIGTIGLIKSINTFKPDKNIKLATYASRCIENEILMYLRRNNKT--- 137
Cdd:COG1191   15 EAREELIEEYLPLVKKIASRLAGRLPaELDDLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRGAILDYLRDEDWVprs 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009 138 ------------------------------RLEVSIDE--------------PLNVDWDGNELLLSDILGTDEDVIYRDI 173
Cdd:COG1191   95 vrelarkieeaieeleqelgreptdeeiaeELGISLEEvqealeaanayqllSLDEPLEDGDDLLDLLESGDPEEELEHE 174

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 496546009 174 ENeveRKLLLKAINKLTDREKTIINLRFGlntpdgQEMTQKEVATLLGISQSYISRLEKKIMKRLKREM 242
Cdd:COG1191  175 EL---REALAEAIEQLPERERLVLSLYYF------EELTLKEIAEVLGVSESRVSRLHKKALARLREYL 234
SigBFG TIGR02980
RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; This group of similar sigma-70 factors ...
 60-242 1.67e-37

RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.


Pssm-ID: 274373 [Multi-domain]  Cd Length: 227  Bit Score: 131.19  E-value: 1.67e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009   60 EDEAKNILIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKSINTFKPDKNIKLATYASRCIENEILMYLRRNNKT-- 137
Cdd:TIGR02980   1 DKEAREKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIMGEIKRFFRDDTWAvr 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009  138 ----------------------------------RLEVSIDE------------PLNVD-----WDGNELLLSDILGTDE 166
Cdd:TIGR02980  81 vprrlkelgvkinkateeltqrlgrsptiaeiaeRLGVSEEEvvealeagnayqALSLDasiedDDGDPIALLDTLGDED 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 496546009  167 DviyrDIENEVERKLLLKAINKLTDREKTIINLRFGlntpdgQEMTQKEVATLLGISQSYISRLEKKIMKRLKREM 242
Cdd:TIGR02980 161 D----ALETVEDRLALKPLLAALPERERRILLLRFF------EDKTQSEIAERLGISQMHVSRLLRRALKKLREQL 226
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 41-245 6.52e-32

DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 440334 [Multi-domain]  Cd Length: 268  Bit Score: 117.46  E-value: 6.52e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009  41 PPLESEKENEiisdLGTEYED---EAKNILIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKSINTFKPDKNIKLAT 117
Cdd:COG0568   10 PLLTAEEEVE----LARRIQAgdeEAKRKLVEANLRLVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDPERGFRFST 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009 118 YASRCIENEILMYLRRN--------------NK----------------------TRLEVSIDE----------PLNVDW 151
Cdd:COG0568   86 YATWWIRQAITRAIADQwrtirlpvhmaetlNKlrrakrqllqelgreptpeeiaEELGVPEEKvremlrlarePVSLDA 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009 152 ---DGNELLLSDILgTDEDVI--YRDIENEVERKLLLKAINKLTDREKTIINLRFGLNtpDGQEMTQKEVATLLGISQSY 226
Cdd:COG0568  166 pvgDDEDSELGDLL-EDEEAPspEEALEEELLREELREALDTLTEREREILRLRFGLD--DGEPHTLEEIGKEFGVSRER 242

                        250
                 ....*....|....*....
gi 496546009 227 ISRLEKKIMKRLKREMVKE 245
Cdd:COG0568  243 VRQIEAKALRKLRHPLRSR 261
PRK05572 PRK05572
RNA polymerase sporulation sigma factor, SigF/SigG family;
62-242 7.94e-30

RNA polymerase sporulation sigma factor, SigF/SigG family;


Pssm-ID: 180137 [Multi-domain]  Cd Length: 252  Bit Score: 111.60  E-value: 7.94e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009  62 EAKNILIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKSINTFKPDKNIKLATYASRCIENEILMYLRRNNKTRLEV 141
Cdd:PRK05572  32 EARDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDGTVKVSR 111

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009 142 SIDEPLN-VDWDGNELL-----------LSDILGTDE-----------------DVIYRD-----------IENEVER-- 179
Cdd:PRK05572 112 SLKETANkIRKDKDELSkelgreptieeLAEYLGVTPeevvlaqeasrspqsihETVHENdgdpitlldqiADQSEEDwf 191

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 496546009 180 -KLLLK-AINKLTDREKTIINLRFglntpdGQEMTQKEVATLLGISQSYISRLEKKIMKRLKREM 242
Cdd:PRK05572 192 dKIALKeAIRELDERERLIVYLRY------FKDKTQSEVAKRLGISQVQVSRLEKKILKQMKEKL 250
PRK08215 PRK08215
RNA polymerase sporulation sigma factor SigG;
60-240 1.74e-28

RNA polymerase sporulation sigma factor SigG;


Pssm-ID: 181296 [Multi-domain]  Cd Length: 258  Bit Score: 108.50  E-value: 1.74e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009  60 EDEAKNILIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKSINTFKPDKNIKLATYASRCIENEILMYLRRNNKTRL 139
Cdd:PRK08215  35 DKEAREKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNPIRV 114

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009 140 E---------------------------------------------------VSIDEPLNVDwDGNELLLSDILGTDEDv 168
Cdd:PRK08215 115 SrslrdiaykalqvreklinenskeptveeiakelevpreevvfaldaiqdpVSLFEPIYHD-GGDPIYVMDQISDEKN- 192

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 496546009 169 iyRDiENEVERKLLLKAINKLTDREKTIINLRFGlntpDGQemTQKEVATLLGISQSYISRLEKKIMKRLKR 240
Cdd:PRK08215 193 --KD-ENWLEEIALKEAMKKLNDREKLILNLRFF----QGK--TQMEVAEEIGISQAQVSRLEKAALKHMRK 255
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 62-242 4.52e-28

RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 104.74  E-value: 4.52e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009   62 EAKNILIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKSINTFKPDKNIKlaTYASRCIENEILMYLRRNNKTRLEV 141
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFK--AWLFRIARNLILDYLRRKRRLRREL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009  142 SIDEPLNVdwdgnelllsdilgtDEDVIYRDIENEVERKLLLKAINKLTDREKTIINLRFglntpdGQEMTQKEVATLLG 221
Cdd:TIGR02937  79 DLLEELLD---------------SDPSPEEELEQEEEREALREALEKLPEREREVLVLRY------LEGLSYKEIAEILG 137

                         170       180
                  ....*....|....*....|.
gi 496546009  222 ISQSYISRLEKKIMKRLKREM 242
Cdd:TIGR02937 138 ISVGTVKRRLKRARKKLRELL 158
FliA_WhiG TIGR02479
RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar ...
 67-242 6.77e-23

RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.


Pssm-ID: 274153 [Multi-domain]  Cd Length: 224  Bit Score: 92.72  E-value: 6.77e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009   67 LIEHNLRLVVYIAKKF---DNTGVGVEDLISIGTIGLIKSINTFKPDKNIKLATYASRCIENEILMYLRRN--------- 134
Cdd:TIGR02479   1 LIRRYLPLVKRIAGRLsvgLPSSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMLDELRRLdwvprslrq 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009  135 -----NKTRLEVS-----------IDEPLNVDWDG----------------NELLLSDILGTDEDVIYRDIENE-----V 177
Cdd:TIGR02479  81 karklERAIRELEarlgrepteeeIAEELGMDLKEyrqalneinalslvslDELLESGDDGGSLIDRIEDDKSEdpeeeL 160

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 496546009  178 ER----KLLLKAINKLTDREKTIINLRFglntpdGQEMTQKEVATLLGISQSYISRLEKKIMKRLKREM 242
Cdd:TIGR02479 161 EReelrEALAEAIESLSEREQLVLSLYY------YEELNLKEIGEVLGLTESRVSQIHSQALKKLRAKL 223
PRK08583 PRK08583
RNA polymerase sigma factor SigB; Validated
 39-245 1.52e-20

RNA polymerase sigma factor SigB; Validated


Pssm-ID: 236306 [Multi-domain]  Cd Length: 257  Bit Score: 87.44  E-value: 1.52e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009  39 LPPPLESEKENEIISDLGTEYEDEAKNILIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKSINTFKPDKNIKLATY 118
Cdd:PRK08583   6 QPTKLTKEEVNKWIAEYQENQDEEAQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAF 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009 119 ASRCIENEILMYLRrnNKT--------------------------------------RLEV------------------S 142
Cdd:PRK08583  86 AVPTIIGEIKRYLR--DKTwsvhvprrikelgpkikkavdelttelqrspkiseiadRLGVseeevleamemgksyqalS 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009 143 IDEPLNVDWDGNELLLSDILGTDEDVIyrdieNEVERKLLL-KAINKLTDREKTIINLRFGLNtpdgqeMTQKEVATLLG 221
Cdd:PRK08583 164 VDHSIEADSDGSTVTLLDIVGQQEDGY-----ELTEQRMILeKILPVLSDREKSIIQCTFIEN------LSQKETGERLG 232

                        250       260
                 ....*....|....*....|....
gi 496546009 222 ISQSYISRLEKKIMKRLKREMVKE 245
Cdd:PRK08583 233 ISQMHVSRLQRQAIKKLREAAFLD 256
PRK07921 PRK07921
RNA polymerase sigma factor SigB; Reviewed
 62-239 1.61e-19

RNA polymerase sigma factor SigB; Reviewed


Pssm-ID: 181169 [Multi-domain]  Cd Length: 324  Bit Score: 85.55  E-value: 1.61e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009  62 EAKNILIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKSINTFKPDKNIKLATYA---------------SRCI--- 123
Cdd:PRK07921  86 AARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYAtwwirqaitrgmadqSRTIrlp 165

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009 124 -------------------------------------ENEILMYLRRnnkTRLEVSIDEPLNVDwdgNELLLSDILgtdE 166
Cdd:PRK07921 166 vhlveqvnklarikrelhqqlgreatdeelaeesgipEEKIADLLEH---SRDPVSLDMPVGSD---EEAPLGDFI---E 236

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 496546009 167 DVIYRDIENEVERKLLLKAINK----LTDREKTIINLRFGLNtpDGQEMTQKEVATLLGISQSYISRLEKKIMKRLK 239
Cdd:PRK07921 237 DSEATSAENAVIAGLLHTDIRSvlatLDEREQQVIRLRFGLD--DGQPRTLDQIGKLFGLSRERVRQIEREVMSKLR 311
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 67-137 1.41e-18

Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime. The aromatic residues of the recognition helix, found at the C-terminus of this domain are though to mediate strand separation, thereby allowing transcription initiation.


Pssm-ID: 427998 [Multi-domain]  Cd Length: 71  Bit Score: 77.24  E-value: 1.41e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 496546009   67 LIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKSINTFKPDKNIKLATYASRCIENEILMYLRRNNKT 137
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRRT 71
PRK05901 PRK05901
RNA polymerase sigma factor; Provisional
 25-239 8.50e-17

RNA polymerase sigma factor; Provisional


Pssm-ID: 235640 [Multi-domain]  Cd Length: 509  Bit Score: 78.88  E-value: 8.50e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009  25 SGQGDIHYIGGAEVLPPplESEKENEIISDLGteyeDEAKNILIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKSI 104
Cdd:PRK05901 240 AGLYAEELLAEGEKLDP--ELRRDLQWIGRDG----KRAKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAV 313

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009 105 NTFKPDKNIKLATYA--------------------------------SRcIENEILMYLRRN------------------ 134
Cdd:PRK05901 314 EKFDYTKGYKFSTYAtwwirqaitramadqartiripvhmvetinklGR-IERELLQELGREptpeelakemgftpekvr 392

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009 135 --NKTRLE-VSIDEPLNvdwDGNELLLSDILgTDEDVIYRDieNEVERKLLLKAINK----LTDREKTIINLRFGLntPD 207
Cdd:PRK05901 393 eiQKYNREpISLDKTIG---KEGDSQFGDFI-EDSEAVSPV--DAVSFTLLQDQLQEvletLSEREAGVIRMRFGL--TD 464

                        250       260       270
                 ....*....|....*....|....*....|..
gi 496546009 208 GQEMTQKEVATLLGISQSYISRLEKKIMKRLK 239
Cdd:PRK05901 465 GQPKTLDEIGQVYGVTRERIRQIESKTLRKLR 496
PRK07122 PRK07122
RNA polymerase sigma factor SigF; Reviewed
 67-242 6.38e-16

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 168831 [Multi-domain]  Cd Length: 264  Bit Score: 74.81  E-value: 6.38e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009  67 LIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKSINTFKPDKNIKLATYASRCIENEILMYLRRNNKT--------- 137
Cdd:PRK07122  45 IVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWSvkvprrlke 124

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009 138 --------------------------------RLEV-------------SIDEPLNvDWDGNELLLSDILGtDEDVIYRD 172
Cdd:PRK07122 125 lhlrlgrataelsqrlgraptaselaaelgmdREEVveglvagsayntlSIDSGGG-SGDDDARAIADTLG-DVDAGLDQ 202

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 496546009 173 IEN-EVERKLLlkaiNKLTDREKTIINLRFGLNtpdgqeMTQKEVATLLGISQSYISRLEKKIMKRLKREM 242
Cdd:PRK07122 203 IENrEALRPLL----AALPERERTVLVLRFFES------MTQTQIAERVGISQMHVSRLLAKTLARLRDQL 263
fliA PRK06986
flagellar biosynthesis sigma factor; Validated
 87-239 2.19e-15

flagellar biosynthesis sigma factor; Validated


Pssm-ID: 235901 [Multi-domain]  Cd Length: 236  Bit Score: 72.96  E-value: 2.19e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009  87 VGVEDLISIGTIGLIKSINTFKPDKNIKLATYASRCIENEILMYLR----------RNNK------TRLE---------- 140
Cdd:PRK06986  36 VDLDDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDELRsldwvprsvrRNARevaqaiRQLEqelgreptdt 115

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009 141 -------------------------VSIDEPLNVDWDGnellLSDILGTDEDVIYRDIENEVERKLLLKAINKLTDREKT 195
Cdd:PRK06986 116 evaeklglsleeyremlldtnisqlFSIDELRGEHGDS----ILVTEDHQDEDPLQQLEDEELREALVEAIESLPEREQL 191

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 496546009 196 IINLRFGlntpdgQEMTQKEVATLLGISQSYISRLEKKIMKRLK 239
Cdd:PRK06986 192 VLSLYYQ------EELNLKEIGAVLGVSESRVSQIHSQAIKRLR 229
PRK05657 PRK05657
RNA polymerase sigma factor RpoS; Validated
 42-240 2.56e-15

RNA polymerase sigma factor RpoS; Validated


Pssm-ID: 235548 [Multi-domain]  Cd Length: 325  Bit Score: 73.84  E-value: 2.56e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009  42 PLESEKENEIISDLGTEYEDEAKNILIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKSINTFKPDKNIKLATYAS- 120
Cdd:PRK05657  66 PLLTAEEEVYFARRALRGDFAARQRMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATw 145

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009 121 -------RCIEN-------------EILMYLR--------------------RNNKTRLEV-----------SIDEPLNV 149
Cdd:PRK05657 146 wirqtieRAIMNqtrtirlpvhvvkELNVYLRaarelehkldhepsaeeiaeLLDKPVDDVsrmlalneritSLDTPLGG 225

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009 150 DWDGNEL-LLSDILGTDEDVIYRDieNEVErKLLLKAINKLTDREKTIINLRFGLNtpdGQE-MTQKEVATLLGISQSYI 227
Cdd:PRK05657 226 DPEKSLLdILADEQENGPEDTTQD--DDMK-QSIVKWLFELNDKQREVLARRFGLL---GYEaATLEDVAREIGLTRERV 299

                        250
                 ....*....|...
gi 496546009 228 SRLEKKIMKRLKR 240
Cdd:PRK05657 300 RQIQVEALRRLRE 312
PRK05949 PRK05949
RNA polymerase sigma factor; Validated
 61-240 3.15e-15

RNA polymerase sigma factor; Validated


Pssm-ID: 180321 [Multi-domain]  Cd Length: 327  Bit Score: 73.72  E-value: 3.15e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009  61 DEAKNILIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKSINTFKPDKNIKLATYASRCIENEILMYLRRNNKT-RL 139
Cdd:PRK05949  90 KRAKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTiRL 169

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009 140 EVSIDEPLN---------------------------------------------VDW---DGNELLLSDILGTDEDVIYR 171
Cdd:PRK05949 170 PIHITEKLNkikktqrelsqklgrsatpaeiakelelepsqireylsmarqpisLDVrvgDNQDTELSELLEDEGPSPDQ 249

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 496546009 172 DIENEVERKLLLKAINKLTDREKTIINLRFGLNtpDGQEMTQKEVATLLGISQSYISRLEKKIMKRLKR 240
Cdd:PRK05949 250 YITQELLRQDLNNLLAELTPQQREVLTLRFGLE--DGKELSLAKVGERLNLSRERVRQLEHQALAHLRR 316
PRK06288 PRK06288
RNA polymerase sigma factor WhiG; Reviewed
 41-239 7.08e-15

RNA polymerase sigma factor WhiG; Reviewed


Pssm-ID: 235770 [Multi-domain]  Cd Length: 268  Bit Score: 72.03  E-value: 7.08e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009  41 PPLESEKENEIISDLGTEYEDEAKNILIEHNLRLVVYIAKKfdnTGVGV------EDLISIGTIGLIKSINTFKPDKNIK 114
Cdd:PRK06288  10 PKYAQQDETELWREYKKTGDPKIREYLILKYSPLVKYVAGR---IAVGMpqnvefDDLVSYGVFGLIDAIEKFDPEREIK 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009 115 LATYA-------------------------SRCIENEILMY---LRRN-----------------NKTRLE------VSI 143
Cdd:PRK06288  87 FKTYAvtrirgaifdelrsidwiprsvrqkARQIERAIAMLearLGRTpsdeeiadelgisleeyNSLLSKlsgtsvVSL 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009 144 DEPLNVDWDGNELLLSDIL----GTDEDVIyrdIENEVERKLLLKAINKLTDREKTIINLRFglntpdGQEMTQKEVATL 219
Cdd:PRK06288 167 NDLWFGGDEGDEVSLMDTLespaALNPDEI---AEREEIKRVIVEAIKTLPEREKKVLILYY------YEDLTLKEIGKV 237

                        250       260
                 ....*....|....*....|
gi 496546009 220 LGISQSYISRLEKKIMKRLK 239
Cdd:PRK06288 238 LGVTESRISQLHTKAVLQLR 257
PRK07598 PRK07598
RNA polymerase sigma factor SigC; Validated
 63-239 2.23e-14

RNA polymerase sigma factor SigC; Validated


Pssm-ID: 236067 [Multi-domain]  Cd Length: 415  Bit Score: 71.82  E-value: 2.23e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009  63 AKNILIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKSINTFKPDKNIKLATYASRCIENEILMYLRRNNKT-RLEV 141
Cdd:PRK07598 176 AKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTiRLPV 255

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009 142 SIDEPLN-----------------------------------------------------VDWDGNELLLSDILGTDEDV 168
Cdd:PRK07598 256 HITEKLNkikkaqrkisqekgrtptiediaqelemtptqvrevllrvprsvsletkvgkdKDTELGDLLETDDISPEEML 335

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 496546009 169 IYRDIENEVERKLLlkainKLTDREKTIINLRFGLNtpDGQEMTQKEVATLLGISQSYISRLEKKIMKRLK 239
Cdd:PRK07598 336 MRESLQRDLQHLLA-----DLTSRERDVIRMRFGLA--DGHTYSLAEIGRALDLSRERVRQIESKALQKLR 399
PRK06596 PRK06596
RNA polymerase factor sigma-32; Reviewed
 15-242 4.97e-14

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 235838 [Multi-domain]  Cd Length: 284  Bit Score: 69.82  E-value: 4.97e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009  15 MIRREPSFLLSGQGDI-HYIGGAEVLPPpLESEKENEiisdLGTEYED----EAKNILIEHNLRLVVYIAKKFDNTGVGV 89
Cdd:PRK06596   1 MTKALQLLALSPEGNLdAYIQAVNKIPM-LTAEEEYM----LAKRLREhgdlEAAKQLVLSHLRFVVHIARGYRGYGLPQ 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009  90 EDLISIGTIGLIKSINTFKPDKNIKLATYASRCIENEILMYLRRN---------------------NKTRL------EV- 141
Cdd:PRK06596  76 ADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNwrivkvattkaqrklffnlrkAKKRLgwlnpeEVe 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009 142 SIDEPLNV-----------------------DWDGNE-----LLLSDILGTDEDVIYRDIENEVERKLLLKAINKLTDRE 193
Cdd:PRK06596 156 MVAEELGVseeevremesrlsgqdasldapiDDDDEEsgapqDYLEDKSSDPADVLEEDNWEDQRRALLADALEGLDERS 235

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*....
gi 496546009 194 KTIINLRFGLNTPdgqeMTQKEVATLLGISQSYISRLEKKIMKRLKREM 242
Cdd:PRK06596 236 RDIIEARWLDDDK----STLQELAAEYGVSAERVRQIEKNAMKKLKAAI 280
PRK07406 PRK07406
RNA polymerase sigma factor RpoD; Validated
 63-239 9.90e-14

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236012 [Multi-domain]  Cd Length: 373  Bit Score: 69.81  E-value: 9.90e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009  63 AKNILIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKSINTFKPDKNIKLATYASRCIENEILMYLRRNNKT-RLEV 141
Cdd:PRK07406 137 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTiRLPV 216

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009 142 SIDEPLNVDWDGNELL------------------------------------LSDILGTDE-----DVIYRDIEN---EV 177
Cdd:PRK07406 217 HLYETISRIKKTTKVLsqefgrkpteeeiaesmemtieklrfiaksaqlpisLETPIGKEEdsrlgDFIEADGETpedDV 296

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 496546009 178 ERKLL---LKAI-NKLTDREKTIINLRFGLNtpDGQEMTQKEVATLLGISQSYISRLEKKIMKRLK 239
Cdd:PRK07406 297 AKNLLredLEGVlATLSPRERDVLRLRYGLD--DGRMKTLEEIGQIFNVTRERIRQIEAKALRKLR 360
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
46-244 1.38e-13

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 67.24  E-value: 1.38e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009  46 EKENEIISDLGTEYEDEAKNILIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKSINTFKPDKNIKLATYASRCIEN 125
Cdd:PRK08295   8 ELEDEELVELARSGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCITR 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009 126 EI---LMYLRRNNKTRLE--VSIDEPLNVDWDGNELL--LSDILGTD--EDVIYRDIENEVERKLLlkaiNKLTDREKTI 196
Cdd:PRK08295  88 QIitaIKTANRQKHIPLNsyVSLDKPIYDEESDRTLLdvISEAKVTDpeELIISKEELEDIEEKIE----ELLSELEKEV 163

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|..
gi 496546009 197 INLRFglntpDGqeMTQKEVATLLGISQSYI----SRLEKKIMKRLKREMVK 244
Cdd:PRK08295 164 LELYL-----DG--KSYQEIAEELNRHVKSIdnalQRVKRKLEKYLENREIT 208
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 60-243 3.93e-13

DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; DNA-directed RNA polymerase specialized sigma subunit, sigma24 family is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 441203 [Multi-domain]  Cd Length: 181  Bit Score: 65.40  E-value: 3.93e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009  60 EDEAKNILIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKSINTFKPDKNIKlaTYASRCIENEILMYLRRNNktRL 139
Cdd:COG1595   15 DEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFR--AWLYRIARNLAIDHLRKRR--RR 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009 140 EVSIDEPLnvdwdgnELLLSDILGTDEDVIYRDienevERKLLLKAINKLTDREKTIINLRFGlntpdgQEMTQKEVATL 219
Cdd:COG1595   91 RELLDELA-------EELPDEAADPEEALEAEE-----LLEALLAALERLPPRQREVLVLRYL------EGLSYAEIAEI 152

                        170       180
                 ....*....|....*....|....*...
gi 496546009 220 LGIS----QSYISRLEKKIMKRLKREMV 243
Cdd:COG1595  153 LGISegtvKSRLSRARKKLREALEEEGA 180
PRK07408 PRK07408
RNA polymerase sigma factor SigF; Reviewed
 64-245 1.25e-12

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 180965 [Multi-domain]  Cd Length: 256  Bit Score: 65.33  E-value: 1.25e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009  64 KNILIEHNLRLVVYIAKKFDN-TGVGVEDLISIGTIGLIKSINTFKPDKNIKLATYASRCIENEILMYLR---------- 132
Cdd:PRK07408  27 RNQLVELNLGLVRKEAHRWSNqCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRdksptvripr 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009 133 -----------------------------------------------RNnktRLEVSIDEPLNVDWDGNeLLLSDILgtd 165
Cdd:PRK07408 107 rwqelqrqakkvrqelrqelgrqptdqeiaqaldisleewqeiklalQN---RTPLSLDAPVNQDEDGS-TSLGDLL--- 179

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009 166 EDVIYRDIE-NEVERKLLLKAINKLTDREKTIINLRFGlntpdgQEMTQKEVATLLGISQSYISRLEKKIMKRLKREMVK 244
Cdd:PRK07408 180 PDPRYRSFQlAQEDRIRLQQALAQLEERTREVLEFVFL------HDLTQKEAAERLGISPVTVSRRVKKGLDQLKKLLQP 253


                 .
gi 496546009 245 E 245
Cdd:PRK07408 254 E 254
PRK07405 PRK07405
RNA polymerase sigma factor SigD; Validated
 61-240 1.76e-12

RNA polymerase sigma factor SigD; Validated


Pssm-ID: 180963 [Multi-domain]  Cd Length: 317  Bit Score: 65.55  E-value: 1.76e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009  61 DEAKNILIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKSINTFKPDKNIKLATYASRCIENEILMYLRRNNKT-RL 139
Cdd:PRK07405  80 EAAKRKMVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTiRL 159

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009 140 EVSIDEPLNV--------------------------------------------------DWDGNEL--LLSDILGTDED 167
Cdd:PRK07405 160 PIHITEKLNKikkaqrqlsqqlgraatigelaeeleltpkqvreylerarqplsldlrvgDNQDTELgeLLEDTGASPED 239

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 496546009 168 -VIYRDIENEVERKLllkaiNKLTDREKTIINLRFGLNtpDGQEMTQKEVATLLGISQSYISRLEKKIMKRLKR 240
Cdd:PRK07405 240 fATQSSLQLDLERLM-----EDLTPQQKEVIALRFGLE--DGQPLTLAKIGERLNISRERVRQIEREALSKLRK 306
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 179-239 1.12e-11

Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP).


Pssm-ID: 100119 [Multi-domain]  Cd Length: 55  Bit Score: 58.27  E-value: 1.12e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 496546009 179 RKLLLKAINKLTDREKTIINLRFGlntpdgQEMTQKEVATLLGISQSYISRLEKKIMKRLK 239
Cdd:cd06171    1 RERLEEALDKLPEREREVILLRFG------EGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 185-240 1.87e-11

Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.


Pssm-ID: 461347 [Multi-domain]  Cd Length: 50  Bit Score: 57.44  E-value: 1.87e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 496546009  185 AINKLTDREKTIINLRFGlntpdgQEMTQKEVATLLGISQSYISRLEKKIMKRLKR 240
Cdd:pfam04545   1 ALASLPPRERQVLVLRYG------EGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
PRK09210 PRK09210
RNA polymerase sigma factor RpoD; Validated
 60-239 5.13e-11

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 61.54  E-value: 5.13e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009  60 EDEAKNILIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKSINTFKPDKNIKLATYASRCIENEILMYLRRNNKT-R 138
Cdd:PRK09210 127 DEEAKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTiR 206

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009 139 LEVSIDEPLNVDWDGNELLLSDI------------------------------------LGTDED------VIYRDIENE 176
Cdd:PRK09210 207 IPVHMVETINKLIRVQRQLLQELgreptpeeiaeemdmppekvreilkiaqepvsletpIGEEDDshlgdfIEDQDATSP 286

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009 177 VE-------RKLLLKAINKLTDREKTIINLRFGLNtpDGQEMTQKEVATLLGISQSYISRLEKKIMKRLK 239
Cdd:PRK09210 287 ADhaayellKEQLEDVLDTLTDREENVLRLRFGLD--DGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 354
rpoH2 PRK07500
RNA polymerase factor sigma-32; Reviewed
 41-244 7.13e-11

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 236033 [Multi-domain]  Cd Length: 289  Bit Score: 60.82  E-value: 7.13e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009  41 PPLESEKENEIISDLGTEYEDEAKNILIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKSINTFKPDKNIKLATYAS 120
Cdd:PRK07500  19 PYLEREEEHALAYRWKDHRDEDALHRIISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYAT 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009 121 RCIENEILMYLRRN-----------------NKTRLEVSI---DEPLNVD-----------------------WDGNELL 157
Cdd:PRK07500  99 WWIRASIQDYILRNwsivrggtssaqkalffNLRRLRARLaqaDEELTKQeihreiatalgvslsdvemmdarLSGPDAS 178

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009 158 LSDILGTDED------------------VIYRDIENEVERKLLLKAINKLTDREKTIInlRFGLNTPDGQemTQKEVATL 219
Cdd:PRK07500 179 LNAPQSEEDEgrsermdflvddsplpdeQVESSIDGERRRRWLTQALQTLNERELRII--RERRLREDGA--TLEALGEE 254

                        250       260
                 ....*....|....*....|....*
gi 496546009 220 LGISQSYISRLEKKIMKRLKREMVK 244
Cdd:PRK07500 255 LGISKERVRQIEARALEKLRRALLS 279
PRK07670 PRK07670
FliA/WhiG family RNA polymerase sigma factor;
62-240 9.17e-10

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 181075 [Multi-domain]  Cd Length: 251  Bit Score: 57.36  E-value: 9.17e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009  62 EAKNILIEHNLRLVVYIAKKFDNT---GVGVEDLISIGTIGLIKSINTFKPDKNIKLATYASRCIENEILMYLRRNN--- 135
Cdd:PRK07670  22 DAADELIRRYMPLVHYHVQRISVGlpkSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRKEDwlp 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009 136 -----KT--------RLE------VSIDE--------PLNVDWDGNELLLSDILGTDE-----------DVIYRD----- 172
Cdd:PRK07670 102 rsmreKTkkveaaieKLEqrymrnVTPKEvaaelgmtEEEVEATMNEGFFANLLSIDEkthdqddgenvSVTIRDdktpt 181

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 496546009 173 ----IENEVERKLLLKAINKLTDREKTIINLRFglntpdGQEMTQKEVATLLGISQSYISRLEKKIMKRLKR 240
Cdd:PRK07670 182 peekLLKEELIEELAEKIKQLSEKEQLVISLFY------KEELTLTEIGQVLNLSTSRISQIHSKALFKLKK 247
PRK05658 PRK05658
RNA polymerase sigma factor RpoD; Validated
 61-119 4.64e-08

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 235549 [Multi-domain]  Cd Length: 619  Bit Score: 53.26  E-value: 4.64e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 496546009  61 DEAKNILIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKSINTFKPDKNIKLATYA 119
Cdd:PRK05658 379 RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 437
PRK05911 PRK05911
RNA polymerase sigma factor sigma-28; Reviewed
 60-239 1.34e-05

RNA polymerase sigma factor sigma-28; Reviewed


Pssm-ID: 235644 [Multi-domain]  Cd Length: 257  Bit Score: 44.99  E-value: 1.34e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009  60 EDEAKNILIEHNLRLVVYIAKKFDN---TGVGVEDLISIGTIGLIKSINTFKPDKNIKLATYASRCIENEILMYLRRNN- 135
Cdd:PRK05911  21 EIEYRDVLIEFYLPLVKNVAHRLISgmpSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRKQDw 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009 136 --------KTRLEVSID--------EP------------------------------LNVDW-----DGNELLLSDILGT 164
Cdd:PRK05911 101 vprsvhqkANKLADAMDslrqslgkEPtdgelceylnisqqelsgwfssarpalilsLNEEFpcqsdDEAGLALEERIAD 180

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 496546009 165 DEDVIYRDIENEVERKLLL-KAINKLTDREKTIINLRFglntpdGQEMTQKEVATLLGISQSYISRLEKKIMKRLK 239
Cdd:PRK05911 181 ERAETGYDVVDKKEFSSILaEAILALEEKERKVMALYY------YEELVLKEIGKILGVSESRVSQIHSKALLKLR 250
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
211-232 1.28e-04

Transcriptional regulator, contains XRE-family HTH domain [Transcription];


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 39.59  E-value: 1.28e-04
                         10        20
                 ....*....|....*....|..
gi 496546009 211 MTQKEVATLLGISQSYISRLEK 232
Cdd:COG1396   21 LTQEELAERLGVSRSTISRIER 42
PRK12427 PRK12427
FliA/WhiG family RNA polymerase sigma factor;
126-239 2.35e-04

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 183523 [Multi-domain]  Cd Length: 231  Bit Score: 41.39  E-value: 2.35e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009 126 EILMYLRRNNKTRLEvSIDEPLNVDWDGNELllsdilgtdedvIYRDIENE-VERKLLLKAINKLTDREKTIINLRFGln 204
Cdd:PRK12427 133 EYQEYLLLENAGTLE-SLDELLALEAHNDIL------------QSRDLEENiIIEDNLKQALSQLDEREQLILHLYYQ-- 197

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 496546009 205 tpdgQEMTQKEVATLLGISQSYISRLEKKIMKRLK 239
Cdd:PRK12427 198 ----HEMSLKEIALVLDLTEARICQLNKKIAQKIK 228
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 179-234 3.35e-04

Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif.


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 37.44  E-value: 3.35e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009  179 RKLLLKAINKLTDREKTIINLRfglntpDGQEMTQKEVATLLGIS----QSYISRLEKKI 234
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLR------YLEGLSYAEIAELLGISegtvKSRLSRARKKL 54
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
209-232 6.02e-04

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 37.11  E-value: 6.02e-04
                           10        20
                   ....*....|....*....|....
gi 496546009   209 QEMTQKEVATLLGISQSYISRLEK 232
Cdd:smart00530   9 KGLTQEELAEKLGVSRSTLSRIEN 32
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 211-232 1.06e-03

Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.


Pssm-ID: 238045 [Multi-domain]  Cd Length: 58  Bit Score: 36.38  E-value: 1.06e-03
                         10        20
                 ....*....|....*....|..
gi 496546009 211 MTQKEVATLLGISQSYISRLEK 232
Cdd:cd00093   13 LTQEELAEKLGVSRSTISRIEN 34
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 102-223 1.76e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 38.41  E-value: 1.76e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009 102 KSINTFKPDKniKLATYASRCIENEILMYLRRNNKTRLEVSIDEPlNVDWDGNELLLSDILGTDEDVIYRdieNEVeRKL 181
Cdd:PRK11922  70 RALGTFRGDA--SLSTWLSRIVLNEALGRLRRRRRLVNLAEMVMA-STIAGGERTPLADPAEDPERAAAR---REI-RAL 142

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 496546009 182 LLKAINKLTDREKTIINLRfglntpDGQEMTQKEVATLLGIS 223
Cdd:PRK11922 143 LERAIDALPDAFRAVFVLR------VVEELSVEETAQALGLP 178
PRK06930 PRK06930
positive control sigma-like factor; Validated
 166-239 1.93e-03

positive control sigma-like factor; Validated


Pssm-ID: 180757 [Multi-domain]  Cd Length: 170  Bit Score: 37.79  E-value: 1.93e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009 166 EDVIYRDIENEVE-----RKLLLKAINKLTDREKTIINLRfglntpDGQEMTQKEVATLLGIS----QSYISRLEKKIMK 236
Cdd:PRK06930  87 EDLEWDIEEPESVisewdKIRIEDALSVLTEREKEVYLMH------RGYGLSYSEIADYLNIKkstvQSMIERAEKKIAR 160


                 ...
gi 496546009 237 RLK 239
Cdd:PRK06930 161 QIN 163
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 211-231 2.15e-03

Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.


Pssm-ID: 433309 [Multi-domain]  Cd Length: 64  Bit Score: 35.58  E-value: 2.15e-03
                          10        20
                  ....*....|....*....|.
gi 496546009  211 MTQKEVATLLGISQSYISRLE 231
Cdd:pfam13560  15 LSQEALARRLGVSRSTLSRLE 35
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
211-232 3.26e-03

DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 35.21  E-value: 3.26e-03
                         10        20
                 ....*....|....*....|..
gi 496546009 211 MTQKEVATLLGISQSYISRLEK 232
Cdd:COG1476   18 LTQEELAELLGVSRQTISAIEN 39
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 209-232 3.33e-03

Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and CI. Within the protein Swiss:Q5F9C2, the full protein fold incorporates a helix-turn-helix motif, but the function of this member is unlikely to be that of a DNA-binding regulator, the function of most other members, so is not necessarily characteriztic of the whole family.


Pssm-ID: 460181 [Multi-domain]  Cd Length: 55  Bit Score: 34.82  E-value: 3.33e-03
                          10        20
                  ....*....|....*....|....
gi 496546009  209 QEMTQKEVATLLGISQSYISRLEK 232
Cdd:pfam01381   8 LGLSQEELAEKLGVSRSTISKIEN 31
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 105-245 4.44e-03

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 36.85  E-value: 4.44e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496546009 105 NTFKPDKNIKlaTYASRCIENEILMYLR--RNNKTRLEVSIDeplnvdWDGNELLLSdilgTDEDVIYRDienevERKLL 182
Cdd:PRK09639  44 SDFKGIENEK--GWLIKSARNVAYNYLRseKRRRARILGEFQ------WQEVDNEPS----PEEIWIRKE-----EITKV 106

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 496546009 183 LKAINKLTDREKTIINLRFglntpdgQEMTQKEVATLLGISQSYISRLEKKIMKRLKREMVKE 245
Cdd:PRK09639 107 QEVLAKMTERDRTVLLLRF-------SGYSYKEIAEALGIKESSVGTTLARAKKKFRKIYEQM 162
tfx PRK03975
putative transcriptional regulator; Provisional
 189-240 5.56e-03

putative transcriptional regulator; Provisional


Pssm-ID: 179690 [Multi-domain]  Cd Length: 141  Bit Score: 36.02  E-value: 5.56e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 496546009 189 LTDREKTIINLRfglntpdGQEMTQKEVATLLGISQSYISRLEKKIMKRLKR 240
Cdd:PRK03975   7 LTERQIEVLRLR-------ERGLTQQEIADILGTSRANVSSIEKRARENIEK 51
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH