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Conserved domains on  [gi|2556888279|gb|WKZ27433|]
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MAG: sigma-70 family RNA polymerase sigma factor [Candidatus Paceibacterota bacterium]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK09210 super family cl35786
RNA polymerase sigma factor RpoD; Validated
 8-357 2.45e-165

RNA polymerase sigma factor RpoD; Validated


The actual alignment was detected with superfamily member PRK09210:

Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 466.00  E-value: 2.45e-165
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279   8 ALIERGKTRGFVTQAEILSAFPTIEQDIIGLEALYERLEGENITVIESVSVFEETAAKEYEQKKKIEDEFS--EGSS-SD 84
Cdd:PRK09210   17 ELIEKGKKRGTLTYDEIAEKLIPFELDSDQIDDLYERLEDAGISIVDEEGNPSSAQVVEEEEEEELDNDLSvpPGVKiND 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279  85 SVQMYLREIGKYPLLKGEEEIELAKRIERNDESARQKLALSNLRLVVSIAKKYVGRSanLSLLDLIQEGNIGLFKAVEKF 164
Cdd:PRK09210   97 PVRMYLKEIGRVPLLTAEEEIELAKRIEEGDEEAKQRLAEANLRLVVSIAKRYVGRG--MLFLDLIQEGNMGLMKAVEKF 174

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 165 DFRKGFKFSTYATWWIRQAITRALADQARTIRIPVHMVETINKYQQVVRRLVQELGRDPLPEEVAAEMDMDVDKVRHIIK 244
Cdd:PRK09210  175 DYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILK 254

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 245 ISQDTISLETPVGDgkDEDSHLEDFIPDENALGPDVSAGRKILKKYIDEIIGDLSQREQKILDMRFGLTDGVTHTLEEVG 324
Cdd:PRK09210  255 IAQEPVSLETPIGE--EDDSHLGDFIEDQDATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVG 332

                         330       340       350
                  ....*....|....*....|....*....|...
gi 2556888279 325 KVFNVTRERIRQIEAKALEKIRQHENVERLKGY 357
Cdd:PRK09210  333 KVFGVTRERIRQIEAKALRKLRHPSRSKQLKDF 365
 
Name Accession Description Interval E-value
PRK09210 PRK09210
RNA polymerase sigma factor RpoD; Validated
 8-357 2.45e-165

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 466.00  E-value: 2.45e-165
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279   8 ALIERGKTRGFVTQAEILSAFPTIEQDIIGLEALYERLEGENITVIESVSVFEETAAKEYEQKKKIEDEFS--EGSS-SD 84
Cdd:PRK09210   17 ELIEKGKKRGTLTYDEIAEKLIPFELDSDQIDDLYERLEDAGISIVDEEGNPSSAQVVEEEEEEELDNDLSvpPGVKiND 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279  85 SVQMYLREIGKYPLLKGEEEIELAKRIERNDESARQKLALSNLRLVVSIAKKYVGRSanLSLLDLIQEGNIGLFKAVEKF 164
Cdd:PRK09210   97 PVRMYLKEIGRVPLLTAEEEIELAKRIEEGDEEAKQRLAEANLRLVVSIAKRYVGRG--MLFLDLIQEGNMGLMKAVEKF 174

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 165 DFRKGFKFSTYATWWIRQAITRALADQARTIRIPVHMVETINKYQQVVRRLVQELGRDPLPEEVAAEMDMDVDKVRHIIK 244
Cdd:PRK09210  175 DYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILK 254

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 245 ISQDTISLETPVGDgkDEDSHLEDFIPDENALGPDVSAGRKILKKYIDEIIGDLSQREQKILDMRFGLTDGVTHTLEEVG 324
Cdd:PRK09210  255 IAQEPVSLETPIGE--EDDSHLGDFIEDQDATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVG 332

                         330       340       350
                  ....*....|....*....|....*....|...
gi 2556888279 325 KVFNVTRERIRQIEAKALEKIRQHENVERLKGY 357
Cdd:PRK09210  333 KVFGVTRERIRQIEAKALRKLRHPSRSKQLKDF 365
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 88-357 6.04e-150

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: 423.31  E-value: 6.04e-150
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279  88 MYLREIGKYPLLKGEEEIELAKRIERNDESARQKLALSNLRLVVSIAKKYVGRsaNLSLLDLIQEGNIGLFKAVEKFDFR 167
Cdd:COG0568     1 AYLREIGRVPLLTAEEEVELARRIQAGDEEAKRKLVEANLRLVVSIAKKYQGR--GLPLLDLIQEGNLGLMKAVEKFDPE 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 168 KGFKFSTYATWWIRQAITRALADQARTIRIPVHMVETINKYQQVVRRLVQELGRDPLPEEVAAEMDMDVDKVRHIIKISQ 247
Cdd:COG0568    79 RGFRFSTYATWWIRQAITRAIADQWRTIRLPVHMAETLNKLRRAKRQLLQELGREPTPEEIAEELGVPEEKVREMLRLAR 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 248 DTISLETPVGDgkDEDSHLEDFIPDENALGPDVSAGRKILKKYIDEIIGDLSQREQKILDMRFGLTDGVTHTLEEVGKVF 327
Cdd:COG0568   159 EPVSLDAPVGD--DEDSELGDLLEDEEAPSPEEALEEELLREELREALDTLTEREREILRLRFGLDDGEPHTLEEIGKEF 236

                         250       260       270
                  ....*....|....*....|....*....|
gi 2556888279 328 NVTRERIRQIEAKALEKIRQHENVERLKGY 357
Cdd:COG0568   237 GVSRERVRQIEAKALRKLRHPLRSRKLRDY 266
RpoD_Cterm TIGR02393
RNA polymerase sigma factor RpoD, C-terminal domain; This model represents the well-conserved ...
 118-357 1.42e-132

RNA polymerase sigma factor RpoD, C-terminal domain; This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc. [Transcription, Transcription factors]


Pssm-ID: 274108 [Multi-domain]  Cd Length: 238  Bit Score: 378.18  E-value: 1.42e-132
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 118 ARQKLALSNLRLVVSIAKKYVGRSanLSLLDLIQEGNIGLFKAVEKFDFRKGFKFSTYATWWIRQAITRALADQARTIRI 197
Cdd:TIGR02393   1 AKKKLVESNLRLVVSIAKKYTNRG--LSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRI 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 198 PVHMVETINKYQQVVRRLVQELGRDPLPEEVAAEMDMDVDKVRHIIKISQDTISLETPVGDgkDEDSHLEDFIPDENALG 277
Cdd:TIGR02393  79 PVHMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGE--EEDSFLGDFIEDESIES 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 278 PDVSAGRKILKKYIDEIIGDLSQREQKILDMRFGLTDGVTHTLEEVGKVFNVTRERIRQIEAKALEKIRQHENVERLKGY 357
Cdd:TIGR02393 157 PDDAAAKELLREQLDEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLKDF 236
Sigma70_r3 pfam04539
Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the ...
 203-279 1.47e-22

Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but as some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme.


Pssm-ID: 427997 [Multi-domain]  Cd Length: 78  Bit Score: 89.97  E-value: 1.47e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2556888279 203 ETINKYQQVVRRLVQELGRDPLPEEVAAEMDMDVDKVRHIIKISQDTISLETPVGDgkDEDSHLEDFIPDENALGPD 279
Cdd:pfam04539   1 ELLNKIKRAQRELEQELGREPTPEEIAEELGLSPEKVREVLEAAREPVSLDTPVGE--EEDGELGDLLEDDDIESPE 75
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 288-346 3.51e-09

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: 52.11  E-value: 3.51e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2556888279 288 KKYIDEIIGDLSQREQKILDMRFGltdgVTHTLEEVGKVFNVTRERIRQIEAKALEKIR 346
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFG----EGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
PRK09210 PRK09210
RNA polymerase sigma factor RpoD; Validated
 8-357 2.45e-165

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 466.00  E-value: 2.45e-165
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279   8 ALIERGKTRGFVTQAEILSAFPTIEQDIIGLEALYERLEGENITVIESVSVFEETAAKEYEQKKKIEDEFS--EGSS-SD 84
Cdd:PRK09210   17 ELIEKGKKRGTLTYDEIAEKLIPFELDSDQIDDLYERLEDAGISIVDEEGNPSSAQVVEEEEEEELDNDLSvpPGVKiND 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279  85 SVQMYLREIGKYPLLKGEEEIELAKRIERNDESARQKLALSNLRLVVSIAKKYVGRSanLSLLDLIQEGNIGLFKAVEKF 164
Cdd:PRK09210   97 PVRMYLKEIGRVPLLTAEEEIELAKRIEEGDEEAKQRLAEANLRLVVSIAKRYVGRG--MLFLDLIQEGNMGLMKAVEKF 174

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 165 DFRKGFKFSTYATWWIRQAITRALADQARTIRIPVHMVETINKYQQVVRRLVQELGRDPLPEEVAAEMDMDVDKVRHIIK 244
Cdd:PRK09210  175 DYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILK 254

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 245 ISQDTISLETPVGDgkDEDSHLEDFIPDENALGPDVSAGRKILKKYIDEIIGDLSQREQKILDMRFGLTDGVTHTLEEVG 324
Cdd:PRK09210  255 IAQEPVSLETPIGE--EDDSHLGDFIEDQDATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVG 332

                         330       340       350
                  ....*....|....*....|....*....|...
gi 2556888279 325 KVFNVTRERIRQIEAKALEKIRQHENVERLKGY 357
Cdd:PRK09210  333 KVFGVTRERIRQIEAKALRKLRHPSRSKQLKDF 365
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 88-357 6.04e-150

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: 423.31  E-value: 6.04e-150
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279  88 MYLREIGKYPLLKGEEEIELAKRIERNDESARQKLALSNLRLVVSIAKKYVGRsaNLSLLDLIQEGNIGLFKAVEKFDFR 167
Cdd:COG0568     1 AYLREIGRVPLLTAEEEVELARRIQAGDEEAKRKLVEANLRLVVSIAKKYQGR--GLPLLDLIQEGNLGLMKAVEKFDPE 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 168 KGFKFSTYATWWIRQAITRALADQARTIRIPVHMVETINKYQQVVRRLVQELGRDPLPEEVAAEMDMDVDKVRHIIKISQ 247
Cdd:COG0568    79 RGFRFSTYATWWIRQAITRAIADQWRTIRLPVHMAETLNKLRRAKRQLLQELGREPTPEEIAEELGVPEEKVREMLRLAR 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 248 DTISLETPVGDgkDEDSHLEDFIPDENALGPDVSAGRKILKKYIDEIIGDLSQREQKILDMRFGLTDGVTHTLEEVGKVF 327
Cdd:COG0568   159 EPVSLDAPVGD--DEDSELGDLLEDEEAPSPEEALEEELLREELREALDTLTEREREILRLRFGLDDGEPHTLEEIGKEF 236

                         250       260       270
                  ....*....|....*....|....*....|
gi 2556888279 328 NVTRERIRQIEAKALEKIRQHENVERLKGY 357
Cdd:COG0568   237 GVSRERVRQIEAKALRKLRHPLRSRKLRDY 266
PRK05901 PRK05901
RNA polymerase sigma factor; Provisional
 30-357 1.18e-136

RNA polymerase sigma factor; Provisional


Pssm-ID: 235640 [Multi-domain]  Cd Length: 509  Bit Score: 398.60  E-value: 1.18e-136
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279  30 TIEQDIIGLEALYERLEGENITVIESVS-VFEETAAKEYEQKKKIEDEFSE-GSSSDSVQMYLREIGKYPLLKGEEEIEL 107
Cdd:PRK05901  155 DDDEDDDDDDVDDEDEEKKEAKELEKLSdDDDFVWDEDDSEALRQARKDAKlTATADPVKAYLKQIGKVKLLNAEEEVEL 234

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 108 AKRIE---------------------------RNDESARQKLALSNLRLVVSIAKKYVGRSanLSLLDLIQEGNIGLFKA 160
Cdd:PRK05901  235 AKRIEaglyaeellaegekldpelrrdlqwigRDGKRAKNHLLEANLRLVVSLAKRYTNRG--LSFLDLIQEGNLGLIKA 312

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 161 VEKFDFRKGFKFSTYATWWIRQAITRALADQARTIRIPVHMVETINKYQQVVRRLVQELGRDPLPEEVAAEMDMDVDKVR 240
Cdd:PRK05901  313 VEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVETINKLGRIERELLQELGREPTPEELAKEMGFTPEKVR 392

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 241 HIIKISQDTISLETPVGDgkDEDSHLEDFIPDENALGPDVSAGRKILKKYIDEIIGDLSQREQKILDMRFGLTDGVTHTL 320
Cdd:PRK05901  393 EIQKYNREPISLDKTIGK--EGDSQFGDFIEDSEAVSPVDAVSFTLLQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTL 470

                         330       340       350
                  ....*....|....*....|....*....|....*..
gi 2556888279 321 EEVGKVFNVTRERIRQIEAKALEKIRQHENVERLKGY 357
Cdd:PRK05901  471 DEIGQVYGVTRERIRQIESKTLRKLRHPSRSQVLRDF 507
RpoD_Cterm TIGR02393
RNA polymerase sigma factor RpoD, C-terminal domain; This model represents the well-conserved ...
 118-357 1.42e-132

RNA polymerase sigma factor RpoD, C-terminal domain; This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc. [Transcription, Transcription factors]


Pssm-ID: 274108 [Multi-domain]  Cd Length: 238  Bit Score: 378.18  E-value: 1.42e-132
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 118 ARQKLALSNLRLVVSIAKKYVGRSanLSLLDLIQEGNIGLFKAVEKFDFRKGFKFSTYATWWIRQAITRALADQARTIRI 197
Cdd:TIGR02393   1 AKKKLVESNLRLVVSIAKKYTNRG--LSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRI 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 198 PVHMVETINKYQQVVRRLVQELGRDPLPEEVAAEMDMDVDKVRHIIKISQDTISLETPVGDgkDEDSHLEDFIPDENALG 277
Cdd:TIGR02393  79 PVHMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGE--EEDSFLGDFIEDESIES 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 278 PDVSAGRKILKKYIDEIIGDLSQREQKILDMRFGLTDGVTHTLEEVGKVFNVTRERIRQIEAKALEKIRQHENVERLKGY 357
Cdd:TIGR02393 157 PDDAAAKELLREQLDEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLKDF 236
PRK05658 PRK05658
RNA polymerase sigma factor RpoD; Validated
 19-357 6.47e-122

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 235549 [Multi-domain]  Cd Length: 619  Bit Score: 364.50  E-value: 6.47e-122
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279  19 VTQAEILSAFPTIEQDIIGLEAlyerlegenitVIESVSVFEETAAKEYEQKKKIEDEfsegsssdsvqmyLREIGKYPL 98
Cdd:PRK05658  303 MPRKDFLKLFQGNELDITWLEK-----------EIASGKPWSEFLVRVYDEIKKLQQE-------------LEAIEEETG 358

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279  99 LKGEEEIELAKRIERNDESARQ---KLALSNLRLVVSIAKKYVGRSanLSLLDLIQEGNIGLFKAVEKFDFRKGFKFSTY 175
Cdd:PRK05658  359 LTIEELKEINRQISKGEAKARRakkEMVEANLRLVISIAKKYTNRG--LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY 436

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 176 ATWWIRQAITRALADQARTIRIPVHMVETINKYQQVVRRLVQELGRDPLPEEVAAEMDMDVDKVRHIIKISQDTISLETP 255
Cdd:PRK05658  437 ATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETP 516

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 256 VGDgkDEDSHLEDFIPDENALGPDVSAGRKILKKYIDEIIGDLSQREQKILDMRFGLTDGVTHTLEEVGKVFNVTRERIR 335
Cdd:PRK05658  517 IGD--DEDSHLGDFIEDKNAELPIDAAIQESLREATTDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIR 594

                         330       340
                  ....*....|....*....|...
gi 2556888279 336 QIEAKALEKIRqHENV-ERLKGY 357
Cdd:PRK05658  595 QIEAKALRKLR-HPSRsRKLRSF 616
PRK07921 PRK07921
RNA polymerase sigma factor SigB; Reviewed
 79-357 2.57e-109

RNA polymerase sigma factor SigB; Reviewed


Pssm-ID: 181169 [Multi-domain]  Cd Length: 324  Bit Score: 322.45  E-value: 2.57e-109
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279  79 EGSSSDSVQMYLREIGKYPLLKGEEEIELAKRIE---------------------------RNDESARQKLALSNLRLVV 131
Cdd:PRK07921   21 QSPAADLVRVYLNGIGKTALLTAADEVELAKRIEaglyaehlletrkrlsearkrdlaavvRDGEAARRHLLEANLRLVV 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 132 SIAKKYVGRSanLSLLDLIQEGNIGLFKAVEKFDFRKGFKFSTYATWWIRQAITRALADQARTIRIPVHMVETINKYQQV 211
Cdd:PRK07921  101 SLAKRYTGRG--MPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARI 178

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 212 VRRLVQELGRDPLPEEVAAEMDMDVDKVRHIIKISQDTISLETPVGDgkDEDSHLEDFIPDENALGPDVSAGRKILKKYI 291
Cdd:PRK07921  179 KRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGS--DEEAPLGDFIEDSEATSAENAVIAGLLHTDI 256

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2556888279 292 DEIIGDLSQREQKILDMRFGLTDGVTHTLEEVGKVFNVTRERIRQIEAKALEKIRQHENVERLKGY 357
Cdd:PRK07921  257 RSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGERADRLRSY 322
Sig70-cyanoRpoD TIGR02997
RNA polymerase sigma factor, cyanobacterial RpoD-like family; This family includes a number of ...
 84-346 1.54e-108

RNA polymerase sigma factor, cyanobacterial RpoD-like family; This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).


Pssm-ID: 274382 [Multi-domain]  Cd Length: 298  Bit Score: 319.19  E-value: 1.54e-108
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279  84 DSVQMYLREIGKYPLLKGEEEIELAKRIE----------------------------------------RNDESARQKLA 123
Cdd:TIGR02997   1 DLVRLYLQEIGRVPLLTPEEEIELARQVQqmmvleelreeleeqlgrepskeewaaaaglseaelrqrlRQGQRAKEKMI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 124 LSNLRLVVSIAKKYVGRsaNLSLLDLIQEGNIGLFKAVEKFDFRKGFKFSTYATWWIRQAITRALADQARTIRIPVHMVE 203
Cdd:TIGR02997  81 KANLRLVVSVAKKYQNR--GLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITE 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 204 TINKYQQVVRRLVQELGRDPLPEEVAAEMDMDVDKVRHIIKISQDTISLETPVGDgkDEDSHLEDFIPDENALgPDVSAG 283
Cdd:TIGR02997 159 KLNKIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGD--EEDTELGDLLEDDGES-PEEQVE 235

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2556888279 284 RKILKKYIDEIIGDLSQREQKILDMRFGLTDGVTHTLEEVGKVFNVTRERIRQIEAKALEKIR 346
Cdd:TIGR02997 236 RESLRQDLESLLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR 298
PRK07406 PRK07406
RNA polymerase sigma factor RpoD; Validated
 54-357 3.06e-106

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236012 [Multi-domain]  Cd Length: 373  Bit Score: 316.34  E-value: 3.06e-106
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279  54 ESVSVFEETAAKEYEQKKKIEDEFSE--GSSSDSVQMYLREIGKYPLLKGEEEIELAKRI-------------------E 112
Cdd:PRK07406   31 SSSENADELSEKEAKAKALARIKIGPkkVYTEDSIRVYLQEIGRIRLLRPDEEIELARKIadlleleelreqfeselgrE 110

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 113 RNDES---------------------ARQKLALSNLRLVVSIAKKYVGRSanLSLLDLIQEGNIGLFKAVEKFDFRKGFK 171
Cdd:PRK07406  111 PSDKEwaelvdmplpkfrrrlmlgrrAKEKMVQSNLRLVVSIAKKYMNRG--LSFQDLIQEGSLGLIRAAEKFDHEKGYK 188

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 172 FSTYATWWIRQAITRALADQARTIRIPVHMVETINKYQQVVRRLVQELGRDPLPEEVAAEMDMDVDKVRHIIKISQDTIS 251
Cdd:PRK07406  189 FSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPIS 268

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 252 LETPVgdGKDEDSHLEDFIpDENALGPDVSAGRKILKKYIDEIIGDLSQREQKILDMRFGLTDGVTHTLEEVGKVFNVTR 331
Cdd:PRK07406  269 LETPI--GKEEDSRLGDFI-EADGETPEDDVAKNLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTR 345

                         330       340
                  ....*....|....*....|....*.
gi 2556888279 332 ERIRQIEAKALEKIRQHENVERLKGY 357
Cdd:PRK07406  346 ERIRQIEAKALRKLRHPNRNSVLKEY 371
rpoS_proteo TIGR02394
RNA polymerase sigma factor RpoS; A sigma factor is a DNA-binding protein protein that binds ...
 79-346 1.73e-93

RNA polymerase sigma factor RpoS; A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393). [Cellular processes, Adaptations to atypical conditions, Transcription, Transcription factors]


Pssm-ID: 131447 [Multi-domain]  Cd Length: 285  Bit Score: 280.46  E-value: 1.73e-93
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279  79 EGSSSDSVQMYLREIGKYPLLKGEEEIELAKRIERNDESARQKLALSNLRLVVSIAKKYVGRSanLSLLDLIQEGNIGLF 158
Cdd:TIGR02394   8 ETRVADVTQLYLREIGFKPLLTAEEEIAYARRALAGDFEARKVMIESNLRLVVSIAKHYVNRG--LPLLDLIEEGNLGLM 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 159 KAVEKFDFRKGFKFSTYATWWIRQAITRALADQARTIRIPVHMVETINKYQQVVRRLVQELGRDPLPEEVAAEMDMDVDK 238
Cdd:TIGR02394  86 HAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPVHVIKELNVYLRAARQLEKKLGREPSVEEIAELLDKPVED 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 239 VRHIIKISQDTISLETPVGDgkDEDSHLEDFIPDENALGPDVSAGRKILKKYIDEIIGDLSQREQKILDMRFGLTDGVTH 318
Cdd:TIGR02394 166 VSRVLALNERITSLDAPLDD--DSSKSLLDTIADEQSIDPESLVQNDDLKQLIEAWLAELNERQREVLARRFGLLGYEPA 243

                         250       260
                  ....*....|....*....|....*...
gi 2556888279 319 TLEEVGKVFNVTRERIRQIEAKALEKIR 346
Cdd:TIGR02394 244 TLEEVAAEVGLTRERVRQIQVEALKKLR 271
PRK05657 PRK05657
RNA polymerase sigma factor RpoS; Validated
 54-348 3.04e-90

RNA polymerase sigma factor RpoS; Validated


Pssm-ID: 235548 [Multi-domain]  Cd Length: 325  Bit Score: 273.75  E-value: 3.04e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279  54 ESVSVFEETAAKEYEQKKKIEDEFSEGSSS------DSVQMYLREIGKYPLLKGEEEIELAKRIERNDESARQKLALSNL 127
Cdd:PRK05657   17 NGVEVFDEKALVEEEPSDNDLAEEELLSQGatqrvlDATQLYLNEIGYSPLLTAEEEVYFARRALRGDFAARQRMIESNL 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 128 RLVVSIAKKYVGRSanLSLLDLIQEGNIGLFKAVEKFDFRKGFKFSTYATWWIRQAITRALADQARTIRIPVHMVETINK 207
Cdd:PRK05657   97 RLVVKIAKRYLNRG--LALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPVHVVKELNV 174

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 208 YQQVVRRLVQELGRDPLPEEVAAEMDMDVDKVRHIIKISQDTISLETPVgdGKDEDSHLEDFIPDENALGPDVSAGRKIL 287
Cdd:PRK05657  175 YLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPL--GGDPEKSLLDILADEQENGPEDTTQDDDM 252

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2556888279 288 KKYIDEIIGDLSQREQKILDMRFGLTDGVTHTLEEVGKVFNVTRERIRQIEAKALEKIRQH 348
Cdd:PRK05657  253 KQSIVKWLFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREI 313
PRK07598 PRK07598
RNA polymerase sigma factor SigC; Validated
 105-357 7.01e-78

RNA polymerase sigma factor SigC; Validated


Pssm-ID: 236067 [Multi-domain]  Cd Length: 415  Bit Score: 245.16  E-value: 7.01e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 105 IELAKRIERNDESARQKLALSNLRLVVSIAKKYVGRSanLSLLDLIQEGNIGLFKAVEKFDFRKGFKFSTYATWWIRQAI 184
Cdd:PRK07598  163 VEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRG--LELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGI 240

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 185 TRALADQARTIRIPVHMVETINKYQQVVRRLVQELGRDPLPEEVAAEMDMDVDKVRHIIKISQDTISLETPVgdGKDEDS 264
Cdd:PRK07598  241 TRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLLRVPRSVSLETKV--GKDKDT 318

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 265 HLEDFIPDENaLGPDVSAGRKILKKYIDEIIGDLSQREQKILDMRFGLTDGVTHTLEEVGKVFNVTRERIRQIEAKALEK 344
Cdd:PRK07598  319 ELGDLLETDD-ISPEEMLMRESLQRDLQHLLADLTSRERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQK 397

                         250
                  ....*....|...
gi 2556888279 345 IRQHENVERLKGY 357
Cdd:PRK07598  398 LRQPKRRNRIRDY 410
PRK05949 PRK05949
RNA polymerase sigma factor; Validated
 81-347 1.66e-76

RNA polymerase sigma factor; Validated


Pssm-ID: 180321 [Multi-domain]  Cd Length: 327  Bit Score: 238.59  E-value: 1.66e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279  81 SSSDSVQMYLREIGKYPLLKGEEEIELAKRIER----------------------------------------NDESARQ 120
Cdd:PRK05949   15 FSADMVRTYLHEIGRVPLLTHEQEIVYGKQVQQmmslleakealakklgrepslpewaeavnlsetelkqtlkQGKRAKQ 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 121 KLALSNLRLVVSIAKKYVGRsaNLSLLDLIQEGNIGLFKAVEKFDFRKGFKFSTYATWWIRQAITRALADQARTIRIPVH 200
Cdd:PRK05949   95 KMIEANLRLVVAIAKKYQKR--NMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIH 172

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 201 MVETINKYQQVVRRLVQELGRDPLPEEVAAEMDMDVDKVRHIIKISQDTISLETPVGDgkDEDSHLEDFIPDEnALGPDV 280
Cdd:PRK05949  173 ITEKLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGD--NQDTELSELLEDE-GPSPDQ 249

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2556888279 281 SAGRKILKKYIDEIIGDLSQREQKILDMRFGLTDGVTHTLEEVGKVFNVTRERIRQIEAKALEKIRQ 347
Cdd:PRK05949  250 YITQELLRQDLNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRR 316
PRK07405 PRK07405
RNA polymerase sigma factor SigD; Validated
 81-347 3.99e-75

RNA polymerase sigma factor SigD; Validated


Pssm-ID: 180963 [Multi-domain]  Cd Length: 317  Bit Score: 234.65  E-value: 3.99e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279  81 SSSDSVQMYLREIGKYPLLKGEEEIELAKRIER----------------------------------------NDESARQ 120
Cdd:PRK07405    5 TSTDLVRTYLREIGRVPLLTHEEEILYGKQVQRlvalqeireelaeelgreptdaewakaaklseeelrsaiaEGEAAKR 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 121 KLALSNLRLVVSIAKKYVGRsaNLSLLDLIQEGNIGLFKAVEKFDFRKGFKFSTYATWWIRQAITRALADQARTIRIPVH 200
Cdd:PRK07405   85 KMVEANLRLVVSVAKKYLKR--NVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIH 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 201 MVETINKYQQVVRRLVQELGRDPLPEEVAAEMDMDVDKVRHIIKISQDTISLETPVGDgkDEDSHLEDFIPDENALgPDV 280
Cdd:PRK07405  163 ITEKLNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGD--NQDTELGELLEDTGAS-PED 239

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2556888279 281 SAGRKILKKYIDEIIGDLSQREQKILDMRFGLTDGVTHTLEEVGKVFNVTRERIRQIEAKALEKIRQ 347
Cdd:PRK07405  240 FATQSSLQLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRK 306
PRK06596 PRK06596
RNA polymerase factor sigma-32; Reviewed
 89-347 1.80e-46

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 235838 [Multi-domain]  Cd Length: 284  Bit Score: 159.57  E-value: 1.80e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279  89 YLREIGKYPLLKGEEEIELAKRI-ERNDESARQKLALSNLRLVVSIAKKYVGRSanLSLLDLIQEGNIGLFKAVEKFDFR 167
Cdd:PRK06596   19 YIQAVNKIPMLTAEEEYMLAKRLrEHGDLEAAKQLVLSHLRFVVHIARGYRGYG--LPQADLIQEGNIGLMKAVKRFDPE 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 168 KGFKFSTYATWWIRQAItraladQA---RTIRIpVHMVETinKYQQV----VRRLVQELGrdPL-PEEV---AAEMDMDV 236
Cdd:PRK06596   97 VGVRLVSFAVHWIKAEI------HEyilRNWRI-VKVATT--KAQRKlffnLRKAKKRLG--WLnPEEVemvAEELGVSE 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 237 DKVRHI-IKISQDTISLETPVGDGKDEDSHLEDFIPDEnalGPDVSAG----------RKILKkyidEIIGDLSQREQKI 305
Cdd:PRK06596  166 EEVREMeSRLSGQDASLDAPIDDDDEESGAPQDYLEDK---SSDPADVleednwedqrRALLA----DALEGLDERSRDI 238

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|..
gi 2556888279 306 LDMRFgLTDGVThTLEEVGKVFNVTRERIRQIEAKALEKIRQ 347
Cdd:PRK06596  239 IEARW-LDDDKS-TLQELAAEYGVSAERVRQIEKNAMKKLKA 278
rpoH_proteo TIGR02392
alternative sigma factor RpoH; A sigma factor is a DNA-binding protein protein that binds to ...
 84-347 3.75e-44

alternative sigma factor RpoH; A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors. [Cellular processes, Adaptations to atypical conditions, Transcription, Transcription factors]


Pssm-ID: 274107 [Multi-domain]  Cd Length: 270  Bit Score: 153.21  E-value: 3.75e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279  84 DSVQMYLREIGKYPLLKGEEEIELAKRI-ERNDESARQKLALSNLRLVVSIAKKYvgRSANLSLLDLIQEGNIGLFKAVE 162
Cdd:TIGR02392   1 GSLDAYIRAVNRIPMLTPEEEYQLAKRLrEHGDLDAAKKLVLSHLRFVVKIARGY--RGYGLPQADLIQEGNIGLMKAVK 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 163 KFDFRKGFKFSTYATWWIRQAITRALadqARTIRIpVHMVETinKYQQV----VRRLVQELGRDPLPEEV---AAEMDMD 235
Cdd:TIGR02392  79 RFDPERGVRLVSFAVHWIKAEIHEYI---LRNWRL-VKVATT--KAQRKlffnLRKMKKRLQGWLNPEEVeaiAEELGVS 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 236 VDKVRHI-IKISQDTISLETPVGDGKDEDSHLEDFIPDENALGPDVSAGR---KILKKYIDEIIGDLSQREQKILDMRFg 311
Cdd:TIGR02392 153 EREVREMeSRLSGQDMSLNASIDDDEDDGGAPIAYLVDKRSDPEDTLEEEqweELQRQALANALGSLDARSRRIIEARW- 231

                         250       260       270
                  ....*....|....*....|....*....|....*.
gi 2556888279 312 LTDGVThTLEEVGKVFNVTRERIRQIEAKALEKIRQ 347
Cdd:TIGR02392 232 LDDDKL-TLQELAAEYGVSAERIRQIEKNAMKKLKA 266
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 103-348 9.39e-44

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: 151.13  E-value: 9.39e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 103 EEIELAKRIERNDESARQKLALSNLRLVVSIAKKYVGRSaNLSLLDLIQEGNIGLFKAVEKFDFRKGFKFSTYATWWIRQ 182
Cdd:COG1191     1 DLEELLRRYQEGDEEAREELIEEYLPLVKKIASRLAGRL-PAELDDLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 183 AITRALADQArtiRIPVHMVETINKYQQVVRRLVQELGRDPLPEEVAAEMDMDVDKVRHIIKISQ--DTISLETPVGDGK 260
Cdd:COG1191    80 AILDYLRDED---WVPRSVRELARKIEEAIEELEQELGREPTDEEIAEELGISLEEVQEALEAANayQLLSLDEPLEDGD 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 261 DedshLEDFIPDENalgPDVSAGRKILKKYIDEIIGDLSQREQKILDMRF--GLtdgvthTLEEVGKVFNVTRERIRQIE 338
Cdd:COG1191   157 D----LLDLLESGD---PEEELEHEELREALAEAIEQLPERERLVLSLYYfeEL------TLKEIAEVLGVSESRVSRLH 223

                         250
                  ....*....|
gi 2556888279 339 AKALEKIRQH 348
Cdd:COG1191   224 KKALARLREY 233
rpoH2 PRK07500
RNA polymerase factor sigma-32; Reviewed
 95-346 1.30e-36

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 236033 [Multi-domain]  Cd Length: 289  Bit Score: 133.62  E-value: 1.30e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279  95 KYPLLKGEEEIELAKRI-ERNDESARQKLALSNLRLVVSIAKKYvgRSANLSLLDLIQEGNIGLFKAVEKFDFRKGFKFS 173
Cdd:PRK07500   17 KAPYLEREEEHALAYRWkDHRDEDALHRIISAHMRLVISMAGKF--RRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFS 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 174 TYATWWIRQAItraladQARTIRiPVHMVETINKYQQ---------VVRRLVQ---ELGRDPLPEEVAAEMDMDVDKVRH 241
Cdd:PRK07500   95 TYATWWIRASI------QDYILR-NWSIVRGGTSSAQkalffnlrrLRARLAQadeELTKQEIHREIATALGVSLSDVEM 167

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 242 I-IKISQDTISLETPVGDGKDEDSHLEDFIPDENALgPDVSAGRKI----LKKYIDEIIGDLSQREQKILDMRFGLTDGV 316
Cdd:PRK07500  168 MdARLSGPDASLNAPQSEEDEGRSERMDFLVDDSPL-PDEQVESSIdgerRRRWLTQALQTLNERELRIIRERRLREDGA 246

                         250       260       270
                  ....*....|....*....|....*....|
gi 2556888279 317 thTLEEVGKVFNVTRERIRQIEAKALEKIR 346
Cdd:PRK07500  247 --TLEALGEELGISKERVRQIEARALEKLR 274
FliA_WhiG TIGR02479
RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar ...
 122-347 9.59e-35

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: 127.00  E-value: 9.59e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 122 LALSNLRLVVSIAKKYVGR-SANLSLLDLIQEGNIGLFKAVEKFDFRKGFKFSTYATWWIRQAI---TRALADQARTIRI 197
Cdd:TIGR02479   1 LIRRYLPLVKRIAGRLSVGlPSSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMldeLRRLDWVPRSLRQ 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 198 PVHMVEtinkyqQVVRRLVQELGRDPLPEEVAAEMDMDVDKVRHIIK--ISQDTISLETpVGDGKDEDSHLEDFIPDENA 275
Cdd:TIGR02479  81 KARKLE------RAIRELEARLGREPTEEEIAEELGMDLKEYRQALNeiNALSLVSLDE-LLESGDDGGSLIDRIEDDKS 153

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2556888279 276 LGPDVSAGRKILKKYIDEIIGDLSQREQKILDMRF--GLtdgvthTLEEVGKVFNVTRERIRQIEAKALEKIRQ 347
Cdd:TIGR02479 154 EDPEEELEREELREALAEAIESLSEREQLVLSLYYyeEL------NLKEIGEVLGLTESRVSQIHSQALKKLRA 221
PRK08215 PRK08215
RNA polymerase sporulation sigma factor SigG;
95-348 1.18e-32

RNA polymerase sporulation sigma factor SigG;


Pssm-ID: 181296 [Multi-domain]  Cd Length: 258  Bit Score: 122.36  E-value: 1.18e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279  95 KYPLLKGEEEIELAKRIERNDESARQKLALSNLRLVVSIAKKYVGRSANLSllDLIQEGNIGLFKAVEKFDFRKGFKFST 174
Cdd:PRK08215   15 KLPVLKNEEMRELFERMQNGDKEAREKLINGNLRLVLSVIQRFNNRGENVD--DLFQVGCIGLMKAIDNFDLSQNVKFST 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 175 YATWWIRQAITRALADQaRTIRIPVHMVETINKYQQVVRRLVQELGRDPLPEEVAAEMDMDVDKVRHIIKISQDTISLET 254
Cdd:PRK08215   93 YAVPMIIGEIRRYLRDN-NPIRVSRSLRDIAYKALQVREKLINENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFE 171

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 255 PV-GDGKDEdSHLEDFIPDENALgpDVSAGRKILkkyIDEIIGDLSQREQKILDMRFglTDGVTHTleEVGKVFNVTRER 333
Cdd:PRK08215  172 PIyHDGGDP-IYVMDQISDEKNK--DENWLEEIA---LKEAMKKLNDREKLILNLRF--FQGKTQM--EVAEEIGISQAQ 241

                         250
                  ....*....|....*
gi 2556888279 334 IRQIEAKALEKIRQH 348
Cdd:PRK08215  242 VSRLEKAALKHMRKY 256
PRK06288 PRK06288
RNA polymerase sigma factor WhiG; Reviewed
 91-346 2.65e-30

RNA polymerase sigma factor WhiG; Reviewed


Pssm-ID: 235770 [Multi-domain]  Cd Length: 268  Bit Score: 116.33  E-value: 2.65e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279  91 REIGKYPLLKGEEEIELAKRIERN-DESARQKLALSNLRLVVSIAKKY-VGRSANLSLLDLIQEGNIGLFKAVEKFDFRK 168
Cdd:PRK06288    4 KMSGKIPKYAQQDETELWREYKKTgDPKIREYLILKYSPLVKYVAGRIaVGMPQNVEFDDLVSYGVFGLIDAIEKFDPER 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 169 GFKFSTYATWWIRQAI---TRALADQARTIRIPVHMVEtinkyqQVVRRLVQELGRDPLPEEVAAEMDMDVDKVRHII-K 244
Cdd:PRK06288   84 EIKFKTYAVTRIRGAIfdeLRSIDWIPRSVRQKARQIE------RAIAMLEARLGRTPSDEEIADELGISLEEYNSLLsK 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 245 ISQ-DTISLET--PVGDGKDEDShLEDFIPDENALGPDVSAGRKILKKYIDEIIGDLSQREQKILDMRF--GLtdgvthT 319
Cdd:PRK06288  158 LSGtSVVSLNDlwFGGDEGDEVS-LMDTLESPAALNPDEIAEREEIKRVIVEAIKTLPEREKKVLILYYyeDL------T 230

                         250       260
                  ....*....|....*....|....*..
gi 2556888279 320 LEEVGKVFNVTRERIRQIEAKALEKIR 346
Cdd:PRK06288  231 LKEIGKVLGVTESRISQLHTKAVLQLR 257
PRK07670 PRK07670
FliA/WhiG family RNA polymerase sigma factor;
148-347 1.01e-24

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 181075 [Multi-domain]  Cd Length: 251  Bit Score: 100.89  E-value: 1.01e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 148 DLIQEGNIGLFKAVEKFDFRKGFKFSTYATWWIRQAITRALADQ---ARTIRipvhmvETINKYQQVVRRLVQELGRDPL 224
Cdd:PRK07670   54 DLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRKEdwlPRSMR------EKTKKVEAAIEKLEQRYMRNVT 127

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 225 PEEVAAEMDMDVDKVRHIIKIS--QDTISLETPVGDGKDEDSHLEDFIpDENALGPDVSAGRKILKKYIDEIIGDLSQRE 302
Cdd:PRK07670  128 PKEVAAELGMTEEEVEATMNEGffANLLSIDEKTHDQDDGENVSVTIR-DDKTPTPEEKLLKEELIEELAEKIKQLSEKE 206

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 2556888279 303 QKILDMRFglTDGVTHTleEVGKVFNVTRERIRQIEAKALEKIRQ 347
Cdd:PRK07670  207 QLVISLFY--KEELTLT--EIGQVLNLSTSRISQIHSKALFKLKK 247
PRK05572 PRK05572
RNA polymerase sporulation sigma factor, SigF/SigG family;
95-348 1.08e-24

RNA polymerase sporulation sigma factor, SigF/SigG family;


Pssm-ID: 180137 [Multi-domain]  Cd Length: 252  Bit Score: 100.82  E-value: 1.08e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279  95 KYPLLKGEEEIELAKRIERNDESARQKLALSNLRLVVSIAKKYVGRSANLSllDLIQEGNIGLFKAVEKFDFRKGFKFST 174
Cdd:PRK05572   10 KKPQLKDEENKELIKKSQDGDQEARDTLVEKNLRLVWSVVQRFLNRGYEPD--DLFQIGCIGLLKAVDKFDLSYDVKFST 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 175 YATWWIRQAITRALADQArTIRIPVHMVETINKYQQVVRRLVQELGRDPLPEEVAAEMDMDVDKVRHIIKISQDTISLET 254
Cdd:PRK05572   88 YAVPMIIGEIQRFLRDDG-TVKVSRSLKETANKIRKDKDELSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHE 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 255 PVGDGKDEDSHLEDFIPDEnalgpdvSAGRKILKKYIDEIIGDLSQREQKILDMRFgLTDgvtHTLEEVGKVFNVTRERI 334
Cdd:PRK05572  167 TVHENDGDPITLLDQIADQ-------SEEDWFDKIALKEAIRELDERERLIVYLRY-FKD---KTQSEVAKRLGISQVQV 235

                         250
                  ....*....|....
gi 2556888279 335 RQIEAKALEKIRQH 348
Cdd:PRK05572  236 SRLEKKILKQMKEK 249
spore_sigF TIGR02885
RNA polymerase sigma-F factor; Members of this protein family are the RNA polymerase sigma ...
 105-347 1.25e-24

RNA polymerase sigma-F factor; Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore. [Transcription, Transcription factors, Cellular processes, Sporulation and germination]


Pssm-ID: 131931 [Multi-domain]  Cd Length: 231  Bit Score: 100.17  E-value: 1.25e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 105 IELAKRierNDESARQKLALSNLRLVVSIAKKYVGRSANLSllDLIQEGNIGLFKAVEKFDFRKGFKFSTYATWWIRQAI 184
Cdd:TIGR02885   2 IKLAQN---GDKEARDKLIECNLRLVWSIVKRFLNRGYEPE--DLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEI 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 185 TRALADQArTIRIPVHMVETINKYQQVVRRLVQELGRDPLPEEVAAEMDMDVDKVRHIIKISQDTISLETPVGDGKDEDS 264
Cdd:TIGR02885  77 KRFLRDDG-IIKVSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLYDTVHQDDGDPI 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 265 HLEDFIPDENALGPDVsagrkILKKYIDEIIGDLSQREQKILDMRFgLTDgvtHTLEEVGKVFNVTRERIRQIEAKALEK 344
Cdd:TIGR02885 156 YLLDQIADKGSEDSDW-----LEKIALKEAISKLDERERQIIMLRY-FKD---KTQTEVANMLGISQVQVSRLEKKVLKK 226


                  ...
gi 2556888279 345 IRQ 347
Cdd:TIGR02885 227 MKE 229
Sigma70_r3 pfam04539
Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the ...
 203-279 1.47e-22

Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but as some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme.


Pssm-ID: 427997 [Multi-domain]  Cd Length: 78  Bit Score: 89.97  E-value: 1.47e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2556888279 203 ETINKYQQVVRRLVQELGRDPLPEEVAAEMDMDVDKVRHIIKISQDTISLETPVGDgkDEDSHLEDFIPDENALGPD 279
Cdd:pfam04539   1 ELLNKIKRAQRELEQELGREPTPEEIAEELGLSPEKVREVLEAAREPVSLDTPVGE--EEDGELGDLLEDDDIESPE 75
PRK05803 PRK05803
RNA polymerase sporulation sigma factor SigK;
99-345 1.40e-21

RNA polymerase sporulation sigma factor SigK;


Pssm-ID: 180266 [Multi-domain]  Cd Length: 233  Bit Score: 91.93  E-value: 1.40e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279  99 LKGEEEIELAKRIERNDESARQKLALSNLRLVVSIAKKYVGRSANLSllDLIQEGNIGLFKAVEKFDFRKGFKFSTYAtw 178
Cdd:PRK05803   31 LSEEEERKYLELMKEGDEEARNILIERNLRLVAHIVKKFENTGEDVD--DLISIGTIGLIKAIESFDAGKGTKLATYA-- 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 179 wirqaitraladqARTIRIPVHMVETINKyqqvvrrlvqelgrdplpeevaaemdmdvdKVRhiikisqDTISLETPVGD 258
Cdd:PRK05803  107 -------------ARCIENEILMHLRNLK------------------------------KTK-------KEVSLQDPIGV 136

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 259 GKD--EDShLEDFIPDENALGPDVsAGRKILKKYIDEIIGDLSQREQKILDMRFGLTDGVTHTLEEVGKVFNVTRERIRQ 336
Cdd:PRK05803  137 DKEgnEIS-LIDILGSEEDDVIEQ-VELKMEVEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSR 214


                  ....*....
gi 2556888279 337 IEAKALEKI 345
Cdd:PRK05803  215 IEKRALKKL 223
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 122-194 3.94e-21

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: 85.72  E-value: 3.94e-21
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2556888279 122 LALSNLRLVVSIAKKYVGRSAnlSLLDLIQEGNIGLFKAVEKFDFRKGFKFSTYATWWIRQAITRALADQART 194
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGA--DAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRRT 71
PRK07408 PRK07408
RNA polymerase sigma factor SigF; Reviewed
 115-272 1.32e-20

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 180965 [Multi-domain]  Cd Length: 256  Bit Score: 89.59  E-value: 1.32e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 115 DESARQKLALSNLRLVVSIAKKYVGRSaNLSLLDLIQEGNIGLFKAVEKFDFRKGFKFSTYATWWIRQAITRALADQART 194
Cdd:PRK07408   23 SIALRNQLVELNLGLVRKEAHRWSNQC-SEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPT 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 195 IRIPVHMVETINKYQQVVRRLVQELGRDPLPEEVAAEMDMDVDKVRHIIKISQ--DTISLETPVGDGKDEDSHLEDFIPD 272
Cdd:PRK07408  102 VRIPRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQnrTPLSLDAPVNQDEDGSTSLGDLLPD 181
fliA PRK06986
flagellar biosynthesis sigma factor; Validated
 118-347 4.87e-20

flagellar biosynthesis sigma factor; Validated


Pssm-ID: 235901 [Multi-domain]  Cd Length: 236  Bit Score: 87.60  E-value: 4.87e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 118 ARQKLALSNLRLVVSIAKKYVGR-SANLSLLDLIQEGNIGLFKAVEKFDFRKGFKFSTYATWWIRQAI---TRALADQAR 193
Cdd:PRK06986    9 DQDELVEQYAPLVKRIALRLKARlPASVDLDDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMldeLRSLDWVPR 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 194 TIRIPVHMVEtinkyqQVVRRLVQELGRDPLPEEVAAEMDMDVDKVRHI---IKISQdTISLETPVGDGKDEDSHLEDFI 270
Cdd:PRK06986   89 SVRRNAREVA------QAIRQLEQELGREPTDTEVAEKLGLSLEEYREMlldTNISQ-LFSIDELRGEHGDSILVTEDHQ 161

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2556888279 271 PDEnalgPDVSAGRKILKKYIDEIIGDLSQREQKILDM--RFGLtdgvthTLEEVGKVFNVTRERIRQIEAKALEKIRQ 347
Cdd:PRK06986  162 DED----PLQQLEDEELREALVEAIESLPEREQLVLSLyyQEEL------NLKEIGAVLGVSESRVSQIHSQAIKRLRA 230
PRK07122 PRK07122
RNA polymerase sigma factor SigF; Reviewed
 106-346 2.07e-19

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 168831 [Multi-domain]  Cd Length: 264  Bit Score: 86.37  E-value: 2.07e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 106 ELAKRIERNDESARQKLALSN--LRLVVSIAKKYVGRSANLSllDLIQEGNIGLFKAVEKFDFRKGFKFSTYATWWIRQA 183
Cdd:PRK07122   27 ELAGLPAGSPEFQRQRDRIVTrcLPLADHIARRFDGRGEPRD--DLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGE 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 184 ITRALADQARTIRIPVHMVETINKYQQVVRRLVQELGRDPLPEEVAAEMDMDVDKVRH--IIKISQDTISLETPVGDGKD 261
Cdd:PRK07122  105 VRRHFRDNSWSVKVPRRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEglVAGSAYNTLSIDSGGGSGDD 184

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 262 EDSHLEDFIPDENAlGPDVSAGRKILKKYIDEiigdLSQREQKILDMRF--GLTDgvTHTLEEVGkvfnVTRERIRQIEA 339
Cdd:PRK07122  185 DARAIADTLGDVDA-GLDQIENREALRPLLAA----LPERERTVLVLRFfeSMTQ--TQIAERVG----ISQMHVSRLLA 253


                  ....*..
gi 2556888279 340 KALEKIR 346
Cdd:PRK07122  254 KTLARLR 260
PRK05911 PRK05911
RNA polymerase sigma factor sigma-28; Reviewed
 119-346 1.82e-16

RNA polymerase sigma factor sigma-28; Reviewed


Pssm-ID: 235644 [Multi-domain]  Cd Length: 257  Bit Score: 78.12  E-value: 1.82e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 119 RQKLALSNLRLVVSIAKKYV-GRSANLSLLDLIQEGNIGLFKAVEKFDFRKGFKFSTYATWWIRQAITRALADQArtiRI 197
Cdd:PRK05911   25 RDVLIEFYLPLVKNVAHRLIsGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRKQD---WV 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 198 PVHMVETINKYQQVVRRLVQELGRDPLPEEVAAEMDMDVDKVRHIIKISQDT--ISL--ETPVGDGKDEDSHLEDFIPDE 273
Cdd:PRK05911  102 PRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPAliLSLneEFPCQSDDEAGLALEERIADE 181

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2556888279 274 NA-LGPDVsAGRKILKKYIDEIIGDLSQREQKILDMRFgLTDGVthtLEEVGKVFNVTRERIRQIEAKALEKIR 346
Cdd:PRK05911  182 RAeTGYDV-VDKKEFSSILAEAILALEEKERKVMALYY-YEELV---LKEIGKILGVSESRVSQIHSKALLKLR 250
PRK05658 PRK05658
RNA polymerase sigma factor RpoD; Validated
 1-112 1.99e-16

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 235549 [Multi-domain]  Cd Length: 619  Bit Score: 80.22  E-value: 1.99e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279   1 MSESATLALIERGKTRGFVTQAEILSAFP----TIEQ--DIIGLealyerLEGENITVIESVSVFEETAAKEYEQKKKIE 74
Cdd:PRK05658    8 NPQSQLKKLIKRGKERGYLTYAELNDHLPedivDSEQieDIIAM------LNDMGIQVVEEAPDADDLLLAENEADAQTD 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2556888279  75 DE------------FSEGSSSDS-VQMYLREIGKYPLLKGEEEIELAKRIE 112
Cdd:PRK05658   82 EDaeeeaaaalssvESEIGRTDDpVRMYLREMGTVELLTREGEIEIAKRIE 132
PRK08301 PRK08301
RNA polymerase sporulation sigma factor SigE;
97-347 9.21e-14

RNA polymerase sporulation sigma factor SigE;


Pssm-ID: 236228 [Multi-domain]  Cd Length: 234  Bit Score: 69.88  E-value: 9.21e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279  97 PLLKGEEEIELAKRIERNDESARQKLALSNLRLVVSIAKKYVGRSANLSllDLIQEGNIGLFKAVEKFDFRKGFKFSTYA 176
Cdd:PRK08301   32 PPLSKEEEEYLLNKLPKGDEAVRSLLIERNLRLVVYIARKFENTGINIE--DLISIGTIGLIKAVNTFNPEKKIKLATYA 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 177 TWWIRQAITRALADQARTiRIPVHMVETINkyqqvvrrlvqelgrdplpeevaaeMDMDVDKvrhiIKISqDTIsletpv 256
Cdd:PRK08301  110 SRCIENEILMYLRRNNKV-KAEVSFDEPLN-------------------------IDWDGNE----LLLS-DVL------ 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 257 gdGKDED---SHLEDFIPdenalgpdvsagRKILKKYIDEiigdLSQREQKILDMRFGLTDGVTHTLEEVGKVFNVTRER 333
Cdd:PRK08301  153 --GTDNDiiyKDIEDEVD------------RKLLKKALKK----LSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSY 214

                         250
                  ....*....|....
gi 2556888279 334 IRQIEAKALEKIRQ 347
Cdd:PRK08301  215 ISRLEKRIIKRLKK 228
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 117-348 2.02e-13

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: 67.37  E-value: 2.02e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 117 SARQKLALSNLRLVVSIAKKYVGRSANLSllDLIQEGNIGLFKAVEKFDFRKgfKFSTYATWWIRQAITRALADQARtir 196
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAE--DLVQEAFLKLLEALDRFDPEG--SFKAWLFRIARNLILDYLRRKRR--- 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 197 ipvhmvetinkYQQVVRRLVQELGRDPLPEEvaaemdmdvdkvrhiikisqdtisletpvgdgkdedshledfipdenal 276
Cdd:TIGR02937  74 -----------LRRELDLLEELLDSDPSPEE------------------------------------------------- 93

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2556888279 277 gpdvSAGRKILKKYIDEIIGDLSQREQKILDMRFGltDGVTHtlEEVGKVFNVTRERIRQIEAKALEKIRQH 348
Cdd:TIGR02937  94 ----ELEQEEEREALREALEKLPEREREVLVLRYL--EGLSY--KEIAEILGISVGTVKRRLKRARKKLREL 157
Sigma70_r1_2 pfam00140
Sigma-70 factor, region 1.2;
84-116 1.77e-12

Sigma-70 factor, region 1.2;


Pssm-ID: 425482 [Multi-domain]  Cd Length: 34  Bit Score: 60.79  E-value: 1.77e-12
                          10        20        30
                  ....*....|....*....|....*....|...
gi 2556888279  84 DSVQMYLREIGKYPLLKGEEEIELAKRIERNDE 116
Cdd:pfam00140   1 DSVRLYLKEIGRIPLLTAEEEVELAKRIEAGDE 33
PRK08583 PRK08583
RNA polymerase sigma factor SigB; Validated
 99-347 1.68e-11

RNA polymerase sigma factor SigB; Validated


Pssm-ID: 236306 [Multi-domain]  Cd Length: 257  Bit Score: 63.56  E-value: 1.68e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279  99 LKGEEEIELAKRIERN-DESARQKLALSNLRLVVSIAKKYV-GRSANLsllDLIQEGNIGLFKAVEKFDFRKGFKFSTYA 176
Cdd:PRK08583   10 LTKEEVNKWIAEYQENqDEEAQEKLVKHYKNLVESLAYKYSkGQSHHE---DLVQVGMVGLLGAIRRYDPSFGRSFEAFA 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 177 TWWIRQAITRALADQARTIRIPVHMVETINKYQQVVRRLVQELGRDPLPEEVAAEMDMDVDKVRHIIKISQ--DTISLET 254
Cdd:PRK08583   87 VPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEVLEAMEMGKsyQALSVDH 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 255 PVGDGKDEDS-HLEDFIPDENAlGPDVSAGRKILKKyideIIGDLSQREQKILDMRFglTDGVTHtlEEVGKVFNVTRER 333
Cdd:PRK08583  167 SIEADSDGSTvTLLDIVGQQED-GYELTEQRMILEK----ILPVLSDREKSIIQCTF--IENLSQ--KETGERLGISQMH 237

                         250
                  ....*....|....
gi 2556888279 334 IRQIEAKALEKIRQ 347
Cdd:PRK08583  238 VSRLQRQAIKKLRE 251
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 295-347 3.54e-10

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: 54.74  E-value: 3.54e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2556888279 295 IGDLSQREQKILDMRFGltdgVTHTLEEVGKVFNVTRERIRQIEAKALEKIRQ 347
Cdd:pfam04545   2 LASLPPRERQVLVLRYG----EGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 288-346 3.51e-09

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: 52.11  E-value: 3.51e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2556888279 288 KKYIDEIIGDLSQREQKILDMRFGltdgVTHTLEEVGKVFNVTRERIRQIEAKALEKIR 346
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFG----EGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK12427 PRK12427
FliA/WhiG family RNA polymerase sigma factor;
148-346 6.37e-06

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 183523 [Multi-domain]  Cd Length: 231  Bit Score: 46.78  E-value: 6.37e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 148 DLIQEGNIGLFKAVEKFDFRKGfKFSTYATWWIRQAIT---RALADQARTIRIPVHmvetinKYQQVVRRLVQELGRDPL 224
Cdd:PRK12427   47 DMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILdelRELDWRPRRLRQKTH------KTNDAIREIAKRLGHEPN 119

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279 225 PEEVAAEMDMDVDKVrhiikisqdtisLETPVGDGKDEDSHLEDFIPDENALGPDVSAGRK---ILKKYIDEIIGDLSQR 301
Cdd:PRK12427  120 FEEISAELNLTAEEY------------QEYLLLENAGTLESLDELLALEAHNDILQSRDLEeniIIEDNLKQALSQLDER 187

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 2556888279 302 EQKILDMRFgltdgvTH--TLEEVGKVFNVTRERIRQIEAKALEKIR 346
Cdd:PRK12427  188 EQLILHLYY------QHemSLKEIALVLDLTEARICQLNKKIAQKIK 228
Sigma70_r1_1 pfam03979
Sigma-70 factor, region 1.1; Region 1.1 modulates DNA binding by region 2 and 4 when sigma is ...
 8-55 2.19e-05

Sigma-70 factor, region 1.1; Region 1.1 modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase. Region 1.1 is also involved in promoter binding


Pssm-ID: 461117 [Multi-domain]  Cd Length: 69  Bit Score: 41.79  E-value: 2.19e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2556888279   8 ALIERGKTRGFVTQAEILSAFPTIEQDIIGLEALYERLEGENITVIES 55
Cdd:pfam03979   5 ELIKKGKKKGYLTYDEINDALPDDILDSEQIEDIIEMLNDMGIDVVEE 52
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
95-185 2.65e-05

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 44.51  E-value: 2.65e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2556888279  95 KYPLLKGEEEIELAkrieRNDESARQKLALSNLR-LVVSIAKKYVGRSANLSllDLIQEGNIGLFKAVEKFDFRKGFKFS 173
Cdd:PRK08295    5 DYDELEDEELVELA----RSGDKEALEYLIEKYKnFVRAKARSYFLIGADRE--DIVQEGMIGLYKAIRDYDKDKLSSFK 78

                          90
                  ....*....|...
gi 2556888279 174 TYATWWI-RQAIT 185
Cdd:PRK08295   79 SFAELCItRQIIT 91
 
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.
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