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Conserved domains on  [gi|1011904185|ref|WP_062719737|]
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sigma-70 family RNA polymerase sigma factor [Fusobacterium necrophorum]

Protein Classification

sigma-70 family RNA polymerase sigma factor( domain architecture ID 11439701)

sigma-70 family RNA polymerase sigma factor is an initiation factor that promotes the attachment of RNA polymerase to specific initiation sites and is then released

Gene Ontology:  GO:0016987|GO:0003677|GO:0006352|GO:0003899|GO:0006355

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 5-188 6.22e-18

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: 78.71  E-value: 6.22e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185   5 ETLELIRLAKQGDIKARNELIEKNINLVHKI-----NCMYGNKEDGFQEGILAFCHAIDKFDETKKVKLSSYAFHWIHQR 79
Cdd:COG1191     1 DLEELLRRYQEGDEEAREELIEEYLPLVKKIasrlaGRLPAELDDLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRGA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185  80 IKRH---------TEKEKYRLLNHVIERMKKEE----------RKRRID----------------------YEYRDSVKE 118
Cdd:COG1191    81 ILDYlrdedwvprSVRELARKIEEAIEELEQELgreptdeeiaEELGISleevqealeaanayqllsldepLEDGDDLLD 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1011904185 119 EDKISDEEDSICLKTTLEQYIKLAC--SEREAFIVRKIYFEGYQQHELAKEMGVCRQRVNTIVKRSLNKIRR 188
Cdd:COG1191   161 LLESGDPEEELEHEELREALAEAIEqlPERERLVLSLYYFEELTLKEIAEVLGVSESRVSRLHKKALARLRE 232
 
Name Accession Description Interval E-value
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 5-188 6.22e-18

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: 78.71  E-value: 6.22e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185   5 ETLELIRLAKQGDIKARNELIEKNINLVHKI-----NCMYGNKEDGFQEGILAFCHAIDKFDETKKVKLSSYAFHWIHQR 79
Cdd:COG1191     1 DLEELLRRYQEGDEEAREELIEEYLPLVKKIasrlaGRLPAELDDLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRGA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185  80 IKRH---------TEKEKYRLLNHVIERMKKEE----------RKRRID----------------------YEYRDSVKE 118
Cdd:COG1191    81 ILDYlrdedwvprSVRELARKIEEAIEELEQELgreptdeeiaEELGISleevqealeaanayqllsldepLEDGDDLLD 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1011904185 119 EDKISDEEDSICLKTTLEQYIKLAC--SEREAFIVRKIYFEGYQQHELAKEMGVCRQRVNTIVKRSLNKIRR 188
Cdd:COG1191   161 LLESGDPEEELEHEELREALAEAIEqlPERERLVLSLYYFEELTLKEIAEVLGVSESRVSRLHKKALARLRE 232
PRK05572 PRK05572
RNA polymerase sporulation sigma factor, SigF/SigG family;
4-188 1.03e-16

RNA polymerase sporulation sigma factor, SigF/SigG family;


Pssm-ID: 180137 [Multi-domain]  Cd Length: 252  Bit Score: 75.78  E-value: 1.03e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185   4 KETLELIRLAKQGDIKARNELIEKNINLVHKINCMYGNK----EDGFQEGILAFCHAIDKFDETKKVKLSSYAFHWIHQR 79
Cdd:PRK05572   17 EENKELIKKSQDGDQEARDTLVEKNLRLVWSVVQRFLNRgyepDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGE 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185  80 IKRHTE-----------KEKYRLLNHVIERM-KKEERKRRID--YEYRDSVKEE-------------------------- 119
Cdd:PRK05572   97 IQRFLRddgtvkvsrslKETANKIRKDKDELsKELGREPTIEelAEYLGVTPEEvvlaqeasrspqsihetvhendgdpi 176

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1011904185 120 ---DKISDEE-----DSICLKTTLEQYiklacSEREAFIVRKIYFEGYQQHELAKEMGVCRQRVNTIVKRSLNKIRR 188
Cdd:PRK05572  177 tllDQIADQSeedwfDKIALKEAIREL-----DERERLIVYLRYFKDKTQSEVAKRLGISQVQVSRLEKKILKQMKE 248
spore_sigF TIGR02885
RNA polymerase sigma-F factor; Members of this protein family are the RNA polymerase sigma ...
 9-188 1.94e-16

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: 74.37  E-value: 1.94e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185   9 LIRLAKQGDIKARNELIEKNINLVHKINCMYGNK----EDGFQEGILAFCHAIDKFDETKKVKLSSYAFHWIHQRIKRH- 83
Cdd:TIGR02885   1 LIKLAQNGDKEARDKLIECNLRLVWSIVKRFLNRgyepEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFl 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185  84 ----------TEKEKYRLLNHVIERMKKE-ERKRRID--YEYRDSVKEE-----------------------------DK 121
Cdd:TIGR02885  81 rddgiikvsrSLKELARKIRYMKEELSKElGREPTINelAEALGVSPEEivmalesarspqslydtvhqddgdpiyllDQ 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185 122 ISD---EEDSICLKTTLEQYIKlACSEREAFIVRKIYFEGYQQHELAKEMGVCRQRVNTIVKRSLNKIRR 188
Cdd:TIGR02885 161 IADkgsEDSDWLEKIALKEAIS-KLDERERQIIMLRYFKDKTQTEVANMLGISQVQVSRLEKKVLKKMKE 229
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 24-83 1.02e-07

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: 47.20  E-value: 1.02e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1011904185  24 LIEKNINLVHKINCMYGNK----EDGFQEGILAFCHAIDKFDETKKVKLSSYAFHWIHQRIKRH 83
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDgadaEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDY 64
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 132-187 2.13e-04

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: 37.85  E-value: 2.13e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1011904185 132 KTTLEQYIKlACSEREAFIVRKIYFEGYQQHELAKEMGVCRQRVNTIVKRSLNKIR 187
Cdd:cd06171     1 RERLEEALD-KLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 5-188 6.22e-18

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: 78.71  E-value: 6.22e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185   5 ETLELIRLAKQGDIKARNELIEKNINLVHKI-----NCMYGNKEDGFQEGILAFCHAIDKFDETKKVKLSSYAFHWIHQR 79
Cdd:COG1191     1 DLEELLRRYQEGDEEAREELIEEYLPLVKKIasrlaGRLPAELDDLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRGA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185  80 IKRH---------TEKEKYRLLNHVIERMKKEE----------RKRRID----------------------YEYRDSVKE 118
Cdd:COG1191    81 ILDYlrdedwvprSVRELARKIEEAIEELEQELgreptdeeiaEELGISleevqealeaanayqllsldepLEDGDDLLD 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1011904185 119 EDKISDEEDSICLKTTLEQYIKLAC--SEREAFIVRKIYFEGYQQHELAKEMGVCRQRVNTIVKRSLNKIRR 188
Cdd:COG1191   161 LLESGDPEEELEHEELREALAEAIEqlPERERLVLSLYYFEELTLKEIAEVLGVSESRVSRLHKKALARLRE 232
PRK05572 PRK05572
RNA polymerase sporulation sigma factor, SigF/SigG family;
4-188 1.03e-16

RNA polymerase sporulation sigma factor, SigF/SigG family;


Pssm-ID: 180137 [Multi-domain]  Cd Length: 252  Bit Score: 75.78  E-value: 1.03e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185   4 KETLELIRLAKQGDIKARNELIEKNINLVHKINCMYGNK----EDGFQEGILAFCHAIDKFDETKKVKLSSYAFHWIHQR 79
Cdd:PRK05572   17 EENKELIKKSQDGDQEARDTLVEKNLRLVWSVVQRFLNRgyepDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGE 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185  80 IKRHTE-----------KEKYRLLNHVIERM-KKEERKRRID--YEYRDSVKEE-------------------------- 119
Cdd:PRK05572   97 IQRFLRddgtvkvsrslKETANKIRKDKDELsKELGREPTIEelAEYLGVTPEEvvlaqeasrspqsihetvhendgdpi 176

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1011904185 120 ---DKISDEE-----DSICLKTTLEQYiklacSEREAFIVRKIYFEGYQQHELAKEMGVCRQRVNTIVKRSLNKIRR 188
Cdd:PRK05572  177 tllDQIADQSeedwfDKIALKEAIREL-----DERERLIVYLRYFKDKTQSEVAKRLGISQVQVSRLEKKILKQMKE 248
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 5-188 1.45e-16

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: 75.48  E-value: 1.45e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185   5 ETLELIRLAKQGDIKARNELIEKNINLVHKINCMYGNK----EDGFQEGILAFCHAIDKFDETKKVKLSSYAFHWIHQRI 80
Cdd:COG0568    16 EEVELARRIQAGDEEAKRKLVEANLRLVVSIAKKYQGRglplLDLIQEGNLGLMKAVEKFDPERGFRFSTYATWWIRQAI 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185  81 KRhtekekY--------RLLNHVIE---RMKKEERKRRIDYEYRDSVKE-------------------------EDKISD 124
Cdd:COG0568    96 TR------AiadqwrtiRLPVHMAEtlnKLRRAKRQLLQELGREPTPEEiaeelgvpeekvremlrlarepvslDAPVGD 169

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185 125 EEDS----------------ICLKTTLEQYIKLA---CSEREAFIVRKIY-FEGYQQH---ELAKEMGVCRQRVNTIVKR 181
Cdd:COG0568   170 DEDSelgdlledeeapspeeALEEELLREELREAldtLTEREREILRLRFgLDDGEPHtleEIGKEFGVSRERVRQIEAK 249


                  ....*..
gi 1011904185 182 SLNKIRR 188
Cdd:COG0568   250 ALRKLRH 256
spore_sigF TIGR02885
RNA polymerase sigma-F factor; Members of this protein family are the RNA polymerase sigma ...
 9-188 1.94e-16

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: 74.37  E-value: 1.94e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185   9 LIRLAKQGDIKARNELIEKNINLVHKINCMYGNK----EDGFQEGILAFCHAIDKFDETKKVKLSSYAFHWIHQRIKRH- 83
Cdd:TIGR02885   1 LIKLAQNGDKEARDKLIECNLRLVWSIVKRFLNRgyepEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFl 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185  84 ----------TEKEKYRLLNHVIERMKKE-ERKRRID--YEYRDSVKEE-----------------------------DK 121
Cdd:TIGR02885  81 rddgiikvsrSLKELARKIRYMKEELSKElGREPTINelAEALGVSPEEivmalesarspqslydtvhqddgdpiyllDQ 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185 122 ISD---EEDSICLKTTLEQYIKlACSEREAFIVRKIYFEGYQQHELAKEMGVCRQRVNTIVKRSLNKIRR 188
Cdd:TIGR02885 161 IADkgsEDSDWLEKIALKEAIS-KLDERERQIIMLRYFKDKTQTEVANMLGISQVQVSRLEKKVLKKMKE 229
SigBFG TIGR02980
RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; This group of similar sigma-70 factors ...
 17-188 1.45e-13

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: 66.48  E-value: 1.45e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185  17 DIKARNELIEKNINLVHKINCMYGNK----EDGFQEGILAFCHAIDKFDETKKVKLSSYAFHWIHQRIKRHTE------- 85
Cdd:TIGR02980   1 DKEAREKLVELNLPLVRSIARRFRNRgephEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIMGEIKRFFRddtwavr 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185  86 -----KEKYRLLNHVIE-------------------RMKKEE-----------RKRRIDYEYRDSVKEE----DKISDEE 126
Cdd:TIGR02980  81 vprrlKELGVKINKATEeltqrlgrsptiaeiaerlGVSEEEvvealeagnayQALSLDASIEDDDGDPiallDTLGDED 160

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1011904185 127 DSIclkTTLEQYIKL-----ACSEREAFIVRKIYFEGYQQHELAKEMGVCRQRVNTIVKRSLNKIRR 188
Cdd:TIGR02980 161 DAL---ETVEDRLALkpllaALPERERRILLLRFFEDKTQSEIAERLGISQMHVSRLLRRALKKLRE 224
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
1-187 4.48e-13

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 64.93  E-value: 4.48e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185   1 METKETLELIRLAKQGDIKARNELIEKNINLVHKINCMY----GNKEDGFQEGILAFCHAIDKFDETKKVKLSSYAFHWI 76
Cdd:PRK08295    6 YDELEDEELVELARSGDKEALEYLIEKYKNFVRAKARSYfligADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCI 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185  77 HQR----IKRHTEKeKYRLLNHVI---ERMKKEERKRRI---DYEYRDSVKEEDKISDEEDSICLKTTLEQyikLACSER 146
Cdd:PRK08295   86 TRQiitaIKTANRQ-KHIPLNSYVsldKPIYDEESDRTLldvISEAKVTDPEELIISKEELEDIEEKIEEL---LSELEK 161

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1011904185 147 EAFivrKIYFEGYQQHELAKEMGVCRQRV-NTI--VKRSLNKIR 187
Cdd:PRK08295  162 EVL---ELYLDGKSYQEIAEELNRHVKSIdNALqrVKRKLEKYL 202
PRK05657 PRK05657
RNA polymerase sigma factor RpoS; Validated
 4-82 9.88e-13

RNA polymerase sigma factor RpoS; Validated


Pssm-ID: 235548 [Multi-domain]  Cd Length: 325  Bit Score: 65.36  E-value: 9.88e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185   4 KETLELIRLAKQGDIKARNELIEKNINLVHKINCMYGNKE----DGFQEGILAFCHAIDKFDETKKVKLSSYAFHWIHQR 79
Cdd:PRK05657   71 EEEVYFARRALRGDFAARQRMIESNLRLVVKIAKRYLNRGlallDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 150


                  ...
gi 1011904185  80 IKR 82
Cdd:PRK05657  151 IER 153
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 19-188 1.35e-12

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: 62.75  E-value: 1.35e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185  19 KARNELIEKNINLVHKI-NCMYGNK---EDGFQEGILAFCHAIDKFDETKKvkLSSYAFHWIHqrikrhtekekyrllNH 94
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYaRRYLGDDadaEDLVQEAFLKLLEALDRFDPEGS--FKAWLFRIAR---------------NL 63

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185  95 VIERMKKEERKRRIDYEYRDSVKEEDKISDEEDSICLKTTLEQYIKlACSEREAFIVRKIYFEGYQQHELAKEMGVCRQR 174
Cdd:TIGR02937  64 ILDYLRRKRRLRRELDLLEELLDSDPSPEEELEQEEEREALREALE-KLPEREREVLVLRYLEGLSYKEIAEILGISVGT 142

                         170
                  ....*....|....
gi 1011904185 175 VNTIVKRSLNKIRR 188
Cdd:TIGR02937 143 VKRRLKRARKKLRE 156
PRK08215 PRK08215
RNA polymerase sporulation sigma factor SigG;
4-188 3.17e-11

RNA polymerase sporulation sigma factor SigG;


Pssm-ID: 181296 [Multi-domain]  Cd Length: 258  Bit Score: 60.73  E-value: 3.17e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185   4 KETLELIRLAKQGDIKARNELIEKNINLV----HKINCMYGNKEDGFQEGILAFCHAIDKFDETKKVKLSSYAFHWIHQR 79
Cdd:PRK08215   22 EEMRELFERMQNGDKEAREKLINGNLRLVlsviQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGE 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185  80 IKRHTE-------------------KEKYRLLNH------VIE-----RMKKEERKRRID--------YE--YRDS---V 116
Cdd:PRK08215  102 IRRYLRdnnpirvsrslrdiaykalQVREKLINEnskeptVEEiakelEVPREEVVFALDaiqdpvslFEpiYHDGgdpI 181

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1011904185 117 KEEDKISDEEDS-------ICLKTTLEqyiKLacSEREAFIVRKIYFEGYQQHELAKEMGVCRQRVNTIVKRSLNKIRR 188
Cdd:PRK08215  182 YVMDQISDEKNKdenwleeIALKEAMK---KL--NDREKLILNLRFFQGKTQMEVAEEIGISQAQVSRLEKAALKHMRK 255
PRK07921 PRK07921
RNA polymerase sigma factor SigB; Reviewed
 1-187 7.04e-11

RNA polymerase sigma factor SigB; Reviewed


Pssm-ID: 181169 [Multi-domain]  Cd Length: 324  Bit Score: 60.13  E-value: 7.04e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185   1 METKETL------ELIRLAKQGDiKARNELIEKNINLVHKINCMYGNKE----DGFQEGILAFCHAIDKFDETKKVKLSS 70
Cdd:PRK07921   63 LETRKRLsearkrDLAAVVRDGE-AARRHLLEANLRLVVSLAKRYTGRGmpllDLIQEGNLGLIRAMEKFDYTKGFKFST 141

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185  71 YAFHWIHQRIKRHT--EKEKYRLLNHVIERMKKEERKRRIDYEY--RDSVKEE---------DKI--------------- 122
Cdd:PRK07921  142 YATWWIRQAITRGMadQSRTIRLPVHLVEQVNKLARIKRELHQQlgREATDEElaeesgipeEKIadllehsrdpvsldm 221

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185 123 ---SDEE---------------DSICLKTTLEQYIK--LAC-SEREAFIVRKIY-FEGYQQH---ELAKEMGVCRQRVNT 177
Cdd:PRK07921  222 pvgSDEEaplgdfiedseatsaENAVIAGLLHTDIRsvLATlDEREQQVIRLRFgLDDGQPRtldQIGKLFGLSRERVRQ 301

                         250
                  ....*....|
gi 1011904185 178 IVKRSLNKIR 187
Cdd:PRK07921  302 IEREVMSKLR 311
PRK07598 PRK07598
RNA polymerase sigma factor SigC; Validated
 8-105 7.50e-11

RNA polymerase sigma factor SigC; Validated


Pssm-ID: 236067 [Multi-domain]  Cd Length: 415  Bit Score: 60.27  E-value: 7.50e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185   8 ELIRLAKQGdIKARNELIEKNINLVHKINCMYGNKE----DGFQEGILAFCHAIDKFDETKKVKLSSYAFHWIHQRIKR- 82
Cdd:PRK07598  165 ELEQIQKQG-LRAKEHMIKANLRLVVSVAKKYQNRGlellDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRa 243

                          90       100
                  ....*....|....*....|....*..
gi 1011904185  83 -HTEKEKYRLLNHVIE---RMKKEERK 105
Cdd:PRK07598  244 iATQSRTIRLPVHITEklnKIKKAQRK 270
PRK05803 PRK05803
RNA polymerase sporulation sigma factor SigK;
4-193 2.97e-10

RNA polymerase sporulation sigma factor SigK;


Pssm-ID: 180266 [Multi-domain]  Cd Length: 233  Bit Score: 57.65  E-value: 2.97e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185   4 KETLELIRLAKQGDIKARNELIEKNINLVHKINCMYGN----KEDGFQEGILAFCHAIDKFDETKKVKLSSYAFHWIHQR 79
Cdd:PRK05803   34 EEERKYLELMKEGDEEARNILIERNLRLVAHIVKKFENtgedVDDLISIGTIGLIKAIESFDAGKGTKLATYAARCIENE 113

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185  80 IKRHTEKEKyrllnhvieRMKKE--------ERKRRIDYEYRDSVK-EEDKISDE-EDSICLKTTLEQYIKLACSEREAF 149
Cdd:PRK05803  114 ILMHLRNLK---------KTKKEvslqdpigVDKEGNEISLIDILGsEEDDVIEQvELKMEVEKLYKKIDILDEREKEVI 184

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1011904185 150 IVRKIYFEGYQ--QHELAKEMGVCRQRVNTIVKRSLNKIRRVFYES 193
Cdd:PRK05803  185 EMRYGLGNGKEktQREIAKALGISRSYVSRIEKRALKKLFKELYRA 230
PRK05949 PRK05949
RNA polymerase sigma factor; Validated
 8-107 8.02e-10

RNA polymerase sigma factor; Validated


Pssm-ID: 180321 [Multi-domain]  Cd Length: 327  Bit Score: 57.16  E-value: 8.02e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185   8 ELIRLAKQGDiKARNELIEKNINLVHKINCMYGNKE----DGFQEGILAFCHAIDKFDETKKVKLSSYAFHWIHQRIKRH 83
Cdd:PRK05949   81 ELKQTLKQGK-RAKQKMIEANLRLVVAIAKKYQKRNmeflDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRA 159

                          90       100
                  ....*....|....*....|....*.
gi 1011904185  84 TEKE--KYRLLNHVIERMKKEERKRR 107
Cdd:PRK05949  160 IAQQarTIRLPIHITEKLNKIKKTQR 185
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 8-188 1.78e-08

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: 51.92  E-value: 1.78e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185   8 ELIRLAKQGDIKARNELIEKNINLVHK-INCMYGNKEDG---FQEGILAFCHAIDKFDETKKVKlsSYAFhwihqRIkrh 83
Cdd:COG1595     6 ELLERLRAGDEAAFEELYERYRPRLYRyARRLLGDRADAedlVQETFLRLWRKLDSFRGRGSFR--AWLY-----RI--- 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185  84 tekekyrLLNHVIERMKKEERKRRIDYEYRDSVKE-----EDKISDEEDSICLKTTLEQyikLACSEREAFIVRkiYFEG 158
Cdd:COG1595    76 -------ARNLAIDHLRKRRRRRELLDELAEELPDeaadpEEALEAEELLEALLAALER---LPPRQREVLVLR--YLEG 143

                         170       180       190
                  ....*....|....*....|....*....|
gi 1011904185 159 YQQHELAKEMGVCRQRVNTIVKRSLNKIRR 188
Cdd:COG1595   144 LSYAEIAEILGISEGTVKSRLSRARKKLRE 173
PRK09210 PRK09210
RNA polymerase sigma factor RpoD; Validated
 8-82 2.18e-08

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 53.07  E-value: 2.18e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185   8 ELIRLAK---QGDIKARNELIEKNINLVHKINCMYGNKE----DGFQEGILAFCHAIDKFDETKKVKLSSYAFHWIHQRI 80
Cdd:PRK09210  115 EEIELAKrieEGDEEAKQRLAEANLRLVVSIAKRYVGRGmlflDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAI 194


                  ..
gi 1011904185  81 KR 82
Cdd:PRK09210  195 TR 196
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 24-83 1.02e-07

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: 47.20  E-value: 1.02e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1011904185  24 LIEKNINLVHKINCMYGNK----EDGFQEGILAFCHAIDKFDETKKVKLSSYAFHWIHQRIKRH 83
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDgadaEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDY 64
PRK08311 PRK08311
RNA polymerase sigma factor SigI;
2-141 2.59e-07

RNA polymerase sigma factor SigI;


Pssm-ID: 236233 [Multi-domain]  Cd Length: 237  Bit Score: 49.10  E-value: 2.59e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185   2 ETKETLELIRLAKQGDIKARNELIEKNINLVHKINCMYGNK------EDGFQEGILAFCHAIDKFDETKKVKLSSYAFHW 75
Cdd:PRK08311    1 RKKSLEDILEKIKNGDEELREELIEEYKPFIAKVVSSVCGRyidwenDDELSIGLIAFNEAIDSYDEEKGKSFLSFAELV 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1011904185  76 IHQRIKRHTEKEKyrlLNHVIERMKKEERKRRIDYEYRDSVkeeDKISDEEDSICLKTTLEQYIKL 141
Cdd:PRK08311   81 IKRRLIDYFRKES---KHNLVLSNSDEEDEEENDIEIELSL---EEYQEEEENEERREEIEEFKKE 140
PRK05901 PRK05901
RNA polymerase sigma factor; Provisional
 1-82 7.56e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 235640 [Multi-domain]  Cd Length: 509  Bit Score: 48.45  E-value: 7.56e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185   1 METKETLELIRLAKQGDiKARNELIEKNINLVHKINCMYGNK----EDGFQEGILAFCHAIDKFDETKKVKLSSYAFHWI 76
Cdd:PRK05901  254 LDPELRRDLQWIGRDGK-RAKNHLLEANLRLVVSLAKRYTNRglsfLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWI 332


                  ....*.
gi 1011904185  77 HQRIKR 82
Cdd:PRK05901  333 RQAITR 338
PRK07406 PRK07406
RNA polymerase sigma factor RpoD; Validated
 19-101 2.55e-06

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236012 [Multi-domain]  Cd Length: 373  Bit Score: 46.70  E-value: 2.55e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185  19 KARNELIEKNINLVHKINCMYGNK----EDGFQEGILAFCHAIDKFDETKKVKLSSYAFHWIHQRIKRHT--EKEKYRLL 92
Cdd:PRK07406  136 RAKEKMVQSNLRLVVSIAKKYMNRglsfQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIadQSRTIRLP 215

                          90
                  ....*....|..
gi 1011904185  93 NHVIE---RMKK 101
Cdd:PRK07406  216 VHLYEtisRIKK 227
PRK07405 PRK07405
RNA polymerase sigma factor SigD; Validated
 8-107 6.91e-06

RNA polymerase sigma factor SigD; Validated


Pssm-ID: 180963 [Multi-domain]  Cd Length: 317  Bit Score: 45.52  E-value: 6.91e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185   8 ELIRLAKQGDIkARNELIEKNINLVHKINCMYGNKE----DGFQEGILAFCHAIDKFDETKKVKLSSYAFHWIHQRIKRH 83
Cdd:PRK07405   71 ELRSAIAEGEA-AKRKMVEANLRLVVSVAKKYLKRNvdllDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRA 149

                          90       100
                  ....*....|....*....|....*.
gi 1011904185  84 -TEKEK-YRLLNHVIERMKKEERKRR 107
Cdd:PRK07405  150 iAEKSRtIRLPIHITEKLNKIKKAQR 175
PRK07408 PRK07408
RNA polymerase sigma factor SigF; Reviewed
 5-76 1.09e-05

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 180965 [Multi-domain]  Cd Length: 256  Bit Score: 44.53  E-value: 1.09e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1011904185   5 ETLELIRL-AKQGDIKARNELIEKNINLVHKI-----NCMYGNKEDGFQEGILAFCHAIDKFDETKKVKLSSYAFHWI 76
Cdd:PRK07408   10 ETMELLRAyQQNPSIALRNQLVELNLGLVRKEahrwsNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYI 87
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 144-188 1.35e-05

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: 40.87  E-value: 1.35e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1011904185 144 SEREAFIVRKIYFEGYQQHELAKEMGVCRQRVNTIVKRSLNKIRR 188
Cdd:pfam04545   6 PPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
rpoH2 PRK07500
RNA polymerase factor sigma-32; Reviewed
 1-188 1.59e-04

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 236033 [Multi-domain]  Cd Length: 289  Bit Score: 41.17  E-value: 1.59e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185   1 METKETLEL-IRLAKQGDIKARNELIEKNINLVHKINCMYGN----KEDGFQEGILAFCHAIDKFDETKKVKLSSYAFHW 75
Cdd:PRK07500   21 LEREEEHALaYRWKDHRDEDALHRIISAHMRLVISMAGKFRRfglpMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWW 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185  76 IH-----------------------------QRIKRHTEKEKYRLLNHVIERM--------------------------- 99
Cdd:PRK07500  101 IRasiqdyilrnwsivrggtssaqkalffnlRRLRARLAQADEELTKQEIHREiatalgvslsdvemmdarlsgpdasln 180

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185 100 -----KKEERKRRIDYEYRDSVKEEDKISDEEDSICLKTTLEQYIKlACSEREAFIV--RKIYFEGYQQHELAKEMGVCR 172
Cdd:PRK07500  181 apqseEDEGRSERMDFLVDDSPLPDEQVESSIDGERRRRWLTQALQ-TLNERELRIIreRRLREDGATLEALGEELGISK 259

                         250
                  ....*....|....*.
gi 1011904185 173 QRVNTIVKRSLNKIRR 188
Cdd:PRK07500  260 ERVRQIEARALEKLRR 275
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 132-187 2.13e-04

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: 37.85  E-value: 2.13e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1011904185 132 KTTLEQYIKlACSEREAFIVRKIYFEGYQQHELAKEMGVCRQRVNTIVKRSLNKIR 187
Cdd:cd06171     1 RERLEEALD-KLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK06759 PRK06759
RNA polymerase factor sigma-70; Validated
 23-187 5.30e-04

RNA polymerase factor sigma-70; Validated


Pssm-ID: 235857 [Multi-domain]  Cd Length: 154  Bit Score: 39.03  E-value: 5.30e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185  23 ELIEKNINLVHKINCMYGNKEDGFQEGILAFCHAIDKFDETKKvKLSSYAFHWIHQRIkrhtekekyrllnhvIERMKKE 102
Cdd:PRK06759   11 VLYEGLIVNQIKKLGIYQDYEEYYQCGLIGLWHAYERYDEKKG-SFPAYAVVTVRGYI---------------LERLKKE 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185 103 ErkrridyeyrdSVKEEDKISDEEDSICLKTTLEQYIKLACS---EREAFIVRKIYFEGYQQHELAKEMGVCRQRVNTIV 179
Cdd:PRK06759   75 F-----------AVQEKCVCVGEYEDHFHFEDVEMKVKDFMSvldEKEKYIIFERFFVGKTMGEIALETEMTYYQVRWIY 143


                  ....*...
gi 1011904185 180 KRSLNKIR 187
Cdd:PRK06759  144 RQALEKMR 151
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 1-188 6.93e-03

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 35.77  E-value: 6.93e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185   1 METKETlELIRLAKQGDIKARNELIEKNINLVH----KINCMYGNKEDGFQEGILAFCHAIDKFdeTKKVKLSSYAFHWI 76
Cdd:PRK09638    1 MQMDEK-ELIQKAKKGDDAALTTLFQQHYSFLYkyllKLTLDPDLAEDLVQETMLKAIENLSSF--QGRSKFSTWLISIA 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1011904185  77 HQRIKRHTEKEK-YRLLnhviERMKKEERKRRIdyeyrdsvKEEDKISDEEdsicLKTTLEQYIKLACSEREAFIVRKIY 155
Cdd:PRK09638   78 SRLYKDHLRKQKrEKLR----LQRAKEETLRKE--------KWEAAIKGAE----WSEMLDALSKLDPEFRAPVILKHYY 141

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1011904185 156 feGYQQHELAKEMGVCRQRVNTIVKRSLNKIRR 188
Cdd:PRK09638  142 --GYTYEEIAKMLNIPEGTVKSRVHHGIKQLRK 172
PRK06596 PRK06596
RNA polymerase factor sigma-32; Reviewed
 11-76 7.10e-03

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 235838 [Multi-domain]  Cd Length: 284  Bit Score: 36.31  E-value: 7.10e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1011904185  11 RLAKQGDIKARNELIEKNINLVHKInCM----YG-NKEDGFQEGILAFCHAIDKFDETKKVKLSSYAFHWI 76
Cdd:PRK06596   40 RLREHGDLEAAKQLVLSHLRFVVHI-ARgyrgYGlPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWI 109
PRK08301 PRK08301
RNA polymerase sporulation sigma factor SigE;
1-72 9.27e-03

RNA polymerase sporulation sigma factor SigE;


Pssm-ID: 236228 [Multi-domain]  Cd Length: 234  Bit Score: 35.99  E-value: 9.27e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1011904185   1 METKETLELIRLAKQGDIKARNELIEKNINLVHKINCMYGNK----EDGFQEGILAFCHAIDKFDETKKVKLSSYA 72
Cdd:PRK08301   34 LSKEEEEYLLNKLPKGDEAVRSLLIERNLRLVVYIARKFENTginiEDLISIGTIGLIKAVNTFNPEKKIKLATYA 109
 
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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