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Conserved domains on  [gi|1879190669|ref|WP_180918027|]
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RNA polymerase sigma factor [Ochrobactrum teleogrylli]

Protein Classification

RNA polymerase sigma factor( domain architecture ID 11446377)

RNA polymerase sigma factor plays a role in bacterial signal transduction and is regulated by anti-sigma factors. May belong to the ECF-type subfamily. Generally, sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released.

CATH:  1.10.1740.10
Gene Ontology:  GO:0016987|GO:0006352|GO:0003677
PubMed:  28575802
SCOP:  4003741

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 5-155 2.73e-28

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: 103.15  E-value: 2.73e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1879190669   5 FERFFVRERSRLKRFAIKLLGNAHDADDILQETYIKL--SSRELSDGD--RGLVVRTLTTLAIDHIRTRNVHDAGGKAAS 80
Cdd:COG1595    19 FEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLwrKLDSFRGRGsfRAWLYRIARNLAIDHLRKRRRRRELLDELA 98

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1879190669  81 DEVFVEHIQPERIVSSKHDLAVLLDAINHLPRRRAKIFLLARVDGMAYGQIAQTLHVSLSTVEKEMAAAIAFCHK 155
Cdd:COG1595    99 EELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLRE 173
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 5-155 2.73e-28

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: 103.15  E-value: 2.73e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1879190669   5 FERFFVRERSRLKRFAIKLLGNAHDADDILQETYIKL--SSRELSDGD--RGLVVRTLTTLAIDHIRTRNVHDAGGKAAS 80
Cdd:COG1595    19 FEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLwrKLDSFRGRGsfRAWLYRIARNLAIDHLRKRRRRRELLDELA 98

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1879190669  81 DEVFVEHIQPERIVSSKHDLAVLLDAINHLPRRRAKIFLLARVDGMAYGQIAQTLHVSLSTVEKEMAAAIAFCHK 155
Cdd:COG1595    99 EELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLRE 173
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 5-152 1.23e-21

RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.


Pssm-ID: 274376 [Multi-domain]  Cd Length: 161  Bit Score: 85.31  E-value: 1.23e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1879190669   5 FERFFVRERSRLKRFAIKLLGNAHDADDILQETYIKL----SSRELSDGDRGLVVRTLTTLAIDHIRTRNVHDAggkaaS 80
Cdd:TIGR02985   3 FEQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLwenrETLEISESIKAYLFTIVKNRCLNYLRHKQVEEK-----Y 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1879190669  81 DEVFVEHIQ-------PERIVSSKHDLAVLLDAINHLPRRRAKIFLLARVDGMAYGQIAQTLHVSLSTVEKEMAAAIAF 152
Cdd:TIGR02985  78 QEELAEIEErelseadPEEELEAKELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKF 156
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 1-153 3.56e-20

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 81.94  E-value: 3.56e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1879190669   1 MNAVFERFFVRERSRLKRFAIKLLGNAHDADDILQETYIKLSSRELSDGDRGLVVRTLTTLAIDHI-----RTRNVHDAG 75
Cdd:PRK11924   11 DKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCydllrRRRREKAVL 90

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1879190669  76 GKAASDEVFVE-HIQPERIVSSKHDLAVLLDAINHLPRRRAKIFLLARVDGMAYGQIAQTLHVSLSTVEKEMAAAIAFC 153
Cdd:PRK11924   91 SDDALEPEFAEtAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQLL 169
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 103-153 4.83e-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.


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 52.46  E-value: 4.83e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1879190669 103 LLDAINHLPRRRAKIFLLARVDGMAYGQIAQTLHVSLSTVEKEMAAAIAFC 153
Cdd:pfam08281   4 LLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 100-151 4.43e-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: 36.31  E-value: 4.43e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1879190669 100 LAVLLDAINHLPRRRAKIFLLARVDGMAYGQIAQTLHVSLSTVEKEMAAAIA 151
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALK 52
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 5-155 2.73e-28

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: 103.15  E-value: 2.73e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1879190669   5 FERFFVRERSRLKRFAIKLLGNAHDADDILQETYIKL--SSRELSDGD--RGLVVRTLTTLAIDHIRTRNVHDAGGKAAS 80
Cdd:COG1595    19 FEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLwrKLDSFRGRGsfRAWLYRIARNLAIDHLRKRRRRRELLDELA 98

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1879190669  81 DEVFVEHIQPERIVSSKHDLAVLLDAINHLPRRRAKIFLLARVDGMAYGQIAQTLHVSLSTVEKEMAAAIAFCHK 155
Cdd:COG1595    99 EELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLRE 173
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 5-152 1.23e-21

RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.


Pssm-ID: 274376 [Multi-domain]  Cd Length: 161  Bit Score: 85.31  E-value: 1.23e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1879190669   5 FERFFVRERSRLKRFAIKLLGNAHDADDILQETYIKL----SSRELSDGDRGLVVRTLTTLAIDHIRTRNVHDAggkaaS 80
Cdd:TIGR02985   3 FEQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLwenrETLEISESIKAYLFTIVKNRCLNYLRHKQVEEK-----Y 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1879190669  81 DEVFVEHIQ-------PERIVSSKHDLAVLLDAINHLPRRRAKIFLLARVDGMAYGQIAQTLHVSLSTVEKEMAAAIAF 152
Cdd:TIGR02985  78 QEELAEIEErelseadPEEELEAKELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKF 156
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 5-155 2.82e-20

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: 81.62  E-value: 2.82e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1879190669   5 FERFFVRERSRLKRFAIKLLGNAHDADDILQETYIKL----SSRELSDGDRGLVVRTLTTLAIDHIRTRNVHDAGGKAAs 80
Cdd:TIGR02937   3 FEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLlealDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDLL- 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1879190669  81 DEVFVEHIQPERIVSSKHDLAVLLDAINHLPRRRAKIFLLARVDGMAYGQIAQTLHVSLSTVEKEMAAAIAFCHK 155
Cdd:TIGR02937  82 EELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRE 156
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 1-153 3.56e-20

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 81.94  E-value: 3.56e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1879190669   1 MNAVFERFFVRERSRLKRFAIKLLGNAHDADDILQETYIKLSSRELSDGDRGLVVRTLTTLAIDHI-----RTRNVHDAG 75
Cdd:PRK11924   11 DKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCydllrRRRREKAVL 90

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1879190669  76 GKAASDEVFVE-HIQPERIVSSKHDLAVLLDAINHLPRRRAKIFLLARVDGMAYGQIAQTLHVSLSTVEKEMAAAIAFC 153
Cdd:PRK11924   91 SDDALEPEFAEtAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQLL 169
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 3-142 2.72e-15

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 69.45  E-value: 2.72e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1879190669   3 AVFERFFVRERSRLKRFAIKLLGNAHDADDILQETYIKLSsRELSDGDRGLVVRT-----LTTLAIDHIRT--RNVHDAG 75
Cdd:PRK09652   10 AAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAY-RALHSFRGGAAFYTwlyriARNTAINYLRKqgRRPPASD 88

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1879190669  76 GKAASDEVF-----VEHI-QPERIVSSKHDLAVLLDAINHLPRRRAKIFLLARVDGMAYGQIAQTLHVSLSTV 142
Cdd:PRK09652   89 VDAEEAEDFdladaLRDIsTPENELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTV 161
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 1-142 1.65e-12

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 61.92  E-value: 1.65e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1879190669   1 MNAVFERFfvreRSRLKRFAIKLLGNAHDADDILQETYIKLSSR--ELSDGD--RGLVVRTLTTLAIDHIRTRNVHDAgg 76
Cdd:PRK09637    3 LESIWSEY----KAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNlhSLKDGSsiKSWLYQIANNTIIDFYRKKNRSEE-- 76

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1879190669  77 kAASDEVFVEHiqpERIVSSKHDLAV-LLDAINHLPRRRAKIFLLARVDGMAYGQIAQTLHVSLSTV 142
Cdd:PRK09637   77 -LPDDLLFEDE---EREENAKKELAPcLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGA 139
PRK12528 PRK12528
RNA polymerase sigma factor; Provisional
 24-154 4.01e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 171561 [Multi-domain]  Cd Length: 161  Bit Score: 60.63  E-value: 4.01e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1879190669  24 LGNAHDADDILQETYIK-LSSRELS--DGDRGLvvrtLTTLA----IDHIRTRNVHDAGGKAASDevfvehiQPERIVSS 96
Cdd:PRK12528   25 LGCPQSAADLAQDTFVKvLVARETAqiIEPRAF----LTTIAkrvlCNHYRRQDLERAYLEALAQ-------LPERVAPS 93

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1879190669  97 KHDLAVLLDAI-------NHLPRRRAKIFLLARVDGMAYGQIAQTLHVSLSTVEKEMAAAIAFCH 154
Cdd:PRK12528   94 EEERAIILETLveldqllDGLPPLVKRAFLLAQVDGLGYGEIATELGISLATVKRYLNKAAMRCY 158
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 10-142 1.02e-11

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 60.18  E-value: 1.02e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1879190669  10 VRERS-RLKRFAIKLLGNAHDADDILQETYIKLsSRELSDGD----RGLVVRTLTTLAIDHIRTRNV--HDAGGKAAsDE 82
Cdd:PRK09647   34 VRQHAdRVYRLAYRLSGNQHDAEDLTQETFIRV-FRSLQNYQpgtfEGWLHRITTNLFLDMVRRRARirMEALPEDY-DR 111

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1879190669  83 VFVEHIQPERIVSSKH---DLAVLLDAINhlPRRRAKIfLLARVDGMAYGQIAQTLHVSLSTV 142
Cdd:PRK09647  112 VPGDEPNPEQIYHDARldpDLQAALDSLP--PEFRAAV-VLCDIEGLSYEEIAATLGVKLGTV 171
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 16-153 2.22e-11

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 58.63  E-value: 2.22e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1879190669  16 LKRFAIKLLGNAHDADDILQETYIKL---SSRELSDGDRGLVVRTLTTLAIDHIRTRNVHDAGG-KAASDEVFVEHIQPE 91
Cdd:PRK12527    8 LVRFLSARLGNRQAAEDVAHDAYLRVlerSSSAQIEHPRAFLYRTALNLVVDRHRRHRVRQAEPlEVLDEEERLHSPSPQ 87

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1879190669  92 RIVSSKHDLAVLLDAINHLPRRRAKIFLLARVDGMAYGQIAQTLHVSLSTVEKEMAAAIAFC 153
Cdd:PRK12527   88 TRLDLGQRLALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKHC 149
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 18-142 3.64e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 55.84  E-value: 3.64e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1879190669  18 RFAIKLLGNAHDADDILQETYIKLSSRELSDGDRGLVVRTLTTL----AIDHIRTRnvhdagGKAASdevFVEHIQPERI 93
Cdd:PRK12519   44 GLALKILGNSQEAEDLTQEIFLSLWRKSSYDPKRGSLSSYLLTLtrsrAIDRLRSR------RSRQR---LLERWQQELL 114

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1879190669  94 VSSKHDLAV-----------LLDAINHLPRRRAKIFLLARVDGMAYGQIAQTLHVSLSTV 142
Cdd:PRK12519  115 GEASEDTPLeqaslaersqrVQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTV 174
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 103-153 4.83e-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.


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 52.46  E-value: 4.83e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1879190669 103 LLDAINHLPRRRAKIFLLARVDGMAYGQIAQTLHVSLSTVEKEMAAAIAFC 153
Cdd:pfam08281   4 LLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
 9-160 7.76e-10

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 54.31  E-value: 7.76e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1879190669   9 FVRERSRLKRFAIKLLGNAHDADDILQETYIKLSSRELSDGDR---GLVVRTLTTLAIDHIRTRNVHD--AGGKAASDEV 83
Cdd:PRK07037    4 FVDNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQDAVKqpvAYLFRIVRNLAIDHYRRQALENkyHGDEEDGLDV 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1879190669  84 FVEHIQPERIVSSKHDLAVLLDAINHLPRRRAKIFLLARVDGMAYGQIAQTLHVSLSTVEKEMAAAIAFCHKWQQSH 160
Cdd:PRK07037   84 PSPEASPEAALINRDTLRHVADALSELPARTRYAFEMYRLHGETQKDIARELGVSPTLVNFMIRDALVHCRKCLDAC 160
PRK09651 PRK09651
RNA polymerase sigma factor FecI; Provisional
 5-161 1.32e-09

RNA polymerase sigma factor FecI; Provisional


Pssm-ID: 182018 [Multi-domain]  Cd Length: 172  Bit Score: 54.05  E-value: 1.32e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1879190669   5 FERFFVRERSRLKRFAIKLLGNAHDADDILQETYIKLSSrelsdGDRGLVVRT----LTTLA----IDHIRtRNvhdagg 76
Cdd:PRK09651   12 FESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMV-----SETLSTIRDprsfLCTIAkrvmVDLFR-RN------ 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1879190669  77 kaASDEVFVEHI--QPERIVSSKHDLAVLLDA-------INHLPRRRAKIFLLARVDGMAYGQIAQTLHVSLSTVEKEMA 147
Cdd:PRK09651   80 --ALEKAYLEMLalMPEGGAPSPEERESQLETlqlldsmLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVA 157

                         170
                  ....*....|....
gi 1879190669 148 AAIAFCHKWQQSHG 161
Cdd:PRK09651  158 KATEHCLLFRLEYG 171
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 3-151 2.14e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 53.92  E-value: 2.14e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1879190669   3 AVFERFFVRERSRLKRFAIKLLGNAHDADDILQETYIKLSSRELSDGDRGLVVRTLTTLA----IDHIRTRNVHDAGGKA 78
Cdd:PRK12513   26 AAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPRARFRTWLYQIArnllIDHWRRHGARQAPSLD 105

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1879190669  79 ASDEVFV---EHIQPERIVSSKHDLAVLLDAINHLPRRRAKIFLLARVDGMAYGQIAQTLHVSLSTVEKEMAAAIA 151
Cdd:PRK12513  106 ADEQLHAladDGAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREHGDLELEEIAELTGVPEETVKSRLRYALQ 181
PRK12529 PRK12529
RNA polymerase sigma factor; Provisional
 30-153 1.83e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 183574 [Multi-domain]  Cd Length: 178  Bit Score: 51.09  E-value: 1.83e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1879190669  30 ADDILQETYIK-LSSRELSDGD-----RGLVVRTLTTLAIDHIRTRNVHDAGGKAASDEVFVEHIQPER---IVSSKHDL 100
Cdd:PRK12529   42 ADDLAHDIFLRiLASRDGGQREairqpRAYLARIANCVLVSWRRRQSLELAWLEALATLPEPLHPSPEQqsvILETLHEI 121

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1879190669 101 AVLLDAINhlPRRRaKIFLLARVDGMAYGQIAQTLHVSLSTVEKEMAAAIAFC 153
Cdd:PRK12529  122 DALLDTLR--PRVK-QAFLMATLDGMKQKDIAQALDIALPTVKKYIHQAYVTC 171
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 1-152 2.15e-08

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 50.72  E-value: 2.15e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1879190669   1 MNAVFERFFVRERSRLKRFAIKLLGNAHDADDILQETYIKL--SSRELSDGDRGLVVRTLTTLAIDHIRTRNVHdaggKA 78
Cdd:PRK09639    1 SDETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLyrSDFKGIENEKGWLIKSARNVAYNYLRSEKRR----RA 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1879190669  79 ASDEVFVEH-----IQPERIVSSKHDLAVLLDAINHLPRRRAKIFLLaRVDGMAYGQIAQTLHVSLSTVEKEMAAAIAF 152
Cdd:PRK09639   77 RILGEFQWQevdnePSPEEIWIRKEEITKVQEVLAKMTERDRTVLLL-RFSGYSYKEIAEALGIKESSVGTTLARAKKK 154
PRK12523 PRK12523
RNA polymerase sigma factor; Reviewed
 30-154 2.43e-07

RNA polymerase sigma factor; Reviewed


Pssm-ID: 183572 [Multi-domain]  Cd Length: 172  Bit Score: 47.92  E-value: 2.43e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1879190669  30 ADDILQETYIKLSSRELSDG---DRGLVVRTLTTLAIDHIRtrnvhdaggKAASDEVFV---------EHIQPERIVSSK 97
Cdd:PRK12523   37 AEDLSQDTFVRLLGRPELPTprePRAFLAAVAKGLMFDHFR---------RAALEQAYLaelalvpeaEQPSPEEQHLIL 107

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1879190669  98 HDLAVLLDAINHLPRRRAKIFLLARVDGMAYGQIAQTLHVSLSTVEKEMAAAIAFCH 154
Cdd:PRK12523  108 EDLKAIDRLLGKLSSKARAAFLYNRLDGMGHAEIAERLGVSVSRVRQYLAQGLRQCY 164
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 5-146 3.90e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 47.24  E-value: 3.90e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1879190669   5 FERFFVRERSRLKRFAIKLLGNAHDADDILQETYIKLSSRelSDGDRGLVVRT-LTTLA----IDHIRTRNvhdaggKAA 79
Cdd:PRK12541    7 LEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVH--IDYYKGEEIRPwLFTIAynafIDWYRKEK------KYK 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1879190669  80 SDEVFVEHIQP----ERIVSSKHDLAVLLDAINHLPRRRAKIFLLARVDGMAYGQIAQTLHVSLSTVEKEM 146
Cdd:PRK12541   79 TTTIEEFHLPNvpstEHEYFIKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIEL 149
PRK12525 PRK12525
RNA polymerase sigma factor; Provisional
 2-155 1.61e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 139037 [Multi-domain]  Cd Length: 168  Bit Score: 45.71  E-value: 1.61e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1879190669   2 NAVFERFFVRERSRLKRFAIKLLGNAHDADDILQETYIK-------LSSRElsdgDRGLvvrtLTTLAidhirTRNVHDA 74
Cdd:PRK12525    8 NTLIGQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQvlalpdpASIRE----PRAL----LTTIA-----RRLMYEG 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1879190669  75 GGKAASDEVFVEHIQ--PERIVSSKHDLAVL---LDAINHL-----PRRRAkIFLLARVDGMAYGQIAQTLHVSLSTVEK 144
Cdd:PRK12525   75 WRRQDLERAYLQSLAeaPEAVQPSPEEQWMVietLLAIDRLldglsGKARA-AFLMSQLEGLTYVEIGERLGVSLSRIHQ 153

                         170
                  ....*....|.
gi 1879190669 145 EMAAAIAFCHK 155
Cdd:PRK12525  154 YMVEAFKCCYQ 164
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 8-70 2.31e-06

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: 42.96  E-value: 2.31e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1879190669   8 FFVRERSRLKRFAIKLLGNAHDADDILQETYIKL-SSRELSDGDRGLVVRT-LTT----LAIDHIRTRN 70
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLwRAIERFDPERGVSFSTwLYTiirnAIIDYLRKQR 69
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 17-142 2.56e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 45.20  E-value: 2.56e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1879190669  17 KRFAI--KLLGNAHDADDILQETYIKLSSRELSDGDRGLVVRT-LTTL----AIDHIRTRNVHDAGGKAASDeVFVEHIQ 89
Cdd:PRK12514   31 KLFGIclRVLKDRSEAEEALQDVYVKIWTKADRFAVSGLSPMTwLITIarnhAIDRLRARKAVAVDIDEAHD-LADPSPG 109

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1879190669  90 PERIVSSKHDLAVLLDAINHLPRRRAKIFLLARVDGMAYGQIAQTLHVSLSTV 142
Cdd:PRK12514  110 PEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYLEGLSYKELAERHDVPLNTM 162
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 18-142 4.38e-06

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 44.69  E-value: 4.38e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1879190669  18 RFAIKLLGNAHDADDILQET----YIKLSSRELSDGDRGLVVRTLTTLAIDHIRTRN--------VHDAGGKAASDEVFV 85
Cdd:PRK09641   33 QLCYRMLGNRHEAEDAAQEAfiraYVNIDSYDINRKFSTWLYRIATNLTIDRLRKRKpdyyldaeVAGTEGLTMYSQLAA 112

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1879190669  86 EHIQPERIVSSKHDLAVLLDAINHLPRRRAKIFLLARVDGMAYGQIAQTLHVSLSTV 142
Cdd:PRK09641  113 DDALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYIEDLSLKEISEILDLPVGTV 169
sigI PRK09635
RNA polymerase sigma factor SigI; Provisional
 11-141 4.73e-06

RNA polymerase sigma factor SigI; Provisional


Pssm-ID: 182008 [Multi-domain]  Cd Length: 290  Bit Score: 44.96  E-value: 4.73e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1879190669  11 RERSRLKRFAIKLLGNAHDADDILQETYIKLSSRELSDGD--RGLVVRTLTTLAIDHIRT-RNVHDAGGKAA---SDEVF 84
Cdd:PRK09635   13 AHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVGDIDdeRGWLIVVTSRLCLDHIKSaSTRRERPQDIAawhDGDAS 92

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1879190669  85 VEHIQP-ERIVSSKHDLAVLLDAINHLPRRRAKIFLLARVDGMAYGQIAQTLHVSLST 141
Cdd:PRK09635   93 VSSVDPaDRVTLDDEVRLALLIMLERLGPAERVVFVLHEIFGLPYQQIATTIGSQAST 150
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 3-155 2.91e-05

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 41.93  E-value: 2.91e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1879190669   3 AVFERFFVRERSRLKRFAIKLLGNAHDADDILQET----YIKLSSRELSDGDRGLVVRTLTTLAIDHIRTRNVHDAGGKA 78
Cdd:PRK09638   18 AALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETmlkaIENLSSFQGRSKFSTWLISIASRLYKDHLRKQKREKLRLQR 97

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1879190669  79 ASDEvfVEHIQPERIVSSKHDLAVLLDAINHLPRRRAKIFLLARVDGMAYGQIAQTLHVSLSTVEKEMAAAIAFCHK 155
Cdd:PRK09638   98 AKEE--TLRKEKWEAAIKGAEWSEMLDALSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRK 172
Sig70_famx1 TIGR02943
RNA polymerase sigma-70 factor, TIGR02943 family; This group of sigma factors are members of ...
 12-142 5.34e-05

RNA polymerase sigma-70 factor, TIGR02943 family; This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.


Pssm-ID: 274359 [Multi-domain]  Cd Length: 188  Bit Score: 41.29  E-value: 5.34e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1879190669  12 ERSRLKRFAIKLLGNAHDADDILQETYIK-LSSRELSDGDRGL---VVRTLTTLAIDHI----RTRNVHDAGGKaASDEV 83
Cdd:TIGR02943  11 LRRDLLRFARLQLRDRDLAEDAVQETLLAaLSHRDSFAGRSALktwLFAILKNKIIDALrakgREVKVSDLDDE-LDDEA 89

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1879190669  84 FVEHI----------------QPERIVSSKHDLAVLLDAINHLPRRRAKIFLLARVDGMAYGQIAQTLHVSLSTV 142
Cdd:TIGR02943  90 FNALFtqnghwaqhgqpqhwnTPEKQLENKEFWEVFEACLYHLPEQTARVFMMREVLGFESDEICQELEISTSNC 164
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 5-133 6.74e-05

RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).


Pssm-ID: 274379 [Multi-domain]  Cd Length: 159  Bit Score: 40.77  E-value: 6.74e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1879190669   5 FERFFVRERSRLKRFAIKLLGNAHDADDILQETYI----KLSSRELSDGdrglVVRTLTTLAIDHIR-----TRNVHDAG 75
Cdd:TIGR02989   3 FVRLLTRHERALRAFVRSLVADRDDVDDVLQETFVvawrKFDQFDPGTN----FVAWARGIARNKVLnyrrkLGRDRLVF 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1879190669  76 GKAASDEVFVEHIqPERIVSSKHDLAVLLDAINHLPRRRAKIFLLARVDGMAYGQIAQ 133
Cdd:TIGR02989  79 DDDLLEALAAEAE-PTEAERLSDDRQALEGCLEKLPERQRELLDLRYQRGQKATALAE 135
PRK06930 PRK06930
positive control sigma-like factor; Validated
 89-149 8.36e-05

positive control sigma-like factor; Validated


Pssm-ID: 180757 [Multi-domain]  Cd Length: 170  Bit Score: 40.87  E-value: 8.36e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1879190669  89 QPERIVSSkHDLAVLLDAINHLPRRRAKIFLLARVDGMAYGQIAQTLHVSLSTVEKEMAAA 149
Cdd:PRK06930   95 EPESVISE-WDKIRIEDALSVLTEREKEVYLMHRGYGLSYSEIADYLNIKKSTVQSMIERA 154
PRK09636 PRK09636
RNA polymerase sigma factor SigJ; Provisional
 13-149 8.38e-05

RNA polymerase sigma factor SigJ; Provisional


Pssm-ID: 236600 [Multi-domain]  Cd Length: 293  Bit Score: 41.45  E-value: 8.38e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1879190669  13 RSRLKRFAIKLLGNAHDADDILQETYIKLSS------RELsdgdRGLVVRTLTTLAIDHIRTrnvhdaggKAASDEVFVE 86
Cdd:PRK09636   14 RPHLLSVAYRMLGSVADAEDIVQEAWLRWNNadraqiRDP----RAWLTRVVTRLCLDRLRS--------ARHRRETYVG 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1879190669  87 HIQPERIV----------SSKHDLAV-LLDAINHL-PRRRAkIFLLARVDGMAYGQIAqtlhvslSTVEKEMAAA 149
Cdd:PRK09636   82 PWLPEPVVeelddpleavVAAEDLSLaLMLALERLsPLERA-AFLLHDVFGVPFDEIA-------STLGRSPAAC 148
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 2-149 3.64e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 39.18  E-value: 3.64e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1879190669   2 NAVFERFFVRERSRLKRFAIKLLGNAHDADDILQETYIKLSSR----ELSDGDRGLVVRTLTTLAIDHIRT--RNVHDag 75
Cdd:PRK12516    9 TPPFKRELLAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKqdhfEVGTNMKAWLFTILRNEFYSQMRKrgREVQD-- 86

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1879190669  76 gkaaSDEVFVEH--IQPERIVSSkhDLAVLLDAINHLPRRRAKIFLLARVDGMAYGQIAQTLHVSLSTVEKEMAAA 149
Cdd:PRK12516   87 ----TDGMFTEQlaVHPSQYGTL--DLQDFRAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRA 156
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 100-151 4.43e-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: 36.31  E-value: 4.43e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1879190669 100 LAVLLDAINHLPRRRAKIFLLARVDGMAYGQIAQTLHVSLSTVEKEMAAAIA 151
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALK 52
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 6-142 5.63e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 38.60  E-value: 5.63e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1879190669   6 ERFFVRERSRLKRFAIKLLGNAHDADDILQETYIKLSSRELS-----DGDRGLVVRTLTTLAIDHIR--TRNVHdaggka 78
Cdd:PRK12537   26 QALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASfdparGSARGWIYSVTRHLALNVLRdtRREVV------ 99

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1879190669  79 ASDEVFVEHIQPERIVSS---KHDLAVLLDAINHLPRRRAKIFLLARVDGMAYGQIAQTLHVSLSTV 142
Cdd:PRK12537  100 LDDDAEETAQTLHEIIDDfdlWANSGKIHRCLEQLEPARRNCILHAYVDGCSHAEIAQRLGAPLGTV 166
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
16-142 7.35e-04

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 38.14  E-value: 7.35e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1879190669  16 LKRFAIKLLGNAHDADDILQETYIKLSSRELSDGDRGLVVRT-LTT----LAIDHIRTRNVHDAGGKAASDEVfvehiqP 90
Cdd:PRK09645   22 LWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTGRSARAwLFTvarnLVIDERRSARARPVEGGDDVLGV------P 95

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1879190669  91 ERIVSSKHDLAV----LLDAINHL-PRRRAKIfLLARVDGMAYGQIAQTLHVSLSTV 142
Cdd:PRK09645   96 EQSAPDEVDRALdrllVADALAQLsPEHRAVL-VRSYYRGWSTAQIAADLGIPEGTV 151
PRK06704 PRK06704
RNA polymerase subunit sigma-70;
1-146 1.09e-03

RNA polymerase subunit sigma-70;


Pssm-ID: 180663 [Multi-domain]  Cd Length: 228  Bit Score: 38.08  E-value: 1.09e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1879190669   1 MNAVFERFFVRERSRLKRFAIKLLGNAHDADDILQETYIK-LSSRELSDGDRGLVVRTLTTLAIDHIRTRNVHDaggKAA 79
Cdd:PRK06704   15 MNHSNINFLIEQYGELKRYCTFLTKNKWDGEDLAQETVCKvLQKYSNKDICMTLVYKIARNRWLDQIKSKSVHE---KIR 91

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1879190669  80 SDEVFVEhiqPERIVSSKHDLAVllDAINHLPRRRAKIFLLARVDGMAYGQIAQTLHVSLSTVEKEM 146
Cdd:PRK06704   92 DQITFEE---PHEKIADLHEMVG--KVLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASL 153
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 5-158 1.57e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 37.02  E-value: 1.57e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1879190669   5 FERFFVRERSRLKRFAIKLLGNAHDADDILQETYIKL-SSRELSDGDR-------GLVVRTLTTLAIDHIRTRNVHDagg 76
Cdd:PRK12543    9 FSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLwESLRKYDSNRpfrfwliGLVIKQIHSWRRKRWRRFRIFE--- 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1879190669  77 KAASDEVFVEHIQPERIVsSKHDLAVLLDAINHLPRRRAKIFLLARVDGMAYGQIAQTLHVSLSTVEKEMAAAIAFCHKW 156
Cdd:PRK12543   86 KAEEQRKPVSIDFSEDVL-SKESNQELIELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQK 164


                  ..
gi 1879190669 157 QQ 158
Cdd:PRK12543  165 EQ 166
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 3-142 1.88e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 37.25  E-value: 1.88e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1879190669   3 AVFERFFVRERSRLKRFAIKLLGNAHDADDILQETYIKlSSRELSD--GDRGL---VVRTLTTLAIDHIRTRNVHDAGGK 77
Cdd:PRK11922   30 AAFEALMRRHNRRLYRTARAILRNDAEAEDVVQEAYLR-AFRALGTfrGDASLstwLSRIVLNEALGRLRRRRRLVNLAE 108

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1879190669  78 AASDEVFVEHIQ---------PERIVSSKHDLAVLLDAINHLPRRRAKIFLLARVDGMAYGQIAQTLHVSLSTV 142
Cdd:PRK11922  109 MVMASTIAGGERtpladpaedPERAAARREIRALLERAIDALPDAFRAVFVLRVVEELSVEETAQALGLPEETV 182
PRK12526 PRK12526
RNA polymerase sigma factor; Provisional
 5-151 2.15e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237127 [Multi-domain]  Cd Length: 206  Bit Score: 37.09  E-value: 2.15e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1879190669   5 FERFFVRERSRLKRFAIKLLGNAHDADDILQETYIKLSSR-ELSDGDRG-------LVVRTLTTLAIDHIRTRNVHDAGG 76
Cdd:PRK12526   40 FTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKaHLYNGDKGaattwvyTVMRNAAFDMLRKIKAKKEQNLGD 119

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1879190669  77 KAASDEVFVEHIQPERIVSSKHDL-AVLLDAINHLPRRRAKIFLLARVDGMAYGQIAQTLHVSLSTVEKEMAAAIA 151
Cdd:PRK12526  120 DIWPIEQALAESQSESEEFSDHLMdKQILSYIEKLPEAQQTVVKGVYFQELSQEQLAQQLNVPLGTVKSRLRLALA 195
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 15-143 2.21e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 36.79  E-value: 2.21e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1879190669  15 RLKRFAIKLLGNAHDADDILQETYIKL--SSRELSDGDRGL---VVRTLTTLAIDHIRTRN----VHDAGGKAASDEVFV 85
Cdd:PRK12524   38 RALAVATRVLGDRAEAEDVTQEAMLRLwrIAPDWRQGEARVstwLYRVVCNLCTDRLRRRRrasvDLDDAPEPADAAPGA 117

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1879190669  86 EHIQPERivsskHDLAVLLDAINHLPRRRAKIFLLARVDGMAYGQIAQTLHVSLSTVE 143
Cdd:PRK12524  118 EEALIEG-----DRMRALDAALAALPERQRQAVVLRHIEGLSNPEIAEVMEIGVEAVE 170
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 5-152 3.02e-03

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 36.46  E-value: 3.02e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1879190669   5 FERFFVRERSRLKRFAIKLLGNAHDADDILQETYIKLSSrELSDGDRGLVVRT-LTTLAIDHIRTRNVHDAGGKAASDEV 83
Cdd:PRK09640   28 YEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLY-GLKNFEGKSKFKTwLYSITYNECITQYRKERRKRRLMDAL 106

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1879190669  84 FVEHI-QPERIVSSKHDLAVLLDA-INHLPRRRAKIFLLARVDGMAYGQIAQTLHVSLSTVEKEMAAAIAF 152
Cdd:PRK09640  107 SLDPLeEASEEKAPKPEERGGLDRwLVHVNPIDREILVLRFVAELEFQEIADIMHMGLSATKMRYKRALDK 177
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 16-151 5.25e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 35.92  E-value: 5.25e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1879190669  16 LKRFAIKLLGNAHDADDILQETYIKLSSRELS-DGDRGLVVRTLTTLA---IDHIRTRNVHDAGGKAASDEVFVEHIQPE 91
Cdd:PRK12511   17 LRRYARSLTRDSAEAEDLVHDALVRALERRASfRSGGNLRTWLMSILHnafIDELRRRRVEARRADELAVLADASLPAAQ 96

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1879190669  92 rivSSKHDLAVLLDAINHLP-RRRAKIFLLArVDGMAYGQIAQTLHVSLSTVEKEMAAAIA 151
Cdd:PRK12511   97 ---EHAVRLAQIRDAFFDLPeEQRAALHLVA-IEGLSYQEAAAVLGIPIGTLMSRIGRARA 153
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 18-149 5.63e-03

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 35.62  E-value: 5.63e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1879190669  18 RFAIKLLGNAHDADDILQET----YIKLSSRELSDGDRGLVVRTLTTLaIDHIRTRNVHDAGGKAASDEVFVEhiQPERI 93
Cdd:PRK09644   16 RYLFSLTKSHHAAEDLLQETfyraYIYLEDYDNQKVKPWLFKVAYHTF-IDFVRKEKKVSFVGTDEIEAIQAE--STEEY 92

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1879190669  94 VSSKHDLAVLLDAINHLPRRRAKIFLLARVDGMAYGQIAQTLHVSLSTVEKEMAAA 149
Cdd:PRK09644   93 VVAKNSYEKLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRG 148
PRK08241 PRK08241
RNA polymerase subunit sigma-70;
5-40 7.41e-03

RNA polymerase subunit sigma-70;


Pssm-ID: 236196 [Multi-domain]  Cd Length: 339  Bit Score: 35.68  E-value: 7.41e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1879190669   5 FERFFVRERSRLKRFAIKLLGNAHDADDILQETYIK 40
Cdd:PRK08241   21 FAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLR 56
 
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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