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Conserved domains on  [gi|1756728420|gb|QFG27167|]
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RNA polymerase sigma factor [Actinomadura sp. WMMB 499]

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]; ...
 13-184 6.16e-34

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: 119.33  E-value: 6.16e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  13 LRAAQDGDEASFRLLYRDTQPRLIRFAAALVG--ADAEDVTSEAWLQIARDLPGFRGDlDGFRGWTATITRHRALDQLRR 90
Cdd:COG1595     8 LERLRAGDEAAFEELYERYRPRLYRYARRLLGdrADAEDLVQETFLRLWRKLDSFRGR-GSFRAWLYRIARNLAIDHLRK 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  91 TARRPAAgLPDEVFTALASGGDTEADALDGIATRDALRLIAELPPDQAEAVLLRVVVGLDAKRAGKVVGKRPGAVRTAAH 170
Cdd:COG1595    87 RRRRREL-LDELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLS 165

                         170
                  ....*....|....
gi 1756728420 171 RGLRRLADRLAADG 184
Cdd:COG1595   166 RARKKLREALEEEG 179
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 13-184 6.16e-34

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: 119.33  E-value: 6.16e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  13 LRAAQDGDEASFRLLYRDTQPRLIRFAAALVG--ADAEDVTSEAWLQIARDLPGFRGDlDGFRGWTATITRHRALDQLRR 90
Cdd:COG1595     8 LERLRAGDEAAFEELYERYRPRLYRYARRLLGdrADAEDLVQETFLRLWRKLDSFRGR-GSFRAWLYRIARNLAIDHLRK 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  91 TARRPAAgLPDEVFTALASGGDTEADALDGIATRDALRLIAELPPDQAEAVLLRVVVGLDAKRAGKVVGKRPGAVRTAAH 170
Cdd:COG1595    87 RRRRREL-LDELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLS 165

                         170
                  ....*....|....
gi 1756728420 171 RGLRRLADRLAADG 184
Cdd:COG1595   166 RARKKLREALEEEG 179
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 22-180 1.24e-22

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: 89.33  E-value: 1.24e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  22 ASFRLLYRDTQPRLIRFAAALVG--ADAEDVTSEAWLQIARDLPGFRGDlDGFRGWTATITRHRALDQLRRTARRPAagL 99
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGddADAEDLVQEAFLKLLEALDRFDPE-GSFKAWLFRIARNLILDYLRRKRRLRR--E 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420 100 PDEVFTALASGGDTEADALDGIATRDALRLIAELPPDQAEAVLLRVVVGLDAKRAGKVVGKRPGAVRTAAHRGLRRLADR 179
Cdd:TIGR02937  78 LDLLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLREL 157


                  .
gi 1756728420 180 L 180
Cdd:TIGR02937 158 L 158
PRK09648 PRK09648
RNA polymerase sigma factor ShbA;
6-182 2.87e-19

RNA polymerase sigma factor ShbA;


Pssm-ID: 236607 [Multi-domain]  Cd Length: 189  Bit Score: 81.55  E-value: 2.87e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420   6 DAELSRALRAAQDGDEASFRLLYRDTQPRLIRFAAALVGA------DAEDVTSEAWLQIARDLPGFRGDLDGFRGWTATI 79
Cdd:PRK09648    8 GEELDALVAEAVAGDRRALREVLEIIRPLVVRYCRARLGGverpglSADDVAQEVCLAVITALPRYRDQGRPFLAFVYGI 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  80 TRHRALDQLRRTARR---PAAGLPDEvftalASGGDT-EADALDGIATRDALRLIAELPPDQAEAVLLRVVVGLDAKRAG 155
Cdd:PRK09648   88 AAHKVADAHRAAGRDkavPTEEVPER-----PSDDAGpEERALRSESSNRMRELLDTLPEKQREILILRVVVGLSAEETA 162

                         170       180
                  ....*....|....*....|....*..
gi 1756728420 156 KVVGKRPGAVRTAAHRGLRRLADRLAA 182
Cdd:PRK09648  163 EAVGSTPGAVRVAQHRALARLRAEIEA 189
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 27-94 2.24e-09

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: 51.82  E-value: 2.24e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1756728420  27 LYRDTQPRLIRFAAALVG--ADAEDVTSEAWLQIARDLPGFRGDLDG-FRGWTATITRHRALDQLRRTARR 94
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGdgADAEDLVQEGFLGLWRAIERFDPERGVsFSTWLYTIIRNAIIDYLRKQRRT 71
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 127-176 8.73e-05

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: 39.01  E-value: 8.73e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1756728420 127 LRLIAELPPDQAEAVLLRVVVGLDAKRAGKVVGKRPGAVRTAAHRGLRRL 176
Cdd:cd06171     5 EEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 13-184 6.16e-34

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: 119.33  E-value: 6.16e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  13 LRAAQDGDEASFRLLYRDTQPRLIRFAAALVG--ADAEDVTSEAWLQIARDLPGFRGDlDGFRGWTATITRHRALDQLRR 90
Cdd:COG1595     8 LERLRAGDEAAFEELYERYRPRLYRYARRLLGdrADAEDLVQETFLRLWRKLDSFRGR-GSFRAWLYRIARNLAIDHLRK 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  91 TARRPAAgLPDEVFTALASGGDTEADALDGIATRDALRLIAELPPDQAEAVLLRVVVGLDAKRAGKVVGKRPGAVRTAAH 170
Cdd:COG1595    87 RRRRREL-LDELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLS 165

                         170
                  ....*....|....
gi 1756728420 171 RGLRRLADRLAADG 184
Cdd:COG1595   166 RARKKLREALEEEG 179
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 22-180 1.24e-22

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: 89.33  E-value: 1.24e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  22 ASFRLLYRDTQPRLIRFAAALVG--ADAEDVTSEAWLQIARDLPGFRGDlDGFRGWTATITRHRALDQLRRTARRPAagL 99
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGddADAEDLVQEAFLKLLEALDRFDPE-GSFKAWLFRIARNLILDYLRRKRRLRR--E 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420 100 PDEVFTALASGGDTEADALDGIATRDALRLIAELPPDQAEAVLLRVVVGLDAKRAGKVVGKRPGAVRTAAHRGLRRLADR 179
Cdd:TIGR02937  78 LDLLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLREL 157


                  .
gi 1756728420 180 L 180
Cdd:TIGR02937 158 L 158
PRK09648 PRK09648
RNA polymerase sigma factor ShbA;
6-182 2.87e-19

RNA polymerase sigma factor ShbA;


Pssm-ID: 236607 [Multi-domain]  Cd Length: 189  Bit Score: 81.55  E-value: 2.87e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420   6 DAELSRALRAAQDGDEASFRLLYRDTQPRLIRFAAALVGA------DAEDVTSEAWLQIARDLPGFRGDLDGFRGWTATI 79
Cdd:PRK09648    8 GEELDALVAEAVAGDRRALREVLEIIRPLVVRYCRARLGGverpglSADDVAQEVCLAVITALPRYRDQGRPFLAFVYGI 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  80 TRHRALDQLRRTARR---PAAGLPDEvftalASGGDT-EADALDGIATRDALRLIAELPPDQAEAVLLRVVVGLDAKRAG 155
Cdd:PRK09648   88 AAHKVADAHRAAGRDkavPTEEVPER-----PSDDAGpEERALRSESSNRMRELLDTLPEKQREILILRVVVGLSAEETA 162

                         170       180
                  ....*....|....*....|....*..
gi 1756728420 156 KVVGKRPGAVRTAAHRGLRRLADRLAA 182
Cdd:PRK09648  163 EAVGSTPGAVRVAQHRALARLRAEIEA 189
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 13-181 7.76e-18

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 77.54  E-value: 7.76e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  13 LRAAQDGDEASFRLLYRDTQPRLIRFAAALVG--ADAEDVTSEAWLQIARDLPGFRGDLdGFRGWTATITRHRALDQLRR 90
Cdd:PRK09652    1 VERVQRGDRAAFALLVRRYQPRVKRLLSRLTRdpADAEDLVQETFIKAYRALHSFRGGA-AFYTWLYRIARNTAINYLRK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  91 TARRPAAGLPD-------EVFTALASGGDTEADALDGIATRDALRLIAELPPDQAEAVLLRVVVGLDAKRAGKVVGKRPG 163
Cdd:PRK09652   80 QGRRPPASDVDaeeaedfDLADALRDISTPENELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIG 159

                         170
                  ....*....|....*...
gi 1756728420 164 AVRTAAHRGLRRLADRLA 181
Cdd:PRK09652  160 TVRSRIFRAREALRAKLQ 177
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 10-183 3.04e-16

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 73.08  E-value: 3.04e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  10 SRALRAAQDGDEASFRLLYRDTQPRLIRFAAALVG--ADAEDVTSEAWLQIARDLPGFRGDLDGfRGWTATITRHRALDQ 87
Cdd:PRK11924    1 GQLMPVDATGDKEAFSELFRPHAPDLLRYARRQLGdrALAEDAVQEAFLRAWRKADLFNGKGSA-RTWLLTIARNVCYDL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  88 LRRTARRPAAGLPDEVFTALASGGDT-EADALDGIATRDALRLIAELPPDQAEAVLLRVVVGLDAKRAGKVVGKRPGAVR 166
Cdd:PRK11924   80 LRRRRREKAVLSDDALEPEFAETAETpEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVK 159

                         170
                  ....*....|....*..
gi 1756728420 167 TAAHRGLRRLADRLAAD 183
Cdd:PRK11924  160 SRLRRARQLLRECLEAQ 176
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 1-183 1.43e-14

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 69.61  E-value: 1.43e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420   1 MPHERDAELSRALRAaqdGDEASFRLLYRDTQPRLIRFAAALV--GADAEDVTSEAWLQIARDLPGFRGDlDGFRGWTAT 78
Cdd:PRK11922   12 LSAASDRELVARVLA---GDEAAFEALMRRHNRRLYRTARAILrnDAEAEDVVQEAYLRAFRALGTFRGD-ASLSTWLSR 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  79 ITRHRALDQLRRTARRPAAgLPDEVFTALASGGDTEADALD-----GIATRDALRL----IAELPPDQAEAVLLRVVVGL 149
Cdd:PRK11922   88 IVLNEALGRLRRRRRLVNL-AEMVMASTIAGGERTPLADPAedperAAARREIRALleraIDALPDAFRAVFVLRVVEEL 166

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1756728420 150 DAKRAGKVVGKRPGAVRTAAHRGLRRLADRLAAD 183
Cdd:PRK11922  167 SVEETAQALGLPEETVKTRLHRARRLLRESLARE 200
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 13-184 1.67e-14

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 68.60  E-value: 1.67e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  13 LRAAQDGDEASFRLLYRDTQPRLIRFAAALVG--ADAEDVTSEAWLQIARDLPGFRGDlDGFRGWTATITRHRALDQLRR 90
Cdd:PRK12515   13 LARIAQGDRTAMQTLYGRHHVRVYRFGLRLVRdeQTAEDLVSEVFLDVWRQAGQFEGR-SQVSTWLLSIARFKALSALRR 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  91 tarRPAAGLPDEVFTALASGGDTEADALDGIATRDALR-LIAELPPDQAEAVLLRVVVGLDAKRAGKVVGKRPGAVRTAA 169
Cdd:PRK12515   92 ---RKHEEIDDEAAAAIEDGADTPEVALQKSDTSAALRaCLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKTRM 168

                         170
                  ....*....|....*
gi 1756728420 170 HRGLRRLADRLAADG 184
Cdd:PRK12515  169 FYARKKLAELLKAAG 183
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 13-187 2.19e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 65.87  E-value: 2.19e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  13 LRAAQDGDEASFRLLYRDTQPRLIRFAAALVG--ADAEDVTSEAWLQIARDLPGFRGDLdGFRGWTATITRHRALDQLRR 90
Cdd:PRK12513   17 MLRYRAGDAAAFEALYARHRTGLYRFLLRLARdrALAEDIFQETWLRVIRARAQYQPRA-RFRTWLYQIARNLLIDHWRR 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  91 TARRPAAGL-PDEVFTALASGGDTEADALDGIATRDALRL-IAELPPDQAEAVLLRVVVGLDAKRAGKVVGKRPGAVRTA 168
Cdd:PRK12513   96 HGARQAPSLdADEQLHALADDGAAPEQQLSLFRDRRRLQAaLETLPDEQREVFLLREHGDLELEEIAELTGVPEETVKSR 175

                         170
                  ....*....|....*....
gi 1756728420 169 AHRGLRRLADRLAADGHAA 187
Cdd:PRK12513  176 LRYALQKLRELLAEEVAVA 194
PRK12512 PRK12512
RNA polymerase sigma factor; Provisional
 4-180 1.49e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 171551 [Multi-domain]  Cd Length: 184  Bit Score: 63.18  E-value: 1.49e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420   4 ERDAELSRALRAAQDGDEASFRLLYRDTQPRLIRFA------AALVGADAEDVTSEAWLQIarDLPGFRGDLDG-FRGWT 76
Cdd:PRK12512    4 GREDEWTDLMRSANAGDAAAYRRLLKAVTPVLRAAArrglarAGQPADQAEDIVQEILLAV--HLKRHTWDPGApFAPWL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  77 ATITRHRALDQLRRTARRPAAGLpDEVFTALASggdteADALDGIATRDALRLIAELPPDQAEAVLLRVVVGLDAKRAGK 156
Cdd:PRK12512   82 FAIARNKLIDALRRRGRRVFVDI-DDFAETLPA-----EPATETLPAGDVGRHLETLPPRQRDVVQSISVEGASIKETAA 155

                         170       180
                  ....*....|....*....|....
gi 1756728420 157 VVGKRPGAVRTAAHRGLRRLADRL 180
Cdd:PRK12512  156 KLSMSEGAVRVALHRGLAALAAKF 179
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 1-184 2.48e-11

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 60.05  E-value: 2.48e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420   1 MPHERDAELsraLRAAQDGDEASFRLLYRDTQPRLIRFAAALVG--ADAEDVTSEAWLQIARDLPGFRGDLDGFRGWTAT 78
Cdd:PRK05602    2 MDADPDEEL---LARVAAGDPAAFRVLVARKLPRLLALATRMLGdpAEAEDVAQETFLRIWKQAPSWRPGEARFDTWLHR 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  79 ITRHRALDQLRRTARRPAAGLPDEVftalasggDTEADALDGIATRDALRLI----AELPPDQAEAVLLRVVVGLDAKRA 154
Cdd:PRK05602   79 VVLNLCYDRLRRRREVPVEDAPDVP--------DPAPGPDAGLEARQRARRVeqalAALPERQREAIVLQYYQGLSNIEA 150

                         170       180       190
                  ....*....|....*....|....*....|
gi 1756728420 155 GKVVGKRPGAVRTAAHRGLRRLADRLAADG 184
Cdd:PRK05602  151 AAVMDISVDALESLLARGRRALRAQLADLP 180
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 23-143 8.26e-11

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: 57.96  E-value: 8.26e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  23 SFRLLYRDTQPRLIRFAAALVG--ADAEDVTSEA--WLQIARDlpgFRGDLDGFRGWTATITRHRALDQLRRTARRpaag 98
Cdd:TIGR02985   2 AFEQLYRRYYPKLCAFARRYVKdeEDAEDIVQDVflKLWENRE---TLEISESIKAYLFTIVKNRCLNYLRHKQVE---- 74

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1756728420  99 lpDEVFTALASGGDTE---ADALDGIATRDALRLIAE----LPPDQAEAVLL 143
Cdd:TIGR02985  75 --EKYQEELAEIEERElseADPEEELEAKELEEIIEEaiekLPEQCREIFIL 124
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 1-196 4.13e-10

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 57.10  E-value: 4.13e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420   1 MPHERDAELSRALRAAQDGDEA---SFRLLYRDTQPRLIRFAAALVG--ADAEDVTSEAWLQIARDLPGFRGDLdgFRGW 75
Cdd:PRK09647    4 DWVEPSDELTGTAVFDATGDKAtmpSWEELVRQHADRVYRLAYRLSGnqHDAEDLTQETFIRVFRSLQNYQPGT--FEGW 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  76 TATITRHRALDQLRRTARRPAAGLPDEVFTALASGGDTEADALDGIATRDALRLIAELPPDQAEAVLLRVVVGLDAKRAG 155
Cdd:PRK09647   82 LHRITTNLFLDMVRRRARIRMEALPEDYDRVPGDEPNPEQIYHDARLDPDLQAALDSLPPEFRAAVVLCDIEGLSYEEIA 161

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1756728420 156 KVVGKRPGAVRTAAHRGLRRLADRLAadgHAAPRPGVRPLL 196
Cdd:PRK09647  162 ATLGVKLGTVRSRIHRGRQQLRAALA---AHAPHAECAALL 199
PRK12534 PRK12534
RNA polymerase sigma factor; Provisional
 1-176 4.75e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 183576 [Multi-domain]  Cd Length: 187  Bit Score: 56.60  E-value: 4.75e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420   1 MPHERDAELSRALRAAQDGDEASFRLLYRDTQPRLIRFAAALVG--ADAEDVTSEAWLQIARDLPGFrgDLDGFRG--WT 76
Cdd:PRK12534    4 IPGHDDDETGRLLTATAGGDRHAFEALYRQTSPKLFGVCLRMIPqrAEAEEVLQDVFTLIWHKAGQF--DPSRARGltWL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  77 ATITRHRALDQLRRTARRPAAGLPDEVFTALASGGDTEADALDGIATRDALRLIAELPPDQAEAVLLRVVVGLDAKRAGK 156
Cdd:PRK12534   82 AMIARNKAIDHLRANAPQRRNVALDDAGELRAADASPLERTERASTRRRIDHCLAELEPPRSELIRTAFFEGITYEELAA 161

                         170       180
                  ....*....|....*....|
gi 1756728420 157 VVGKRPGAVRTAAHRGLRRL 176
Cdd:PRK12534  162 RTDTPIGTVKSWIRRGLAKL 181
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
14-189 6.97e-10

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 55.86  E-value: 6.97e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  14 RAAQDGDEASFRLLYRDTQPRLIRFAAALVG--ADAEDVTSEAWLQIARDLPGFRGDLDGFRGWTATITRHRALDQLRRT 91
Cdd:PRK09645    1 SGMATAEAALMRALYDEHAAPLWRYALRLTGdrARAEDVVQETLLRAWQHPEVLADTGRSARAWLFTVARNLVIDERRSA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  92 ARRPAAGLPDEVFTALASGGDTEADALDGIATRDALrliAELPPDQAEAVLLRVVVGLDAKRAGKVVGKRPGAVRTAAHR 171
Cdd:PRK09645   81 RARPVEGGDDVLGVPEQSAPDEVDRALDRLLVADAL---AQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHY 157

                         170
                  ....*....|....*...
gi 1756728420 172 GLRRLadRLAADGHAAPR 189
Cdd:PRK09645  158 ALRAL--RLALQERGVTR 173
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 19-183 9.80e-10

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 55.69  E-value: 9.80e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  19 GDEASFRLLYRDTQPRLIRFA--AALVGADAEDVTSEAWLQIARDLPGFRGDLDGFRGWTATITRHRALDQLRRTARRPA 96
Cdd:PRK13919   20 GEEEALRALFRRYAGAFLALArrMGLDGAAAEDVVQEVFIRVWKKAKEFDPRRGSARAWLLALAHHAAVDHVRRRAARPQ 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  97 AGLPD----EVFTALASGGDTEAdALDGIATRDALrliAELPPDQAEAVLLRVVVGLDAKRAGKVVGKRPGAVRTAAHRG 172
Cdd:PRK13919  100 PLEPDerepEAFDLPGPGLDEEG-HLDRTRLGRAL---KALSPEERRVIEVLYYQGYTHREAAQLLGLPLGTLKTRARRA 175

                         170
                  ....*....|.
gi 1756728420 173 LRRLADRLAAD 183
Cdd:PRK13919  176 LSRLKEVLREP 186
PRK09643 PRK09643
RNA polymerase sigma factor SigM; Reviewed
 6-181 1.86e-09

RNA polymerase sigma factor SigM; Reviewed


Pssm-ID: 236604 [Multi-domain]  Cd Length: 192  Bit Score: 55.10  E-value: 1.86e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420   6 DAELsraLRAAQDGDEASFRLLYRDTQPRLIRFAAALVGA--DAEDVTSEAWLQIARDLPGFRGDlDGFRGWTATITRHR 83
Cdd:PRK09643   14 DAEL---LAAHVAGDRYAFGELFRRHHRRLWAVARRTSGTreDAADALQDAMLSAHRAAGSFRGD-AAVSSWLHRIVVNA 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  84 ALDQLRRTARRPAAGLPDEVFTALASGGDTEADALdgiaTRDALRLIAELPPDQAEAVLLRVVVGLDAKRAGKVVGKRPG 163
Cdd:PRK09643   90 CLDRLRRAKARPTVPLDDVYPVAQLERDPTARVET----ALAVQRALMRLPVEQRAALVAVDMQGYSVADAARMLGVAEG 165

                         170
                  ....*....|....*...
gi 1756728420 164 AVRTAAHRGLRRLADRLA 181
Cdd:PRK09643  166 TVKSRCARGRARLAELLG 183
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 27-94 2.24e-09

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: 51.82  E-value: 2.24e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1756728420  27 LYRDTQPRLIRFAAALVG--ADAEDVTSEAWLQIARDLPGFRGDLDG-FRGWTATITRHRALDQLRRTARR 94
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGdgADAEDLVQEGFLGLWRAIERFDPERGVsFSTWLYTIIRNAIIDYLRKQRRT 71
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 1-176 3.07e-09

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 54.26  E-value: 3.07e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420   1 MPHErDAELsraLRAAQDGDEASFRLLYRDTQPRLIRFAAALVG--ADAEDVTSEAWLQIARDLPGFRGDLDgFRGWTAT 78
Cdd:PRK09638    1 MQMD-EKEL---IQKAKKGDDAALTTLFQQHYSFLYKYLLKLTLdpDLAEDLVQETMLKAIENLSSFQGRSK-FSTWLIS 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  79 ITRHRALDQLRRTARRPaagLPDEVFTALASGGDTEADALDGIATRDALRLIAELPPDQAEAVLLRVVVGLDAKRAGKVV 158
Cdd:PRK09638   76 IASRLYKDHLRKQKREK---LRLQRAKEETLRKEKWEAAIKGAEWSEMLDALSKLDPEFRAPVILKHYYGYTYEEIAKML 152

                         170
                  ....*....|....*...
gi 1756728420 159 GKRPGAVRTAAHRGLRRL 176
Cdd:PRK09638  153 NIPEGTVKSRVHHGIKQL 170
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 19-178 3.21e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 54.06  E-value: 3.21e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  19 GDEASFRLLYRDTQPRLIRFAAALVG--ADAEDVTSEAWLQIARDLPGFRGDLDGFRGWTATITRHRALDQLRrtARRPA 96
Cdd:PRK12514   16 GDRDAFSSLYDATSAKLFGICLRVLKdrSEAEEALQDVYVKIWTKADRFAVSGLSPMTWLITIARNHAIDRLR--ARKAV 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  97 AGLPDEVFTALASGGDTEADALDGIATRDALRLIAELPPDQAEAVLLRVVVGLDAKRAGKVVGKRPGAVRTAAHRGLRRL 176
Cdd:PRK12514   94 AVDIDEAHDLADPSPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMRTWLRRSLLKL 173


                  ..
gi 1756728420 177 AD 178
Cdd:PRK12514  174 RE 175
PRK09649 PRK09649
RNA polymerase sigma factor SigC; Reviewed
 15-183 6.45e-09

RNA polymerase sigma factor SigC; Reviewed


Pssm-ID: 137458 [Multi-domain]  Cd Length: 185  Bit Score: 53.51  E-value: 6.45e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  15 AAQDGDEASFRLLYRDTQPRLIRFAAALVGA-DAEDVTSEAWLQIARDLPGFRGDLDGfRGWTATITRHRALDQLRRTAR 93
Cdd:PRK09649   17 SAAKGNGRALEAFIKATQQDVWRFVAYLSDVgSADDLTQETFLRAIGAIPRFSARSSA-RTWLLAIARHVVADHIRHVRS 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  94 RPAAGLpdEVFTALASGGDTEADALDGIAtrDALRLIAELPPDQAEAVLLRVVVGLDAKRAGKVVGKRPGAVRTAAHRGl 173
Cdd:PRK09649   96 RPRTTR--GARPEHLIDGDRHARGFEDLV--EVTTMIADLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARA- 170

                         170
                  ....*....|
gi 1756728420 174 rrlADRLAAD 183
Cdd:PRK09649  171 ---RDALLAD 177
PRK12535 PRK12535
RNA polymerase sigma factor; Provisional
 12-184 7.48e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 237130 [Multi-domain]  Cd Length: 196  Bit Score: 53.36  E-value: 7.48e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  12 ALRAAQdGDEASFRLLYRDTQPRLIRFAAALVGAD-AEDVTSEAWLQIARDLPGFRGDLDGfRGWTATITRHRALDQLRR 90
Cdd:PRK12535   16 ALAAGR-GDRAALTEFIRETQDDVWRLLAHLGGHDiADDLTQETYLRVMSALPRFAARSSA-RTWLLSLARRVWVDNIRH 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  91 TARRP-AAGLPDEVFTALASGGDTEADALDGIATRDalrLIAELPPDQAEAVLLRVVVGLDAKRAGKVVGKRPGAVRTaa 169
Cdd:PRK12535   94 DMARPrKSATEYEDAAATTASNETTGSWSEWIDVRT---LIDALPPERREALILTQVLGYTYEEAAKIADVRVGTIRS-- 168

                         170
                  ....*....|....*
gi 1756728420 170 hRGLRRLADRLAADG 184
Cdd:PRK12535  169 -RVARARADLIAATA 182
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 18-181 3.82e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 51.43  E-value: 3.82e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  18 DGDEASFRLLYRDTQPRLIRFAAALVG--ADAEDVTSEAWLQIARDLPGFRGDLDGFRGWTATITRHRALDQLRRTARRP 95
Cdd:PRK12524   22 NGDPAAARALTLRLAPRALAVATRVLGdrAEAEDVTQEAMLRLWRIAPDWRQGEARVSTWLYRVVCNLCTDRLRRRRRAS 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  96 AAGLPDEVFTALASGGdteADALDGIATRDALRL-IAELPPDQAEAVLLRVVVGLDAKRAGKVVGKRPGAVRTAAHRGLR 174
Cdd:PRK12524  102 VDLDDAPEPADAAPGA---EEALIEGDRMRALDAaLAALPERQRQAVVLRHIEGLSNPEIAEVMEIGVEAVESLTARGKR 178


                  ....*..
gi 1756728420 175 RLADRLA 181
Cdd:PRK12524  179 ALAALLA 185
algU PRK11923
RNA polymerase sigma factor AlgU; Provisional
 16-171 6.30e-08

RNA polymerase sigma factor AlgU; Provisional


Pssm-ID: 171347 [Multi-domain]  Cd Length: 193  Bit Score: 50.57  E-value: 6.30e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  16 AQDGDEASFRLLYRDTQPRLIRFAAALV--GADAEDVTSEAWLQIARDLPGFRGDlDGFRGWTATITRHRALDQLRRTAR 93
Cdd:PRK11923   14 VQRGDKRAFDLLVLKYQHKILGLIVRFVhdTAEAQDVAQEAFIKAYRALGNFRGD-SAFYTWLYRIAINTAKNHLVSRGR 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  94 RPAAGLPDEVFTALASGGDT--EADALDGIATRDAL-----RLIAELPPDQAEAVLLRVVVGLDAKRAGKVVGKRPGAVR 166
Cdd:PRK11923   93 RPPDSDVSSEDAEFYDGDHAlkDIESPERALLRDEIegtvhRTIQQLPEDLRTALTLREFDGLSYEDIASVMQCPVGTVR 172


                  ....*
gi 1756728420 167 TAAHR 171
Cdd:PRK11923  173 SRIFR 177
PRK12539 PRK12539
RNA polymerase sigma factor SigF;
8-177 8.49e-08

RNA polymerase sigma factor SigF;


Pssm-ID: 237132 [Multi-domain]  Cd Length: 184  Bit Score: 50.11  E-value: 8.49e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420   8 ELSRALRAAQDGDEASFRLLYRDTQPRLI-----RFAAALVGAD-AEDVTSEAWLQIARDlpgfRGDLDG---FRGWTAT 78
Cdd:PRK12539    7 ELKALMLASLDGDAAAHRALLERLSGHLRayykgKLARIGRGAEeAEDLVQEALMAIHTR----RHTYDPeqpLTPWVYA 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  79 ITRHRALDQLRRTaRRPAAGLP-DEVFTALASGGDTEADAldgiaTRDALRLIAELPPDQAEAVLLRVVVGLDAKRAGKV 157
Cdd:PRK12539   83 IARYKLIDHLRRT-RASLADVPiDDADELVAHDDHAAVES-----TLDLGRLLARLPEKMRLAIQAVKLEGLSVAEAATR 156

                         170       180
                  ....*....|....*....|
gi 1756728420 158 VGKRPGAVRTAAHRGLRRLA 177
Cdd:PRK12539  157 SGMSESAVKVSVHRGLKALA 176
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 127-176 8.59e-08

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: 47.07  E-value: 8.59e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1756728420 127 LRLIAELPPDQAEAVLLRVVVGLDAKRAGKVVGKRPGAVRTAAHRGLRRL 176
Cdd:pfam08281   5 LRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 6-180 9.28e-08

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 50.08  E-value: 9.28e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420   6 DAELSRALRAAQDGDEASFRL---LYRDtqpRLIRFAAALVG--ADAEDVTSEAWLQIARDLPGFRGDLDgFRGWTATIT 80
Cdd:PRK09641    2 DLLIKRLIKQVKKGDQNAFAElvdLYKD---KIYQLCYRMLGnrHEAEDAAQEAFIRAYVNIDSYDINRK-FSTWLYRIA 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  81 RHRALDQLRRtaRRPAAGLPDEV--------FTALASGGDTEADALDGIATRDAL-RLIAELPPDQAEAVLLRVVVGLDA 151
Cdd:PRK09641   78 TNLTIDRLRK--RKPDYYLDAEVagtegltmYSQLAADDALPEEQVVSLELQETIqEAILQLPEKYRTVIVLKYIEDLSL 155

                         170       180
                  ....*....|....*....|....*....
gi 1756728420 152 KRAGKVVGKRPGAVRTAAHRGLRRLADRL 180
Cdd:PRK09641  156 KEISEILDLPVGTVKTRIHRGREALRKQL 184
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 1-183 1.12e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 50.06  E-value: 1.12e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420   1 MPHERDAELSRALRAaqdGDEASFRLLYRDTQPRLIRFAAALVG--ADAEDVTSEAWLQIARDlPGFRGDLDGFRGWTAT 78
Cdd:PRK12519   11 LSSRSDAELFSALKA---GQSAALGVLYDRHAGLVYGLALKILGnsQEAEDLTQEIFLSLWRK-SSYDPKRGSLSSYLLT 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  79 ITRHRALDQLRrtARRPAAGLPDEVFTALASG--GDTEADALDGIATRDALR-LIAELPPDQAEAVLLRVVVGLDAKRAG 155
Cdd:PRK12519   87 LTRSRAIDRLR--SRRSRQRLLERWQQELLGEasEDTPLEQASLAERSQRVQtALAQLPESQRQVLELAYYEGLSQSEIA 164

                         170       180
                  ....*....|....*....|....*...
gi 1756728420 156 KVVGKRPGAVRTAAHRGLRRLADRLAAD 183
Cdd:PRK12519  165 KRLGIPLGTVKARARQGLLKLRELLQDL 192
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 16-97 1.44e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 49.33  E-value: 1.44e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  16 AQDGDEASFRLLYRDTQPRLIRFAAALVGADA-EDVTSEAWLQIARDLPGFRGDlDGFRGWTATITRHRALDQLRRTARR 94
Cdd:PRK12518    5 CQRGDRQSFRQLYRRYQQKVRSTLYQLCGRELlDDLVQEVFLRVWKGLPKLRNP-AYFSTWLYRITWNVATDARRQFAQR 83


                  ...
gi 1756728420  95 PAA 97
Cdd:PRK12518   84 PSR 86
PRK12536 PRK12536
RNA polymerase sigma factor; Provisional
 3-180 1.66e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 237131 [Multi-domain]  Cd Length: 181  Bit Score: 49.28  E-value: 1.66e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420   3 HERDAELSRALRAAQDGDEASFRLLYRDTQPRL---IRFAAALVGADAEDVTSEAWLQIARDLPGFRGDlDGFRGWTATI 79
Cdd:PRK12536    2 SAAEARLRALLLRGLAGDAAAYRQFLSELAAHLrgfLRRRLPQLPDEVEDLVQEILLAVHNARHTYRAD-QPLTAWVHAI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  80 TRHRALDQLRRTARRPAAGLP-DEVFTALASGGDTEADAldgiaTRDALRLIAELPPDQAEAVLLRVVVGLDAKRAGKVV 158
Cdd:PRK12536   81 ARYKLMDFLRSRARREALHDPlDDESELFATSDDEAAEA-----RRDLGKLLEQLPDRQRLPIVHVKLEGLSVAETAQLT 155

                         170       180
                  ....*....|....*....|..
gi 1756728420 159 GKRPGAVRTAAHRGLRRLADRL 180
Cdd:PRK12536  156 GLSESAVKVGIHRGLKALAAKI 177
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 20-186 2.08e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 49.19  E-value: 2.08e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  20 DEASFRLLYRDTQPRLIRFAAALVG----AD--AEDVTSEAWLQIARDLPGfrgdlDGFRGWTATITRHRALDQLRRTAR 93
Cdd:PRK12516    8 GTPPFKRELLAALPSLRAFAVSLIGrhdrADdlVQDTIMKAWAKQDHFEVG-----TNMKAWLFTILRNEFYSQMRKRGR 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  94 RPAAglPDEVFTALASGGDTEADALDgiaTRDALRLIAELPPDQAEAVLLRVVVGLDAKRAGKVVGKRPGAVRTAAHRGL 173
Cdd:PRK12516   83 EVQD--TDGMFTEQLAVHPSQYGTLD---LQDFRAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRAR 157

                         170
                  ....*....|...
gi 1756728420 174 RRLADRLAADGHA 186
Cdd:PRK12516  158 QRLQEILQIEGEA 170
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 11-93 2.77e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 48.62  E-value: 2.77e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  11 RALRAAQDGDEASFRLLYRDTQPRLIRFAAALV--GADAEDVTSEAWLQIARDLPGFRGDLDGFRGWTATITRHRALDQL 88
Cdd:PRK12537   12 ACLLACARGDRRALQALYQQESARLLGVARRIVrdRALAEDIVHDAFIKIWTGAASFDPARGSARGWIYSVTRHLALNVL 91


                  ....*
gi 1756728420  89 RRTAR 93
Cdd:PRK12537   92 RDTRR 96
sigI PRK09635
RNA polymerase sigma factor SigI; Provisional
 28-187 6.21e-07

RNA polymerase sigma factor SigI; Provisional


Pssm-ID: 182008 [Multi-domain]  Cd Length: 290  Bit Score: 48.81  E-value: 6.21e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  28 YRDTQPRLIRFAAALVG--ADAEDVTSEAWLQIARdlpGFRGDLDGFRGWTATITRHRALDQLRR-TARRPAAGLPDEVF 104
Cdd:PRK09635   11 WRAHRAYLVDLAFRMVGdiGVAEDMVQEAFSRLLR---APVGDIDDERGWLIVVTSRLCLDHIKSaSTRRERPQDIAAWH 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420 105 TALASGGDTeaDALDGIATRDALRL-----IAELPPDQAEAVLLRVVVGLDAKRAGKVVGKRPGAVRTAAHRGLRRL-AD 178
Cdd:PRK09635   88 DGDASVSSV--DPADRVTLDDEVRLallimLERLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQLAHRARRKInES 165


                  ....*....
gi 1756728420 179 RLAADGHAA 187
Cdd:PRK09635  166 RIAASVEPA 174
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 20-181 9.34e-07

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 47.24  E-value: 9.34e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  20 DEASFRLLYRDTQPRLIRFAAALVG--ADAEDVTSEAWLQIARDLPGFRGDLDgFRGWTATITRHRALDQLRRTaRRPAA 97
Cdd:PRK09640   24 VTRAYEELMRRYQRTLFNVCARYLGndRDADDVCQEVMLKVLYGLKNFEGKSK-FKTWLYSITYNECITQYRKE-RRKRR 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  98 GLPDEVFTALASGGDTEADALDgiaTRDAL-RLIAELPPDQAEAVLLRVVVGLDAKRAGKVVGKRPGAVRTAAHRGLRRL 176
Cdd:PRK09640  102 LMDALSLDPLEEASEEKAPKPE---ERGGLdRWLVHVNPIDREILVLRFVAELEFQEIADIMHMGLSATKMRYKRALDKL 178


                  ....*
gi 1756728420 177 ADRLA 181
Cdd:PRK09640  179 REKFA 183
PRK09636 PRK09636
RNA polymerase sigma factor SigJ; Provisional
 32-178 1.13e-06

RNA polymerase sigma factor SigJ; Provisional


Pssm-ID: 236600 [Multi-domain]  Cd Length: 293  Bit Score: 47.99  E-value: 1.13e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  32 QPRLIRFAAALVG--ADAEDVTSEAWLQIARdlpGFRGDLDGFRGWTATITRHRALDQLRRTARR----PAAGLPDEVFT 105
Cdd:PRK09636   14 RPHLLSVAYRMLGsvADAEDIVQEAWLRWNN---ADRAQIRDPRAWLTRVVTRLCLDRLRSARHRretyVGPWLPEPVVE 90

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1756728420 106 ALASGGDTEADALDgiATRDALRLIAELPPDQAEAVLLRVVVGLDAKRAGKVVGKRPGAVRTAAHRGLRRLAD 178
Cdd:PRK09636   91 ELDDPLEAVVAAED--LSLALMLALERLSPLERAAFLLHDVFGVPFDEIASTLGRSPAACRQLASRARKHVRA 161
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 23-179 4.28e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 42.23  E-value: 4.28e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  23 SFRLLYRDTQPRLIRFAAALVGAD--AEDVTSEAWLQIARDLPGFRGDldGFRGWTATITRHRALDQLRRTARRPAAGLP 100
Cdd:PRK12541    6 SLEEIYSEHMQDLFRYLLSLTGDShfAEDLMQETFYRMLVHIDYYKGE--EIRPWLFTIAYNAFIDWYRKEKKYKTTTIE 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1756728420 101 DEVFTALASggdTEADALDGIATRDALRLIAELPPDQAEAVLLRVVVGLDAKRAGKVVGKRPGAVRTAAHRGLRRLADR 179
Cdd:PRK12541   84 EFHLPNVPS---TEHEYFIKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKETKSI 159
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 127-176 8.73e-05

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: 39.01  E-value: 8.73e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1756728420 127 LRLIAELPPDQAEAVLLRVVVGLDAKRAGKVVGKRPGAVRTAAHRGLRRL 176
Cdd:cd06171     5 EEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54
PRK12533 PRK12533
RNA polymerase sigma factor; Provisional
 44-205 9.84e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 237129 [Multi-domain]  Cd Length: 216  Bit Score: 41.64  E-value: 9.84e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  44 GADAEDVTSEAWLQIARDLPGFRGdlDGFRGWTATITRHRALDQLRRTARRPAAGLPDEVFTALA------SGGDTEADA 117
Cdd:PRK12533   42 ASDADDVVQEACMRALRFFDSFRG--DNARPWLLAIVRHTWYSEWRRRANAHEVAAPDTLDDADSlddwqpAGEDPLALL 119

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420 118 LDGIATRDALRLIAELPPDQAEAVLLRVVVGLDAKRAGKVVGKRPGAVRTAAHRGLRRLADRLAADGHAAPRPGVRPLLQ 197
Cdd:PRK12533  120 LRAEDVRLVNAALAKLPVEYREVLVLRELEDMSYREIAAIADVPVGTVMSRLARARRRLAALLGGASAAQAAPGERAAGR 199


                  ....*...
gi 1756728420 198 GDRTGGSG 205
Cdd:PRK12533  200 PRRAPAAG 207
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 20-176 2.85e-04

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 39.93  E-value: 2.85e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  20 DEASFRLLYRDTQPRLIRFAAALVGAD--AEDVTSEAWLQIARDLPGFRGDLdgfRGWTATITRHRALDQLRRTARRPAA 97
Cdd:PRK09639    1 SDETFEDLFEQYYPDVVQQIFYIVKDRtqAEDLAQEVFLRLYRSDFKGIENE---KGWLIKSARNVAYNYLRSEKRRRAR 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1756728420  98 GLPDEVFTALASGGDTEADALDGIATRDALRLIAELPPDQAEAVLLRvVVGLDAKRAGKVVGKRPGAVRTAAHRGLRRL 176
Cdd:PRK09639   78 ILGEFQWQEVDNEPSPEEIWIRKEEITKVQEVLAKMTERDRTVLLLR-FSGYSYKEIAEALGIKESSVGTTLARAKKKF 155
PRK09047 PRK09047
RNA polymerase factor sigma-70; Validated
 78-184 5.65e-04

RNA polymerase factor sigma-70; Validated


Pssm-ID: 236367 [Multi-domain]  Cd Length: 161  Bit Score: 39.18  E-value: 5.65e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  78 TITRHRALDQLRRTARR------------PAAGLPDEVFTALASGGDTEADALDGIATRDALRLI----AELPPDQAEAV 141
Cdd:PRK09047   36 RILQNRIHDWFRRQKVRntwvslfssfsdDDDDDDFDPLETLDSADEGAESPADKLERAQVLQLIeeaiQKLPARQREAF 115

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1756728420 142 LLRVVVGLDAKRAGKVVGKRPGAVRTAAHRGLRRLADRLAADG 184
Cdd:PRK09047  116 LLRYWEDMDVAETAAAMGCSEGSVKTHCSRATHALAKALEAKG 158
PRK12547 PRK12547
RNA polymerase sigma factor; Provisional
 33-184 6.15e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 139056 [Multi-domain]  Cd Length: 164  Bit Score: 39.09  E-value: 6.15e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  33 PRLIRFAAALVG-AD-AEDVTSE----AWLQIARDLPGfrgdlDGFRGWTATITRHRALDQLRRTARRPAAGlpDEVFTA 106
Cdd:PRK12547   17 PALRAFAVSLSSkHDkAEDLVQDtlmkAWAKQDSFEMG-----TNLKAWLFTILRNEFYSQMRKRGREVQDS--DGVFTA 89

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1756728420 107 LASGGDTEADALDgiaTRDALRLIAELPPDQAEAVLLRVVVGLDAKRAGKVVGKRPGAVRTAAHRGLRRLADRLAADG 184
Cdd:PRK12547   90 RVAVHPAQYGSLD---LQDFKKALNLLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARNRLQELLKVDG 164
PRK09646 PRK09646
ECF RNA polymerase sigma factor SigK;
7-180 8.31e-04

ECF RNA polymerase sigma factor SigK;


Pssm-ID: 182015 [Multi-domain]  Cd Length: 194  Bit Score: 38.88  E-value: 8.31e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420   7 AELSRALRAAQDGDEASFRLLYRDTQPRLIRFAAALV--GADAEDVTSEAWLQIARDLPGFRGDLDGFRGWTATITRHRA 84
Cdd:PRK09646   15 PDLDALLRRVARGDQDAFAELYDRTSSRVYGLVRRVLrdPGYSEETTQEVYLEVWRTASRFDPARGSALAWLLTLAHRRA 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  85 LDQLR----------RTARRPAAGLPDEVFTALASGGDTEadaldgiATRDALRLIAELppdQAEAVLLRVVVGLDAKRA 154
Cdd:PRK09646   95 VDRVRseqaasqrevRYGARNVDPAFDQVAEEVEARLERE-------RVRDCLDALTDT---QRESVTLAYYGGLTYREV 164

                         170       180
                  ....*....|....*....|....*.
gi 1756728420 155 GKVVGKRPGAVRTAAHRGLRRLADRL 180
Cdd:PRK09646  165 AERLAVPLGTVKTRMRDGLIRLRDCL 190
PRK09642 PRK09642
RNA polymerase sigma factor;
46-142 8.74e-04

RNA polymerase sigma factor;


Pssm-ID: 170031 [Multi-domain]  Cd Length: 160  Bit Score: 38.54  E-value: 8.74e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  46 DAEDVTSEAWLQIARDLPGFRgdLDGFRGWTATITRHRALDQLRRTARRPAA-GLPDEVFTALASGGDTEADALdgiaTR 124
Cdd:PRK09642   21 DAKDVTQEVFVKIHASLPNYQ--FRGLKTWMARIATNHAIDYKRKKARENEElSLCKETEENIKSSHNIEDLLL----TK 94

                          90       100
                  ....*....|....*....|..
gi 1756728420 125 DALRLIA----ELPPDQAEAVL 142
Cdd:PRK09642   95 EQKLLIAqklrELPENYRDVVL 116
PRK12540 PRK12540
RNA polymerase sigma factor; Provisional
 33-200 1.60e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183579 [Multi-domain]  Cd Length: 182  Bit Score: 38.02  E-value: 1.60e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  33 PRLIRFAAALVGAD--AEDVTSEAWLQIARDLPGFRGDLDgFRGWTATITRHRALDQLRRtaRRPAAGLPDEVFTALASG 110
Cdd:PRK12540   16 PSLRAFAISLSGNGdrADDLVQETLLRALANIDSFQPGSN-LPAWLFTILRNLFRSDYRK--RRREVEDADGSYAKTLKS 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420 111 GDTEADALDGIATRDALRliaELPPDQAEAVLLRVVVGLDAKRAGKVVGKRPGAVRTAAHRGLRRLADRLAADGHA--AP 188
Cdd:PRK12540   93 QPGQNAHLEFEEFRAALD---KLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARSKLSALLYVDGAEdfGP 169

                         170
                  ....*....|..
gi 1756728420 189 RPGVRPLLQGDR 200
Cdd:PRK12540  170 DDTVRAVIGGSG 181
PRK08241 PRK08241
RNA polymerase subunit sigma-70;
11-191 2.00e-03

RNA polymerase subunit sigma-70;


Pssm-ID: 236196 [Multi-domain]  Cd Length: 339  Bit Score: 38.38  E-value: 2.00e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  11 RALRAAQDGDEASFRLLYRDTQPRLIRFAAALVG--ADAEDVTSEAWLQIARDLPGFRGDlDGFRGWTATITRHRALDQL 88
Cdd:PRK08241    8 ALLARAAAGDRDAFAALVEPHRRELLAHCYRMLGsvHDAEDAVQETLLRAWRGYDRFEGR-SSLRTWLYRIATNVCLDAL 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  89 RRTARRP-------AAGLPDEVFTAL-----------ASGGDTEADALDGIATRDALRL-----IAELPPDQAEAVLLRV 145
Cdd:PRK08241   87 EGRARRPlptdlgaPAADPVDELVERpevpwlepypdALLDPAAADPAARVVARESVRLafvaaLQHLPPRQRAVLILRD 166

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1756728420 146 VVGLDAKRAGKVVGKRPGAVRTAAHRGLRRLADRLAADGHAAPRPG 191
Cdd:PRK08241  167 VLGWSAAEVAELLDTSVAAVNSALQRARATLAERGPSAADTLREPD 212
Sigma70_ECF pfam07638
ECF sigma factor; These proteins are probably RNA polymerase sigma factors belonging to the ...
 7-165 9.85e-03

ECF sigma factor; These proteins are probably RNA polymerase sigma factors belonging to the extra-cytoplasmic function (ECF) subfamily and show sequence similarity to pfam04542 and pfam04545.


Pssm-ID: 254323 [Multi-domain]  Cd Length: 185  Bit Score: 35.47  E-value: 9.85e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420   7 AELSRALRAAQDGDEASFRLLYRDTQPRLIRFAAALVGADAEDVT-------SEAWLQIAR--DLPGFRGDlDGFRGWTA 77
Cdd:pfam07638   2 QEVTQLLQQVKDGDAAATEQLLPLVYDELRRLAGSKLQNERRGHTlqptalvHEAFVRLVDteDFPDWSGR-GHFFAAAA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756728420  78 TITRHRALDQLRRTARRPAAGlpDEVFTALASGGDT-EADALDGIAT-RDALRLIAELPPDQAEAVLLRVVVGLDAKRAG 155
Cdd:pfam07638  81 EAMRRILIDHARRRQRQKRGG--DVQRRELDEVVDNgDSPNPDLLLDlDEALEQLFSLSPRQARLVELRFFAGLSNDEIA 158

                         170
                  ....*....|
gi 1756728420 156 KVVGKRPGAV 165
Cdd:pfam07638 159 ERLGVSERTV 168
 
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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