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Conserved domains on  [gi|2796099454|ref|WP_372855634|]
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RNA polymerase sigma factor [Pedobacter sp.]

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]; ...
 18-189 1.89e-46

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: 151.30  E-value: 1.89e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  18 NEVQLLIALKSGDRQAFEEIYQNYSPRIFLNILKMIKSIDDSQEILQDVFIKVWEKRDLIDPEQPFKSYLFQISRYTVYN 97
Cdd:COG1595     3 SDEELLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAID 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  98 FFRKANLDKKLKAYLSFENTELYTHIEENIVQRENSQLIMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSSTIND 177
Cdd:COG1595    83 HLRKRRRRRELLDELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKS 162

                         170
                  ....*....|..
gi 2796099454 178 HIVKATKFLRER 189
Cdd:COG1595   163 RLSRARKKLREA 174
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 18-189 1.89e-46

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: 151.30  E-value: 1.89e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  18 NEVQLLIALKSGDRQAFEEIYQNYSPRIFLNILKMIKSIDDSQEILQDVFIKVWEKRDLIDPEQPFKSYLFQISRYTVYN 97
Cdd:COG1595     3 SDEELLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAID 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  98 FFRKANLDKKLKAYLSFENTELYTHIEENIVQRENSQLIMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSSTIND 177
Cdd:COG1595    83 HLRKRRRRRELLDELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKS 162

                         170
                  ....*....|..
gi 2796099454 178 HIVKATKFLRER 189
Cdd:COG1595   163 RLSRARKKLREA 174
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 32-188 6.07e-39

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: 131.53  E-value: 6.07e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  32 QAFEEIYQNYSPRIFLNILKMIKSIDDSQEILQDVFIKVWEKRDLIDPEQPFKSYLFQISRYTVYNFFRKANLDKKLKAY 111
Cdd:TIGR02985   1 EAFEQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETLEISESIKAYLFTIVKNRCLNYLRHKQVEEKYQEE 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2796099454 112 LSF--ENTELYTHIEENIVQRENSQLIMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSSTINDHIVKATKFLRE 188
Cdd:TIGR02985  81 LAEieERELSEADPEEELEAKELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLRK 159
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 28-189 5.77e-26

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 98.73  E-value: 5.77e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  28 SGDRQAFEEIYQNYSPRIFLNILKMIKSIDDSQEILQDVFIKVWEKRDLIDPEQPFKSYLFQISRYTVYNFFRKAN---- 103
Cdd:PRK09652    6 RGDRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRGGAAFYTWLYRIARNTAINYLRKQGrrpp 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454 104 -LDKKLKAYLSFENTELYTHI---EENIVQRENSQLIMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSSTINDHI 179
Cdd:PRK09652   86 aSDVDAEEAEDFDLADALRDIstpENELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRI 165

                         170
                  ....*....|
gi 2796099454 180 VKATKFLRER 189
Cdd:PRK09652  166 FRAREALRAK 175
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 133-186 4.68e-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: 53.23  E-value: 4.68e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2796099454 133 SQLIMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSSTINDHIVKATKFL 186
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 134-187 1.29e-06

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: 44.02  E-value: 1.29e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2796099454 134 QLIMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSSTINDHIVKATKFLR 187
Cdd:cd06171     2 ERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 18-189 1.89e-46

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: 151.30  E-value: 1.89e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  18 NEVQLLIALKSGDRQAFEEIYQNYSPRIFLNILKMIKSIDDSQEILQDVFIKVWEKRDLIDPEQPFKSYLFQISRYTVYN 97
Cdd:COG1595     3 SDEELLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAID 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  98 FFRKANLDKKLKAYLSFENTELYTHIEENIVQRENSQLIMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSSTIND 177
Cdd:COG1595    83 HLRKRRRRRELLDELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKS 162

                         170
                  ....*....|..
gi 2796099454 178 HIVKATKFLRER 189
Cdd:COG1595   163 RLSRARKKLREA 174
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 32-188 6.07e-39

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: 131.53  E-value: 6.07e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  32 QAFEEIYQNYSPRIFLNILKMIKSIDDSQEILQDVFIKVWEKRDLIDPEQPFKSYLFQISRYTVYNFFRKANLDKKLKAY 111
Cdd:TIGR02985   1 EAFEQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETLEISESIKAYLFTIVKNRCLNYLRHKQVEEKYQEE 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2796099454 112 LSF--ENTELYTHIEENIVQRENSQLIMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSSTINDHIVKATKFLRE 188
Cdd:TIGR02985  81 LAEieERELSEADPEEELEAKELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLRK 159
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 32-189 4.91e-31

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: 111.29  E-value: 4.91e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  32 QAFEEIYQNYSPRIFLNILKMIKSIDDSQEILQDVFIKVWEKRDLIDPEQPFKSYLFQISRYTVYNFFRKANLDKKLKAy 111
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELD- 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2796099454 112 LSFENTELYTHIEENIVQRENSQLIMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSSTINDHIVKATKFLRER 189
Cdd:TIGR02937  80 LLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLREL 157
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 28-189 5.77e-26

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 98.73  E-value: 5.77e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  28 SGDRQAFEEIYQNYSPRIFLNILKMIKSIDDSQEILQDVFIKVWEKRDLIDPEQPFKSYLFQISRYTVYNFFRKAN---- 103
Cdd:PRK09652    6 RGDRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRGGAAFYTWLYRIARNTAINYLRKQGrrpp 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454 104 -LDKKLKAYLSFENTELYTHI---EENIVQRENSQLIMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSSTINDHI 179
Cdd:PRK09652   86 aSDVDAEEAEDFDLADALRDIstpENELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRI 165

                         170
                  ....*....|
gi 2796099454 180 VKATKFLRER 189
Cdd:PRK09652  166 FRAREALRAK 175
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 28-189 3.95e-21

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 86.18  E-value: 3.95e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  28 SGDRQAFEEIYQNYSPRIFLNILKMIKSIDDSQEILQDVFIKVWEKRDLIDPEQPFKSYLFQISRYTVYNFFRKANLDKK 107
Cdd:PRK11924    9 TGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCYDLLRRRRREKA 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454 108 LKAYLSFENTELYTH--IEENIVQRENSQLIMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSSTINDHIVKATKF 185
Cdd:PRK11924   89 VLSDDALEPEFAETAetPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQL 168


                  ....
gi 2796099454 186 LRER 189
Cdd:PRK11924  169 LREC 172
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 35-188 4.81e-19

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 80.41  E-value: 4.81e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  35 EEIYQNYSPRIFLNILKMIKSIDDSQEILQDVFIKVWEKRDLIDPEQPFKSYLFQISRYTVYNFFRKANLDKKLKAYLSF 114
Cdd:PRK09637    4 ESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDGSSIKSWLYQIANNTIIDFYRKKNRSEELPDDLLF 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2796099454 115 ENTElythIEENIVQrENSQLIMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSSTINDHIVKATKFLRE 188
Cdd:PRK09637   84 EDEE----REENAKK-ELAPCLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKE 152
PRK12534 PRK12534
RNA polymerase sigma factor; Provisional
 21-187 2.85e-17

RNA polymerase sigma factor; Provisional


Pssm-ID: 183576 [Multi-domain]  Cd Length: 187  Bit Score: 76.25  E-value: 2.85e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  21 QLLIALKSGDRQAFEEIYQNYSPRIFLNILKMIKSIDDSQEILQDVFIKVWEKRDLIDPEQPFK-SYLFQISRYTVYNFF 99
Cdd:PRK12534   14 RLLTATAGGDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRARGlTWLAMIARNKAIDHL 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454 100 RkANLDKKLKAYLSfENTELYTHIEENIVQRE---NSQLIMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSSTIN 176
Cdd:PRK12534   94 R-ANAPQRRNVALD-DAGELRAADASPLERTErasTRRRIDHCLAELEPPRSELIRTAFFEGITYEELAARTDTPIGTVK 171

                         170
                  ....*....|.
gi 2796099454 177 DHIVKATKFLR 187
Cdd:PRK12534  172 SWIRRGLAKLK 182
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 30-188 2.98e-17

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 75.37  E-value: 2.98e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  30 DRQAFEEIYQNYSPRIFLNILKMIKSIDDSQEILQDVFIKVWeKRDLIDPEQPfKSYLFQISRYTVYNFFRKANlDKKLK 109
Cdd:PRK09639    1 SDETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLY-RSDFKGIENE-KGWLIKSARNVAYNYLRSEK-RRRAR 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454 110 AYLSFENTELYTHI--EENIVQRENSQLIMNAIEELPPqRKQIYKLCKIEGRSYAEVAMQLGISSSTINDHIVKATKFLR 187
Cdd:PRK09639   78 ILGEFQWQEVDNEPspEEIWIRKEEITKVQEVLAKMTE-RDRTVLLLRFSGYSYKEIAEALGIKESSVGTTLARAKKKFR 156


                  .
gi 2796099454 188 E 188
Cdd:PRK09639  157 K 157
PRK06811 PRK06811
RNA polymerase factor sigma-70; Validated
 16-189 4.07e-17

RNA polymerase factor sigma-70; Validated


Pssm-ID: 180707 [Multi-domain]  Cd Length: 189  Bit Score: 75.75  E-value: 4.07e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  16 NLNEVQLLIALKSGDRQAFEEIYQNYSPRIFLNILKMIKSIDDSQ---EILQDVFIKVWEKRDLIDPEQ-PFKSYLFQIS 91
Cdd:PRK06811    2 KINEDNFIKELKKKNEKALEFIVDTYGNLVKKIVHKVLGTVNYSQlieECVNDIFLSIWNNIDKFDEEKgSFKKWIAAIS 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  92 RYTVYNFFRKANldKKLKAYLSFENTELY-THIEENIVQRENSQLIMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGI 170
Cdd:PRK06811   82 KYKAIDYKRKLT--KNNEIDSIDEFILISeESIENEIILKENKEEILKLINDLEKLDREIFIRRYLLGEKIEEIAKKLGL 159

                         170
                  ....*....|....*....
gi 2796099454 171 SSSTINDHIVKATKFLRER 189
Cdd:PRK06811  160 TRSAIDNRLSRGRKKLQKN 178
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 19-189 1.59e-16

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 73.96  E-value: 1.59e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  19 EVQLLIALKSGDRQAFEEIYQNYSPRIFLNILKMIKSIDDSQEILQDVFIKVWEKRDLIDPEQPFKSYLFQISRYTVYNF 98
Cdd:PRK09641    5 IKRLIKQVKKGDQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINRKFSTWLYRIATNLTIDR 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  99 FRKANLDKKLKAYLS-FENTELYTHI-------EENIVQRENSQLIMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGI 170
Cdd:PRK09641   85 LRKRKPDYYLDAEVAgTEGLTMYSQLaaddalpEEQVVSLELQETIQEAILQLPEKYRTVIVLKYIEDLSLKEISEILDL 164

                         170
                  ....*....|....*....
gi 2796099454 171 SSSTINDHIVKATKFLRER 189
Cdd:PRK09641  165 PVGTVKTRIHRGREALRKQ 183
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 19-190 6.36e-16

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 72.79  E-value: 6.36e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  19 EVQLLIALKSGDRQAFEEIYQNYSPRIFLNILKMIKSIDDSQEILQDVFIKVWEKRDLiDPEQ-PFKSYLFQISRYTVYN 97
Cdd:PRK12519   16 DAELFSALKAGQSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRKSSY-DPKRgSLSSYLLTLTRSRAID 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  98 FFR----KANLDKKLKAYLSFENTELYTHieENIVQRENSQLIMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSS 173
Cdd:PRK12519   95 RLRsrrsRQRLLERWQQELLGEASEDTPL--EQASLAERSQRVQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLG 172

                         170
                  ....*....|....*..
gi 2796099454 174 TindhiVKAtkflRERQ 190
Cdd:PRK12519  173 T-----VKA----RARQ 180
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 18-188 3.69e-15

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 70.24  E-value: 3.69e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  18 NEVQLLIALKS-GDRQAFEEIYQNYSPRIFLNILKMIKSIDDSQEILQDVFIKVWEKRDL--IDPEQPFkSYLFQISRYT 94
Cdd:PRK12514    4 DDIEKLIVRVSlGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRfaVSGLSPM-TWLITIARNH 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  95 VYNFFRK-----ANLDKklkaylSFENTELYTHIEENIVQRENSQLIMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLG 169
Cdd:PRK12514   83 AIDRLRArkavaVDIDE------AHDLADPSPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYLEGLSYKELAERHD 156

                         170
                  ....*....|....*....
gi 2796099454 170 ISSSTINDHIVKATKFLRE 188
Cdd:PRK12514  157 VPLNTMRTWLRRSLLKLRE 175
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 35-188 1.47e-13

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 65.67  E-value: 1.47e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  35 EEIYQNYSPRIFLNILKMIKSIDDSQEILQDVFIKVWEKRDLIDpEQPFKSYLFQISRYTVYNFFRKanldKKLKAYLSF 114
Cdd:PRK09644    4 EEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYD-NQKVKPWLFKVAYHTFIDFVRK----EKKVSFVGT 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2796099454 115 ENTE--LYTHIEENIVQRENSQLIMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSSTINDHIVKATKFLRE 188
Cdd:PRK09644   79 DEIEaiQAESTEEYVVAKNSYEKLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRLKA 154
PRK12528 PRK12528
RNA polymerase sigma factor; Provisional
 57-182 1.72e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 171561 [Multi-domain]  Cd Length: 161  Bit Score: 65.25  E-value: 1.72e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  57 DDSQEILQDVFIKVWEKRD---LIDPeqpfKSYLFQISRYTVYNFFRKANLDKklkAYLsfentELYTHIEENIVQRENS 133
Cdd:PRK12528   29 QSAADLAQDTFVKVLVAREtaqIIEP----RAFLTTIAKRVLCNHYRRQDLER---AYL-----EALAQLPERVAPSEEE 96

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2796099454 134 QLIM--------NAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSSTINDHIVKA 182
Cdd:PRK12528   97 RAIIletlveldQLLDGLPPLVKRAFLLAQVDGLGYGEIATELGISLATVKRYLNKA 153
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 23-188 1.78e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 63.26  E-value: 1.78e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  23 LIALKSGDRQAFEEIYQNYSPRIFLNILKMIKSIDDSQEILQDVFIKVWEKRDLIDPEQ-PFKSYLFQISRYTVYNFFRk 101
Cdd:PRK12537   14 LLACARGDRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPARgSARGWIYSVTRHLALNVLR- 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454 102 anlDKKLKAYLSFENTELYTHIEENIVQRE---NSQLIMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSSTINDH 178
Cdd:PRK12537   93 ---DTRREVVLDDDAEETAQTLHEIIDDFDlwaNSGKIHRCLEQLEPARRNCILHAYVDGCSHAEIAQRLGAPLGTVKAW 169

                         170
                  ....*....|
gi 2796099454 179 IVKATKFLRE 188
Cdd:PRK12537  170 IKRSLKALRE 179
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 33-189 2.17e-12

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: 62.34  E-value: 2.17e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  33 AFEEIYQNYSPRIFLNILKMIKSIDDSQEILQDVFIKVWEKRDLIDPEQPFKSYLFQISRYTVYNFFRKANLDKKLkayL 112
Cdd:TIGR02989   2 AFVRLLTRHERALRAFVRSLVADRDDVDDVLQETFVVAWRKFDQFDPGTNFVAWARGIARNKVLNYRRKLGRDRLV---F 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454 113 SFENTELYTHIEENIVQRENS---QLIMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSSTindhIVKATKFLRER 189
Cdd:TIGR02989  79 DDDLLEALAAEAEPTEAERLSddrQALEGCLEKLPERQRELLDLRYQRGQKATALAEQTGRTVNA----VYKALQRIRVS 154
PRK09651 PRK09651
RNA polymerase sigma factor FecI; Provisional
 34-184 3.46e-12

RNA polymerase sigma factor FecI; Provisional


Pssm-ID: 182018 [Multi-domain]  Cd Length: 172  Bit Score: 62.13  E-value: 3.46e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  34 FEEIYQNYSPRIFLNILKMIKSIDDSQEILQDVFIKVWEKRDLIDPEQPfKSYLFQISRYTVYNFFRKANLDKKLKAYLS 113
Cdd:PRK09651   12 FESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVSETLSTIRDP-RSFLCTIAKRVMVDLFRRNALEKAYLEMLA 90

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2796099454 114 FENTELYTHIEENIVQRENSQLIMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSSTINDHIVKATK 184
Cdd:PRK09651   91 LMPEGGAPSPEERESQLETLQLLDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKATE 161
SigE-fam_strep TIGR02983
RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors ...
 28-189 5.65e-12

RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.


Pssm-ID: 132028 [Multi-domain]  Cd Length: 162  Bit Score: 61.25  E-value: 5.65e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  28 SGDRQAFEEIYQNYSPRIFLNILKMIKSIDDSQEILQDVFIKVWEKRDLI-DPEQPfKSYLfqisRYTVYNFFRKANLDK 106
Cdd:TIGR02983   2 SATEEEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIrDPDAP-DAYV----RRVLVNLARSRWRRR 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454 107 KLKAYLSFENTElyTHIEENIVQRENSQLIMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSSTINDHIVKATKFL 186
Cdd:TIGR02983  77 RLLELPTRELPD--AAAPDPAPDVALRAALARALRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALARL 154


                  ...
gi 2796099454 187 RER 189
Cdd:TIGR02983 155 REL 157
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 22-194 1.64e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 60.86  E-value: 1.64e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  22 LLIALKSGDRQAFEEIYQNYSPRIFLNILKMIKSIDDSQEILQDVFIKVWEKRDLIDPEQPFKSYLFQISRYTVYNFFRK 101
Cdd:PRK12513   16 LMLRYRAGDAAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPRARFRTWLYQIARNLLIDHWRR 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454 102 AnldkKLKAYLSFE-NTELYTHI------EENIVQRENSQLIMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSST 174
Cdd:PRK12513   96 H----GARQAPSLDaDEQLHALAddgaapEQQLSLFRDRRRLQAALETLPDEQREVFLLREHGDLELEEIAELTGVPEET 171

                         170       180
                  ....*....|....*....|
gi 2796099454 175 INDHIVKATKFLRERQSSFG 194
Cdd:PRK12513  172 VKSRLRYALQKLRELLAEEV 191
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 26-188 5.24e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 58.98  E-value: 5.24e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  26 LKSGDRQAFEEIYQNYSPRIFLNILKMIKSIDDSQEILQDVFIKVWEKRDLIDPEQPFKSYLF-----QISRYTVYNFFR 100
Cdd:PRK12543    1 MLSGDQEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNRPFRFWLIglvikQIHSWRRKRWRR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454 101 KANLDKKlkayLSFENTELYThIEENIVQRENSQLIMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSSTINDHIV 180
Cdd:PRK12543   81 FRIFEKA----EEQRKPVSID-FSEDVLSKESNQELIELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIH 155


                  ....*...
gi 2796099454 181 KATKFLRE 188
Cdd:PRK12543  156 AALKKLRQ 163
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 22-188 4.19e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 56.66  E-value: 4.19e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  22 LLIALKSGDRQAFEEIYQNYSPRIFLNILKMIKSIDDSQEILQDVFIKVWEKRDLIDPEQPFKSYLFQISRYTVYNFFRK 101
Cdd:PRK12515   12 LLARIAQGDRTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGRSQVSTWLLSIARFKALSALRR 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454 102 ---ANLDKklKAYLSFENTelyTHIEENIVQRENSQLIMNA-IEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSSTIND 177
Cdd:PRK12515   92 rkhEEIDD--EAAAAIEDG---ADTPEVALQKSDTSAALRAcLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKT 166

                         170
                  ....*....|.
gi 2796099454 178 HIVKATKFLRE 188
Cdd:PRK12515  167 RMFYARKKLAE 177
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 133-186 4.68e-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: 53.23  E-value: 4.68e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2796099454 133 SQLIMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSSTINDHIVKATKFL 186
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 17-187 4.71e-10

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 56.18  E-value: 4.71e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  17 LNEVQLLIALKSGDRQAFEEIYQNYSPRIFLNILKMIKSIDDSQEILQDVFIKVWEKRDLIDPEQPFKSYLFQISRYTVY 96
Cdd:PRK09638    3 MDEKELIQKAKKGDDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGRSKFSTWLISIASRLYK 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  97 NFFRKanldKKLKAYLSFENTELYTHIEENIVQRENSQL--IMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSST 174
Cdd:PRK09638   83 DHLRK----QKREKLRLQRAKEETLRKEKWEAAIKGAEWseMLDALSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGT 158

                         170
                  ....*....|...
gi 2796099454 175 INDHIVKATKFLR 187
Cdd:PRK09638  159 VKSRVHHGIKQLR 171
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 58-189 1.21e-09

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 54.78  E-value: 1.21e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  58 DSQEILQDVFIKVWEKRDLIDPEQPfKSYLFQISRYTVYNFFRKaNLDKKLKAYLSFENTELYTH--IEENIVQRENSQL 135
Cdd:PRK12527   21 AAEDVAHDAYLRVLERSSSAQIEHP-RAFLYRTALNLVVDRHRR-HRVRQAEPLEVLDEEERLHSpsPQTRLDLGQRLAL 98

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2796099454 136 IMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSSTINDHIVKATKFLRER 189
Cdd:PRK12527   99 LQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVR 152
PRK12539 PRK12539
RNA polymerase sigma factor SigF;
22-190 3.02e-09

RNA polymerase sigma factor SigF;


Pssm-ID: 237132 [Multi-domain]  Cd Length: 184  Bit Score: 54.35  E-value: 3.02e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  22 LLIALKSGDRQAFEEIYQNYSPRI---FLNILKMI-KSIDDSQEILQDVFIKVWEKRDLIDPEQPFKSYLFQISRYTVYN 97
Cdd:PRK12539   11 LMLASLDGDAAAHRALLERLSGHLrayYKGKLARIgRGAEEAEDLVQEALMAIHTRRHTYDPEQPLTPWVYAIARYKLID 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  98 FFRKanlDKKLKAYLSFENTElYTHIEENIVQRENSQLIMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSSTIND 177
Cdd:PRK12539   91 HLRR---TRASLADVPIDDAD-ELVAHDDHAAVESTLDLGRLLARLPEKMRLAIQAVKLEGLSVAEAATRSGMSESAVKV 166

                         170
                  ....*....|....*...
gi 2796099454 178 HIVKATKFL-----RERQ 190
Cdd:PRK12539  167 SVHRGLKALaaligRETQ 184
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
 59-188 8.32e-09

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 52.77  E-value: 8.32e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  59 SQEILQDVFIKVWEKRDLIDPEQPFkSYLFQISRYTVYNFFRKANLDKKlkaYLSFENTELYTHIEE-----NIVQRENS 133
Cdd:PRK07037   25 AEDVVQDAFVKLVEAPNQDAVKQPV-AYLFRIVRNLAIDHYRRQALENK---YHGDEEDGLDVPSPEaspeaALINRDTL 100

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2796099454 134 QLIMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSSTINDHIVKATKFLRE 188
Cdd:PRK07037  101 RHVADALSELPARTRYAFEMYRLHGETQKDIARELGVSPTLVNFMIRDALVHCRK 155
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 29-188 7.17e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 50.10  E-value: 7.17e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  29 GDRQAFEEIYQNYSPRIFLNILKM--IKSIDDsqeILQDVFIKVWEKRDLIDPEQPFKSYLFQISRYTVYNFFRKANLDK 106
Cdd:PRK12518    8 GDRQSFRQLYRRYQQKVRSTLYQLcgRELLDD---LVQEVFLRVWKGLPKLRNPAYFSTWLYRITWNVATDARRQFAQRP 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454 107 KLKAYLSFENTELYTHIEENIVQRENSQLIMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSSTINDHIVKATKFL 186
Cdd:PRK12518   85 SRIQDDSLNDQPSRPSDTPDLMQLHYQDLVQQGLQTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRLFYARRQL 164


                  ..
gi 2796099454 187 RE 188
Cdd:PRK12518  165 RK 166
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 37-103 8.37e-08

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


Pssm-ID: 427998 [Multi-domain]  Cd Length: 71  Bit Score: 47.58  E-value: 8.37e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2796099454  37 IYQNYSPRIFLNILKMIKSIDDSQEILQDVFIKVWEKRDLIDPEQP--FKSYLFQISRYTVYNFFRKAN 103
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGvsFSTWLYTIIRNAIIDYLRKQR 69
PRK12522 PRK12522
RNA polymerase sigma factor; Provisional
 35-188 9.63e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 183571 [Multi-domain]  Cd Length: 173  Bit Score: 49.87  E-value: 9.63e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  35 EEIYQNYSPRIFLNILKMIKSIDDSQEILQDVFIKVWEKRDLIDPEQPFKSYLFQISRYTVYNFFRKAN---------LD 105
Cdd:PRK12522    6 EELIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVENYKKWITTICVRTFYDFYRKKKrwkdrildlFH 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454 106 KKLKAYLSFENTelyTHIEENIVQRENSQLIMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSSTINDHIVKATKF 185
Cdd:PRK12522   86 KEDGGEIEFADD---VNISEEFIQKVEAEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQ 162


                  ...
gi 2796099454 186 LRE 188
Cdd:PRK12522  163 MRE 165
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 23-188 9.82e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 50.73  E-value: 9.82e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  23 LIAL-KSGDRQAFEEIYQNYSPRIFLNILKMIKSIDDSQEILQDVFIKVWEKRDLIDPEQPFKSYLFQISRYTVYNFFRK 101
Cdd:PRK11922   20 LVARvLAGDEAAFEALMRRHNRRLYRTARAILRNDAEAEDVVQEAYLRAFRALGTFRGDASLSTWLSRIVLNEALGRLRR 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454 102 A----NLDKKLKAYLSFENTELYTH-----IEENIVQRENSQLIMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISS 172
Cdd:PRK11922  100 RrrlvNLAEMVMASTIAGGERTPLAdpaedPERAAARREIRALLERAIDALPDAFRAVFVLRVVEELSVEETAQALGLPE 179

                         170
                  ....*....|....*.
gi 2796099454 173 STINDHIVKATKFLRE 188
Cdd:PRK11922  180 ETVKTRLHRARRLLRE 195
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 32-188 1.09e-07

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 49.75  E-value: 1.09e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  32 QAFEEIYQNYSPRIFLNILKMIKSIDDSQEILQDVFIKVWEKRDLIDPEQPFKSYLFQISRYTVYNFFRKANLDKKLKAY 111
Cdd:PRK09415   16 DLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGKSSLKTWLYRIAINHCKDYLKSWHNKKVIVTE 95

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2796099454 112 LSFENTEL-YTHIEENIVQRENSQLIMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSSTINDHIVKATKFLRE 188
Cdd:PRK09415   96 DIFTYMESqKESVEEEVIQNAEDERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKELLKK 173
PRK12525 PRK12525
RNA polymerase sigma factor; Provisional
 59-184 1.10e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 139037 [Multi-domain]  Cd Length: 168  Bit Score: 49.56  E-value: 1.10e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  59 SQEILQDVFIKVWEKRDLIDPEQPfKSYLFQISRYTVYNFFRKANLDKKLKAYLSFENTELYTHIEENIVQRENSQLIMN 138
Cdd:PRK12525   36 AEDIASETFLQVLALPDPASIREP-RALLTTIARRLMYEGWRRQDLERAYLQSLAEAPEAVQPSPEEQWMVIETLLAIDR 114

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2796099454 139 AIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSSTINDHIVKATK 184
Cdd:PRK12525  115 LLDGLSGKARAAFLMSQLEGLTYVEIGERLGVSLSRIHQYMVEAFK 160
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 57-188 1.14e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 49.96  E-value: 1.14e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  57 DDSQEILQDVFIKVWEKRDLIDPEQPFKSYLFQISRYTVYNFFRKANldKKLKAYLSFENTELYTHIEEniVQRENSQLI 136
Cdd:PRK12516   35 DRADDLVQDTIMKAWAKQDHFEVGTNMKAWLFTILRNEFYSQMRKRG--REVQDTDGMFTEQLAVHPSQ--YGTLDLQDF 110

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2796099454 137 MNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSSTINDHIVKATKFLRE 188
Cdd:PRK12516  111 RAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQRLQE 162
algU PRK11923
RNA polymerase sigma factor AlgU; Provisional
 21-182 2.92e-07

RNA polymerase sigma factor AlgU; Provisional


Pssm-ID: 171347 [Multi-domain]  Cd Length: 193  Bit Score: 49.03  E-value: 2.92e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  21 QLLIALKSGDRQAFEEIYQNYSPRIFLNILKMIKSIDDSQEILQDVFIKVWEKRDLIDPEQPFKSYLFQISRYTVYNFFR 100
Cdd:PRK11923    9 QLVERVQRGDKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDSAFYTWLYRIAINTAKNHLV 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454 101 KANlDKKLKAYLSFENTELYTH------IE--ENIVQRENSQ-LIMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGIS 171
Cdd:PRK11923   89 SRG-RRPPDSDVSSEDAEFYDGdhalkdIEspERALLRDEIEgTVHRTIQQLPEDLRTALTLREFDGLSYEDIASVMQCP 167

                         170
                  ....*....|.
gi 2796099454 172 SSTINDHIVKA 182
Cdd:PRK11923  168 VGTVRSRIFRA 178
PRK12536 PRK12536
RNA polymerase sigma factor; Provisional
 57-175 3.22e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 237131 [Multi-domain]  Cd Length: 181  Bit Score: 48.51  E-value: 3.22e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  57 DDSQEILQDVFIKVWEKRDLIDPEQPFKSYLFQISRYTVYNFFRKANLDKKLKAYLSfENTELYTHIEENIVQ--RENSQ 134
Cdd:PRK12536   47 DEVEDLVQEILLAVHNARHTYRADQPLTAWVHAIARYKLMDFLRSRARREALHDPLD-DESELFATSDDEAAEarRDLGK 125

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 2796099454 135 LimnaIEELPP-QRKQIYKLcKIEGRSYAEVAMQLGISSSTI 175
Cdd:PRK12536  126 L----LEQLPDrQRLPIVHV-KLEGLSVAETAQLTGLSESAV 162
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 17-188 3.23e-07

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 48.76  E-value: 3.23e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  17 LNEVQLLIALKSGDRQAFEEIYQNYSPRIFLNILKMIKSIDDSQEILQDVFIKVWEKRDLIDPEQ-PFKSYLFQISRYTV 95
Cdd:PRK13919    8 LSDEALLALVARGEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRRgSARAWLLALAHHAA 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  96 YNFFRKANL--------DKKLKAY-LSFENTELYTHIEENIVQRensqlimnAIEELPPQRKQIYKLCKIEGRSYAEVAM 166
Cdd:PRK13919   88 VDHVRRRAArpqplepdEREPEAFdLPGPGLDEEGHLDRTRLGR--------ALKALSPEERRVIEVLYYQGYTHREAAQ 159

                         170       180
                  ....*....|....*....|..
gi 2796099454 167 QLGISSSTINDHIVKATKFLRE 188
Cdd:PRK13919  160 LLGLPLGTLKTRARRALSRLKE 181
PRK09646 PRK09646
ECF RNA polymerase sigma factor SigK;
21-175 4.42e-07

ECF RNA polymerase sigma factor SigK;


Pssm-ID: 182015 [Multi-domain]  Cd Length: 194  Bit Score: 48.51  E-value: 4.42e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  21 QLLIALKSGDRQAFEEIYQNYSPRIFLNILKMIKSIDDSQEILQDVFIKVWEKRDLIDPEQ-PFKSYLFQISRYTVYNFF 99
Cdd:PRK09646   19 ALLRRVARGDQDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDPARgSALAWLLTLAHRRAVDRV 98

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2796099454 100 R--KANLDKKLKAYLSFENTElYTHIEENIVQRENSQLIMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSSTI 175
Cdd:PRK09646   99 RseQAASQREVRYGARNVDPA-FDQVAEEVEARLERERVRDCLDALTDTQRESVTLAYYGGLTYREVAERLAVPLGTV 175
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 22-171 6.19e-07

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 47.72  E-value: 6.19e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  22 LLIALKSGDRQAFEEIYQNYSPRIFLNILKMIKSIDDSQEILQDVFIKVWEKRDLIDPEQP-FKSYLFQIsrytVYNffr 100
Cdd:PRK05602   10 LLARVAAGDPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPGEArFDTWLHRV----VLN--- 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454 101 kanldkklkayLSFENTELYTHI---------------EENIVQRENSQLIMNAIEELPP-QRKQIYkLCKIEGRSYAEV 164
Cdd:PRK05602   83 -----------LCYDRLRRRREVpvedapdvpdpapgpDAGLEARQRARRVEQALAALPErQREAIV-LQYYQGLSNIEA 150


                  ....*..
gi 2796099454 165 AMQLGIS 171
Cdd:PRK05602  151 AAVMDIS 157
PRK12512 PRK12512
RNA polymerase sigma factor; Provisional
 22-171 7.64e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 171551 [Multi-domain]  Cd Length: 184  Bit Score: 47.39  E-value: 7.64e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  22 LLIALKSGDRQAFEEIYQNYSP--RIFLN--ILKMIKSIDDSQEILQDVFIKVWEKRDLIDPEQPFKSYLFQISRYTVYN 97
Cdd:PRK12512   12 LMRSANAGDAAAYRRLLKAVTPvlRAAARrgLARAGQPADQAEDIVQEILLAVHLKRHTWDPGAPFAPWLFAIARNKLID 91

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2796099454  98 FFRKanldkklKAYLSFENTElytHIEENIVQRE-----NSQLIMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGIS 171
Cdd:PRK12512   92 ALRR-------RGRRVFVDID---DFAETLPAEPatetlPAGDVGRHLETLPPRQRDVVQSISVEGASIKETAAKLSMS 160
PRK12523 PRK12523
RNA polymerase sigma factor; Reviewed
 59-184 8.50e-07

RNA polymerase sigma factor; Reviewed


Pssm-ID: 183572 [Multi-domain]  Cd Length: 172  Bit Score: 47.15  E-value: 8.50e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  59 SQEILQDVFIKVWEKRDLIDPEQPfKSYLFQISRYTVYNFFRKANLDKklkAYLsfenTELYTHIEENIVQRENSQLIMN 138
Cdd:PRK12523   37 AEDLSQDTFVRLLGRPELPTPREP-RAFLAAVAKGLMFDHFRRAALEQ---AYL----AELALVPEAEQPSPEEQHLILE 108

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2796099454 139 AIEE-------LPPQRKQIYKLCKIEGRSYAEVAMQLGISSSTINDHIVKATK 184
Cdd:PRK12523  109 DLKAidrllgkLSSKARAAFLYNRLDGMGHAEIAERLGVSVSRVRQYLAQGLR 161
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 134-187 1.29e-06

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: 44.02  E-value: 1.29e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2796099454 134 QLIMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSSTINDHIVKATKFLR 187
Cdd:cd06171     2 ERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK12531 PRK12531
RNA polymerase sigma factor; Provisional
 26-187 1.60e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 105726 [Multi-domain]  Cd Length: 194  Bit Score: 46.85  E-value: 1.60e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  26 LKSGDRQAFEEIYQNYSPRIFLNILKMIKSIDDSQEILQDVFIKVWEKRDLIDPEQ-PFKSYLFQISRYTVYNFFRKanl 104
Cdd:PRK12531   21 VKSRDKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQKsALSTWIYTIIRNLCFDLLRK--- 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454 105 DKKLKAYLSFENTELYTHIEENIVQR---ENSQL---IMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSSTINDH 178
Cdd:PRK12531   98 QKGKDLHIHADDIWPSDYYPPDLVDHyspEQDMLkeqVMKFLDRLPKAQRDVLQAVYLEELPHQQVAEMFDIPLGTVKSR 177


                  ....*....
gi 2796099454 179 IVKATKFLR 187
Cdd:PRK12531  178 LRLAVEKLR 186
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 31-190 9.28e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 44.16  E-value: 9.28e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  31 RQAFEEIYQNYSPRIFLNILKMIKSIDDSQEILQDVFIKVWEKRDLIDPEQpFKSYLFQISRYTVYNFFRKanlDKKLKA 110
Cdd:PRK12541    4 KQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGEE-IRPWLFTIAYNAFIDWYRK---EKKYKT 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454 111 YL--SFENTELYTHIEENIVQRENSQLiMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSSTINDHIVKATKFLRE 188
Cdd:PRK12541   80 TTieEFHLPNVPSTEHEYFIKHEIASW-LDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKETKS 158


                  ..
gi 2796099454 189 RQ 190
Cdd:PRK12541  159 IK 160
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 139-188 9.49e-06

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


Pssm-ID: 461347 [Multi-domain]  Cd Length: 50  Bit Score: 41.64  E-value: 9.49e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2796099454 139 AIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSSTINDHIVKATKFLRE 188
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
PRK12526 PRK12526
RNA polymerase sigma factor; Provisional
 30-175 9.67e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 237127 [Multi-domain]  Cd Length: 206  Bit Score: 44.79  E-value: 9.67e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  30 DRQAFEEIYQNYSPRIFLNILKMIKSIDDSQEILQDVFIKVWEKRDLIDPEQPFKSYLfqisrytVYNFFRKANLD--KK 107
Cdd:PRK12526   36 DKQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKGAATTW-------VYTVMRNAAFDmlRK 108

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2796099454 108 LKAYLSFENTELYTHIEENIVQRENSQL----------IMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSSTI 175
Cdd:PRK12526  109 IKAKKEQNLGDDIWPIEQALAESQSESEefsdhlmdkqILSYIEKLPEAQQTVVKGVYFQELSQEQLAQQLNVPLGTV 186
PRK09643 PRK09643
RNA polymerase sigma factor SigM; Reviewed
 8-175 2.00e-05

RNA polymerase sigma factor SigM; Reviewed


Pssm-ID: 236604 [Multi-domain]  Cd Length: 192  Bit Score: 43.54  E-value: 2.00e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454   8 IMHQERVNNLNEVQLLIALKSGDRQAFEEIYQNYSPRIFLNILKMIKSIDDSQEILQDVFIKVWEKRDLIDPEQPFKSYL 87
Cdd:PRK09643    3 YCPAVGFGERSDAELLAAHVAGDRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGDAAVSSWL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  88 FQIsrytVYNffrkANLD----KKLKAYLSFENTE-LYTHIEENIVQRENSQLIMNAIEELPPQRKQIYKLCKIEGRSYA 162
Cdd:PRK09643   83 HRI----VVN----ACLDrlrrAKARPTVPLDDVYpVAQLERDPTARVETALAVQRALMRLPVEQRAALVAVDMQGYSVA 154

                         170
                  ....*....|...
gi 2796099454 163 EVAMQLGISSSTI 175
Cdd:PRK09643  155 DAARMLGVAEGTV 167
PRK12542 PRK12542
RNA polymerase sigma factor; Provisional
 30-184 2.33e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183581 [Multi-domain]  Cd Length: 185  Bit Score: 43.50  E-value: 2.33e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  30 DRQAFEEIYQNYSPRIFLNILKMIKSIDDSQEILQDVFIKVWEKRDLIDP--EQPFKSYLFQISRYTVYNFFRKanlDKK 107
Cdd:PRK12542    7 DYEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSlnTQELKRYILRVAKNKAIDSYRK---NKR 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454 108 LKAYLSFENTELYTHIEENIVQRENSQL----IMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSSTINDHIVKAT 183
Cdd:PRK12542   84 HETFLEEYERESIEAVDENIEEWEKRKMsevqIDTLLKELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERAR 163


                  .
gi 2796099454 184 K 184
Cdd:PRK12542  164 K 164
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
 55-203 3.27e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 42.90  E-value: 3.27e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  55 SIDDsqeILQDVFIKVWEKRDLIDPEQPFKSYLFQISRYTVYNFFRK-----ANLDKKLKAYLSfentELYTHieenivq 129
Cdd:PRK12546   33 VADD---LVQDTIVKAWTNFDKFQEGTNLRAWLFTILRNTFYSDRRKhkrevPDPEGVHAASLA----VKPAH------- 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454 130 reNSQLIMN----AIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSSTINDHIVKATKFLRER-QSSFGTAL------T 198
Cdd:PRK12546   99 --DGRLAMSdfraAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARARLAELlQLEEGEELemtdgaT 176


                  ....*
gi 2796099454 199 LSIVS 203
Cdd:PRK12546  177 LAVMS 181
PRK12547 PRK12547
RNA polymerase sigma factor; Provisional
 50-188 5.08e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 139056 [Multi-domain]  Cd Length: 164  Bit Score: 42.17  E-value: 5.08e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  50 LKMIKSIDDSQEILQDVFIKVWEKRDLIDPEQPFKSYLFQISRYTVYNFFRKANLDKKLKAYLSFENTELYTHIEENIvq 129
Cdd:PRK12547   24 VSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGTNLKAWLFTILRNEFYSQMRKRGREVQDSDGVFTARVAVHPAQYGSL-- 101

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2796099454 130 reNSQLIMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSSTINDHIVKATKFLRE 188
Cdd:PRK12547  102 --DLQDFKKALNLLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARNRLQE 158
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 35-188 8.16e-05

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 42.08  E-value: 8.16e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  35 EEIYQNYSPRIFLNILKMIKSIDDSQEILQDVFIKVWekRDLIDpEQP--FKSYLFQISRytvyNFFrkanLDK-KLKAY 111
Cdd:PRK09647   31 EELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVF--RSLQN-YQPgtFEGWLHRITT----NLF----LDMvRRRAR 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454 112 LSFEN-TELYTHIEENIVQRE----NSQL---IMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSSTINDHIVKAT 183
Cdd:PRK09647  100 IRMEAlPEDYDRVPGDEPNPEqiyhDARLdpdLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGR 179


                  ....*
gi 2796099454 184 KFLRE 188
Cdd:PRK09647  180 QQLRA 184
PRK09642 PRK09642
RNA polymerase sigma factor;
39-188 1.07e-04

RNA polymerase sigma factor;


Pssm-ID: 170031 [Multi-domain]  Cd Length: 160  Bit Score: 41.24  E-value: 1.07e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  39 QNYSPRIFLNILKMIKSIDDSQEILQDVFIKVWEKRdlidPEQPF---KSYLFQISRYTVYNFFRKANLDKKLKAYL--S 113
Cdd:PRK09642    2 QTYRHYIFQVIFSILRHEEDAKDVTQEVFVKIHASL----PNYQFrglKTWMARIATNHAIDYKRKKARENEELSLCkeT 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2796099454 114 FENTELYTHIEENIVQRENSQLIMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSSTINDHIVKATKFLRE 188
Cdd:PRK09642   78 EENIKSSHNIEDLLLTKEQKLLIAQKLRELPENYRDVVLAHYLEEKSYQEIALQEKIEVKTVEMKLYRARKWIKK 152
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 30-191 2.38e-04

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 40.31  E-value: 2.38e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  30 DRQAFEEIYQNYSPRIFLNILKMIKSIDDSQEILQDVFIKVWEKRDLIDPEQPFKSYLFQISRYTVYNFFRKANLDKKLK 109
Cdd:PRK09640   24 VTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGKSKFKTWLYSITYNECITQYRKERRKRRLM 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454 110 AYLSFENTELYTHieENIVQRENSQLIMNAIEELPPQRKQIYKLCKIEGRSYAEVA--MQLGISSSTINDHivKATKFLR 187
Cdd:PRK09640  104 DALSLDPLEEASE--EKAPKPEERGGLDRWLVHVNPIDREILVLRFVAELEFQEIAdiMHMGLSATKMRYK--RALDKLR 179


                  ....
gi 2796099454 188 ERQS 191
Cdd:PRK09640  180 EKFA 183
PRK06930 PRK06930
positive control sigma-like factor; Validated
 113-191 2.64e-04

positive control sigma-like factor; Validated


Pssm-ID: 180757 [Multi-domain]  Cd Length: 170  Bit Score: 40.10  E-value: 2.64e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2796099454 113 SFENTELYTHIEENIVQRENSQLIMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSSTINDHIVKATKFLRERQS 191
Cdd:PRK06930   85 SMEDLEWDIEEPESVISEWDKIRIEDALSVLTEREKEVYLMHRGYGLSYSEIADYLNIKKSTVQSMIERAEKKIARQIN 163
PRK09047 PRK09047
RNA polymerase factor sigma-70; Validated
 57-197 1.26e-03

RNA polymerase factor sigma-70; Validated


Pssm-ID: 236367 [Multi-domain]  Cd Length: 161  Bit Score: 38.03  E-value: 1.26e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454  57 DDSQEILQDVFIKVWEK-RDliDPEQPFKSyLFQ-ISRYTVYNFFRKANLDKKLKAYLSF-------------ENTELYT 121
Cdd:PRK09047    5 DAALDIVQDAMIKLAEKyGD--RPAAEWPP-LFQrILQNRIHDWFRRQKVRNTWVSLFSSfsdddddddfdplETLDSAD 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2796099454 122 HIEEN----IVQRENSQLIMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSSTINDHIVKATKFLRERQSSFGTAL 197
Cdd:PRK09047   82 EGAESpadkLERAQVLQLIEEAIQKLPARQREAFLLRYWEDMDVAETAAAMGCSEGSVKTHCSRATHALAKALEAKGITL 161
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 124-175 5.22e-03

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


Pssm-ID: 440804 [Multi-domain]  Cd Length: 236  Bit Score: 36.73  E-value: 5.22e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2796099454 124 EENIVQRENSQLIMNAIEELPPQRKQIYKLCKIEGRSYAEVAMQLGISSSTI 175
Cdd:COG1191   168 EEELEHEELREALAEAIEQLPERERLVLSLYYFEELTLKEIAEVLGVSESRV 219
 
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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