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Conserved domains on  [gi|924285938|ref|WP_053473258|]
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MULTISPECIES: RNA polymerase sigma factor [Flavobacterium]

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]; ...
 2-175 4.07e-39

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: 131.27  E-value: 4.07e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938   2 SQEELLVLIYKKDERAFTHLYDMYSKSLFSVINVLIKNREEAEDVLQEVFVKIWKNIDSYNEsKGRFYTWILNIARNTSI 81
Cdd:COG1595    3 SDEELLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRG-RGSFRAWLYRIARNLAI 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938  82 DKLRSKnfnNSQKNLSSDNFVNLLDDS----NKLINRIDTIGIQEFVKKLKPKCIEIIDLLFFKGYTQQEASEELALPLG 157
Cdd:COG1595   82 DHLRKR---RRRRELLDELAEELPDEAadpeEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEG 158

                        170
                 ....*....|....*...
gi 924285938 158 TIKTQNRNCINDLRNYLK 175
Cdd:COG1595  159 TVKSRLSRARKKLREALE 176
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 2-175 4.07e-39

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: 131.27  E-value: 4.07e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938   2 SQEELLVLIYKKDERAFTHLYDMYSKSLFSVINVLIKNREEAEDVLQEVFVKIWKNIDSYNEsKGRFYTWILNIARNTSI 81
Cdd:COG1595    3 SDEELLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRG-RGSFRAWLYRIARNLAI 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938  82 DKLRSKnfnNSQKNLSSDNFVNLLDDS----NKLINRIDTIGIQEFVKKLKPKCIEIIDLLFFKGYTQQEASEELALPLG 157
Cdd:COG1595   82 DHLRKR---RRRRELLDELAEELPDEAadpeEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEG 158

                        170
                 ....*....|....*...
gi 924285938 158 TIKTQNRNCINDLRNYLK 175
Cdd:COG1595  159 TVKSRLSRARKKLREALE 176
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 1-175 4.74e-30

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 108.46  E-value: 4.74e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938   1 MSQEELLVLIYKKDERAFTHLYDMYSKSLFSVINVLIKNREEAEDVLQEVFVKIWKNIDSYNESKGRFYTWILNIARNTS 80
Cdd:PRK13919   8 LSDEALLALVARGEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRRGSARAWLLALAHHAA 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938  81 IDKLRSKNFNNS--QKNLSSDNFVNL----LDDSNKLinriDTIGIQEFVKKLKPKCIEIIDLLFFKGYTQQEASEELAL 154
Cdd:PRK13919  88 VDHVRRRAARPQplEPDEREPEAFDLpgpgLDEEGHL----DRTRLGRALKALSPEERRVIEVLYYQGYTHREAAQLLGL 163

                        170       180
                 ....*....|....*....|.
gi 924285938 155 PLGTIKTQNRNCINDLRNYLK 175
Cdd:PRK13919 164 PLGTLKTRARRALSRLKEVLR 184
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 16-174 2.68e-29

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: 105.51  E-value: 2.68e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938   16 RAFTHLYDMYSKSLFSVINVLIKNREEAEDVLQEVFVKIWKNIDSYNEsKGRFYTWILNIARNTSIDKLRSKNFNNSQKN 95
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDP-EGSFKAWLFRIARNLILDYLRRKRRLRRELD 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 924285938   96 LSSDNFVNLLDDSNKLINRIDTIGIQEFVKKLKPKCIEIIDLLFFKGYTQQEASEELALPLGTIKTQNRNCINDLRNYL 174
Cdd:TIGR02937  80 LLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 21-88 2.67e-15

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: 66.84  E-value: 2.67e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 924285938   21 LYDMYSKSLFSVINVLIKNREEAEDVLQEVFVKIWKNIDSYNESKG-RFYTWILNIARNTSIDKLRSKN 88
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGvSFSTWLYTIIRNAIIDYLRKQR 69
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 120-161 6.26e-04

Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP).


Pssm-ID: 100119 [Multi-domain]  Cd Length: 55  Bit Score: 36.31  E-value: 6.26e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 924285938 120 IQEFVKKLKPKCIEIIDLLFFKGYTQQEASEELALPLGTIKT 161
Cdd:cd06171    4 LEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQ 45
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 2-175 4.07e-39

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: 131.27  E-value: 4.07e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938   2 SQEELLVLIYKKDERAFTHLYDMYSKSLFSVINVLIKNREEAEDVLQEVFVKIWKNIDSYNEsKGRFYTWILNIARNTSI 81
Cdd:COG1595    3 SDEELLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRG-RGSFRAWLYRIARNLAI 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938  82 DKLRSKnfnNSQKNLSSDNFVNLLDDS----NKLINRIDTIGIQEFVKKLKPKCIEIIDLLFFKGYTQQEASEELALPLG 157
Cdd:COG1595   82 DHLRKR---RRRRELLDELAEELPDEAadpeEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEG 158

                        170
                 ....*....|....*...
gi 924285938 158 TIKTQNRNCINDLRNYLK 175
Cdd:COG1595  159 TVKSRLSRARKKLREALE 176
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 1-175 4.74e-30

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 108.46  E-value: 4.74e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938   1 MSQEELLVLIYKKDERAFTHLYDMYSKSLFSVINVLIKNREEAEDVLQEVFVKIWKNIDSYNESKGRFYTWILNIARNTS 80
Cdd:PRK13919   8 LSDEALLALVARGEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRRGSARAWLLALAHHAA 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938  81 IDKLRSKNFNNS--QKNLSSDNFVNL----LDDSNKLinriDTIGIQEFVKKLKPKCIEIIDLLFFKGYTQQEASEELAL 154
Cdd:PRK13919  88 VDHVRRRAARPQplEPDEREPEAFDLpgpgLDEEGHL----DRTRLGRALKALSPEERRVIEVLYYQGYTHREAAQLLGL 163

                        170       180
                 ....*....|....*....|.
gi 924285938 155 PLGTIKTQNRNCINDLRNYLK 175
Cdd:PRK13919 164 PLGTLKTRARRALSRLKEVLR 184
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 16-174 2.68e-29

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: 105.51  E-value: 2.68e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938   16 RAFTHLYDMYSKSLFSVINVLIKNREEAEDVLQEVFVKIWKNIDSYNEsKGRFYTWILNIARNTSIDKLRSKNFNNSQKN 95
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDP-EGSFKAWLFRIARNLILDYLRRKRRLRRELD 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 924285938   96 LSSDNFVNLLDDSNKLINRIDTIGIQEFVKKLKPKCIEIIDLLFFKGYTQQEASEELALPLGTIKTQNRNCINDLRNYL 174
Cdd:TIGR02937  80 LLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 12-171 4.92e-27

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 100.43  E-value: 4.92e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938  12 KKDERAFTHLYDMYSKSLFSVINVLIKNREEAEDVLQEVFVKIWKNIDSYNeSKGRFYTWILNIARNTSIDKLRSKNFNN 91
Cdd:PRK11924   9 TGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFN-GKGSARTWLLTIARNVCYDLLRRRRREK 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938  92 ---SQKNLSSDNFVNLLDDSNKLINRIDTIGIQEFVKKLKPKCIEIIDLLFFKGYTQQEASEELALPLGTIKTQNRNCIN 168
Cdd:PRK11924  88 avlSDDALEPEFAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQ 167


                 ...
gi 924285938 169 DLR 171
Cdd:PRK11924 168 LLR 170
PRK12534 PRK12534
RNA polymerase sigma factor; Provisional
 5-175 1.37e-24

RNA polymerase sigma factor; Provisional


Pssm-ID: 183576 [Multi-domain]  Cd Length: 187  Bit Score: 94.35  E-value: 1.37e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938   5 ELLVLIYKKDERAFTHLYDMYSKSLFSVINVLIKNREEAEDVLQEVFVKIWKNIDSYNESKGRFYTWILNIARNTSIDKL 84
Cdd:PRK12534  14 RLLTATAGGDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRARGLTWLAMIARNKAIDHL 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938  85 RSKnfNNSQKNLSSDNFVNLLDDSNKLINRIDTIG----IQEFVKKLKPKCIEIIDLLFFKGYTQQEASEELALPLGTIK 160
Cdd:PRK12534  94 RAN--APQRRNVALDDAGELRAADASPLERTERAStrrrIDHCLAELEPPRSELIRTAFFEGITYEELAARTDTPIGTVK 171

                        170
                 ....*....|....*
gi 924285938 161 TQNRNCINDLRNYLK 175
Cdd:PRK12534 172 SWIRRGLAKLKACLE 186
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 5-161 2.00e-24

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 93.61  E-value: 2.00e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938   5 ELLVLIYKKDERAFTHLYDMYSKSLFSVINVLIKNREEAEDVLQEVFVKIWKNIDSYNESKgRFYTWILNIARNTSIDKL 84
Cdd:PRK09641   7 RLIKQVKKGDQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINR-KFSTWLYRIATNLTIDRL 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938  85 RSKNFN-------------NSQKNLSSDNfvNLLDDSNKLINRIDTigIQEFVKKLKPKCIEIIDLLFFKGYTQQEASEE 151
Cdd:PRK09641  86 RKRKPDyyldaevagteglTMYSQLAADD--ALPEEQVVSLELQET--IQEAILQLPEKYRTVIVLKYIEDLSLKEISEI 161

                        170
                 ....*....|
gi 924285938 152 LALPLGTIKT 161
Cdd:PRK09641 162 LDLPVGTVKT 171
PRK09646 PRK09646
ECF RNA polymerase sigma factor SigK;
4-174 2.53e-24

ECF RNA polymerase sigma factor SigK;


Pssm-ID: 182015 [Multi-domain]  Cd Length: 194  Bit Score: 93.58  E-value: 2.53e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938   4 EELLVLIYKKDERAFTHLYDMYSKSLFSVINVLIKNREEAEDVLQEVFVKIWKNIDSYNESKGRFYTWILNIARNTSIDK 83
Cdd:PRK09646  18 DALLRRVARGDQDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDPARGSALAWLLTLAHRRAVDR 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938  84 LRSknfnnSQKNLSSDNFVNLLD-----D--SNKLINRIDTIGIQEFVKKLKPKCIEIIDLLFFKGYTQQEASEELALPL 156
Cdd:PRK09646  98 VRS-----EQAASQREVRYGARNvdpafDqvAEEVEARLERERVRDCLDALTDTQRESVTLAYYGGLTYREVAERLAVPL 172

                        170
                 ....*....|....*...
gi 924285938 157 GTIKTQNRNCINDLRNYL 174
Cdd:PRK09646 173 GTVKTRMRDGLIRLRDCL 190
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 1-174 4.54e-23

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 90.27  E-value: 4.54e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938   1 MSQEELLVLIYK---KDERAFTHLYDMYSKSLFSVINVLIKNREEAEDVLQEVFVKIWKNIDSYNESKGRFYTWILNIAR 77
Cdd:PRK12514   1 TQPDDIEKLIVRvslGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSGLSPMTWLITIAR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938  78 NTSIDKLRSKNfnnsQKNLSSDNFVNLLDDS----NKLINRIDTIGIQEFVKKLKPKCIEIIDLLFFKGYTQQEASEELA 153
Cdd:PRK12514  81 NHAIDRLRARK----AVAVDIDEAHDLADPSpgpeAEVIAGDEGQRIDACLEELEKDRAAAVRRAYLEGLSYKELAERHD 156

                        170       180
                 ....*....|....*....|.
gi 924285938 154 LPLGTIKTQNRNCINDLRNYL 174
Cdd:PRK12514 157 VPLNTMRTWLRRSLLKLRECL 177
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 17-174 3.55e-22

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: 87.23  E-value: 3.55e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938   17 AFTHLYDMYSKSLFSVINVLIKNREEAEDVLQEVFVKIWKNIDSYNESKgRFYTWILNIARNTSIDKLRSKNFNNSQKNL 96
Cdd:TIGR02985   2 AFEQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETLEISE-SIKAYLFTIVKNRCLNYLRHKQVEEKYQEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938   97 SSDNFVNLLDDSNKL-------INRIdtigIQEFVKKLKPKCIEIIDLLFFKGYTQQEASEELALPLGTIKTQNRNCIND 169
Cdd:TIGR02985  81 LAEIEERELSEADPEeeleakeLEEI----IEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKF 156


                  ....*
gi 924285938  170 LRNYL 174
Cdd:TIGR02985 157 LRKEL 161
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 2-175 5.38e-22

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 87.81  E-value: 5.38e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938   2 SQEELLVLIYKKDERAFTHLYDMYSKSLFSVINVLIKNREEAEDVLQEVFVKIWKNIdSYNESKGRFYTWILNIARNTSI 81
Cdd:PRK12519  15 SDAELFSALKAGQSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRKS-SYDPKRGSLSSYLLTLTRSRAI 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938  82 DKLRSKnfNNSQKNLSSDNFVNLLDDS-----NKLINRIDTIGIQEFVKKLKPKCIEIIDLLFFKGYTQQEASEELALPL 156
Cdd:PRK12519  94 DRLRSR--RSRQRLLERWQQELLGEASedtplEQASLAERSQRVQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPL 171

                        170
                 ....*....|....*....
gi 924285938 157 GTIKTQNRNCINDLRNYLK 175
Cdd:PRK12519 172 GTVKARARQGLLKLRELLQ 190
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 14-160 6.85e-21

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 84.47  E-value: 6.85e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938  14 DERAFTHLYDMYSKSLFSVINVLIKNREEAEDVLQEVFVKIWKNIDSYNEsKGRFYTWILNIARNTSIDKLRSKNFNNSQ 93
Cdd:PRK09652   8 DRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRG-GAAFYTWLYRIARNTAINYLRKQGRRPPA 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938  94 KNLSS------DNFVNLLDDSN-------KLINRIdtigIQEFVKKLKPKCIEIIDLLFFKGYTQQEASEELALPLGTIK 160
Cdd:PRK09652  87 SDVDAeeaedfDLADALRDISTpenellsAELEQR----VRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVR 162
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
14-161 2.72e-16

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 72.03  E-value: 2.72e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938  14 DERAFTHLYDMYSKSLFSVINVLIKNREEAEDVLQEVFVKIWKNIDSYNESKGRFYTWILNIARNTSIDKLRSKNFNNsq 93
Cdd:PRK09645   7 EAALMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTGRSARAWLFTVARNLVIDERRSARARP-- 84

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 924285938  94 KNLSSDNFVNLLDDSNKLINR-IDTIGIQEFVKKLKPKCIEIIDLLFFKGYTQQEASEELALPLGTIKT 161
Cdd:PRK09645  85 VEGGDDVLGVPEQSAPDEVDRaLDRLLVADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKS 153
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 1-175 6.44e-16

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 71.32  E-value: 6.44e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938   1 MSQEELLVLIYKKDERAFTHLYDMYSKSLFSVINVLIKNREEAEDVLQEVFVKIWKNIDSYNeSKGRFYTWILNIARNTS 80
Cdd:PRK09415   1 MEELTIEAFEIEDKEDLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYK-GKSSLKTWLYRIAINHC 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938  81 IDKLRSknFNNSQKNLSSDNFVNLLDDSN----KLINRIDTIGIQEFVKKLKPKCIEIIDLLFFKGYTQQEASEELALPL 156
Cdd:PRK09415  80 KDYLKS--WHNKKVIVTEDIFTYMESQKEsveeEVIQNAEDERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNE 157

                        170
                 ....*....|....*....
gi 924285938 157 GTIKTQNRNCINDLRNYLK 175
Cdd:PRK09415 158 NTVKTRLKKAKELLKKGLE 176
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 2-85 9.02e-16

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 71.22  E-value: 9.02e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938   2 SQEELLVLIYKKDERAFTHLYDMYSKSLFSVINVLIKNREEAEDVLQEVFVKIWKNIDSYNESKGRFYTWILNIARNTSI 81
Cdd:PRK05602   6 PDEELLARVAAGDPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPGEARFDTWLHRVVLNLCY 85


                 ....
gi 924285938  82 DKLR 85
Cdd:PRK05602  86 DRLR 89
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 20-160 2.21e-15

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 70.01  E-value: 2.21e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938  20 HLYDMYSKSLFSVINVLIKNREEAEDVLQEVFVKIWKNIDSYNeSKGRFYTWILNIARNTSIDKLRSKNfnnsQKNLSSD 99
Cdd:PRK09637   5 SIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLK-DGSSIKSWLYQIANNTIIDFYRKKN----RSEELPD 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 924285938 100 NFVNLLDDSNKLINRIDTIGIQEFVKKLKPKCIEIIDLLFFKGYTQQEASEELALPLGTIK 160
Cdd:PRK09637  80 DLLFEDEEREENAKKELAPCLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAK 140
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 21-88 2.67e-15

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: 66.84  E-value: 2.67e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 924285938   21 LYDMYSKSLFSVINVLIKNREEAEDVLQEVFVKIWKNIDSYNESKG-RFYTWILNIARNTSIDKLRSKN 88
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGvSFSTWLYTIIRNAIIDYLRKQR 69
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 2-162 3.52e-15

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 69.76  E-value: 3.52e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938   2 SQEELLVLIYKKDERAFTHLYDMYSKSLFSVINVLIKNREEAEDVLQEVFVKIWKNIDSYnESKGRFYTWILNIARNTSI 81
Cdd:PRK12515   8 TDEMLLARIAQGDRTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQF-EGRSQVSTWLLSIARFKAL 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938  82 DKLRSKNFnnsqKNLSSDNFVNLLDDSNK---LINRIDTIGI-QEFVKKLKPKCIEIIDLLFFKGYTQQEASEELALPLG 157
Cdd:PRK12515  87 SALRRRKH----EEIDDEAAAAIEDGADTpevALQKSDTSAAlRACLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPES 162


                 ....*
gi 924285938 158 TIKTQ 162
Cdd:PRK12515 163 TVKTR 167
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 14-172 7.32e-15

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 68.61  E-value: 7.32e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938  14 DERAFTHLYDMYSKSLFSVINVLIKNREEAEDVLQEVFVKIWKNIDSYNESKGrFYTWILNIARNtSIDKLRSKNFN--- 90
Cdd:PRK12543   5 DQEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNRP-FRFWLIGLVIK-QIHSWRRKRWRrfr 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938  91 --NSQKNLSSDNFVnllDDSNKLINRIDTIGIQEFVKKLKPKCIEIIDLLFFKGYTQQEASEELALPLGTIKTQNRNCIN 168
Cdd:PRK12543  83 ifEKAEEQRKPVSI---DFSEDVLSKESNQELIELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAALK 159


                 ....
gi 924285938 169 DLRN 172
Cdd:PRK12543 160 KLRQ 163
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 14-171 1.54e-14

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 67.88  E-value: 1.54e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938  14 DERAFTHLYDMYSKSLFSVINVLIKNREEAEDVLQEVFVKIWKNIDSYNESKGRFYTWILNIARNTSIDKLRsknfnNSQ 93
Cdd:PRK12537  21 DRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPARGSARGWIYSVTRHLALNVLR-----DTR 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938  94 KN--LSSDNFvnllDDSNKLINRIDTIGIQEFVKKLKpKCIEIID------LL--FFKGYTQQEASEELALPLGTIKTQN 163
Cdd:PRK12537  96 REvvLDDDAE----ETAQTLHEIIDDFDLWANSGKIH-RCLEQLEparrncILhaYVDGCSHAEIAQRLGAPLGTVKAWI 170


                 ....*...
gi 924285938 164 RNCINDLR 171
Cdd:PRK12537 171 KRSLKALR 178
PRK12526 PRK12526
RNA polymerase sigma factor; Provisional
 12-174 1.32e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 237127 [Multi-domain]  Cd Length: 206  Bit Score: 65.59  E-value: 1.32e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938  12 KKDERAFTHLYDMYSKSLFSVINVLIKNREEAEDVLQEVFVKIWKNIDSYNESKGRFYTWILNIARNTSIDKLRSKNFNN 91
Cdd:PRK12526  34 SRDKQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKGAATTWVYTVMRNAAFDMLRKIKAKK 113

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938  92 SQkNLSSD------NFVNLLDDSNKLINRIDTIGIQEFVKKLKPKCIEIIDLLFFKGYTQQEASEELALPLGTIKTQNRN 165
Cdd:PRK12526 114 EQ-NLGDDiwpieqALAESQSESEEFSDHLMDKQILSYIEKLPEAQQTVVKGVYFQELSQEQLAQQLNVPLGTVKSRLRL 192


                 ....*....
gi 924285938 166 CINDLRNYL 174
Cdd:PRK12526 193 ALAKLKVQM 201
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 4-85 2.58e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 64.71  E-value: 2.58e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938   4 EELLVLIYKK-DERAFTHLYDMYSKSLFSVINVLIKNREEAEDVLQEVFVKIWKNIDSYnESKGRFYTWILNIARNTSID 82
Cdd:PRK12513  13 DEALMLRYRAgDAAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQY-QPRARFRTWLYQIARNLLID 91


                 ...
gi 924285938  83 KLR 85
Cdd:PRK12513  92 HWR 94
PRK06811 PRK06811
RNA polymerase factor sigma-70; Validated
 1-159 3.67e-12

RNA polymerase factor sigma-70; Validated


Pssm-ID: 180707 [Multi-domain]  Cd Length: 189  Bit Score: 61.49  E-value: 3.67e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938   1 MSQEELLVLIYKKDERAFTHLYDMYSKSLFSVI-NVL--IKNREEAEDVLQEVFVKIWKNIDSYNESKGRFYTWILNIAR 77
Cdd:PRK06811   3 INEDNFIKELKKKNEKALEFIVDTYGNLVKKIVhKVLgtVNYSQLIEECVNDIFLSIWNNIDKFDEEKGSFKKWIAAISK 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938  78 NTSIDKLRSKNFNNSQKNLSSDNFVNLLDDSNKLINRIDTIGIQEFVKKLKPKCIEIIDLLFFKGYTQQEASEELALPLG 157
Cdd:PRK06811  83 YKAIDYKRKLTKNNEIDSIDEFILISEESIENEIILKENKEEILKLINDLEKLDREIFIRRYLLGEKIEEIAKKLGLTRS 162


                 ..
gi 924285938 158 TI 159
Cdd:PRK06811 163 AI 164
PRK12522 PRK12522
RNA polymerase sigma factor; Provisional
 21-175 6.18e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 183571 [Multi-domain]  Cd Length: 173  Bit Score: 60.65  E-value: 6.18e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938  21 LYDMYSKSLFSVINVLIKNREEAEDVLQEVFVKIWKNIDSYNESKgRFYTWILNIARNTSIDKLRSKnfnNSQKNLSSDN 100
Cdd:PRK12522   8 LIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVE-NYKKWITTICVRTFYDFYRKK---KRWKDRILDL 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938 101 F-------VNLLDDSN---KLINRIDTIGIQEFVKKLKPKCIEIIDLLFFKGYTQQEASEELALPLGTIKTQNRNCINDL 170
Cdd:PRK12522  84 FhkedggeIEFADDVNiseEFIQKVEAEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQM 163


                 ....*
gi 924285938 171 RNYLK 175
Cdd:PRK12522 164 REHLE 168
algU PRK11923
RNA polymerase sigma factor AlgU; Provisional
 2-162 8.29e-12

RNA polymerase sigma factor AlgU; Provisional


Pssm-ID: 171347 [Multi-domain]  Cd Length: 193  Bit Score: 60.59  E-value: 8.29e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938   2 SQEELLVLIYKKDERAFTHLYDMYSKSLFSVINVLIKNREEAEDVLQEVFVKIWKNIDSYnESKGRFYTWILNIARNTsi 81
Cdd:PRK11923   6 EDQQLVERVQRGDKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNF-RGDSAFYTWLYRIAINT-- 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938  82 dklrSKNFNNSQKNLSSDNFVNLLD----DSNKLINRIDT-----------IGIQEFVKKLKPKCIEIIDLLFFKGYTQQ 146
Cdd:PRK11923  83 ----AKNHLVSRGRRPPDSDVSSEDaefyDGDHALKDIESperallrdeieGTVHRTIQQLPEDLRTALTLREFDGLSYE 158

                        170
                 ....*....|....*.
gi 924285938 147 EASEELALPLGTIKTQ 162
Cdd:PRK11923 159 DIASVMQCPVGTVRSR 174
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 1-171 6.72e-11

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 57.72  E-value: 6.72e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938   1 MSQEELLVLIYKKDERAFTHLYDMYSKSLFSVINVLIKNREEAEDVLQEVFVKIWKNIDSYN-ESKgrFYTWILNIARNT 79
Cdd:PRK09638   3 MDEKELIQKAKKGDDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQgRSK--FSTWLISIASRL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938  80 SIDKLRSKNFNNSQKNLSSDNFVNLLDDSNKLINrIDTIGIQEFVKKLKPKCIEIIDLLFFKGYTQQEASEELALPLGTI 159
Cdd:PRK09638  81 YKDHLRKQKREKLRLQRAKEETLRKEKWEAAIKG-AEWSEMLDALSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTV 159

                        170
                 ....*....|..
gi 924285938 160 KTQNRNCINDLR 171
Cdd:PRK09638 160 KSRVHHGIKQLR 171
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 14-161 6.85e-11

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 57.65  E-value: 6.85e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938  14 DERAFTHLYDMYSKSLFSVINVLIKNREEAEDVLQEVFVKIWKNIDSYNESKGrfyTWILNIARNTSIDKLRS-KNFNNS 92
Cdd:PRK09639   1 SDETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRSDFKGIENEK---GWLIKSARNVAYNYLRSeKRRRAR 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938  93 QKNLSSDNFVNLLDDSNKLINRIDTIG-IQEFVKKLKPKCIEIIdLLFFKGYTQQEASEELALPLGTIKT 161
Cdd:PRK09639  78 ILGEFQWQEVDNEPSPEEIWIRKEEITkVQEVLAKMTERDRTVL-LLRFSGYSYKEIAEALGIKESSVGT 146
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 1-175 7.46e-11

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 58.03  E-value: 7.46e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938   1 MSQEELLVLIYKK---DERAFTHLYDMYSKSLFSVINVLIKNREEAEDVLQEVFVKIWKNIDSYnESKGRFYTWILNIAR 77
Cdd:PRK09640   8 LNDEELVARVHVElfhVTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNF-EGKSKFKTWLYSITY 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938  78 NTSIDKLRSKNFNNSQKN-LSSDNFVNLLDDSNKLINriDTIGIQEFVKKLKPKCIEIIDLLFFKGYTQQEASEELALPL 156
Cdd:PRK09640  87 NECITQYRKERRKRRLMDaLSLDPLEEASEEKAPKPE--ERGGLDRWLVHVNPIDREILVLRFVAELEFQEIADIMHMGL 164

                        170
                 ....*....|....*....
gi 924285938 157 GTIKTQNRNCINDLRNYLK 175
Cdd:PRK09640 165 SATKMRYKRALDKLREKFA 183
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 14-175 1.09e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 54.72  E-value: 1.09e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938  14 DERAFTHLYDMYSKSLFSVINVLIkNREEAEDVLQEVFVKIWKNIDSYnESKGRFYTWILNIARNTSIDKLRSKNFNNSQ 93
Cdd:PRK12518   9 DRQSFRQLYRRYQQKVRSTLYQLC-GRELLDDLVQEVFLRVWKGLPKL-RNPAYFSTWLYRITWNVATDARRQFAQRPSR 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938  94 KNLSSDNFVNLLDDSNKLINRIDTigiQEFVKK----LKPKCIEIIDLLFFKGYTQQEASEELALPLGTIKTQNRNCIND 169
Cdd:PRK12518  87 IQDDSLNDQPSRPSDTPDLMQLHY---QDLVQQglqtLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRLFYARRQ 163


                 ....*.
gi 924285938 170 LRNYLK 175
Cdd:PRK12518 164 LRKFLQ 169
PRK12531 PRK12531
RNA polymerase sigma factor; Provisional
 13-171 1.15e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 105726 [Multi-domain]  Cd Length: 194  Bit Score: 54.94  E-value: 1.15e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938  13 KDERAFTHLYDMYSKSLFSVINVLIKNREEAEDVLQEVFVKIWKNIDSYNESKGRFYTWILNIARNTSIDKLRSKNFNN- 91
Cdd:PRK12531  24 RDKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQKSALSTWIYTIIRNLCFDLLRKQKGKDl 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938  92 ---SQKNLSSDNFVNLLDDSNKLINRIDTIGIQEFVKKLKPKCIEIIDLLFFKGYTQQEASEELALPLGTIKTQNRNCIN 168
Cdd:PRK12531 104 hihADDIWPSDYYPPDLVDHYSPEQDMLKEQVMKFLDRLPKAQRDVLQAVYLEELPHQQVAEMFDIPLGTVKSRLRLAVE 183


                 ...
gi 924285938 169 DLR 171
Cdd:PRK12531 184 KLR 186
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 2-86 2.49e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 54.20  E-value: 2.49e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938   2 SQEELLVLIYKKDERAFTHLYDMYSKSLFSVINVLIKNREEAEDVLQEVFVKIWKNIDSYnESKGRFYTWILNIARNTSI 81
Cdd:PRK11922  16 SDRELVARVLAGDEAAFEALMRRHNRRLYRTARAILRNDAEAEDVVQEAYLRAFRALGTF-RGDASLSTWLSRIVLNEAL 94


                 ....*
gi 924285938  82 DKLRS 86
Cdd:PRK11922  95 GRLRR 99
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 1-85 7.76e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 52.58  E-value: 7.76e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938   1 MSQEELLVLIYKKDERAFTHLYDMYSKSLFSVINVLIKNREEAEDVLQEVFVKIWKNIDSYNESKGRFYTWILNIARNTS 80
Cdd:PRK12524  11 VSDEALLVLYANGDPAAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQGEARVSTWLYRVVCNLC 90


                 ....*
gi 924285938  81 IDKLR 85
Cdd:PRK12524  91 TDRLR 95
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
 4-87 2.64e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 51.40  E-value: 2.64e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938   4 EELLVLIYKKDERAFTHLYDMYSKSLFSVINVLIKNREEAEDVLQEVFVKIWKNIDSYNESKGRFYTWILNIARNTSIDk 83
Cdd:PRK12538  51 EELLDRLATDDEAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRAKFSTWLYRVVSNRCID- 129


                 ....
gi 924285938  84 LRSK 87
Cdd:PRK12538 130 LRRK 133
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 16-164 7.24e-08

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: 49.24  E-value: 7.24e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938   16 RAFTHLYDMYSKSLFSVINVLIKNREEAEDVLQEVFVKIWKNIDSYNESKGrFYTWILNIARNtsidKLRsknfnNSQKN 95
Cdd:TIGR02989   1 KAFVRLLTRHERALRAFVRSLVADRDDVDDVLQETFVVAWRKFDQFDPGTN-FVAWARGIARN----KVL-----NYRRK 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938   96 LSSDNFVnlLDDSnkLINRI--------------DTIGIQEFVKKLKPKCIEIIDLLFFKGYTQQEASEELALPLGTI-K 160
Cdd:TIGR02989  71 LGRDRLV--FDDD--LLEALaaeaepteaerlsdDRQALEGCLEKLPERQRELLDLRYQRGQKATALAEQTGRTVNAVyK 146


                  ....
gi 924285938  161 TQNR 164
Cdd:TIGR02989 147 ALQR 150
PRK08241 PRK08241
RNA polymerase subunit sigma-70;
42-88 1.11e-06

RNA polymerase subunit sigma-70;


Pssm-ID: 236196 [Multi-domain]  Cd Length: 339  Bit Score: 47.24  E-value: 1.11e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 924285938  42 EAEDVLQEVFVKIWKNIDSYnESKGRFYTWILNIARNTSIDKLRSKN 88
Cdd:PRK08241  45 DAEDAVQETLLRAWRGYDRF-EGRSSLRTWLYRIATNVCLDALEGRA 90
PRK12542 PRK12542
RNA polymerase sigma factor; Provisional
 10-162 1.32e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183581 [Multi-domain]  Cd Length: 185  Bit Score: 46.20  E-value: 1.32e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938  10 IYKKDERAFTHLYDMYSKSLFSVINVLIKNREEAEDVLQEVFVKIWKNIDS-YNESKGRFYTWILNIARNTSIDKLRSKN 88
Cdd:PRK12542   3 VTNNDYEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKlHSLNTQELKRYILRVAKNKAIDSYRKNK 82

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 924285938  89 FNNSQKNLSSDNFVNLLDDSNKLINR--IDTIGIQEFVKKLKPKCIEIIDLLFFKGYTQQEASEELALPLGTIKTQ 162
Cdd:PRK12542  83 RHETFLEEYERESIEAVDENIEEWEKrkMSEVQIDTLLKELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQ 158
PRK12530 PRK12530
RNA polymerase sigma factor; Provisional
 37-88 4.23e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 237128 [Multi-domain]  Cd Length: 189  Bit Score: 44.76  E-value: 4.23e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 924285938  37 IKNREEAEDVLQEVFVKIWKNIDSYnESKGRFYTWILNIARNTSIDKLRSKN 88
Cdd:PRK12530  28 LKDADLAEDVVQEALVSAYKNADSF-KGQSALKTWIFAILKNKIIDLIRYRK 78
PRK09643 PRK09643
RNA polymerase sigma factor SigM; Reviewed
 2-161 5.49e-06

RNA polymerase sigma factor SigM; Reviewed


Pssm-ID: 236604 [Multi-domain]  Cd Length: 192  Bit Score: 44.70  E-value: 5.49e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938   2 SQEELLVLIYKKDERAFTHLYDMYSKSLFSVINVLIKNREEAEDVLQEVFVKIWKNIDSYN-ESKGRfyTWILNIARNTS 80
Cdd:PRK09643  13 SDAELLAAHVAGDRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRgDAAVS--SWLHRIVVNAC 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938  81 IDKLRSknfNNSQKNLSSDNFVNLLDDSNKLINRIDT-IGIQEFVKKLKPK---CIEIIDLLffkGYTQQEASEELALPL 156
Cdd:PRK09643  91 LDRLRR---AKARPTVPLDDVYPVAQLERDPTARVETaLAVQRALMRLPVEqraALVAVDMQ---GYSVADAARMLGVAE 164


                 ....*
gi 924285938 157 GTIKT 161
Cdd:PRK09643 165 GTVKS 169
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 21-161 5.65e-06

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 44.10  E-value: 5.65e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938  21 LYDMYSKSLFSVINVLIKNREEAEDVLQEVFVKIWKNIDSYNESKGRfyTWILNIARNTSIDKLR--------SKNFNNS 92
Cdd:PRK09644   6 IYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDNQKVK--PWLFKVAYHTFIDFVRkekkvsfvGTDEIEA 83

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 924285938  93 QKNLSSDNFVNLLDDSNKLINRIDTigiqefvkkLKPKCIEIIDLLFFKGYTQQEASEELALPLGTIKT 161
Cdd:PRK09644  84 IQAESTEEYVVAKNSYEKLIQIIHT---------LPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKS 143
PRK12547 PRK12547
RNA polymerase sigma factor; Provisional
 36-176 1.71e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 139056 [Multi-domain]  Cd Length: 164  Bit Score: 42.94  E-value: 1.71e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938  36 LIKNREEAEDVLQEVFVKIWKNIDSYnESKGRFYTWILNIARNTSIDKLRSKNfnnsqknlssdnfVNLLDDSNKLINRI 115
Cdd:PRK12547  26 LSSKHDKAEDLVQDTLMKAWAKQDSF-EMGTNLKAWLFTILRNEFYSQMRKRG-------------REVQDSDGVFTARV 91

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 924285938 116 D-------TIGIQEFVK---KLKPKCIEIIDLLFFKGYTQQEASEELALPLGTIKTQNRNCINDLRNYLKI 176
Cdd:PRK12547  92 AvhpaqygSLDLQDFKKalnLLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARNRLQELLKV 162
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 13-160 1.76e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 43.00  E-value: 1.76e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938  13 KDERAFTHLYDMYSKSLFSVINVLIKNREEAEDVLQEVFVKIWKNIDSYNESKGRfyTWILNIARNTSIDKLRsKNFNNS 92
Cdd:PRK12541   2 KRKQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGEEIR--PWLFTIAYNAFIDWYR-KEKKYK 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 924285938  93 QKNLSSDNFVNLLDDSNKLINRIDTIGIQEFVKKLKPKCIEIIDLLFFKGYTQQEASEELALPLGTIK 160
Cdd:PRK12541  79 TTTIEEFHLPNVPSTEHEYFIKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVK 146
PRK08215 PRK08215
RNA polymerase sporulation sigma factor SigG;
106-175 2.44e-05

RNA polymerase sporulation sigma factor SigG;


Pssm-ID: 181296 [Multi-domain]  Cd Length: 258  Bit Score: 43.01  E-value: 2.44e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938 106 DDSNKLINRIDTIGIQEFVKKLKPKCIEIIDLLFFKGYTQQEASEELALPLGTIKTQNRNCINDLRNYLK 175
Cdd:PRK08215 189 DEKNKDENWLEEIALKEAMKKLNDREKLILNLRFFQGKTQMEVAEEIGISQAQVSRLEKAALKHMRKYIQ 258
PRK09642 PRK09642
RNA polymerase sigma factor;
25-109 5.81e-05

RNA polymerase sigma factor;


Pssm-ID: 170031 [Multi-domain]  Cd Length: 160  Bit Score: 41.24  E-value: 5.81e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938  25 YSKSLFSVINVLIKNREEAEDVLQEVFVKIWKNIDSYnESKGrFYTWILNIARNTSIDKLRSKNFNNSQKNLSSDNFVNL 104
Cdd:PRK09642   4 YRHYIFQVIFSILRHEEDAKDVTQEVFVKIHASLPNY-QFRG-LKTWMARIATNHAIDYKRKKARENEELSLCKETEENI 81


                 ....*
gi 924285938 105 LDDSN 109
Cdd:PRK09642  82 KSSHN 86
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
 36-164 8.04e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 41.36  E-value: 8.04e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938  36 LIKNREEAEDVLQEVFVKIWKNIDSYNESKgRFYTWILNIARNT--SIDKLRSKNFNNSQKNLSSDNFVNLLDDSnklin 113
Cdd:PRK12546  27 LTRNVAVADDLVQDTIVKAWTNFDKFQEGT-NLRAWLFTILRNTfySDRRKHKREVPDPEGVHAASLAVKPAHDG----- 100

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 924285938 114 RIDTIGIQEFVKKLKPKCIEIIDLLFFKGYTQQEASEELALPLGTIKTQ-NR 164
Cdd:PRK12546 101 RLAMSDFRAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRaNR 152
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 36-176 9.60e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 41.10  E-value: 9.60e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938  36 LIKNREEAEDVLQEVFVKIWKNIDSYnESKGRFYTWILNIARNTSIDKLRS--KNFNNSQKNLSSDNFVNllddsnklIN 113
Cdd:PRK12516  30 LIGRHDRADDLVQDTIMKAWAKQDHF-EVGTNMKAWLFTILRNEFYSQMRKrgREVQDTDGMFTEQLAVH--------PS 100

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 924285938 114 RIDTIGIQEFVK---KLKPKCIEIIDLLFFKGYTQQEASEELALPLGTIKTQNRNCINDLRNYLKI 176
Cdd:PRK12516 101 QYGTLDLQDFRAaldQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQRLQEILQI 166
PRK12544 PRK12544
RNA polymerase factor sigma-70;
43-108 1.35e-04

RNA polymerase factor sigma-70;


Pssm-ID: 183583 [Multi-domain]  Cd Length: 206  Bit Score: 40.94  E-value: 1.35e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 924285938  43 AEDVLQEVFVKIWKNIDSYnesKGR--FYTWILNIARNTSIDKLRSKNFNNSQKNLSSD-----NFVNLLDDS 108
Cdd:PRK12544  45 AEDAVQEALIGALKNADSF---AGRaaFKTWVFAILKNKIIDLLRQKKRHVSASSLLRDeeeeeDFEELFDES 114
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 36-88 3.03e-04

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 39.77  E-value: 3.03e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 924285938  36 LIKNREEAEDVLQEVFVKIWKNIDSYneSKGRFYTWILNIARNTSIDKLRSKN 88
Cdd:PRK09647  48 LSGNQHDAEDLTQETFIRVFRSLQNY--QPGTFEGWLHRITTNLFLDMVRRRA 98
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 120-161 6.26e-04

Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP).


Pssm-ID: 100119 [Multi-domain]  Cd Length: 55  Bit Score: 36.31  E-value: 6.26e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 924285938 120 IQEFVKKLKPKCIEIIDLLFFKGYTQQEASEELALPLGTIKT 161
Cdd:cd06171    4 LEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQ 45
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 125-172 6.90e-04

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: 35.87  E-value: 6.90e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 924285938  125 KKLKPKCIEIIDLLFFKGYTQQEASEELALPLGTIKTQNRNCINDLRN 172
Cdd:pfam04545   3 ASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 36-159 8.85e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 38.23  E-value: 8.85e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938  36 LIKNREEAEDVLQEVFVKIWKNIDSYnESKGRFYTWILNIARNTSIDKLRSKNFNNSQknlsSDNFVNLLDDSNKLI--N 113
Cdd:PRK12511  24 LTRDSAEAEDLVHDALVRALERRASF-RSGGNLRTWLMSILHNAFIDELRRRRVEARR----ADELAVLADASLPAAqeH 98

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 924285938 114 RIDTIGIQEFVKKLKPKCIEIIDLLFFKGYTQQEASEELALPLGTI 159
Cdd:PRK12511  99 AVRLAQIRDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTL 144
PRK12517 PRK12517
RNA polymerase sigma factor; Provisional
 36-161 1.02e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183569 [Multi-domain]  Cd Length: 188  Bit Score: 38.13  E-value: 1.02e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 924285938  36 LIKNREEAEDVLQEVFVKIWKNIDSYNESKGRfYTWILNIARNTSIDKLRSKNFNNS--QKNLSSDNFVNLLDDSnklin 113
Cdd:PRK12517  43 LCKDKHIAEDLVQETFLRAWRSLDSLKDEKAA-KAWLITILRRENARRFERKQFDLVdiEDDSIEDDASHSSEEE----- 116

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 924285938 114 rIDTIGIQEFVKKLKPKCIEIIDLLFFKGYTQQEASEELALPLGTIKT 161
Cdd:PRK12517 117 -MEQEWLRRQIAKLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMT 163
PRK12533 PRK12533
RNA polymerase sigma factor; Provisional
 39-79 3.95e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237129 [Multi-domain]  Cd Length: 216  Bit Score: 36.63  E-value: 3.95e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 924285938  39 NREEAEDVLQEVFVKIWKNIDSYNESKGRfyTWILNIARNT 79
Cdd:PRK12533  41 NASDADDVVQEACMRALRFFDSFRGDNAR--PWLLAIVRHT 79
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
 36-91 9.96e-03

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 35.05  E-value: 9.96e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 924285938  36 LIKNREEAEDVLQEVFVKIwknIDSYNESKGRFY-TWILNIARNTSIDKLRSKNFNN 91
Cdd:PRK07037  18 IVGCRSRAEDVVQDAFVKL---VEAPNQDAVKQPvAYLFRIVRNLAIDHYRRQALEN 71
 
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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