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Conserved domains on  [gi|489052855|ref|WP_002963053|]
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MULTISPECIES: RNA polymerase sigma factor [Pseudoalteromonas]

Protein Classification

RNA polymerase sigma factor( domain architecture ID 11446377)

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 13-177 1.30e-49

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: 158.23  E-value: 1.30e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  13 EAALIERVKSGDQGAYTTLYELHIKRVYGLCLRLLADQAHAEDAAQEVFVQVWHKIALFDGRSQFSTWLYSVASNVAISY 92
Cdd:COG1595    4 DEELLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDH 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  93 LRKQKNWLQKVVSIEHSGMD-----EQSANDCKGLNGLDKLIVRLPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQ 167
Cdd:COG1595   84 LRKRRRRRELLDELAEELPDeaadpEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSR 163

                        170
                 ....*....|
gi 489052855 168 YHRARQLLQE 177
Cdd:COG1595  164 LSRARKKLRE 173
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 13-177 1.30e-49

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: 158.23  E-value: 1.30e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  13 EAALIERVKSGDQGAYTTLYELHIKRVYGLCLRLLADQAHAEDAAQEVFVQVWHKIALFDGRSQFSTWLYSVASNVAISY 92
Cdd:COG1595    4 DEELLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDH 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  93 LRKQKNWLQKVVSIEHSGMD-----EQSANDCKGLNGLDKLIVRLPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQ 167
Cdd:COG1595   84 LRKRRRRRELLDELAEELPDeaadpEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSR 163

                        170
                 ....*....|
gi 489052855 168 YHRARQLLQE 177
Cdd:COG1595  164 LSRARKKLRE 173
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 17-177 6.78e-41

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 136.09  E-value: 6.78e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  17 IERVKSGDQGAYTTLYELHIKRVYGLCLRLLADQAHAEDAAQEVFVQVWHKIALFDGRSQFSTWLYSVASNVAISYLRKQ 96
Cdd:PRK09652   1 VERVQRGDRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRGGAAFYTWLYRIARNTAINYLRKQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  97 KNWLQKVVSIEHSGMDEQSANDCKGLNGLDKL-------------IVRLPERARMVFVLFAIEGYRHEEIAEQLGMAVGS 163
Cdd:PRK09652  81 GRRPPASDVDAEEAEDFDLADALRDISTPENEllsaeleqrvraaIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGT 160

                        170
                 ....*....|....
gi 489052855 164 SKSQYHRARQLLQE 177
Cdd:PRK09652 161 VRSRIFRAREALRA 174
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 27-177 8.10e-37

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: 125.15  E-value: 8.10e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855   27 AYTTLYELHIKRVYGLCLRLLADQAHAEDAAQEVFVQVWHKIALFDGRSQFSTWLYSVASNVAISYLRKQKNWLQKVVSI 106
Cdd:TIGR02937   2 AFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDLL 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489052855  107 ----EHSGMDEQSANDCKGLNGLDKLIVRLPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQYHRARQLLQE 177
Cdd:TIGR02937  82 eellDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRE 156
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 31-97 2.37e-17

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: 72.24  E-value: 2.37e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489052855   31 LYELHIKRVYGLCLRLLADQAHAEDAAQEVFVQVWHKIALFD-GRSQ-FSTWLYSVASNVAISYLRKQK 97
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDpERGVsFSTWLYTIIRNAIIDYLRKQR 69
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 125-176 5.56e-08

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: 47.48  E-value: 5.56e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 489052855 125 LDKLIVRLPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQYHRARQLLQ 176
Cdd:cd06171    4 LEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 13-177 1.30e-49

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: 158.23  E-value: 1.30e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  13 EAALIERVKSGDQGAYTTLYELHIKRVYGLCLRLLADQAHAEDAAQEVFVQVWHKIALFDGRSQFSTWLYSVASNVAISY 92
Cdd:COG1595    4 DEELLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDH 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  93 LRKQKNWLQKVVSIEHSGMD-----EQSANDCKGLNGLDKLIVRLPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQ 167
Cdd:COG1595   84 LRKRRRRRELLDELAEELPDeaadpEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSR 163

                        170
                 ....*....|
gi 489052855 168 YHRARQLLQE 177
Cdd:COG1595  164 LSRARKKLRE 173
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 17-177 6.78e-41

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 136.09  E-value: 6.78e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  17 IERVKSGDQGAYTTLYELHIKRVYGLCLRLLADQAHAEDAAQEVFVQVWHKIALFDGRSQFSTWLYSVASNVAISYLRKQ 96
Cdd:PRK09652   1 VERVQRGDRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRGGAAFYTWLYRIARNTAINYLRKQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  97 KNWLQKVVSIEHSGMDEQSANDCKGLNGLDKL-------------IVRLPERARMVFVLFAIEGYRHEEIAEQLGMAVGS 163
Cdd:PRK09652  81 GRRPPASDVDAEEAEDFDLADALRDISTPENEllsaeleqrvraaIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGT 160

                        170
                 ....*....|....
gi 489052855 164 SKSQYHRARQLLQE 177
Cdd:PRK09652 161 VRSRIFRAREALRA 174
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 27-177 8.10e-37

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: 125.15  E-value: 8.10e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855   27 AYTTLYELHIKRVYGLCLRLLADQAHAEDAAQEVFVQVWHKIALFDGRSQFSTWLYSVASNVAISYLRKQKNWLQKVVSI 106
Cdd:TIGR02937   2 AFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDLL 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489052855  107 ----EHSGMDEQSANDCKGLNGLDKLIVRLPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQYHRARQLLQE 177
Cdd:TIGR02937  82 eellDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRE 156
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 13-178 6.69e-36

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 123.21  E-value: 6.69e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  13 EAALIERVKSGDQGAYTTLYELHIKRVYGLCLRLLADQAHAEDAAQEVFVQVWHKIALFDGRSQFSTWLYSVASNVAISY 92
Cdd:PRK09638   5 EKELIQKAKKGDDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGRSKFSTWLISIASRLYKDH 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  93 LRKQKNWLQKVVSIEHSGMDEQSANDC-KGLNGLD--KLIVRLPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQYH 169
Cdd:PRK09638  85 LRKQKREKLRLQRAKEETLRKEKWEAAiKGAEWSEmlDALSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTVKSRVH 164

                        170
                 ....*....|
gi 489052855 170 RA-RQLLQEW 178
Cdd:PRK09638 165 HGiKQLRKEW 174
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 16-176 2.73e-33

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 116.72  E-value: 2.73e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  16 LIERVKSGDQGAYTTLYELHIKRVYGLCLRLLADQAHAEDAAQEVFVQVWHKIALFDGRSQFSTWLYSVASNVAISYLRK 95
Cdd:PRK09641   8 LIKQVKKGDQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINRKFSTWLYRIATNLTIDRLRK 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  96 QKN--WLQKVVSiEHSGMDEQSANDCKGLNGLDKL------------IVRLPERARMVFVLFAIEGYRHEEIAEQLGMAV 161
Cdd:PRK09641  88 RKPdyYLDAEVA-GTEGLTMYSQLAADDALPEEQVvslelqetiqeaILQLPEKYRTVIVLKYIEDLSLKEISEILDLPV 166

                        170
                 ....*....|....*
gi 489052855 162 GSSKSQYHRARQLLQ 176
Cdd:PRK09641 167 GTVKTRIHRGREALR 181
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 22-182 1.13e-30

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 109.68  E-value: 1.13e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  22 SGDQGAYTTLYELHIKRVYGLCLRLLADQAHAEDAAQEVFVQVWHKIALFDGRSQFSTWLYSVASNVAISYLRkqKNWLQ 101
Cdd:PRK11924   9 TGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCYDLLR--RRRRE 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855 102 KVVSI----------EHSGMDEQSANDCKGLNgLDKLIVRLPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQYHRA 171
Cdd:PRK11924  87 KAVLSddalepefaeTAETPEAALLAKDDLAR-IDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRA 165

                        170
                 ....*....|.
gi 489052855 172 RQLLQEWYENE 182
Cdd:PRK11924 166 RQLLRECLEAQ 176
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 5-177 1.49e-29

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 108.51  E-value: 1.49e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855   5 KPEPTPLCEAALIERVKSGDQGAYTTLYELHIKRVYGLCLRLLADQAHAEDAAQEVFVQVWHKIALFDGRSQFSTWLYSV 84
Cdd:PRK11922   9 PPPLSAASDRELVARVLAGDEAAFEALMRRHNRRLYRTARAILRNDAEAEDVVQEAYLRAFRALGTFRGDASLSTWLSRI 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  85 ASNVAISYLRKQKNwLQKVVSIEhsgMDEQSANDCKGLNG------------------LDKLIVRLPERARMVFVLFAIE 146
Cdd:PRK11922  89 VLNEALGRLRRRRR-LVNLAEMV---MASTIAGGERTPLAdpaedperaaarreiralLERAIDALPDAFRAVFVLRVVE 164

                        170       180       190
                 ....*....|....*....|....*....|.
gi 489052855 147 GYRHEEIAEQLGMAVGSSKSQYHRARQLLQE 177
Cdd:PRK11922 165 ELSVEETAQALGLPEETVKTRLHRARRLLRE 195
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 27-177 4.29e-25

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: 94.94  E-value: 4.29e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855   27 AYTTLYELHIKRVYGLCLRLLADQAHAEDAAQEVFVQVWHKIALFDGRSQFSTWLYSVASNVAISYLRKQKN------WL 100
Cdd:TIGR02985   2 AFEQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETLEISESIKAYLFTIVKNRCLNYLRHKQVeekyqeEL 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489052855  101 QKVVSIEHSGMDEQSANDCKGLNG-LDKLIVRLPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQYHRARQLLQE 177
Cdd:TIGR02985  82 AEIEERELSEADPEEELEAKELEEiIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLRK 159
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 16-182 1.01e-24

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 94.40  E-value: 1.01e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  16 LIERVKSGDQGAYTTLYELHIKRVYGLcLRLLADQAHAEDAAQEVFVQVWHKIALFDGRSQFSTWLYSVASNVAISYlRK 95
Cdd:PRK12518   1 LILRCQRGDRQSFRQLYRRYQQKVRST-LYQLCGRELLDDLVQEVFLRVWKGLPKLRNPAYFSTWLYRITWNVATDA-RR 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  96 QKNWLQKVVSIEHSGMDEQSANDCKGLNGLD--KLIVR----LPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQYH 169
Cdd:PRK12518  79 QFAQRPSRIQDDSLNDQPSRPSDTPDLMQLHyqDLVQQglqtLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRLF 158

                        170
                 ....*....|...
gi 489052855 170 RARQLLQEWYENE 182
Cdd:PRK12518 159 YARRQLRKFLQQQ 171
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 13-177 1.82e-24

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 93.95  E-value: 1.82e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  13 EAALIERVKSGDQGAYTTLYELHIKRVYGLCLRLLADQAHAEDAAQEVFVQVWHKIALFD-GRSQFSTWLYSVASNVAIS 91
Cdd:PRK05602   7 DEELLARVAAGDPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRpGEARFDTWLHRVVLNLCYD 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  92 YLRKqknwlQKVVSIEHSG--MDEQSANDCKGLNGLDKLIVR-----LPERARMVFVLFAIEGYRHEEIAEQLGMAVGSS 164
Cdd:PRK05602  87 RLRR-----RREVPVEDAPdvPDPAPGPDAGLEARQRARRVEqalaaLPERQREAIVLQYYQGLSNIEAAAVMDISVDAL 161

                        170
                 ....*....|...
gi 489052855 165 KSQYHRARQLLQE 177
Cdd:PRK05602 162 ESLLARGRRALRA 174
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 15-177 6.40e-24

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 92.87  E-value: 6.40e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  15 ALIERVKSGDQGAYTTLYELHIKRVYGLCLRLLADQAHAEDAAQEVFVQVWHKIALFDGRSQFSTWLYSVASNVAISYLR 94
Cdd:PRK12515  11 MLLARIAQGDRTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGRSQVSTWLLSIARFKALSALR 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  95 KQKN-WL--QKVVSIEHSGMDEQSANDCKGLNG-LDKLIVRLPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQYHR 170
Cdd:PRK12515  91 RRKHeEIddEAAAAIEDGADTPEVALQKSDTSAaLRACLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKTRMFY 170


                 ....*..
gi 489052855 171 ARQLLQE 177
Cdd:PRK12515 171 ARKKLAE 177
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
 6-177 1.18e-22

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 90.69  E-value: 1.18e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855   6 PEPTPLCEAA------LIERVKSGDQGAYTTLYELHIKRVYGLCLRLLADQAHAEDAAQEVFVQVW-HKIALFDGRSQFS 78
Cdd:PRK12538  37 PDPPPVADAVfdedeeLLDRLATDDEAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWtHRGRWQHGRAKFS 116

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  79 TWLYSVASNVAISYLRKQKNWLQKVVSIEHSGMDEQSA----NDCKGLngLDKLIVRLPERARMVFVLFAIEGYRHEEIA 154
Cdd:PRK12538 117 TWLYRVVSNRCIDLRRKPRTENVDAVPEVADGKPDAVSvierNELSDL--LEAAMQRLPEQQRIAVILSYHENMSNGEIA 194

                        170       180
                 ....*....|....*....|...
gi 489052855 155 EQLGMAVGSSKSQYHRARQLLQE 177
Cdd:PRK12538 195 EVMDTTVAAVESLLKRGRQQLRD 217
PRK12534 PRK12534
RNA polymerase sigma factor; Provisional
 16-171 2.36e-22

RNA polymerase sigma factor; Provisional


Pssm-ID: 183576 [Multi-domain]  Cd Length: 187  Bit Score: 88.57  E-value: 2.36e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  16 LIERVKSGDQGAYTTLYELHIKRVYGLCLRLLADQAHAEDAAQEVFVQVWHKIALFD-GRSQFSTWLYSVASNVAISYLR 94
Cdd:PRK12534  15 LLTATAGGDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDpSRARGLTWLAMIARNKAIDHLR 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  95 KQKNWLQKvVSIEHSGmdEQSANDCKGLNGLDKLIVRL----------PERARMVFVLFaIEGYRHEEIAEQLGMAVGSS 164
Cdd:PRK12534  95 ANAPQRRN-VALDDAG--ELRAADASPLERTERASTRRridhclaelePPRSELIRTAF-FEGITYEELAARTDTPIGTV 170


                 ....*..
gi 489052855 165 KSQYHRA 171
Cdd:PRK12534 171 KSWIRRG 177
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 31-182 5.35e-22

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 86.93  E-value: 5.35e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  31 LYELHIKRVYGLCLRLLADQAHAEDAAQEVFVQVWHkiALFDGRSQFSTWLYSVASNVAISYLRKQKNWLQKV--VSIEH 108
Cdd:PRK09639   8 LFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYR--SDFKGIENEKGWLIKSARNVAYNYLRSEKRRRARIlgEFQWQ 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855 109 SGMDEQSANDC--------KGLNGLDKlivrLPERARMVFVL-FAieGYRHEEIAEQLGMAVGSSKSQYHRARQLLQEWY 179
Cdd:PRK09639  86 EVDNEPSPEEIwirkeeitKVQEVLAK----MTERDRTVLLLrFS--GYSYKEIAEALGIKESSVGTTLARAKKKFRKIY 159


                 ...
gi 489052855 180 ENE 182
Cdd:PRK09639 160 EQM 162
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 13-175 1.01e-20

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 84.34  E-value: 1.01e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  13 EAALIERVKSGDQGAYTTLYELHIKRVYGLCLRLLADQAHAEDAAQEVFVQVWHKIALFDGRSQFSTWLYSVASNVAISY 92
Cdd:PRK12519  16 DAELFSALKAGQSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRKSSYDPKRGSLSSYLLTLTRSRAIDR 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  93 LRKQKN-------WLQKVVS-------IEHSGMDEQSANDCKGLNgldklivRLPERARMVFVLFAIEGYRHEEIAEQLG 158
Cdd:PRK12519  96 LRSRRSrqrllerWQQELLGeasedtpLEQASLAERSQRVQTALA-------QLPESQRQVLELAYYEGLSQSEIAKRLG 168

                        170
                 ....*....|....*..
gi 489052855 159 MAVGSSKSqyhRARQLL 175
Cdd:PRK12519 169 IPLGTVKA---RARQGL 182
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 7-177 1.89e-20

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 83.83  E-value: 1.89e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855   7 EPTPLCEAALIERVKSG---DQGAYTTLYELHIKRVYGLCLRLLADQAHAEDAAQEVFVQVWHKIALFDGRSQFSTWLYS 83
Cdd:PRK09640   4 DPRELNDEELVARVHVElfhVTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGKSKFKTWLYS 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  84 VASNVAISYLRKQ--KNWLQKVVS---IEHSGMDEQSANDCKGlnGLDKLIVRLPERARMVFVLFAIEGYRHEEIAEQLG 158
Cdd:PRK09640  84 ITYNECITQYRKErrKRRLMDALSldpLEEASEEKAPKPEERG--GLDRWLVHVNPIDREILVLRFVAELEFQEIADIMH 161

                        170
                 ....*....|....*....
gi 489052855 159 MAVGSSKSQYHRARQLLQE 177
Cdd:PRK09640 162 MGLSATKMRYKRALDKLRE 180
algU PRK11923
RNA polymerase sigma factor AlgU; Provisional
 8-173 2.75e-20

RNA polymerase sigma factor AlgU; Provisional


Pssm-ID: 171347 [Multi-domain]  Cd Length: 193  Bit Score: 83.31  E-value: 2.75e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855   8 PTPLCEAALIERVKSGDQGAYTTLYELHIKRVYGLCLRLLADQAHAEDAAQEVFVQVWHKIALFDGRSQFSTWLYSVASN 87
Cdd:PRK11923   2 LTQEEDQQLVERVQRGDKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDSAFYTWLYRIAIN 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  88 VAISYL----RKQKNWLQKVVSIEHSGMDEQsandCKGLNGLDKLIVR-------------LPERARMVFVLFAIEGYRH 150
Cdd:PRK11923  82 TAKNHLvsrgRRPPDSDVSSEDAEFYDGDHA----LKDIESPERALLRdeiegtvhrtiqqLPEDLRTALTLREFDGLSY 157

                        170       180
                 ....*....|....*....|...
gi 489052855 151 EEIAEQLGMAVGSSKSQYHRARQ 173
Cdd:PRK11923 158 EDIASVMQCPVGTVRSRIFRARE 180
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 13-177 3.10e-20

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 83.20  E-value: 3.10e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  13 EAALIERVKSGDQGAYTTLYELHIKRVYGLCLRLLADQAHAEDAAQEVFVQVWHKIALFDGRSQFSTWLYSVASNVAISY 92
Cdd:PRK12513  13 DEALMLRYRAGDAAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPRARFRTWLYQIARNLLIDH 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  93 LRKQKnwLQKVVSIE-----HSGMD-----EQSANDCKGLNGLDKLIVRLPERARMVFVLFAIEGYRHEEIAEQLGMAVG 162
Cdd:PRK12513  93 WRRHG--ARQAPSLDadeqlHALADdgaapEQQLSLFRDRRRLQAALETLPDEQREVFLLREHGDLELEEIAELTGVPEE 170

                        170
                 ....*....|....*
gi 489052855 163 SSKSQYHRARQLLQE 177
Cdd:PRK12513 171 TVKSRLRYALQKLRE 185
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 1-175 1.70e-19

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 81.47  E-value: 1.70e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855   1 MLHVKPEPTPLCEAALIERVKSGDQGAYTTLYELHIKRVYGLCLRLLADQAHAEDAAQEVFVQVWhKIA--LFDGRSQFS 78
Cdd:PRK12524   1 MTMPFDALSDVSDEALLVLYANGDPAAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLW-RIApdWRQGEARVS 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  79 TWLYSVASNVAISYLRKQKNwlqkvvsiEHSGMDE--QSANDCKG----------LNGLDKLIVRLPERARMVFVLFAIE 146
Cdd:PRK12524  80 TWLYRVVCNLCTDRLRRRRR--------ASVDLDDapEPADAAPGaeealiegdrMRALDAALAALPERQRQAVVLRHIE 151

                        170       180
                 ....*....|....*....|....*....
gi 489052855 147 GYRHEEIAEQLGMAVGSSKSQYHRARQLL 175
Cdd:PRK12524 152 GLSNPEIAEVMEIGVEAVESLTARGKRAL 180
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 21-182 4.64e-19

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 79.78  E-value: 4.64e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  21 KSGDQGAYTTLYELHIKRVYGLCLRLLADQAHAEDAAQEVFVQVWHKIALFDGRSQFSTWLYSVASNVAISYLRKQknW- 99
Cdd:PRK12543   2 LSGDQEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNRPFRFWLIGLVIKQIHSWRRKR--Wr 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855 100 ----LQKVVSIEHS-GMDEQSANDCKGLNG-LDKLIVRLPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQYHRARQ 173
Cdd:PRK12543  80 rfriFEKAEEQRKPvSIDFSEDVLSKESNQeLIELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAALK 159


                 ....*....
gi 489052855 174 LLQEWYENE 182
Cdd:PRK12543 160 KLRQKEQIE 168
PRK09643 PRK09643
RNA polymerase sigma factor SigM; Reviewed
 13-177 1.15e-18

RNA polymerase sigma factor SigM; Reviewed


Pssm-ID: 236604 [Multi-domain]  Cd Length: 192  Bit Score: 78.98  E-value: 1.15e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  13 EAALIERVKSGDQGAYTTLYELHIKRVYGLCLRLLADQAHAEDAAQEVFVQVWHKIALFDGRSQFSTWLYSVASNVAISY 92
Cdd:PRK09643  14 DAELLAAHVAGDRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGDAAVSSWLHRIVVNACLDR 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  93 LRKQKNwlQKVVSIEHSGMDEQSANDCKGLNGLDKLIVR----LPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQY 168
Cdd:PRK09643  94 LRRAKA--RPTVPLDDVYPVAQLERDPTARVETALAVQRalmrLPVEQRAALVAVDMQGYSVADAARMLGVAEGTVKSRC 171


                 ....*....
gi 489052855 169 HRARQLLQE 177
Cdd:PRK09643 172 ARGRARLAE 180
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 27-177 2.83e-18

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: 77.36  E-value: 2.83e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855   27 AYTTLYELHIKRVYGLCLRLLADQAHAEDAAQEVFVQVWHKIALFDGRSQFSTWLYSVASNVAISYLRKQK-------NW 99
Cdd:TIGR02989   2 AFVRLLTRHERALRAFVRSLVADRDDVDDVLQETFVVAWRKFDQFDPGTNFVAWARGIARNKVLNYRRKLGrdrlvfdDD 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489052855  100 LQKVVSIEHSG-MDEQSANDckgLNGLDKLIVRLPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQYHRARQLLQE 177
Cdd:TIGR02989  82 LLEALAAEAEPtEAERLSDD---RQALEGCLEKLPERQRELLDLRYQRGQKATALAEQTGRTVNAVYKALQRIRVSLRE 157
PRK08241 PRK08241
RNA polymerase subunit sigma-70;
8-177 7.37e-18

RNA polymerase subunit sigma-70;


Pssm-ID: 236196 [Multi-domain]  Cd Length: 339  Bit Score: 79.21  E-value: 7.37e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855   8 PTPLCEAALIERVKSGDQGAYTTLYELHIKRVYGLCLRLLADQAHAEDAAQEVFVQVWHKIALFDGRSQFSTWLYSVASN 87
Cdd:PRK08241   1 DPATAAAALLARAAAGDRDAFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGYDRFEGRSSLRTWLYRIATN 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  88 VAISYLRKQK-------------------------NWLQKVVSIEHSGMDEQSAndckglnglDKLIVR----------- 131
Cdd:PRK08241  81 VCLDALEGRArrplptdlgapaadpvdelverpevPWLEPYPDALLDPAAADPA---------ARVVAResvrlafvaal 151

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 489052855 132 --LPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQYHRARQLLQE 177
Cdd:PRK08241 152 qhLPPRQRAVLILRDVLGWSAAEVAELLDTSVAAVNSALQRARATLAE 199
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 14-97 1.18e-17

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 76.01  E-value: 1.18e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  14 AALIERVKSGDQGAYTTLYELHIKRVYGLCLRLLADQAHAEDAAQEVFVQVWHKIALFD-GRSQFSTWLYSVASNVAISY 92
Cdd:PRK12514   7 EKLIVRVSLGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAvSGLSPMTWLITIARNHAIDR 86


                 ....*
gi 489052855  93 LRKQK 97
Cdd:PRK12514  87 LRARK 91
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 31-97 2.37e-17

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: 72.24  E-value: 2.37e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489052855   31 LYELHIKRVYGLCLRLLADQAHAEDAAQEVFVQVWHKIALFD-GRSQ-FSTWLYSVASNVAISYLRKQK 97
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDpERGVsFSTWLYTIIRNAIIDYLRKQR 69
PRK09646 PRK09646
ECF RNA polymerase sigma factor SigK;
3-166 6.38e-17

ECF RNA polymerase sigma factor SigK;


Pssm-ID: 182015 [Multi-domain]  Cd Length: 194  Bit Score: 74.71  E-value: 6.38e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855   3 HVKPEPTPLCEA-ALIERVKSGDQGAYTTLYELHIKRVYGLCLRLLADQAHAEDAAQEVFVQVWHKIALFD-GRSQFSTW 80
Cdd:PRK09646   6 PMTGPPAESPDLdALLRRVARGDQDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDpARGSALAW 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  81 LYSVASNVAISYLRKQKNWLQK--------------VVSIE-HSGMDEQSANDCkglngLDKLIvrlpERARMVFVLFAI 145
Cdd:PRK09646  86 LLTLAHRRAVDRVRSEQAASQRevrygarnvdpafdQVAEEvEARLERERVRDC-----LDALT----DTQRESVTLAYY 156

                        170       180
                 ....*....|....*....|.
gi 489052855 146 EGYRHEEIAEQLGMAVGSSKS 166
Cdd:PRK09646 157 GGLTYREVAERLAVPLGTVKT 177
SigM_subfam TIGR02950
RNA polymerase sigma factor, SigM family; This family of RNA polymerase sigma factors is a ...
 32-180 1.56e-16

RNA polymerase sigma factor, SigM family; This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot:


Pssm-ID: 274361 [Multi-domain]  Cd Length: 154  Bit Score: 72.49  E-value: 1.56e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855   32 YELHIKRVYGLCLRLLADQAHAEDAAQEVFVQVWHKIALFDGrSQFSTWLYSVASNVAISYLRKQKnwlqKVVSIEHS-- 109
Cdd:TIGR02950   1 YREYMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKD-SSIKPWLFRIARNAFIDWYRKDK----KIQTIDDDai 75

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489052855  110 --------GMDEQSANDCKGLNGLDKLIVRLPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQYHRARQLLQEWYE 180
Cdd:TIGR02950  76 gdleqhpvESPEHHLLIKIEQEEITHHLSRLPENYRTVLILREFKEFSYKEIAELLNLSLAKVKSNLFRARKELKKLLE 154
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 11-177 1.73e-16

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 73.41  E-value: 1.73e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  11 LCEAALIERVKSGDQGAYTTLYELHIKRVYGLCLRLLADQAHAEDAAQEVFVQVWHKIALFD-GRSQFSTWLYSVASNVA 89
Cdd:PRK13919   8 LSDEALLALVARGEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDpRRGSARAWLLALAHHAA 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  90 ISYLRKQKNWLQKVVSIEhsgmDEQSANDCKG-----LNGLDKLIVRL------PERARMVFVLFaIEGYRHEEIAEQLG 158
Cdd:PRK13919  88 VDHVRRRAARPQPLEPDE----REPEAFDLPGpgldeEGHLDRTRLGRalkalsPEERRVIEVLY-YQGYTHREAAQLLG 162

                        170
                 ....*....|....*....
gi 489052855 159 MAVGSSKSQYHRARQLLQE 177
Cdd:PRK13919 163 LPLGTLKTRARRALSRLKE 181
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 22-182 8.34e-16

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 71.74  E-value: 8.34e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  22 SGDQGAYTTLYEL---HIKRVYGLCLRLLADQAHAEDAAQEVFVQVWHKIALFDGRSqFSTWLYSVASNVAISYLRKQkn 98
Cdd:PRK09647  21 TGDKATMPSWEELvrqHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQPGT-FEGWLHRITTNLFLDMVRRR-- 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  99 wlQKVvSIEHSGMD-----------EQSANDCKGLNGLDKLIVRLPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQ 167
Cdd:PRK09647  98 --ARI-RMEALPEDydrvpgdepnpEQIYHDARLDPDLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSR 174

                        170
                 ....*....|....*
gi 489052855 168 YHRARQLLQEWYENE 182
Cdd:PRK09647 175 IHRGRQQLRAALAAH 189
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 6-177 3.26e-15

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 69.81  E-value: 3.26e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855   6 PEPTPLCEAALiERVKSGDQGAYTTLYELHIKRVYGLCLRLLADQAHAEDAAQEVFVQVWHKIALFD-GRSQFSTWLYSV 84
Cdd:PRK12537   4 PEAPFDYEACL-LACARGDRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDpARGSARGWIYSV 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  85 ASNVAISYLRkqkNWLQKVV----SIEHSGMDEQSANDCKGLNGLDKLIVRLP--ERARMVFVLFA-IEGYRHEEIAEQL 157
Cdd:PRK12537  83 TRHLALNVLR---DTRREVVldddAEETAQTLHEIIDDFDLWANSGKIHRCLEqlEPARRNCILHAyVDGCSHAEIAQRL 159

                        170       180
                 ....*....|....*....|
gi 489052855 158 GMAVGSSKSQYHRARQLLQE 177
Cdd:PRK12537 160 GAPLGTVKAWIKRSLKALRE 179
PRK12522 PRK12522
RNA polymerase sigma factor; Provisional
 30-182 8.93e-15

RNA polymerase sigma factor; Provisional


Pssm-ID: 183571 [Multi-domain]  Cd Length: 173  Bit Score: 68.36  E-value: 8.93e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  30 TLYELHIKRVYGLCLRLLADQAHAEDAAQEVFVQVWHKIALFDGRSQFSTWLYSVASNVAISYLRKQKNWLQKVVSIEHS 109
Cdd:PRK12522   7 ELIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVENYKKWITTICVRTFYDFYRKKKRWKDRILDLFHK 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855 110 G-----MDEQSAN-DCKGLNGLDKLIVR-----LPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQYHRARQLLQEW 178
Cdd:PRK12522  87 EdggeiEFADDVNiSEEFIQKVEAEMIReviqlLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQMREH 166


                 ....
gi 489052855 179 YENE 182
Cdd:PRK12522 167 LEGF 170
SigZ TIGR02959
RNA polymerase sigma factor, SigZ family; This family of RNA polymerase sigma factors is a ...
 48-181 3.08e-14

RNA polymerase sigma factor, SigZ family; This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).


Pssm-ID: 132004 [Multi-domain]  Cd Length: 170  Bit Score: 67.01  E-value: 3.08e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855   48 ADQAHAEDAAQEVFVQVWHKIALFDGRSQFSTWLYSVASNVAISYLRKQKNWLQKVVSIEHSGMDE-----QSANDCkgl 122
Cdd:TIGR02959  17 SDASDVEDLLQEVFIKIHRNLPSLKDGQKIQSWLYQIARNTIIDFYRSKSRSVELPESLLAADSAReetfvKELSQC--- 93

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 489052855  123 ngLDKLIVRLPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQYHRARQLLQEWYEN 181
Cdd:TIGR02959  94 --IPPMIKELPDEYREAIRLTELEGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLET 150
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
 35-177 4.07e-14

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 66.79  E-value: 4.07e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  35 HIKRVYGLCLRLLADQAHAEDAAQEVFVQVWHKIALFDGRSQFSTWLYSVASNVAISYLRKQKNWLQKVVSIEHSGMDEQ 114
Cdd:PRK12546  16 HLPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEGTNLRAWLFTILRNTFYSDRRKHKREVPDPEGVHAASLAVK 95

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489052855 115 SANDCK-GLNGLDKLIVRLPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQYHRARQLLQE 177
Cdd:PRK12546  96 PAHDGRlAMSDFRAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARARLAE 159
PRK12531 PRK12531
RNA polymerase sigma factor; Provisional
 14-176 2.31e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 105726 [Multi-domain]  Cd Length: 194  Bit Score: 64.95  E-value: 2.31e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  14 AALIERVKSGDQGAYTTLYELHIKRVYGLCLRLLADQAHAEDAAQEVFVQVWHKIALFDG-RSQFSTWLYSVASNVAISY 92
Cdd:PRK12531  15 LECMEKVKSRDKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGqKSALSTWIYTIIRNLCFDL 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  93 LRKQKN----------W--------LQKVVSIEHSGMDEQSAndckglngldKLIVRLPERARMVFVLFAIEGYRHEEIA 154
Cdd:PRK12531  95 LRKQKGkdlhihaddiWpsdyyppdLVDHYSPEQDMLKEQVM----------KFLDRLPKAQRDVLQAVYLEELPHQQVA 164

                        170       180
                 ....*....|....*....|..
gi 489052855 155 EQLGMAVGSSKSQYHRARQLLQ 176
Cdd:PRK12531 165 EMFDIPLGTVKSRLRLAVEKLR 186
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
31-177 6.12e-13

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 63.56  E-value: 6.12e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  31 LYELHIKRVYGLCLRLLADQAHAEDAAQEVFVQVW-HKIALFDGRSQFSTWLYSVASNVAISYLRKQKNwLQKVVSIEHS 109
Cdd:PRK09645  14 LYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWqHPEVLADTGRSARAWLFTVARNLVIDERRSARA-RPVEGGDDVL 92

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489052855 110 GMDEQSANDcKGLNGLDKLIVR-----LPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQYHRA----RQLLQE 177
Cdd:PRK09645  93 GVPEQSAPD-EVDRALDRLLVAdalaqLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYAlralRLALQE 168
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 125-175 8.64e-13

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: 59.78  E-value: 8.64e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 489052855  125 LDKLIVRLPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQYHRARQLL 175
Cdd:pfam08281   4 LLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 49-182 1.04e-12

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 62.84  E-value: 1.04e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  49 DQAHAEDAAQEVFVQVWHKIALFDGRSQFSTWLYSVASNVAISYLrkqKNWLQKVVSIEHSGMDE-------------QS 115
Cdd:PRK09415  39 NKEVAEDLTQEIFVKCYKSLHTYKGKSSLKTWLYRIAINHCKDYL---KSWHNKKVIVTEDIFTYmesqkesveeeviQN 115

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489052855 116 ANDckglNGLDKLIVRLPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQYHRARQLLQEWYENE 182
Cdd:PRK09415 116 AED----ERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKELLKKGLEEE 178
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 46-177 1.49e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 62.68  E-value: 1.49e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  46 LLADQAHAEDAAQEVFVQVWHKIALFDGRSQFSTWLYSVASNVAISYLRKQKNWLQkvvsiEHSGM-DEQSANDCKGLNG 124
Cdd:PRK12516  30 LIGRHDRADDLVQDTIMKAWAKQDHFEVGTNMKAWLFTILRNEFYSQMRKRGREVQ-----DTDGMfTEQLAVHPSQYGT 104

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 489052855 125 LD-----KLIVRLPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQYHRARQLLQE 177
Cdd:PRK12516 105 LDlqdfrAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQRLQE 162
PRK06811 PRK06811
RNA polymerase factor sigma-70; Validated
 16-182 6.80e-12

RNA polymerase factor sigma-70; Validated


Pssm-ID: 180707 [Multi-domain]  Cd Length: 189  Bit Score: 61.11  E-value: 6.80e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  16 LIERVKSGDQGAYTTLYELHIKRVYGLCLRLL---ADQAHAEDAAQEVFVQVWHKIALFDG-RSQFSTWLYSVASNVAIS 91
Cdd:PRK06811   8 FIKELKKKNEKALEFIVDTYGNLVKKIVHKVLgtvNYSQLIEECVNDIFLSIWNNIDKFDEeKGSFKKWIAAISKYKAID 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  92 YLRK--QKNWLQKV--------VSIEHSGMDEQSANDckglngLDKLIVRLPERARMVFVLFAIEGYRHEEIAEQLGMAV 161
Cdd:PRK06811  88 YKRKltKNNEIDSIdefiliseESIENEIILKENKEE------ILKLINDLEKLDREIFIRRYLLGEKIEEIAKKLGLTR 161

                        170       180
                 ....*....|....*....|.
gi 489052855 162 GSSKSQYHRARQLLQEWYENE 182
Cdd:PRK06811 162 SAIDNRLSRGRKKLQKNKLNI 182
PRK12547 PRK12547
RNA polymerase sigma factor; Provisional
 38-177 2.07e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 139056 [Multi-domain]  Cd Length: 164  Bit Score: 59.12  E-value: 2.07e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  38 RVYGLCLRLLADQAhaEDAAQEVFVQVWHKIALFDGRSQFSTWLYSVASNVAISYLRKQKNWLQK---VVSIEHSGMDEQ 114
Cdd:PRK12547  20 RAFAVSLSSKHDKA--EDLVQDTLMKAWAKQDSFEMGTNLKAWLFTILRNEFYSQMRKRGREVQDsdgVFTARVAVHPAQ 97

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489052855 115 SANdcKGLNGLDKLIVRLPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQYHRARQLLQE 177
Cdd:PRK12547  98 YGS--LDLQDFKKALNLLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARNRLQE 158
SigX4 TIGR02957
RNA polymerase sigma-70 factor, TIGR02957 family; This group of sigma factors are members of ...
 31-177 3.37e-11

RNA polymerase sigma-70 factor, TIGR02957 family; This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.


Pssm-ID: 132002 [Multi-domain]  Cd Length: 281  Bit Score: 60.06  E-value: 3.37e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855   31 LYELHIKRVYGLCLRLLADQAHAEDAAQEVFVQvWHKIALFDGRSQFStWLYSVASNVAISYL---RKQKN-----WLQK 102
Cdd:TIGR02957   2 EFEALRPLLFSLAYRMLGSVADAEDIVQETFLR-WQEADRAQIENPKA-YLTKVVTRRCIDVLrsaRARREvyvgpWLPE 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489052855  103 VVSIEHSGMDEQSANDCKGLNGLDKLIVRLPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQYHRARQLLQE 177
Cdd:TIGR02957  80 PLLTTSADPAESVELAESLSMAYLLLLERLSPLERAVFVLREVFDYPYEEIASIVGKSEANCRQLVSRARRHLDA 154
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 31-180 5.34e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 58.02  E-value: 5.34e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  31 LYELHIKRVYGLCLRLLADQAHAEDAAQEVFVQVWHKIALFDGRsQFSTWLYSVASNVAISYLRKQKNW---------LQ 101
Cdd:PRK12541  10 IYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGE-EIRPWLFTIAYNAFIDWYRKEKKYktttieefhLP 88

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489052855 102 KVVSIEHSGMDEQSANdckglNGLDKLIVRLPERaRMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQYHRARQLLQEWYE 180
Cdd:PRK12541  89 NVPSTEHEYFIKHEIA-----SWLDSLSSLPLER-RNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKETKSIKE 161
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 48-181 7.55e-11

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 58.07  E-value: 7.55e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  48 ADQAHAEDAAQEVFVQVWHKIALFDGRSQFSTWLYSVASNVAISYLRKqKNWLQKVVSIEHSGMDEQSANDCKGLNG-LD 126
Cdd:PRK09637  23 SNEADVDDLLQEVLIKTHSNLHSLKDGSSIKSWLYQIANNTIIDFYRK-KNRSEELPDDLLFEDEEREENAKKELAPcLR 101

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 489052855 127 KLIVRLPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQYHRARQLLQEWYEN 181
Cdd:PRK09637 102 PFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLEG 156
Sig70_famx1 TIGR02943
RNA polymerase sigma-70 factor, TIGR02943 family; This group of sigma factors are members of ...
 47-181 1.21e-10

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


Pssm-ID: 274359 [Multi-domain]  Cd Length: 188  Bit Score: 57.47  E-value: 1.21e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855   47 LADQAHAEDAAQEVFVQVWHKIALFDGRSQFSTWLYSVASNVAISYLRKQKNwlQKVVSIEHSGMDEQSANDCKGLNG-- 124
Cdd:TIGR02943  23 LRDRDLAEDAVQETLLAALSHRDSFAGRSALKTWLFAILKNKIIDALRAKGR--EVKVSDLDDELDDEAFNALFTQNGhw 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  125 ------------------------LDKLIVRLPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQYHRARQLLQEWYE 180
Cdd:TIGR02943 101 aqhgqpqhwntpekqlenkefwevFEACLYHLPEQTARVFMMREVLGFESDEICQELEISTSNCHVLLYRARLSLRACLS 180


                  .
gi 489052855  181 N 181
Cdd:TIGR02943 181 I 181
PRK12526 PRK12526
RNA polymerase sigma factor; Provisional
 8-177 1.22e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 237127 [Multi-domain]  Cd Length: 206  Bit Score: 57.89  E-value: 1.22e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855   8 PTPLCeAALIERVKSGDQGAYTTLYELHIKRVYGLCLRLLADQAHAEDAAQEVFVQVWHKIALFDG-RSQFSTWLYSVAS 86
Cdd:PRK12526  21 PTELS-QWLILVAISRDKQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGdKGAATTWVYTVMR 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  87 NVAISYLRKQKNWLQKVVS-----IEHSGMDEQSANDCKGLNGLDKLIVR----LPERARMVFVLFAIEGYRHEEIAEQL 157
Cdd:PRK12526 100 NAAFDMLRKIKAKKEQNLGddiwpIEQALAESQSESEEFSDHLMDKQILSyiekLPEAQQTVVKGVYFQELSQEQLAQQL 179

                        170       180
                 ....*....|....*....|
gi 489052855 158 GMAVGSSKSQYHRARQLLQE 177
Cdd:PRK12526 180 NVPLGTVKSRLRLALAKLKV 199
PRK09649 PRK09649
RNA polymerase sigma factor SigC; Reviewed
 47-175 1.33e-09

RNA polymerase sigma factor SigC; Reviewed


Pssm-ID: 137458 [Multi-domain]  Cd Length: 185  Bit Score: 54.66  E-value: 1.33e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  47 LADQAHAEDAAQEVFVQVWHKIALFDGRSQFSTWLYSVASNVAISYLRKqknwLQKVVSIEHSGMDEQSANDCKGLNGLD 126
Cdd:PRK09649  44 LSDVGSADDLTQETFLRAIGAIPRFSARSSARTWLLAIARHVVADHIRH----VRSRPRTTRGARPEHLIDGDRHARGFE 119

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 489052855 127 KL------IVRLPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQYHRARQLL 175
Cdd:PRK09649 120 DLvevttmIADLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARARDAL 174
PRK12535 PRK12535
RNA polymerase sigma factor; Provisional
 15-172 1.76e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 237130 [Multi-domain]  Cd Length: 196  Bit Score: 54.52  E-value: 1.76e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  15 ALIERVKSGDQGAYTTLYELHIKRVYGLcLRLLADQAHAEDAAQEVFVQVWHKIALFDGRSQFSTWLYSVASNVAISYLR 94
Cdd:PRK12535  14 DLALAAGRGDRAALTEFIRETQDDVWRL-LAHLGGHDIADDLTQETYLRVMSALPRFAARSSARTWLLSLARRVWVDNIR 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  95 KQKNWLQK-VVSIEHSGMDEQSANDCKGLN---GLDKLIVRLPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQYHR 170
Cdd:PRK12535  93 HDMARPRKsATEYEDAAATTASNETTGSWSewiDVRTLIDALPPERREALILTQVLGYTYEEAAKIADVRVGTIRSRVAR 172


                 ..
gi 489052855 171 AR 172
Cdd:PRK12535 173 AR 174
PRK12542 PRK12542
RNA polymerase sigma factor; Provisional
 19-176 4.93e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 183581 [Multi-domain]  Cd Length: 185  Bit Score: 53.13  E-value: 4.93e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  19 RVKSGDQGAYTTLYELHIKRVYGLCLRLLADQAHAEDAAQEVFVQVWHKIALFDGRS--QFSTWLYSVASNVAISYLRKQ 96
Cdd:PRK12542   2 KVTNNDYEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNtqELKRYILRVAKNKAIDSYRKN 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  97 K-------NWLQKVVSIEHSGMDEQSANDCKGLNgLDKLIVRLPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQYH 169
Cdd:PRK12542  82 KrhetfleEYERESIEAVDENIEEWEKRKMSEVQ-IDTLLKELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFE 160


                 ....*..
gi 489052855 170 RARQLLQ 176
Cdd:PRK12542 161 RARKRVQ 167
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 30-182 5.15e-09

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 52.96  E-value: 5.15e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  30 TLYELHIKRVYGLCLRLLADQAHAEDAAQEVFVQVWHKIALFDgRSQFSTWLYSVASNVAISYLRKQKnwlqKVVSIEHS 109
Cdd:PRK09644   5 EIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYD-NQKVKPWLFKVAYHTFIDFVRKEK----KVSFVGTD 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855 110 GMD-------EQSANDCKGLNGLDKLIVRLPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQYHRARQLLQEWYENE 182
Cdd:PRK09644  80 EIEaiqaestEEYVVAKNSYEKLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLKEE 159
sigI PRK09635
RNA polymerase sigma factor SigI; Provisional
 42-177 5.93e-09

RNA polymerase sigma factor SigI; Provisional


Pssm-ID: 182008 [Multi-domain]  Cd Length: 290  Bit Score: 53.82  E-value: 5.93e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  42 LCLRLLADQAHAEDAAQEVFVQVWHKIA--LFDGRSqfstWLYSVASNVAISYLRKQKNWLQK--VVSIEHSGMDEQSAN 117
Cdd:PRK09635  21 LAFRMVGDIGVAEDMVQEAFSRLLRAPVgdIDDERG----WLIVVTSRLCLDHIKSASTRRERpqDIAAWHDGDASVSSV 96

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489052855 118 DCKGLNGLDK------LIV--RLPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQYHRARQLLQE 177
Cdd:PRK09635  97 DPADRVTLDDevrlalLIMleRLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQLAHRARRKINE 164
PRK12529 PRK12529
RNA polymerase sigma factor; Provisional
 22-171 5.97e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 183574 [Multi-domain]  Cd Length: 178  Bit Score: 53.02  E-value: 5.97e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  22 SGDQGAYTTLYELHIKRVYG-LCLRLLA-DQAHAEDAAQEVFVQVW--HKIALFDGRSQFSTWLYSVASNVAISYLRKQ- 96
Cdd:PRK12529   9 SADRDKVATLYRENHAWLRNwLAYRLRSwGRGVADDLAHDIFLRILasRDGGQREAIRQPRAYLARIANCVLVSWRRRQs 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  97 --KNWLQKVVSI---EHSGMDEQSANdCKGLNGLDKLIVRLPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQYHRA 171
Cdd:PRK12529  89 leLAWLEALATLpepLHPSPEQQSVI-LETLHEIDALLDTLRPRVKQAFLMATLDGMKQKDIAQALDIALPTVKKYIHQA 167
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 125-176 5.56e-08

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: 47.48  E-value: 5.56e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 489052855 125 LDKLIVRLPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQYHRARQLLQ 176
Cdd:cd06171    4 LEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK12532 PRK12532
RNA polymerase sigma factor; Provisional
 44-181 7.65e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 171564 [Multi-domain]  Cd Length: 195  Bit Score: 49.93  E-value: 7.65e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  44 LRLLADQAHAEDAAQEVFVQVWHKIALFDGRSQFSTWLYSVASNVAISYLRKQKNWLQKVVSIEHSGMDE---------- 113
Cdd:PRK12532  24 LQLPDHPDLAEDLVQETLLSAYSAGDSFQGRALVNSWLFAILKNKIIDALRQIGRQRKVFTLLDDELLDEafeshfsqng 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855 114 --------QSANDC-KGLNG------LDKLIVRLPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQYHRARQLLQEW 178
Cdd:PRK12532 104 hwtpegqpQHWNTPeKSLNNnefqkiLQSCLYNLPENTARVFTLKEILGFSSDEIQQMCGISTSNYHTIMHRARESLRQC 183


                 ...
gi 489052855 179 YEN 181
Cdd:PRK12532 184 LQI 186
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 46-182 3.49e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 47.86  E-value: 3.49e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  46 LLADQAHAEDAAQEVFVQVWHKIALFDGRSQFSTWLYSVASNVAISYLRKQKNWLQKVVSIEHSGMDEQSANDCKG--LN 123
Cdd:PRK12511  24 LTRDSAEAEDLVHDALVRALERRASFRSGGNLRTWLMSILHNAFIDELRRRRVEARRADELAVLADASLPAAQEHAvrLA 103

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 489052855 124 GLDKLIVRLPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQYHRARQLLQEWYENE 182
Cdd:PRK12511 104 QIRDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAALRAFEEGT 162
PRK12540 PRK12540
RNA polymerase sigma factor; Provisional
 38-177 7.03e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183579 [Multi-domain]  Cd Length: 182  Bit Score: 47.27  E-value: 7.03e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  38 RVYGLCLRLLADQAhaEDAAQEVFVQVWHKIALFDGRSQFSTWLYSVASNVAISYLRKQKnwlQKVVSIEHSGMDEQSAN 117
Cdd:PRK12540  19 RAFAISLSGNGDRA--DDLVQETLLRALANIDSFQPGSNLPAWLFTILRNLFRSDYRKRR---REVEDADGSYAKTLKSQ 93

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489052855 118 DCKGLN--------GLDKlivrLPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQYHRARQLLQE 177
Cdd:PRK12540  94 PGQNAHlefeefraALDK----LPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARSKLSA 157
PRK12523 PRK12523
RNA polymerase sigma factor; Reviewed
 31-177 9.62e-07

RNA polymerase sigma factor; Reviewed


Pssm-ID: 183572 [Multi-domain]  Cd Length: 172  Bit Score: 46.77  E-value: 9.62e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  31 LYELHIKRVYGLCLRLLADQAHAEDAAQEVFVQVWHKIALFDGRSQfSTWLYSVASNVAISYLRK---QKNWLQKVVSI- 106
Cdd:PRK12523  15 LYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGRPELPTPREP-RAFLAAVAKGLMFDHFRRaalEQAYLAELALVp 93

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489052855 107 --EHSGMDEQSAnDCKGLNGLDKLIVRLPERARMVFVLFAIEGYRHEEIAEQLGMAVGssksqyhRARQLLQE 177
Cdd:PRK12523  94 eaEQPSPEEQHL-ILEDLKAIDRLLGKLSSKARAAFLYNRLDGMGHAEIAERLGVSVS-------RVRQYLAQ 158
PRK12539 PRK12539
RNA polymerase sigma factor SigF;
1-170 9.12e-06

RNA polymerase sigma factor SigF;


Pssm-ID: 237132 [Multi-domain]  Cd Length: 184  Bit Score: 43.95  E-value: 9.12e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855   1 MLHVKPEPTPLCEAALiervkSGDQGAYTTLYEL---HIKRVY-GLCLRLLADQAHAEDAAQEVFVQVWHKIALFDGRSQ 76
Cdd:PRK12539   1 MMSQENELKALMLASL-----DGDAAAHRALLERlsgHLRAYYkGKLARIGRGAEEAEDLVQEALMAIHTRRHTYDPEQP 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  77 FSTWLYSVASNVAISYLRKQKNWLQKVVSIEHSGM---DEQSANDCKglNGLDKLIVRLPERARMVFVLFAIEGYRHEEI 153
Cdd:PRK12539  76 LTPWVYAIARYKLIDHLRRTRASLADVPIDDADELvahDDHAAVEST--LDLGRLLARLPEKMRLAIQAVKLEGLSVAEA 153

                        170
                 ....*....|....*..
gi 489052855 154 AEQLGMAVGSSKSQYHR 170
Cdd:PRK12539 154 ATRSGMSESAVKVSVHR 170
PRK12544 PRK12544
RNA polymerase factor sigma-70;
47-181 1.17e-05

RNA polymerase factor sigma-70;


Pssm-ID: 183583 [Multi-domain]  Cd Length: 206  Bit Score: 44.02  E-value: 1.17e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  47 LADQAHAEDAAQEVFVQVWHKIALFDGRSQFSTWLYSVASNVAISYLRKQKnwlqKVVSIEHSGMDEQSANDCKGL---N 123
Cdd:PRK12544  39 LSDLHLAEDAVQEALIGALKNADSFAGRAAFKTWVFAILKNKIIDLLRQKK----RHVSASSLLRDEEEEEDFEELfdeS 114

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855 124 G--------------------------LDKLIVRLPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQYHRARQLLQE 177
Cdd:PRK12544 115 GhwqkderpqawgnpeesleqeqfwriFEACLDGLPAKYARVFMMREFIELETNEICHAVDLSVSNLNVLLYRARLRLRE 194


                 ....
gi 489052855 178 WYEN 181
Cdd:PRK12544 195 CLEN 198
PRK09642 PRK09642
RNA polymerase sigma factor;
39-182 1.32e-05

RNA polymerase sigma factor;


Pssm-ID: 170031 [Multi-domain]  Cd Length: 160  Bit Score: 43.17  E-value: 1.32e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  39 VYGLCLRLLADQAHAEDAAQEVFVQVWHKIALFDGRSqFSTWLYSVASNVAISYLRKQKNWLQKVVSIEHSGMDEQSAND 118
Cdd:PRK09642   8 IFQVIFSILRHEEDAKDVTQEVFVKIHASLPNYQFRG-LKTWMARIATNHAIDYKRKKARENEELSLCKETEENIKSSHN 86

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489052855 119 CKGL--NGLDKLIV-----RLPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQYHRARQLLQE-WYENE 182
Cdd:PRK09642  87 IEDLllTKEQKLLIaqklrELPENYRDVVLAHYLEEKSYQEIALQEKIEVKTVEMKLYRARKWIKKhWKEEE 158
PRK09648 PRK09648
RNA polymerase sigma factor ShbA;
53-171 1.41e-05

RNA polymerase sigma factor ShbA;


Pssm-ID: 236607 [Multi-domain]  Cd Length: 189  Bit Score: 43.42  E-value: 1.41e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  53 AEDAAQEVFVQVWHKIALFD--GRSqFSTWLYSVASN-VAISYLRKQKNWLQKVVSIEHSGMD----EQSANDCKGLNGL 125
Cdd:PRK09648  55 ADDVAQEVCLAVITALPRYRdqGRP-FLAFVYGIAAHkVADAHRAAGRDKAVPTEEVPERPSDdagpEERALRSESSNRM 133

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 489052855 126 DKLIVRLPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQYHRA 171
Cdd:PRK09648 134 RELLDTLPEKQREILILRVVVGLSAEETAEAVGSTPGAVRVAQHRA 179
PRK12517 PRK12517
RNA polymerase sigma factor; Provisional
 40-177 1.43e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183569 [Multi-domain]  Cd Length: 188  Bit Score: 43.52  E-value: 1.43e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  40 YGLClrllADQAHAEDAAQEVFVQVWHKI-ALFDGRSQFStWLYSVA--SNvAISYLRKQKNWL---QKVVSIEHSGMDE 113
Cdd:PRK12517  41 YWLC----KDKHIAEDLVQETFLRAWRSLdSLKDEKAAKA-WLITILrrEN-ARRFERKQFDLVdieDDSIEDDASHSSE 114

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489052855 114 QSANDckglNGLDKLIVRLPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQYHRARQLLQE 177
Cdd:PRK12517 115 EEMEQ----EWLRRQIAKLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMTRLFRARNQLKE 174
PRK09651 PRK09651
RNA polymerase sigma factor FecI; Provisional
 28-171 1.67e-05

RNA polymerase sigma factor FecI; Provisional


Pssm-ID: 182018 [Multi-domain]  Cd Length: 172  Bit Score: 43.26  E-value: 1.67e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  28 YTTLYELHIKRVYGLCLRLLADQAHAEDAAQEVFVQVWHKIALFDGRSQFStWLYSVASNVAISYLRK---QKNWLQKVV 104
Cdd:PRK09651  12 FESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVSETLSTIRDPRS-FLCTIAKRVMVDLFRRnalEKAYLEMLA 90

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489052855 105 SIEHSGMDEQSANDC--KGLNGLDKLIVRLPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQYHRA 171
Cdd:PRK09651  91 LMPEGGAPSPEERESqlETLQLLDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKA 159
PRK12525 PRK12525
RNA polymerase sigma factor; Provisional
 53-177 3.04e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 139037 [Multi-domain]  Cd Length: 168  Bit Score: 42.24  E-value: 3.04e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  53 AEDAAQEVFVQVWhkiALFDGRSQFS--TWLYSVASNVAISYLRKQ---KNWLQKVVSIE---HSGMDEQsANDCKGLNG 124
Cdd:PRK12525  36 AEDIASETFLQVL---ALPDPASIREprALLTTIARRLMYEGWRRQdleRAYLQSLAEAPeavQPSPEEQ-WMVIETLLA 111

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 489052855 125 LDKLIVRLPERARMVFVLFAIEGYRHEEIAEQLGMAVGS----SKSQYHRARQLLQE 177
Cdd:PRK12525 112 IDRLLDGLSGKARAAFLMSQLEGLTYVEIGERLGVSLSRihqyMVEAFKCCYQGFQE 168
PRK12545 PRK12545
RNA polymerase factor sigma-70;
47-106 3.12e-05

RNA polymerase factor sigma-70;


Pssm-ID: 183584 [Multi-domain]  Cd Length: 201  Bit Score: 42.64  E-value: 3.12e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  47 LADQAHAEDAAQEVFVQVWHKIALFDGRSQFSTWLYSVASNVAISYLRKQknwlQKVVSI 106
Cdd:PRK12545  29 LRDADAAEDAVQEALAAAWSQAGRFAGQSAHKTWVFGILRNKLIDTLRAR----QRTVNL 84
PRK12520 PRK12520
RNA polymerase sigma factor; Provisional
 47-177 3.17e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 237126 [Multi-domain]  Cd Length: 191  Bit Score: 42.41  E-value: 3.17e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  47 LADQAHAEDAAQEVFVQVWHKIALFDGRSQFSTWLYSVASNVAISYLRKQKNWLQKVVSIEHSGMDEQSANDCKGLNG-- 124
Cdd:PRK12520  23 LRDPALAEDAVSETLLAVLEHPERFAGQSSLKTYLVGILKHKIIDAIRSGRREVRLSLDDADEQSDDDLFDALFAADGhy 102

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489052855 125 ----------------------LDKLIVRLPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQYHRARQLLQE 177
Cdd:PRK12520 103 reppsdwgdpdaalsrreffevLQACVDRLPPRTGRVFMMREWLELETEEICQELQITATNAWVLLYRARMRLRE 177
PRK12528 PRK12528
RNA polymerase sigma factor; Provisional
 30-173 3.24e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 171561 [Multi-domain]  Cd Length: 161  Bit Score: 42.14  E-value: 3.24e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  30 TLYELHIKRVYGLCLRLLADQAHAEDAAQEVFVQVW---HKIALFDGRSqfstWLYSVASNVAISYLRKQ---KNWLQKV 103
Cdd:PRK12528   8 GLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLvarETAQIIEPRA----FLTTIAKRVLCNHYRRQdleRAYLEAL 83

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489052855 104 VSI--EHSGMDEQSANDCKGLNGLDKLIVRLPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQYHRARQ 173
Cdd:PRK12528  84 AQLpeRVAPSEEERAIILETLVELDQLLDGLPPLVKRAFLLAQVDGLGYGEIATELGISLATVKRYLNKAAM 155
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 128-177 3.50e-05

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


Pssm-ID: 461347 [Multi-domain]  Cd Length: 50  Bit Score: 39.72  E-value: 3.50e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 489052855  128 LIVRLPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQYHRARQLLQE 177
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
PRK12530 PRK12530
RNA polymerase sigma factor; Provisional
 47-97 1.80e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 237128 [Multi-domain]  Cd Length: 189  Bit Score: 40.52  E-value: 1.80e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 489052855  47 LADQAHAEDAAQEVFVQVWHKIALFDGRSQFSTWLYSVASNVAISYLRKQK 97
Cdd:PRK12530  28 LKDADLAEDVVQEALVSAYKNADSFKGQSALKTWIFAILKNKIIDLIRYRK 78
PRK12512 PRK12512
RNA polymerase sigma factor; Provisional
 43-171 2.09e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 171551 [Multi-domain]  Cd Length: 184  Bit Score: 40.07  E-value: 2.09e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  43 CLRLLADQAHAEDAAQEVFVQVWHKIALFDGRSQFSTWLYSVASNVAISYLRKQKNwlQKVVSIEHSGMDEQSANDCKGL 122
Cdd:PRK12512  43 LARAGQPADQAEDIVQEILLAVHLKRHTWDPGAPFAPWLFAIARNKLIDALRRRGR--RVFVDIDDFAETLPAEPATETL 120

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 489052855 123 NGLD--KLIVRLPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQYHRA 171
Cdd:PRK12512 121 PAGDvgRHLETLPPRQRDVVQSISVEGASIKETAAKLSMSEGAVRVALHRG 171
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
 53-158 5.42e-04

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 38.90  E-value: 5.42e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  53 AEDAAQEVFVQVWHKIALFDGRSQFStWLYSVASNVAISYLRKQkNWLQKVVSIEHSGMD--------EQSANDCKGLNG 124
Cdd:PRK07037  25 AEDVVQDAFVKLVEAPNQDAVKQPVA-YLFRIVRNLAIDHYRRQ-ALENKYHGDEEDGLDvpspeaspEAALINRDTLRH 102

                         90       100       110
                 ....*....|....*....|....*....|....
gi 489052855 125 LDKLIVRLPERARMVFVLFAIEGYRHEEIAEQLG 158
Cdd:PRK07037 103 VADALSELPARTRYAFEMYRLHGETQKDIARELG 136
PRK09047 PRK09047
RNA polymerase factor sigma-70; Validated
 125-177 9.93e-04

RNA polymerase factor sigma-70; Validated


Pssm-ID: 236367 [Multi-domain]  Cd Length: 161  Bit Score: 38.03  E-value: 9.93e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 489052855 125 LDKLIVRLPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQYHRARQLLQE 177
Cdd:PRK09047 100 IEEAIQKLPARQREAFLLRYWEDMDVAETAAAMGCSEGSVKTHCSRATHALAK 152
PRK12536 PRK12536
RNA polymerase sigma factor; Provisional
 15-170 1.75e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237131 [Multi-domain]  Cd Length: 181  Bit Score: 37.34  E-value: 1.75e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  15 ALIERVKSGDQGAYTTLYELHIKRVYGLCLRLLAD-QAHAEDAAQEVFVQVWHKIALFDGRSQFSTWLYSVASNVAISYL 93
Cdd:PRK12536  10 ALLLRGLAGDAAAYRQFLSELAAHLRGFLRRRLPQlPDEVEDLVQEILLAVHNARHTYRADQPLTAWVHAIARYKLMDFL 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  94 RK--QKNWLQKVVSIEH---SGMDEQSANDCKGLNgldKLIVRLPERARMVFVLFAIEGYRHEEIAEQLGMAVGSSKSQY 168
Cdd:PRK12536  90 RSraRREALHDPLDDESelfATSDDEAAEARRDLG---KLLEQLPDRQRLPIVHVKLEGLSVAETAQLTGLSESAVKVGI 166


                 ..
gi 489052855 169 HR 170
Cdd:PRK12536 167 HR 168
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 42-161 1.85e-03

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 37.06  E-value: 1.85e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489052855  42 LCLRLLADQAhAEDAAQEVFVQVWHKIAlfDGR-SQFSTWLYSVASNVAISylRKQKNWLQKVVSIE--------HSGMD 112
Cdd:PRK12527  12 LSARLGNRQA-AEDVAHDAYLRVLERSS--SAQiEHPRAFLYRTALNLVVD--RHRRHRVRQAEPLEvldeeerlHSPSP 86

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 489052855 113 EQSANDCKGLNGLDKLIVRLPERARMVFVLFAIEGYRHEEIAEQLGMAV 161
Cdd:PRK12527  87 QTRLDLGQRLALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISR 135
 
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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