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Conserved domains on  [gi|59479680|gb|AAW85467|]
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RNA polymerase ECF-type sigma factor [Aliivibrio fischeri ES114]

Protein Classification

PRK09637 family protein( domain architecture ID 11484433)

PRK09637 family protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 1-179 1.13e-101

RNA polymerase sigma factor SigZ; Provisional


:

Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 290.35  E-value: 1.13e-101
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680    1 MLSEWQNHKAQLRNYVYKRVDDASAVDDILQDVYIKASSNLHQLKSKGSLKGWLYKIAYNTIMDFYRDKLPYDELPEDLV 80
Cdd:PRK09637   3 LESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDGSSIKSWLYQIANNTIIDFYRKKNRSEELPDDLL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680   81 AEDEDAVEESRKEIAECMRPLIDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGRVKFRENLMTCCDFEI 160
Cdd:PRK09637  83 FEDEEREENAKKELAPCLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLEGCCDFEI 162

                        170
                 ....*....|....*....
gi 59479680  161 NDGGMVTGYTPKKTNCSSP 179
Cdd:PRK09637 163 DRQGNLIDYEQKSTECKKC 181
 
Name Accession Description Interval E-value
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 1-179 1.13e-101

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 290.35  E-value: 1.13e-101
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680    1 MLSEWQNHKAQLRNYVYKRVDDASAVDDILQDVYIKASSNLHQLKSKGSLKGWLYKIAYNTIMDFYRDKLPYDELPEDLV 80
Cdd:PRK09637   3 LESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDGSSIKSWLYQIANNTIIDFYRKKNRSEELPDDLL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680   81 AEDEDAVEESRKEIAECMRPLIDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGRVKFRENLMTCCDFEI 160
Cdd:PRK09637  83 FEDEEREENAKKELAPCLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLEGCCDFEI 162

                        170
                 ....*....|....*....
gi 59479680  161 NDGGMVTGYTPKKTNCSSP 179
Cdd:PRK09637 163 DRQGNLIDYEQKSTECKKC 181
SigZ TIGR02959
RNA polymerase sigma factor, SigZ family; This family of RNA polymerase sigma factors is a ...
 5-174 2.38e-96

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: 276.17  E-value: 2.38e-96
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680     5 WQNHKAQLRNYVYKRVDDASAVDDILQDVYIKASSNLHQLKSKGSLKGWLYKIAYNTIMDFYRDKLPYDELPEDLVAEDE 84
Cdd:TIGR02959   1 WDEFRSELKAFIKSRVSDASDVEDLLQEVFIKIHRNLPSLKDGQKIQSWLYQIARNTIIDFYRSKSRSVELPESLLAADS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680    85 DAVEESRKEIAECMRPLIDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGRVKFRENLMTCCDFEINDGG 164
Cdd:TIGR02959  81 AREETFVKELSQCIPPMIKELPDEYREAIRLTELEGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLETCCHFEFDRVG 160

                         170
                  ....*....|
gi 59479680   165 MVTGYTPKKT 174
Cdd:TIGR02959 161 NLIDYEPKGT 170
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 5-152 2.28e-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: 132.04  E-value: 2.28e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680   5 WQNHKAQLRNYVYKRVDDASAVDDILQDVYIKASSNLHQLKSKGSLKGWLYKIAYNTIMDFYR----DKLPYDELPEDLV 80
Cdd:COG1595  23 YERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHLRkrrrRRELLDELAEELP 102

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 59479680  81 AEDEDAVEE-SRKEIAECMRPLIDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGRVKFRENL 152
Cdd:COG1595 103 DEAADPEEAlEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREAL 175
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 101-147 2.31e-09

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: 50.92  E-value: 2.31e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 59479680   101 LIDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGRVK 147
Cdd:pfam08281   7 ALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKK 53
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 96-149 1.01e-07

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: 46.71  E-value: 1.01e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 59479680  96 ECMRPLIDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGRVKFR 149
Cdd:cd06171   2 ERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 1-179 1.13e-101

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 290.35  E-value: 1.13e-101
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680    1 MLSEWQNHKAQLRNYVYKRVDDASAVDDILQDVYIKASSNLHQLKSKGSLKGWLYKIAYNTIMDFYRDKLPYDELPEDLV 80
Cdd:PRK09637   3 LESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDGSSIKSWLYQIANNTIIDFYRKKNRSEELPDDLL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680   81 AEDEDAVEESRKEIAECMRPLIDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGRVKFRENLMTCCDFEI 160
Cdd:PRK09637  83 FEDEEREENAKKELAPCLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLEGCCDFEI 162

                        170
                 ....*....|....*....
gi 59479680  161 NDGGMVTGYTPKKTNCSSP 179
Cdd:PRK09637 163 DRQGNLIDYEQKSTECKKC 181
SigZ TIGR02959
RNA polymerase sigma factor, SigZ family; This family of RNA polymerase sigma factors is a ...
 5-174 2.38e-96

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: 276.17  E-value: 2.38e-96
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680     5 WQNHKAQLRNYVYKRVDDASAVDDILQDVYIKASSNLHQLKSKGSLKGWLYKIAYNTIMDFYRDKLPYDELPEDLVAEDE 84
Cdd:TIGR02959   1 WDEFRSELKAFIKSRVSDASDVEDLLQEVFIKIHRNLPSLKDGQKIQSWLYQIARNTIIDFYRSKSRSVELPESLLAADS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680    85 DAVEESRKEIAECMRPLIDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGRVKFRENLMTCCDFEINDGG 164
Cdd:TIGR02959  81 AREETFVKELSQCIPPMIKELPDEYREAIRLTELEGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLETCCHFEFDRVG 160

                         170
                  ....*....|
gi 59479680   165 MVTGYTPKKT 174
Cdd:TIGR02959 161 NLIDYEPKGT 170
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 5-152 2.28e-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: 132.04  E-value: 2.28e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680   5 WQNHKAQLRNYVYKRVDDASAVDDILQDVYIKASSNLHQLKSKGSLKGWLYKIAYNTIMDFYR----DKLPYDELPEDLV 80
Cdd:COG1595  23 YERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHLRkrrrRRELLDELAEELP 102

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 59479680  81 AEDEDAVEE-SRKEIAECMRPLIDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGRVKFRENL 152
Cdd:COG1595 103 DEAADPEEAlEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREAL 175
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 8-152 1.72e-31

RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 111.29  E-value: 1.72e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680     8 HKAQLRNYVYKRVDDASAVDDILQDVYIKASSNLHQLKSKGSLKGWLYKIAYNTIMDFYRDK---LPYDELPEDLVAEDE 84
Cdd:TIGR02937  10 YLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKrrlRRELDLLEELLDSDP 89

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 59479680    85 DAVEE-SRKEIAECMRPLIDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGRVKFRENL 152
Cdd:TIGR02937  90 SPEEElEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 8-152 4.56e-26

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 98.12  E-value: 4.56e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680    8 HKAQLRNYVYKRVDDASAVDDILQDVYIKASSNLHQLKSKGSLKGWLYKIAYNTIMDFYRDKLP-----YDELPEDLVAE 82
Cdd:PRK11924  22 HAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCYDLLRRRRRekavlSDDALEPEFAE 101

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 59479680   83 DEDAVEES--RKEIAECMRPLIDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGRVKFRENL 152
Cdd:PRK11924 102 TAETPEAAllAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQLLRECL 173
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 11-152 2.34e-25

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 96.03  E-value: 2.34e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680   11 QLRNYVYKRVDDASAVDDILQDVYIKASSNLHQLKSKGSLKGWLYKIAYNTIMDFYRDK--LPYDELPEDLVAEDEDAVE 88
Cdd:PRK09652  22 RVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRGGAAFYTWLYRIARNTAINYLRKQgrRPPASDVDAEEAEDFDLAD 101

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 59479680   89 ESR-----------KEIAECMRPLIDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGRVKFRENL 152
Cdd:PRK09652 102 ALRdistpenellsAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRIFRAREALRAKL 176
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 8-152 4.26e-20

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: 81.84  E-value: 4.26e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680     8 HKAQLRNYVYKRVDDASAVDDILQDVYIKASSNLHQLKSKGSLKGWLYKIAYNTIMDFYRDKL----PYDELPEDLVAED 83
Cdd:TIGR02985  10 YYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETLEISESIKAYLFTIVKNRCLNYLRHKQveekYQEELAEIEEREL 89

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 59479680    84 EDAVEES---RKEIAECMRPLIDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGRVKFRENL 152
Cdd:TIGR02985  90 SEADPEEeleAKELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLRKEL 161
SigM_subfam TIGR02950
RNA polymerase sigma factor, SigM family; This family of RNA polymerase sigma factors is a ...
 5-145 1.99e-17

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: 74.80  E-value: 1.99e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680     5 WQNHKAQLRNYVYKRVDDASAVDDILQDVYIKASSNLHQLKSKgSLKGWLYKIAYNTIMDFYRDKLPYDELPEDLVAEDE 84
Cdd:TIGR02950   1 YREYMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKDS-SIKPWLFRIARNAFIDWYRKDKKIQTIDDDAIGDLE 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 59479680    85 -DAVEESR-----KEIAECMRPLIDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGR 145
Cdd:TIGR02950  80 qHPVESPEhhlliKIEQEEITHHLSRLPENYRTVLILREFKEFSYKEIAELLNLSLAKVKSNLFRAR 146
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 8-152 5.16e-17

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 74.73  E-value: 5.16e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680    8 HKAQLRNYVYKRVDDASAVDDILQDVYIKASSNLHQLKSKGSLKGWLYKIAYNTIMDFYRDKLP---------------- 71
Cdd:PRK09641  27 YKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINRKFSTWLYRIATNLTIDRLRKRKPdyyldaevagtegltm 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680   72 YDELPEDlVAEDEDAVEESrkEIAECMRPLIDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGRVKFREN 151
Cdd:PRK09641 107 YSQLAAD-DALPEEQVVSL--ELQETIQEAILQLPEKYRTVIVLKYIEDLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183


                 .
gi 59479680  152 L 152
Cdd:PRK09641 184 L 184
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 5-150 7.05e-16

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: 70.81  E-value: 7.05e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680     5 WQNHKAQLRNYVYKRVDDASAVDDILQDVYIKASSNLHQLKSKGSLKGWLYKIAYNTIMDFYRDK-----LPYDELPEDL 79
Cdd:TIGR02989   7 LTRHERALRAFVRSLVADRDDVDDVLQETFVVAWRKFDQFDPGTNFVAWARGIARNKVLNYRRKLgrdrlVFDDDLLEAL 86

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 59479680    80 VAEDEDAVEESRKEIAECMRPLIDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGRVKFRE 150
Cdd:TIGR02989  87 AAEAEPTEAERLSDDRQALEGCLEKLPERQRELLDLRYQRGQKATALAEQTGRTVNAVYKALQRIRVSLRE 157
PRK12522 PRK12522
RNA polymerase sigma factor; Provisional
 8-152 4.09e-14

RNA polymerase sigma factor; Provisional


Pssm-ID: 183571 [Multi-domain]  Cd Length: 173  Bit Score: 66.82  E-value: 4.09e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680    8 HKAQLRNYVYKRVDDASAVDDILQDVYIKASSNLHQLKSKGSLKGWLYKIAYNTIMDFYRDKLPYDELPEDLV-AEDEDA 86
Cdd:PRK12522  12 YKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVENYKKWITTICVRTFYDFYRKKKRWKDRILDLFhKEDGGE 91

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 59479680   87 VEES----------RKEIAECMRPLIDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGRVKFRENL 152
Cdd:PRK12522  92 IEFAddvniseefiQKVEAEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQMREHL 167
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 27-152 5.89e-14

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 66.73  E-value: 5.89e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680   27 DDILQDVYIKASSNLhQLKSKGSLKGWLYKIAYNTIMDFYR--DKLPYDELPED---LVAED---EDAVEESRKEIAecM 98
Cdd:PRK09647  56 EDLTQETFIRVFRSL-QNYQPGTFEGWLHRITTNLFLDMVRrrARIRMEALPEDydrVPGDEpnpEQIYHDARLDPD--L 132

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 59479680   99 RPLIDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGRVKFRENL 152
Cdd:PRK09647 133 QAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAAL 186
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 1-152 1.01e-13

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 65.54  E-value: 1.01e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680    1 MLSEWQNHKAQ-LRNYVYKRVDDASAVDDILQDVYIKASSNLHQLKSKGSLKGWLYKIAYNTIMDF-----YRDKLPYDE 74
Cdd:PRK09415  17 LIDEIMNEYGQeVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGKSSLKTWLYRIAINHCKDYlkswhNKKVIVTED 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680   75 LPEDLVAEdEDAVEES--RKEIAECMRPLIDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGRVKFRENL 152
Cdd:PRK09415  97 IFTYMESQ-KESVEEEviQNAEDERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKELLKKGL 175
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 12-150 4.39e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 64.04  E-value: 4.39e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680   12 LRNYVYKRVDDASAVDDILQDVYIKASSNLHQLKSKGSLKGWLYKIAYNTIMDFYRDKLPYDELPEDLVAEDEDAV---E 88
Cdd:PRK12511  17 LRRYARSLTRDSAEAEDLVHDALVRALERRASFRSGGNLRTWLMSILHNAFIDELRRRRVEARRADELAVLADASLpaaQ 96

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 59479680   89 ESRKEIAEcMRPLIDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGRVKFRE 150
Cdd:PRK12511  97 EHAVRLAQ-IRDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAALRA 157
PRK12536 PRK12536
RNA polymerase sigma factor; Provisional
 10-144 6.95e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 237131 [Multi-domain]  Cd Length: 181  Bit Score: 63.53  E-value: 6.95e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680   10 AQLRNYVYKRVDDASA-VDDILQDVYIKASSNLHQLKSKGSLKGWLYKIAYNTIMDFYRDKLPYDELPE------DLVAE 82
Cdd:PRK12536  32 AHLRGFLRRRLPQLPDeVEDLVQEILLAVHNARHTYRADQPLTAWVHAIARYKLMDFLRSRARREALHDplddesELFAT 111

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 59479680   83 DEDAVEESRKEIAEcmrpLIDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRG 144
Cdd:PRK12536 112 SDDEAAEARRDLGK----LLEQLPDRQRLPIVHVKLEGLSVAETAQLTGLSESAVKVGIHRG 169
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 21-152 7.74e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 64.22  E-value: 7.74e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680   21 DDASAvDDILQDVYIKASSNLHQLKSKGSLKGWLYKIAYNTIMDFYR------DKLPYDE---------LPEDLVAED-E 84
Cdd:PRK11922  53 NDAEA-EDVVQEAYLRAFRALGTFRGDASLSTWLSRIVLNEALGRLRrrrrlvNLAEMVMastiaggerTPLADPAEDpE 131

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 59479680   85 DAVeeSRKEIAECMRPLIDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGRVKFRENL 152
Cdd:PRK11922 132 RAA--ARREIRALLERAIDALPDAFRAVFVLRVVEELSVEETAQALGLPEETVKTRLHRARRLLRESL 197
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 12-152 4.67e-12

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 61.49  E-value: 4.67e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680   12 LRNYVYKRVDDASAVDDILQDVYIKASSNLHQLKSKGSLKGWLYKIAYNTIMDFYRDKLPYDELPEDLVAEDEDAVEESR 91
Cdd:PRK09640  39 LFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGKSKFKTWLYSITYNECITQYRKERRKRRLMDALSLDPLEEASEEK 118

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 59479680   92 KEIAE----CMRPLIDELP-DKYSVPLR-LAELDGipqQEIADKLGLSLSGAKSRIQRGRVKFRENL 152
Cdd:PRK09640 119 APKPEerggLDRWLVHVNPiDREILVLRfVAELEF---QEIADIMHMGLSATKMRYKRALDKLREKF 182
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 15-150 7.33e-12

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 60.28  E-value: 7.33e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680   15 YVYKRVDDASAVDDILQDVYIKASSNLHQLKSKgSLKGWLYKIAYNTIMDFYRD--KLPY--DELPEDLVAEdedAVEE- 89
Cdd:PRK09644  17 YLFSLTKSHHAAEDLLQETFYRAYIYLEDYDNQ-KVKPWLFKVAYHTFIDFVRKekKVSFvgTDEIEAIQAE---STEEy 92

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 59479680   90 -SRKEIAECMRPLIDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGRVKFRE 150
Cdd:PRK09644  93 vVAKNSYEKLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRLKA 154
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 6-152 1.04e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 60.47  E-value: 1.04e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680    6 QNHKAQLRNYVYKRVDDASAVDDILQDVY---IKASSnlhQLKSKGSLKGWLYKIAYNTIMDFYRD----KLPYDELPED 78
Cdd:PRK12513  33 ARHRTGLYRFLLRLARDRALAEDIFQETWlrvIRARA---QYQPRARFRTWLYQIARNLLIDHWRRhgarQAPSLDADEQ 109

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 59479680   79 LVAEDEDAVEESRKEIAECMRPLID----ELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGRVKFRENL 152
Cdd:PRK12513 110 LHALADDGAAPEQQLSLFRDRRRLQaaleTLPDEQREVFLLREHGDLELEEIAELTGVPEETVKSRLRYALQKLRELL 187
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 5-152 1.21e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 60.12  E-value: 1.21e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680    5 WQNHKAQLRNYVYKrVDDASAVDDILQDVYIKASSNLHQLKSKGSLKGWLYKIAYNTIMDfYRDKLPYDELpedLVAEDE 84
Cdd:PRK12518  17 YRRYQQKVRSTLYQ-LCGRELLDDLVQEVFLRVWKGLPKLRNPAYFSTWLYRITWNVATD-ARRQFAQRPS---RIQDDS 91

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 59479680   85 DAVEESRKEIAECMRPL---------IDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGRVKFRENL 152
Cdd:PRK12518  92 LNDQPSRPSDTPDLMQLhyqdlvqqgLQTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFL 168
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
 4-152 5.12e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 58.70  E-value: 5.12e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680    4 EWQNHKAQLRNYVYKRVDDASAVDDILQDVYIKASSNLHQLKSKGSLKGWLYKIAYNTimdFYRDKLPYDELPEDLVAED 83
Cdd:PRK12546  12 ELVEHLPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEGTNLRAWLFTILRNT---FYSDRRKHKREVPDPEGVH 88

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 59479680   84 EDAVEES-----RKEIAEcMRPLIDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGRVKFRENL 152
Cdd:PRK12546  89 AASLAVKpahdgRLAMSD-FRAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARARLAELL 161
PRK12539 PRK12539
RNA polymerase sigma factor SigF;
12-144 1.57e-10

RNA polymerase sigma factor SigF;


Pssm-ID: 237132 [Multi-domain]  Cd Length: 184  Bit Score: 57.05  E-value: 1.57e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680   12 LRNYVYKRVD----DASAVDDILQDVYIKASSNLHQLKSKGSLKGWLYKIAYNTIMDFYRDK------LPYDELpEDLVA 81
Cdd:PRK12539  34 LRAYYKGKLArigrGAEEAEDLVQEALMAIHTRRHTYDPEQPLTPWVYAIARYKLIDHLRRTrasladVPIDDA-DELVA 112

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 59479680   82 EDEDAVEESRKEIAEcmrpLIDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRG 144
Cdd:PRK12539 113 HDDHAAVESTLDLGR----LLARLPEKMRLAIQAVKLEGLSVAEAATRSGMSESAVKVSVHRG 171
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 5-145 1.91e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 56.48  E-value: 1.91e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680    5 WQNHKAQLRNYVYKRVDDASAVDDILQDVYIKASSNLHQLKSKgSLKGWLYKIAYNTIMDFYRDKLPYD-------ELPE 77
Cdd:PRK12541  11 YSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGE-EIRPWLFTIAYNAFIDWYRKEKKYKtttieefHLPN 89

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 59479680   78 DLVAEDEDAVeesRKEIAECMRPLIDELPDKYSVPLrLAELDGIPQQEIADKLGLSLSGAKSRIQRGR 145
Cdd:PRK12541  90 VPSTEHEYFI---KHEIASWLDSLSSLPLERRNVLL-LRDYYGFSYKEIAEMTGLSLAKVKIELHRGR 153
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 15-150 2.26e-10

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 56.50  E-value: 2.26e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680   15 YVYKR----VDDASAVDDILQDVYIKASSNlhQLKSKGSLKGWLYKIAYNTIMDFYR----------DKLPYDELPEDLV 80
Cdd:PRK09639  15 DVVQQifyiVKDRTQAEDLAQEVFLRLYRS--DFKGIENEKGWLIKSARNVAYNYLRsekrrrarilGEFQWQEVDNEPS 92

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680   81 AEDEDAVEESRKEIAECMRPLIDElpDKYSVPLRLAeldGIPQQEIADKLGLSLSGAKSRIQRGRVKFRE 150
Cdd:PRK09639  93 PEEIWIRKEEITKVQEVLAKMTER--DRTVLLLRFS---GYSYKEIAEALGIKESSVGTTLARAKKKFRK 157
PRK08241 PRK08241
RNA polymerase subunit sigma-70;
8-150 6.30e-10

RNA polymerase subunit sigma-70;


Pssm-ID: 236196 [Multi-domain]  Cd Length: 339  Bit Score: 56.87  E-value: 6.30e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680    8 HKAQLRNYVYK---RVDDAsavDDILQDVYIKASSNLHQLKSKGSLKGWLYKIAYNTIMDFYRDKlPYDELPEDLVAEDE 84
Cdd:PRK08241  28 HRRELLAHCYRmlgSVHDA---EDAVQETLLRAWRGYDRFEGRSSLRTWLYRIATNVCLDALEGR-ARRPLPTDLGAPAA 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680   85 DAVEESRkEIAEcmRPLIDELPDKYSVP--------------LRLA-------------------ELDGIPQQEIADKLG 131
Cdd:PRK08241 104 DPVDELV-ERPE--VPWLEPYPDALLDPaaadpaarvvaresVRLAfvaalqhlpprqravlilrDVLGWSAAEVAELLD 180

                        170
                 ....*....|....*....
gi 59479680  132 LSLSGAKSRIQRGRVKFRE 150
Cdd:PRK08241 181 TSVAAVNSALQRARATLAE 199
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 101-147 2.31e-09

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: 50.92  E-value: 2.31e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 59479680   101 LIDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGRVK 147
Cdd:pfam08281   7 ALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKK 53
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 20-151 2.59e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 53.97  E-value: 2.59e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680   20 VDDASAVDDILQDVYIKASSNLHQLKSKGSLKGWLYKIAYNTIMDFYRDKL-------PYDELPEDLVAEDEDAV--EES 90
Cdd:PRK12543  28 VEDKQDVDDVVNEIYIQLWESLRKYDSNRPFRFWLIGLVIKQIHSWRRKRWrrfrifeKAEEQRKPVSIDFSEDVlsKES 107

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 59479680   91 RKEIAEcmrpLIDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGRVKFREN 151
Cdd:PRK12543 108 NQELIE----LIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQK 164
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 6-152 2.63e-09

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 53.87  E-value: 2.63e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680    6 QNHKAQLRNYVYKRVDDASAVDDILQDVYIKASSNLHQLKSKGSLKGWLYKIAYNTIMDFYRDKLPYDELpedlvaEDED 85
Cdd:PRK09638  25 QQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGRSKFSTWLISIASRLYKDHLRKQKREKLR------LQRA 98

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 59479680   86 AVEESRKEIAECMRP---------LIDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGRVKFRENL 152
Cdd:PRK09638  99 KEETLRKEKWEAAIKgaewsemldALSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRKEW 174
algU PRK11923
RNA polymerase sigma factor AlgU; Provisional
 20-145 6.62e-09

RNA polymerase sigma factor AlgU; Provisional


Pssm-ID: 171347 [Multi-domain]  Cd Length: 193  Bit Score: 52.88  E-value: 6.62e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680   20 VDDASAVDDILQDVYIKASSNLHQLKSKGSLKGWLYKIAYNTIMDFY--RDKLPYDelpEDLVAED------EDAVEE-- 89
Cdd:PRK11923  41 VHDTAEAQDVAQEAFIKAYRALGNFRGDSAFYTWLYRIAINTAKNHLvsRGRRPPD---SDVSSEDaefydgDHALKDie 117

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 59479680   90 ------SRKEIAECMRPLIDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGR 145
Cdd:PRK11923 118 speralLRDEIEGTVHRTIQQLPEDLRTALTLREFDGLSYEDIASVMQCPVGTVRSRIFRAR 179
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 8-69 1.16e-08

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


Pssm-ID: 427998 [Multi-domain]  Cd Length: 71  Bit Score: 49.51  E-value: 1.16e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 59479680     8 HKAQLRNYVYKRVDDASAVDDILQDVYIKASSNLHQLK-SKG-SLKGWLYKIAYNTIMDFYRDK 69
Cdd:pfam04542   5 YLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDpERGvSFSTWLYTIIRNAIIDYLRKQ 68
PRK12531 PRK12531
RNA polymerase sigma factor; Provisional
 5-154 5.57e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 105726 [Multi-domain]  Cd Length: 194  Bit Score: 50.31  E-value: 5.57e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680    5 WQNHKAQLRNYVYKRVDDASAVDDILQDVYIKASSNLHQLK-SKGSLKGWLYKIAYNTIMDFYR------------DKLP 71
Cdd:PRK12531  33 FSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDgQKSALSTWIYTIIRNLCFDLLRkqkgkdlhihadDIWP 112

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680   72 YDELPEDLV---AEDEDAVEEsrkeiaECMRpLIDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGRVKF 148
Cdd:PRK12531 113 SDYYPPDLVdhySPEQDMLKE------QVMK-FLDRLPKAQRDVLQAVYLEELPHQQVAEMFDIPLGTVKSRLRLAVEKL 185


                 ....*.
gi 59479680  149 RENLMT 154
Cdd:PRK12531 186 RHSMDA 191
PRK06811 PRK06811
RNA polymerase factor sigma-70; Validated
 26-151 8.52e-08

RNA polymerase factor sigma-70; Validated


Pssm-ID: 180707 [Multi-domain]  Cd Length: 189  Bit Score: 49.55  E-value: 8.52e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680   26 VDDILQDVYIKASSNLHQLKS-KGSLKGWLYKIAYNTIMDFYR--------DKLPYDELPEDLVAEDEDAVEESRKEIAE 96
Cdd:PRK06811  48 IEECVNDIFLSIWNNIDKFDEeKGSFKKWIAAISKYKAIDYKRkltknneiDSIDEFILISEESIENEIILKENKEEILK 127

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 59479680   97 cmrpLIDELP--DKYSVPLRLaeLDGIPQQEIADKLGLSLSGAKSRIQRGRVKFREN 151
Cdd:PRK06811 128 ----LINDLEklDREIFIRRY--LLGEKIEEIAKKLGLTRSAIDNRLSRGRKKLQKN 178
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 96-149 1.01e-07

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: 46.71  E-value: 1.01e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 59479680  96 ECMRPLIDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGRVKFR 149
Cdd:cd06171   2 ERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 22-152 1.46e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 49.05  E-value: 1.46e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680   22 DASAVDDILQDVYIKASSNLHQLK-SKGSLKGWLYKIAYNTIMDFYRDKLPY-DELPE--DLVAEDED------AVEESR 91
Cdd:PRK12514  42 DRSEAEEALQDVYVKIWTKADRFAvSGLSPMTWLITIARNHAIDRLRARKAVaVDIDEahDLADPSPGpeaeviAGDEGQ 121

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 59479680   92 KeIAECMRplidELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGRVKFRENL 152
Cdd:PRK12514 122 R-IDACLE----ELEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMRTWLRRSLLKLRECL 177
PRK12534 PRK12534
RNA polymerase sigma factor; Provisional
 27-152 2.37e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183576 [Multi-domain]  Cd Length: 187  Bit Score: 48.51  E-value: 2.37e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680   27 DDILQDVYIKASSNLHQLK-SKGSLKGWLYKIAYNTIMDFYRDKLP------YDELPEdLVAEDEDAVEES-----RKEI 94
Cdd:PRK12534  53 EEVLQDVFTLIWHKAGQFDpSRARGLTWLAMIARNKAIDHLRANAPqrrnvaLDDAGE-LRAADASPLERTerastRRRI 131

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 59479680   95 AECMrpliDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGRVKFRENL 152
Cdd:PRK12534 132 DHCL----AELEPPRSELIRTAFFEGITYEELAARTDTPIGTVKSWIRRGLAKLKACL 185
PRK09651 PRK09651
RNA polymerase sigma factor FecI; Provisional
 3-138 3.10e-07

RNA polymerase sigma factor FecI; Provisional


Pssm-ID: 182018 [Multi-domain]  Cd Length: 172  Bit Score: 47.88  E-value: 3.10e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680    3 SEWQNHKAQLRNYVYKRVDDASAVDDILQDVYIKASSNlHQLKSKGSLKGWLYKIAYNTIMDFYR----DKLPYD---EL 75
Cdd:PRK09651  14 SLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVS-ETLSTIRDPRSFLCTIAKRVMVDLFRrnalEKAYLEmlaLM 92

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 59479680   76 PEDLVAEDEdaVEESRKEIAECMRPLIDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAK 138
Cdd:PRK09651  93 PEGGAPSPE--ERESQLETLQLLDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVK 153
PRK09643 PRK09643
RNA polymerase sigma factor SigM; Reviewed
 27-152 1.19e-06

RNA polymerase sigma factor SigM; Reviewed


Pssm-ID: 236604 [Multi-domain]  Cd Length: 192  Bit Score: 46.63  E-value: 1.19e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680   27 DDILQDVYIKASSNLHQLKSKGSLKGWLYKIAYNTIMDFYR-----------DKLPYDELPEDLVAEDEDAVEESRKeia 95
Cdd:PRK09643  55 ADALQDAMLSAHRAAGSFRGDAAVSSWLHRIVVNACLDRLRrakarptvpldDVYPVAQLERDPTARVETALAVQRA--- 131

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 59479680   96 ecmrplIDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGRVKFRENL 152
Cdd:PRK09643 132 ------LMRLPVEQRAALVAVDMQGYSVADAARMLGVAEGTVKSRCARGRARLAELL 182
PRK12517 PRK12517
RNA polymerase sigma factor; Provisional
 15-152 1.27e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183569 [Multi-domain]  Cd Length: 188  Bit Score: 46.60  E-value: 1.27e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680   15 YVYKRVDDASAVDDILQDVYIKASSNLHQLKSKGSLKGWLYkiaynTIMD------FYRDKLPYDELPEDLVaEDEDAVE 88
Cdd:PRK12517  39 YAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDEKAAKAWLI-----TILRrenarrFERKQFDLVDIEDDSI-EDDASHS 112

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 59479680   89 ESRKEIAECMRPLIDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGRVKFRENL 152
Cdd:PRK12517 113 SEEEMEQEWLRRQIAKLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMTRLFRARNQLKEAL 176
PRK09649 PRK09649
RNA polymerase sigma factor SigC; Reviewed
 20-145 2.00e-06

RNA polymerase sigma factor SigC; Reviewed


Pssm-ID: 137458 [Multi-domain]  Cd Length: 185  Bit Score: 45.80  E-value: 2.00e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680   20 VDDASAVDDILQDVYIKASSNLHQLKSKGSLKGWLYKIAYNTIMDFYRD-----KLPYDELPEDLVAED------EDAVE 88
Cdd:PRK09649  44 LSDVGSADDLTQETFLRAIGAIPRFSARSSARTWLLAIARHVVADHIRHvrsrpRTTRGARPEHLIDGDrhargfEDLVE 123

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 59479680   89 esrkeiaecMRPLIDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGR 145
Cdd:PRK09649 124 ---------VTTMIADLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARAR 171
PRK12544 PRK12544
RNA polymerase factor sigma-70;
6-152 2.07e-06

RNA polymerase factor sigma-70;


Pssm-ID: 183583 [Multi-domain]  Cd Length: 206  Bit Score: 45.95  E-value: 2.07e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680    6 QNHKAQLRNYVYKRVDDASAVDDILQDVYIKASSNLHQLKSKGSLKGWLYKIAYNTIMDFYRDKLPYDELPEDLVAEDED 85
Cdd:PRK12544  25 EDLRKQMIKFATLQLSDLHLAEDAVQEALIGALKNADSFAGRAAFKTWVFAILKNKIIDLLRQKKRHVSASSLLRDEEEE 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680   86 A-VEE------------------SRKEIAE----------CMrpliDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSG 136
Cdd:PRK12544 105 EdFEElfdesghwqkderpqawgNPEESLEqeqfwrifeaCL----DGLPAKYARVFMMREFIELETNEICHAVDLSVSN 180

                        170
                 ....*....|....*.
gi 59479680  137 AKSRIQRGRVKFRENL 152
Cdd:PRK12544 181 LNVLLYRARLRLRECL 196
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
 8-133 2.22e-06

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 45.45  E-value: 2.22e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680    8 HKAQLRNYVYKRVDDASAVDDILQDVYIKASSNLHQLKSKGSLkGWLYKIAYNTIMDFYRD---KLPYDELPED-LVAED 83
Cdd:PRK07037   7 NRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQDAVKQPV-AYLFRIVRNLAIDHYRRqalENKYHGDEEDgLDVPS 85

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 59479680   84 EDAVEES---RKEIAECMRPLIDELPDKYSVPLRLAELDGIPQQEIADKLGLS 133
Cdd:PRK07037  86 PEASPEAaliNRDTLRHVADALSELPARTRYAFEMYRLHGETQKDIARELGVS 138
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 6-150 3.23e-06

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 44.77  E-value: 3.23e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680    6 QNHKAQLRNYVYKRVDDASAVDDILQDVYIKAssnlhqLKSKGSL-----KGWLYKIAYNTIMDFYRDKLPYDELPEDLV 80
Cdd:PRK12527   2 ENYYRELVRFLSARLGNRQAAEDVAHDAYLRV------LERSSSAqiehpRAFLYRTALNLVVDRHRRHRVRQAEPLEVL 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680   81 AEDE-------DAVEESRKEIAECMRPLiDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRG----RVKFR 149
Cdd:PRK12527  76 DEEErlhspspQTRLDLGQRLALLQRAL-AELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAmkhcRVRMR 154


                 .
gi 59479680  150 E 150
Cdd:PRK12527 155 Q 155
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 22-152 4.31e-06

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 44.90  E-value: 4.31e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680   22 DASAVDDILQDVYIKASSNLHQL-KSKGSLKGWLYKIAYNTIMDFYRDKL-------PYDELPE--DLVAEDEDavEESR 91
Cdd:PRK13919  46 DGAAAEDVVQEVFIRVWKKAKEFdPRRGSARAWLLALAHHAAVDHVRRRAarpqplePDEREPEafDLPGPGLD--EEGH 123

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 59479680   92 KEIAECMRPLIDELPDKYSVpLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGRVKFRENL 152
Cdd:PRK13919 124 LDRTRLGRALKALSPEERRV-IEVLYYQGYTHREAAQLLGLPLGTLKTRARRALSRLKEVL 183
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 5-150 4.74e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 44.77  E-value: 4.74e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680    5 WQNHKAQLRNYVYKRVDDASAVDDILQDVYIKASSNLHQLK-SKGSLKGWLYKI----AYNTIMDFYRDkLPYDELPED- 78
Cdd:PRK12537  29 YQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDpARGSARGWIYSVtrhlALNVLRDTRRE-VVLDDDAEEt 107

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 59479680   79 -----LVAEDEDAVEESRKeIAECMRPLideLPDKYSVPLRlAELDGIPQQEIADKLGLSLSGAKSRIQRGRVKFRE 150
Cdd:PRK12537 108 aqtlhEIIDDFDLWANSGK-IHRCLEQL---EPARRNCILH-AYVDGCSHAEIAQRLGAPLGTVKAWIKRSLKALRE 179
PRK12523 PRK12523
RNA polymerase sigma factor; Reviewed
 5-144 1.14e-05

RNA polymerase sigma factor; Reviewed


Pssm-ID: 183572 [Multi-domain]  Cd Length: 172  Bit Score: 43.69  E-value: 1.14e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680    5 WQNHKAQLRNYVYKRVDDASAVDDILQDVYIKASSNlHQLKSKGSLKGWLYKIAYNTIMD-FYRDKLPYDELPE-DLVAE 82
Cdd:PRK12523  16 YRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGR-PELPTPREPRAFLAAVAKGLMFDhFRRAALEQAYLAElALVPE 94

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 59479680   83 DEDAVEESRKEIAECMRPlIDELPDKYSVPLRLA----ELDGIPQQEIADKLGLSLSGAKSRIQRG 144
Cdd:PRK12523  95 AEQPSPEEQHLILEDLKA-IDRLLGKLSSKARAAflynRLDGMGHAEIAERLGVSVSRVRQYLAQG 159
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 86-152 1.17e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 43.90  E-value: 1.17e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 59479680   86 AVEESRKEIAECMrpliDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGRVKFRENL 152
Cdd:PRK12519 127 SLAERSQRVQTAL----AQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKARARQGLLKLRELL 189
PRK12528 PRK12528
RNA polymerase sigma factor; Provisional
 5-138 2.45e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 171561 [Multi-domain]  Cd Length: 161  Bit Score: 42.52  E-value: 2.45e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680    5 WQNHKAQLRNYVYKRVDDASAVDDILQDVYIKassnLHQLKSKGSL---KGWLYKIAYNTIMDFYR----DKLPYDELPE 77
Cdd:PRK12528  10 YSAHHHWLTGWLRRRLGCPQSAADLAQDTFVK----VLVARETAQIiepRAFLTTIAKRVLCNHYRrqdlERAYLEALAQ 85

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 59479680   78 dlVAEDEDAVEESRKEIAECMRPLiDELPDKYSVPLR----LAELDGIPQQEIADKLGLSLSGAK 138
Cdd:PRK12528  86 --LPERVAPSEEERAIILETLVEL-DQLLDGLPPLVKraflLAQVDGLGYGEIATELGISLATVK 147
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 12-152 2.87e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 42.64  E-value: 2.87e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680   12 LRNYVYKRVDDASAVDDILQDVYIKASSNLHQLKSKGSLKGWLYKIAYNTIMDFYRDKLPYDELPEDLVAEdEDAVEESR 91
Cdd:PRK12516  23 LRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVGTNMKAWLFTILRNEFYSQMRKRGREVQDTDGMFTE-QLAVHPSQ 101

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 59479680   92 KEIAEC--MRPLIDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGRVKFRENL 152
Cdd:PRK12516 102 YGTLDLqdFRAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQRLQEIL 164
PRK12540 PRK12540
RNA polymerase sigma factor; Provisional
 12-152 4.14e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183579 [Multi-domain]  Cd Length: 182  Bit Score: 42.26  E-value: 4.14e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680   12 LRNYVYKRVDDASAVDDILQDVYIKASSNLHQLKSKGSLKGWLYKIAYNTIMDFYRDKLPYDELPEDLVAE--DEDAVEE 89
Cdd:PRK12540  18 LRAFAISLSGNGDRADDLVQETLLRALANIDSFQPGSNLPAWLFTILRNLFRSDYRKRRREVEDADGSYAKtlKSQPGQN 97

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 59479680   90 SRKEIAEcMRPLIDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGRVKFRENL 152
Cdd:PRK12540  98 AHLEFEE-FRAALDKLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARSKLSALL 159
sigI PRK09635
RNA polymerase sigma factor SigI; Provisional
 5-150 4.69e-05

RNA polymerase sigma factor SigI; Provisional


Pssm-ID: 182008 [Multi-domain]  Cd Length: 290  Bit Score: 42.65  E-value: 4.69e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680    5 WQNHKAQLRNYVYKRVDDASAVDDILQDVYIK-ASSNLHQLKSKgslKGWLYKIAYNTIMDFYRDKLPYDELPEDL-VAE 82
Cdd:PRK09635  11 WRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRlLRAPVGDIDDE---RGWLIVVTSRLCLDHIKSASTRRERPQDIaAWH 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680   83 DEDAV-------------EESRKEIAECMRplidELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGRVKFR 149
Cdd:PRK09635  88 DGDASvssvdpadrvtldDEVRLALLIMLE----RLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQLAHRARRKIN 163


                 .
gi 59479680  150 E 150
Cdd:PRK09635 164 E 164
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 20-152 7.98e-05

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 41.18  E-value: 7.98e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680   20 VDDASAVDDILQDVYIKASSNLHQLKSKG-SLKGWLYKIAYNTIMDFYRDK--LPYDELPEdlVAEDEDAVEES--RKEI 94
Cdd:PRK05602  41 LGDPAEAEDVAQETFLRIWKQAPSWRPGEaRFDTWLHRVVLNLCYDRLRRRreVPVEDAPD--VPDPAPGPDAGleARQR 118

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 59479680   95 AECMRPLIDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGRVKFRENL 152
Cdd:PRK05602 119 ARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALESLLARGRRALRAQL 176
PRK09646 PRK09646
ECF RNA polymerase sigma factor SigK;
31-152 9.75e-05

ECF RNA polymerase sigma factor SigK;


Pssm-ID: 182015 [Multi-domain]  Cd Length: 194  Bit Score: 41.19  E-value: 9.75e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680   31 QDVYIKASSNLHQLK-SKGSLKGWLYKIAYNTIMDFYRDK----------------LPYDELPEDLVAEDEdaveesRKE 93
Cdd:PRK09646  62 QEVYLEVWRTASRFDpARGSALAWLLTLAHRRAVDRVRSEqaasqrevrygarnvdPAFDQVAEEVEARLE------RER 135

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 59479680   94 IAECMRPLIDElpDKYSVplRLAELDGIPQQEIADKLGLSLSGAKSRIQRGRVKFRENL 152
Cdd:PRK09646 136 VRDCLDALTDT--QRESV--TLAYYGGLTYREVAERLAVPLGTVKTRMRDGLIRLRDCL 190
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 101-150 1.30e-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: 38.18  E-value: 1.30e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 59479680   101 LIDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGRVKFRE 150
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
 20-152 1.97e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 40.61  E-value: 1.97e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680   20 VDDASAVDDILQDVYIKASSNLHQLK-SKGSLKGWLYKIAYNTIMDFYRDKLP--YDELPEdlVAEDE-DAVEE-SRKEI 94
Cdd:PRK12538  84 VGNRADAEDVVQDTMLKVWTHRGRWQhGRAKFSTWLYRVVSNRCIDLRRKPRTenVDAVPE--VADGKpDAVSViERNEL 161

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 59479680   95 AECMRPLIDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGRVKFRENL 152
Cdd:PRK12538 162 SDLLEAAMQRLPEQQRIAVILSYHENMSNGEIAEVMDTTVAAVESLLKRGRQQLRDLL 219
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 8-152 3.61e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 39.33  E-value: 3.61e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680    8 HKAQLRNYVYKRVDDASAVDDILQDVYIKASSNLHQLKSKGSLKGWLYKIAYNTIMDFYRDKlPYDELPEDLVAEDEDAV 87
Cdd:PRK12515  31 HHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGRSQVSTWLLSIARFKALSALRRR-KHEEIDDEAAAAIEDGA 109

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680   88 EE-----SRKEIAECMRPLIDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGRVKFRENL 152
Cdd:PRK12515 110 DTpevalQKSDTSAALRACLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKTRMFYARKKLAELL 179
PRK12530 PRK12530
RNA polymerase sigma factor; Provisional
 19-69 6.70e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 237128 [Multi-domain]  Cd Length: 189  Bit Score: 38.59  E-value: 6.70e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 59479680   19 RVDDASAVDDILQDVYIKASSNLHQLKSKGSLKGWLYKIAYNTIMDFYRDK 69
Cdd:PRK12530  27 QLKDADLAEDVVQEALVSAYKNADSFKGQSALKTWIFAILKNKIIDLIRYR 77
PRK12542 PRK12542
RNA polymerase sigma factor; Provisional
 17-145 7.85e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183581 [Multi-domain]  Cd Length: 185  Bit Score: 38.49  E-value: 7.85e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680   17 YKRVDDASAVDDILQDVYIKASSNLHQLKSKGS--LKGWLYKIAYNTIMDFYRDKLPYDELPEDLVAEDEDAVEES---- 90
Cdd:PRK12542  27 YSILNNIQQAEDAVQETFITLYKNLEKLHSLNTqeLKRYILRVAKNKAIDSYRKNKRHETFLEEYERESIEAVDENieew 106

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 59479680   91 -RKEIAEC-MRPLIDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGR 145
Cdd:PRK12542 107 eKRKMSEVqIDTLLKELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERAR 163
PRK12529 PRK12529
RNA polymerase sigma factor; Provisional
 5-146 2.71e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183574 [Multi-domain]  Cd Length: 178  Bit Score: 36.84  E-value: 2.71e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680    5 WQNHKAQLRNYVYKRVDD--ASAVDDILQDVYIK--ASSNLHQLKSKGSLKGWLYKIAYNTIMDFYRDK---LPYDE--- 74
Cdd:PRK12529  19 YRENHAWLRNWLAYRLRSwgRGVADDLAHDIFLRilASRDGGQREAIRQPRAYLARIANCVLVSWRRRQsleLAWLEala 98

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 59479680   75 -LPEDL--VAEDEDAVEESRKEIaecmRPLIDELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGRV 146
Cdd:PRK12529  99 tLPEPLhpSPEQQSVILETLHEI----DALLDTLRPRVKQAFLMATLDGMKQKDIAQALDIALPTVKKYIHQAYV 169
PRK12535 PRK12535
RNA polymerase sigma factor; Provisional
 27-145 3.18e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237130 [Multi-domain]  Cd Length: 196  Bit Score: 36.80  E-value: 3.18e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 59479680   27 DDILQDVYIKASSNLHQLKSKGSLKGWLYKIAYNTIMDFYRDKL--PYDELPEDLVAEDEDAVEESRKEIAECM--RPLI 102
Cdd:PRK12535  52 DDLTQETYLRVMSALPRFAARSSARTWLLSLARRVWVDNIRHDMarPRKSATEYEDAAATTASNETTGSWSEWIdvRTLI 131

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 59479680  103 DELPDKYSVPLRLAELDGIPQQEIADKLGLSLSGAKSRIQRGR 145
Cdd:PRK12535 132 DALPPERREALILTQVLGYTYEEAAKIADVRVGTIRSRVARAR 174
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 68-145 7.71e-03

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


Pssm-ID: 440804 [Multi-domain]  Cd Length: 236  Bit Score: 35.96  E-value: 7.71e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 59479680  68 DKLPYDELPEDLVAEDEDAVEESRKEIAECMRPLIDELPDKYSVPLRLAELDGIPQQEIADKLGLSlsgaKSRIQRGR 145
Cdd:COG1191 150 EPLEDGDDLLDLLESGDPEEELEHEELREALAEAIEQLPERERLVLSLYYFEELTLKEIAEVLGVS----ESRVSRLH 223
HTH_24 pfam13412
Winged helix-turn-helix DNA-binding;
120-143 9.75e-03

Winged helix-turn-helix DNA-binding;


Pssm-ID: 404317 [Multi-domain]  Cd Length: 45  Bit Score: 32.79  E-value: 9.75e-03
                          10        20
                  ....*....|....*....|....
gi 59479680   120 GIPQQEIADKLGLSLSGAKSRIQR 143
Cdd:pfam13412  15 RISQRELAERLGLSPSTVNRRLKR 38
 
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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