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Conserved domains on  [gi|1897049147|ref|WP_186975241|]
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MULTISPECIES: RNA polymerase sigma-70 factor [Butyricimonas]

Protein Classification

RNA polymerase sigma-70 factor( domain architecture ID 11496275)

RNA polymerase sigma-70 factor; sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 14-168 4.24e-51

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: 161.96  E-value: 4.24e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  14 FEDIFKQHFATLCTHATTFVNDPDASKDIVHDVFLSLWSHREEIDFSRPILPYLFSLTRNRAINYLAHRKVEDAHaQQAL 93
Cdd:TIGR02985   3 FEQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETLEISESIKAYLFTIVKNRCLNYLRHKQVEEKY-QEEL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  94 VEEPVYTLSEPSD-----RDELINRIIKRIDQLPERCSRVMKLCFIECKKYKEIAEELNISVNTVKTHVTTGLNILRDEF 168
Cdd:TIGR02985  82 AEIEERELSEADPeeeleAKELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLRKEL 161
 
Name Accession Description Interval E-value
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 14-168 4.24e-51

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: 161.96  E-value: 4.24e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  14 FEDIFKQHFATLCTHATTFVNDPDASKDIVHDVFLSLWSHREEIDFSRPILPYLFSLTRNRAINYLAHRKVEDAHaQQAL 93
Cdd:TIGR02985   3 FEQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETLEISESIKAYLFTIVKNRCLNYLRHKQVEEKY-QEEL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  94 VEEPVYTLSEPSD-----RDELINRIIKRIDQLPERCSRVMKLCFIECKKYKEIAEELNISVNTVKTHVTTGLNILRDEF 168
Cdd:TIGR02985  82 AEIEERELSEADPeeeleAKELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLRKEL 161
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 1-167 4.10e-38

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: 129.34  E-value: 4.10e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147   1 MERVKNKESMCtgFEDIFKQHFATLCTHATTFVNDPDASKDIVHDVFLSLWSHREEIDFSRPILPYLFSLTRNRAINYLA 80
Cdd:COG1595     8 LERLRAGDEAA--FEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHLR 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  81 HRKVEDAHAQQALVEEPVYTLS--EPSDRDELINRIIKRIDQLPERCSRVMKLCFIECKKYKEIAEELNISVNTVKTHVT 158
Cdd:COG1595    86 KRRRRRELLDELAEELPDEAADpeEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLS 165


                  ....*....
gi 1897049147 159 TGLNILRDE 167
Cdd:COG1595   166 RARKKLREA 174
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 14-165 4.11e-19

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 80.40  E-value: 4.11e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  14 FEDIFKQHFATLCTHATTFVNDPDASKDIVHDVFLSLWSHREEIDFSRPILPYLFSLTRNRAINYLAHRKVEDAhAQQAL 93
Cdd:PRK11924   15 FSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCYDLLRRRRREKA-VLSDD 93

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1897049147  94 VEEPVYTLSEPSDRDELIN-----RIIKRIDQLPERCSRVMKLCFIECKKYKEIAEELNISVNTVKTHVTTGLNILR 165
Cdd:PRK11924   94 ALEPEFAETAETPEAALLAkddlaRIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQLLR 170
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 111-157 4.16e-11

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: 55.93  E-value: 4.16e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1897049147 111 INRIIKRIDQLPERCSRVMKLCFIECKKYKEIAEELNISVNTVKTHV 157
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRL 47
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 119-165 1.61e-07

helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 46.37  E-value: 1.61e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1897049147  119 DQLPERCSRVMKLCfIECKKYKEIAEELNISVNTVKTHVTtglNILR 165
Cdd:smart00421   2 ASLTPREREVLRLL-AEGLTNKEIAERLGISEKTVKTHLS---NIMR 44
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 111-165 1.74e-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: 46.33  E-value: 1.74e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1897049147 111 INRIIKRIDQLPERCSRVMKLCFIECKKYKEIAEELNISVNTVKTHVTTGLNILR 165
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 14-168 4.24e-51

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: 161.96  E-value: 4.24e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  14 FEDIFKQHFATLCTHATTFVNDPDASKDIVHDVFLSLWSHREEIDFSRPILPYLFSLTRNRAINYLAHRKVEDAHaQQAL 93
Cdd:TIGR02985   3 FEQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETLEISESIKAYLFTIVKNRCLNYLRHKQVEEKY-QEEL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  94 VEEPVYTLSEPSD-----RDELINRIIKRIDQLPERCSRVMKLCFIECKKYKEIAEELNISVNTVKTHVTTGLNILRDEF 168
Cdd:TIGR02985  82 AEIEERELSEADPeeeleAKELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLRKEL 161
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 1-167 4.10e-38

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: 129.34  E-value: 4.10e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147   1 MERVKNKESMCtgFEDIFKQHFATLCTHATTFVNDPDASKDIVHDVFLSLWSHREEIDFSRPILPYLFSLTRNRAINYLA 80
Cdd:COG1595     8 LERLRAGDEAA--FEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHLR 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  81 HRKVEDAHAQQALVEEPVYTLS--EPSDRDELINRIIKRIDQLPERCSRVMKLCFIECKKYKEIAEELNISVNTVKTHVT 158
Cdd:COG1595    86 KRRRRRELLDELAEELPDEAADpeEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLS 165


                  ....*....
gi 1897049147 159 TGLNILRDE 167
Cdd:COG1595   166 RARKKLREA 174
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 14-168 1.45e-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: 112.06  E-value: 1.45e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  14 FEDIFKQHFATLCTHATTFVNDPDASKDIVHDVFLSLWSHREEIDFSRPILPYLFSLTRNRAINYLAHRKVEDAHAQQAL 93
Cdd:TIGR02937   3 FEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDLLE 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1897049147  94 -VEEPVYTLSEPSDRDELINRIIKRIDQLPERCSRVMKLCFIECKKYKEIAEELNISVNTVKTHVTTGLNILRDEF 168
Cdd:TIGR02937  83 eLLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 14-165 4.11e-19

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 80.40  E-value: 4.11e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  14 FEDIFKQHFATLCTHATTFVNDPDASKDIVHDVFLSLWSHREEIDFSRPILPYLFSLTRNRAINYLAHRKVEDAhAQQAL 93
Cdd:PRK11924   15 FSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCYDLLRRRRREKA-VLSDD 93

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1897049147  94 VEEPVYTLSEPSDRDELIN-----RIIKRIDQLPERCSRVMKLCFIECKKYKEIAEELNISVNTVKTHVTTGLNILR 165
Cdd:PRK11924   94 ALEPEFAETAETPEAALLAkddlaRIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQLLR 170
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 1-167 7.66e-17

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 74.46  E-value: 7.66e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147   1 MERVKNKESMCtgFEDIFkQHFAT-LCTHATTFVNDPDASKDIVHDVFLSLW----SHREEIDFSrpilPYLFSLTRNRA 75
Cdd:PRK09652    1 VERVQRGDRAA--FALLV-RRYQPrVKRLLSRLTRDPADAEDLVQETFIKAYralhSFRGGAAFY----TWLYRIARNTA 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  76 INYLAHRK----VEDAHAQQALVEEPVYTLSEPSD------RDELINRIIKRIDQLPERCSRVMKLCFIECKKYKEIAEE 145
Cdd:PRK09652   74 INYLRKQGrrppASDVDAEEAEDFDLADALRDISTpenellSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEI 153

                         170       180
                  ....*....|....*....|..
gi 1897049147 146 LNISVNTVKTHVTTGLNILRDE 167
Cdd:PRK09652  154 MGCPIGTVRSRIFRAREALRAK 175
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 35-166 2.49e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 65.08  E-value: 2.49e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  35 DPDASKDIVHDVFLSLWSHREEIDFSRPILPYLFSLTRNRAINYLAHR----KVEDAHAQQALVEEPVYTLSEPSDRDEL 110
Cdd:PRK12519   52 NSQEAEDLTQEIFLSLWRKSSYDPKRGSLSSYLLTLTRSRAIDRLRSRrsrqRLLERWQQELLGEASEDTPLEQASLAER 131

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147 111 INRIIKRIDQLPERCSRVMKLCFIECKKYKEIAEELNISVNTVKTHVTTGL----NILRD 166
Cdd:PRK12519  132 SQRVQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKARARQGLlklrELLQD 191
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 17-166 2.22e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 62.49  E-value: 2.22e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  17 IFKQHFATLCTHATTFVNDPDASKDIVHDVFLSLWSHREEIDFSR-PILPYLFSLTRNRAINYLAHRK----VEDAHAQQ 91
Cdd:PRK12537   28 LYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPARgSARGWIYSVTRHLALNVLRDTRrevvLDDDAEET 107

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1897049147  92 ALVEEPVYTLSEPSDRDELINRIIKRIDQLPERCSrvmkLC-FIECKKYKEIAEELNISVNTVKTHVTTGLNILRD 166
Cdd:PRK12537  108 AQTLHEIIDDFDLWANSGKIHRCLEQLEPARRNCI----LHaYVDGCSHAEIAQRLGAPLGTVKAWIKRSLKALRE 179
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 10-168 2.41e-12

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 62.31  E-value: 2.41e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  10 MCTgfEDIFKQHFATLCTHATTFVNDPDASKDIVHDVFLSLWSHREEIDFSRPILPYLFSLTRNRAINYlaHRKVEdahA 89
Cdd:PRK09637    1 MKL--ESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDGSSIKSWLYQIANNTIIDF--YRKKN---R 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  90 QQALVEEPVYTLSEPSD--RDELINRIIKRIDQLPERCSRVMKLCFIECKKYKEIAEELNISVNTVKTHVTTGLNILRDE 167
Cdd:PRK09637   74 SEELPDDLLFEDEEREEnaKKELAPCLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKEL 153


                  .
gi 1897049147 168 F 168
Cdd:PRK09637  154 L 154
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
 16-149 9.06e-12

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 60.47  E-value: 9.06e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  16 DIFKQHFATLCTHATTFVNDPDASKDIVHDVFLSLWSHREEIDFSRPiLPYLFSLTRNRAInylahrkveDAHAQQALve 95
Cdd:PRK07037    2 DVFVDNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQDAVKQP-VAYLFRIVRNLAI---------DHYRRQAL-- 69

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1897049147  96 EPVYTLSE----------PSDRDELINR-----IIKRIDQLPERCSRVMKLCFIECKKYKEIAEELNIS 149
Cdd:PRK07037   70 ENKYHGDEedgldvpspeASPEAALINRdtlrhVADALSELPARTRYAFEMYRLHGETQKDIARELGVS 138
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 14-165 1.06e-11

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 60.35  E-value: 1.06e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  14 FEDIFKQHFATLCTHATTFVNDPDASKDIVHDVFLSL----WSHREEIDfsrpilPYLFSLTRNRAINYL-----AHRKV 84
Cdd:PRK09639    5 FEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLyrsdFKGIENEK------GWLIKSARNVAYNYLrsekrRRARI 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  85 EDAHAQQALVEEPvytlsepsDRDELINRI--IKRIDQLPERCSRVMKLCFI---ECKKYKEIAEELNISVNTVKTHVTT 159
Cdd:PRK09639   79 LGEFQWQEVDNEP--------SPEEIWIRKeeITKVQEVLAKMTERDRTVLLlrfSGYSYKEIAEALGIKESSVGTTLAR 150


                  ....*.
gi 1897049147 160 GLNILR 165
Cdd:PRK09639  151 AKKKFR 156
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
17-165 1.67e-11

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 60.09  E-value: 1.67e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  17 IFKQHFATLCTHATTFVNDPDASKDIVHDVFLSLWSHREEIDFS-RPILPYLFSLTRNRAINylAHRKvedAHAQQALVE 95
Cdd:PRK09645   14 LYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTgRSARAWLFTVARNLVID--ERRS---ARARPVEGG 88

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1897049147  96 EPVYTLSEPSDRDElINRIIKRID------QLPERCSRVMKLCFIECKKYKEIAEELNISVNTVKTHVTTGLNILR 165
Cdd:PRK09645   89 DDVLGVPEQSAPDE-VDRALDRLLvadalaQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYALRALR 163
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 111-157 4.16e-11

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: 55.93  E-value: 4.16e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1897049147 111 INRIIKRIDQLPERCSRVMKLCFIECKKYKEIAEELNISVNTVKTHV 157
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRL 47
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 39-168 3.26e-09

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 53.93  E-value: 3.26e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  39 SKDIVHDVFLSLWSHREEIDFSRPILPYLFSLTRNRAINYLAHRKVE---DAH--------------AQQALVEEPVYTL 101
Cdd:PRK09641   45 AEDAAQEAFIRAYVNIDSYDINRKFSTWLYRIATNLTIDRLRKRKPDyylDAEvagtegltmysqlaADDALPEEQVVSL 124

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1897049147 102 sepsdrdELINRIIKRIDQLPERCSRVMKLCFIECKKYKEIAEELNISVNTVKTHVTTGLNILRDEF 168
Cdd:PRK09641  125 -------ELQETIQEAILQLPEKYRTVIVLKYIEDLSLKEISEILDLPVGTVKTRIHRGREALRKQL 184
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 6-167 9.68e-09

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 52.33  E-value: 9.68e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147   6 NKESMCTgfedIFKQHFATLCTHATTFVNDPDASKDIVHDVFL----SLWSHREEIDFSrpilPYLFSLTRNRAINYLAH 81
Cdd:PRK09638   16 DDAALTT----LFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLkaieNLSSFQGRSKFS----TWLISIASRLYKDHLRK 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  82 RKVEDAHAQQALVEEPVYTLSEPSDRDELINRIIKRIDQLPERCSRVMKLCFIECKKYKEIAEELNISVNTVKTHVTTGL 161
Cdd:PRK09638   88 QKREKLRLQRAKEETLRKEKWEAAIKGAEWSEMLDALSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTVKSRVHHGI 167


                  ....*.
gi 1897049147 162 NILRDE 167
Cdd:PRK09638  168 KQLRKE 173
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 33-155 7.69e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 50.12  E-value: 7.69e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  33 VNDPDASKDIVHDVFLSLWSHREEIDFSRPILPYLFSLTRNRAINYLAHRKVEDahaqqaLVEEPVYTLSEPSDRDELI- 111
Cdd:PRK12515   43 VRDEQTAEDLVSEVFLDVWRQAGQFEGRSQVSTWLLSIARFKALSALRRRKHEE------IDDEAAAAIEDGADTPEVAl 116

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1897049147 112 -----NRIIKR-IDQLPERCSRVMKLCFIECKKYKEIAEELNISVNTVKT 155
Cdd:PRK12515  117 qksdtSAALRAcLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKT 166
SigM_subfam TIGR02950
RNA polymerase sigma factor, SigM family; This family of RNA polymerase sigma factors is a ...
 34-157 8.77e-08

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: 49.38  E-value: 8.77e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  34 NDPDASKDIVHDVFLSLWSHREEIDFSRpILPYLFSLTRNRAINYLAHRKVEDAHAQQALVEEPVYTLSEPSDR---DEL 110
Cdd:TIGR02950  17 KDKHLAEDLLQETFLKAYIHLHSFKDSS-IKPWLFRIARNAFIDWYRKDKKIQTIDDDAIGDLEQHPVESPEHHlliKIE 95

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1897049147 111 INRIIKRIDQLPERCSRVMKLCFIECKKYKEIAEELNISVNTVKTHV 157
Cdd:TIGR02950  96 QEEITHHLSRLPENYRTVLILREFKEFSYKEIAELLNLSLAKVKSNL 142
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 119-165 1.61e-07

helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 46.37  E-value: 1.61e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1897049147  119 DQLPERCSRVMKLCfIECKKYKEIAEELNISVNTVKTHVTtglNILR 165
Cdd:smart00421   2 ASLTPREREVLRLL-AEGLTNKEIAERLGISEKTVKTHLS---NIMR 44
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 111-165 1.74e-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: 46.33  E-value: 1.74e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1897049147 111 INRIIKRIDQLPERCSRVMKLCFIECKKYKEIAEELNISVNTVKTHVTTGLNILR 165
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 15-165 2.88e-07

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 48.34  E-value: 2.88e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  15 EDIFKQHFATLCTHATTFVNDPDASKDIVHDVFLSLWSHREEIDFSRpILPYLFSLTRNRAINYLAHRKVEDAHAQQALV 94
Cdd:PRK09644    4 EEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDNQK-VKPWLFKVAYHTFIDFVRKEKKVSFVGTDEIE 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1897049147  95 EEPVYTLSEPSDRDELINRIIKRIDQLPERCSRVMKLCFIECKKYKEIAEELNISVNTVKTHVTTGLNILR 165
Cdd:PRK09644   83 AIQAESTEEYVVAKNSYEKLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRLK 153
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 17-83 2.98e-07

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: 46.04  E-value: 2.98e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1897049147  17 IFKQHFATLCTHATTFVNDPDASKDIVHDVFLSLWSHREEIDFSRPI--LPYLFSLTRNRAINYLAHRK 83
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVsfSTWLYTIIRNAIIDYLRKQR 69
PRK12512 PRK12512
RNA polymerase sigma factor; Provisional
 36-164 5.69e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 171551 [Multi-domain]  Cd Length: 184  Bit Score: 47.77  E-value: 5.69e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  36 PDASKDIVHDVFLSLWSHREEIDFSRPILPYLFSLTRNRAINYLAH--RKVE---DAHAQQALVEEPVYTLsepSDRDel 110
Cdd:PRK12512   50 ADQAEDIVQEILLAVHLKRHTWDPGAPFAPWLFAIARNKLIDALRRrgRRVFvdiDDFAETLPAEPATETL---PAGD-- 124

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1897049147 111 inrIIKRIDQLPERCSRVMKLCFIECKKYKEIAEELNISVNTVKTHVTTGLNIL 164
Cdd:PRK12512  125 ---VGRHLETLPPRQRDVVQSISVEGASIKETAAKLSMSEGAVRVALHRGLAAL 175
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 14-153 6.33e-07

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: 46.93  E-value: 6.33e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  14 FEDIFKQHFATLCTHATTFVNDPDASKDIVHDVFLSLWSHREEIDFSRPILPYLFSLTRNRAINYLA----HRKVEDAHA 89
Cdd:TIGR02989   3 FVRLLTRHERALRAFVRSLVADRDDVDDVLQETFVVAWRKFDQFDPGTNFVAWARGIARNKVLNYRRklgrDRLVFDDDL 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1897049147  90 QQALVEEPVYTLSEpsdRDELINRIIKR-IDQLPERCSRVMKLCFIECKKYKEIAEELNISVNTV 153
Cdd:TIGR02989  83 LEALAAEAEPTEAE---RLSDDRQALEGcLEKLPERQRELLDLRYQRGQKATALAEQTGRTVNAV 144
PRK12531 PRK12531
RNA polymerase sigma factor; Provisional
 1-165 1.07e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 105726 [Multi-domain]  Cd Length: 194  Bit Score: 46.85  E-value: 1.07e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147   1 MERVKNKESmcTGFEDIFKQHFATLCTHATTFVNDPDASKDIVHDVFLSLWSHREEIDFSRPILP-YLFSLTRNRAINYL 79
Cdd:PRK12531   18 MEKVKSRDK--QAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQKSALStWIYTIIRNLCFDLL 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  80 AHRKVEDAHAQQALVEEPVYTLSEPSDR-----DELINRIIKRIDQLPERCSRVMKLCFIECKKYKEIAEELNISVNTVK 154
Cdd:PRK12531   96 RKQKGKDLHIHADDIWPSDYYPPDLVDHyspeqDMLKEQVMKFLDRLPKAQRDVLQAVYLEELPHQQVAEMFDIPLGTVK 175

                         170
                  ....*....|.
gi 1897049147 155 THVTTGLNILR 165
Cdd:PRK12531  176 SRLRLAVEKLR 186
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 14-166 1.35e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 46.35  E-value: 1.35e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  14 FEDIFKQHFATLCTHATTFVNDPDASKDIVHDVFLSLW--SHREEIDFSRPIlPYLFSLTRNRAINYLAHRK--VEDAHA 89
Cdd:PRK12514   21 FSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWtkADRFAVSGLSPM-TWLITIARNHAIDRLRARKavAVDIDE 99

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1897049147  90 QQALVEEPVYTLSEPSDRDELiNRIIKRIDQLPERCSRVMKLCFIECKKYKEIAEELNISVNTVKTHVTTGLNILRD 166
Cdd:PRK12514  100 AHDLADPSPGPEAEVIAGDEG-QRIDACLEELEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMRTWLRRSLLKLRE 175
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 14-167 1.55e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 46.27  E-value: 1.55e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  14 FEDIFKQHFATLCTHATTFVNDPDASKDIVHDVFLSLWSHREEIDFSRPILPYLFSLT-----RNRAINYLAHRKVEDAH 88
Cdd:PRK12543    9 FSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNRPFRFWLIGLVikqihSWRRKRWRRFRIFEKAE 88

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1897049147  89 AQQalvEEPVYTLSEPSDRDELINRIIKRIDQLPERCSRVMKLCFIECKKYKEIAEELNISVNTVKTHVTTGLNILRDE 167
Cdd:PRK12543   89 EQR---KPVSIDFSEDVLSKESNQELIELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQK 164
PRK12534 PRK12534
RNA polymerase sigma factor; Provisional
 14-165 1.58e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183576 [Multi-domain]  Cd Length: 187  Bit Score: 46.59  E-value: 1.58e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  14 FEDIFKQHFATLCTHATTFVNDPDASKDIVHDVFLSLWSHREEIDFSRPI-LPYLFSLTRNRAINYLAHRkvedAHAQQA 92
Cdd:PRK12534   27 FEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRARgLTWLAMIARNKAIDHLRAN----APQRRN 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  93 LVEEPVYTLSEpSDRDEL--INRII--KRIDQL-----PERcSRVMKLCFIECKKYKEIAEELNISVNTVKTHVTTGLNI 163
Cdd:PRK12534  103 VALDDAGELRA-ADASPLerTERAStrRRIDHClaelePPR-SELIRTAFFEGITYEELAARTDTPIGTVKSWIRRGLAK 180


                  ..
gi 1897049147 164 LR 165
Cdd:PRK12534  181 LK 182
PRK12528 PRK12528
RNA polymerase sigma factor; Provisional
 36-157 1.96e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 171561 [Multi-domain]  Cd Length: 161  Bit Score: 45.99  E-value: 1.96e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  36 PDASKDIVHDVFLSLWSHREEIDFSRPiLPYLFSLTRNRAINYLAHRKVEDAHaQQALVEEPvyTLSEPSDRDE-LINRI 114
Cdd:PRK12528   28 PQSAADLAQDTFVKVLVARETAQIIEP-RAFLTTIAKRVLCNHYRRQDLERAY-LEALAQLP--ERVAPSEEERaIILET 103

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1897049147 115 IKRIDQLPERCSRVMKLCFIECK----KYKEIAEELNISVNTVKTHV 157
Cdd:PRK12528  104 LVELDQLLDGLPPLVKRAFLLAQvdglGYGEIATELGISLATVKRYL 150
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 137-165 2.12e-06

DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal transduction mechanisms, Transcription];


Pssm-ID: 441799 [Multi-domain]  Cd Length: 131  Bit Score: 45.27  E-value: 2.12e-06
                          10        20
                  ....*....|....*....|....*....
gi 1897049147 137 KKYKEIAEELNISVNTVKTHVTtglNILR 165
Cdd:COG2197    85 LSNKEIAERLGISERTVKTHVS---NILR 110
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 118-166 2.87e-06

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


Pssm-ID: 461347 [Multi-domain]  Cd Length: 50  Bit Score: 42.80  E-value: 2.87e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1897049147 118 IDQLPERCSRVMKLCFIECKKYKEIAEELNISVNTVKTHVTTGLNILRD 166
Cdd:pfam04545   2 LASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 28-165 1.23e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 44.01  E-value: 1.23e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  28 HATTFVNDPDASKDIVHDVFLSLWSHREEIDFSRPILPYLFSLTRNRAINYLAHRKVEDAHAQQALVEEPVyTLSEPSDR 107
Cdd:PRK12511   20 YARSLTRDSAEAEDLVHDALVRALERRASFRSGGNLRTWLMSILHNAFIDELRRRRVEARRADELAVLADA-SLPAAQEH 98

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1897049147 108 DELINRIIKRIDQLPERCSRVMKLCFIECKKYKEIAEELNISVNTVKTHVTTGLNILR 165
Cdd:PRK12511   99 AVRLAQIRDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAALR 156
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 103-166 3.79e-05

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: 42.89  E-value: 3.79e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1897049147 103 EPSDRDELINRIIKRIDQLPERCSRVMKLCFIECKKYKEIAEELNISVNTVKTHVTTGLNILRD 166
Cdd:COG1191   169 EELEHEELREALAEAIEQLPERERLVLSLYYFEELTLKEIAEVLGVSESRVSRLHKKALARLRE 232
MalT COG2909
ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];
139-165 7.12e-05

ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];


Pssm-ID: 442153 [Multi-domain]  Cd Length: 184  Bit Score: 41.61  E-value: 7.12e-05
                          10        20
                  ....*....|....*....|....*..
gi 1897049147 139 YKEIAEELNISVNTVKTHVTtglNILR 165
Cdd:COG2909   140 NKEIAERLFISVNTVKTHLR---NIYR 163
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 14-167 7.56e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 41.60  E-value: 7.56e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  14 FEDIFKQHFATLCTHATTFVNDPDASKDIVHDVFLSLWS----HREEIDFSrpilPYLFSLTRNRAINYL---AHRKV-- 84
Cdd:PRK12513   28 FEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRaraqYQPRARFR----TWLYQIARNLLIDHWrrhGARQAps 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  85 ----EDAHAQQALVEEPVYTLSEPSDRDelinRIIKRIDQLPERCSRVMKLCFIECKKYKEIAEELNISVNTVKTHVTTG 160
Cdd:PRK12513  104 ldadEQLHALADDGAAPEQQLSLFRDRR----RLQAALETLPDEQREVFLLREHGDLELEEIAELTGVPEETVKSRLRYA 179


                  ....*..
gi 1897049147 161 LNILRDE 167
Cdd:PRK12513  180 LQKLREL 186
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
79-157 1.48e-04

DNA-binding transcriptional regulator, CsgD family [Transcription];


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 40.89  E-value: 1.48e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1897049147  79 LAHRKVEDAHAQQALVEEPVYTLSEPSDRDELINRIIKRIDQLPERCSRVMKLcFIECKKYKEIAEELNISVNTVKTHV 157
Cdd:COG2771    86 LLLALLALLAALLARLAALLLALALAALLLAALARLLARAPGLTPREREVLRL-LAEGLTLKEIARILGISERTVRTHL 163
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 14-168 1.56e-04

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 40.67  E-value: 1.56e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  14 FEDIFKQHFATLCTHATTFVNDPDASKDIVHDVFLSLWSHREEIDFSR-PILPYLFSLTRNRAINYLAHRKVEDAHAQQA 92
Cdd:PRK13919   25 LRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRRgSARAWLLALAHHAAVDHVRRRAARPQPLEPD 104

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1897049147  93 LVEEPVYTLSEPS-DRDELINRI-IKR-IDQLPERCSRVMKLCFIECKKYKEIAEELNISVNTVKTHVTTGLNILRDEF 168
Cdd:PRK13919  105 EREPEAFDLPGPGlDEEGHLDRTrLGRaLKALSPEERRVIEVLYYQGYTHREAAQLLGLPLGTLKTRARRALSRLKEVL 183
GerE pfam00196
Bacterial regulatory proteins, luxR family;
119-165 1.71e-04

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 37.95  E-value: 1.71e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1897049147 119 DQLPERCSRVMKLCfIECKKYKEIAEELNISVNTVKTHVTtglNILR 165
Cdd:pfam00196   1 DSLSPREREVLRWL-AAGKSNKEIADELGISEKTVKVHRS---NIMR 43
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 38-161 1.81e-04

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 40.14  E-value: 1.81e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  38 ASKDIVHDVFLSLWSHREEIDFSRPiLPYLFSLTRNRAINYLAHRKVEDAHAQQALVEEPVYTLSEPS---DRDELINRI 114
Cdd:PRK12527   21 AAEDVAHDAYLRVLERSSSAQIEHP-RAFLYRTALNLVVDRHRRHRVRQAEPLEVLDEEERLHSPSPQtrlDLGQRLALL 99

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1897049147 115 IKRIDQLPERCSRVMKLCFIECKKYKEIAEELNISVNTVKTHVTTGL 161
Cdd:PRK12527  100 QRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAM 146
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 137-165 1.98e-04

C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental nitrate or nitrite is present under anerobic conditions. FixJ is involved in the transcriptional activation of nitrogen fixation genes. The group also includes small proteins which lack an N-terminal signaling domain, such as Bacillus subtilis GerE. GerE is dimeric and acts in conjunction with sigmaK as an activator or a repressor modulating the expression of various genes in particular those encoding the spore-coat. These LuxR family regulators may share a similar organization of their target binding sites. For example the LuxR dimer binds the lux box, a 20bp inverted repeat, GerE dimers bind two 12bp consensus sequences in inverted orientation having the central four bases overlap, and the NarL dimer binds two 7bp inverted repeats separated by 2 bp.


Pssm-ID: 99777 [Multi-domain]  Cd Length: 57  Bit Score: 37.90  E-value: 1.98e-04
                          10        20
                  ....*....|....*....|....*....
gi 1897049147 137 KKYKEIAEELNISVNTVKTHVTtglNILR 165
Cdd:cd06170    16 KTNKEIADILGISEKTVKTHLR---NIMR 41
PRK09646 PRK09646
ECF RNA polymerase sigma factor SigK;
33-167 2.28e-04

ECF RNA polymerase sigma factor SigK;


Pssm-ID: 182015 [Multi-domain]  Cd Length: 194  Bit Score: 40.42  E-value: 2.28e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  33 VNDPDASKDIVHDVFLSLWSHREEIDFSR-PILPYLFSLTRNRAINYLahRKVEDAHAQQALVEEPVYTLsePSD----- 106
Cdd:PRK09646   51 LRDPGYSEETTQEVYLEVWRTASRFDPARgSALAWLLTLAHRRAVDRV--RSEQAASQREVRYGARNVDP--AFDqvaee 126

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1897049147 107 ---RDELiNRIIKRIDQLPERCSRVMKLCFIECKKYKEIAEELNISVNTVKTHVTTGLNILRDE 167
Cdd:PRK09646  127 veaRLER-ERVRDCLDALTDTQRESVTLAYYGGLTYREVAERLAVPLGTVKTRMRDGLIRLRDC 189
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
 34-166 2.73e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 40.22  E-value: 2.73e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  34 NDPDAsKDIVHDVFLSLWSHREEIDFSRPILP-YLFSLTRNRAINYlaHRKVEdahaqqalvEEPVYTLSEPSD------ 106
Cdd:PRK12538   86 NRADA-EDVVQDTMLKVWTHRGRWQHGRAKFStWLYRVVSNRCIDL--RRKPR---------TENVDAVPEVADgkpdav 153

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1897049147 107 ----RDELINRIIKRIDQLPERCSRVMKLCFIECKKYKEIAEELNISVNTVKTHVTTGLNILRD 166
Cdd:PRK12538  154 svieRNELSDLLEAAMQRLPEQQRIAVILSYHENMSNGEIAEVMDTTVAAVESLLKRGRQQLRD 217
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 140-165 3.96e-04

Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell division, chromosome partitioning, Transcription];


Pssm-ID: 444607 [Multi-domain]  Cd Length: 76  Bit Score: 37.63  E-value: 3.96e-04
                          10        20
                  ....*....|....*....|....*.
gi 1897049147 140 KEIAEELNISVNTVKTHVTtglNILR 165
Cdd:COG5905    31 KEIARQLFISEKTVKNHVS---NILR 53
PRK12523 PRK12523
RNA polymerase sigma factor; Reviewed
 33-161 4.10e-04

RNA polymerase sigma factor; Reviewed


Pssm-ID: 183572 [Multi-domain]  Cd Length: 172  Bit Score: 39.45  E-value: 4.10e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  33 VNDPDASKDIVHDVFLSLWShREEIDFSRPILPYLFSLTRNRAINYLAHRKVEDAH-AQQALVEEPvytlSEPSDRDE-L 110
Cdd:PRK12523   31 VACRQRAEDLSQDTFVRLLG-RPELPTPREPRAFLAAVAKGLMFDHFRRAALEQAYlAELALVPEA----EQPSPEEQhL 105

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1897049147 111 INRIIKRIDQLPERCSRVMKLCFIECK----KYKEIAEELNISVNTVKTHVTTGL 161
Cdd:PRK12523  106 ILEDLKAIDRLLGKLSSKARAAFLYNRldgmGHAEIAERLGVSVSRVRQYLAQGL 160
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 14-160 4.31e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 39.15  E-value: 4.31e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  14 FEDIFKQHFATLCTHATTFVNDPDASKDIVHDVFLSLWSHreeIDFSR--PILPYLFSLTRNRAINYLAHRK------VE 85
Cdd:PRK12541    7 LEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVH---IDYYKgeEIRPWLFTIAYNAFIDWYRKEKkyktttIE 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1897049147  86 DAH-AQQALVEEPVYTLSEpsdrdelINRIIKRIDQLPERCSRVMKLCFIECKKYKEIAEELNISVNTVKTHVTTG 160
Cdd:PRK12541   84 EFHlPNVPSTEHEYFIKHE-------IASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRG 152
PRK12539 PRK12539
RNA polymerase sigma factor SigF;
36-164 6.23e-04

RNA polymerase sigma factor SigF;


Pssm-ID: 237132 [Multi-domain]  Cd Length: 184  Bit Score: 38.94  E-value: 6.23e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  36 PDASKDIVHDVFLSLWSHREEIDFSRPILPYLFSLTRNRAINYL-------AHRKVED-----AHAQQALVEepvytlse 103
Cdd:PRK12539   49 AEEAEDLVQEALMAIHTRRHTYDPEQPLTPWVYAIARYKLIDHLrrtraslADVPIDDadelvAHDDHAAVE-------- 120

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1897049147 104 pSDRDelINRIIKRidqLPE--RCS-RVMKLcfiECKKYKEIAEELNISVNTVKTHVTTGLNIL 164
Cdd:PRK12539  121 -STLD--LGRLLAR---LPEkmRLAiQAVKL---EGLSVAEAATRSGMSESAVKVSVHRGLKAL 175
PRK12522 PRK12522
RNA polymerase sigma factor; Provisional
 16-166 6.66e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183571 [Multi-domain]  Cd Length: 173  Bit Score: 38.70  E-value: 6.66e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  16 DIFKQHFATLCTHATtfvNDPDASKDIVHDVFLSLWSHREEIDFSRPILPYLFSLTRNRAINYLAHRK--------VEDA 87
Cdd:PRK12522   10 DIYKQQIYSLCYKLA---KTKEDAEDIFQETWIKVFSSRHQLSYVENYKKWITTICVRTFYDFYRKKKrwkdrildLFHK 86

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1897049147  88 HAQQALVEEPVYTLSEPSDRDELINRIIKRIDQLPERCSRVMKLCFIECKKYKEIAEELNISVNTVKTHVTTGLNILRD 166
Cdd:PRK12522   87 EDGGEIEFADDVNISEEFIQKVEAEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQMRE 165
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 29-151 8.55e-04

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 38.48  E-value: 8.55e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  29 ATTFVNDPDASKDIVHDVFLSLWSHR-----EEIDFSrpilPYLFSLTRNRAINYLAHRK---VEDAhaqqalvEEPVYT 100
Cdd:PRK05602   37 ATRMLGDPAEAEDVAQETFLRIWKQApswrpGEARFD----TWLHRVVLNLCYDRLRRRRevpVEDA-------PDVPDP 105

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1897049147 101 LSEPSDR---DELINRIIKRIDQLPERCSRVMKLCFIECKKYKEIAEELNISVN 151
Cdd:PRK05602  106 APGPDAGleaRQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVD 159
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
 20-164 1.04e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 38.28  E-value: 1.04e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  20 QHFATLCTHATTFVNDPDASKDIVHDVFLSLWSHREEIDFSRPILPYLFSLTRNRAinYLAHRK----VEDAHAQQA--L 93
Cdd:PRK12546   15 EHLPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEGTNLRAWLFTILRNTF--YSDRRKhkreVPDPEGVHAasL 92

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1897049147  94 VEEPVYtlsepsDRDELINRIIKRIDQLPERCSRVMKLCFIECKKYKEIAEELNISVNTVKTHVTTGLNIL 164
Cdd:PRK12546   93 AVKPAH------DGRLAMSDFRAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARARL 157
PRK12525 PRK12525
RNA polymerase sigma factor; Provisional
 17-161 1.30e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 139037 [Multi-domain]  Cd Length: 168  Bit Score: 38.00  E-value: 1.30e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  17 IFKQHFATLCTHATTFVNDPDASKDIVHDVFLSLW------SHREeidfsrpilPYLFSLTRNRAINYLAHRK--VEDAH 88
Cdd:PRK12525   14 MFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLalpdpaSIRE---------PRALLTTIARRLMYEGWRRqdLERAY 84

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1897049147  89 AQQ-ALVEEPVYtlSEPSDRDELINRIIkRIDQLPERCSRVMKLCFIECK----KYKEIAEELNISVNTVKTHVTTGL 161
Cdd:PRK12525   85 LQSlAEAPEAVQ--PSPEEQWMVIETLL-AIDRLLDGLSGKARAAFLMSQleglTYVEIGERLGVSLSRIHQYMVEAF 159
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 113-156 4.13e-03

DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal transduction mechanisms, Transcription];


Pssm-ID: 443623 [Multi-domain]  Cd Length: 196  Bit Score: 36.62  E-value: 4.13e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1897049147 113 RIIKRIDQLPERCSRVMKLcFIECKKYKEIAEELNISVNTVKTH 156
Cdd:COG4566   130 ELRARLASLTPREREVLDL-VVAGLSNKQIARELGISPRTVEVH 172
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 14-168 4.87e-03

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 36.46  E-value: 4.87e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  14 FEDIFKQHFATLCTHATTFVNDPDASKDIVHDVFLSLWSHREEIDFSRPILPYLFSLTRNRAINYLAHRKvEDAHAQQAL 93
Cdd:PRK09640   28 YEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGKSKFKTWLYSITYNECITQYRKER-RKRRLMDAL 106

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1897049147  94 VEEPvytLSEPSDRDELINRIIKRIDQLPERCS----RVMKLCFIECKKYKEIAEELNISVNTVKTHVTTGLNILRDEF 168
Cdd:PRK09640  107 SLDP---LEEASEEKAPKPEERGGLDRWLVHVNpidrEILVLRFVAELEFQEIADIMHMGLSATKMRYKRALDKLREKF 182
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 35-155 8.46e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 35.46  E-value: 8.46e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1897049147  35 DPDASKDIVHDVFLSLWSH----REEIDFSrpilPYLFSLTRNRAINY---LAHRKVedAHAQQALVEEPVYTLSEPS-- 105
Cdd:PRK12518   33 GRELLDDLVQEVFLRVWKGlpklRNPAYFS----TWLYRITWNVATDArrqFAQRPS--RIQDDSLNDQPSRPSDTPDlm 106

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1897049147 106 --DRDELINRiikRIDQLPERCSRVMKLCFIECKKYKEIAEELNISVNTVKT 155
Cdd:PRK12518  107 qlHYQDLVQQ---GLQTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKS 155
 
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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