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Conserved domains on  [gi|496324952|ref|WP_009034130|]
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RNA polymerase sigma factor [Indibacter alkaliphilus]

Protein Classification

RNA polymerase sigma factor( domain architecture ID 11446377)

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 2-171 1.86e-47

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: 152.84  E-value: 1.86e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952   2 EQHLIQEAKRGDKKSLEMLYKHFYGYAMSIALRYSNGRDEACEIVNDSFMKVFDKLPQYSESNSFKGWFRRILVNTSIDY 81
Cdd:COG1595    4 DEELLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDH 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  82 YRKNAKHYAAMD--IDKVDTESYEPE--IISQLTKDDILNLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTSRTY 157
Cdd:COG1595   84 LRKRRRRRELLDelAEELPDEAADPEeaLEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSR 163

                        170
                 ....*....|....
gi 496324952 158 LARAKQKLREKVTE 171
Cdd:COG1595  164 LSRARKKLREALEE 177
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 2-171 1.86e-47

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: 152.84  E-value: 1.86e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952   2 EQHLIQEAKRGDKKSLEMLYKHFYGYAMSIALRYSNGRDEACEIVNDSFMKVFDKLPQYSESNSFKGWFRRILVNTSIDY 81
Cdd:COG1595    4 DEELLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDH 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  82 YRKNAKHYAAMD--IDKVDTESYEPE--IISQLTKDDILNLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTSRTY 157
Cdd:COG1595   84 LRKRRRRRELLDelAEELPDEAADPEeaLEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSR 163

                        170
                 ....*....|....
gi 496324952 158 LARAKQKLREKVTE 171
Cdd:COG1595  164 LSRARKKLREALEE 177
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 6-172 5.83e-35

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 121.07  E-value: 5.83e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952   6 IQEAKRGDKKSLEMLYKHFYGYAMSIALRYSNGRDEACEIVNDSFMKVFDKLPQYSESNSFKGWFRRILVNTSIDYYRKN 85
Cdd:PRK09652   1 VERVQRGDRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRGGAAFYTWLYRIARNTAINYLRKQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  86 AKHYAAMDIDKVDTESYEP------------EIISQLTKDDILNLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPAST 153
Cdd:PRK09652  81 GRRPPASDVDAEEAEDFDLadalrdistpenELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGT 160

                        170
                 ....*....|....*....
gi 496324952 154 SRTYLARAKQKLREKVTEL 172
Cdd:PRK09652 161 VRSRIFRAREALRAKLQPL 179
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 15-169 8.69e-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: 109.36  E-value: 8.69e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952   15 KSLEMLYKHFYGYAMSIALRYSNGRDEACEIVNDSFMKVFDKLPQYSESNSFKGWFRRILVNTSIDYYRKNAKHYAAMDI 94
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 496324952   95 D---KVDTESYEPEIISQLTKDDILNLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTSRTYLARAKQKLREKV 169
Cdd:TIGR02937  81 LeelLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 112-165 3.65e-12

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: 58.24  E-value: 3.65e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 496324952  112 KDDILNLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTSRTYLARAKQKL 165
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 112-166 6.83e-10

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: 52.49  E-value: 6.83e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 496324952 112 KDDILNLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTSRTYLARAKQKLR 166
Cdd:cd06171    1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 136-165 2.29e-03

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 34.81  E-value: 2.29e-03
                           10        20        30
                   ....*....|....*....|....*....|
gi 496324952   136 EGYSHNEIAEQCGIPASTSRTYLARAKQKL 165
Cdd:smart00421  17 EGLTNKEIAERLGISEKTVKTHLSNIMRKL 46
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 2-171 1.86e-47

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: 152.84  E-value: 1.86e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952   2 EQHLIQEAKRGDKKSLEMLYKHFYGYAMSIALRYSNGRDEACEIVNDSFMKVFDKLPQYSESNSFKGWFRRILVNTSIDY 81
Cdd:COG1595    4 DEELLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDH 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  82 YRKNAKHYAAMD--IDKVDTESYEPE--IISQLTKDDILNLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTSRTY 157
Cdd:COG1595   84 LRKRRRRRELLDelAEELPDEAADPEeaLEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSR 163

                        170
                 ....*....|....
gi 496324952 158 LARAKQKLREKVTE 171
Cdd:COG1595  164 LSRARKKLREALEE 177
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 6-172 5.83e-35

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 121.07  E-value: 5.83e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952   6 IQEAKRGDKKSLEMLYKHFYGYAMSIALRYSNGRDEACEIVNDSFMKVFDKLPQYSESNSFKGWFRRILVNTSIDYYRKN 85
Cdd:PRK09652   1 VERVQRGDRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRGGAAFYTWLYRIARNTAINYLRKQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  86 AKHYAAMDIDKVDTESYEP------------EIISQLTKDDILNLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPAST 153
Cdd:PRK09652  81 GRRPPASDVDAEEAEDFDLadalrdistpenELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGT 160

                        170
                 ....*....|....*....
gi 496324952 154 SRTYLARAKQKLREKVTEL 172
Cdd:PRK09652 161 VRSRIFRAREALRAKLQPL 179
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 15-169 8.69e-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: 109.36  E-value: 8.69e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952   15 KSLEMLYKHFYGYAMSIALRYSNGRDEACEIVNDSFMKVFDKLPQYSESNSFKGWFRRILVNTSIDYYRKNAKHYAAMDI 94
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 496324952   95 D---KVDTESYEPEIISQLTKDDILNLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTSRTYLARAKQKLREKV 169
Cdd:TIGR02937  81 LeelLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 11-167 4.17e-28

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 103.13  E-value: 4.17e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  11 RGDKKSLEMLYKHFYGYAMSIALRYSNGRDEACEIVNDSFMKVFDKLPQYSESNSFKGWFRRILVNTSIDYYRKNA--KH 88
Cdd:PRK11924   9 TGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCYDLLRRRRreKA 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  89 YAAMDIDKVDTESYEPEIISQL-TKDDILNLLR---SLPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTSRTYLARAKQK 164
Cdd:PRK11924  89 VLSDDALEPEFAETAETPEAALlAKDDLARIDRcldALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQL 168


                 ...
gi 496324952 165 LRE 167
Cdd:PRK11924 169 LRE 171
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 15-168 1.21e-23

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: 91.08  E-value: 1.21e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952   15 KSLEMLYKHFYGYAMSIALRYSNGRDEACEIVNDSFMKVFDKLPQYSESNSFKGWFRRILVNTSIDYYRKNAKHYAAMD- 93
Cdd:TIGR02985   1 EAFEQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETLEISESIKAYLFTIVKNRCLNYLRHKQVEEKYQEe 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952   94 -IDKVDTESYEPEIISQLTKDD----ILNLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTSRTYLARAKQKLREK 168
Cdd:TIGR02985  81 lAEIEERELSEADPEEELEAKEleeiIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLRKE 160
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 2-166 5.35e-20

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 81.99  E-value: 5.35e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952   2 EQHLIQEAKRGDKKSLEMLYKHFY----GYAMSIALRYsngrDEACEIVNDSFMKVFDKLPQYSESNSFKGWFRRILVNT 77
Cdd:PRK09638   5 EKELIQKAKKGDDAALTTLFQQHYsflyKYLLKLTLDP----DLAEDLVQETMLKAIENLSSFQGRSKFSTWLISIASRL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  78 SIDYYRKNAKHYAAMDIDKV---DTESYEPEiISQLTKDDILNLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTS 154
Cdd:PRK09638  81 YKDHLRKQKREKLRLQRAKEetlRKEKWEAA-IKGAEWSEMLDALSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTV 159

                        170
                 ....*....|..
gi 496324952 155 RTYLARAKQKLR 166
Cdd:PRK09638 160 KSRVHHGIKQLR 171
algU PRK11923
RNA polymerase sigma factor AlgU; Provisional
 1-172 2.30e-19

RNA polymerase sigma factor AlgU; Provisional


Pssm-ID: 171347 [Multi-domain]  Cd Length: 193  Bit Score: 81.00  E-value: 2.30e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952   1 MEQHLIQEAKRGDKKSLEMLYKHFYGYAMSIALRYSNGRDEACEIVNDSFMKVFDKLPQYSESNSFKGWFRRILVNTSID 80
Cdd:PRK11923   6 EDQQLVERVQRGDKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDSAFYTWLYRIAINTAKN 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  81 YYRKNAKHYAAMDIDKVDTESYE----------PE--IISQLTKDDILNLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCG 148
Cdd:PRK11923  86 HLVSRGRRPPDSDVSSEDAEFYDgdhalkdiesPEraLLRDEIEGTVHRTIQQLPEDLRTALTLREFDGLSYEDIASVMQ 165

                        170       180
                 ....*....|....*....|....
gi 496324952 149 IPASTSRTYLARAKQKLREKVTEL 172
Cdd:PRK11923 166 CPVGTVRSRIFRAREAIDKALQPL 189
PRK06811 PRK06811
RNA polymerase factor sigma-70; Validated
 2-172 1.70e-17

RNA polymerase factor sigma-70; Validated


Pssm-ID: 180707 [Multi-domain]  Cd Length: 189  Bit Score: 75.75  E-value: 1.70e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952   2 EQHLIQEAKRGDKKSLEMLYKHFYGYAMSI---ALRYSNGRDEACEIVNDSFMKVFDKLPQY-SESNSFKGWFRRILVNT 77
Cdd:PRK06811   5 EDNFIKELKKKNEKALEFIVDTYGNLVKKIvhkVLGTVNYSQLIEECVNDIFLSIWNNIDKFdEEKGSFKKWIAAISKYK 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  78 SIDYYRKNAKHYAAMDIDK---VDTESYEPEIISQLTKDDILNLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTS 154
Cdd:PRK06811  85 AIDYKRKLTKNNEIDSIDEfilISEESIENEIILKENKEEILKLINDLEKLDREIFIRRYLLGEKIEEIAKKLGLTRSAI 164

                        170
                 ....*....|....*...
gi 496324952 155 RTYLARAKQKLREKVTEL 172
Cdd:PRK06811 165 DNRLSRGRKKLQKNKLNI 182
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 45-167 1.49e-15

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 70.78  E-value: 1.49e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  45 IVNDSFMKVFDKLPQYSESNSFKGWFRRILVNTSIDYYRKNAKhYAAMDIDKVDTESYEPEIISQLTKDDILNLLRSLPE 124
Cdd:PRK09637  31 LLQEVLIKTHSNLHSLKDGSSIKSWLYQIANNTIIDFYRKKNR-SEELPDDLLFEDEEREENAKKELAPCLRPFIDALPE 109

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 496324952 125 MLRIVFNMYEIEGYSHNEIAEQCGIPASTSRTYLARAKQKLRE 167
Cdd:PRK09637 110 KYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKE 152
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 5-171 2.11e-15

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 70.49  E-value: 2.11e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952   5 LIQEAKRGDKKSLEMLY-KH---FYGYAmsiaLRYSNGRDEACEIVNDSFMKVFDKLPQYSESNSFKGWFRRILVNTSID 80
Cdd:PRK12513  16 LMLRYRAGDAAAFEALYaRHrtgLYRFL----LRLARDRALAEDIFQETWLRVIRARAQYQPRARFRTWLYQIARNLLID 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  81 YYRKNAKHYAAMD-------IDKVDTESYEPEIISQLTKDDILNLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPAST 153
Cdd:PRK12513  92 HWRRHGARQAPSLdadeqlhALADDGAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREHGDLELEEIAELTGVPEET 171

                        170
                 ....*....|....*...
gi 496324952 154 SRTYLARAKQKLREKVTE 171
Cdd:PRK12513 172 VKSRLRYALQKLRELLAE 189
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 5-167 1.89e-14

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 67.44  E-value: 1.89e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952   5 LIQEAKRGDKKSLEMLYKHFYGYAMSIALRYSnGRDEACEIVNDSFMKVFDKLPQYSESNSFKGWFRRILVNTSIDYYRK 84
Cdd:PRK12518   1 LILRCQRGDRQSFRQLYRRYQQKVRSTLYQLC-GRELLDDLVQEVFLRVWKGLPKLRNPAYFSTWLYRITWNVATDARRQ 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  85 NAKHYAAMDIDKVDTESYEPEiisqlTKDDILNL---------LRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTSR 155
Cdd:PRK12518  80 FAQRPSRIQDDSLNDQPSRPS-----DTPDLMQLhyqdlvqqgLQTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVK 154

                        170
                 ....*....|..
gi 496324952 156 TYLARAKQKLRE 167
Cdd:PRK12518 155 SRLFYARRQLRK 166
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 5-167 2.68e-14

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 67.15  E-value: 2.68e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952   5 LIQEAKRGDKKSLEMLYKHFYGYAMSIALRYSNGRDEACEIVNDSFMKVFDKLPQYSESN-SFKGWFRRILVNTSIDYYR 83
Cdd:PRK12514   9 LIVRVSLGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSGlSPMTWLITIARNHAIDRLR 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  84 knAKHYAAMDIDKV-----DTESYEPEIISQLTKDDILNLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTSRTYL 158
Cdd:PRK12514  89 --ARKAVAVDIDEAhdladPSPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMRTWL 166


                 ....*....
gi 496324952 159 ARAKQKLRE 167
Cdd:PRK12514 167 RRSLLKLRE 175
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 1-172 4.29e-14

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 67.03  E-value: 4.29e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952   1 MEQHLIQEAKRGDKKS---LEMLYKHfygYAMSIALRYSNGRDEACEIVNDSFMKVFDKLPQYSESNSFKGWFRRILVNT 77
Cdd:PRK09641   4 LIKRLIKQVKKGDQNAfaeLVDLYKD---KIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINRKFSTWLYRIATNL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  78 SIDYYRKNAKHYAaMDIDKVDTE-------------SYEPEIISQLTKDDILNLLRSLPEMLRIVFNMYEIEGYSHNEIA 144
Cdd:PRK09641  81 TIDRLRKRKPDYY-LDAEVAGTEgltmysqlaaddaLPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYIEDLSLKEIS 159

                        170       180
                 ....*....|....*....|....*...
gi 496324952 145 EQCGIPASTSRTYLARAKQKLREKVTEL 172
Cdd:PRK09641 160 EILDLPVGTVKTRIHRGREALRKQLRHL 187
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 31-167 5.49e-14

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 66.73  E-value: 5.49e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  31 IALRYSNGRDEACEIVNDSFMKVFDKLPQYsESNSFKGWFRRILVNTSIDYYRKNAK-HYAAM--DIDKVDTESYEPEII 107
Cdd:PRK09647  44 LAYRLSGNQHDAEDLTQETFIRVFRSLQNY-QPGTFEGWLHRITTNLFLDMVRRRARiRMEALpeDYDRVPGDEPNPEQI 122

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 496324952 108 SQLTK--DDILNLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTSRTYLARAKQKLRE 167
Cdd:PRK09647 123 YHDARldPDLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQQLRA 184
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 31-171 6.28e-14

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 66.31  E-value: 6.28e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  31 IALRYSNGRDEACEIVNDSFMKVFDKLPQYSESNSFKGWFRRILVNTSIDYYRK--NAKHYAAMDID---KVDTESYEPE 105
Cdd:PRK09415  32 LVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGKSSLKTWLYRIAINHCKDYLKSwhNKKVIVTEDIFtymESQKESVEEE 111

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 496324952 106 IISQLTKDDILNLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTSRTYLARAKQKLREKVTE 171
Cdd:PRK09415 112 VIQNAEDERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKELLKKGLEE 177
PRK12522 PRK12522
RNA polymerase sigma factor; Provisional
 17-169 2.41e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 183571 [Multi-domain]  Cd Length: 173  Bit Score: 64.51  E-value: 2.41e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  17 LEMLYKHFYGYAMSIALRYSNGRDEACEIVNDSFMKVFDKLPQYSESNSFKGWFRRILVNTSIDYYRKNaKHYAAMDIDK 96
Cdd:PRK12522   5 VEELIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVENYKKWITTICVRTFYDFYRKK-KRWKDRILDL 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  97 VDTESYE-----------PEIISQLTKDDILNLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTSRTYLARAKQKL 165
Cdd:PRK12522  84 FHKEDGGeiefaddvnisEEFIQKVEAEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQM 163


                 ....
gi 496324952 166 REKV 169
Cdd:PRK12522 164 REHL 167
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 11-167 1.01e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 63.26  E-value: 1.01e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  11 RGDKKSLEMLYKHFYGYAMSIALRYSNGRDEACEIVNDSFMKVFDKLPQYSES-NSFKGWF----RRILVNTSIDYYRKn 85
Cdd:PRK12537  19 RGDRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPArGSARGWIysvtRHLALNVLRDTRRE- 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  86 akhyAAMDIDKVDTESYEPEIISQL-TKDDILNLLRSL----PEMLRIVFNMYeIEGYSHNEIAEQCGIPASTSRTYLAR 160
Cdd:PRK12537  98 ----VVLDDDAEETAQTLHEIIDDFdLWANSGKIHRCLeqlePARRNCILHAY-VDGCSHAEIAQRLGAPLGTVKAWIKR 172


                 ....*..
gi 496324952 161 AKQKLRE 167
Cdd:PRK12537 173 SLKALRE 179
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 40-171 1.77e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 63.06  E-value: 1.77e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  40 DEACEIVNDSFMKVFDKLPQYSESNSFKGWFRRILVNTSIDYYRKNAKhyaAMDIDKVDTESYEPEIISQLTKDD----- 114
Cdd:PRK11922  55 AEAEDVVQEAYLRAFRALGTFRGDASLSTWLSRIVLNEALGRLRRRRR---LVNLAEMVMASTIAGGERTPLADPaedpe 131

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 496324952 115 -------ILNLLRS----LPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTSRTYLARAKQKLREKVTE 171
Cdd:PRK11922 132 raaarreIRALLERaidaLPDAFRAVFVLRVVEELSVEETAQALGLPEETVKTRLHRARRLLRESLAR 199
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 112-165 3.65e-12

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: 58.24  E-value: 3.65e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 496324952  112 KDDILNLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTSRTYLARAKQKL 165
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 11-171 5.38e-12

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 61.08  E-value: 5.38e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  11 RGDKKSLEMLYKHFYGYAMSIALRYSNGRDEACEIVNDSFMKVFDKLPQYS-ESNSFKGWFRRILVNTSIDYYRKNAKHY 89
Cdd:PRK13919  19 RGEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDpRRGSARAWLLALAHHAAVDHVRRRAARP 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  90 AAMDIDKVDTESYE---PEIiSQLTKDDILNLLRSL----PEMLRIVFNMYeIEGYSHNEIAEQCGIPASTSRTYLARAK 162
Cdd:PRK13919  99 QPLEPDEREPEAFDlpgPGL-DEEGHLDRTRLGRALkalsPEERRVIEVLY-YQGYTHREAAQLLGLPLGTLKTRARRAL 176


                 ....*....
gi 496324952 163 QKLREKVTE 171
Cdd:PRK13919 177 SRLKEVLRE 185
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 7-179 7.88e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 60.75  E-value: 7.88e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952   7 QEAKRGDKKSLEMLYKHFYGYAMSIALRYsngrDEACEIVNDSFMKVFDKLPQYSESNSFKGWFRRILVNTSIDYYRKNA 86
Cdd:PRK12516   6 VEGTPPFKRELLAALPSLRAFAVSLIGRH----DRADDLVQDTIMKAWAKQDHFEVGTNMKAWLFTILRNEFYSQMRKRG 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  87 KHyaAMDIDKVDTES--YEPEIISQLTKDDILNLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTSRTYLARAKQK 164
Cdd:PRK12516  82 RE--VQDTDGMFTEQlaVHPSQYGTLDLQDFRAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQR 159

                        170
                 ....*....|....*
gi 496324952 165 LREKVtelnQIRNEG 179
Cdd:PRK12516 160 LQEIL----QIEGEA 170
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
 12-167 2.49e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 60.26  E-value: 2.49e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  12 GDKKSLEMLYKHFYGYAMSIALRYSNGRDEACEIVNDSFMKVFDKLPQYSESNS-FKGWFRRILVNTSIDYYRKNAKhya 90
Cdd:PRK12538  60 DDEAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRAkFSTWLYRVVSNRCIDLRRKPRT--- 136

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  91 amdiDKVDT----ESYEPEIISQLTKDDILNLL----RSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTSRTYLARAK 162
Cdd:PRK12538 137 ----ENVDAvpevADGKPDAVSVIERNELSDLLeaamQRLPEQQRIAVILSYHENMSNGEIAEVMDTTVAAVESLLKRGR 212


                 ....*
gi 496324952 163 QKLRE 167
Cdd:PRK12538 213 QQLRD 217
SigM_subfam TIGR02950
RNA polymerase sigma factor, SigM family; This family of RNA polymerase sigma factors is a ...
 21-169 2.95e-11

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: 58.62  E-value: 2.95e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952   21 YKHFYGYAMSIALRYSNGRDEACEIVNDSFMKVFDKLPQYSESnSFKGWFRRILVNTSIDYYRKNAK-----HYAAMDID 95
Cdd:TIGR02950   1 YREYMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKDS-SIKPWLFRIARNAFIDWYRKDKKiqtidDDAIGDLE 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 496324952   96 KVDTESYEPEIISQLTKDDILNLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTSRTYLARAKQKLREKV 169
Cdd:TIGR02950  80 QHPVESPEHHLLIKIEQEEITHHLSRLPENYRTVLILREFKEFSYKEIAELLNLSLAKVKSNLFRARKELKKLL 153
PRK09643 PRK09643
RNA polymerase sigma factor SigM; Reviewed
 12-173 2.25e-10

RNA polymerase sigma factor SigM; Reviewed


Pssm-ID: 236604 [Multi-domain]  Cd Length: 192  Bit Score: 57.03  E-value: 2.25e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  12 GDKKSLEMLYKHFYGYAMSIALRYSNGRDEACEIVNDSFMKVFDKlpqyseSNSFKG------WFRRILVNTSIDYYRKN 85
Cdd:PRK09643  24 GDRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRA------AGSFRGdaavssWLHRIVVNACLDRLRRA 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  86 AKHYAAMDIDKVDTESYEPEIISQL-TKDDILNLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTSRTYLARAKQK 164
Cdd:PRK09643  98 KARPTVPLDDVYPVAQLERDPTARVeTALAVQRALMRLPVEQRAALVAVDMQGYSVADAARMLGVAEGTVKSRCARGRAR 177


                 ....*....
gi 496324952 165 LREKVTELN 173
Cdd:PRK09643 178 LAELLGYLR 186
PRK12547 PRK12547
RNA polymerase sigma factor; Provisional
 30-167 2.35e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 139056 [Multi-domain]  Cd Length: 164  Bit Score: 56.42  E-value: 2.35e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  30 SIALRYSNGRDEACEIVNDSFMKVFDKLPQYSESNSFKGWFRRILVNTSIDYYRKNAKHyaAMDIDKVDTE--SYEPEII 107
Cdd:PRK12547  21 AFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGTNLKAWLFTILRNEFYSQMRKRGRE--VQDSDGVFTArvAVHPAQY 98

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952 108 SQLTKDDILNLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTSRTYLARAKQKLRE 167
Cdd:PRK12547  99 GSLDLQDFKKALNLLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARNRLQE 158
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 112-166 6.83e-10

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: 52.49  E-value: 6.83e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 496324952 112 KDDILNLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTSRTYLARAKQKLR 166
Cdd:cd06171    1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK12534 PRK12534
RNA polymerase sigma factor; Provisional
 12-166 1.01e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 183576 [Multi-domain]  Cd Length: 187  Bit Score: 55.06  E-value: 1.01e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  12 GDKKSLEMLYKHFYGYAMSIALRYSNGRDEACEIVNDSFMKVFDKLPQYSESNSfKG--WFRRILVNTSIDYYRKNAKHY 89
Cdd:PRK12534  22 GDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRA-RGltWLAMIARNKAIDHLRANAPQR 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  90 AAMDIDKV-----DTESYEPEIISQLTKDDILNLLRSLP----EMLRIVFnmyeIEGYSHNEIAEQCGIPASTSRTYLAR 160
Cdd:PRK12534 101 RNVALDDAgelraADASPLERTERASTRRRIDHCLAELEpprsELIRTAF----FEGITYEELAARTDTPIGTVKSWIRR 176


                 ....*.
gi 496324952 161 AKQKLR 166
Cdd:PRK12534 177 GLAKLK 182
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 10-178 3.29e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 53.58  E-value: 3.29e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  10 KRGDKKSLEMLY----KHFYGYAMSIAlrySNGRDEAcEIVNDSFMKVFDKLPQYSESNSFKGWFRRILVNTSIDYYRKN 85
Cdd:PRK12543   2 LSGDQEAFSEIYdvtiQEVYKTVHFLV---EDKQDVD-DVVNEIYIQLWESLRKYDSNRPFRFWLIGLVIKQIHSWRRKR 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  86 AKHYAAMDIDKVDTES----YEPEIISQLTKDDILNLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTSRTYLARA 161
Cdd:PRK12543  78 WRRFRIFEKAEEQRKPvsidFSEDVLSKESNQELIELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAA 157

                        170
                 ....*....|....*..
gi 496324952 162 KQKLREKVTELNQIRNE 178
Cdd:PRK12543 158 LKKLRQKEQIEEIFLGE 174
PRK12531 PRK12531
RNA polymerase sigma factor; Provisional
 6-166 4.14e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 105726 [Multi-domain]  Cd Length: 194  Bit Score: 53.40  E-value: 4.14e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952   6 IQEAKRGDKKSLEMLYKHFYGYAMSIALRYSNGRDEACEIVNDSFMKVFDKLPQY-SESNSFKGWFRRILVNTSIDYYRK 84
Cdd:PRK12531  18 MEKVKSRDKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFdGQKSALSTWIYTIIRNLCFDLLRK 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  85 NAK---HYAAMDIDKVD------TESYEPEiiSQLTKDDILNLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTSR 155
Cdd:PRK12531  98 QKGkdlHIHADDIWPSDyyppdlVDHYSPE--QDMLKEQVMKFLDRLPKAQRDVLQAVYLEELPHQQVAEMFDIPLGTVK 175

                        170
                 ....*....|.
gi 496324952 156 TYLARAKQKLR 166
Cdd:PRK12531 176 SRLRLAVEKLR 186
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 20-87 6.51e-09

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: 50.28  E-value: 6.51e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952   20 LYKHFYGYAMSIALRYSNGRDEACEIVNDSFMKVFDKLPQY--SESNSFKGWFRRILVNTSIDYYRKNAK 87
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFdpERGVSFSTWLYTIIRNAIIDYLRKQRR 70
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 39-169 8.30e-09

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: 51.94  E-value: 8.30e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952   39 RDEACEIVNDSFMKVFDKLPQYSESNSFKGWFRRILVNTSIDYYRKNAKHYAAMDIDKVDTESYEPEIISQLTKDDILNL 118
Cdd:TIGR02989  25 RDDVDDVLQETFVVAWRKFDQFDPGTNFVAWARGIARNKVLNYRRKLGRDRLVFDDDLLEALAAEAEPTEAERLSDDRQA 104

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 496324952  119 LRS----LPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTSRTYLARAKQKLREKV 169
Cdd:TIGR02989 105 LEGclekLPERQRELLDLRYQRGQKATALAEQTGRTVNAVYKALQRIRVSLRECV 159
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 2-167 1.09e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 52.37  E-value: 1.09e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952   2 EQHLIQEAKRGDKKSLEMLYKHFYGYAMSIALRYSNGRDEACEIVNDsfmkVFDKLPQYSESNSFKGWFRRILV----NT 77
Cdd:PRK12519  16 DAELFSALKAGQSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQE----IFLSLWRKSSYDPKRGSLSSYLLtltrSR 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  78 SIDYYRknAKHYAAMDIDKVD----TESYEPEIISQLTKDD----ILNLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGI 149
Cdd:PRK12519  92 AIDRLR--SRRSRQRLLERWQqellGEASEDTPLEQASLAErsqrVQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGI 169

                        170
                 ....*....|....*...
gi 496324952 150 PASTSRTYLARAKQKLRE 167
Cdd:PRK12519 170 PLGTVKARARQGLLKLRE 187
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 5-172 1.52e-08

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 51.96  E-value: 1.52e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952   5 LIQEAKRGDKKSLEMLYKHFYGYAMSIALRYSNGRDEACEIVNDSFMKVFDKLPQYSESN-SFKGWFRRILVNTSIDYYR 83
Cdd:PRK05602  10 LLARVAAGDPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPGEaRFDTWLHRVVLNLCYDRLR 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  84 KnAKHYAAMDIDKVDTESYEPE--IISQLTKDDILNLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTSRTYLARA 161
Cdd:PRK05602  90 R-RREVPVEDAPDVPDPAPGPDagLEARQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALESLLARG 168

                        170
                 ....*....|.
gi 496324952 162 KQKLREKVTEL 172
Cdd:PRK05602 169 RRALRAQLADL 179
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
 31-149 1.80e-08

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 51.22  E-value: 1.80e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  31 IALRYSNGRDEACEIVNDSFMKVFDkLPQYSESNSFKGWFRRILVNTSIDYYRKNA--KHYAAMDIDKVDTESYE--PE- 105
Cdd:PRK07037  14 IAARIVGCRSRAEDVVQDAFVKLVE-APNQDAVKQPVAYLFRIVRNLAIDHYRRQAleNKYHGDEEDGLDVPSPEasPEa 92

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 496324952 106 -IISQLTKDDILNLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGI 149
Cdd:PRK07037  93 aLINRDTLRHVADALSELPARTRYAFEMYRLHGETQKDIARELGV 137
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
 26-169 2.15e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 51.38  E-value: 2.15e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  26 GYAMSIAlrysngRDEAC--EIVNDSFMKVFDKLPQYSESNSFKGWFRRILVNTSIDYYRKNAKHYAamDIDKVDTESY- 102
Cdd:PRK12546  22 AFAISLT------RNVAVadDLVQDTIVKAWTNFDKFQEGTNLRAWLFTILRNTFYSDRRKHKREVP--DPEGVHAASLa 93

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 496324952 103 -EPEIISQLTKDDILNLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTSRTYLARAKQKLREKV 169
Cdd:PRK12546  94 vKPAHDGRLAMSDFRAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARARLAELL 161
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 16-167 2.31e-08

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 51.10  E-value: 2.31e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  16 SLEMLYKHFYGYAMSIALRYSNGRDEACEIVNDSFMKVFDKLPQYSESnsFKGWFRRILVNTSIDYYRKNAKHYAamdid 95
Cdd:PRK09639   4 TFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRSDFKGIEN--EKGWLIKSARNVAYNYLRSEKRRRA----- 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  96 KVDTESYEPEIISQLTKDDILNLLRSLPEMLRIVFNMYEIE---------GYSHNEIAEQCGIPASTSRTYLARAKQKLR 166
Cdd:PRK09639  77 RILGEFQWQEVDNEPSPEEIWIRKEEITKVQEVLAKMTERDrtvlllrfsGYSYKEIAEALGIKESSVGTTLARAKKKFR 156


                 .
gi 496324952 167 E 167
Cdd:PRK09639 157 K 157
Sigma70_ECF pfam07638
ECF sigma factor; These proteins are probably RNA polymerase sigma factors belonging to the ...
 4-162 3.28e-08

ECF sigma factor; These proteins are probably RNA polymerase sigma factors belonging to the extra-cytoplasmic function (ECF) subfamily and show sequence similarity to pfam04542 and pfam04545.


Pssm-ID: 254323 [Multi-domain]  Cd Length: 185  Bit Score: 50.88  E-value: 3.28e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952    4 HLIQEAKRGDKKSLEMLYKHFYGYAMSIALRYSN-----GRDEACEIVNDSFMKVFD--KLPQYSESNSFKGW----FRR 72
Cdd:pfam07638   6 QLLQQVKDGDAAATEQLLPLVYDELRRLAGSKLQnerrgHTLQPTALVHEAFVRLVDteDFPDWSGRGHFFAAaaeaMRR 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952   73 ILV-NTSIDYYRKNAKHYAAMDIDKVDTESYEPEIISQLTKDDILNLLRSL-PEMLRIVFNMYeIEGYSHNEIAEQCGIP 150
Cdd:pfam07638  86 ILIdHARRRQRQKRGGDVQRRELDEVVDNGDSPNPDLLLDLDEALEQLFSLsPRQARLVELRF-FAGLSNDEIAERLGVS 164

                         170
                  ....*....|....
gi 496324952  151 AST--SRTYLARAK 162
Cdd:pfam07638 165 ERTveRNWALARAW 178
PRK09642 PRK09642
RNA polymerase sigma factor;
21-171 3.03e-07

RNA polymerase sigma factor;


Pssm-ID: 170031 [Multi-domain]  Cd Length: 160  Bit Score: 47.79  E-value: 3.03e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  21 YKHFYGYAMSIALRYsngRDEACEIVNDSFMKVFDKLPQYsESNSFKGWFRRILVNTSIDYYRKNAKHYAAMDIDKVDTE 100
Cdd:PRK09642   4 YRHYIFQVIFSILRH---EEDAKDVTQEVFVKIHASLPNY-QFRGLKTWMARIATNHAIDYKRKKARENEELSLCKETEE 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 496324952 101 SY------EPEIISQLTKDDILNLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTSRTYLARAKQKLREKVTE 171
Cdd:PRK09642  80 NIksshniEDLLLTKEQKLLIAQKLRELPENYRDVVLAHYLEEKSYQEIALQEKIEVKTVEMKLYRARKWIKKHWKE 156
PRK12532 PRK12532
RNA polymerase sigma factor; Provisional
 33-167 3.44e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 171564 [Multi-domain]  Cd Length: 195  Bit Score: 48.00  E-value: 3.44e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  33 LRYSNGRDEACEIVNDSFMKVFDKLPQYSESNSFKGWFRRILVNTSIDYYRKNAKHYAAMDI--DKVDTESYE------- 103
Cdd:PRK12532  24 LQLPDHPDLAEDLVQETLLSAYSAGDSFQGRALVNSWLFAILKNKIIDALRQIGRQRKVFTLldDELLDEAFEshfsqng 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952 104 -------------PEiiSQLTKDDILNLLRS----LPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTSRTYLARAKQKLR 166
Cdd:PRK12532 104 hwtpegqpqhwntPE--KSLNNNEFQKILQSclynLPENTARVFTLKEILGFSSDEIQQMCGISTSNYHTIMHRARESLR 181


                 .
gi 496324952 167 E 167
Cdd:PRK12532 182 Q 182
PRK12526 PRK12526
RNA polymerase sigma factor; Provisional
 3-171 3.62e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 237127 [Multi-domain]  Cd Length: 206  Bit Score: 48.26  E-value: 3.62e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952   3 QHLIQEAKRGDKKSLEMLYKHFYGYAMSIALRYSNGRDEACEIVNDSFMKVFDKLPQYsesNSFKG----WFRRILVNTS 78
Cdd:PRK12526  26 QWLILVAISRDKQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLY---NGDKGaattWVYTVMRNAA 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  79 IDYYRK---NAKHYAAMDI---DKVDTESY-EPEIIS-QLTKDDILNLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIP 150
Cdd:PRK12526 103 FDMLRKikaKKEQNLGDDIwpiEQALAESQsESEEFSdHLMDKQILSYIEKLPEAQQTVVKGVYFQELSQEQLAQQLNVP 182

                        170       180
                 ....*....|....*....|.
gi 496324952 151 ASTSRTYLARAKQKLREKVTE 171
Cdd:PRK12526 183 LGTVKSRLRLALAKLKVQMGE 203
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 14-166 5.52e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 47.24  E-value: 5.52e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  14 KKSLEMLYKHFYGYAMSIALRYSNGRDEACEIVNDSFMKVFDKLpQYSESNSFKGWFRRILVNTSIDYYRKNaKHYAAMD 93
Cdd:PRK12541   4 KQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHI-DYYKGEEIRPWLFTIAYNAFIDWYRKE-KKYKTTT 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 496324952  94 IDKV---DTESYEPEIISQLTKDDILNLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTSRTYLARAKQKLR 166
Cdd:PRK12541  82 IEEFhlpNVPSTEHEYFIKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKETK 157
PRK12542 PRK12542
RNA polymerase sigma factor; Provisional
 13-166 6.43e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183581 [Multi-domain]  Cd Length: 185  Bit Score: 47.35  E-value: 6.43e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  13 DKKSLEMLYKHFYGYAMSIALRYSNGRDEACEIVNDSFMKVFDKLPQYSESNS--FKGWFRRILVNTSIDYYRKNAKH-- 88
Cdd:PRK12542   7 DYEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTqeLKRYILRVAKNKAIDSYRKNKRHet 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  89 ----YAAMDIDKVD--TESYEPEIISQLTKDdilNLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTSRTYLARAK 162
Cdd:PRK12542  87 fleeYERESIEAVDenIEEWEKRKMSEVQID---TLLKELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERAR 163


                 ....
gi 496324952 163 QKLR 166
Cdd:PRK12542 164 KRVQ 167
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 16-171 8.84e-07

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 46.80  E-value: 8.84e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  16 SLEMLYKHFYGYAMSIALRYSNGRDEACEIVNDSFMKVFDKLPQYsESNSFKGWFRRILVNTSIDYYRKNAKHYAAMD-- 93
Cdd:PRK09644   2 EIEEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDY-DNQKVKPWLFKVAYHTFIDFVRKEKKVSFVGTde 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 496324952  94 IDKVDTESYEPEIISQLTKDDILNLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTSRTYLARAKQKLREKVTE 171
Cdd:PRK09644  81 IEAIQAESTEEYVVAKNSYEKLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLKE 158
PRK12540 PRK12540
RNA polymerase sigma factor; Provisional
 30-167 2.46e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183579 [Multi-domain]  Cd Length: 182  Bit Score: 45.73  E-value: 2.46e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  30 SIALRYSNGRDEACEIVNDSFMKVFDKLPQYSESNSFKGWFRRILVNTSIDYYRKNAKHYAAMDIDKVDTESYEPEIISQ 109
Cdd:PRK12540  20 AFAISLSGNGDRADDLVQETLLRALANIDSFQPGSNLPAWLFTILRNLFRSDYRKRRREVEDADGSYAKTLKSQPGQNAH 99

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 496324952 110 LTKDDILNLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTSRTYLARAKQKLRE 167
Cdd:PRK12540 100 LEFEEFRAALDKLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARSKLSA 157
PRK09047 PRK09047
RNA polymerase factor sigma-70; Validated
 37-173 2.91e-06

RNA polymerase factor sigma-70; Validated


Pssm-ID: 236367 [Multi-domain]  Cd Length: 161  Bit Score: 44.96  E-value: 2.91e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  37 NGRDEACEIVNDSFMKVFDKLPQYSESnSFKGWFRRILVNTSIDYYRKNA-------------KHYAAMDIDKVDT-ESY 102
Cdd:PRK09047   2 RDDDAALDIVQDAMIKLAEKYGDRPAA-EWPPLFQRILQNRIHDWFRRQKvrntwvslfssfsDDDDDDDFDPLETlDSA 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 496324952 103 EPEIIS---QLTKDDILNL----LRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTSRTYLARAKQKLREKVTELN 173
Cdd:PRK09047  81 DEGAESpadKLERAQVLQLieeaIQKLPARQREAFLLRYWEDMDVAETAAAMGCSEGSVKTHCSRATHALAKALEAKG 158
PRK12523 PRK12523
RNA polymerase sigma factor; Reviewed
 20-167 3.32e-06

RNA polymerase sigma factor; Reviewed


Pssm-ID: 183572 [Multi-domain]  Cd Length: 172  Bit Score: 45.23  E-value: 3.32e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  20 LYKHFYGYAMSIALRYSNGRDEACEIVNDSFMKVF--DKLPQYSESNSFKGWFRRILVntsIDYYRKNA--KHYAAMDID 95
Cdd:PRK12523  15 LYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLgrPELPTPREPRAFLAAVAKGLM---FDHFRRAAleQAYLAELAL 91

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 496324952  96 KVDTESYEPE----IISQLTKDDilNLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTSRTYLArakQKLRE 167
Cdd:PRK12523  92 VPEAEQPSPEeqhlILEDLKAID--RLLGKLSSKARAAFLYNRLDGMGHAEIAERLGVSVSRVRQYLA---QGLRQ 162
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 12-165 4.23e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 45.27  E-value: 4.23e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  12 GDKKSLEMLYKHFYGYAMSIALRYSNGRDEACEIVNDSFMKVFDKLPQYSESNS-FKGWFRRILVNTSIDYYRKNAKHYA 90
Cdd:PRK12524  23 GDPAAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQGEArVSTWLYRVVCNLCTDRLRRRRRASV 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  91 AMDIDK--VDTESYEPEIISQLTKDDILNL-LRSLPEMLRIVFNMYEIEGYSHNEIAE--QCGIPASTSRTylARAKQKL 165
Cdd:PRK12524 103 DLDDAPepADAAPGAEEALIEGDRMRALDAaLAALPERQRQAVVLRHIEGLSNPEIAEvmEIGVEAVESLT--ARGKRAL 180
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 40-167 5.13e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 44.78  E-value: 5.13e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  40 DEACEIVNDSFMKVFDKLPQYSESNSFKGWFRRILVNTSIDYYRKN----AKHYAAMDIDKvdtESYEPEIISQLTKDDI 115
Cdd:PRK12511  29 AEAEDLVHDALVRALERRASFRSGGNLRTWLMSILHNAFIDELRRRrveaRRADELAVLAD---ASLPAAQEHAVRLAQI 105

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 496324952 116 LNLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTSRTYLARAKQKLRE 167
Cdd:PRK12511 106 RDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAALRA 157
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 22-171 8.59e-06

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 43.61  E-value: 8.59e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  22 KHFYGYAMSIALRYSNGRDEACEIVNDSFMKVFDKLPQYSESNSfKGWFRRILVNTSIDYYRKNAKHyAAMDIDKVDTES 101
Cdd:PRK12527   2 ENYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQIEHP-RAFLYRTALNLVVDRHRRHRVR-QAEPLEVLDEEE 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 496324952 102 --YEPEIISQLTKDDILNLLR----SLPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTSRTYLARAKQKLREKVTE 171
Cdd:PRK12527  80 rlHSPSPQTRLDLGQRLALLQralaELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMRQ 155
sigI PRK09635
RNA polymerase sigma factor SigI; Provisional
 21-167 1.25e-05

RNA polymerase sigma factor SigI; Provisional


Pssm-ID: 182008 [Multi-domain]  Cd Length: 290  Bit Score: 44.19  E-value: 1.25e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  21 YKHFYGYAMSIALRYSNGRDEACEIVNDSFMKVFDKlpQYSESNSFKGWFRRILVNTSIDYYRK-NAKHYAAMDIDKVDT 99
Cdd:PRK09635  11 WRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRA--PVGDIDDERGWLIVVTSRLCLDHIKSaSTRRERPQDIAAWHD 88

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 496324952 100 ESYEPEIIS---QLTKDD-----ILNLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTSRTYLARAKQKLRE 167
Cdd:PRK09635  89 GDASVSSVDpadRVTLDDevrlaLLIMLERLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQLAHRARRKINE 164
PRK09651 PRK09651
RNA polymerase sigma factor FecI; Provisional
 16-161 1.37e-05

RNA polymerase sigma factor FecI; Provisional


Pssm-ID: 182018 [Multi-domain]  Cd Length: 172  Bit Score: 43.26  E-value: 1.37e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  16 SLEMLYKHFYGYAMSIALRYSNGRDEACEIVNDSFMKVF--DKLPQYSESNSFKGWF-RRILVntsiDYYRKNA--KHYA 90
Cdd:PRK09651  11 TFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMvsETLSTIRDPRSFLCTIaKRVMV----DLFRRNAleKAYL 86

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 496324952  91 AMDIDKVDTESYEPEII-SQL-TKDDILNLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTSRTYLARA 161
Cdd:PRK09651  87 EMLALMPEGGAPSPEEReSQLeTLQLLDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKA 159
PRK12539 PRK12539
RNA polymerase sigma factor SigF;
17-152 1.42e-05

RNA polymerase sigma factor SigF;


Pssm-ID: 237132 [Multi-domain]  Cd Length: 184  Bit Score: 43.57  E-value: 1.42e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  17 LEMLYKHFYGYAMSIALRYSNGRDEACEIVNDSFMKVFDKLPQYSESNSFKGWFRRILVNTSIDYYRKNAKHYAAMDIDK 96
Cdd:PRK12539  27 LERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHTRRHTYDPEQPLTPWVYAIARYKLIDHLRRTRASLADVPIDD 106

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 496324952  97 VDTESYEPEIISQLTKDDILNLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPAS 152
Cdd:PRK12539 107 ADELVAHDDHAAVESTLDLGRLLARLPEKMRLAIQAVKLEGLSVAEAATRSGMSES 162
PRK12535 PRK12535
RNA polymerase sigma factor; Provisional
 38-165 2.33e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 237130 [Multi-domain]  Cd Length: 196  Bit Score: 42.96  E-value: 2.33e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  38 GRDEACEIVNDSFMKVFDKLPQYSESNSFKGWF----RRILV-NTSIDYYRKNAKHYAAMDIDKVDTESYEPEIISQLTk 112
Cdd:PRK12535  47 GHDIADDLTQETYLRVMSALPRFAARSSARTWLlslaRRVWVdNIRHDMARPRKSATEYEDAAATTASNETTGSWSEWI- 125

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 496324952 113 dDILNLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTSRTYLARAKQKL 165
Cdd:PRK12535 126 -DVRTLIDALPPERREALILTQVLGYTYEEAAKIADVRVGTIRSRVARARADL 177
PRK12528 PRK12528
RNA polymerase sigma factor; Provisional
 40-164 3.31e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 171561 [Multi-domain]  Cd Length: 161  Bit Score: 42.14  E-value: 3.31e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  40 DEACEIVNDSFMKVFD--KLPQYSESNSFKGWF-RRILVNtsidyyrknakHYAAMDIDK--VDTESYEPEII--SQLTK 112
Cdd:PRK12528  29 QSAADLAQDTFVKVLVarETAQIIEPRAFLTTIaKRVLCN-----------HYRRQDLERayLEALAQLPERVapSEEER 97

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 496324952 113 DDIL-------NLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTSRTYLARAKQK 164
Cdd:PRK12528  98 AIILetlveldQLLDGLPPLVKRAFLLAQVDGLGYGEIATELGISLATVKRYLNKAAMR 156
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 13-174 3.77e-05

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 42.23  E-value: 3.77e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  13 DKKSLEMLYKHFYGYAMSIALRYSNGRDEACEIVNDSFMKVFDKLPQYSESNSFKGWFRRILVNTSIDYYRKNAKHYAAM 92
Cdd:PRK09640  24 VTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGKSKFKTWLYSITYNECITQYRKERRKRRLM 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  93 DIDKVD-----TESYEPEIISQLTKDDILNLLRSLPEMLRIVFNMYEIEgysHNEIAEQCGIPASTSRTYLARAKQKLRE 167
Cdd:PRK09640 104 DALSLDpleeaSEEKAPKPEERGGLDRWLVHVNPIDREILVLRFVAELE---FQEIADIMHMGLSATKMRYKRALDKLRE 180


                 ....*..
gi 496324952 168 KVTELNQ 174
Cdd:PRK09640 181 KFAGLAE 187
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 118-167 6.94e-05

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


Pssm-ID: 461347 [Multi-domain]  Cd Length: 50  Bit Score: 38.95  E-value: 6.94e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 496324952  118 LLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTSRTYLARAKQKLRE 167
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
PRK12517 PRK12517
RNA polymerase sigma factor; Provisional
 42-176 1.18e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183569 [Multi-domain]  Cd Length: 188  Bit Score: 40.83  E-value: 1.18e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  42 ACEIVNDSFMKVFDKLPQYSESNSFKGWFRRILvntsidyYRKNAKHYAAMDIDKVDTESYEPEIISQLTKDDILN--LL 119
Cdd:PRK12517  50 AEDLVQETFLRAWRSLDSLKDEKAAKAWLITIL-------RRENARRFERKQFDLVDIEDDSIEDDASHSSEEEMEqeWL 122

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 496324952 120 RSL----------PEMLRIVFnmyeieGYSHNEIAEQCGIPASTSRTYLARAKQKLREKVTELNQIR 176
Cdd:PRK12517 123 RRQiakldpeyrePLLLQVIG------GFSGEEIAEILDLNKNTVMTRLFRARNQLKEALEKPDVQR 183
PRK06930 PRK06930
positive control sigma-like factor; Validated
 91-174 1.84e-04

positive control sigma-like factor; Validated


Pssm-ID: 180757 [Multi-domain]  Cd Length: 170  Bit Score: 40.10  E-value: 1.84e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  91 AMDIDKVDTESYEPEIiSQLTKDDILNLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTSRTYLARAKQKLREKVT 170
Cdd:PRK06930  85 SMEDLEWDIEEPESVI-SEWDKIRIEDALSVLTEREKEVYLMHRGYGLSYSEIADYLNIKKSTVQSMIERAEKKIARQIN 163


                 ....
gi 496324952 171 ELNQ 174
Cdd:PRK06930 164 ESLF 167
PRK09649 PRK09649
RNA polymerase sigma factor SigC; Reviewed
 9-165 3.10e-04

RNA polymerase sigma factor SigC; Reviewed


Pssm-ID: 137458 [Multi-domain]  Cd Length: 185  Bit Score: 39.64  E-value: 3.10e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952   9 AKRGDKKSLEMLYK-------HFYGYAMSIAlrysngrdEACEIVNDSFMKVFDKLPQYSESNSFKGWFRRILVNTSIDY 81
Cdd:PRK09649  18 AAKGNGRALEAFIKatqqdvwRFVAYLSDVG--------SADDLTQETFLRAIGAIPRFSARSSARTWLLAIARHVVADH 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  82 YRK-NAKHYAAMDIDkvdtesyePEIIsqLTKD----------DILNLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIP 150
Cdd:PRK09649  90 IRHvRSRPRTTRGAR--------PEHL--IDGDrhargfedlvEVTTMIADLTTDQREALLLTQLLGLSYADAAAVCGCP 159

                        170
                 ....*....|....*
gi 496324952 151 ASTSRTYLARAKQKL 165
Cdd:PRK09649 160 VGTIRSRVARARDAL 174
PRK12533 PRK12533
RNA polymerase sigma factor; Provisional
 41-171 5.39e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 237129 [Multi-domain]  Cd Length: 216  Bit Score: 39.33  E-value: 5.39e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  41 EACEIVNDSFMKVFDKLpqysesNSFKG-----WFRRILVNTSIDYYRKNAK-HYAAMDIDKVDTES------YEPEIIS 108
Cdd:PRK12533  44 DADDVVQEACMRALRFF------DSFRGdnarpWLLAIVRHTWYSEWRRRANaHEVAAPDTLDDADSlddwqpAGEDPLA 117

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 496324952 109 QLTKDDILNLLRS----LPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTSRTYLARAKQKLREKVTE 171
Cdd:PRK12533 118 LLLRAEDVRLVNAalakLPVEYREVLVLRELEDMSYREIAAIADVPVGTVMSRLARARRRLAALLGG 184
PRK12530 PRK12530
RNA polymerase sigma factor; Provisional
 40-166 7.54e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 237128 [Multi-domain]  Cd Length: 189  Bit Score: 38.59  E-value: 7.54e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  40 DEACEIVNDSFMKVFDKLPQYSESNSFKGWFRRILVNTSIDYYRKNAKHYAAMDIDKVDT-------------ESYEP-- 104
Cdd:PRK12530  32 DLAEDVVQEALVSAYKNADSFKGQSALKTWIFAILKNKIIDLIRYRKRFVNESELIEEDSpnsffdekghwkpEYYEPse 111

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 496324952 105 --EIISQLTKDDILNL----LRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTSRTYLARAKQKLR 166
Cdd:PRK12530 112 wqEVENTVYKEEFWLIfeacLNHLPAQQARVFMMREYLELSSEQICQECDISTSNLHVLLYRARLQLQ 179
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 94-171 7.61e-04

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: 38.65  E-value: 7.61e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 496324952  94 IDKVDTESYEPEIISQLTKDDILNLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPAST-SRtYLARAKQKLREKVTE 171
Cdd:COG1191  159 LDLLESGDPEEELEHEELREALAEAIEQLPERERLVLSLYYFEELTLKEIAEVLGVSESRvSR-LHKKALARLREYLKE 236
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 5-167 8.74e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 38.56  E-value: 8.74e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952   5 LIQEAKRGDKKSLEMLYKHFYGYAMSIALRYSngRDE--ACEIVNDSFMKVFDKLPQYSESNSFKGWFRRILVNTSIDYY 82
Cdd:PRK12515  12 LLARIAQGDRTAMQTLYGRHHVRVYRFGLRLV--RDEqtAEDLVSEVFLDVWRQAGQFEGRSQVSTWLLSIARFKALSAL 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  83 RKNaKHY-----AAMDI-DKVDTesyePEIISQltKDDILNLLR----SLPEMLRIVFNMYEIEGYSHNEIAEQCGIPAS 152
Cdd:PRK12515  90 RRR-KHEeiddeAAAAIeDGADT----PEVALQ--KSDTSAALRaclaKLSPAHREIIDLVYYHEKSVEEVGEIVGIPES 162

                        170
                 ....*....|....*
gi 496324952 153 TSRTYLARAKQKLRE 167
Cdd:PRK12515 163 TVKTRMFYARKKLAE 177
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 136-165 2.29e-03

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 34.81  E-value: 2.29e-03
                           10        20        30
                   ....*....|....*....|....*....|
gi 496324952   136 EGYSHNEIAEQCGIPASTSRTYLARAKQKL 165
Cdd:smart00421  17 EGLTNKEIAERLGISEKTVKTHLSNIMRKL 46
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
136-165 2.89e-03

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 37.04  E-value: 2.89e-03
                         10        20        30
                 ....*....|....*....|....*....|
gi 496324952 136 EGYSHNEIAEQCGIPASTSRTYLARAKQKL 165
Cdd:COG2771  141 EGLTLKEIARILGISERTVRTHLKRIYRKL 170
PRK09636 PRK09636
RNA polymerase sigma factor SigJ; Provisional
 29-168 5.82e-03

RNA polymerase sigma factor SigJ; Provisional


Pssm-ID: 236600 [Multi-domain]  Cd Length: 293  Bit Score: 36.44  E-value: 5.82e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496324952  29 MSIALRYSNGRDEACEIVNDSFMKvFDKLPQySESNSFKGWFRRILVNTSIDYYRkNAKH----YAAMDI-DKVDTESYE 103
Cdd:PRK09636  18 LSVAYRMLGSVADAEDIVQEAWLR-WNNADR-AQIRDPRAWLTRVVTRLCLDRLR-SARHrretYVGPWLpEPVVEELDD 94

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 496324952 104 PeIISQLTKDDI----LNLLRSLPEMLRIVFNMYEIEGYSHNEIAEQCGIPASTSRTYLARAKQKLREK 168
Cdd:PRK09636  95 P-LEAVVAAEDLslalMLALERLSPLERAAFLLHDVFGVPFDEIASTLGRSPAACRQLASRARKHVRAA 162
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 136-165 7.33e-03

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: 34.87  E-value: 7.33e-03
                         10        20        30
                 ....*....|....*....|....*....|
gi 496324952 136 EGYSHNEIAEQCGIPASTSRTYLARAKQKL 165
Cdd:COG2197   83 EGLSNKEIAERLGISERTVKTHVSNILRKL 112
GerE pfam00196
Bacterial regulatory proteins, luxR family;
136-166 8.21e-03

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 33.33  E-value: 8.21e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 496324952  136 EGYSHNEIAEQCGIPASTSRTYLARAKQKLR 166
Cdd:pfam00196  16 AGKSNKEIADELGISEKTVKVHRSNIMRKLN 46
 
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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