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Conserved domains on  [gi|696249455|ref|WP_032827217|]
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MULTISPECIES: sigma-70 family RNA polymerase sigma factor [Pseudoalteromonas]

Protein Classification

sigma-70 family RNA polymerase sigma factor( domain architecture ID 11485959)

sigma-70 family RNA polymerase sigma 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
PRK12517 PRK12517
RNA polymerase sigma factor; Provisional
 1-179 3.37e-113

RNA polymerase sigma factor; Provisional


:

Pssm-ID: 183569 [Multi-domain]  Cd Length: 188  Bit Score: 319.71  E-value: 3.37e-113
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455   1 MLGKKKSNNQVLIDMAEKQKRYEALVHVYNKELYRFAYWLCRDPHIADDLVQETFLRAWRSLDSLLDQKAAKPWLLTILR 80
Cdd:PRK12517   4 NFRKKSSESPVSSDMLSKQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDEKAAKAWLITILR 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  81 RENARRFERKQFDYSDVENDTLVDETSHSLDDEMEQTVIQRQIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMT 160
Cdd:PRK12517  84 RENARRFERKQFDLVDIEDDSIEDDASHSSEEEMEQEWLRRQIAKLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMT 163

                        170
                 ....*....|....*....
gi 696249455 161 RLYRARNQLKEALSRDDEQ 179
Cdd:PRK12517 164 RLFRARNQLKEALEKPDVQ 182
 
Name Accession Description Interval E-value
PRK12517 PRK12517
RNA polymerase sigma factor; Provisional
 1-179 3.37e-113

RNA polymerase sigma factor; Provisional


Pssm-ID: 183569 [Multi-domain]  Cd Length: 188  Bit Score: 319.71  E-value: 3.37e-113
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455   1 MLGKKKSNNQVLIDMAEKQKRYEALVHVYNKELYRFAYWLCRDPHIADDLVQETFLRAWRSLDSLLDQKAAKPWLLTILR 80
Cdd:PRK12517   4 NFRKKSSESPVSSDMLSKQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDEKAAKAWLITILR 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  81 RENARRFERKQFDYSDVENDTLVDETSHSLDDEMEQTVIQRQIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMT 160
Cdd:PRK12517  84 RENARRFERKQFDLVDIEDDSIEDDASHSSEEEMEQEWLRRQIAKLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMT 163

                        170
                 ....*....|....*....
gi 696249455 161 RLYRARNQLKEALSRDDEQ 179
Cdd:PRK12517 164 RLFRARNQLKEALEKPDVQ 182
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 7-178 6.01e-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: 128.57  E-value: 6.01e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455   7 SNNQVLIDMAEK--QKRYEALVHVYNKELYRFAYWLCRDPHIADDLVQETFLRAWRSLDSLLDQKAAKPWLLTILRRE-- 82
Cdd:COG1595    2 SSDEELLERLRAgdEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLai 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  83 NARRFERKQFDYSDVENDTLVDETS---HSLDDEMEQTVIQRQIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVM 159
Cdd:COG1595   82 DHLRKRRRRRELLDELAEELPDEAAdpeEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVK 161

                        170
                 ....*....|....*....
gi 696249455 160 TRLYRARNQLKEALSRDDE 178
Cdd:COG1595  162 SRLSRARKKLREALEEEGA 180
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 22-173 1.50e-27

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: 101.27  E-value: 1.50e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455   22 YEALVHVYNKELYRFAYWLCRDPHIADDLVQETFLRAWRSLDSLLDQKAAKPWLLTILRRENARRFERKQFDYSDVENDT 101
Cdd:TIGR02937   3 FEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDLLE 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 696249455  102 LVDETSHSLDDEMEQTVIQRQ----IALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMTRLYRARNQLKEAL 173
Cdd:TIGR02937  83 ELLDSDPSPEEELEQEEEREAlreaLEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 25-91 2.08e-12

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: 59.52  E-value: 2.08e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 696249455   25 LVHVYNKELYRFAYWLCRDPHIADDLVQETFLRAWRSLDSLLDQKAAKP--WLLTILRRENARRFERKQ 91
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFstWLYTIIRNAIIDYLRKQR 69
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 116-170 4.33e-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: 44.79  E-value: 4.33e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 696249455 116 QTVIQRQIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMTRLYRARNQLK 170
Cdd:cd06171    1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
PRK12517 PRK12517
RNA polymerase sigma factor; Provisional
 1-179 3.37e-113

RNA polymerase sigma factor; Provisional


Pssm-ID: 183569 [Multi-domain]  Cd Length: 188  Bit Score: 319.71  E-value: 3.37e-113
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455   1 MLGKKKSNNQVLIDMAEKQKRYEALVHVYNKELYRFAYWLCRDPHIADDLVQETFLRAWRSLDSLLDQKAAKPWLLTILR 80
Cdd:PRK12517   4 NFRKKSSESPVSSDMLSKQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDEKAAKAWLITILR 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  81 RENARRFERKQFDYSDVENDTLVDETSHSLDDEMEQTVIQRQIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMT 160
Cdd:PRK12517  84 RENARRFERKQFDLVDIEDDSIEDDASHSSEEEMEQEWLRRQIAKLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMT 163

                        170
                 ....*....|....*....
gi 696249455 161 RLYRARNQLKEALSRDDEQ 179
Cdd:PRK12517 164 RLFRARNQLKEALEKPDVQ 182
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 7-178 6.01e-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: 128.57  E-value: 6.01e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455   7 SNNQVLIDMAEK--QKRYEALVHVYNKELYRFAYWLCRDPHIADDLVQETFLRAWRSLDSLLDQKAAKPWLLTILRRE-- 82
Cdd:COG1595    2 SSDEELLERLRAgdEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLai 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  83 NARRFERKQFDYSDVENDTLVDETS---HSLDDEMEQTVIQRQIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVM 159
Cdd:COG1595   82 DHLRKRRRRRELLDELAEELPDEAAdpeEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVK 161

                        170
                 ....*....|....*....
gi 696249455 160 TRLYRARNQLKEALSRDDE 178
Cdd:COG1595  162 SRLSRARKKLREALEEEGA 180
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 11-179 6.10e-31

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 110.83  E-value: 6.10e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  11 VLIDMAEKQKRYEALVHVYNKELYRFAYWLCRDPHIADDLVQETFLRAWRSLDSLLDQKAAKPWLLTILRRENARRFERK 90
Cdd:PRK11924   4 MPVDATGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCYDLLRRR 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  91 QFDYSDVENDTLVDETSHSLDDEMEQTV-------IQRQIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMTRLY 163
Cdd:PRK11924  84 RREKAVLSDDALEPEFAETAETPEAALLakddlarIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLR 163

                        170
                 ....*....|....*.
gi 696249455 164 RARNQLKEALSRDDEQ 179
Cdd:PRK11924 164 RARQLLRECLEAQWEA 179
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 22-173 1.50e-27

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: 101.27  E-value: 1.50e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455   22 YEALVHVYNKELYRFAYWLCRDPHIADDLVQETFLRAWRSLDSLLDQKAAKPWLLTILRRENARRFERKQFDYSDVENDT 101
Cdd:TIGR02937   3 FEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDLLE 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 696249455  102 LVDETSHSLDDEMEQTVIQRQ----IALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMTRLYRARNQLKEAL 173
Cdd:TIGR02937  83 ELLDSDPSPEEELEQEEEREAlreaLEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 11-173 3.78e-27

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 101.04  E-value: 3.78e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  11 VLIDMAEKQKRYEALVHVYNKELYRFAYWLCRDPHIADDLVQETFLRAWRSLDSLLDQKAAKPWLLTILR-------REN 83
Cdd:PRK09652   1 VERVQRGDRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRGGAAFYTWLYRIARntainylRKQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  84 ARRFERKQFDYSDVENDTLVDETSHS-------LDDEMEQTVIQRqIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKN 156
Cdd:PRK09652  81 GRRPPASDVDAEEAEDFDLADALRDIstpenelLSAELEQRVRAA-IESLPEELRTAITLREIEGLSYEEIAEIMGCPIG 159

                        170
                 ....*....|....*..
gi 696249455 157 TVMTRLYRARNQLKEAL 173
Cdd:PRK09652 160 TVRSRIFRAREALRAKL 176
PRK12533 PRK12533
RNA polymerase sigma factor; Provisional
 14-184 1.18e-23

RNA polymerase sigma factor; Provisional


Pssm-ID: 237129 [Multi-domain]  Cd Length: 216  Bit Score: 92.87  E-value: 1.18e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  14 DMAEKQKRYEALVHVYNKELYRFAYWLCRDPHIADDLVQETFLRAWRSLDSLLDQKaAKPWLLTILRR----ENARRFER 89
Cdd:PRK12533  12 DAAARGERFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSFRGDN-ARPWLLAIVRHtwysEWRRRANA 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  90 KQFDYSD-VENDTLVDETSHSLDDEMEQTV-------IQRQIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMTR 161
Cdd:PRK12533  91 HEVAAPDtLDDADSLDDWQPAGEDPLALLLraedvrlVNAALAKLPVEYREVLVLRELEDMSYREIAAIADVPVGTVMSR 170

                        170       180
                 ....*....|....*....|...
gi 696249455 162 LYRARNQLKEALSRDDEQLKGAS 184
Cdd:PRK12533 171 LARARRRLAALLGGASAAQAAPG 193
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 22-176 1.42e-22

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 90.41  E-value: 1.42e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  22 YEALVHVYNKELYRFAYWLCRDPHIADDLVQETFLRAWRSLDSLLDQKAAKPWLLTI--------LRRenARRFERKQFD 93
Cdd:PRK11922  32 FEALMRRHNRRLYRTARAILRNDAEAEDVVQEAYLRAFRALGTFRGDASLSTWLSRIvlnealgrLRR--RRRLVNLAEM 109

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  94 YSDVENDTLVDETSHSLDDEMEQTVIQRQ--------IALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMTRLYRA 165
Cdd:PRK11922 110 VMASTIAGGERTPLADPAEDPERAAARREiralleraIDALPDAFRAVFVLRVVEELSVEETAQALGLPEETVKTRLHRA 189

                        170
                 ....*....|.
gi 696249455 166 RNQLKEALSRD 176
Cdd:PRK11922 190 RRLLRESLARE 200
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 23-179 4.14e-20

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 82.23  E-value: 4.14e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  23 EALVHVYNKELYRFAYWLCRDPHIADDLVQETFLRAWRSLDSLLDQKAaKPWLLTILRRE--NARRFERKQFDYSDVEND 100
Cdd:PRK09644   4 EEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDNQKV-KPWLFKVAYHTfiDFVRKEKKVSFVGTDEIE 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455 101 TLVDETSHSLDDEME-QTVIQRQIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMTRLYRARNQLKEALSRDDEQ 179
Cdd:PRK09644  83 AIQAESTEEYVVAKNsYEKLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLKEEKSQ 162
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
 15-182 1.22e-19

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 81.81  E-value: 1.22e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  15 MAEKQKRYEALVHVynKELYRFAYWLCRDPHIADDLVQETFLRAWRSLDSLLDQKAAKPWLLTILRRE--NARRFERKQF 92
Cdd:PRK12546   4 AKHRDPRDELVEHL--PALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEGTNLRAWLFTILRNTfySDRRKHKREV 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  93 DYSD-VENDTLVDETSHslDDEMEQTVIQRQIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMTRLYRARNQLKE 171
Cdd:PRK12546  82 PDPEgVHAASLAVKPAH--DGRLAMSDFRAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARARLAE 159

                        170
                 ....*....|..
gi 696249455 172 ALS-RDDEQLKG 182
Cdd:PRK12546 160 LLQlEEGEELEM 171
PRK12522 PRK12522
RNA polymerase sigma factor; Provisional
 19-173 1.48e-19

RNA polymerase sigma factor; Provisional


Pssm-ID: 183571 [Multi-domain]  Cd Length: 173  Bit Score: 81.07  E-value: 1.48e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  19 QKRYEALVHVYNKELYRFAYWLCRDPHIADDLVQETFLRAWRSLDSLLDQKAAKPWLLTILRRENARRFERKQ------F 92
Cdd:PRK12522   2 EEKVEELIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVENYKKWITTICVRTFYDFYRKKKrwkdriL 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  93 DYSDVENDTLVDETSHSLDDE-----MEQTVIQRQIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMTRLYRARN 167
Cdd:PRK12522  82 DLFHKEDGGEIEFADDVNISEefiqkVEAEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKK 161


                 ....*.
gi 696249455 168 QLKEAL 173
Cdd:PRK12522 162 QMREHL 167
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
23-173 1.82e-19

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 80.89  E-value: 1.82e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  23 EALVHVYNKE----LYRFAYWLCRDPHIADDLVQETFLRAWRSLDSL-LDQKAAKPWLLTILRR-----ENARRFeRKQF 92
Cdd:PRK09645   8 AALMRALYDEhaapLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLaDTGRSARAWLFTVARNlvideRRSARA-RPVE 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  93 DYSDVENDTLVDETSHSlDDEMEQTVIQRQIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMTRLYRARNQLKEA 172
Cdd:PRK09645  87 GGDDVLGVPEQSAPDEV-DRALDRLLVADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYALRALRLA 165


                 .
gi 696249455 173 L 173
Cdd:PRK09645 166 L 166
PRK09649 PRK09649
RNA polymerase sigma factor SigC; Reviewed
 16-177 3.90e-19

RNA polymerase sigma factor SigC; Reviewed


Pssm-ID: 137458 [Multi-domain]  Cd Length: 185  Bit Score: 80.47  E-value: 3.90e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  16 AEKQKR-YEALVHVYNKELYRFAYWLcRDPHIADDLVQETFLRAWRSLDSLLDQKAAKPWLLTILRR---ENARRFERKQ 91
Cdd:PRK09649  19 AKGNGRaLEAFIKATQQDVWRFVAYL-SDVGSADDLTQETFLRAIGAIPRFSARSSARTWLLAIARHvvaDHIRHVRSRP 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  92 FDYSDVENDTLVDETSHS--LDDEMEQTVIqrqIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMTRLYRARNQL 169
Cdd:PRK09649  98 RTTRGARPEHLIDGDRHArgFEDLVEVTTM---IADLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARARDAL 174


                 ....*...
gi 696249455 170 KEALSRDD 177
Cdd:PRK09649 175 LADAEPDD 182
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 20-173 5.37e-19

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: 79.14  E-value: 5.37e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455   20 KRYEALVHVYNKELYRFAYWLCRDPHIADDLVQETFLRAWRSLDSLLDQKAAKPWLLTILRRENARRFERKQF--DYSDV 97
Cdd:TIGR02985   1 EAFEQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETLEISESIKAYLFTIVKNRCLNYLRHKQVeeKYQEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455   98 ENDTLVDETShSLDDEME------QTVIQRQIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMTRLYRARNQLKE 171
Cdd:TIGR02985  81 LAEIEERELS-EADPEEEleakelEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLRK 159


                  ..
gi 696249455  172 AL 173
Cdd:TIGR02985 160 EL 161
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 12-173 1.38e-18

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 78.97  E-value: 1.38e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  12 LIDMAEK--QKRYEALVHVYNKELYRFAYWLCRDPHIADDLVQETFLRAWRSLDSLLDQKAAKPWLLTILRRENARRFER 89
Cdd:PRK09641   8 LIKQVKKgdQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINRKFSTWLYRIATNLTIDRLRK 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  90 KQFDYS-DVENDTLVDETSHSL--------DDEME----QTVIQRQIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKN 156
Cdd:PRK09641  88 RKPDYYlDAEVAGTEGLTMYSQlaaddalpEEQVVslelQETIQEAILQLPEKYRTVIVLKYIEDLSLKEISEILDLPVG 167

                        170
                 ....*....|....*..
gi 696249455 157 TVMTRLYRARNQLKEAL 173
Cdd:PRK09641 168 TVKTRIHRGREALRKQL 184
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 22-175 1.72e-18

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 79.06  E-value: 1.72e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  22 YEALVHVYNKELYRFAYWLCRDPHIADDLVQETFLRAWRSLDSLldqkaaKP-----WL--------LTILRRENARRFE 88
Cdd:PRK09647  30 WEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNY------QPgtfegWLhrittnlfLDMVRRRARIRME 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  89 RKQFDYSDVENDTLVDETSHS---LDDEmeqtvIQRQIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMTRLYRA 165
Cdd:PRK09647 104 ALPEDYDRVPGDEPNPEQIYHdarLDPD-----LQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRG 178

                        170
                 ....*....|
gi 696249455 166 RNQLKEALSR 175
Cdd:PRK09647 179 RQQLRAALAA 188
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 1-175 2.12e-18

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 78.23  E-value: 2.12e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455   1 MLGKKKSNNQVLIDMAEKQKRyeALVHV----YNKELYRFAYWLCRDPHIADDLVQETFLRAWRSLDSLLDQKAAKPWLL 76
Cdd:PRK12515   1 IIAAQATTDEMLLARIAQGDR--TAMQTlygrHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGRSQVSTWLL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  77 TILRRENARRFERKQFDYSDVENDTLVDETSH----SLDDEMEQTVIQRQIALLSDEYREPLLLQVVMGCSGEEIAGILN 152
Cdd:PRK12515  79 SIARFKALSALRRRKHEEIDDEAAAAIEDGADtpevALQKSDTSAALRACLAKLSPAHREIIDLVYYHEKSVEEVGEIVG 158

                        170       180
                 ....*....|....*....|...
gi 696249455 153 LNKNTVMTRLYRARNQLKEALSR 175
Cdd:PRK12515 159 IPESTVKTRMFYARKKLAELLKA 181
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 31-173 2.84e-18

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 77.84  E-value: 2.84e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  31 KELYR--------FAYWLCrDPHIADDLVQETFLRAWRSLDSLLDQKAAKPWLLTIL-------RRENARRFERKQfdyS 95
Cdd:PRK12518  14 RQLYRryqqkvrsTLYQLC-GRELLDDLVQEVFLRVWKGLPKLRNPAYFSTWLYRITwnvatdaRRQFAQRPSRIQ---D 89

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 696249455  96 DVENDTLV-DETSHSLDDEMEQTVIQRQIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMTRLYRARNQLKEAL 173
Cdd:PRK12518  90 DSLNDQPSrPSDTPDLMQLHYQDLVQQGLQTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFL 168
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 13-177 9.59e-17

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 73.63  E-value: 9.59e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  13 IDMAEKQKRYEALVHV---YNKELYRFAYWLCRDPHIADDLVQETFLRAWRSLDSLLDQKAAKPWLLTI--------LRR 81
Cdd:PRK09415   6 IEAFEIEDKEDLIDEImneYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGKSSLKTWLYRIainhckdyLKS 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  82 ENARR--FERKQFDYSDVENDTlVDET--SHSLDDEMEQTVIQrqialLSDEYREPLLLQVVMGCSGEEIAGILNLNKNT 157
Cdd:PRK09415  86 WHNKKviVTEDIFTYMESQKES-VEEEviQNAEDERLASAVMS-----LPIKYREVIYLFYYEELSIKEIAEVTGVNENT 159

                        170       180
                 ....*....|....*....|
gi 696249455 158 VMTRLYRARNQLKEALSRDD 177
Cdd:PRK09415 160 VKTRLKKAKELLKKGLEEEV 179
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 22-174 2.82e-16

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 72.80  E-value: 2.82e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  22 YEALVHVYNKELYRFAYWLCRDPHIADDLVQETFLRAWRSLDSLLDQKAAKPWLLTI--------LRRENARRfeRKQFD 93
Cdd:PRK12513  28 FEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPRARFRTWLYQIarnllidhWRRHGARQ--APSLD 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  94 YsDVENDTLVDETSHS---LDDEMEQTVIQRQIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMTRLYRARNQLK 170
Cdd:PRK12513 106 A-DEQLHALADDGAAPeqqLSLFRDRRRLQAALETLPDEQREVFLLREHGDLELEEIAELTGVPEETVKSRLRYALQKLR 184


                 ....
gi 696249455 171 EALS 174
Cdd:PRK12513 185 ELLA 188
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 20-171 1.40e-15

RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).


Pssm-ID: 274379 [Multi-domain]  Cd Length: 159  Bit Score: 70.43  E-value: 1.40e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455   20 KRYEALVHVYNKELYRFAYWLCRDPHIADDLVQETFLRAWRSLDSLLDQKAAKPWLLTILRREnARRFERKQFDYSDVEN 99
Cdd:TIGR02989   1 KAFVRLLTRHERALRAFVRSLVADRDDVDDVLQETFVVAWRKFDQFDPGTNFVAWARGIARNK-VLNYRRKLGRDRLVFD 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 696249455  100 DTLVDETSHSLDDEMEQTVIQRQIAL------LSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMTRLYRARNQLKE 171
Cdd:TIGR02989  80 DDLLEALAAEAEPTEAERLSDDRQALegclekLPERQRELLDLRYQRGQKATALAEQTGRTVNAVYKALQRIRVSLRE 157
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 15-171 5.88e-15

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 69.04  E-value: 5.88e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  15 MAEKQKRYEALVHVynKELYRFAYWLCRDPHIADDLVQETFLRAWRSLDSLLDQKAAKPWLLTILRRENARRFERKQFDy 94
Cdd:PRK12511   1 MERKSKRFDVLDQL--VPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRSGGNLRTWLMSILHNAFIDELRRRRVE- 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  95 sDVENDTLVDETSHSLDDEMEQTV----IQRQIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMTRLYRARNQLK 170
Cdd:PRK12511  78 -ARRADELAVLADASLPAAQEHAVrlaqIRDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAALR 156


                 .
gi 696249455 171 E 171
Cdd:PRK12511 157 A 157
PRK12535 PRK12535
RNA polymerase sigma factor; Provisional
 43-177 9.28e-15

RNA polymerase sigma factor; Provisional


Pssm-ID: 237130 [Multi-domain]  Cd Length: 196  Bit Score: 68.77  E-value: 9.28e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  43 DPHIADDLVQETFLRAWRSLDSLLDQKAAKPWLLTILRR---ENAR----RFERKQFDYSDVENDTLVDETSHSLDDEME 115
Cdd:PRK12535  47 GHDIADDLTQETYLRVMSALPRFAARSSARTWLLSLARRvwvDNIRhdmaRPRKSATEYEDAAATTASNETTGSWSEWID 126

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 696249455 116 qtvIQRQIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMTRLYRARNQLKEALSRDD 177
Cdd:PRK12535 127 ---VRTLIDALPPERREALILTQVLGYTYEEAAKIADVRVGTIRSRVARARADLIAATATGQ 185
Sig70_famx1 TIGR02943
RNA polymerase sigma-70 factor, TIGR02943 family; This group of sigma factors are members of ...
 31-174 1.22e-14

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


Pssm-ID: 274359 [Multi-domain]  Cd Length: 188  Bit Score: 68.25  E-value: 1.22e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455   31 KELYRFAYWLCRDPHIADDLVQETFLRAWRSLDSLLDQKAAKPWLLTILRRE--NARRFERKQFDYSDVENDT------- 101
Cdd:TIGR02943  13 RDLLRFARLQLRDRDLAEDAVQETLLAALSHRDSFAGRSALKTWLFAILKNKiiDALRAKGREVKVSDLDDELddeafna 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  102 LVDETSHSLDDEM-------EQTVIQRQIALLSDE--YREP------LLLQVVMGCSGEEIAGILNLNKNTVMTRLYRAR 166
Cdd:TIGR02943  93 LFTQNGHWAQHGQpqhwntpEKQLENKEFWEVFEAclYHLPeqtarvFMMREVLGFESDEICQELEISTSNCHVLLYRAR 172


                  ....*...
gi 696249455  167 NQLKEALS 174
Cdd:TIGR02943 173 LSLRACLS 180
PRK12547 PRK12547
RNA polymerase sigma factor; Provisional
 33-176 1.61e-14

RNA polymerase sigma factor; Provisional


Pssm-ID: 139056 [Multi-domain]  Cd Length: 164  Bit Score: 67.59  E-value: 1.61e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  33 LYRFAYWLCRDPHIADDLVQETFLRAWRSLDSLLDQKAAKPWLLTILRRE-----NARRFERKQFDYSDVENDTLVDETS 107
Cdd:PRK12547  19 LRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGTNLKAWLFTILRNEfysqmRKRGREVQDSDGVFTARVAVHPAQY 98

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 696249455 108 HSLDDEMeqtvIQRQIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMTRLYRARNQLKEALSRD 176
Cdd:PRK12547  99 GSLDLQD----FKKALNLLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARNRLQELLKVD 163
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 33-178 1.17e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 65.76  E-value: 1.17e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  33 LYRFAYWLCRDPHIADDLVQETFLRAWRSLDSLLDQKAAKPWLLTILRRE---NARRFERKQFDYSDVENDTLVDETSH- 108
Cdd:PRK12516  23 LRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVGTNMKAWLFTILRNEfysQMRKRGREVQDTDGMFTEQLAVHPSQy 102

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 696249455 109 -SLDDEMeqtvIQRQIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMTRLYRARNQLKEALSRDDE 178
Cdd:PRK12516 103 gTLDLQD----FRAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQRLQEILQIEGE 169
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 12-175 1.53e-13

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 65.04  E-value: 1.53e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  12 LIDMAEK--QKRYEALVHVYNKELYRFAYWLCRDPHIADDLVQETFLRAWRSLDSLLDQKAAKPWLLTI--------LRR 81
Cdd:PRK09638   8 LIQKAKKgdDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGRSKFSTWLISIasrlykdhLRK 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  82 EnaRRFERKQFDYSDVENDTLVDETSHSLDDEMEqtvIQRQIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMTR 161
Cdd:PRK09638  88 Q--KREKLRLQRAKEETLRKEKWEAAIKGAEWSE---MLDALSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTVKSR 162

                        170
                 ....*....|....
gi 696249455 162 LYRARNQLKEALSR 175
Cdd:PRK09638 163 VHHGIKQLRKEWGQ 176
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 22-180 5.61e-13

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 63.43  E-value: 5.61e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  22 YEALVHVYNKELYRFAYWLCRDPHIADDLVQETFLRAWRSldSLLDQKAAKPWLLTI--------LRRE-NARRFERKQF 92
Cdd:PRK09639   5 FEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRS--DFKGIENEKGWLIKSarnvaynyLRSEkRRRARILGEF 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  93 DYSDVENDTLVDETSHSLDdemEQTVIQRQIALLSDEYREPLLLQvVMGCSGEEIAGILNLNKNTVMTRLYRARNQLKEA 172
Cdd:PRK09639  83 QWQEVDNEPSPEEIWIRKE---EITKVQEVLAKMTERDRTVLLLR-FSGYSYKEIAEALGIKESSVGTTLARAKKKFRKI 158


                 ....*...
gi 696249455 173 LSRDDEQL 180
Cdd:PRK09639 159 YEQMEEEE 166
SigE-fam_strep TIGR02983
RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors ...
 22-173 6.48e-13

RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.


Pssm-ID: 132028 [Multi-domain]  Cd Length: 162  Bit Score: 63.18  E-value: 6.48e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455   22 YEALVHVYNKELYRFAYWLCRDPHIADDLVQETFLRAWRSLDSLLDQKAAKPWLLTILRRENARRFERKQFDYSDVEN-- 99
Cdd:TIGR02983   8 FTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRDPDAPDAYVRRVLVNLARSRWRRRRLLELPTRElp 87

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 696249455  100 DTLVDETShslDDEMEQTVIQRQIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMTRLYRARNQLKEAL 173
Cdd:TIGR02983  88 DAAAPDPA---PDVALRAALARALRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALARLRELL 158
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 25-91 2.08e-12

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: 59.52  E-value: 2.08e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 696249455   25 LVHVYNKELYRFAYWLCRDPHIADDLVQETFLRAWRSLDSLLDQKAAKP--WLLTILRRENARRFERKQ 91
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFstWLYTIIRNAIIDYLRKQR 69
PRK12540 PRK12540
RNA polymerase sigma factor; Provisional
 33-179 2.15e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 183579 [Multi-domain]  Cd Length: 182  Bit Score: 62.29  E-value: 2.15e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  33 LYRFAYWLCRDPHIADDLVQETFLRAWRSLDSLLDQKAAKPWLLTILR---RENARRFERKQFDYSDVENDTLVDETSHS 109
Cdd:PRK12540  18 LRAFAISLSGNGDRADDLVQETLLRALANIDSFQPGSNLPAWLFTILRnlfRSDYRKRRREVEDADGSYAKTLKSQPGQN 97

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455 110 LDDEMEQtvIQRQIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMTRLYRARNQLKEALSRDDEQ 179
Cdd:PRK12540  98 AHLEFEE--FRAALDKLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARSKLSALLYVDGAE 165
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 29-173 2.50e-12

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 61.92  E-value: 2.50e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  29 YNKELYRFAYWLCRDPHIADDLVQETFLRAWRSLDSLLDQKAAKPWLLTILRRENArRFERKQFDYSDVENDTLVDETSH 108
Cdd:PRK09637  10 YKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDGSSIKSWLYQIANNTII-DFYRKKNRSEELPDDLLFEDEER 88

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 696249455 109 SLDDEMEQTV-IQRQIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMTRLYRARNQLKEAL 173
Cdd:PRK09637  89 EENAKKELAPcLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELL 154
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 33-177 4.22e-11

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 58.90  E-value: 4.22e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  33 LYRFAYWLCRDPHIADDLVQETFLRAWRSLDSLlDQKAAK--PWLLTI--------LRRenarRFERKQFDYSDVEND-T 101
Cdd:PRK05602  33 LLALATRMLGDPAEAEDVAQETFLRIWKQAPSW-RPGEARfdTWLHRVvlnlcydrLRR----RREVPVEDAPDVPDPaP 107

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 696249455 102 LVDETSHSLDdemEQTVIQRQIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMTRLYRARNQLKEALSRDD 177
Cdd:PRK05602 108 GPDAGLEARQ---RARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALESLLARGRRALRAQLADLP 180
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 20-170 5.68e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 58.02  E-value: 5.68e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  20 KRYEALVHVYNK---ELYRFAYWLCRDPHIADDLVQETFLRAWRSLDSLLDQKaAKPWLLTILRRENARRFeRKQFDYSD 96
Cdd:PRK12541   2 KRKQSLEEIYSEhmqDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGEE-IRPWLFTIAYNAFIDWY-RKEKKYKT 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 696249455  97 VEND----TLVDETSHSLDDEMEQTVIQRQIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMTRLYRARNQLK 170
Cdd:PRK12541  80 TTIEefhlPNVPSTEHEYFIKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKETK 157
PRK08241 PRK08241
RNA polymerase subunit sigma-70;
22-180 6.34e-11

RNA polymerase subunit sigma-70;


Pssm-ID: 236196 [Multi-domain]  Cd Length: 339  Bit Score: 59.95  E-value: 6.34e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  22 YEALVHVYNKELYRFAYWLCRDPHIADDLVQETFLRAWRSLDSLLDQKAAKPWL--------LTILRRENARRFERKQFD 93
Cdd:PRK08241  21 FAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGYDRFEGRSSLRTWLyriatnvcLDALEGRARRPLPTDLGA 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  94 YSDVENDTLV------------DETSHSLDDEMEQTVIQRQ------IA---LLSDEYREPLLLQVVMGCSGEEIAGILN 152
Cdd:PRK08241 101 PAADPVDELVerpevpwlepypDALLDPAAADPAARVVAREsvrlafVAalqHLPPRQRAVLILRDVLGWSAAEVAELLD 180

                        170       180
                 ....*....|....*....|....*...
gi 696249455 153 LNKNTVMTRLYRARNQLKEALSRDDEQL 180
Cdd:PRK08241 181 TSVAAVNSALQRARATLAERGPSAADTL 208
algU PRK11923
RNA polymerase sigma factor AlgU; Provisional
 9-174 1.53e-10

RNA polymerase sigma factor AlgU; Provisional


Pssm-ID: 171347 [Multi-domain]  Cd Length: 193  Bit Score: 57.50  E-value: 1.53e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455   9 NQVLIDMAEK--QKRYEALVHVYNKELYRFAYWLCRDPHIADDLVQETFLRAWRSLDSLLDQKAAKPWLLTILRR----- 81
Cdd:PRK11923   7 DQQLVERVQRgdKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDSAFYTWLYRIAINtaknh 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  82 --ENARRFERKQFDYSDVE----NDTLVDETS---HSLDDEMEqTVIQRQIALLSDEYREPLLLQVVMGCSGEEIAGILN 152
Cdd:PRK11923  87 lvSRGRRPPDSDVSSEDAEfydgDHALKDIESperALLRDEIE-GTVHRTIQQLPEDLRTALTLREFDGLSYEDIASVMQ 165

                        170       180
                 ....*....|....*....|..
gi 696249455 153 LNKNTVMTRLYRARNQLKEALS 174
Cdd:PRK11923 166 CPVGTVRSRIFRAREAIDKALQ 187
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 43-176 1.54e-10

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 57.23  E-value: 1.54e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  43 DPHIADDLVQETFLRAWRSLDSLLDQK-AAKPWLLTI----LRRENARRFERKQFDYSDVENDTLVDETSHSLDDE--ME 115
Cdd:PRK13919  46 DGAAAEDVVQEVFIRVWKKAKEFDPRRgSARAWLLALahhaAVDHVRRRAARPQPLEPDEREPEAFDLPGPGLDEEghLD 125

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 696249455 116 QTVIQRQIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMTRLYRARNQLKEALSRD 176
Cdd:PRK13919 126 RTRLGRALKALSPEERRVIEVLYYQGYTHREAAQLLGLPLGTLKTRARRALSRLKEVLREP 186
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 19-171 6.82e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 55.51  E-value: 6.82e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  19 QKRYEALVHVYNKELYRFAYWLCRDPHIADDLVQETFLRAWRSLDSLLDQKAAKPWLLTIL-------RRENARR---FE 88
Cdd:PRK12543   6 QEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNRPFRFWLIGLVikqihswRRKRWRRfriFE 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  89 RKQfdysDVENDTLVDETSHSLDDEMEQTVIQrQIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMTRLYRARNQ 168
Cdd:PRK12543  86 KAE----EQRKPVSIDFSEDVLSKESNQELIE-LIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAALKK 160


                 ...
gi 696249455 169 LKE 171
Cdd:PRK12543 161 LRQ 163
PRK12532 PRK12532
RNA polymerase sigma factor; Provisional
 31-175 7.71e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 171564 [Multi-domain]  Cd Length: 195  Bit Score: 55.71  E-value: 7.71e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  31 KELYRFAYWLCRD-PHIADDLVQETFLRAWRSLDSLLDQKAAKPWLLTILRRE--NARRFERKQFDYSDVENDTLVDET- 106
Cdd:PRK12532  16 KLLLHFARLQLPDhPDLAEDLVQETLLSAYSAGDSFQGRALVNSWLFAILKNKiiDALRQIGRQRKVFTLLDDELLDEAf 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455 107 ----------------------SHSLDDEMEQTVIQRQIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMTRLYR 164
Cdd:PRK12532  96 eshfsqnghwtpegqpqhwntpEKSLNNNEFQKILQSCLYNLPENTARVFTLKEILGFSSDEIQQMCGISTSNYHTIMHR 175

                        170
                 ....*....|.
gi 696249455 165 ARNQLKEALSR 175
Cdd:PRK12532 176 ARESLRQCLQI 186
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 119-169 5.65e-09

Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif.


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 50.15  E-value: 5.65e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 696249455  119 IQRQIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMTRLYRARNQL 169
Cdd:pfam08281   4 LLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK09643 PRK09643
RNA polymerase sigma factor SigM; Reviewed
 22-173 3.17e-08

RNA polymerase sigma factor SigM; Reviewed


Pssm-ID: 236604 [Multi-domain]  Cd Length: 192  Bit Score: 51.25  E-value: 3.17e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  22 YEALVHVYNKELYRFAYWLCRDPHIADDLVQETFLRAWRSLDSLLDQKAAKPWLLTI--------LRRENArrfeRKQFD 93
Cdd:PRK09643  29 FGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGDAAVSSWLHRIvvnacldrLRRAKA----RPTVP 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  94 YSDVEnDTLVDETSHSLDDEMEQTViQRQIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMTRLYRARNQLKEAL 173
Cdd:PRK09643 105 LDDVY-PVAQLERDPTARVETALAV-QRALMRLPVEQRAALVAVDMQGYSVADAARMLGVAEGTVKSRCARGRARLAELL 182
PRK12530 PRK12530
RNA polymerase sigma factor; Provisional
 32-175 1.46e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 237128 [Multi-domain]  Cd Length: 189  Bit Score: 49.38  E-value: 1.46e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  32 ELYRFAYWLCRDPHIADDLVQETFLRAWRSLDSLLDQKAAKPWLLTILR-------RENARRFERKQFDYSDVENdTLVD 104
Cdd:PRK12530  19 QMLKFATLQLKDADLAEDVVQEALVSAYKNADSFKGQSALKTWIFAILKnkiidliRYRKRFVNESELIEEDSPN-SFFD 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455 105 ETSH--------SLDDEMEQTVIQRQIALLSDEYREPLLLQ---VVM-----GCSGEEIAGILNLNKNTVMTRLYRARNQ 168
Cdd:PRK12530  98 EKGHwkpeyyepSEWQEVENTVYKEEFWLIFEACLNHLPAQqarVFMmreylELSSEQICQECDISTSNLHVLLYRARLQ 177


                 ....*..
gi 696249455 169 LKEALSR 175
Cdd:PRK12530 178 LQACLSK 184
PRK12544 PRK12544
RNA polymerase factor sigma-70;
31-174 1.60e-07

RNA polymerase factor sigma-70;


Pssm-ID: 183583 [Multi-domain]  Cd Length: 206  Bit Score: 49.41  E-value: 1.60e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  31 KELYRFAYWLCRDPHIADDLVQETFLRAWRSLDSLLDQKAAKPWLLTILR-------RENARRFERKQFDYSDVEN---D 100
Cdd:PRK12544  29 KQMIKFATLQLSDLHLAEDAVQEALIGALKNADSFAGRAAFKTWVFAILKnkiidllRQKKRHVSASSLLRDEEEEedfE 108

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455 101 TLVDETSHSLDDE-----------MEQ----TVIQRQIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMTRLYRA 165
Cdd:PRK12544 109 ELFDESGHWQKDErpqawgnpeesLEQeqfwRIFEACLDGLPAKYARVFMMREFIELETNEICHAVDLSVSNLNVLLYRA 188


                 ....*....
gi 696249455 166 RNQLKEALS 174
Cdd:PRK12544 189 RLRLRECLE 197
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 116-170 4.33e-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: 44.79  E-value: 4.33e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 696249455 116 QTVIQRQIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMTRLYRARNQLK 170
Cdd:cd06171    1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 22-178 4.55e-07

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 48.01  E-value: 4.55e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  22 YEALVHVYNKELYRFAYWLCRDPHIADDLVQETFLRAWRSLDSLLDQKAAKPWLLTILRRE--NARRFERKQFDYSDVEN 99
Cdd:PRK09640  28 YEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGKSKFKTWLYSITYNEciTQYRKERRKRRLMDALS 107

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455 100 DTLVDETSHSLDDEMEQ-TVIQRQIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMTRLYRARNQLKEALSRDDE 178
Cdd:PRK09640 108 LDPLEEASEEKAPKPEErGGLDRWLVHVNPIDREILVLRFVAELEFQEIADIMHMGLSATKMRYKRALDKLREKFAGLAE 187
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 24-173 1.02e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 46.69  E-value: 1.02e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  24 ALVHVYNKELYRF---AYWLCRDPHIADDLVQETFLRAWRSLDSLlDQK--AAKPWLLTILRRE--NARRFERKQFDYSD 96
Cdd:PRK12537  24 ALQALYQQESARLlgvARRIVRDRALAEDIVHDAFIKIWTGAASF-DPArgSARGWIYSVTRHLalNVLRDTRREVVLDD 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  97 VENDTLvdETSHSLDDEMEQTV----IQRQIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMTRLYRARNQLKEA 172
Cdd:PRK12537 103 DAEETA--QTLHEIIDDFDLWAnsgkIHRCLEQLEPARRNCILHAYVDGCSHAEIAQRLGAPLGTVKAWIKRSLKALREC 180


                 .
gi 696249455 173 L 173
Cdd:PRK12537 181 M 181
PRK12525 PRK12525
RNA polymerase sigma factor; Provisional
 15-175 2.73e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 139037 [Multi-domain]  Cd Length: 168  Bit Score: 45.32  E-value: 2.73e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  15 MAEKQKRYEALVHVYNKElYRfayWLCRD-------PHIADDLVQETFLRAWrSLDSLLDQKAAKPWLLTILRRENARRF 87
Cdd:PRK12525   1 MGQGSIKNTLIGQMFQQD-YD---WLCKKlsrqlgcPHSAEDIASETFLQVL-ALPDPASIREPRALLTTIARRLMYEGW 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  88 ERKQFDYSDVENDTLVDETSHSLDDEMEQTV-----IQRQIALLSDEYREPLLLQVVMGCSGEEIAGILNLNkntvmtrL 162
Cdd:PRK12525  76 RRQDLERAYLQSLAEAPEAVQPSPEEQWMVIetllaIDRLLDGLSGKARAAFLMSQLEGLTYVEIGERLGVS-------L 148

                        170
                 ....*....|...
gi 696249455 163 YRARNQLKEALSR 175
Cdd:PRK12525 149 SRIHQYMVEAFKC 161
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 16-178 6.02e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 44.67  E-value: 6.02e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  16 AEKQKRYEALVHVYNKE---LYRFAYWLCRDPHIADDLVQETFLRAWRSLDSLLDQKAAKPWLLTILR----------RE 82
Cdd:PRK12519  22 ALKAGQSAALGVLYDRHaglVYGLALKILGNSQEAEDLTQEIFLSLWRKSSYDPKRGSLSSYLLTLTRsraidrlrsrRS 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  83 NARRFERKQfdySDVENDTLVDETSHSLD-DEMEQTViQRQIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMTR 161
Cdd:PRK12519 102 RQRLLERWQ---QELLGEASEDTPLEQASlAERSQRV-QTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKAR 177

                        170
                 ....*....|....*..
gi 696249455 162 LYRARNQLKEALSRDDE 178
Cdd:PRK12519 178 ARQGLLKLRELLQDLLE 194
PRK12545 PRK12545
RNA polymerase factor sigma-70;
31-174 1.61e-05

RNA polymerase factor sigma-70;


Pssm-ID: 183584 [Multi-domain]  Cd Length: 201  Bit Score: 43.41  E-value: 1.61e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  31 KELYRFAYWLCRDPHIADDLVQETFLRAWRSLDSLLDQKAAKPWLLTILRRENARRFERKQFDYSDVENDTLVDETShSL 110
Cdd:PRK12545  19 HDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQSAHKTWVFGILRNKLIDTLRARQRTVNLSALDAELDGEA-LL 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455 111 DDEM------------------EQTVIQRQ---------IALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMTRLY 163
Cdd:PRK12545  98 DRELfkdnghwaahakprpwpkPETILQQQqfwtlfetcLDHLPEQIGRVFMMREFLDFEIDDICTELTLTANHCSVLLY 177

                        170
                 ....*....|.
gi 696249455 164 RARNQLKEALS 174
Cdd:PRK12545 178 RARTRLRTCLS 188
PRK12520 PRK12520
RNA polymerase sigma factor; Provisional
 33-173 2.00e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 237126 [Multi-domain]  Cd Length: 191  Bit Score: 43.18  E-value: 2.00e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  33 LYRFAYWLCRDPHIADDLVQETFLRAWRSLDSLLDQKAAKPWLLTIL-----------RRENARRFERKQFDYSDVENDT 101
Cdd:PRK12520  15 LLRFARLQLRDPALAEDAVSETLLAVLEHPERFAGQSSLKTYLVGILkhkiidairsgRREVRLSLDDADEQSDDDLFDA 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455 102 LVDETSHSLD-----DEMEQTVIQRQIALLSDEYREPL--------LLQVVMGCSGEEIAGILNLNKNTVMTRLYRARNQ 168
Cdd:PRK12520  95 LFAADGHYREppsdwGDPDAALSRREFFEVLQACVDRLpprtgrvfMMREWLELETEEICQELQITATNAWVLLYRARMR 174


                 ....*
gi 696249455 169 LKEAL 173
Cdd:PRK12520 175 LRECL 179
PRK06811 PRK06811
RNA polymerase factor sigma-70; Validated
 45-170 2.89e-05

RNA polymerase factor sigma-70; Validated


Pssm-ID: 180707 [Multi-domain]  Cd Length: 189  Bit Score: 42.62  E-value: 2.89e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  45 HIADDLVQETFLRAWRSLDSLLDQKAA-KPWLLTILRRE--NARRFERKQFDYSDVENDTLVDETS---HSLDDEMEQTV 118
Cdd:PRK06811  46 QLIEECVNDIFLSIWNNIDKFDEEKGSfKKWIAAISKYKaiDYKRKLTKNNEIDSIDEFILISEESienEIILKENKEEI 125

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 696249455 119 IqRQIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMTRLYRARNQLK 170
Cdd:PRK06811 126 L-KLINDLEKLDREIFIRRYLLGEKIEEIAKKLGLTRSAIDNRLSRGRKKLQ 176
PRK09646 PRK09646
ECF RNA polymerase sigma factor SigK;
42-173 8.42e-05

ECF RNA polymerase sigma factor SigK;


Pssm-ID: 182015 [Multi-domain]  Cd Length: 194  Bit Score: 41.58  E-value: 8.42e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  42 RDPHIADDLVQETFLRAWRSLDSL-LDQKAAKPWLLTILRR---------ENARRFERKqfdYSDVENDTLVDETSHSLD 111
Cdd:PRK09646  52 RDPGYSEETTQEVYLEVWRTASRFdPARGSALAWLLTLAHRravdrvrseQAASQREVR---YGARNVDPAFDQVAEEVE 128

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 696249455 112 DEMEQTVIQRQIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMTRLYRARNQLKEAL 173
Cdd:PRK09646 129 ARLERERVRDCLDALTDTQRESVTLAYYGGLTYREVAERLAVPLGTVKTRMRDGLIRLRDCL 190
sigI PRK09635
RNA polymerase sigma factor SigI; Provisional
 33-172 1.66e-04

RNA polymerase sigma factor SigI; Provisional


Pssm-ID: 182008 [Multi-domain]  Cd Length: 290  Bit Score: 41.11  E-value: 1.66e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  33 LYRFAYWLCRDPHIADDLVQETFLRAWRSLDSLLDQKAAkpWLLTI--------LRRENARRfERKQfDYSDVEND---- 100
Cdd:PRK09635  18 LVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVGDIDDERG--WLIVVtsrlcldhIKSASTRR-ERPQ-DIAAWHDGdasv 93

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 696249455 101 TLVDETSH-SLDDEMeQTVIQRQIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMTRLYRARNQLKEA 172
Cdd:PRK09635  94 SSVDPADRvTLDDEV-RLALLIMLERLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQLAHRARRKINES 165
PRK12542 PRK12542
RNA polymerase sigma factor; Provisional
 20-170 3.08e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183581 [Multi-domain]  Cd Length: 185  Bit Score: 39.65  E-value: 3.08e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  20 KRYEALVHVYNKELYRFAYWLCRDPHIADDLVQETFLRAWRSLDSL--LDQKAAKPWLLTILRR---ENARRFERKQFDY 94
Cdd:PRK12542   9 EKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLhsLNTQELKRYILRVAKNkaiDSYRKNKRHETFL 88

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 696249455  95 SDVENDTL--VDETSHSLDD-EMEQTVIQRQIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMTRLYRARNQLK 170
Cdd:PRK12542  89 EEYERESIeaVDENIEEWEKrKMSEVQIDTLLKELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERARKRVQ 167
PRK09648 PRK09648
RNA polymerase sigma factor ShbA;
42-175 3.90e-04

RNA polymerase sigma factor ShbA;


Pssm-ID: 236607 [Multi-domain]  Cd Length: 189  Bit Score: 39.57  E-value: 3.90e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  42 RDPHIADDLVQETFLRAWRSLDSLLDQkaAKPWL---LTILRRENA---RRFERKQFDYSDVENDTLVDETS---HSLDD 112
Cdd:PRK09648  50 RPGLSADDVAQEVCLAVITALPRYRDQ--GRPFLafvYGIAAHKVAdahRAAGRDKAVPTEEVPERPSDDAGpeeRALRS 127

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 696249455 113 EMEQTViQRQIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMTRLYRARNQLKEALSR 175
Cdd:PRK09648 128 ESSNRM-RELLDTLPEKQREILILRVVVGLSAEETAEAVGSTPGAVRVAQHRALARLRAEIEA 189
PRK12512 PRK12512
RNA polymerase sigma factor; Provisional
 47-165 2.99e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 171551 [Multi-domain]  Cd Length: 184  Bit Score: 36.98  E-value: 2.99e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  47 ADDLVQETFL------RAWrsldsllDQKAA-KPWLLTILRR---ENARRFERKQF-DYSDVEnDTLVDETSHSLDDEME 115
Cdd:PRK12512  53 AEDIVQEILLavhlkrHTW-------DPGAPfAPWLFAIARNkliDALRRRGRRVFvDIDDFA-ETLPAEPATETLPAGD 124

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 696249455 116 qtvIQRQIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMTRLYRA 165
Cdd:PRK12512 125 ---VGRHLETLPPRQRDVVQSISVEGASIKETAAKLSMSEGAVRVALHRG 171
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 47-180 6.82e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 36.02  E-value: 6.82e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  47 ADDLVQETFLRAWRSLDSlLDQKAAKP--WLLTILRRENARRFERKQFDYSDVENDTLVDETSHSLDDEMEQT----VIQ 120
Cdd:PRK12524  53 AEDVTQEAMLRLWRIAPD-WRQGEARVstWLYRVVCNLCTDRLRRRRRASVDLDDAPEPADAAPGAEEALIEGdrmrALD 131

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455 121 RQIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMTRLYRARNQLKEALSRDDEQL 180
Cdd:PRK12524 132 AALAALPERQRQAVVLRHIEGLSNPEIAEVMEIGVEAVESLTARGKRALAALLAGQRAEL 191
PRK09651 PRK09651
RNA polymerase sigma factor FecI; Provisional
 47-165 8.17e-03

RNA polymerase sigma factor FecI; Provisional


Pssm-ID: 182018 [Multi-domain]  Cd Length: 172  Bit Score: 35.56  E-value: 8.17e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  47 ADDLVQETFLRAWRSlDSLLDQKAAKPWLLTILRRENARRFERKQFDYSDVENDTLVDETSHSLDDEMEQTV-----IQR 121
Cdd:PRK09651  37 ADDIAQDTFLRVMVS-ETLSTIRDPRSFLCTIAKRVMVDLFRRNALEKAYLEMLALMPEGGAPSPEERESQLetlqlLDS 115

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 696249455 122 QIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMTRLYRA 165
Cdd:PRK09651 116 MLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKA 159
PRK06930 PRK06930
positive control sigma-like factor; Validated
 88-173 8.76e-03

positive control sigma-like factor; Validated


Pssm-ID: 180757 [Multi-domain]  Cd Length: 170  Bit Score: 35.48  E-value: 8.76e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  88 ERKQFDYSDVENDTLVDETSHSlddEMEQTVIQRQIALLSDEYREPLLLQVVMGCSGEEIAGILNLNKNTVMTRLYRAR- 166
Cdd:PRK06930  80 QRYFRSMEDLEWDIEEPESVIS---EWDKIRIEDALSVLTEREKEVYLMHRGYGLSYSEIADYLNIKKSTVQSMIERAEk 156

                         90
                 ....*....|
gi 696249455 167 ---NQLKEAL 173
Cdd:PRK06930 157 kiaRQINESL 166
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
 47-183 9.68e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 35.60  E-value: 9.68e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 696249455  47 ADDLVQETFLRAWRSLDSLLDQKAA-KPWLLTI-------LRR----ENARRFERKQFDYSDVENDTLVDETSHSLDDEM 114
Cdd:PRK12538  90 AEDVVQDTMLKVWTHRGRWQHGRAKfSTWLYRVvsnrcidLRRkprtENVDAVPEVADGKPDAVSVIERNELSDLLEAAM 169

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 696249455 115 EQTVIQRQIALLSdEYREPLllqvvmgcSGEEIAGILNLNKNTVMTRLYRARNQLKEALSRDDEQLKGA 183
Cdd:PRK12538 170 QRLPEQQRIAVIL-SYHENM--------SNGEIAEVMDTTVAAVESLLKRGRQQLRDLLRRHERDIRHA 229
 
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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