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Conserved domains on  [gi|2524879493|ref|WP_286832899|]
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MULTISPECIES: RNA polymerase sigma-70 factor [unclassified Proteiniphilum]

Protein Classification

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 22-179 3.50e-45

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: 146.55  E-value: 3.50e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  22 KAFEHIFHFYYNQVYTFVLNTLFNKTFAEDITQTVFITLWEKRETIDPDTNIAPLLYTIAKNHVYRQTEQLLRKYKYEQT 101
Cdd:TIGR02985   1 EAFEQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETLEISESIKAYLFTIVKNRCLNYLRHKQVEEKYQEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493 102 QQEIMP---EESNPEEDVNNLFLEKILSELIEKLPTARRKIFLLSRKENLSNKDIASRLNISEKTVETQIRRSLIFLNEK 178
Cdd:TIGR02985  81 LAEIEErelSEADPEEELEAKELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLRKE 160


                  .
gi 2524879493 179 L 179
Cdd:TIGR02985 161 L 161
 
Name Accession Description Interval E-value
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 22-179 3.50e-45

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: 146.55  E-value: 3.50e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  22 KAFEHIFHFYYNQVYTFVLNTLFNKTFAEDITQTVFITLWEKRETIDPDTNIAPLLYTIAKNHVYRQTEQLLRKYKYEQT 101
Cdd:TIGR02985   1 EAFEQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETLEISESIKAYLFTIVKNRCLNYLRHKQVEEKYQEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493 102 QQEIMP---EESNPEEDVNNLFLEKILSELIEKLPTARRKIFLLSRKENLSNKDIASRLNISEKTVETQIRRSLIFLNEK 178
Cdd:TIGR02985  81 LAEIEErelSEADPEEELEAKELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLRKE 160


                  .
gi 2524879493 179 L 179
Cdd:TIGR02985 161 L 161
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 13-185 5.47e-41

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: 136.66  E-value: 5.47e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  13 LRLLQEGDEKAFEHIFHFYYNQVYTFVLNTLFNKTFAEDITQTVFITLWEKRETIDPDTNIAPLLYTIAKNHVYRQteql 92
Cdd:COG1595     8 LERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDH---- 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  93 LRKYKYEQT-----QQEIMPEESNPEEDVNNLFLEKILSELIEKLPTARRKIFLLSRKENLSNKDIASRLNISEKTVETQ 167
Cdd:COG1595    84 LRKRRRRRElldelAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSR 163

                         170
                  ....*....|....*...
gi 2524879493 168 IRRSLIFLNEKLKHYLNL 185
Cdd:COG1595   164 LSRARKKLREALEEEGAL 181
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 19-181 6.52e-23

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 90.03  E-value: 6.52e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  19 GDEKAFEHIFHFYYNQVYTFVLNTLFNKTFAEDITQTVFITLWEKRETIDPDTNIAPLLYTIAKNHVYrqteQLLRKYKY 98
Cdd:PRK11924   10 GDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCY----DLLRRRRR 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  99 EQT-------QQEIMPEESNPEEDVNNLFLEKILSELIEKLPTARRKIFLLSRKENLSNKDIASRLNISEKTVETQIRRS 171
Cdd:PRK11924   86 EKAvlsddalEPEFAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRA 165

                         170
                  ....*....|
gi 2524879493 172 LIFLNEKLKH 181
Cdd:PRK11924  166 RQLLRECLEA 175
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 124-175 8.27e-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: 57.47  E-value: 8.27e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2524879493 124 ILSELIEKLPTARRKIFLLSRKENLSNKDIASRLNISEKTVETQIRRSLIFL 175
Cdd:pfam08281   3 ALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 125-172 1.18e-05

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: 41.32  E-value: 1.18e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2524879493 125 LSELIEKLPTARRKIFLLSRKENLSNKDIASRLNISEKTVETQIRRSL 172
Cdd:cd06171     4 LEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRAL 51
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 148-170 2.10e-05

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 40.59  E-value: 2.10e-05
                           10        20
                   ....*....|....*....|...
gi 2524879493  148 LSNKDIASRLNISEKTVETQIRR 170
Cdd:smart00421  19 LTNKEIAERLGISEKTVKTHLSN 41
 
Name Accession Description Interval E-value
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 22-179 3.50e-45

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: 146.55  E-value: 3.50e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  22 KAFEHIFHFYYNQVYTFVLNTLFNKTFAEDITQTVFITLWEKRETIDPDTNIAPLLYTIAKNHVYRQTEQLLRKYKYEQT 101
Cdd:TIGR02985   1 EAFEQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETLEISESIKAYLFTIVKNRCLNYLRHKQVEEKYQEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493 102 QQEIMP---EESNPEEDVNNLFLEKILSELIEKLPTARRKIFLLSRKENLSNKDIASRLNISEKTVETQIRRSLIFLNEK 178
Cdd:TIGR02985  81 LAEIEErelSEADPEEELEAKELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLRKE 160


                  .
gi 2524879493 179 L 179
Cdd:TIGR02985 161 L 161
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 13-185 5.47e-41

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: 136.66  E-value: 5.47e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  13 LRLLQEGDEKAFEHIFHFYYNQVYTFVLNTLFNKTFAEDITQTVFITLWEKRETIDPDTNIAPLLYTIAKNHVYRQteql 92
Cdd:COG1595     8 LERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDH---- 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  93 LRKYKYEQT-----QQEIMPEESNPEEDVNNLFLEKILSELIEKLPTARRKIFLLSRKENLSNKDIASRLNISEKTVETQ 167
Cdd:COG1595    84 LRKRRRRRElldelAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSR 163

                         170
                  ....*....|....*...
gi 2524879493 168 IRRSLIFLNEKLKHYLNL 185
Cdd:COG1595   164 LSRARKKLREALEEEGAL 181
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 22-179 7.02e-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: 99.73  E-value: 7.02e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  22 KAFEHIFHFYYNQVYTFVLNTLFNKTFAEDITQTVFITLWEKRETIDPDTNIAPLLYTIAKNHVYRQTEQLLRKYKYEQT 101
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2524879493 102 QQEIMPEESNPEEDVNNLFLEKILSELIEKLPTARRKIFLLSRKENLSNKDIASRLNISEKTVETQIRRSLIFLNEKL 179
Cdd:TIGR02937  81 LEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 19-181 6.52e-23

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 90.03  E-value: 6.52e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  19 GDEKAFEHIFHFYYNQVYTFVLNTLFNKTFAEDITQTVFITLWEKRETIDPDTNIAPLLYTIAKNHVYrqteQLLRKYKY 98
Cdd:PRK11924   10 GDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCY----DLLRRRRR 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  99 EQT-------QQEIMPEESNPEEDVNNLFLEKILSELIEKLPTARRKIFLLSRKENLSNKDIASRLNISEKTVETQIRRS 171
Cdd:PRK11924   86 EKAvlsddalEPEFAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRA 165

                         170
                  ....*....|
gi 2524879493 172 LIFLNEKLKH 181
Cdd:PRK11924  166 RQLLRECLEA 175
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 13-183 3.37e-19

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 80.24  E-value: 3.37e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  13 LRLLQEGDEKAFEHIFHFYYNQVYTFVLNTLFNKTFAEDITQTVFITLWEKRETIDPDTNIAPLLYTIAKNHVYRQteql 92
Cdd:PRK09652    1 VERVQRGDRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRGGAAFYTWLYRIARNTAINY---- 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  93 LRKYKYEQTQQEIMPEE-------------SNPEEDVNNLFLEKILSELIEKLPTARRKIFLLSRKENLSNKDIASRLNI 159
Cdd:PRK09652   77 LRKQGRRPPASDVDAEEaedfdladalrdiSTPENELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGC 156

                         170       180
                  ....*....|....*....|....
gi 2524879493 160 SEKTVETQIRRSLIFLNEKLKHYL 183
Cdd:PRK09652  157 PIGTVRSRIFRAREALRAKLQPLL 180
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 11-181 7.85e-17

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 74.35  E-value: 7.85e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  11 RTLRLLQEGDEKAFEHIFHFYYNQVYTFVLNTLFNKTFAEDITQTVFITLWEKRETIDPDTNIAPLLYTIAKNhvyrQTE 90
Cdd:PRK09641    7 RLIKQVKKGDQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINRKFSTWLYRIATN----LTI 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  91 QLLRKYKYE-------------QTQQEIMPEESNPEEDVNNLFLEKILSELIEKLPTARRKIFLLSRKENLSNKDIASRL 157
Cdd:PRK09641   83 DRLRKRKPDyyldaevagteglTMYSQLAADDALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYIEDLSLKEISEIL 162

                         170       180
                  ....*....|....*....|....
gi 2524879493 158 NISEKTVETQIRRSLIFLNEKLKH 181
Cdd:PRK09641  163 DLPVGTVKTRIHRGREALRKQLRH 186
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 16-183 1.72e-14

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 68.16  E-value: 1.72e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  16 LQEGDEKAFEHIFHFYYNQVYTFVLNTLFNKTFAEDITQTVFITLWEKrETIDPDT-NIAPLLYTIAKNHVYRQTEQLLR 94
Cdd:PRK12519   23 LKAGQSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRK-SSYDPKRgSLSSYLLTLTRSRAIDRLRSRRS 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  95 KYKYEQTQQEIMPEESNPEEDVNNLFLEKILSEL---IEKLPTARRKIFLLSRKENLSNKDIASRLNISEKTVETQIRRS 171
Cdd:PRK12519  102 RQRLLERWQQELLGEASEDTPLEQASLAERSQRVqtaLAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKARARQG 181

                         170
                  ....*....|..
gi 2524879493 172 LIFLNEKLKHYL 183
Cdd:PRK12519  182 LLKLRELLQDLL 193
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 1-180 1.76e-13

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 65.15  E-value: 1.76e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493   1 MKNKTIDINSrtlrllQEGDEKAFEHIFHFYYNQVYTFVLNTLFNKTFAEDITQTVFITLWEKRETIDPDTNIAPLLYTI 80
Cdd:PRK09415    1 MEELTIEAFE------IEDKEDLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGKSSLKTWLYRI 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  81 AKNHV--YRQTEQLLRKYKYEQTQQEIMPEESNPEEDVNNLFLEKILSELIEKLPTARRKIFLLSRKENLSNKDIASRLN 158
Cdd:PRK09415   75 AINHCkdYLKSWHNKKVIVTEDIFTYMESQKESVEEEVIQNAEDERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTG 154

                         170       180
                  ....*....|....*....|..
gi 2524879493 159 ISEKTVETQIRRSLIFLNEKLK 180
Cdd:PRK09415  155 VNENTVKTRLKKAKELLKKGLE 176
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 17-184 3.93e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 64.71  E-value: 3.93e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  17 QEGDEKAFEHIFHFYYNQVYTFVLNTLFNKTFAEDITQTVFITLWEKRETIDPDTNIAPLLYTIAKN----HVYRQTEQL 92
Cdd:PRK12513   21 RAGDAAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPRARFRTWLYQIARNllidHWRRHGARQ 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  93 LRKYKYEQTQQEIMPEESNPEEDVNNLFLEKILSELIEKLPTARRKIFLLSRKENLSNKDIASRLNISEKTVETQIRRSL 172
Cdd:PRK12513  101 APSLDADEQLHALADDGAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREHGDLELEEIAELTGVPEETVKSRLRYAL 180

                         170
                  ....*....|..
gi 2524879493 173 iflnEKLKHYLN 184
Cdd:PRK12513  181 ----QKLRELLA 188
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 20-177 2.40e-12

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 61.89  E-value: 2.40e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  20 DEKAFEHIFHFYYNQVYTFVLNTLFNKTFAEDITQTVFITLWekRETIDPDTNIAPLLYTIAKNHVYR--QTEQLLRKYK 97
Cdd:PRK09639    1 SDETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLY--RSDFKGIENEKGWLIKSARNVAYNylRSEKRRRARI 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  98 YEQTQQEIMPEESNPEEDVNNLFLEKILSELIEKLpTARRKIFLLSRKENLSNKDIASRLNISEKTVETQIRRSLIFLNE 177
Cdd:PRK09639   79 LGEFQWQEVDNEPSPEEIWIRKEEITKVQEVLAKM-TERDRTVLLLRFSGYSYKEIAEALGIKESSVGTTLARAKKKFRK 157
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 124-175 8.27e-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: 57.47  E-value: 8.27e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2524879493 124 ILSELIEKLPTARRKIFLLSRKENLSNKDIASRLNISEKTVETQIRRSLIFL 175
Cdd:pfam08281   3 ALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK12531 PRK12531
RNA polymerase sigma factor; Provisional
 20-184 3.22e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 105726 [Multi-domain]  Cd Length: 194  Bit Score: 59.56  E-value: 3.22e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  20 DEKAFEHIFHFYYNQVYTFVLNTLFNKTFAEDITQTVFITLWEKRETIDPD-TNIAPLLYTIAKNHVYrqteQLLRKYKY 98
Cdd:PRK12531   25 DKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQkSALSTWIYTIIRNLCF----DLLRKQKG 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  99 EQTQ---QEIMPEESNPEEDVNNL-----FLEKILSELIEKLPTARRKIFLLSRKENLSNKDIASRLNISEKTVETQIRR 170
Cdd:PRK12531  101 KDLHihaDDIWPSDYYPPDLVDHYspeqdMLKEQVMKFLDRLPKAQRDVLQAVYLEELPHQQVAEMFDIPLGTVKSRLRL 180

                         170
                  ....*....|....
gi 2524879493 171 SLiflnEKLKHYLN 184
Cdd:PRK12531  181 AV----EKLRHSMD 190
PRK12528 PRK12528
RNA polymerase sigma factor; Provisional
 49-165 2.13e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 171561 [Multi-domain]  Cd Length: 161  Bit Score: 56.78  E-value: 2.13e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  49 AEDITQTVFITLWEKRET---IDPDTniapLLYTIAK----NHVYRQteQLLRKYkYEQTQQeiMPEESNPEEDVNNLFL 121
Cdd:PRK12528   31 AADLAQDTFVKVLVARETaqiIEPRA----FLTTIAKrvlcNHYRRQ--DLERAY-LEALAQ--LPERVAPSEEERAIIL 101

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2524879493 122 EKI--LSELIEKLPTARRKIFLLSRKENLSNKDIASRLNISEKTVE 165
Cdd:PRK12528  102 ETLveLDQLLDGLPPLVKRAFLLAQVDGLGYGEIATELGISLATVK 147
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 22-173 3.09e-10

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: 56.18  E-value: 3.09e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  22 KAFEHIFHFYYNQVYTFVLNTLFNKTFAEDITQTVFITLWEKRETIDPDTNIAPLLYTIAKNHVYRQteqlLRKYKYEQT 101
Cdd:TIGR02989   1 KAFVRLLTRHERALRAFVRSLVADRDDVDDVLQETFVVAWRKFDQFDPGTNFVAWARGIARNKVLNY----RRKLGRDRL 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493 102 Q-----QEIMPEESNPEEDVNNLFLEKILSELIEKLPTARRKIFLLSRKENLSNKDIASRlniSEKTVET------QIRR 170
Cdd:TIGR02989  77 VfdddlLEALAAEAEPTEAERLSDDRQALEGCLEKLPERQRELLDLRYQRGQKATALAEQ---TGRTVNAvykalqRIRV 153


                  ...
gi 2524879493 171 SLI 173
Cdd:TIGR02989 154 SLR 156
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 25-180 1.37e-09

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 54.61  E-value: 1.37e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  25 EHIFHFYYNQVYTFVLNTLFNKTFAEDITQTVFITLWEKRETIDPDTNIAPLLYTIAKNHV---YRQteqllrkykyEQT 101
Cdd:PRK09637    4 ESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDGSSIKSWLYQIANNTIidfYRK----------KNR 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493 102 QQEIMPEESNPEEDVNNLFLEKI---LSELIEKLPTARRKIFLLSRKENLSNKDIASRLNISEKTVETQIRRSliflNEK 178
Cdd:PRK09637   74 SEELPDDLLFEDEEREENAKKELapcLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRG----RVK 149


                  ..
gi 2524879493 179 LK 180
Cdd:PRK09637  150 LK 151
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
 7-180 2.52e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 54.86  E-value: 2.52e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493   7 DINSRTLRLLQEGDEKAFEHIFHFYYNQVYTFVLNTLFNKTFAEDITQTVFITLWEKRETIDPD-TNIAPLLYTIAKNHV 85
Cdd:PRK12538   48 DEDEELLDRLATDDEAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGrAKFSTWLYRVVSNRC 127

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  86 YrqteQLLRKYKYEQTqqEIMPEESNPEEDVNNLFLEKILSELIE----KLPTARRKIFLLSRKENLSNKDIASRLNISE 161
Cdd:PRK12538  128 I----DLRRKPRTENV--DAVPEVADGKPDAVSVIERNELSDLLEaamqRLPEQQRIAVILSYHENMSNGEIAEVMDTTV 201

                         170
                  ....*....|....*....
gi 2524879493 162 KTVETQIRRSLIFLNEKLK 180
Cdd:PRK12538  202 AAVESLLKRGRQQLRDLLR 220
PRK12526 PRK12526
RNA polymerase sigma factor; Provisional
 20-179 1.15e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 237127 [Multi-domain]  Cd Length: 206  Bit Score: 52.50  E-value: 1.15e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  20 DEKAFEHIFHFYYNQVYTFVLNTLFNKTFAEDITQTVFITLWEKRETIDPDTNIAPL-LYTIAKNHVYrqteQLLRKYKY 98
Cdd:PRK12526   36 DKQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKGAATTwVYTVMRNAAF----DMLRKIKA 111

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  99 EQTQ---------QEIMPEESNPEEDVNNLFLEKILSELIEKLPTARRKIFLLSRKENLSNKDIASRLNISEKTVETQIR 169
Cdd:PRK12526  112 KKEQnlgddiwpiEQALAESQSESEEFSDHLMDKQILSYIEKLPEAQQTVVKGVYFQELSQEQLAQQLNVPLGTVKSRLR 191

                         170
                  ....*....|
gi 2524879493 170 RSLIFLNEKL 179
Cdd:PRK12526  192 LALAKLKVQM 201
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 19-179 1.60e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 51.75  E-value: 1.60e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  19 GDEKAFEHIFHFYYNQVYTFVLNTLFNKTFAEDITQTVFITLWEKRETID-PDTNIAPLLYTIAKNHVYRQteqlLRKYK 97
Cdd:PRK12514   16 GDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAvSGLSPMTWLITIARNHAIDR----LRARK 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  98 YEQTQ----QEIMPEESNPEEDVNNLFLEKILSELIEKLPTARRKIFLLSRKENLSNKDIASRLNISEKTVETQIRRSLI 173
Cdd:PRK12514   92 AVAVDideaHDLADPSPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMRTWLRRSLL 171


                  ....*.
gi 2524879493 174 FLNEKL 179
Cdd:PRK12514  172 KLRECL 177
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 13-168 2.26e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 51.66  E-value: 2.26e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  13 LRLLQEGDEKAFEHIFHFYYNQVYTFVLNTLFNKTFAEDITQTVFITLWEKRETIDPDTNIAPLLYTIAKnhvyRQTEQL 92
Cdd:PRK12515   13 LARIAQGDRTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGRSQVSTWLLSIAR----FKALSA 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  93 LRKYKYEQTQQE----IMPEESNPEEDVNNLFLEKILSELIEKLPTARRKIFLLSRKENLSNKDIASRLNISEKTVETQI 168
Cdd:PRK12515   89 LRRRKHEEIDDEaaaaIEDGADTPEVALQKSDTSAALRACLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKTRM 168
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 17-180 3.60e-08

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 50.79  E-value: 3.60e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  17 QEGDEKAFEHIFHFYYNQVYTFVLNTLFNKTFAEDITQTVFITLWEKRETIDPDTNIAPLLYTIAKnhvyRQTEQLLRKY 96
Cdd:PRK09638   13 KKGDDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGRSKFSTWLISIAS----RLYKDHLRKQ 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  97 KYEQTQQEIMPEESNPEEDVN----NLFLEKILsELIEKLPTARRKIFLLSRKENLSNKDIASRLNISEKTVETQIRRSL 172
Cdd:PRK09638   89 KREKLRLQRAKEETLRKEKWEaaikGAEWSEML-DALSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTVKSRVHHGI 167


                  ....*...
gi 2524879493 173 IFLNEKLK 180
Cdd:PRK09638  168 KQLRKEWG 175
PRK12522 PRK12522
RNA polymerase sigma factor; Provisional
 21-184 4.18e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 183571 [Multi-domain]  Cd Length: 173  Bit Score: 50.64  E-value: 4.18e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  21 EKAFEHIFHFYYNQVYTFVLNTLFNKTFAEDITQTVFITLWEKRETIDPDTNIAPLLYTIAKNHVY------RQTEQLLR 94
Cdd:PRK12522    2 EEKVEELIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVENYKKWITTICVRTFYdfyrkkKRWKDRIL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  95 KYKYEQTQQEIM-PEESNPEEDVNNLFLEKILSELIEKLPTARRKIFLLSRKENLSNKDIASRLNISEKTVETQIRRSLI 173
Cdd:PRK12522   82 DLFHKEDGGEIEfADDVNISEEFIQKVEAEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKK 161

                         170
                  ....*....|.
gi 2524879493 174 FLNEKLKHYLN 184
Cdd:PRK12522  162 QMREHLEGFVH 172
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 16-178 5.65e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 50.12  E-value: 5.65e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  16 LQEGDEKAFEHIFHFYYNQVYTFVLNTLFNKTFAEDITQTVFITLWEKRETIDPDTNIAPLLYTIAKNHVYRQTEQLLRK 95
Cdd:PRK12543    1 MLSGDQEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNRPFRFWLIGLVIKQIHSWRRKRWRR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  96 YKYEQTQQEIMPEES-NPEEDVNNLFLEKILSELIEKLPTARRKIFLLSRKENLSNKDIASRLNISEKTVETQIRRSLIF 174
Cdd:PRK12543   81 FRIFEKAEEQRKPVSiDFSEDVLSKESNQELIELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAALKK 160


                  ....
gi 2524879493 175 LNEK 178
Cdd:PRK12543  161 LRQK 164
PRK12512 PRK12512
RNA polymerase sigma factor; Provisional
 49-180 5.74e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 171551 [Multi-domain]  Cd Length: 184  Bit Score: 50.47  E-value: 5.74e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  49 AEDITQTVFITLWEKRETIDPDTNIAPLLYTIAKNHVYrqteQLLRKYKYEQTQQ-----EIMPEESnPEEDVNNLFLEK 123
Cdd:PRK12512   53 AEDIVQEILLAVHLKRHTWDPGAPFAPWLFAIARNKLI----DALRRRGRRVFVDiddfaETLPAEP-ATETLPAGDVGR 127

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2524879493 124 ILseliEKLPTARRKIFLLSRKENLSNKDIASRLNISEKTVETQIRRSLIFLNEKLK 180
Cdd:PRK12512  128 HL----ETLPPRQRDVVQSISVEGASIKETAAKLSMSEGAVRVALHRGLAALAAKFR 180
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 17-172 1.10e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 49.33  E-value: 1.10e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  17 QEGDEKAFEHIFHFYYNQVYTfVLNTLFNKTFAEDITQTVFITLWEKRETIDPDTNIAPLLYTIAKNHVYRQTEQLL-RK 95
Cdd:PRK12518    6 QRGDRQSFRQLYRRYQQKVRS-TLYQLCGRELLDDLVQEVFLRVWKGLPKLRNPAYFSTWLYRITWNVATDARRQFAqRP 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  96 YKYEQTQQEIMPEESNPEEDVNNLFLEKILSELIEKLPTARRKIFLLSRKENLSNKDIASRLNISEKTVETQI---RRSL 172
Cdd:PRK12518   85 SRIQDDSLNDQPSRPSDTPDLMQLHYQDLVQQGLQTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRLfyaRRQL 164
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 127-179 2.48e-07

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: 47.58  E-value: 2.48e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2524879493 127 ELIEKLPTAR-RKIFLLSRkENLSNKDIASRLNISEKTVETQIRRslIFlnEKL 179
Cdd:COG2197    64 EALRRLLTPReREVLRLLA-EGLSNKEIAERLGISERTVKTHVSN--IL--RKL 112
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 13-180 4.35e-07

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 47.99  E-value: 4.35e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  13 LRLLQEGDEKAFEHIFHFYYNQVYTFVLNTLFNKTFAEDITQTVFITLWEKRETIDPDTNIA-PLLYTIAK----NHVYR 87
Cdd:PRK13919   14 LALVARGEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRRGSArAWLLALAHhaavDHVRR 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  88 QteqllrkykyEQTQQEIMPEESNPE---------EDVNNLFLEKILSELIEKLPTARRKIFLLSRkENLSNKDIASRLN 158
Cdd:PRK13919   94 R----------AARPQPLEPDEREPEafdlpgpglDEEGHLDRTRLGRALKALSPEERRVIEVLYY-QGYTHREAAQLLG 162

                         170       180
                  ....*....|....*....|..
gi 2524879493 159 ISEKTVETQIRRSLIFLNEKLK 180
Cdd:PRK13919  163 LPLGTLKTRARRALSRLKEVLR 184
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 31-87 4.70e-07

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


Pssm-ID: 427998 [Multi-domain]  Cd Length: 71  Bit Score: 45.27  E-value: 4.70e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2524879493  31 YYNQVYTFVLNTLFNKTFAEDITQTVFITLWEKRETIDPDTNIAPL--LYTIAKNHVYR 87
Cdd:pfam04542   5 YLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFStwLYTIIRNAIID 63
PRK09651 PRK09651
RNA polymerase sigma factor FecI; Provisional
 49-165 1.00e-06

RNA polymerase sigma factor FecI; Provisional


Pssm-ID: 182018 [Multi-domain]  Cd Length: 172  Bit Score: 46.73  E-value: 1.00e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  49 AEDITQTVF--ITLWEKRETI-DPDTniapLLYTIAKnhvyRQTEQLLRKYKYEQTQQEI---MPEESNPEEDVNNLFLE 122
Cdd:PRK09651   37 ADDIAQDTFlrVMVSETLSTIrDPRS----FLCTIAK----RVMVDLFRRNALEKAYLEMlalMPEGGAPSPEERESQLE 108

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 2524879493 123 --KILSELIEKLPTARRKIFLLSRKENLSNKDIASRLNISEKTVE 165
Cdd:PRK09651  109 tlQLLDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVK 153
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 108-184 1.07e-06

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: 47.13  E-value: 1.07e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2524879493 108 EESNPEEDVNNLFLEKILSELIEKLPTARRKIFLLSRKENLSNKDIASRLNISEKTVEtQIRRSLIflnEKLKHYLN 184
Cdd:COG1191   163 ESGDPEEELEHEELREALAEAIEQLPERERLVLSLYYFEELTLKEIAEVLGVSESRVS-RLHKKAL---ARLREYLK 235
PRK12539 PRK12539
RNA polymerase sigma factor SigF;
49-172 1.27e-06

RNA polymerase sigma factor SigF;


Pssm-ID: 237132 [Multi-domain]  Cd Length: 184  Bit Score: 46.65  E-value: 1.27e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  49 AEDITQTVFITLWEKRETIDPDTNIAPLLYTIAK----NHVyRQTEQLLRKYKYEQTqQEIMPEESNPEEDvNNLFLEKI 124
Cdd:PRK12539   52 AEDLVQEALMAIHTRRHTYDPEQPLTPWVYAIARykliDHL-RRTRASLADVPIDDA-DELVAHDDHAAVE-STLDLGRL 128

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 2524879493 125 LSELIEKLPTARRKIFLlsrkENLSNKDIASRLNISEKTVETQIRRSL 172
Cdd:PRK12539  129 LARLPEKMRLAIQAVKL----EGLSVAEAATRSGMSESAVKVSVHRGL 172
PRK06811 PRK06811
RNA polymerase factor sigma-70; Validated
 16-171 3.21e-06

RNA polymerase factor sigma-70; Validated


Pssm-ID: 180707 [Multi-domain]  Cd Length: 189  Bit Score: 45.32  E-value: 3.21e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  16 LQEGDEKAFEHIFHFYYNQVY---TFVLNTLFNKTFAEDITQTVFITLWEKRETIDPD-TNIAPLLYTIAKNHVYRQTEQ 91
Cdd:PRK06811   12 LKKKNEKALEFIVDTYGNLVKkivHKVLGTVNYSQLIEECVNDIFLSIWNNIDKFDEEkGSFKKWIAAISKYKAIDYKRK 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  92 LLRKYKYEQTQQEIMPEESNPEEDVNNLFLEKILSELIEKLPTARRKIFLLSRKENLSNKDIASRLNISEKTVETQIRRS 171
Cdd:PRK06811   92 LTKNNEIDSIDEFILISEESIENEIILKENKEEILKLINDLEKLDREIFIRRYLLGEKIEEIAKKLGLTRSAIDNRLSRG 171
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 31-172 4.82e-06

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 44.77  E-value: 4.82e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  31 YYNQVYTFVLNTLFNKTFAEDITQTVFITLWEkRETIDPDTNIAPLLYTIA--------KNHVYRQTEQLlrkykyEQTQ 102
Cdd:PRK12527    4 YYRELVRFLSARLGNRQAAEDVAHDAYLRVLE-RSSSAQIEHPRAFLYRTAlnlvvdrhRRHRVRQAEPL------EVLD 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493 103 QEIMPEESNPEEDVNNLFLEKILSELIEKLPTARRKIFLLSRKENLSNKDIASRLNISEKTVETQIRRSL 172
Cdd:PRK12527   77 EEERLHSPSPQTRLDLGQRLALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAM 146
PRK12534 PRK12534
RNA polymerase sigma factor; Provisional
 7-172 5.32e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183576 [Multi-domain]  Cd Length: 187  Bit Score: 45.05  E-value: 5.32e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493   7 DINSRTLRLLQEGDEKAFEHIFHFYYNQVYTFVLNTLFNKTFAEDITQTVFITLWEKRETIDPDTNIA-PLLYTIAKNHV 85
Cdd:PRK12534   10 DETGRLLTATAGGDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRARGlTWLAMIARNKA 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  86 --YRQTEQLLRKYKYEQTQQEIMPEESNPEEDVNNLFLEKILSELIEKLPTARRKIFLLSRKENLSNKDIASRLNISEKT 163
Cdd:PRK12534   90 idHLRANAPQRRNVALDDAGELRAADASPLERTERASTRRRIDHCLAELEPPRSELIRTAFFEGITYEELAARTDTPIGT 169


                  ....*....
gi 2524879493 164 VETQIRRSL 172
Cdd:PRK12534  170 VKSWIRRGL 178
PRK12547 PRK12547
RNA polymerase sigma factor; Provisional
 38-180 5.93e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 139056 [Multi-domain]  Cd Length: 164  Bit Score: 44.48  E-value: 5.93e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  38 FVLNTLFNKTFAEDITQTVFITLWEKRETIDPDTNIAPLLYTIAKNHVYRQteqlLRKYKYE-QTQQEIMPEE-SNPEED 115
Cdd:PRK12547   22 FAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGTNLKAWLFTILRNEFYSQ----MRKRGREvQDSDGVFTARvAVHPAQ 97

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2524879493 116 VNNLFLEKILSELiEKLPTARRKIFLLSRKENLSNKDIASRLNISEKTVETQIRRSLIFLNEKLK 180
Cdd:PRK12547   98 YGSLDLQDFKKAL-NLLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARNRLQELLK 161
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
 49-173 8.07e-06

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 43.91  E-value: 8.07e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  49 AEDITQTVFITLWEKRETIDPDTNIApLLYTIAKN----HVYRQTEQLlrKYKYEQ------TQQEIMPEESNPEEDVnn 118
Cdd:PRK07037   25 AEDVVQDAFVKLVEAPNQDAVKQPVA-YLFRIVRNlaidHYRRQALEN--KYHGDEedgldvPSPEASPEAALINRDT-- 99

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2524879493 119 lfLEKIlSELIEKLPTARRKIFLLSRKENLSNKDIASRLNISEKTVETQIRRSLI 173
Cdd:PRK07037  100 --LRHV-ADALSELPARTRYAFEMYRLHGETQKDIARELGVSPTLVNFMIRDALV 151
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 125-172 1.18e-05

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: 41.32  E-value: 1.18e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2524879493 125 LSELIEKLPTARRKIFLLSRKENLSNKDIASRLNISEKTVETQIRRSL 172
Cdd:cd06171     4 LEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRAL 51
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 49-180 1.35e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 43.80  E-value: 1.35e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  49 AEDITQTVFITLWEKRETIDPDTNIAPLLYTIAKNHVYRQteqlLRKYKYEQTQQEIMPEES---NPEEdVNNLFLEKIL 125
Cdd:PRK12516   37 ADDLVQDTIMKAWAKQDHFEVGTNMKAWLFTILRNEFYSQ----MRKRGREVQDTDGMFTEQlavHPSQ-YGTLDLQDFR 111

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2524879493 126 SELiEKLPTARRKIFLLSRKENLSNKDIASRLNISEKTVETQIRRSLIFLNEKLK 180
Cdd:PRK12516  112 AAL-DQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQRLQEILQ 165
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 11-177 1.49e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 43.61  E-value: 1.49e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  11 RTLRLLQEGDEKAFEHIFHFYYNQVYTFVLNTLFNKTFAEDITQTVFITLWEKRETIDPDTNIAP-LLYTIAKNHVYrqt 89
Cdd:PRK12537   12 ACLLACARGDRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPARGSARgWIYSVTRHLAL--- 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  90 eQLLRKYKYE-QTQQEIMPEESNPEEDVNNLFLEKILSEL---IEKLPTARRKIFLLSRKENLSNKDIASRLNISEKTVE 165
Cdd:PRK12537   89 -NVLRDTRREvVLDDDAEETAQTLHEIIDDFDLWANSGKIhrcLEQLEPARRNCILHAYVDGCSHAEIAQRLGAPLGTVK 167

                         170
                  ....*....|..
gi 2524879493 166 TQIRRSLIFLNE 177
Cdd:PRK12537  168 AWIKRSLKALRE 179
Sigma70_ECF pfam07638
ECF sigma factor; These proteins are probably RNA polymerase sigma factors belonging to the ...
 10-184 1.70e-05

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: 43.18  E-value: 1.70e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  10 SRTLRLLQEGDEKAFEHIFHFYYNQVYTFVLNTLFNKTFAEDITQTV-----FITLWEKRETIDPD------TNIAPLLY 78
Cdd:pfam07638   5 TQLLQQVKDGDAAATEQLLPLVYDELRRLAGSKLQNERRGHTLQPTAlvheaFVRLVDTEDFPDWSgrghffAAAAEAMR 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  79 TIAKNHVYRQTEQllrKYKYEQTQQEIMPEESNPEEDVNNLFLEkiLSELIEKL---PTARRKIFLLSRKENLSNKDIAS 155
Cdd:pfam07638  85 RILIDHARRRQRQ---KRGGDVQRRELDEVVDNGDSPNPDLLLD--LDEALEQLfslSPRQARLVELRFFAGLSNDEIAE 159

                         170       180
                  ....*....|....*....|....*....
gi 2524879493 156 RLNISEKTVEtqirRSLIFLNEKLKHYLN 184
Cdd:pfam07638 160 RLGVSERTVE----RNWALARAWLHRELR 184
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
119-170 1.75e-05

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 43.59  E-value: 1.75e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2524879493 119 LFLEKILSELIEKLPTARRKIFLLSRKE---------NLSNKDIASRLNISEKTVETQIRR 170
Cdd:COG2771   105 LLALALAALLLAALARLLARAPGLTPRErevlrllaeGLTLKEIARILGISERTVRTHLKR 165
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 148-170 2.10e-05

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 40.59  E-value: 2.10e-05
                           10        20
                   ....*....|....*....|...
gi 2524879493  148 LSNKDIASRLNISEKTVETQIRR 170
Cdd:smart00421  19 LTNKEIAERLGISEKTVKTHLSN 41
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
49-164 2.88e-05

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 42.76  E-value: 2.88e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  49 AEDITQTVFITLWEKRETI-DPDTNIAPLLYTIAKNHVYRQTEQllRKYKYEQTQQEIMPEESNPEEDVNNLFLEKIL-S 126
Cdd:PRK09645   36 AEDVVQETLLRAWQHPEVLaDTGRSARAWLFTVARNLVIDERRS--ARARPVEGGDDVLGVPEQSAPDEVDRALDRLLvA 113

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 2524879493 127 ELIEKLPTARRKIFLLSRKENLSNKDIASRLNISEKTV 164
Cdd:PRK09645  114 DALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTV 151
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 25-170 3.91e-05

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 42.17  E-value: 3.91e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  25 EHIFHFYYNQVYTFVLNTLFNKTFAEDITQTVFITLWEKRETIDpDTNIAPLLYTIAKnHVYRQTEQLLRKYKYEQTQQE 104
Cdd:PRK09644    4 EEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYD-NQKVKPWLFKVAY-HTFIDFVRKEKKVSFVGTDEI 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2524879493 105 IMPEESNPEEDVNNLFLEKILSELIEKLPTARRKIFLLSRKENLSNKDIASRLNISEKTVETQIRR 170
Cdd:PRK09644   82 EAIQAESTEEYVVAKNSYEKLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFR 147
MalT COG2909
ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];
146-179 3.99e-05

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


Pssm-ID: 442153 [Multi-domain]  Cd Length: 184  Bit Score: 42.38  E-value: 3.99e-05
                          10        20        30
                  ....*....|....*....|....*....|....
gi 2524879493 146 ENLSNKDIASRLNISEKTVETQIRRslifLNEKL 179
Cdd:COG2909   136 EGLSNKEIAERLFISVNTVKTHLRN----IYRKL 165
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 148-179 4.82e-05

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


Pssm-ID: 443623 [Multi-domain]  Cd Length: 196  Bit Score: 42.01  E-value: 4.82e-05
                          10        20        30
                  ....*....|....*....|....*....|..
gi 2524879493 148 LSNKDIASRLNISEKTVEtqIRRSLIFlnEKL 179
Cdd:COG4566   153 LSNKQIARELGISPRTVE--VHRANVM--EKL 180
PRK12529 PRK12529
RNA polymerase sigma factor; Provisional
 49-173 5.88e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183574 [Multi-domain]  Cd Length: 178  Bit Score: 41.84  E-value: 5.88e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  49 AEDITQTVFITLWEKRETIDPDTNIAPLLY-TIAKNHV---YRQTEQLLRKYkYEQTQQeiMPEESNPEEDVNNLFLEKi 124
Cdd:PRK12529   42 ADDLAHDIFLRILASRDGGQREAIRQPRAYlARIANCVlvsWRRRQSLELAW-LEALAT--LPEPLHPSPEQQSVILET- 117

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2524879493 125 LSELIEKLPTAR---RKIFLLSRKENLSNKDIASRLNISEKTVETQIRRSLI 173
Cdd:PRK12529  118 LHEIDALLDTLRprvKQAFLMATLDGMKQKDIAQALDIALPTVKKYIHQAYV 169
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 21-170 6.16e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 41.46  E-value: 6.16e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  21 EKAFEHIFHFYYNQVYTFVLNTLFNKTFAEDITQTVFITLWEKRETIDPDtNIAPLLYTIAKNHV---YRQTeqllRKYK 97
Cdd:PRK12541    4 KQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGE-EIRPWLFTIAYNAFidwYRKE----KKYK 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2524879493  98 YEQTQQEIMPEESNPEEDVnnLFLEKILSEL--IEKLPTARRKIFLLSRKENLSNKDIASRLNISEKTVETQIRR 170
Cdd:PRK12541   79 TTTIEEFHLPNVPSTEHEY--FIKHEIASWLdsLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHR 151
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 146-172 3.23e-04

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


Pssm-ID: 444607 [Multi-domain]  Cd Length: 76  Bit Score: 37.63  E-value: 3.23e-04
                          10        20
                  ....*....|....*....|....*..
gi 2524879493 146 ENLSNKDIASRLNISEKTVETQIRRSL 172
Cdd:COG5905    26 EGLTNKEIARQLFISEKTVKNHVSNIL 52
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 20-180 5.07e-04

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 39.15  E-value: 5.07e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  20 DEKAFEHIFHFYYNQVYTFVLNTLFNKTFAEDITQTVFITLWEKRETIDPDTNIAPLLYTIAKNHVYRQTEQLLRKyKYE 99
Cdd:PRK09640   24 VTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGKSKFKTWLYSITYNECITQYRKERRK-RRL 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493 100 QTQQEIMPEESNPEEDVNNLFLEKILSELIEKLPTARRKIFLLSRKENLSNKDIASRLNISEKTVETQIRRSLIFLNEKL 179
Cdd:PRK09640  103 MDALSLDPLEEASEEKAPKPEERGGLDRWLVHVNPIDREILVLRFVAELEFQEIADIMHMGLSATKMRYKRALDKLREKF 182


                  .
gi 2524879493 180 K 180
Cdd:PRK09640  183 A 183
GerE pfam00196
Bacterial regulatory proteins, luxR family;
148-170 5.22e-04

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 36.79  E-value: 5.22e-04
                          10        20
                  ....*....|....*....|...
gi 2524879493 148 LSNKDIASRLNISEKTVETQIRR 170
Cdd:pfam00196  18 KSNKEIADELGISEKTVKVHRSN 40
PRK12542 PRK12542
RNA polymerase sigma factor; Provisional
 20-171 5.30e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183581 [Multi-domain]  Cd Length: 185  Bit Score: 39.26  E-value: 5.30e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  20 DEKAFEHIFHFYYNQVYTFVLNTLFNKTFAEDITQTVFITLWEKRETIDP--DTNIAPLLYTIAKNHV---YRQT---EQ 91
Cdd:PRK12542    7 DYEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSlnTQELKRYILRVAKNKAidsYRKNkrhET 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  92 LLRKYKYEQTQQeimpEESNPEEDVNNLFLEKILSELIEKLPTARRKIFLLSRKENLSNKDIASRLNISEKTVETQIRRS 171
Cdd:PRK12542   87 FLEEYERESIEA----VDENIEEWEKRKMSEVQIDTLLKELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERA 162
PRK10403 PRK10403
nitrate/nitrite response regulator protein NarP;
114-176 5.92e-04

nitrate/nitrite response regulator protein NarP;


Pssm-ID: 182431 [Multi-domain]  Cd Length: 215  Bit Score: 39.07  E-value: 5.92e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2524879493 114 EDVNNLFLEKILSELIE---KLPTARRKIFLLSRKENLSNKDIASRLNISEKTVETQIRRSLIFLN 176
Cdd:PRK10403  132 ERVNQYLREREMFGAEEdpfSVLTERELDVLHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKLN 197
PRK12536 PRK12536
RNA polymerase sigma factor; Provisional
 50-180 6.30e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 237131 [Multi-domain]  Cd Length: 181  Bit Score: 38.88  E-value: 6.30e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  50 EDITQTVFITLWEKRETIDPDTNIAPLLYTIAKnhvYRQTEqLLRKYKYEQTQQEimpeesnPEEDVNNLFLE------- 122
Cdd:PRK12536   50 EDLVQEILLAVHNARHTYRADQPLTAWVHAIAR---YKLMD-FLRSRARREALHD-------PLDDESELFATsddeaae 118

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493 123 --KILSELIEKLPTARRKIFLLSRKENLSNKDIASRLNISEKTVETQIRRSLIFLNEKLK 180
Cdd:PRK12536  119 arRDLGKLLEQLPDRQRLPIVHVKLEGLSVAETAQLTGLSESAVKVGIHRGLKALAAKIR 178
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 142-170 7.39e-04

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


Pssm-ID: 99777 [Multi-domain]  Cd Length: 57  Bit Score: 36.36  E-value: 7.39e-04
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 2524879493 142 LSRKEN---------LSNKDIASRLNISEKTVETQIRR 170
Cdd:cd06170     1 LTPRERevlrllaegKTNKEIADILGISEKTVKTHLRN 38
PRK09646 PRK09646
ECF RNA polymerase sigma factor SigK;
12-179 7.69e-04

ECF RNA polymerase sigma factor SigK;


Pssm-ID: 182015 [Multi-domain]  Cd Length: 194  Bit Score: 38.50  E-value: 7.69e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  12 TLRLLQEGDEKAFEHIFHFYYNQVYTFVLNTLFNKTFAEDITQTVFITLWEKRETIDPDTNiAPL--LYTIA-KNHVYR- 87
Cdd:PRK09646   20 LLRRVARGDQDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDPARG-SALawLLTLAhRRAVDRv 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  88 QTEQL--LRKYKYEQTQQEimPEESNPEEDVNNLFLEKILSELIEKLPTARRKIFLLSRKENLSNKDIASRLNISEKTVE 165
Cdd:PRK09646   99 RSEQAasQREVRYGARNVD--PAFDQVAEEVEARLERERVRDCLDALTDTQRESVTLAYYGGLTYREVAERLAVPLGTVK 176

                         170
                  ....*....|....
gi 2524879493 166 TQIRRSLIFLNEKL 179
Cdd:PRK09646  177 TRMRDGLIRLRDCL 190
COG3398 COG3398
Predicted transcriptional regulator, contains two HTH domains [Transcription];
133-170 1.14e-03

Predicted transcriptional regulator, contains two HTH domains [Transcription];


Pssm-ID: 442625 [Multi-domain]  Cd Length: 159  Bit Score: 37.94  E-value: 1.14e-03
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 2524879493 133 PTARRKIFLLSRKENLSNKDIASRLNISEKTVETQIRR 170
Cdd:COG3398    97 ETPRRILLYLLENPGATNKELAEELGISRSTVSWHLKR 134
PRK06930 PRK06930
positive control sigma-like factor; Validated
 121-171 1.15e-03

positive control sigma-like factor; Validated


Pssm-ID: 180757 [Multi-domain]  Cd Length: 170  Bit Score: 37.79  E-value: 1.15e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2524879493 121 LEKILSELIEKlptaRRKIFLLSRKENLSNKDIASRLNISEKTVETQIRRS 171
Cdd:PRK06930  108 IEDALSVLTER----EKEVYLMHRGYGLSYSEIADYLNIKKSTVQSMIERA 154
PRK06704 PRK06704
RNA polymerase subunit sigma-70;
45-171 2.66e-03

RNA polymerase subunit sigma-70;


Pssm-ID: 180663 [Multi-domain]  Cd Length: 228  Bit Score: 37.31  E-value: 2.66e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  45 NKTFAEDITQTVFITLWEKRETIDPdtnIAPLLYTIAKNhvyRQTEQLLRKYKYEQTQQEIMPEEsnPEEDVNNL--FLE 122
Cdd:PRK06704   40 NKWDGEDLAQETVCKVLQKYSNKDI---CMTLVYKIARN---RWLDQIKSKSVHEKIRDQITFEE--PHEKIADLheMVG 111

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 2524879493 123 KILSELIEKLPTarrkIFLLSRKENLSNKDIASRLNISEKTVETQIRRS 171
Cdd:PRK06704  112 KVLSSLNVQQSA----ILLLKDVFQYSIADIAKVCSVSEGAVKASLFRS 156
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 128-181 3.12e-03

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: 34.33  E-value: 3.12e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2524879493 128 LIEKLPTARRKIFLLSRKENLSNKDIASRLNISEKTVETQIRRSLiflnEKLKH 181
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRAL----RKLRK 50
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 49-172 4.55e-03

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 36.17  E-value: 4.55e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524879493  49 AEDITQTVFITLWEKRETIDPDtnIAPL---LYTIAKNHVYRQteqlLRKYKYEQTQQ--EIMPEESNPEEDVNNLFLEK 123
Cdd:PRK05602   47 AEDVAQETFLRIWKQAPSWRPG--EARFdtwLHRVVLNLCYDR----LRRRREVPVEDapDVPDPAPGPDAGLEARQRAR 120

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2524879493 124 ILSELIEKLPTARRKIFLLSRKENLSNKDIASRLNISEKTVETQI---RRSL 172
Cdd:PRK05602  121 RVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALESLLargRRAL 172
 
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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