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Conserved domains on  [gi|496494726|ref|WP_009203262|]
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RNA polymerase sigma factor [Anaerostipes hadrus]

Protein Classification

RNA polymerase sigma factor( domain architecture ID 11446377)

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 1-189 4.34e-36

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: 124.34  E-value: 4.34e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726   1 MLIEQKLIKRIKKkQDKEAANALISYYYKEVYAYVYRQTGNEELAKDLTQDIFIQILQKITIFDHkKASFRTWMYRIASN 80
Cdd:COG1595    1 MSSDEELLERLRA-GDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRG-RGSFRAWLYRIARN 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  81 KICDHYRSKVHRLSLkqeqidmtdenLELHSGNLGTAVRDLSELIIHKELIEDIMEIVSLYKQEWQEIFYMKCFEERTFQ 160
Cdd:COG1595   79 LAIDHLRKRRRRREL-----------LDELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYA 147

                        170       180
                 ....*....|....*....|....*....
gi 496494726 161 DISQTLNISENTVKSRFYKMIRQIKSEVD 189
Cdd:COG1595  148 EIAEILGISEGTVKSRLSRARKKLREALE 176
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 1-189 4.34e-36

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: 124.34  E-value: 4.34e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726   1 MLIEQKLIKRIKKkQDKEAANALISYYYKEVYAYVYRQTGNEELAKDLTQDIFIQILQKITIFDHkKASFRTWMYRIASN 80
Cdd:COG1595    1 MSSDEELLERLRA-GDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRG-RGSFRAWLYRIARN 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  81 KICDHYRSKVHRLSLkqeqidmtdenLELHSGNLGTAVRDLSELIIHKELIEDIMEIVSLYKQEWQEIFYMKCFEERTFQ 160
Cdd:COG1595   79 LAIDHLRKRRRRREL-----------LDELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYA 147

                        170       180
                 ....*....|....*....|....*....
gi 496494726 161 DISQTLNISENTVKSRFYKMIRQIKSEVD 189
Cdd:COG1595  148 EIAEILGISEGTVKSRLSRARKKLREALE 176
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 14-187 2.75e-25

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 96.19  E-value: 2.75e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  14 KQDKEAANALISYYYKEVYAYVYRQTGNEELAKDLTQDIFIQILQKITIFdHKKASFRTWMYRIASNKICDHYRSKVHRl 93
Cdd:PRK11924   9 TGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLF-NGKGSARTWLLTIARNVCYDLLRRRRRE- 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  94 slKQEQIDMTDENLELHSGNlgtavrDLSELIIHKELIEDIMEIVSLYKQEWQEIFYMKCFEERTFQDISQTLNISENTV 173
Cdd:PRK11924  87 --KAVLSDDALEPEFAETAE------TPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTV 158

                        170
                 ....*....|....
gi 496494726 174 KSRFYKMIRQIKSE 187
Cdd:PRK11924 159 KSRLRRARQLLREC 172
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 18-188 6.41e-25

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: 94.72  E-value: 6.41e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726   18 EAANALISYYYKEVYAYVYRQTGNEELAKDLTQDIFIQILQKITIFDHKKaSFRTWMYRIASNKICDHYRSKVHRLSLKQ 97
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEG-SFKAWLFRIARNLILDYLRRKRRLRRELD 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726   98 EQIDMTDEnlelhsgnlgtaVRDLSELIIHKELIEDIMEIVSLYKQEWQEIFYMKCFEERTFQDISQTLNISENTVKSRF 177
Cdd:TIGR02937  80 LLEELLDS------------DPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRL 147

                         170
                  ....*....|.
gi 496494726  178 YKMIRQIKSEV 188
Cdd:TIGR02937 148 KRARKKLRELL 158
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 23-89 2.65e-14

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: 64.53  E-value: 2.65e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 496494726   23 LISYYYKEVYAYVYRQTGNEELAKDLTQDIFIQILQKITIFDH-KKASFRTWMYRIASNKICDHYRSK 89
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPeRGVSFSTWLYTIIRNAIIDYLRKQ 68
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 146-185 1.29e-03

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: 35.54  E-value: 1.29e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 496494726 146 QEIFYMKCFEERTFQDISQTLNISENTVKSRFYKMIRQIK 185
Cdd:cd06171   16 REVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 1-189 4.34e-36

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: 124.34  E-value: 4.34e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726   1 MLIEQKLIKRIKKkQDKEAANALISYYYKEVYAYVYRQTGNEELAKDLTQDIFIQILQKITIFDHkKASFRTWMYRIASN 80
Cdd:COG1595    1 MSSDEELLERLRA-GDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRG-RGSFRAWLYRIARN 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  81 KICDHYRSKVHRLSLkqeqidmtdenLELHSGNLGTAVRDLSELIIHKELIEDIMEIVSLYKQEWQEIFYMKCFEERTFQ 160
Cdd:COG1595   79 LAIDHLRKRRRRREL-----------LDELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYA 147

                        170       180
                 ....*....|....*....|....*....
gi 496494726 161 DISQTLNISENTVKSRFYKMIRQIKSEVD 189
Cdd:COG1595  148 EIAEILGISEGTVKSRLSRARKKLREALE 176
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 14-187 2.75e-25

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 96.19  E-value: 2.75e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  14 KQDKEAANALISYYYKEVYAYVYRQTGNEELAKDLTQDIFIQILQKITIFdHKKASFRTWMYRIASNKICDHYRSKVHRl 93
Cdd:PRK11924   9 TGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLF-NGKGSARTWLLTIARNVCYDLLRRRRRE- 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  94 slKQEQIDMTDENLELHSGNlgtavrDLSELIIHKELIEDIMEIVSLYKQEWQEIFYMKCFEERTFQDISQTLNISENTV 173
Cdd:PRK11924  87 --KAVLSDDALEPEFAETAE------TPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTV 158

                        170
                 ....*....|....
gi 496494726 174 KSRFYKMIRQIKSE 187
Cdd:PRK11924 159 KSRLRRARQLLREC 172
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 18-188 6.41e-25

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: 94.72  E-value: 6.41e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726   18 EAANALISYYYKEVYAYVYRQTGNEELAKDLTQDIFIQILQKITIFDHKKaSFRTWMYRIASNKICDHYRSKVHRLSLKQ 97
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEG-SFKAWLFRIARNLILDYLRRKRRLRRELD 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726   98 EQIDMTDEnlelhsgnlgtaVRDLSELIIHKELIEDIMEIVSLYKQEWQEIFYMKCFEERTFQDISQTLNISENTVKSRF 177
Cdd:TIGR02937  80 LLEELLDS------------DPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRL 147

                         170
                  ....*....|.
gi 496494726  178 YKMIRQIKSEV 188
Cdd:TIGR02937 148 KRARKKLRELL 158
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 16-190 1.70e-21

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 86.67  E-value: 1.70e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  16 DKEAANALISYYYKEVYAYVYRQTGNEELAKDLTQDIFIQILQKITIFDHKkASFRTWMYRIASNKICDHYRSKVHRLSL 95
Cdd:PRK12513  24 DAAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPR-ARFRTWLYQIARNLLIDHWRRHGARQAP 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  96 KQEQidmtDENLELHSGNLGTAVRDLSELIIHKEL---IEDIMEivslykqEWQEIFYMKCFEERTFQDISQTLNISENT 172
Cdd:PRK12513 103 SLDA----DEQLHALADDGAAPEQQLSLFRDRRRLqaaLETLPD-------EQREVFLLREHGDLELEEIAELTGVPEET 171

                        170       180
                 ....*....|....*....|..
gi 496494726 173 VKSRF-Y---KMIRQIKSEVDY 190
Cdd:PRK12513 172 VKSRLrYalqKLRELLAEEVAV 193
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 10-188 8.88e-21

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 84.47  E-value: 8.88e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  10 RIKKKQDKEAANALISYYYKEVYAYVYRQTGNEELAKDLTQDIFIQILQKITIFDhKKASFRTWMYRIASNKICDHYRSK 89
Cdd:PRK09652   2 ERVQRGDRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFR-GGAAFYTWLYRIARNTAINYLRKQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  90 VHRLSlkqeQIDMTDENLELHsgNLGTAVRDLS---ELIIHKELIEDIMEIVSLYKQEWQEIFYMKCFEERTFQDISQTL 166
Cdd:PRK09652  81 GRRPP----ASDVDAEEAEDF--DLADALRDIStpeNELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIM 154

                        170       180
                 ....*....|....*....|..
gi 496494726 167 NISENTVKSRFYKMIRQIKSEV 188
Cdd:PRK09652 155 GCPIGTVRSRIFRAREALRAKL 176
SigM_subfam TIGR02950
RNA polymerase sigma factor, SigM family; This family of RNA polymerase sigma factors is a ...
 27-186 8.28e-18

RNA polymerase sigma factor, SigM family; This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot:


Pssm-ID: 274361 [Multi-domain]  Cd Length: 154  Bit Score: 76.34  E-value: 8.28e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726   27 YYKEVYAYVYRQTGNEELAKDLTQDIFIQILQKITIFDHkkASFRTWMYRIASNKICDHYRSKvhrlslKQEQIDMTDEN 106
Cdd:TIGR02950   4 YMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKD--SSIKPWLFRIARNAFIDWYRKD------KKIQTIDDDAI 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  107 LELHSGNLGTAVRDLseliIHKELIEDIMEIVSLYKQEWQEIFYMKCFEERTFQDISQTLNISENTVKSRFYKMIRQIKS 186
Cdd:TIGR02950  76 GDLEQHPVESPEHHL----LIKIEQEEITHHLSRLPENYRTVLILREFKEFSYKEIAELLNLSLAKVKSNLFRARKELKK 151
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 4-187 1.06e-17

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 76.60  E-value: 1.06e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726   4 EQKLIKRiKKKQDKEAANALISYYYKEVYAYVYRQTGNEELAKDLTQDIFIQILQKITIFdHKKASFRTWMYRIASNKIC 83
Cdd:PRK09638   5 EKELIQK-AKKGDDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSF-QGRSKFSTWLISIASRLYK 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  84 DHYRsKVHRLSLKQEQIdmTDEnlelhsgnlgTAVRDLSELIIHKELIEDIMEIVSLYKQEWQEIFYMKCFEERTFQDIS 163
Cdd:PRK09638  83 DHLR-KQKREKLRLQRA--KEE----------TLRKEKWEAAIKGAEWSEMLDALSKLDPEFRAPVILKHYYGYTYEEIA 149

                        170       180
                 ....*....|....*....|....
gi 496494726 164 QTLNISENTVKSRFYKMIRQIKSE 187
Cdd:PRK09638 150 KMLNIPEGTVKSRVHHGIKQLRKE 173
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 2-179 1.42e-17

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 76.27  E-value: 1.42e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726   2 LIEQKLIKRIKKKqDKEAANALISYYYKEVYAYVYRQTGNEELAKDLTQDIFIQILQKITIFDHKKaSFRTWMYRIASNK 81
Cdd:PRK09641   3 LLIKRLIKQVKKG-DQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINR-KFSTWLYRIATNL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  82 ICDHYRSKVHRLSLKQEQIDMtdENLELHSgNLGTAVRDLSELIIHKELIEDIMEIVSLYKQEWQEIFYMKCFEERTFQD 161
Cdd:PRK09641  81 TIDRLRKRKPDYYLDAEVAGT--EGLTMYS-QLAADDALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYIEDLSLKE 157

                        170
                 ....*....|....*...
gi 496494726 162 ISQTLNISENTVKSRFYK 179
Cdd:PRK09641 158 ISEILDLPVGTVKTRIHR 175
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 18-187 1.74e-16

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: 72.98  E-value: 1.74e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726   18 EAANALISYYYKEVYAYVYRQTGNEELAKDLTQDIFIQILQKITIFDHKKaSFRTWMYRIASNKICDHYRSKVHRLSLKQ 97
Cdd:TIGR02985   1 EAFEQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETLEISE-SIKAYLFTIVKNRCLNYLRHKQVEEKYQE 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726   98 EQIDMTDENLELhsgnlgtavRDLSELIIHKELIEDIMEIVSLYKQEWQEIFYMKCFEERTFQDISQTLNISENTVKSRF 177
Cdd:TIGR02985  80 ELAEIEERELSE---------ADPEEELEAKELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHI 150

                         170
                  ....*....|
gi 496494726  178 YKMIRQIKSE 187
Cdd:TIGR02985 151 TKALKFLRKE 160
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 15-179 5.30e-16

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 72.09  E-value: 5.30e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  15 QDKEAA-NALISYYYKEVYAYVYRQTGNEELAKDLTQDIFIQILQKITIFDhKKASFRTWMYRIASNKICDHYRSKVHRl 93
Cdd:PRK09415  12 EDKEDLiDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYK-GKSSLKTWLYRIAINHCKDYLKSWHNK- 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  94 slkqeQIDMTDENLElhsgNLGTAVRDLSELIIHKELIEDIMEIVSLYKQEWQEIFYMKCFEERTFQDISQTLNISENTV 173
Cdd:PRK09415  90 -----KVIVTEDIFT----YMESQKESVEEEVIQNAEDERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTV 160


                 ....*.
gi 496494726 174 KSRFYK 179
Cdd:PRK09415 161 KTRLKK 166
SigW_bacill TIGR02948
RNA polymerase sigma-W factor; This sigma factor is restricted to certain lineages of the ...
 2-179 9.24e-16

RNA polymerase sigma-W factor; This sigma factor is restricted to certain lineages of the order Bacillales.


Pssm-ID: 131993 [Multi-domain]  Cd Length: 187  Bit Score: 71.46  E-value: 9.24e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726    2 LIEQKLIKRIKKKqDKEAANALISYYYKEVYAYVYRQTGNEELAKDLTQDIFIQILQKITIFDHKKaSFRTWMYRIASNK 81
Cdd:TIGR02948   3 SIIKKRIKEVRKG-DENAFADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIRAYTNIDTYDIQR-KFSTWLYRIATNL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726   82 ICDHYRSKVHRLSLkQEQIDMTDeNLELHSgNLGTAVRDLSELIIHKELIEDIMEIVSLYKQEWQEIFYMKCFEERTFQD 161
Cdd:TIGR02948  81 TIDRLRKRKPDFYL-DDEVQGTD-GLTMES-QLAADEAPPEDQVISLELRDTIQQEIQALPPKYRMVIVLKYMEDLSLKE 157

                         170
                  ....*....|....*...
gi 496494726  162 ISQTLNISENTVKSRFYK 179
Cdd:TIGR02948 158 ISEILDLPVGTVKTRIHR 175
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 23-89 2.65e-14

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: 64.53  E-value: 2.65e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 496494726   23 LISYYYKEVYAYVYRQTGNEELAKDLTQDIFIQILQKITIFDH-KKASFRTWMYRIASNKICDHYRSK 89
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPeRGVSFSTWLYTIIRNAIIDYLRKQ 68
PRK06811 PRK06811
RNA polymerase factor sigma-70; Validated
 4-188 1.27e-13

RNA polymerase factor sigma-70; Validated


Pssm-ID: 180707 [Multi-domain]  Cd Length: 189  Bit Score: 65.73  E-value: 1.27e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726   4 EQKLIKRIKKKqDKEAANALISYYYKEVYAYVY---RQTGNEELAKDLTQDIFIQILQKITIFDHKKASFRTWMYRIASN 80
Cdd:PRK06811   5 EDNFIKELKKK-NEKALEFIVDTYGNLVKKIVHkvlGTVNYSQLIEECVNDIFLSIWNNIDKFDEEKGSFKKWIAAISKY 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  81 KICDHYRS--KVHRLSLKQEQIDMTDENLElhsgnlgtavrdlsELIIHKELIEDIMEIVSLYKQEWQEIFYMKCFEERT 158
Cdd:PRK06811  84 KAIDYKRKltKNNEIDSIDEFILISEESIE--------------NEIILKENKEEILKLINDLEKLDREIFIRRYLLGEK 149

                        170       180       190
                 ....*....|....*....|....*....|
gi 496494726 159 FQDISQTLNISENTVKSRFYKMIRQIKSEV 188
Cdd:PRK06811 150 IEEIAKKLGLTRSAIDNRLSRGRKKLQKNK 179
PRK12531 PRK12531
RNA polymerase sigma factor; Provisional
 13-189 1.49e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 105726 [Multi-domain]  Cd Length: 194  Bit Score: 63.03  E-value: 1.49e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  13 KKQDKEAANALISYYYKEVYAYVYRQTGNEELAKDLTQDIFIQILQKITIFDHKKASFRTWMYRIASNKICDHYRskvhr 92
Cdd:PRK12531  22 KSRDKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQKSALSTWIYTIIRNLCFDLLR----- 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  93 lslKQEQIDmtdenLELHSGNLGTAVRDLSELIIHKE-----LIEDIMEIVSLYKQEWQEIFYMKCFEERTFQDISQTLN 167
Cdd:PRK12531  97 ---KQKGKD-----LHIHADDIWPSDYYPPDLVDHYSpeqdmLKEQVMKFLDRLPKAQRDVLQAVYLEELPHQQVAEMFD 168

                        170       180
                 ....*....|....*....|..
gi 496494726 168 ISENTVKSRFYKMIRQIKSEVD 189
Cdd:PRK12531 169 IPLGTVKSRLRLAVEKLRHSMD 190
SigZ TIGR02959
RNA polymerase sigma factor, SigZ family; This family of RNA polymerase sigma factors is a ...
 27-176 5.30e-12

RNA polymerase sigma factor, SigZ family; This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).


Pssm-ID: 132004 [Multi-domain]  Cd Length: 170  Bit Score: 61.23  E-value: 5.30e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726   27 YYKEVYAYVYRQTGNEELAKDLTQDIFIQILQKITIFDhKKASFRTWMYRIASNKICDHYRSKVHRLSLKQEQIDMTDEN 106
Cdd:TIGR02959   4 FRSELKAFIKSRVSDASDVEDLLQEVFIKIHRNLPSLK-DGQKIQSWLYQIARNTIIDFYRSKSRSVELPESLLAADSAR 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 496494726  107 LElhsgnlgTAVRDLSELI--IHKELIEDIMEIVSLYKqewqeifymkcFEERTFQDISQTLNISENTVKSR 176
Cdd:TIGR02959  83 EE-------TFVKELSQCIppMIKELPDEYREAIRLTE-----------LEGLSQQEIAEKLGLSLSGAKSR 136
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
18-185 6.44e-12

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 60.86  E-value: 6.44e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  18 EAANALISYYYKE----VYAYVYRQTGNEELAKDLTQDIFIQILQKITIFDHKKASFRTWMYRIASNKICDHYRSKVHRl 93
Cdd:PRK09645   5 TAEAALMRALYDEhaapLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTGRSARAWLFTVARNLVIDERRSARAR- 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  94 slKQEQIDMTDENLE----------LHSGNLGTAVRDLSELiiHKELIEDImeivslYKQEWqeifymkcfeerTFQDIS 163
Cdd:PRK09645  84 --PVEGGDDVLGVPEqsapdevdraLDRLLVADALAQLSPE--HRAVLVRS------YYRGW------------STAQIA 141

                        170       180
                 ....*....|....*....|..
gi 496494726 164 QTLNISENTVKSRFYKMIRQIK 185
Cdd:PRK09645 142 ADLGIPEGTVKSRLHYALRALR 163
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 16-185 7.58e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 58.19  E-value: 7.58e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  16 DKEAANALISYYYKEVYAYVYRQTGNEELaKDLTQDIFIQILQKITIFDHKkASFRTWMYRIASNKICDHYRSKVHRLSL 95
Cdd:PRK12518   9 DRQSFRQLYRRYQQKVRSTLYQLCGRELL-DDLVQEVFLRVWKGLPKLRNP-AYFSTWLYRITWNVATDARRQFAQRPSR 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  96 KQEQIDMTDENLELHSGNLGTavrdlselIIHKELIEDIMEIVSLykqEWQEIFYMKCFEERTFQDISQTLNISENTVKS 175
Cdd:PRK12518  87 IQDDSLNDQPSRPSDTPDLMQ--------LHYQDLVQQGLQTLSL---EHRAVLVLHDLEDLPQKEIAEILNIPVGTVKS 155

                        170
                 ....*....|
gi 496494726 176 RFYKMIRQIK 185
Cdd:PRK12518 156 RLFYARRQLR 165
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 25-176 3.19e-10

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 56.53  E-value: 3.19e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  25 SYYYKEVYAYVYRQTGNEELAKDLTQDIFIQILQKITIFDhKKASFRTWMYRIASNKICDHYRskvhrlslKQEQIDMTD 104
Cdd:PRK09637   8 SEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLK-DGSSIKSWLYQIANNTIIDFYR--------KKNRSEELP 78

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 496494726 105 ENLELHSGNLGTAVRD-LSELI--IHKELIEDIMEIVSLYKqewqeifymkcFEERTFQDISQTLNISENTVKSR 176
Cdd:PRK09637  79 DDLLFEDEEREENAKKeLAPCLrpFIDALPEKYAEALRLTE-----------LEGLSQKEIAEKLGLSLSGAKSR 142
PRK12522 PRK12522
RNA polymerase sigma factor; Provisional
 17-189 1.02e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 183571 [Multi-domain]  Cd Length: 173  Bit Score: 54.88  E-value: 1.02e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  17 KEAANALISYYYKEVYAYVYRQTGNEELAKDLTQDIFIQILQKITIFDHKKaSFRTWMYRIASNKICDHYRSKVHRLSLK 96
Cdd:PRK12522   2 EEKVEELIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVE-NYKKWITTICVRTFYDFYRKKKRWKDRI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  97 QEQIDMTD-ENLELHSGNlgtavrDLSELIIHKELIEDIMEIVSLYKQEWQEIFYMKCFEERTFQDISQTLNISENTVKS 175
Cdd:PRK12522  81 LDLFHKEDgGEIEFADDV------NISEEFIQKVEAEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKY 154

                        170
                 ....*....|....
gi 496494726 176 RFYKMIRQIKSEVD 189
Cdd:PRK12522 155 RLNYAKKQMREHLE 168
algU PRK11923
RNA polymerase sigma factor AlgU; Provisional
 4-179 2.95e-09

RNA polymerase sigma factor AlgU; Provisional


Pssm-ID: 171347 [Multi-domain]  Cd Length: 193  Bit Score: 54.04  E-value: 2.95e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726   4 EQKLIKRIKKKqDKEAANALISYYYKEVYAYVYRQTGNEELAKDLTQDIFIQILQKITIFDHKKAsFRTWMYRIASNKIC 83
Cdd:PRK11923   7 DQQLVERVQRG-DKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDSA-FYTWLYRIAINTAK 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  84 DHYRSKVHRlslkQEQIDMTDENLELHSGNLGTAVRDLSELIIHKELIED-IMEIVSLYKQEWQEIFYMKCFEERTFQDI 162
Cdd:PRK11923  85 NHLVSRGRR----PPDSDVSSEDAEFYDGDHALKDIESPERALLRDEIEGtVHRTIQQLPEDLRTALTLREFDGLSYEDI 160

                        170
                 ....*....|....*..
gi 496494726 163 SQTLNISENTVKSRFYK 179
Cdd:PRK11923 161 ASVMQCPVGTVRSRIFR 177
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 7-178 4.44e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 53.58  E-value: 4.44e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726   7 LIKRIKKKqDKEAANALISYYYKEVYAYVYRQTGNEELAKDLTQDIFIQILQKITIFDhKKASFRTWMYRIASNKICDHY 86
Cdd:PRK12515  12 LLARIAQG-DRTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFE-GRSQVSTWLLSIARFKALSAL 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  87 RSKvhrlslKQEQIDmTDENLELHSGNlgtavrDLSELIIHKELIEDIM-EIVSLYKQEWQEIFYMKCFEERTFQDISQT 165
Cdd:PRK12515  90 RRR------KHEEID-DEAAAAIEDGA------DTPEVALQKSDTSAALrACLAKLSPAHREIIDLVYYHEKSVEEVGEI 156

                        170
                 ....*....|....
gi 496494726 166 LNISENTVKSR-FY 178
Cdd:PRK12515 157 VGIPESTVKTRmFY 170
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 2-187 5.67e-09

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 53.40  E-value: 5.67e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726   2 LIEQKLIKRIKKK--QDKEAANALISYYYKEVYAYVYRQTGNEELAKDLTQDIFIQILQKITIFDhKKASFRTWMYRIAS 79
Cdd:PRK09640   8 LNDEELVARVHVElfHVTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFE-GKSKFKTWLYSITY 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  80 NKICDHYRSKVHRlslKQEQIDMTDENLELHSGNLGTAVRD---LSELIIHKELIEdimeivslykqewQEIFYMKCFEE 156
Cdd:PRK09640  87 NECITQYRKERRK---RRLMDALSLDPLEEASEEKAPKPEErggLDRWLVHVNPID-------------REILVLRFVAE 150

                        170       180       190
                 ....*....|....*....|....*....|.
gi 496494726 157 RTFQDISQTLNISENTVKSRFYKMIRQIKSE 187
Cdd:PRK09640 151 LEFQEIADIMHMGLSATKMRYKRALDKLREK 181
SigX5 TIGR02960
RNA polymerase sigma-70 factor, TIGR02960 family; This group of sigma factors are members of ...
 16-92 9.37e-09

RNA polymerase sigma-70 factor, TIGR02960 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: 132005 [Multi-domain]  Cd Length: 324  Bit Score: 53.71  E-value: 9.37e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 496494726   16 DKEAANALISYYYKEVYAYVYRQTGNEELAKDLTQDIFIQILQKITIFDhKKASFRTWMYRIASNKICDHY--RSKVHR 92
Cdd:TIGR02960   3 DGAAFTALAEPHRRELLAHCYRMLGSLHEAEDLVQETLLRAWRARDRFE-GRSSVRTWLYRIATNACLDALeaRQRRPR 80
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 16-189 6.96e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 50.12  E-value: 6.96e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  16 DKEAANALISYYYKEVYAYVYRQTGNEELAKDLTQDIFIQILQKITIFDHKKaSFRTWMYRIASNKICDHYRSKVHRLSL 95
Cdd:PRK12543   5 DQEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNR-PFRFWLIGLVIKQIHSWRRKRWRRFRI 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  96 KQEQIDMTDEnlelhsgnlgtAVRDLSELIIHKELIEDIMEIVSLYKQEWQEIFYMKCFEERTFQDISQTLNISENTVKS 175
Cdd:PRK12543  84 FEKAEEQRKP-----------VSIDFSEDVLSKESNQELIELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKS 152

                        170
                 ....*....|....
gi 496494726 176 RFYKMIRQIKSEVD 189
Cdd:PRK12543 153 RIHAALKKLRQKEQ 166
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 23-179 8.67e-08

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 50.17  E-value: 8.67e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  23 LISYYYKEVYAYVYRQTGNEELAKDLTQDIFIQILQKITifDHKKASFRTWMYRIASNKICDHYRskvHRLSLKQEQI-- 100
Cdd:PRK09647  33 LVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQ--NYQPGTFEGWLHRITTNLFLDMVR---RRARIRMEALpe 107

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726 101 --------DMTDENLeLHSGNLGTAVRdlSELiihKELIEDIMEIVSLykqewqeifymkC-FEERTFQDISQTLNISEN 171
Cdd:PRK09647 108 dydrvpgdEPNPEQI-YHDARLDPDLQ--AAL---DSLPPEFRAAVVL------------CdIEGLSYEEIAATLGVKLG 169


                 ....*...
gi 496494726 172 TVKSRFYK 179
Cdd:PRK09647 170 TVRSRIHR 177
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 16-188 9.09e-08

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 49.91  E-value: 9.09e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  16 DKEAANALISYYYKEVYAYVYRQTGNEELAKDLTQDIFIQILQKITIFDHKKASFRTWMYRIASNKICDHYRSKVHR-LS 94
Cdd:PRK13919  21 EEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRRGSARAWLLALAHHAAVDHVRRRAARpQP 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  95 L-----KQEQIDMT----DENLELHSGNLGTAVRDLSELiiHKELIEdimeivSLYKQEWqeifymkcfeerTFQDISQT 165
Cdd:PRK13919 101 LepderEPEAFDLPgpglDEEGHLDRTRLGRALKALSPE--ERRVIE------VLYYQGY------------THREAAQL 160

                        170       180
                 ....*....|....*....|...
gi 496494726 166 LNISENTVKSRFYKMIRQIKSEV 188
Cdd:PRK13919 161 LGLPLGTLKTRARRALSRLKEVL 183
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 28-174 3.87e-07

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 47.64  E-value: 3.87e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  28 YKEVYAYVYRQ----TGNEELAKDLTQDIFIQILQkiTIFDHkKASFRTWMYRIASNKICDHYRSKVHRLSLKQEQIDMT 103
Cdd:PRK09639   9 FEQYYPDVVQQifyiVKDRTQAEDLAQEVFLRLYR--SDFKG-IENEKGWLIKSARNVAYNYLRSEKRRRARILGEFQWQ 85

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 496494726 104 DENLELhsgnlgtavrDLSELIIHKELIEDIMEIVSLYKQEWQEIFYMKcFEERTFQDISQTLNISENTVK 174
Cdd:PRK09639  86 EVDNEP----------SPEEIWIRKEEITKVQEVLAKMTERDRTVLLLR-FSGYSYKEIAEALGIKESSVG 145
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 13-176 4.26e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 48.13  E-value: 4.26e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  13 KKQDKEAANALISYYYKEVYAYVYRQTGNEELAKDLTQDIFIQILQKITiFDHKKASFRTWMYRIASNKICDHYRSKVHR 92
Cdd:PRK12519  24 KAGQSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRKSS-YDPKRGSLSSYLLTLTRSRAIDRLRSRRSR 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  93 LS-LKQEQIDMTDEN----------LELHSGNLGTAVRDLSEliihkeliedimeivslyKQewQEIFYMKCFEERTFQD 161
Cdd:PRK12519 103 QRlLERWQQELLGEAsedtpleqasLAERSQRVQTALAQLPE------------------SQ--RQVLELAYYEGLSQSE 162

                        170
                 ....*....|....*
gi 496494726 162 ISQTLNISENTVKSR 176
Cdd:PRK12519 163 IAKRLGIPLGTVKAR 177
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 16-87 1.15e-06

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 46.57  E-value: 1.15e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 496494726  16 DKEAANALISYYYKEVYAYVYRQTGNEELAKDLTQDIFIQILQKITIFDHKKASFRTWMYRIASNKICDHYR 87
Cdd:PRK05602  18 DPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPGEARFDTWLHRVVLNLCYDRLR 89
PRK12542 PRK12542
RNA polymerase sigma factor; Provisional
 15-186 3.07e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183581 [Multi-domain]  Cd Length: 185  Bit Score: 45.43  E-value: 3.07e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  15 QDKEAANALISYYYKEVYAYVYRQTGNEELAKDLTQDIFIQILQKIT-IFDHKKASFRTWMYRIASNKICDHYR-SKVHR 92
Cdd:PRK12542   6 NDYEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEkLHSLNTQELKRYILRVAKNKAIDSYRkNKRHE 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  93 LSLKQ---EQIDMTDENLELHSGnlgtavRDLSELIIHKELIEdimeivslYKQEWQEIFYMKCFEERTFQDISQTLNIS 169
Cdd:PRK12542  86 TFLEEyerESIEAVDENIEEWEK------RKMSEVQIDTLLKE--------LNESNRQVFKYKVFYNLTYQEISSVMGIT 151

                        170
                 ....*....|....*..
gi 496494726 170 ENTVKSRFYKMIRQIKS 186
Cdd:PRK12542 152 EANVRKQFERARKRVQN 168
PRK08241 PRK08241
RNA polymerase subunit sigma-70;
27-80 6.14e-06

RNA polymerase subunit sigma-70;


Pssm-ID: 236196 [Multi-domain]  Cd Length: 339  Bit Score: 45.31  E-value: 6.14e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 496494726  27 YYKEVYAYVYRQTGNEELAKDLTQDIFIQILQKITIFDhKKASFRTWMYRIASN 80
Cdd:PRK08241  28 HRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGYDRFE-GRSSLRTWLYRIATN 80
PRK12534 PRK12534
RNA polymerase sigma factor; Provisional
 16-89 6.67e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183576 [Multi-domain]  Cd Length: 187  Bit Score: 44.66  E-value: 6.67e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 496494726  16 DKEAANALISYYYKEVYAYVYRQTGNEELAKDLTQDIFIQILQKITIFDHKKASFRTWMYRIASNKICDHYRSK 89
Cdd:PRK12534  23 DRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRARGLTWLAMIARNKAIDHLRAN 96
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 27-185 6.89e-06

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 44.48  E-value: 6.89e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  27 YYKEVYAYVYRQTGNEELAKDLTQDIFIQILQKITIFDHKKAsfRTWMYRIASNKICDHYRSKVHRLSLKQEQIDMTDEN 106
Cdd:PRK09644  10 YINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDNQKV--KPWLFKVAYHTFIDFVRKEKKVSFVGTDEIEAIQAE 87

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 496494726 107 lelhsgnlgtavrDLSELIIHKELIEDIMEIVSLYKQEWQEIFYMKCFEERTFQDISQTLNISENTVKSRFYKMIRQIK 185
Cdd:PRK09644  88 -------------STEEYVVAKNSYEKLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRLK 153
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
 16-87 8.41e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 44.85  E-value: 8.41e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 496494726  16 DKEAANALISYYYKEVYAYVYRQTGNEELAKDLTQDIFIQILQKITIFDHKKASFRTWMYRIASNKICDHYR 87
Cdd:PRK12538  61 DEAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRAKFSTWLYRVVSNRCIDLRR 132
PRK09642 PRK09642
RNA polymerase sigma factor;
27-185 1.34e-05

RNA polymerase sigma factor;


Pssm-ID: 170031 [Multi-domain]  Cd Length: 160  Bit Score: 43.55  E-value: 1.34e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  27 YYKEVYAYVYRQTGNEELAKDLTQDIFIQIlqKITIFDHKKASFRTWMYRIASNKICDHYRSKVhRLSLKQEQIDMTDEN 106
Cdd:PRK09642   4 YRHYIFQVIFSILRHEEDAKDVTQEVFVKI--HASLPNYQFRGLKTWMARIATNHAIDYKRKKA-RENEELSLCKETEEN 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 496494726 107 LElhsgnlgtAVRDLSELIIHKELIEDIMEIVSLYKQEWQEIFYMKCFEERTFQDISQTLNISENTVKSRFYKMIRQIK 185
Cdd:PRK09642  81 IK--------SSHNIEDLLLTKEQKLLIAQKLRELPENYRDVVLAHYLEEKSYQEIALQEKIEVKTVEMKLYRARKWIK 151
PRK12530 PRK12530
RNA polymerase sigma factor; Provisional
 38-106 2.25e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 237128 [Multi-domain]  Cd Length: 189  Bit Score: 43.22  E-value: 2.25e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 496494726  38 QTGNEELAKDLTQDIFIQILQKITIFDHKKAsFRTWMYRIASNKICDHYRSKvHRLSLKQEQIDMTDEN 106
Cdd:PRK12530  27 QLKDADLAEDVVQEALVSAYKNADSFKGQSA-LKTWIFAILKNKIIDLIRYR-KRFVNESELIEEDSPN 93
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 41-183 3.08e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 43.03  E-value: 3.08e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  41 NEELAKDLTQDIFIQILQKITIFdHKKASFRTWMYRIASNKICDHYRsKVHRLSLKQEqIDMTDENLELHSGNLGTAVRD 120
Cdd:PRK11922  53 NDAEAEDVVQEAYLRAFRALGTF-RGDASLSTWLSRIVLNEALGRLR-RRRRLVNLAE-MVMASTIAGGERTPLADPAED 129

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 496494726 121 lseliIHKEL----IEDIME--IVSLyKQEWQEIFYMKCFEERTFQDISQTLNISENTVKSRFY---KMIRQ 183
Cdd:PRK11922 130 -----PERAAarreIRALLEraIDAL-PDAFRAVFVLRVVEELSVEETAQALGLPEETVKTRLHrarRLLRE 195
Sig70_famx1 TIGR02943
RNA polymerase sigma-70 factor, TIGR02943 family; This group of sigma factors are members of ...
 38-179 6.17e-05

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: 41.67  E-value: 6.17e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726   38 QTGNEELAKDLTQDIFIQILQKITIFdHKKASFRTWMYRIASNKICDHYRSKVHRLSLKQEQIDMTDENLELHSGNLG-- 115
Cdd:TIGR02943  22 QLRDRDLAEDAVQETLLAALSHRDSF-AGRSALKTWLFAILKNKIIDALRAKGREVKVSDLDDELDDEAFNALFTQNGhw 100

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  116 ---TAVRDLSE---LIIHKELIEDIMEIVSLYKQEWQEIFYMKCFEERTFQDISQTLNISENTVKSRFYK 179
Cdd:TIGR02943 101 aqhGQPQHWNTpekQLENKEFWEVFEACLYHLPEQTARVFMMREVLGFESDEICQELEISTSNCHVLLYR 170
PRK09649 PRK09649
RNA polymerase sigma factor SigC; Reviewed
 16-124 6.90e-05

RNA polymerase sigma factor SigC; Reviewed


Pssm-ID: 137458 [Multi-domain]  Cd Length: 185  Bit Score: 41.56  E-value: 6.90e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  16 DKEAANALISYYYKEVYAYV--YRQTGNeelAKDLTQDIFIQILQKITIFDhKKASFRTWMYRIASNKICDHYRskvhRL 93
Cdd:PRK09649  22 NGRALEAFIKATQQDVWRFVayLSDVGS---ADDLTQETFLRAIGAIPRFS-ARSSARTWLLAIARHVVADHIR----HV 93

                         90       100       110
                 ....*....|....*....|....*....|.
gi 496494726  94 SLKQEQIDMTDENLELHSGNLGTAVRDLSEL 124
Cdd:PRK09649  94 RSRPRTTRGARPEHLIDGDRHARGFEDLVEV 124
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
 37-182 9.09e-05

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 41.21  E-value: 9.09e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  37 RQTGNEELAKDLTQDIFIQiLQKITIFDHKKASFrTWMYRIASNKICDHYRskvhRLSLKQEQIDMTDENLELHSGNLGT 116
Cdd:PRK07037  17 RIVGCRSRAEDVVQDAFVK-LVEAPNQDAVKQPV-AYLFRIVRNLAIDHYR----RQALENKYHGDEEDGLDVPSPEASP 90

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 496494726 117 avrdlSELIIHKELIEDIMEIVSLYKQEWQEIFYMKCFEERTFQDISQTLNISENTVKsrFykMIR 182
Cdd:PRK07037  91 -----EAALINRDTLRHVADALSELPARTRYAFEMYRLHGETQKDIARELGVSPTLVN--F--MIR 147
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 27-173 1.23e-04

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 40.53  E-value: 1.23e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  27 YYKEVYAYVYRQTGNEELAKDLTQDIFIQILQKI--TIFDHKKAsfrtWMYRIASNKICDHYRSkvHRLSlKQEQIDMTD 104
Cdd:PRK12527   4 YYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSssAQIEHPRA----FLYRTALNLVVDRHRR--HRVR-QAEPLEVLD 76

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 496494726 105 ENLELHSGNlgtavrdLSELIIHKELIEDIMEIVSLYKQEWQEIFYMKCFEERTFQDISQTLNISENTV 173
Cdd:PRK12527  77 EEERLHSPS-------PQTRLDLGQRLALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLV 138
PRK12526 PRK12526
RNA polymerase sigma factor; Provisional
 8-188 1.47e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 237127 [Multi-domain]  Cd Length: 206  Bit Score: 40.94  E-value: 1.47e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726   8 IKRIKKKQDKEAANALISYYYKEVYAYVYRQTGNEELAKDLTQDIFIQILQKITIFDHKKASFRTWMYRIASNKICDHYR 87
Cdd:PRK12526  28 LILVAISRDKQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKGAATTWVYTVMRNAAFDMLR 107

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  88 skvhRLSLKQEQidmtdenlelhsgNLGTAV----RDLSELIIHKELIED------IMEIVSLYKQEWQEIFYMKCFEER 157
Cdd:PRK12526 108 ----KIKAKKEQ-------------NLGDDIwpieQALAESQSESEEFSDhlmdkqILSYIEKLPEAQQTVVKGVYFQEL 170

                        170       180       190
                 ....*....|....*....|....*....|.
gi 496494726 158 TFQDISQTLNISENTVKSRFYKMIRQIKSEV 188
Cdd:PRK12526 171 SQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 44-124 2.96e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 39.76  E-value: 2.96e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  44 LAKDLTQDIFIQILQKITIFDHKKASFRTWMYRI----ASNKICDHYRSKV---HRLSLKQEQIDMTDEnLELHSgNLGT 116
Cdd:PRK12537  49 LAEDIVHDAFIKIWTGAASFDPARGSARGWIYSVtrhlALNVLRDTRREVVlddDAEETAQTLHEIIDD-FDLWA-NSGK 126


                 ....*...
gi 496494726 117 AVRDLSEL 124
Cdd:PRK12537 127 IHRCLEQL 134
PRK12544 PRK12544
RNA polymerase factor sigma-70;
38-109 4.20e-04

RNA polymerase factor sigma-70;


Pssm-ID: 183583 [Multi-domain]  Cd Length: 206  Bit Score: 39.40  E-value: 4.20e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 496494726  38 QTGNEELAKDLTQDIFIQILQKITIFDhKKASFRTWMYRIASNKICDHYRSKvHRLSLKQEQIDmtDENLEL 109
Cdd:PRK12544  38 QLSDLHLAEDAVQEALIGALKNADSFA-GRAAFKTWVFAILKNKIIDLLRQK-KRHVSASSLLR--DEEEEE 105
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 11-186 4.73e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 39.15  E-value: 4.73e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  11 IKKKQDKEAanaLISYYYKEVYAYVYRQTGNEELAKDLTQDIFIQILQKITIFdhKKASFRTWMYRIASNKICDHYRskv 90
Cdd:PRK12541   1 MKRKQSLEE---IYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYY--KGEEIRPWLFTIAYNAFIDWYR--- 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  91 hrlslkQEQIDMTDENLELHSGNLGTAvrdlSELIIHKELIEDIMEIVSLYKQEWQEIFYMKCFEERTFQDISQTLNISE 170
Cdd:PRK12541  73 ------KEKKYKTTTIEEFHLPNVPST----EHEYFIKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSL 142

                        170
                 ....*....|....*.
gi 496494726 171 NTVKSRFYKMIRQIKS 186
Cdd:PRK12541 143 AKVKIELHRGRKETKS 158
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 146-179 4.96e-04

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


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 36.67  E-value: 4.96e-04
                          10        20        30
                  ....*....|....*....|....*....|....
gi 496494726  146 QEIFYMKCFEERTFQDISQTLNISENTVKSRFYK 179
Cdd:pfam08281  16 REVFLLRYLEGLSYAEIAELLGISEGTVKSRLSR 49
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 16-87 1.24e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 38.33  E-value: 1.24e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 496494726  16 DKEAANALISYYYKEVYAYVYRQTGNEELAKDLTQDIFIQILQKITIFDHKKASFRTWMYRIASNKICDHYR 87
Cdd:PRK12524  24 DPAAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQGEARVSTWLYRVVCNLCTDRLR 95
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 146-185 1.29e-03

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: 35.54  E-value: 1.29e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 496494726 146 QEIFYMKCFEERTFQDISQTLNISENTVKSRFYKMIRQIK 185
Cdd:cd06171   16 REVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK06704 PRK06704
RNA polymerase subunit sigma-70;
21-186 2.35e-03

RNA polymerase subunit sigma-70;


Pssm-ID: 180663 [Multi-domain]  Cd Length: 228  Bit Score: 37.70  E-value: 2.35e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726  21 NALISYYyKEVYAYVYRQTGNEELAKDLTQDIFIQILQKITifdhKKASFRTWMYRIASNKICDHYRSKVHRLSLKQEQi 100
Cdd:PRK06704  21 NFLIEQY-GELKRYCTFLTKNKWDGEDLAQETVCKVLQKYS----NKDICMTLVYKIARNRWLDQIKSKSVHEKIRDQI- 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496494726 101 dmtdeNLELHSGNLGtavrDLSELIihkeliediMEIVSLYKQEWQEIFYMKCFEERTFQDISQTLNISENTVKSRFYKM 180
Cdd:PRK06704  95 -----TFEEPHEKIA----DLHEMV---------GKVLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRS 156


                 ....*.
gi 496494726 181 IRQIKS 186
Cdd:PRK06704 157 RNRLKT 162
PRK12532 PRK12532
RNA polymerase sigma factor; Provisional
 44-110 6.24e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 171564 [Multi-domain]  Cd Length: 195  Bit Score: 36.06  E-value: 6.24e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 496494726  44 LAKDLTQDIFIQILQKITIFdHKKASFRTWMYRIASNKICDHYR-SKVHRLSLKQEQIDMTDENLELH 110
Cdd:PRK12532  32 LAEDLVQETLLSAYSAGDSF-QGRALVNSWLFAILKNKIIDALRqIGRQRKVFTLLDDELLDEAFESH 98
 
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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