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Conserved domains on  [gi|2570555548|ref|WP_307681313|]
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sigma-70 family RNA polymerase sigma factor [Thermoanaerobacter pentosaceus]

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]; ...
 4-177 6.78e-55

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: 172.10  E-value: 6.78e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548   4 EDLLGRAKAGETEAFEILVSEHQKYIYNVILKIVFDKEEALDLTQETLLKAYLNIKKFRGNSSIRTWLYRIAINCAIDYL 83
Cdd:COG1595     5 EELLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHL 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  84 RKRNVEKSNFKEIEEFENEikDFETPEEVLDKRLTAEMLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVKS 163
Cdd:COG1595    85 RKRRRRRELLDELAEELPD--EAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKS 162

                         170
                  ....*....|....
gi 2570555548 164 RLWRARNLLKERIK 177
Cdd:COG1595   163 RLSRARKKLREALE 176
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 4-177 6.78e-55

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: 172.10  E-value: 6.78e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548   4 EDLLGRAKAGETEAFEILVSEHQKYIYNVILKIVFDKEEALDLTQETLLKAYLNIKKFRGNSSIRTWLYRIAINCAIDYL 83
Cdd:COG1595     5 EELLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHL 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  84 RKRNVEKSNFKEIEEFENEikDFETPEEVLDKRLTAEMLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVKS 163
Cdd:COG1595    85 RKRRRRRELLDELAEELPD--EAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKS 162

                         170
                  ....*....|....
gi 2570555548 164 RLWRARNLLKERIK 177
Cdd:COG1595   163 RLSRARKKLREALE 176
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 9-181 7.55e-55

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 171.91  E-value: 7.55e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548   9 RAKAGETEAFEILVSEHQKYIYNVILKIVFDKEEALDLTQETLLKAYLNIKKFRGNSSIRTWLYRIAINCAIDYLRK--R 86
Cdd:PRK09652    3 RVQRGDRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRGGAAFYTWLYRIARNTAINYLRKqgR 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  87 NVEKSNFKEIEEFENEI----KDFETPEEVLDKRLTAEMLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVK 162
Cdd:PRK09652   83 RPPASDVDAEEAEDFDLadalRDISTPENELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVR 162

                         170
                  ....*....|....*....
gi 2570555548 163 SRLWRARNLLKERIKSLSE 181
Cdd:PRK09652  163 SRIFRAREALRAKLQPLLD 181
RpoE_Sigma70 TIGR02939
RNA polymerase sigma factor RpoE; A sigma factor is a DNA-binding protein protein that binds ...
 6-179 2.11e-41

RNA polymerase sigma factor RpoE; A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.


Pssm-ID: 131985 [Multi-domain]  Cd Length: 190  Bit Score: 138.04  E-value: 2.11e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548   6 LLGRAKAGETEAFEILVSEHQKYIYNVILKIVFDKEEALDLTQETLLKAYLNIKKFRGNSSIRTWLYRIAINCAIDYL-- 83
Cdd:TIGR02939  10 LVERVQRGEKQAFDLLVRKYQHKVVALVGRYVRDSSEVEDVAQEAFVKAYRALSSFRGDSAFYTWLYRIAVNTAKNHLva 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  84 RKRNVEKSNF--KEIEEFE--NEIKDFETPEEVLDKRLTAEMLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLG 159
Cdd:TIGR02939  90 QGRRPPTSDVeiEDAEHFEgaDRLREIDTPERLLLSRELEQTVMRAVEALPEDLRTAITLRELEGLSYEDIARIMDCPVG 169

                         170       180
                  ....*....|....*....|
gi 2570555548 160 TVKSRLWRARNLLKERIKSL 179
Cdd:TIGR02939 170 TVRSRIFRAREAIAIRLRPL 189
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 21-87 3.74e-15

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: 66.84  E-value: 3.74e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2570555548  21 LVSEHQKYIYNVILKIVFDKEEALDLTQETLLKAYLNIKKFRG--NSSIRTWLYRIAINCAIDYLRKRN 87
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPerGVSFSTWLYTIIRNAIIDYLRKQR 69
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 120-173 2.13e-10

Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP).


Pssm-ID: 100119 [Multi-domain]  Cd Length: 55  Bit Score: 54.03  E-value: 2.13e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2570555548 120 EMLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVKSRLWRARNLLK 173
Cdd:cd06171     2 ERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
CAS_III-E_sigma NF041236
type III-E CRISPR-associated RpoE-like sigma factor;
35-178 1.50e-08

type III-E CRISPR-associated RpoE-like sigma factor;


Pssm-ID: 469138 [Multi-domain]  Cd Length: 192  Bit Score: 51.99  E-value: 1.50e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  35 KIVFDKEEALDLTQETLLKAYLNIKKFRG--NSSIRTWLYRIAINCAIDYLRKRNVEKSNFKEIEEFENEIKDFetPEEV 112
Cdd:NF041236   42 YTGIPPEDREDILSETVEAVQRGIGKFEGrrGAKFSTWVWRIFRNKRVDYFRKKYKKKEYSLPLEGAEDDQEEE--PEDD 119

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2570555548 113 LDKRLTAEMLMREINKLPADYKIALI--LRDI-----EGLNYEEISKIMNLNLGTVKSRLWRARNLLKERIKS 178
Cdd:NF041236  120 IEEMFAAEDIIECLKKKVDDGETGCIrlLLDLyrwfkEGLTQKEMAESYGLKPNTLNQRISRCRKRIKQLLEE 192
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 4-177 6.78e-55

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: 172.10  E-value: 6.78e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548   4 EDLLGRAKAGETEAFEILVSEHQKYIYNVILKIVFDKEEALDLTQETLLKAYLNIKKFRGNSSIRTWLYRIAINCAIDYL 83
Cdd:COG1595     5 EELLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHL 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  84 RKRNVEKSNFKEIEEFENEikDFETPEEVLDKRLTAEMLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVKS 163
Cdd:COG1595    85 RKRRRRRELLDELAEELPD--EAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKS 162

                         170
                  ....*....|....
gi 2570555548 164 RLWRARNLLKERIK 177
Cdd:COG1595   163 RLSRARKKLREALE 176
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 9-181 7.55e-55

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 171.91  E-value: 7.55e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548   9 RAKAGETEAFEILVSEHQKYIYNVILKIVFDKEEALDLTQETLLKAYLNIKKFRGNSSIRTWLYRIAINCAIDYLRK--R 86
Cdd:PRK09652    3 RVQRGDRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRGGAAFYTWLYRIARNTAINYLRKqgR 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  87 NVEKSNFKEIEEFENEI----KDFETPEEVLDKRLTAEMLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVK 162
Cdd:PRK09652   83 RPPASDVDAEEAEDFDLadalRDISTPENELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVR 162

                         170
                  ....*....|....*....
gi 2570555548 163 SRLWRARNLLKERIKSLSE 181
Cdd:PRK09652  163 SRIFRAREALRAKLQPLLD 181
algU PRK11923
RNA polymerase sigma factor AlgU; Provisional
 4-181 1.91e-41

RNA polymerase sigma factor AlgU; Provisional


Pssm-ID: 171347 [Multi-domain]  Cd Length: 193  Bit Score: 138.40  E-value: 1.91e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548   4 EDLLGRAKAGETEAFEILVSEHQKYIYNVILKIVFDKEEALDLTQETLLKAYLNIKKFRGNSSIRTWLYRIAINCAIDYL 83
Cdd:PRK11923    8 QQLVERVQRGDKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDSAFYTWLYRIAINTAKNHL 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  84 RKRNVEK-SNFKEIEEFE-----NEIKDFETPEEVLDKRLTAEMLMREINKLPADYKIALILRDIEGLNYEEISKIMNLN 157
Cdd:PRK11923   88 VSRGRRPpDSDVSSEDAEfydgdHALKDIESPERALLRDEIEGTVHRTIQQLPEDLRTALTLREFDGLSYEDIASVMQCP 167

                         170       180
                  ....*....|....*....|....
gi 2570555548 158 LGTVKSRLWRARNLLKERIKSLSE 181
Cdd:PRK11923  168 VGTVRSRIFRAREAIDKALQPLLQ 191
RpoE_Sigma70 TIGR02939
RNA polymerase sigma factor RpoE; A sigma factor is a DNA-binding protein protein that binds ...
 6-179 2.11e-41

RNA polymerase sigma factor RpoE; A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.


Pssm-ID: 131985 [Multi-domain]  Cd Length: 190  Bit Score: 138.04  E-value: 2.11e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548   6 LLGRAKAGETEAFEILVSEHQKYIYNVILKIVFDKEEALDLTQETLLKAYLNIKKFRGNSSIRTWLYRIAINCAIDYL-- 83
Cdd:TIGR02939  10 LVERVQRGEKQAFDLLVRKYQHKVVALVGRYVRDSSEVEDVAQEAFVKAYRALSSFRGDSAFYTWLYRIAVNTAKNHLva 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  84 RKRNVEKSNF--KEIEEFE--NEIKDFETPEEVLDKRLTAEMLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLG 159
Cdd:TIGR02939  90 QGRRPPTSDVeiEDAEHFEgaDRLREIDTPERLLLSRELEQTVMRAVEALPEDLRTAITLRELEGLSYEDIARIMDCPVG 169

                         170       180
                  ....*....|....*....|
gi 2570555548 160 TVKSRLWRARNLLKERIKSL 179
Cdd:TIGR02939 170 TVRSRIFRAREAIAIRLRPL 189
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 6-179 1.30e-37

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 128.28  E-value: 1.30e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548   6 LLGRAKAGETEAFEILVSEHQKYIYNVILKIVFDKEEALDLTQETLLKAYLNIKKFRGNSSIRTWLYRIAINCAIDYLRK 85
Cdd:PRK09641    8 LIKQVKKGDQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINRKFSTWLYRIATNLTIDRLRK 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  86 RNVEKSNFKEIEEFENEI------KDFETPEEVLDKRLTAEMLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLG 159
Cdd:PRK09641   88 RKPDYYLDAEVAGTEGLTmysqlaADDALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYIEDLSLKEISEILDLPVG 167

                         170       180
                  ....*....|....*....|
gi 2570555548 160 TVKSRLWRARNLLKERIKSL 179
Cdd:PRK09641  168 TVKTRIHRGREALRKQLRHL 187
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 16-176 1.60e-37

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: 127.08  E-value: 1.60e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  16 EAFEILVSEHQKYIYNVILKIVFDKEEALDLTQETLLKAYLNIKKFRGNSSIRTWLYRIAINCAIDYLRKRNVEKSNFKE 95
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  96 IEEFENEIkdfETPEEVLDKRLTAEMLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVKSRLWRARNLLKER 175
Cdd:TIGR02937  81 LEELLDSD---PSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLREL 157


                  .
gi 2570555548 176 I 176
Cdd:TIGR02937 158 L 158
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 15-176 1.59e-36

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 125.08  E-value: 1.59e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  15 TEAFEILVSEHQKYIYNVILKIVFDKEEALDLTQETLLKAYLNIKKFRGNSSIRTWLYRIAINCAIDYLRKRNVEKSNFK 94
Cdd:PRK11924   12 KEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCYDLLRRRRREKAVLS 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  95 EIEEFENEIKDFETPEEVLDKRLTAEMLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVKSRLWRARNLLKE 174
Cdd:PRK11924   92 DDALEPEFAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQLLRE 171


                  ..
gi 2570555548 175 RI 176
Cdd:PRK11924  172 CL 173
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 1-181 1.17e-35

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 122.82  E-value: 1.17e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548   1 MGREDLLGRAKAGETEAFEILVSEHQKYIYNVILKIVFDKEEALDLTQETLLKAYLNIKKFRGNSSIRTWLYRIAINCAI 80
Cdd:PRK09638    3 MDEKELIQKAKKGDDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGRSKFSTWLISIASRLYK 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  81 DYLRKR-NVEKSNFKEIEEFENEIKdfetpEEVLDKRLTAEMLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLG 159
Cdd:PRK09638   83 DHLRKQkREKLRLQRAKEETLRKEK-----WEAAIKGAEWSEMLDALSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEG 157

                         170       180
                  ....*....|....*....|..
gi 2570555548 160 TVKSRLWRArnlLKERIKSLSE 181
Cdd:PRK09638  158 TVKSRVHHG---IKQLRKEWGQ 176
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 4-176 1.88e-35

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 123.92  E-value: 1.88e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548   4 EDLLGRAKAGETEAFEILVSEHQKYIYNVILKIVFDKEEALDLTQETLLKAYLNIKKFRGNSSIRTWLYRIAINCAIDYL 83
Cdd:PRK11922   18 RELVARVLAGDEAAFEALMRRHNRRLYRTARAILRNDAEAEDVVQEAYLRAFRALGTFRGDASLSTWLSRIVLNEALGRL 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  84 RKR--------NVEKSNFKEIEEFENEIKDfETPEEVLDKRLTAEMLMREINKLPADYKIALILRDIEGLNYEEISKIMN 155
Cdd:PRK11922   98 RRRrrlvnlaeMVMASTIAGGERTPLADPA-EDPERAAARREIRALLERAIDALPDAFRAVFVLRVVEELSVEETAQALG 176

                         170       180
                  ....*....|....*....|.
gi 2570555548 156 LNLGTVKSRLWRARNLLKERI 176
Cdd:PRK11922  177 LPEETVKTRLHRARRLLRESL 197
PRK09643 PRK09643
RNA polymerase sigma factor SigM; Reviewed
 5-179 7.36e-32

RNA polymerase sigma factor SigM; Reviewed


Pssm-ID: 236604 [Multi-domain]  Cd Length: 192  Bit Score: 113.65  E-value: 7.36e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548   5 DLLGRAKAGETEAFEILVSEHQKYIYNVILKIVFDKEEALDLTQETLLKAYLNIKKFRGNSSIRTWLYRIAINCAIDYLR 84
Cdd:PRK09643   16 ELLAAHVAGDRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGDAAVSSWLHRIVVNACLDRLR 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  85 KRNVEK-SNFKEIEEFENEIKDfetPEEVLDKRLTaemLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVKS 163
Cdd:PRK09643   96 RAKARPtVPLDDVYPVAQLERD---PTARVETALA---VQRALMRLPVEQRAALVAVDMQGYSVADAARMLGVAEGTVKS 169

                         170
                  ....*....|....*.
gi 2570555548 164 RLWRARNLLKERIKSL 179
Cdd:PRK09643  170 RCARGRARLAELLGYL 185
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 11-177 1.63e-29

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 107.14  E-value: 1.63e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  11 KAGETEAFEILVSEHQKYIYNVILKIVF----DKEEALDLTQETLLKAYLNIKKFRGNSSIRTWLYRIAINCAIDYLRKR 86
Cdd:PRK09415    7 EAFEIEDKEDLIDEIMNEYGQEVLQLVYsyvkNKEVAEDLTQEIFVKCYKSLHTYKGKSSLKTWLYRIAINHCKDYLKSW 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  87 NVEKSNFKEiEEFENEIKDFETPEEVLDKRLTAEMLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVKSRLW 166
Cdd:PRK09415   87 HNKKVIVTE-DIFTYMESQKESVEEEVIQNAEDERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLK 165

                         170
                  ....*....|.
gi 2570555548 167 RARNLLKERIK 177
Cdd:PRK09415  166 KAKELLKKGLE 176
SigW_bacill TIGR02948
RNA polymerase sigma-W factor; This sigma factor is restricted to certain lineages of the ...
 11-179 1.85e-29

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: 107.29  E-value: 1.85e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  11 KAGETEAFEILVSEHQKYIYNVILKIVFDKEEALDLTQETLLKAYLNIKKFRGNSSIRTWLYRIAINCAIDYLRKRnveK 90
Cdd:TIGR02948  13 RKGDENAFADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIRAYTNIDTYDIQRKFSTWLYRIATNLTIDRLRKR---K 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  91 SNFKEIEEFENE---------IKDFETPEEVLDKRLTAEMLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTV 161
Cdd:TIGR02948  90 PDFYLDDEVQGTdgltmesqlAADEAPPEDQVISLELRDTIQQEIQALPPKYRMVIVLKYMEDLSLKEISEILDLPVGTV 169

                         170
                  ....*....|....*...
gi 2570555548 162 KSRLWRARNLLKERIKSL 179
Cdd:TIGR02948 170 KTRIHRGREALRKQLRHL 187
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 4-176 8.58e-29

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 105.93  E-value: 8.58e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548   4 EDLLGRAKAGETEAFEILVSEHQKYIYNVILKIVFDKEEALDLTQETLLKAYLNIKKFRGNSSIRTWLYRIAINCAIDYL 83
Cdd:PRK12513   14 EALMLRYRAGDAAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPRARFRTWLYQIARNLLIDHW 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  84 RK-RNVEKSNFKEIEEFENEIKDFETPEEVLDKRLTAEMLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVK 162
Cdd:PRK12513   94 RRhGARQAPSLDADEQLHALADDGAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREHGDLELEEIAELTGVPEETVK 173

                         170
                  ....*....|....
gi 2570555548 163 SRLWRARNLLKERI 176
Cdd:PRK12513  174 SRLRYALQKLRELL 187
SigM_subfam TIGR02950
RNA polymerase sigma factor, SigM family; This family of RNA polymerase sigma factors is a ...
 23-176 1.04e-28

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: 104.46  E-value: 1.04e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  23 SEHQKYIYNVILKIVFDKEEALDLTQETLLKAYLNIKKFRGnSSIRTWLYRIAINCAIDYLRKRNVEKSNF-KEIEEFEn 101
Cdd:TIGR02950   2 REYMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKD-SSIKPWLFRIARNAFIDWYRKDKKIQTIDdDAIGDLE- 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2570555548 102 eIKDFETPEEVLDKRLTAEMLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVKSRLWRARNLLKERI 176
Cdd:TIGR02950  80 -QHPVESPEHHLLIKIEQEEITHHLSRLPENYRTVLILREFKEFSYKEIAELLNLSLAKVKSNLFRARKELKKLL 153
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 6-174 2.35e-28

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 104.03  E-value: 2.35e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548   6 LLGRAKAGETEAFEILVSEHQKYIYNVILKIVfDKEEALDLTQETLLKAYLNIKKFRGNSSIRTWLYRIAINCAIDYLRK 85
Cdd:PRK12518    1 LILRCQRGDRQSFRQLYRRYQQKVRSTLYQLC-GRELLDDLVQEVFLRVWKGLPKLRNPAYFSTWLYRITWNVATDARRQ 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  86 RNVEKSNFKEIEEFENEIKDFETPEEvldKRLTAEMLMRE-INKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVKSR 164
Cdd:PRK12518   80 FAQRPSRIQDDSLNDQPSRPSDTPDL---MQLHYQDLVQQgLQTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSR 156

                         170
                  ....*....|
gi 2570555548 165 LWRARNLLKE 174
Cdd:PRK12518  157 LFYARRQLRK 166
Sig70_famx3 TIGR02954
RNA polymerase sigma-70 factor, TIGR02954 family; This group of sigma factors are members of ...
 1-177 8.33e-28

RNA polymerase sigma-70 factor, TIGR02954 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. This family is found in certain Bacillus and Clostridium species.


Pssm-ID: 213752 [Multi-domain]  Cd Length: 169  Bit Score: 102.48  E-value: 8.33e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548   1 MGREDLLGRAKAGETEAFEILVSEHQKYIYNVILKIVFDKEEALDLTQETLLKAYLNIKKFRGNSSIRTWLYRIAINCAI 80
Cdd:TIGR02954   1 MNDEELVKKAKRGNKPAFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHPKYFNTWLTRILINECI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  81 DYLRKRnveksnfKEIEEFENEIKDFETPEEV-LDKRLTaemLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLG 159
Cdd:TIGR02954  81 DLLKKK-------KKVIPFDPNTSIEKGECEThADSRLD---LYKAIDTLNDKYQTAIILRYYHDLTIKEIAEVMNKPEG 150

                         170
                  ....*....|....*...
gi 2570555548 160 TVKSRLWRARNLLKERIK 177
Cdd:TIGR02954 151 TVKTYLHRALKKLKKRLE 168
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 23-174 3.09e-25

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 96.21  E-value: 3.09e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  23 SEHQKYIYNVILKIVFDKEEALDLTQETLLKAYLNIKKFRGNSSIRTWLYRIAINCAIDYLRKRNveksnfKEIEEFENE 102
Cdd:PRK09637    8 SEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDGSSIKSWLYQIANNTIIDFYRKKN------RSEELPDDL 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2570555548 103 IKDFETPEEVLDKRLtAEMLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVKSRLWRARNLLKE 174
Cdd:PRK09637   82 LFEDEEREENAKKEL-APCLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKE 152
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 16-176 8.13e-25

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: 94.55  E-value: 8.13e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  16 EAFEILVSEHQKYIYNVILKIVFDKEEALDLTQETLLKAYLNIKKFRGNSSIRTWLYRIAINCAIDYLRKRNVEKsNFKE 95
Cdd:TIGR02985   1 EAFEQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETLEISESIKAYLFTIVKNRCLNYLRHKQVEE-KYQE 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  96 --IEEFENEIKDFETPEEVLDKRLTaEMLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVKSRLWRARNLLK 173
Cdd:TIGR02985  80 elAEIEERELSEADPEEELEAKELE-EIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLR 158


                  ...
gi 2570555548 174 ERI 176
Cdd:TIGR02985 159 KEL 161
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 12-174 1.76e-24

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 94.85  E-value: 1.76e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  12 AGETEAFEILVSEHQKYIYNVILKIVFDKEEALDLTQETLLKAYLNIKK-----FRGnssirtWLYRIAINCAIDYLRKR 86
Cdd:PRK09647   24 KATMPSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNyqpgtFEG------WLHRITTNLFLDMVRRR 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  87 NveKSNFKEI-EEFENEIKDFETPEEVL-DKRLTAEmLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVKSR 164
Cdd:PRK09647   98 A--RIRMEALpEDYDRVPGDEPNPEQIYhDARLDPD-LQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSR 174

                         170
                  ....*....|
gi 2570555548 165 LWRARNLLKE 174
Cdd:PRK09647  175 IHRGRQQLRA 184
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 16-181 2.95e-23

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 90.78  E-value: 2.95e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  16 EAFEILVSEHQKYIYNVILKIVFDKEEALDLTQETLLKAYLNikKFRGNSSIRTWLYRIAINCAIDYLRKRNVEKSnfKE 95
Cdd:PRK09639    3 ETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRS--DFKGIENEKGWLIKSARNVAYNYLRSEKRRRA--RI 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  96 IEEFE-NEIKDFETPEEVLDKRLTAEMLMREINKLPADYKIALILRdIEGLNYEEISKIMNLNLGTVKSRLWRARNLLKE 174
Cdd:PRK09639   79 LGEFQwQEVDNEPSPEEIWIRKEEITKVQEVLAKMTERDRTVLLLR-FSGYSYKEIAEALGIKESSVGTTLARAKKKFRK 157


                  ....*..
gi 2570555548 175 RIKSLSE 181
Cdd:PRK09639  158 IYEQMEE 164
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 4-178 2.23e-22

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 89.02  E-value: 2.23e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548   4 EDLLGRAKAGETEAFEILVSEHQKYIYNVILKIVFDKEEALDLTQETLLKAYLNIKKFRGNSSIRTWLYRIAINCAIDYL 83
Cdd:PRK12515   10 EMLLARIAQGDRTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGRSQVSTWLLSIARFKALSAL 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  84 RKRNVEksnfkEIE-EFENEIKD-FETPEEVLDKRLTAEMLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTV 161
Cdd:PRK12515   90 RRRKHE-----EIDdEAAAAIEDgADTPEVALQKSDTSAALRACLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTV 164

                         170
                  ....*....|....*..
gi 2570555548 162 KSRLWRARNLLKERIKS 178
Cdd:PRK12515  165 KTRMFYARKKLAELLKA 181
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 4-174 2.60e-22

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 88.56  E-value: 2.60e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548   4 EDLLGRAKAGETEAFEILVSEHQKYIYNVILKIVFDKEEALDLTQETLLKAYLNIKKFR-GNSSIRTWLYRIAINCAIDY 82
Cdd:PRK05602    8 EELLARVAAGDPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRpGEARFDTWLHRVVLNLCYDR 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  83 LRKRNVEksnfkEIEEFENEIKDFETPEEVLDKRLTAEMLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVK 162
Cdd:PRK05602   88 LRRRREV-----PVEDAPDVPDPAPGPDAGLEARQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALE 162

                         170
                  ....*....|..
gi 2570555548 163 SRLWRARNLLKE 174
Cdd:PRK05602  163 SLLARGRRALRA 174
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 29-190 7.44e-22

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 86.86  E-value: 7.44e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  29 IYNVILKIVFDKEEALDLTQETLLKAYLNIKKFRgNSSIRTWLYRIAINCAIDYLRKRnvEKSNFKEIEEFENeiKDFET 108
Cdd:PRK09644   14 VYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYD-NQKVKPWLFKVAYHTFIDFVRKE--KKVSFVGTDEIEA--IQAES 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548 109 PEEVLDKRLTAEMLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVKSRLWRARNLLKERIKslseflslEER 188
Cdd:PRK09644   89 TEEYVVAKNSYEKLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLK--------EEK 160


                  ..
gi 2570555548 189 GQ 190
Cdd:PRK09644  161 SQ 162
PRK12517 PRK12517
RNA polymerase sigma factor; Provisional
 18-190 1.72e-20

RNA polymerase sigma factor; Provisional


Pssm-ID: 183569 [Multi-domain]  Cd Length: 188  Bit Score: 83.97  E-value: 1.72e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  18 FEILVSEHQKYIYNVILKIVFDKEEALDLTQETLLKAYLNIKKFRGNSSIRTWLYRIaincaidyLRKRNV---EKSNFK 94
Cdd:PRK12517   25 YEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDEKAAKAWLITI--------LRRENArrfERKQFD 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  95 --EIEEFENEIKDFETPEEVLDKrltaEMLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVKSRLWRARNLL 172
Cdd:PRK12517   97 lvDIEDDSIEDDASHSSEEEMEQ----EWLRRQIAKLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMTRLFRARNQL 172

                         170
                  ....*....|....*...
gi 2570555548 173 KERIKSlseflSLEERGQ 190
Cdd:PRK12517  173 KEALEK-----PDVQRGQ 185
SigE-fam_strep TIGR02983
RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors ...
 12-175 2.47e-20

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


Pssm-ID: 132028 [Multi-domain]  Cd Length: 162  Bit Score: 82.82  E-value: 2.47e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  12 AGETEAFEILVSEHQKYIYNVILKIVFDKEEALDLTQETLLKAYLNIKKFRGNSSIRTWLYRIAINCAIDYLRKRNVEKS 91
Cdd:TIGR02983   2 SATEEEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRDPDAPDAYVRRVLVNLARSRWRRRRLLEL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  92 NFKEIeefeneiKDFETPEEVLDKRLTAEmLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVKSRLWRARNL 171
Cdd:TIGR02983  82 PTREL-------PDAAAPDPAPDVALRAA-LARALRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALAR 153


                  ....
gi 2570555548 172 LKER 175
Cdd:TIGR02983 154 LREL 157
PRK12522 PRK12522
RNA polymerase sigma factor; Provisional
 16-177 6.98e-20

RNA polymerase sigma factor; Provisional


Pssm-ID: 183571 [Multi-domain]  Cd Length: 173  Bit Score: 82.22  E-value: 6.98e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  16 EAFEILVSEHQKYIYNVILKIVFDKEEALDLTQETLLKAYLNIKKFRGNSSIRTWLYRIAINCAIDYLRKR----NVEKS 91
Cdd:PRK12522    3 EKVEELIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVENYKKWITTICVRTFYDFYRKKkrwkDRILD 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  92 NFKEIEEFENEIKDFETPEEVLDKRLTAEMLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVKSRLWRARNL 171
Cdd:PRK12522   83 LFHKEDGGEIEFADDVNISEEFIQKVEAEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQ 162


                  ....*.
gi 2570555548 172 LKERIK 177
Cdd:PRK12522  163 MREHLE 168
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 15-181 7.27e-20

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 82.29  E-value: 7.27e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  15 TEAFEILVSEHQKYIYNVILKIVFDKEEALDLTQETLLKAYLNIKKFRGNSSIRTWLYRIAINCAIDYLRKRNvEKSNFK 94
Cdd:PRK09640   25 TRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGKSKFKTWLYSITYNECITQYRKER-RKRRLM 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  95 EIEEFENEIKDFETPEEVLDKRLTAEMLMREINklPADYKIaLILRDIEGLNYEEISKIMNLNLGTVKSRLWRARNLLKE 174
Cdd:PRK09640  104 DALSLDPLEEASEEKAPKPEERGGLDRWLVHVN--PIDREI-LVLRFVAELEFQEIADIMHMGLSATKMRYKRALDKLRE 180


                  ....*..
gi 2570555548 175 RIKSLSE 181
Cdd:PRK09640  181 KFAGLAE 187
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 11-184 9.35e-20

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 82.09  E-value: 9.35e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  11 KAGETEAFEILVSEHQKYIYNVILKIVFDKEEALDLTQETLLKAYLNIKKFRGNSSIRTWLYRIAINCAIDYLRKRNVEK 90
Cdd:PRK12543    2 LSGDQEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNRPFRFWLIGLVIKQIHSWRRKRWRRF 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  91 SNFKEIEEFENEIKdFETPEEVLDKRlTAEMLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVKSRLWRARN 170
Cdd:PRK12543   82 RIFEKAEEQRKPVS-IDFSEDVLSKE-SNQELIELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAALK 159

                         170
                  ....*....|....
gi 2570555548 171 LLKERIKSLSEFLS 184
Cdd:PRK12543  160 KLRQKEQIEEIFLG 173
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 16-175 7.09e-19

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 79.21  E-value: 7.09e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  16 EAFEILVSEHQKYIYNVILKIVFDKEEALDLTQETLLKAYLNIKKFRGnSSIRTWLYRIAINCAIDYLRKRNVEKSNfkE 95
Cdd:PRK12541    5 QSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKG-EEIRPWLFTIAYNAFIDWYRKEKKYKTT--T 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  96 IEEFENEIKDfETPEEVLDKRLTAEMLMReINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVKSRLWRARNLLKER 175
Cdd:PRK12541   82 IEEFHLPNVP-STEHEYFIKHEIASWLDS-LSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKETKSI 159
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
 43-191 1.01e-18

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 79.50  E-value: 1.01e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  43 ALDLTQETLLKAYLNIKKFRGNSSIRTWLYRIAINCAIDYLRKRNveksnfKEIEEFENEIKD--FETPEEvlDKRLTAE 120
Cdd:PRK12546   34 ADDLVQDTIVKAWTNFDKFQEGTNLRAWLFTILRNTFYSDRRKHK------REVPDPEGVHAAslAVKPAH--DGRLAMS 105

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2570555548 121 MLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVKSRLWRARNllkerikSLSEFLSLEERGQL 191
Cdd:PRK12546  106 DFRAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARA-------RLAELLQLEEGEEL 169
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
 4-177 2.65e-18

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 79.13  E-value: 2.65e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548   4 EDLLGRAKAGETEAFEILVSEHQKYIYNVILKIVFDKEEALDLTQETLLKAYLNIKKFR-GNSSIRTWLYRIAINCAIDY 82
Cdd:PRK12538   51 EELLDRLATDDEAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQhGRAKFSTWLYRVVSNRCIDL 130

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  83 LRKRNVEksNFKEIEEFENEIKDFETpeeVLDKRLTAEMLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVK 162
Cdd:PRK12538  131 RRKPRTE--NVDAVPEVADGKPDAVS---VIERNELSDLLEAAMQRLPEQQRIAVILSYHENMSNGEIAEVMDTTVAAVE 205

                         170
                  ....*....|....*
gi 2570555548 163 SRLWRARNLLKERIK 177
Cdd:PRK12538  206 SLLKRGRQQLRDLLR 220
SigX5 TIGR02960
RNA polymerase sigma-70 factor, TIGR02960 family; This group of sigma factors are members of ...
 12-175 3.03e-18

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: 80.67  E-value: 3.03e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  12 AGETEAFEILVSEHQKYIYNVILKIVFDKEEALDLTQETLLKAYLNIKKFRGNSSIRTWLYRIAINCAIDYLRKRN---- 87
Cdd:TIGR02960   1 SVDGAAFTALAEPHRRELLAHCYRMLGSLHEAEDLVQETLLRAWRARDRFEGRSSVRTWLYRIATNACLDALEARQrrpr 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  88 ---------------VEKSNFKEIE-----EFENEIKDFETPEEVLDKRLTAEM-LMREINKLPADYKIALILRDIEGLN 146
Cdd:TIGR02960  81 pvglgapsadgtaaaSEAAEVTWLEplpdlTLDLDDPAAADPSVAAGSRESVRLaFVAAIQYLPPRQRAVLLLRDVLGWR 160

                         170       180
                  ....*....|....*....|....*....
gi 2570555548 147 YEEISKIMNLNLGTVKSRLWRARNLLKER 175
Cdd:TIGR02960 161 AAETAELLGTSTASVNSALQRARATLDEV 189
PRK12535 PRK12535
RNA polymerase sigma factor; Provisional
 5-169 5.19e-18

RNA polymerase sigma factor; Provisional


Pssm-ID: 237130 [Multi-domain]  Cd Length: 196  Bit Score: 77.63  E-value: 5.19e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548   5 DLLGRAKAGETEAFEILVSEHQKYIYNvILKIVFDKEEALDLTQETLLKAYLNIKKFRGNSSIRTWLYRIAINCAIDYLR 84
Cdd:PRK12535   14 DLALAAGRGDRAALTEFIRETQDDVWR-LLAHLGGHDIADDLTQETYLRVMSALPRFAARSSARTWLLSLARRVWVDNIR 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  85 KRNVEKSnfKEIEEFENEIKDFETPE------EVLDKRLTaemlmreINKLPADYKIALILRDIEGLNYEEISKIMNLNL 158
Cdd:PRK12535   93 HDMARPR--KSATEYEDAAATTASNEttgswsEWIDVRTL-------IDALPPERREALILTQVLGYTYEEAAKIADVRV 163

                         170
                  ....*....|.
gi 2570555548 159 GTVKSRLWRAR 169
Cdd:PRK12535  164 GTIRSRVARAR 174
PRK08241 PRK08241
RNA polymerase subunit sigma-70;
5-175 6.87e-18

RNA polymerase subunit sigma-70;


Pssm-ID: 236196 [Multi-domain]  Cd Length: 339  Bit Score: 79.60  E-value: 6.87e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548   5 DLLGRAKAGETEAFEILVSEHQK----YIYNvILKIVFDKEealDLTQETLLKAYLNIKKFRGNSSIRTWLYRIAINCAI 80
Cdd:PRK08241    8 ALLARAAAGDRDAFAALVEPHRRellaHCYR-MLGSVHDAE---DAVQETLLRAWRGYDRFEGRSSLRTWLYRIATNVCL 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  81 DYLRKRN-------------------VEKSNFKEIEEFENEIKDFET--PEEVLDKRLTAEM-LMREINKLPADYKIALI 138
Cdd:PRK08241   84 DALEGRArrplptdlgapaadpvdelVERPEVPWLEPYPDALLDPAAadPAARVVARESVRLaFVAALQHLPPRQRAVLI 163

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 2570555548 139 LRDIEGLNYEEISKIMNLNLGTVKSRLWRARNLLKER 175
Cdd:PRK08241  164 LRDVLGWSAAEVAELLDTSVAAVNSALQRARATLAER 200
PRK12540 PRK12540
RNA polymerase sigma factor; Provisional
 41-174 2.39e-17

RNA polymerase sigma factor; Provisional


Pssm-ID: 183579 [Multi-domain]  Cd Length: 182  Bit Score: 75.77  E-value: 2.39e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  41 EEALDLTQETLLKAYLNIKKFRGNSSIRTWLYRIAINCAIDYLRKRNveksnfKEIEEFENEIKDFETPEEVLDKRLTAE 120
Cdd:PRK12540   30 DRADDLVQETLLRALANIDSFQPGSNLPAWLFTILRNLFRSDYRKRR------REVEDADGSYAKTLKSQPGQNAHLEFE 103

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2570555548 121 MLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVKSRLWRARNLLKE 174
Cdd:PRK12540  104 EFRAALDKLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARSKLSA 157
PRK09649 PRK09649
RNA polymerase sigma factor SigC; Reviewed
 5-172 2.85e-17

RNA polymerase sigma factor SigC; Reviewed


Pssm-ID: 137458 [Multi-domain]  Cd Length: 185  Bit Score: 75.46  E-value: 2.85e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548   5 DLLGRAKAGETEAFEILVSEHQKYIYNVILKIVfDKEEALDLTQETLLKAYLNIKKFRGNSSIRTWLYRIAINCAIDYLR 84
Cdd:PRK09649   13 ALALSAAKGNGRALEAFIKATQQDVWRFVAYLS-DVGSADDLTQETFLRAIGAIPRFSARSSARTWLLAIARHVVADHIR 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  85 KRNVEKSNFKEIEefeneikdfetPEEVLDKRLTA---EMLMR---EINKLPADYKIALILRDIEGLNYEEISKIMNLNL 158
Cdd:PRK09649   92 HVRSRPRTTRGAR-----------PEHLIDGDRHArgfEDLVEvttMIADLTTDQREALLLTQLLGLSYADAAAVCGCPV 160

                         170
                  ....*....|....
gi 2570555548 159 GTVKSRLWRARNLL 172
Cdd:PRK09649  161 GTIRSRVARARDAL 174
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 39-174 7.19e-16

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 71.74  E-value: 7.19e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  39 DKEEALDLTQETLLKAYLNIKKFRGNSSIRTWLYRIAINCAIDYLRKRNVEKsnfKEIEEFENEIKDFETPEEVLDKRLt 118
Cdd:PRK12511   27 DSAEAEDLVHDALVRALERRASFRSGGNLRTWLMSILHNAFIDELRRRRVEA---RRADELAVLADASLPAAQEHAVRL- 102

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2570555548 119 aeMLMRE-INKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVKSRLWRARNLLKE 174
Cdd:PRK12511  103 --AQIRDaFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAALRA 157
PRK09642 PRK09642
RNA polymerase sigma factor;
25-183 1.26e-15

RNA polymerase sigma factor;


Pssm-ID: 170031 [Multi-domain]  Cd Length: 160  Bit Score: 70.51  E-value: 1.26e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  25 HQKYIYNVILKIVFDKEEALDLTQETLLKAYLNIK--KFRGnssIRTWLYRIAINCAIDYLRKRNVEKSNFKEIEEFENE 102
Cdd:PRK09642    4 YRHYIFQVIFSILRHEEDAKDVTQEVFVKIHASLPnyQFRG---LKTWMARIATNHAIDYKRKKARENEELSLCKETEEN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548 103 IKDFETPEEVLDKRLTAEMLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVKSRLWRARNLLKERIKSlSEF 182
Cdd:PRK09642   81 IKSSHNIEDLLLTKEQKLLIAQKLRELPENYRDVVLAHYLEEKSYQEIALQEKIEVKTVEMKLYRARKWIKKHWKE-EEF 159


                  .
gi 2570555548 183 L 183
Cdd:PRK09642  160 L 160
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 4-173 1.77e-15

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 71.07  E-value: 1.77e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548   4 EDLLGRAKAGETEAFEILVSEHQKYIYNVILKIVFDKEEALDLTQETLLKAYLNIKKFR-GNSSIRTWLYRIAINCAIDY 82
Cdd:PRK12524   14 EALLVLYANGDPAAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRqGEARVSTWLYRVVCNLCTDR 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  83 LRKRNVEKSNFKEIEEFENeikDFETPEEVLDKRLTAEMLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVK 162
Cdd:PRK12524   94 LRRRRRASVDLDDAPEPAD---AAPGAEEALIEGDRMRALDAALAALPERQRQAVVLRHIEGLSNPEIAEVMEIGVEAVE 170

                         170
                  ....*....|.
gi 2570555548 163 SRLWRARNLLK 173
Cdd:PRK12524  171 SLTARGKRALA 181
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 21-87 3.74e-15

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: 66.84  E-value: 3.74e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2570555548  21 LVSEHQKYIYNVILKIVFDKEEALDLTQETLLKAYLNIKKFRG--NSSIRTWLYRIAINCAIDYLRKRN 87
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPerGVSFSTWLYTIIRNAIIDYLRKQR 69
PRK12533 PRK12533
RNA polymerase sigma factor; Provisional
 8-172 5.48e-15

RNA polymerase sigma factor; Provisional


Pssm-ID: 237129 [Multi-domain]  Cd Length: 216  Bit Score: 70.14  E-value: 5.48e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548   8 GRAKAGETEAFEILVSEHQKYIYNVILKIVFDKEEALDLTQETLLKAYLNIKKFRGNSSiRTWLYRIAINCAIDYLRKRN 87
Cdd:PRK12533   10 AMDAAARGERFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSFRGDNA-RPWLLAIVRHTWYSEWRRRA 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  88 -----VEKSNFKEIEEFENEIKDFETPEEVL----DKRLTAEMLMReinkLPADYKIALILRDIEGLNYEEISKIMNLNL 158
Cdd:PRK12533   89 nahevAAPDTLDDADSLDDWQPAGEDPLALLlraeDVRLVNAALAK----LPVEYREVLVLRELEDMSYREIAAIADVPV 164

                         170
                  ....*....|....
gi 2570555548 159 GTVKSRLWRARNLL 172
Cdd:PRK12533  165 GTVMSRLARARRRL 178
Sig-70_plancto1 TIGR02984
RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1; This group of sigma ...
 10-174 9.83e-15

RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1; This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).


Pssm-ID: 274375 [Multi-domain]  Cd Length: 189  Bit Score: 68.89  E-value: 9.83e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  10 AKAGETEAFEILVSEHQKYIYNV----ILKIVFDKEEALDLTQETLLKAYLNIKKFRGNS--SIRTWLYRIAINCAIDYL 83
Cdd:TIGR02984   1 ARGGDREALGELLDRYRNYLRLLarvqLDPRLRRRVDPSDLVQETLLEAHRRFDQFRGKTegEFAGWLRGILSNVLADAL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  84 R------KRNVEK----SNFKEIEE----FENEIKDFE-TPEEVLDKRLTAEMLMREINKLPADYKIALILRDIEGLNYE 148
Cdd:TIGR02984  81 RrhlgaqKRDIRReqslDAGGRLDEssvrLEAQLAADGpSPSQVAARRESAVRLAQALAKLPEDYREVILLRHLEGLSFA 160

                         170       180
                  ....*....|....*....|....*.
gi 2570555548 149 EISKIMNLNLGTVKSRLWRARNLLKE 174
Cdd:TIGR02984 161 EVAERMDRSEGAVSMLWVRGLARLRQ 186
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
14-189 4.82e-14

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 66.64  E-value: 4.82e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  14 ETEAFEILVSEHQKYIYNVILKIVFDKEEALDLTQETLLKAYLNIKKF-RGNSSIRTWLYRIAINCAIDYLRKRnveKSN 92
Cdd:PRK09645    7 EAALMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLaDTGRSARAWLFTVARNLVIDERRSA---RAR 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  93 FKEIEEFENEIKDFETPEEVlDKRLTAeMLMRE-INKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVKSRLWRARNL 171
Cdd:PRK09645   84 PVEGGDDVLGVPEQSAPDEV-DRALDR-LLVADaLAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYALRA 161

                         170
                  ....*....|....*...
gi 2570555548 172 LKerikslsefLSLEERG 189
Cdd:PRK09645  162 LR---------LALQERG 170
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 41-177 4.91e-14

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 66.91  E-value: 4.91e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  41 EEALDLTQETLLKAYLNIKKFRGNSSIRTWLYRIAINCAIDYLRKRNVEKSNFKEIeeFENEIKDFETPEEVLDkrltAE 120
Cdd:PRK12516   35 DRADDLVQDTIMKAWAKQDHFEVGTNMKAWLFTILRNEFYSQMRKRGREVQDTDGM--FTEQLAVHPSQYGTLD----LQ 108

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2570555548 121 MLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVKSRLWRARNLLKERIK 177
Cdd:PRK12516  109 DFRAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQRLQEILQ 165
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 11-181 5.80e-14

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 67.01  E-value: 5.80e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  11 KAGETEAFEILVSEHQKYIYNVILKIVFDKEEALDLTQETLL----KAYLNIKkfRGnsSIRTWLYRIAINCAIDYLRKR 86
Cdd:PRK12519   24 KAGQSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLslwrKSSYDPK--RG--SLSSYLLTLTRSRAIDRLRSR 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  87 nveKSNFKEIEEFENEIKDfETPEEVLDKRLTAEMLMREIN----KLPADYKIALILRDIEGLNYEEISKIMNLNLGTVK 162
Cdd:PRK12519  100 ---RSRQRLLERWQQELLG-EASEDTPLEQASLAERSQRVQtalaQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVK 175

                         170
                  ....*....|....*....
gi 2570555548 163 SRLWRARNLLKERIKSLSE 181
Cdd:PRK12519  176 ARARQGLLKLRELLQDLLE 194
PRK09047 PRK09047
RNA polymerase factor sigma-70; Validated
 39-177 7.69e-14

RNA polymerase factor sigma-70; Validated


Pssm-ID: 236367 [Multi-domain]  Cd Length: 161  Bit Score: 65.76  E-value: 7.69e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  39 DKEEALDLTQETLLKAylnIKKFrGNSSIRTW---LYRIAINCAIDYLRKRNV---------------EKSNFKEIEEFE 100
Cdd:PRK09047    3 DDDAALDIVQDAMIKL---AEKY-GDRPAAEWpplFQRILQNRIHDWFRRQKVrntwvslfssfsdddDDDDFDPLETLD 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2570555548 101 NEIKDFETPEEVLDKRLTAEMLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVKSRLWRARNLLKERIK 177
Cdd:PRK09047   79 SADEGAESPADKLERAQVLQLIEEAIQKLPARQREAFLLRYWEDMDVAETAAAMGCSEGSVKTHCSRATHALAKALE 155
PRK12547 PRK12547
RNA polymerase sigma factor; Provisional
 41-177 8.21e-14

RNA polymerase sigma factor; Provisional


Pssm-ID: 139056 [Multi-domain]  Cd Length: 164  Bit Score: 66.05  E-value: 8.21e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  41 EEALDLTQETLLKAYLNIKKFRGNSSIRTWLYRIAINCAIDYLRKRNveksnfKEIEEFENEIKDFETPEEVLDKRLTAE 120
Cdd:PRK12547   31 DKAEDLVQDTLMKAWAKQDSFEMGTNLKAWLFTILRNEFYSQMRKRG------REVQDSDGVFTARVAVHPAQYGSLDLQ 104

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2570555548 121 MLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVKSRLWRARNLLKERIK 177
Cdd:PRK12547  105 DFKKALNLLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARNRLQELLK 161
Sig70_famx1 TIGR02943
RNA polymerase sigma-70 factor, TIGR02943 family; This group of sigma factors are members of ...
 39-174 2.13e-13

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: 65.17  E-value: 2.13e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  39 DKEEALDLTQETLLKAYLNIKKFRGNSSIRTWLYRIAINCAIDYLRKRNVEKSNFKEIEEFENE---------------- 102
Cdd:TIGR02943  25 DRDLAEDAVQETLLAALSHRDSFAGRSALKTWLFAILKNKIIDALRAKGREVKVSDLDDELDDEafnalftqnghwaqhg 104

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2570555548 103 -IKDFETPEEVLDKRLTAEMLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVKSRLWRARNLLKE 174
Cdd:TIGR02943 105 qPQHWNTPEKQLENKEFWEVFEACLYHLPEQTARVFMMREVLGFESDEICQELEISTSNCHVLLYRARLSLRA 177
PRK12531 PRK12531
RNA polymerase sigma factor; Provisional
 1-165 2.86e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 105726 [Multi-domain]  Cd Length: 194  Bit Score: 64.95  E-value: 2.86e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548   1 MGRED---LLGRAKAGETEAFEILVSEHQKYIYNVILKIVFDKEEALDLTQETLLKAYLNIKKFRGN-SSIRTWLYRIAI 76
Cdd:PRK12531    9 FGRQEwleCMEKVKSRDKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQkSALSTWIYTIIR 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  77 NCAIDYLRKR-----NVEKSNFKEIEEFENEIKDFETPEEVLDKrltaEMLMREINKLPADYKIALILRDIEGLNYEEIS 151
Cdd:PRK12531   89 NLCFDLLRKQkgkdlHIHADDIWPSDYYPPDLVDHYSPEQDMLK----EQVMKFLDRLPKAQRDVLQAVYLEELPHQQVA 164

                         170
                  ....*....|....
gi 2570555548 152 KIMNLNLGTVKSRL 165
Cdd:PRK12531  165 EMFDIPLGTVKSRL 178
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 4-175 7.59e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 63.69  E-value: 7.59e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548   4 EDLLGRAKAGETEAFEILVSEHQKYIYNVILKIVFDKEEALDLTQETLLKAYLNIKKFR-GNSSIRTWLYRIAINCAIDY 82
Cdd:PRK12514    7 EKLIVRVSLGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAvSGLSPMTWLITIARNHAIDR 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  83 LRKRNVEKSNFKEIEEFENEIKDFETPEEVLDKRLTAEMLMREinkLPADYKIALILRDIEGLNYEEISKIMNLNLGTVk 162
Cdd:PRK12514   87 LRARKAVAVDIDEAHDLADPSPGPEAEVIAGDEGQRIDACLEE---LEKDRAAAVRRAYLEGLSYKELAERHDVPLNTM- 162

                         170
                  ....*....|...
gi 2570555548 163 sRLWRARNLLKER 175
Cdd:PRK12514  163 -RTWLRRSLLKLR 174
PRK06811 PRK06811
RNA polymerase factor sigma-70; Validated
 1-181 1.70e-12

RNA polymerase factor sigma-70; Validated


Pssm-ID: 180707 [Multi-domain]  Cd Length: 189  Bit Score: 62.65  E-value: 1.70e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548   1 MGREDLLGRAKAGETEAFEILVSEHQKYIYNVILKI---VFDKEEALDLTQETLLKAYLNIKKFRGN-SSIRTWLYRIAI 76
Cdd:PRK06811    3 INEDNFIKELKKKNEKALEFIVDTYGNLVKKIVHKVlgtVNYSQLIEECVNDIFLSIWNNIDKFDEEkGSFKKWIAAISK 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  77 NCAIDYLRKrNVEKSNFKEIEEFEneIKDFETPEEVLDKRLTAEMLMREINKL-PADYKIaLILRDIEGLNYEEISKIMN 155
Cdd:PRK06811   83 YKAIDYKRK-LTKNNEIDSIDEFI--LISEESIENEIILKENKEEILKLINDLeKLDREI-FIRRYLLGEKIEEIAKKLG 158

                         170       180
                  ....*....|....*....|....*.
gi 2570555548 156 LNLGTVKSRLWRARNLLKERIKSLSE 181
Cdd:PRK06811  159 LTRSAIDNRLSRGRKKLQKNKLNISL 184
PRK12534 PRK12534
RNA polymerase sigma factor; Provisional
 6-173 4.64e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 183576 [Multi-domain]  Cd Length: 187  Bit Score: 61.61  E-value: 4.64e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548   6 LLGRAKAGETEAFEILVSEHQKYIYNVILKIVFDKEEALDLTQETLLKAYLNIKKF-----RGnssiRTWLYRIAINCAI 80
Cdd:PRK12534   15 LLTATAGGDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFdpsraRG----LTWLAMIARNKAI 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  81 DYLRKRNVEKSNFKeIEEFENEIKDFETPEEVLDKRLTAEMLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGT 160
Cdd:PRK12534   91 DHLRANAPQRRNVA-LDDAGELRAADASPLERTERASTRRRIDHCLAELEPPRSELIRTAFFEGITYEELAARTDTPIGT 169

                         170
                  ....*....|...
gi 2570555548 161 VKSrlWRARNLLK 173
Cdd:PRK12534  170 VKS--WIRRGLAK 180
PRK12532 PRK12532
RNA polymerase sigma factor; Provisional
 43-174 6.41e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 171564 [Multi-domain]  Cd Length: 195  Bit Score: 61.48  E-value: 6.41e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  43 ALDLTQETLLKAYLNIKKFRGNSSIRTWLYRIAINCAIDYLRKRNVEKSNFKEI------EEFENEIK------------ 104
Cdd:PRK12532   33 AEDLVQETLLSAYSAGDSFQGRALVNSWLFAILKNKIIDALRQIGRQRKVFTLLddelldEAFESHFSqnghwtpegqpq 112

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548 105 DFETPEEVLDKRLTAEMLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVKSRLWRARNLLKE 174
Cdd:PRK12532  113 HWNTPEKSLNNNEFQKILQSCLYNLPENTARVFTLKEILGFSSDEIQQMCGISTSNYHTIMHRARESLRQ 182
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 120-172 1.74e-11

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


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 56.70  E-value: 1.74e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2570555548 120 EMLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVKSRLWRARNLL 172
Cdd:pfam08281   2 EALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 1-177 3.44e-11

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 59.16  E-value: 3.44e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548   1 MGREDLLGRAKAGETEAFEILVSEHQKYIYNVILKIVFDKEEALDLTQETLLKAYLNIKKFR-GNSSIRTWLYRIAINCA 79
Cdd:PRK13919    8 LSDEALLALVARGEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDpRRGSARAWLLALAHHAA 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  80 IDYLRKRNVEKsnfKEIEEFENEIKDFETPEEVLDK--RLTAEMLMREINKLPADYKIALILRDIEGLNYEEISKIMNLN 157
Cdd:PRK13919   88 VDHVRRRAARP---QPLEPDEREPEAFDLPGPGLDEegHLDRTRLGRALKALSPEERRVIEVLYYQGYTHREAAQLLGLP 164

                         170       180
                  ....*....|....*....|
gi 2570555548 158 LGTVKSRLWRARNLLKERIK 177
Cdd:PRK13919  165 LGTLKTRARRALSRLKEVLR 184
PRK06704 PRK06704
RNA polymerase subunit sigma-70;
39-175 5.64e-11

RNA polymerase subunit sigma-70;


Pssm-ID: 180663 [Multi-domain]  Cd Length: 228  Bit Score: 59.27  E-value: 5.64e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  39 DKEEALDLTQETLLKAylnIKKFRGNSSIRTWLYRIAINCAIDYLRKRNVEksnfkeiEEFENEIKdFETPEEVLDKrlT 118
Cdd:PRK06704   40 NKWDGEDLAQETVCKV---LQKYSNKDICMTLVYKIARNRWLDQIKSKSVH-------EKIRDQIT-FEEPHEKIAD--L 106

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2570555548 119 AEMLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVKSRLWRARNLLKER 175
Cdd:PRK06704  107 HEMVGKVLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRLKTV 163
PRK12544 PRK12544
RNA polymerase factor sigma-70;
39-174 2.08e-10

RNA polymerase factor sigma-70;


Pssm-ID: 183583 [Multi-domain]  Cd Length: 206  Bit Score: 57.50  E-value: 2.08e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  39 DKEEALDLTQETLLKAYLNIKKFRGNSSIRTWLYRIAINCAIDYLR--KRNVEKSN-FKEIEEFEN-----EIKDFETPE 110
Cdd:PRK12544   41 DLHLAEDAVQEALIGALKNADSFAGRAAFKTWVFAILKNKIIDLLRqkKRHVSASSlLRDEEEEEDfeelfDESGHWQKD 120

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2570555548 111 EVLDKRLTAEMLMRE----------INKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVKSRLWRARNLLKE 174
Cdd:PRK12544  121 ERPQAWGNPEESLEQeqfwrifeacLDGLPAKYARVFMMREFIELETNEICHAVDLSVSNLNVLLYRARLRLRE 194
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 120-173 2.13e-10

Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP).


Pssm-ID: 100119 [Multi-domain]  Cd Length: 55  Bit Score: 54.03  E-value: 2.13e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2570555548 120 EMLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVKSRLWRARNLLK 173
Cdd:cd06171     2 ERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 16-174 1.03e-09

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


Pssm-ID: 274379 [Multi-domain]  Cd Length: 159  Bit Score: 54.63  E-value: 1.03e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  16 EAFEILVSEHQKYIYNVILKIVFDKEEALDLTQETLLKAYLNIKKFRGNSSIRTWLYRIAINCAIDYLRKRNveksnfKE 95
Cdd:TIGR02989   1 KAFVRLLTRHERALRAFVRSLVADRDDVDDVLQETFVVAWRKFDQFDPGTNFVAWARGIARNKVLNYRRKLG------RD 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  96 IEEFENEIKDF--ETPEEVLDKRLTAEM--LMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVKSRLWRARNL 171
Cdd:TIGR02989  75 RLVFDDDLLEAlaAEAEPTEAERLSDDRqaLEGCLEKLPERQRELLDLRYQRGQKATALAEQTGRTVNAVYKALQRIRVS 154


                  ...
gi 2570555548 172 LKE 174
Cdd:TIGR02989 155 LRE 157
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 39-177 1.24e-08

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 51.70  E-value: 1.24e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  39 DKEEALDLTQEtllkAYLNIKKFRGNSSI---RTWLYRIAINCAIDYLRKRNVEKSnfKEIEEFENEIKDFE-TPEEVLD 114
Cdd:PRK12527   18 NRQAAEDVAHD----AYLRVLERSSSAQIehpRAFLYRTALNLVVDRHRRHRVRQA--EPLEVLDEEERLHSpSPQTRLD 91

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2570555548 115 KRLTAEMLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVKSRLWRARNLLKERIK 177
Cdd:PRK12527   92 LGQRLALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMR 154
CAS_III-E_sigma NF041236
type III-E CRISPR-associated RpoE-like sigma factor;
35-178 1.50e-08

type III-E CRISPR-associated RpoE-like sigma factor;


Pssm-ID: 469138 [Multi-domain]  Cd Length: 192  Bit Score: 51.99  E-value: 1.50e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  35 KIVFDKEEALDLTQETLLKAYLNIKKFRG--NSSIRTWLYRIAINCAIDYLRKRNVEKSNFKEIEEFENEIKDFetPEEV 112
Cdd:NF041236   42 YTGIPPEDREDILSETVEAVQRGIGKFEGrrGAKFSTWVWRIFRNKRVDYFRKKYKKKEYSLPLEGAEDDQEEE--PEDD 119

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2570555548 113 LDKRLTAEMLMREINKLPADYKIALI--LRDI-----EGLNYEEISKIMNLNLGTVKSRLWRARNLLKERIKS 178
Cdd:NF041236  120 IEEMFAAEDIIECLKKKVDDGETGCIrlLLDLyrwfkEGLTQKEMAESYGLKPNTLNQRISRCRKRIKQLLEE 192
PRK09646 PRK09646
ECF RNA polymerase sigma factor SigK;
4-165 1.52e-08

ECF RNA polymerase sigma factor SigK;


Pssm-ID: 182015 [Multi-domain]  Cd Length: 194  Bit Score: 51.98  E-value: 1.52e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548   4 EDLLGRAKAGETEAFEILVSEHQKYIYNVILKIVFDKEEALDLTQETLLKAYLNIKKF---RGnsSIRTWLYRIAINCAI 80
Cdd:PRK09646   18 DALLRRVARGDQDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFdpaRG--SALAWLLTLAHRRAV 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  81 DylRKRNVEKSNFKEIEEfenEIKDFETP-----EEVlDKRLTAEMLMREINKLPADYKIALILRDIEGLNYEEISKIMN 155
Cdd:PRK09646   96 D--RVRSEQAASQREVRY---GARNVDPAfdqvaEEV-EARLERERVRDCLDALTDTQRESVTLAYYGGLTYREVAERLA 169

                         170
                  ....*....|
gi 2570555548 156 LNLGTVKSRL 165
Cdd:PRK09646  170 VPLGTVKTRM 179
PRK12530 PRK12530
RNA polymerase sigma factor; Provisional
 39-169 4.44e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 237128 [Multi-domain]  Cd Length: 189  Bit Score: 50.92  E-value: 4.44e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  39 DKEEALDLTQETLLKAYLNIKKFRGNSSIRTWLYRIAINCAIDYL--RKRNVEKSNFKEiEEFEN--------------E 102
Cdd:PRK12530   30 DADLAEDVVQEALVSAYKNADSFKGQSALKTWIFAILKNKIIDLIryRKRFVNESELIE-EDSPNsffdekghwkpeyyE 108

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2570555548 103 IKDFETPEEVLDKRLTAEMLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVKSRLWRAR 169
Cdd:PRK12530  109 PSEWQEVENTVYKEEFWLIFEACLNHLPAQQARVFMMREYLELSSEQICQECDISTSNLHVLLYRAR 175
PRK12526 PRK12526
RNA polymerase sigma factor; Provisional
 42-176 9.52e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 237127 [Multi-domain]  Cd Length: 206  Bit Score: 47.10  E-value: 9.52e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  42 EALDLTQETLLKAYLNIKKFRGNS-SIRTWLYRIAINCAIDYLR--KRNVEKSNFKEIEEFENEIKDFETPEEVLDKRLT 118
Cdd:PRK12526   64 QANELVQETMSNVWRKAHLYNGDKgAATTWVYTVMRNAAFDMLRkiKAKKEQNLGDDIWPIEQALAESQSESEEFSDHLM 143

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2570555548 119 AEMLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVKSRLWRARNLLKERI 176
Cdd:PRK12526  144 DKQILSYIEKLPEAQQTVVKGVYFQELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201
PRK12542 PRK12542
RNA polymerase sigma factor; Provisional
 16-176 1.01e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183581 [Multi-domain]  Cd Length: 185  Bit Score: 46.97  E-value: 1.01e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  16 EAFEILVSEHQKYIYNVILKIVFDKEEALDLTQETLLKAYLNIKKFRGNSS--IRTWLYRIAINCAIDYLRKRNVEKSNF 93
Cdd:PRK12542    9 EKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTqeLKRYILRVAKNKAIDSYRKNKRHETFL 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  94 KEIEEFENEIKDfETPEEVLDKRLTAEMLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVKSRLWRARNLLK 173
Cdd:PRK12542   89 EEYERESIEAVD-ENIEEWEKRKMSEVQIDTLLKELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERARKRVQ 167


                  ...
gi 2570555548 174 ERI 176
Cdd:PRK12542  168 NMI 170
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
 24-155 4.84e-06

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 44.68  E-value: 4.84e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  24 EHQKYIYNVILKIVFDKEEALDLTQEtllkAYLNIKKFRGNSSIRT---WLYRIAINCAIDYLRKRNVEKSNFKEIEEFE 100
Cdd:PRK07037    6 DNRSMLVKIAARIVGCRSRAEDVVQD----AFVKLVEAPNQDAVKQpvaYLFRIVRNLAIDHYRRQALENKYHGDEEDGL 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2570555548 101 NEIKDFETPEEVLDKRLTAEMLMREINKLPADYKIALILRDIEGLNYEEISKIMN 155
Cdd:PRK07037   82 DVPSPEASPEAALINRDTLRHVADALSELPARTRYAFEMYRLHGETQKDIARELG 136
PRK12545 PRK12545
RNA polymerase factor sigma-70;
39-173 1.05e-05

RNA polymerase factor sigma-70;


Pssm-ID: 183584 [Multi-domain]  Cd Length: 201  Bit Score: 44.18  E-value: 1.05e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  39 DKEEALDLTQETLLKAYLNIKKFRGNSSIRTWLYRIAINCAIDYLRKRN-----------------VEKSNFKEIEEFEN 101
Cdd:PRK12545   31 DADAAEDAVQEALAAAWSQAGRFAGQSAHKTWVFGILRNKLIDTLRARQrtvnlsaldaeldgealLDRELFKDNGHWAA 110

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2570555548 102 EIK--DFETPEEVLDKRLTAEMLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVKSRLWRARNLLK 173
Cdd:PRK12545  111 HAKprPWPKPETILQQQQFWTLFETCLDHLPEQIGRVFMMREFLDFEIDDICTELTLTANHCSVLLYRARTRLR 184
PRK12520 PRK12520
RNA polymerase sigma factor; Provisional
 43-174 1.56e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 237126 [Multi-domain]  Cd Length: 191  Bit Score: 43.57  E-value: 1.56e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  43 ALDLTQETLLKAYLNIKKFRGNSSIRTWLYRIAINCAIDYLR--KRNVEKSN---------------FKEIEEFENEIKD 105
Cdd:PRK12520   29 AEDAVSETLLAVLEHPERFAGQSSLKTYLVGILKHKIIDAIRsgRREVRLSLddadeqsdddlfdalFAADGHYREPPSD 108

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2570555548 106 FETPEEVLDKRLTAEMLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVKSRLWRARNLLKE 174
Cdd:PRK12520  109 WGDPDAALSRREFFEVLQACVDRLPPRTGRVFMMREWLELETEEICQELQITATNAWVLLYRARMRLRE 177
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 13-174 1.75e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 43.23  E-value: 1.75e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  13 GETEAFEILVSEHQKYIYNVILKIVFDKEEALDLTQETLLKAYLNIKKF---RGnsSIRTWLYRIAINCAIDYLRKRNve 89
Cdd:PRK12537   20 GDRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFdpaRG--SARGWIYSVTRHLALNVLRDTR-- 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  90 ksnfKEIEEFENEIKDFETPEEVLDK-RLTAEM--LMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVKSRLW 166
Cdd:PRK12537   96 ----REVVLDDDAEETAQTLHEIIDDfDLWANSgkIHRCLEQLEPARRNCILHAYVDGCSHAEIAQRLGAPLGTVKAWIK 171


                  ....*...
gi 2570555548 167 RARNLLKE 174
Cdd:PRK12537  172 RSLKALRE 179
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 126-174 4.58e-05

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


Pssm-ID: 461347 [Multi-domain]  Cd Length: 50  Bit Score: 39.33  E-value: 4.58e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2570555548 126 INKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVKSRLWRARNLLKE 174
Cdd:pfam04545   2 LASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
PRK12512 PRK12512
RNA polymerase sigma factor; Provisional
 42-178 4.59e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 171551 [Multi-domain]  Cd Length: 184  Bit Score: 41.99  E-value: 4.59e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  42 EALDLTQETLLKAYLNIKKFRGNSSIRTWLYRIAINCAIDYLRKRNveKSNFKEIEEFENEIKDfETPEEVLDKRLTAEM 121
Cdd:PRK12512   52 QAEDIVQEILLAVHLKRHTWDPGAPFAPWLFAIARNKLIDALRRRG--RRVFVDIDDFAETLPA-EPATETLPAGDVGRH 128

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2570555548 122 LmreiNKLPADYKIalILRDI--EGLNYEEISKIMNLNLGTVKSRLWRARNLLKERIKS 178
Cdd:PRK12512  129 L----ETLPPRQRD--VVQSIsvEGASIKETAAKLSMSEGAVRVALHRGLAALAAKFRS 181
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 93-178 2.57e-04

DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA polymerase specialized sigma subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 440804 [Multi-domain]  Cd Length: 236  Bit Score: 40.19  E-value: 2.57e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  93 FKEIEEFENEIKDF---ETPEEVLDKRLTAEMLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVKSRLWRAR 169
Cdd:COG1191   148 LDEPLEDGDDLLDLlesGDPEEELEHEELREALAEAIEQLPERERLVLSLYYFEELTLKEIAEVLGVSESRVSRLHKKAL 227


                  ....*....
gi 2570555548 170 NLLKERIKS 178
Cdd:COG1191   228 ARLREYLKE 236
PRK12528 PRK12528
RNA polymerase sigma factor; Provisional
 15-168 6.94e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 171561 [Multi-domain]  Cd Length: 161  Bit Score: 38.67  E-value: 6.94e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  15 TEAFEILVSEHQKYIYNVILKIVFDKEEALDLTQETllkaYLNIKKFRGNSSI---RTWLYRIAINCAIDYLRKRNVEKS 91
Cdd:PRK12528    3 SATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDT----FVKVLVARETAQIiepRAFLTTIAKRVLCNHYRRQDLERA 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2570555548  92 NFKEIEEFENEIKDFETPEEVLDKRLTAemLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVKSRLWRA 168
Cdd:PRK12528   79 YLEALAQLPERVAPSEEERAIILETLVE--LDQLLDGLPPLVKRAFLLAQVDGLGYGEIATELGISLATVKRYLNKA 153
sigI PRK09635
RNA polymerase sigma factor SigI; Provisional
 24-169 8.83e-04

RNA polymerase sigma factor SigI; Provisional


Pssm-ID: 182008 [Multi-domain]  Cd Length: 290  Bit Score: 39.18  E-value: 8.83e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  24 EHQKYIYNVILKIVFDKEEALDLTQETLLKayLNIKKFRGNSSIRTWLYRIAINCAIDYLRKRNVEKSNFKEIEEFENE- 102
Cdd:PRK09635   13 AHRAYLVDLAFRMVGDIGVAEDMVQEAFSR--LLRAPVGDIDDERGWLIVVTSRLCLDHIKSASTRRERPQDIAAWHDGd 90

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548 103 --IKDFETPEEV-LDKRLTAEMLMReINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVKSRLWRAR 169
Cdd:PRK09635   91 asVSSVDPADRVtLDDEVRLALLIM-LERLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQLAHRAR 159
PRK12539 PRK12539
RNA polymerase sigma factor SigF;
41-162 1.08e-03

RNA polymerase sigma factor SigF;


Pssm-ID: 237132 [Multi-domain]  Cd Length: 184  Bit Score: 38.17  E-value: 1.08e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  41 EEALDLTQETLLKAYLNIKKFRGNSSIRTWLYRIAINCAIDYLRkRNVEKSNFKEIEEFENEIK--DFETPEEVLDkrlt 118
Cdd:PRK12539   50 EEAEDLVQEALMAIHTRRHTYDPEQPLTPWVYAIARYKLIDHLR-RTRASLADVPIDDADELVAhdDHAAVESTLD---- 124

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 2570555548 119 aemLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVK 162
Cdd:PRK12539  125 ---LGRLLARLPEKMRLAIQAVKLEGLSVAEAATRSGMSESAVK 165
PRK09651 PRK09651
RNA polymerase sigma factor FecI; Provisional
 18-168 1.95e-03

RNA polymerase sigma factor FecI; Provisional


Pssm-ID: 182018 [Multi-domain]  Cd Length: 172  Bit Score: 37.48  E-value: 1.95e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  18 FEILVSEHQKYIYNVILKIVFDKEEALDLTQETLLKAYLNikkfRGNSSIR---TWLYRIAINCAIDYLRKRNVEKSNFK 94
Cdd:PRK09651   12 FESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVS----ETLSTIRdprSFLCTIAKRVMVDLFRRNALEKAYLE 87

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2570555548  95 EIEEFENEIkdFETPEEVLDKRLTAEMLMREINKLPADYKIALILRDIEGLNYEEISKIMNLNLGTVKSRLWRA 168
Cdd:PRK09651   88 MLALMPEGG--APSPEERESQLETLQLLDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKA 159
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
1-182 2.38e-03

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 37.20  E-value: 2.38e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548   1 MGREDLLGRAKAGETEAFEILVsehQKYiYNVILKIVF-------DKEealDLTQETLLKAYLNIKKFRG--NSSIRTWL 71
Cdd:PRK08295    9 LEDEELVELARSGDKEALEYLI---EKY-KNFVRAKARsyfligaDRE---DIVQEGMIGLYKAIRDYDKdkLSSFKSFA 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570555548  72 YRI---AINCAIDYL-RKRN--------VEKSNF-KEIEEFENEI---KDFETPEEVLDKRLTAEMLMREINKLPADYKI 135
Cdd:PRK08295   82 ELCitrQIITAIKTAnRQKHiplnsyvsLDKPIYdEESDRTLLDViseAKVTDPEELIISKEELEDIEEKIEELLSELEK 161

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 2570555548 136 ALILRDIEGLNYEEISKIMNLNLGTVKSRLWRARNLLkERIKSLSEF 182
Cdd:PRK08295  162 EVLELYLDGKSYQEIAEELNRHVKSIDNALQRVKRKL-EKYLENREI 207
 
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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