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Conserved domains on  [gi|1085001966|gb|OGS11904|]
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hypothetical protein A2386_08450 [Elusimicrobia bacterium RIFOXYB1_FULL_48_9]

Protein Classification

RNA polymerase sigma factor( domain architecture ID 11446377)

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

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

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
1-183 9.65e-46

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: 148.60  E-value: 9.65e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966   1 MDISKDIIERAARGEIPAFEEIYKSSSGFVYNVALRISASEHEASEITQDVFVKLFSGLKSFNHKSSFNTWLYRVAVNEA 80
Cdd:COG1595     1 MSSDEELLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLA 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  81 LNRRKKsnlENSRRAEFDESVEANPALREDPVgKSVNENIDKDKVAELLSLVNEEHRVVLVLREMQGLNYEEMSRVLGIN 160
Cdd:COG1595    81 IDHLRK---RRRRRELLDELAEELPDEAADPE-EALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGIS 156
                         170       180
                  ....*....|....*....|...
gi 1085001966 161 INTVRTRLKRAREILIKKVKENG 183
Cdd:COG1595   157 EGTVKSRLSRARKKLREALEEEG 179
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
1-183 9.65e-46

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: 148.60  E-value: 9.65e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966   1 MDISKDIIERAARGEIPAFEEIYKSSSGFVYNVALRISASEHEASEITQDVFVKLFSGLKSFNHKSSFNTWLYRVAVNEA 80
Cdd:COG1595     1 MSSDEELLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLA 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  81 LNRRKKsnlENSRRAEFDESVEANPALREDPVgKSVNENIDKDKVAELLSLVNEEHRVVLVLREMQGLNYEEMSRVLGIN 160
Cdd:COG1595    81 IDHLRK---RRRRRELLDELAEELPDEAADPE-EALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGIS 156
                         170       180
                  ....*....|....*....|...
gi 1085001966 161 INTVRTRLKRAREILIKKVKENG 183
Cdd:COG1595   157 EGTVKSRLSRARKKLREALEEEG 179
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
18-179 4.49e-32

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: 112.83  E-value: 4.49e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  18 AFEEIYKSSSGFVYNVALRISASEHEASEITQDVFVKLFSGLKSFNHKSSFNTWLYRVAVNEALNRRKKsnlenSRRAEF 97
Cdd:TIGR02937   2 AFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRR-----KRRLRR 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  98 DESVEANPALREDPVGKSVNENIDKDKVAELLSLVNEEHRVVLVLREMQGLNYEEMSRVLGININTVRTRLKRAREILIK 177
Cdd:TIGR02937  77 ELDLLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRE 156

                  ..
gi 1085001966 178 KV 179
Cdd:TIGR02937 157 LL 158
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
8-181 5.96e-31

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 110.67  E-value: 5.96e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966   8 IERAARGEIPAFEEIYKSSSGFVYNVALRISASEHEASEITQDVFVKLFSGLKSFNHKSSFNTWLYRVAVNEALN---RR 84
Cdd:PRK09652    1 VERVQRGDRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRGGAAFYTWLYRIARNTAINylrKQ 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  85 KKSNLENSRRAEFDESVEANPALREDPVGKSV-NENIDKDKVAELLSLVNEEHRVVLVLREMQGLNYEEMSRVLGININT 163
Cdd:PRK09652   81 GRRPPASDVDAEEAEDFDLADALRDISTPENElLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGT 160
                         170
                  ....*....|....*...
gi 1085001966 164 VRTRLKRAREILIKKVKE 181
Cdd:PRK09652  161 VRSRIFRAREALRAKLQP 178
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
122-175 2.83e-10

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


Pssm-ID: 100119 [Multi-domain]  Cd Length: 55  Bit Score: 53.26  E-value: 2.83e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1085001966 122 KDKVAELLSLVNEEHRVVLVLREMQGLNYEEMSRVLGININTVRTRLKRAREIL 175
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
122-175 1.16e-08

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: 48.99  E-value: 1.16e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1085001966 122 KDKVAELLSLVNEEHRVVLVLREMQGLNYEEMSRVLGININTVRTRLKRAREIL 175
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
1-183 9.65e-46

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: 148.60  E-value: 9.65e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966   1 MDISKDIIERAARGEIPAFEEIYKSSSGFVYNVALRISASEHEASEITQDVFVKLFSGLKSFNHKSSFNTWLYRVAVNEA 80
Cdd:COG1595     1 MSSDEELLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLA 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  81 LNRRKKsnlENSRRAEFDESVEANPALREDPVgKSVNENIDKDKVAELLSLVNEEHRVVLVLREMQGLNYEEMSRVLGIN 160
Cdd:COG1595    81 IDHLRK---RRRRRELLDELAEELPDEAADPE-EALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGIS 156
                         170       180
                  ....*....|....*....|...
gi 1085001966 161 INTVRTRLKRAREILIKKVKENG 183
Cdd:COG1595   157 EGTVKSRLSRARKKLREALEEEG 179
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
18-179 4.49e-32

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: 112.83  E-value: 4.49e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  18 AFEEIYKSSSGFVYNVALRISASEHEASEITQDVFVKLFSGLKSFNHKSSFNTWLYRVAVNEALNRRKKsnlenSRRAEF 97
Cdd:TIGR02937   2 AFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRR-----KRRLRR 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  98 DESVEANPALREDPVGKSVNENIDKDKVAELLSLVNEEHRVVLVLREMQGLNYEEMSRVLGININTVRTRLKRAREILIK 177
Cdd:TIGR02937  77 ELDLLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRE 156

                  ..
gi 1085001966 178 KV 179
Cdd:TIGR02937 157 LL 158
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
8-181 5.96e-31

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 110.67  E-value: 5.96e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966   8 IERAARGEIPAFEEIYKSSSGFVYNVALRISASEHEASEITQDVFVKLFSGLKSFNHKSSFNTWLYRVAVNEALN---RR 84
Cdd:PRK09652    1 VERVQRGDRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRGGAAFYTWLYRIARNTAINylrKQ 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  85 KKSNLENSRRAEFDESVEANPALREDPVGKSV-NENIDKDKVAELLSLVNEEHRVVLVLREMQGLNYEEMSRVLGININT 163
Cdd:PRK09652   81 GRRPPASDVDAEEAEDFDLADALRDISTPENElLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGT 160
                         170
                  ....*....|....*...
gi 1085001966 164 VRTRLKRAREILIKKVKE 181
Cdd:PRK09652  161 VRSRIFRAREALRAKLQP 178
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
7-185 5.26e-26

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 97.87  E-value: 5.26e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966   7 IIERAARGEIPAFEEIYKSSSGFVYNVALRISASEhEASEITQDVFVKLFSGLKSFNHKSSFNTWLYRVAVNEALNRRKK 86
Cdd:PRK12518    1 LILRCQRGDRQSFRQLYRRYQQKVRSTLYQLCGRE-LLDDLVQEVFLRVWKGLPKLRNPAYFSTWLYRITWNVATDARRQ 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  87 SNLENSRRAEFDESVEANPALREDPVGKSVNEnidkDKVAELLSLVNEEHRVVLVLREMQGLNYEEMSRVLGININTVRT 166
Cdd:PRK12518   80 FAQRPSRIQDDSLNDQPSRPSDTPDLMQLHYQ----DLVQQGLQTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKS 155
                         170
                  ....*....|....*....
gi 1085001966 167 RLKRAREILIKKVKENGMQ 185
Cdd:PRK12518  156 RLFYARRQLRKFLQQQGVL 174
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
13-175 4.71e-25

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 96.01  E-value: 4.71e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  13 RGEIPAFEEIYKSSSGFVYNVALRISASEHEASEITQDVFVKLFSGLKSFNhKSSFNTWLYRVAVNEALNR-RKKSNLen 91
Cdd:PRK09647   24 KATMPSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQ-PGTFEGWLHRITTNLFLDMvRRRARI-- 100
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  92 sRRAEFDESVEANPALREDPVGKSVNENIDKDKVAELLSLvNEEHRVVLVLREMQGLNYEEMSRVLGININTVRTRLKRA 171
Cdd:PRK09647  101 -RMEALPEDYDRVPGDEPNPEQIYHDARLDPDLQAALDSL-PPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRG 178

                  ....
gi 1085001966 172 REIL 175
Cdd:PRK09647  179 RQQL 182
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
6-175 6.19e-25

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 96.57  E-value: 6.19e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966   6 DIIERAARGEIPAFEEIYKSSSGFVYNVALRISASEHEASEITQDVFVKLFSGLKSFNHKSSFNTWLYRVAVNEALNRRK 85
Cdd:PRK11922   19 ELVARVLAGDEAAFEALMRRHNRRLYRTARAILRNDAEAEDVVQEAYLRAFRALGTFRGDASLSTWLSRIVLNEALGRLR 98
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  86 KSnlenSRRAEFDESVEAN-PALREDPVGKSVNENIDKDKV-AELLSLVN-------EEHRVVLVLREMQGLNYEEMSRV 156
Cdd:PRK11922   99 RR----RRLVNLAEMVMAStIAGGERTPLADPAEDPERAAArREIRALLEraidalpDAFRAVFVLRVVEELSVEETAQA 174
                         170
                  ....*....|....*....
gi 1085001966 157 LGININTVRTRLKRAREIL 175
Cdd:PRK11922  175 LGLPEETVKTRLHRARRLL 193
SigW_bacill TIGR02948
RNA polymerase sigma-W factor; This sigma factor is restricted to certain lineages of the ...
1-181 1.62e-24

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: 94.19  E-value: 1.62e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966   1 MD-ISKDIIERAARGEIPAFEEIYKSSSGFVYNVALRISASEHEASEITQDVFVKLFSGLKSFNHKSSFNTWLYRVAVNE 79
Cdd:TIGR02948   1 MDsIIKKRIKEVRKGDENAFADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIRAYTNIDTYDIQRKFSTWLYRIATNL 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  80 ALNRRKKSN----LENSRRAEFDESVEANPALREDPVGKSVNENIDKDKVAELLSLVNEEHRVVLVLREMQGLNYEEMSR 155
Cdd:TIGR02948  81 TIDRLRKRKpdfyLDDEVQGTDGLTMESQLAADEAPPEDQVISLELRDTIQQEIQALPPKYRMVIVLKYMEDLSLKEISE 160
                         170       180
                  ....*....|....*....|....*.
gi 1085001966 156 VLGININTVRTRLKRAREILIKKVKE 181
Cdd:TIGR02948 161 ILDLPVGTVKTRIHRGREALRKQLRH 186
algU PRK11923
RNA polymerase sigma factor AlgU; Provisional
7-180 2.44e-24

RNA polymerase sigma factor AlgU; Provisional


Pssm-ID: 171347 [Multi-domain]  Cd Length: 193  Bit Score: 94.10  E-value: 2.44e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966   7 IIERAARGEIPAFEEIYKSSSGFVYNVALRISASEHEASEITQDVFVKLFSGLKSFNHKSSFNTWLYRVAVNEALN---- 82
Cdd:PRK11923   10 LVERVQRGDKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDSAFYTWLYRIAINTAKNhlvs 89
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  83 --RRKKSNLENSRRAEFdesVEANPALR--EDPVGKSVNENIdKDKVAELLSLVNEEHRVVLVLREMQGLNYEEMSRVLG 158
Cdd:PRK11923   90 rgRRPPDSDVSSEDAEF---YDGDHALKdiESPERALLRDEI-EGTVHRTIQQLPEDLRTALTLREFDGLSYEDIASVMQ 165
                         170       180
                  ....*....|....*....|..
gi 1085001966 159 ININTVRTRLKRAREILIKKVK 180
Cdd:PRK11923  166 CPVGTVRSRIFRAREAIDKALQ 187
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
1-178 2.31e-23

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 91.30  E-value: 2.31e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966   1 MD-ISKDIIERAARGEIPAFEEI---YKSSsgfVYNVALRISASEHEASEITQDVFVKLFSGLKSFNHKSSFNTWLYRVA 76
Cdd:PRK09641    1 MDlLIKRLIKQVKKGDQNAFAELvdlYKDK---IYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINRKFSTWLYRIA 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  77 VNEALNRRKKSNLENSRRAEFDES--------VEANPALREDPVGKSVNENIDKDKVAELlslvNEEHRVVLVLREMQGL 148
Cdd:PRK09641   78 TNLTIDRLRKRKPDYYLDAEVAGTegltmysqLAADDALPEEQVVSLELQETIQEAILQL----PEKYRTVIVLKYIEDL 153
                         170       180       190
                  ....*....|....*....|....*....|
gi 1085001966 149 NYEEMSRVLGININTVRTRLKRAREILIKK 178
Cdd:PRK09641  154 SLKEISEILDLPVGTVKTRIHRGREALRKQ 183
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
18-175 1.25e-22

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 89.26  E-value: 1.25e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  18 AFEEIYKSSSGFVYNVALRISASEHEASEITQDVFVKLFSGLKSFNHKSSFNTWLYRVAVN---EALNRRKKSNLENSRR 94
Cdd:PRK11924   14 AFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNvcyDLLRRRRREKAVLSDD 93
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  95 AEFDESVEANPALREDPVGKSVNENIDKdKVAELlslvNEEHRVVLVLREMQGLNYEEMSRVLGININTVRTRLKRAREI 174
Cdd:PRK11924   94 ALEPEFAETAETPEAALLAKDDLARIDR-CLDAL----PVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQL 168

                  .
gi 1085001966 175 L 175
Cdd:PRK11924  169 L 169
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
5-181 4.00e-22

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 87.77  E-value: 4.00e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966   5 KDIIERAARGEIPAFEEIYKSSSGFVYNVALRISASEHEASEITQDVFVKLFSGLKSFNHKSSFNTWLYRVAVNEALN-- 82
Cdd:PRK09638    6 KELIQKAKKGDDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGRSKFSTWLISIASRLYKDhl 85
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  83 RRKKsnleNSRRAEFDESVEANPALREDPVGKsvneNIDKDKVAELLSLVNEEHRVVLVLREMQGLNYEEMSRVLGININ 162
Cdd:PRK09638   86 RKQK----REKLRLQRAKEETLRKEKWEAAIK----GAEWSEMLDALSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEG 157
                         170
                  ....*....|....*....
gi 1085001966 163 TVRTRLKRAREILIKKVKE 181
Cdd:PRK09638  158 TVKSRVHHGIKQLRKEWGQ 176
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
10-175 5.25e-20

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 82.81  E-value: 5.25e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  10 RAARGEIPAFEEIYKSSSGFVYNVALRISASEHEASEITQDVFVKLFSGLKSFNHKSSFNTWLYRVAVNEALNRRKKSNL 89
Cdd:PRK12513   19 RYRAGDAAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPRARFRTWLYQIARNLLIDHWRRHGA 98
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  90 ENSRRAEFDESVEANPALREDPvGKSVNENIDKDKVAELLSLVNEEHRVVLVLREMQGLNYEEMSRVLGININTVRTRLK 169
Cdd:PRK12513   99 RQAPSLDADEQLHALADDGAAP-EQQLSLFRDRRRLQAALETLPDEQREVFLLREHGDLELEEIAELTGVPEETVKSRLR 177

                  ....*.
gi 1085001966 170 RAREIL 175
Cdd:PRK12513  178 YALQKL 183
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
18-175 7.27e-20

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: 81.45  E-value: 7.27e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  18 AFEEIYKSSSGFVYNVALRISASEHEASEITQDVFVKLFSGLKSFNHKSSFNTWLYRVAVNEALNRRKKSNLENSRRAEF 97
Cdd:TIGR02985   2 AFEQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETLEISESIKAYLFTIVKNRCLNYLRHKQVEEKYQEEL 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  98 DESVEanpalREDPVGKSVNENIDKDKVAELLSLVN---EEHRVVLVLREMQGLNYEEMSRVLGININTVRTRLKRAREI 174
Cdd:TIGR02985  82 AEIEE-----RELSEADPEEELEAKELEEIIEEAIEklpEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKF 156

                  .
gi 1085001966 175 L 175
Cdd:TIGR02985 157 L 157
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
17-177 1.10e-19

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 81.15  E-value: 1.10e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  17 PAFEEIYKSSSGFVYNVALRISASEHEASEITQDVFVKLFSglKSFNHKSSFNTWLYRVAVNEALNRRKKsnlENSRRAE 96
Cdd:PRK09639    3 ETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYR--SDFKGIENEKGWLIKSARNVAYNYLRS---EKRRRAR 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  97 FDESVEANPALREDPVGKSVNENIDKDKVAELLSLVNEEHRVVLVLREmQGLNYEEMSRVLGININTVRTRLKRAREILI 176
Cdd:PRK09639   78 ILGEFQWQEVDNEPSPEEIWIRKEEITKVQEVLAKMTERDRTVLLLRF-SGYSYKEIAEALGIKESSVGTTLARAKKKFR 156

                  .
gi 1085001966 177 K 177
Cdd:PRK09639  157 K 157
PRK09643 PRK09643
RNA polymerase sigma factor SigM; Reviewed
5-172 1.73e-19

RNA polymerase sigma factor SigM; Reviewed


Pssm-ID: 236604 [Multi-domain]  Cd Length: 192  Bit Score: 81.29  E-value: 1.73e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966   5 KDIIERAARGEIPAFEEIYKSSSGFVYNVALRISASEHEASEITQDVFVKLFSGLKSFNHKSSFNTWLYRVAVNEALNR- 83
Cdd:PRK09643   15 AELLAAHVAGDRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGDAAVSSWLHRIVVNACLDRl 94
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  84 RKKSnlenSRRAEFDESVEANPALREDPVGKsVNENIDkdkVAELLSLVNEEHRVVLVLREMQGLNYEEMSRVLGININT 163
Cdd:PRK09643   95 RRAK----ARPTVPLDDVYPVAQLERDPTAR-VETALA---VQRALMRLPVEQRAALVAVDMQGYSVADAARMLGVAEGT 166

                  ....*....
gi 1085001966 164 VRTRLKRAR 172
Cdd:PRK09643  167 VKSRCARGR 175
SigM_subfam TIGR02950
RNA polymerase sigma factor, SigM family; This family of RNA polymerase sigma factors is a ...
30-181 7.50e-18

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


Pssm-ID: 274361 [Multi-domain]  Cd Length: 154  Bit Score: 75.95  E-value: 7.50e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  30 VYNVALRISASEHEASEITQDVFVKLFSGLKSFNHkSSFNTWLYRVAVNEALNR-RKKSNLENSrraefdeSVEANPALR 108
Cdd:TIGR02950   8 VFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKD-SSIKPWLFRIARNAFIDWyRKDKKIQTI-------DDDAIGDLE 79
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1085001966 109 EDPVGKSVNENIDKDKVAELLSLVN---EEHRVVLVLREMQGLNYEEMSRVLGININTVRTRLKRAREILiKKVKE 181
Cdd:TIGR02950  80 QHPVESPEHHLLIKIEQEEITHHLSrlpENYRTVLILREFKEFSYKEIAELLNLSLAKVKSNLFRARKEL-KKLLE 154
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
40-183 8.00e-18

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 76.71  E-value: 8.00e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  40 SEHEASEITQDVFVKLFSGLKSFNHKSSFNTWLYRVAVNEALNRRKKSnleNSRRAEFDESVEANPALREDPVGKSVnen 119
Cdd:PRK09415   39 NKEVAEDLTQEIFVKCYKSLHTYKGKSSLKTWLYRIAINHCKDYLKSW---HNKKVIVTEDIFTYMESQKESVEEEV--- 112
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1085001966 120 IDKDKVAELLSLVNE---EHRVVLVLREMQGLNYEEMSRVLGININTVRTRLKRAREILIKKVKENG 183
Cdd:PRK09415  113 IQNAEDERLASAVMSlpiKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKELLKKGLEEEV 179
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
18-182 4.21e-17

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 74.98  E-value: 4.21e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  18 AFEEIYKSSSGFVYNVALRISASEHEASEITQDVFVKLFSGLKSFNHKSSFNTWLYRVAVNEALN----RRKKSNLENSR 93
Cdd:PRK09640   27 AYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGKSKFKTWLYSITYNECITqyrkERRKRRLMDAL 106
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  94 RAEFDESVEANPALREDpvgksvneniDKDKVAELLSLVNEEHRVVLVLREMQGLNYEEMSRVLGININTVRTRLKRARE 173
Cdd:PRK09640  107 SLDPLEEASEEKAPKPE----------ERGGLDRWLVHVNPIDREILVLRFVAELEFQEIADIMHMGLSATKMRYKRALD 176

                  ....*....
gi 1085001966 174 ILIKKVKEN 182
Cdd:PRK09640  177 KLREKFAGL 185
PRK12522 PRK12522
RNA polymerase sigma factor; Provisional
21-180 3.48e-15

RNA polymerase sigma factor; Provisional


Pssm-ID: 183571 [Multi-domain]  Cd Length: 173  Bit Score: 69.51  E-value: 3.48e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  21 EIYKSssgFVYNVALRISASEHEASEITQDVFVKLFSGLKSFNHKSSFNTWLYRVAVNEALNR-RKKSNLENSRRAEFDE 99
Cdd:PRK12522   10 DIYKQ---QIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVENYKKWITTICVRTFYDFyRKKKRWKDRILDLFHK 86
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966 100 SVEANPALREDP-VGKSVNENIDKDKVAELLSLVNEEHRVVLVLREMQGLNYEEMSRVLGININTVRTRLKRAREILIKK 178
Cdd:PRK12522   87 EDGGEIEFADDVnISEEFIQKVEAEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQMREH 166

                  ..
gi 1085001966 179 VK 180
Cdd:PRK12522  167 LE 168
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
6-183 9.90e-15

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 68.53  E-value: 9.90e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966   6 DIIERAARGEIPAFEEIYKSSSGFVYNVALRISASEHEASEITQDVFVKLFSGLKSFNHK-SSFNTWLYRVAVNEALNRR 84
Cdd:PRK05602    9 ELLARVAAGDPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPGeARFDTWLHRVVLNLCYDRL 88
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  85 KKsnlensRRaefdESVEANPALREDPvGKSVNENI----DKDKVAELLSLVNEEHRVVLVLREMQGLNYEEMSRVLGIN 160
Cdd:PRK05602   89 RR------RR----EVPVEDAPDVPDP-APGPDAGLearqRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDIS 157
                         170       180
                  ....*....|....*....|...
gi 1085001966 161 INTVRTRLKRAREILIKKVKENG 183
Cdd:PRK05602  158 VDALESLLARGRRALRAQLADLP 180
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
13-175 1.27e-14

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 68.55  E-value: 1.27e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  13 RGEIPAFEEIYKSSSGFVYNVALRISASEHEASEITQDVFVKLFSGlKSFNHK-SSFNTWLYRVAVNEALN--RRKKSNL 89
Cdd:PRK12519   25 AGQSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRK-SSYDPKrGSLSSYLLTLTRSRAIDrlRSRRSRQ 103
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  90 ENSRRAEFDESVEAnpalREDPVGKSVNENIDKDKVAELLSLVNEEHRVVLVLREMQGLNYEEMSRVLGININTVRTRLK 169
Cdd:PRK12519  104 RLLERWQQELLGEA----SEDTPLEQASLAERSQRVQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKARAR 179
                         170
                  ....*....|
gi 1085001966 170 RA----REIL 175
Cdd:PRK12519  180 QGllklRELL 189
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
6-185 5.96e-14

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 66.68  E-value: 5.96e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966   6 DIIERAARGEIPAFEEIYKSSSGFVYNVALRISASEHEASEITQDVFVKLFSGLKSFNHKSSFNTWLYRVAVNEALN--- 82
Cdd:PRK12515   11 MLLARIAQGDRTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGRSQVSTWLLSIARFKALSalr 90
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  83 RRKKSNLEnsrraefDESVEANPALREDPvgksvNENIDKDKVAELL----SLVNEEHRVVLVLREMQGLNYEEMSRVLG 158
Cdd:PRK12515   91 RRKHEEID-------DEAAAAIEDGADTP-----EVALQKSDTSAALraclAKLSPAHREIIDLVYYHEKSVEEVGEIVG 158
                         170       180
                  ....*....|....*....|....*..
gi 1085001966 159 ININTVRTRLKRAREILIKKVKENGMQ 185
Cdd:PRK12515  159 IPESTVKTRMFYARKKLAELLKAAGVE 185
PRK09649 PRK09649
RNA polymerase sigma factor SigC; Reviewed
11-184 8.44e-14

RNA polymerase sigma factor SigC; Reviewed


Pssm-ID: 137458 [Multi-domain]  Cd Length: 185  Bit Score: 66.22  E-value: 8.44e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  11 AARGEIPAFEEIYKSSSGFVYNVALRISASEHeASEITQDVFVKLFSGLKSFNHKSSFNTWLYRVAVNEALNRRKKsnLE 90
Cdd:PRK09649   18 AAKGNGRALEAFIKATQQDVWRFVAYLSDVGS-ADDLTQETFLRAIGAIPRFSARSSARTWLLAIARHVVADHIRH--VR 94
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  91 NSRRAEFDesveANPALREDpVGKSVNENIDKDKVAELLSLVNEEHRVVLVLREMQGLNYEEMSRVLGININTVRTRLKR 170
Cdd:PRK09649   95 SRPRTTRG----ARPEHLID-GDRHARGFEDLVEVTTMIADLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVAR 169
                         170
                  ....*....|....
gi 1085001966 171 AREILIKKVKENGM 184
Cdd:PRK09649  170 ARDALLADAEPDDL 183
PRK09646 PRK09646
ECF RNA polymerase sigma factor SigK;
6-169 9.73e-14

ECF RNA polymerase sigma factor SigK;


Pssm-ID: 182015 [Multi-domain]  Cd Length: 194  Bit Score: 66.23  E-value: 9.73e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966   6 DIIERAARGEIPAFEEIYKSSSGFVYNVALRISASEHEASEITQDVFVKLFSGLKSFN-HKSSFNTWLYRVAVNEALNRR 84
Cdd:PRK09646   19 ALLRRVARGDQDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDpARGSALAWLLTLAHRRAVDRV 98
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  85 KKSNLENSRRAEFDESVEANPAlreDPVGKSVNENIDKDKVAELLSLVNEEHRVVLVLREMQGLNYEEMSRVLGININTV 164
Cdd:PRK09646   99 RSEQAASQREVRYGARNVDPAF---DQVAEEVEARLERERVRDCLDALTDTQRESVTLAYYGGLTYREVAERLAVPLGTV 175

                  ....*
gi 1085001966 165 RTRLK 169
Cdd:PRK09646  176 KTRMR 180
SigE-fam_strep TIGR02983
RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors ...
18-172 1.48e-13

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


Pssm-ID: 132028 [Multi-domain]  Cd Length: 162  Bit Score: 65.10  E-value: 1.48e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  18 AFEEIYKSSSGFVYNVALRISASEHEASEITQDVFVKLFSGLKSFNHKSSFNTWLYRVAVNEALNR-RKKSNLENSRRaE 96
Cdd:TIGR02983   7 EFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRDPDAPDAYVRRVLVNLARSRwRRRRLLELPTR-E 85
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1085001966  97 FDESVEANPALREDpvgksvneniDKDKVAELLSLVNEEHRVVLVLREMQGLNYEEMSRVLGININTVRTRLKRAR 172
Cdd:TIGR02983  86 LPDAAAPDPAPDVA----------LRAALARALRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRAL 151
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
2-175 3.95e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 65.26  E-value: 3.95e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966   2 DISKDIIERAARGEIPAFEEIYKSSSGFVYNVALRISASEHEASEITQDVFVKLFSGLKSFNH-KSSFNTWLYRVAVNEA 80
Cdd:PRK12538   48 DEDEELLDRLATDDEAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHgRAKFSTWLYRVVSNRC 127
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  81 LNRRKKSNLENsrraefdesVEANPalrEDPVGK-SVNENIDKDKVAELLSL----VNEEHRVVLVLREMQGLNYEEMSR 155
Cdd:PRK12538  128 IDLRRKPRTEN---------VDAVP---EVADGKpDAVSVIERNELSDLLEAamqrLPEQQRIAVILSYHENMSNGEIAE 195
                         170       180
                  ....*....|....*....|
gi 1085001966 156 VLGININTVRTRLKRAREIL 175
Cdd:PRK12538  196 VMDTTVAAVESLLKRGRQQL 215
PRK12535 PRK12535
RNA polymerase sigma factor; Provisional
10-176 1.31e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 237130 [Multi-domain]  Cd Length: 196  Bit Score: 62.99  E-value: 1.31e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  10 RAARGEIPAFEEIYKSSSGFVYNVALRISASEhEASEITQDVFVKLFSGLKSFNHKSSFNTWLYRVA-------VNEALN 82
Cdd:PRK12535   18 AAGRGDRAALTEFIRETQDDVWRLLAHLGGHD-IADDLTQETYLRVMSALPRFAARSSARTWLLSLArrvwvdnIRHDMA 96
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  83 RRKKSNlensrrAEFDESVEANPAlreDPVGKSVNENIDkdkVAELLSLVNEEHRVVLVLREMQGLNYEEMSRVLGININ 162
Cdd:PRK12535   97 RPRKSA------TEYEDAAATTAS---NETTGSWSEWID---VRTLIDALPPERREALILTQVLGYTYEEAAKIADVRVG 164
                         170
                  ....*....|....
gi 1085001966 163 TVRTRLKRAREILI 176
Cdd:PRK12535  165 TIRSRVARARADLI 178
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
2-171 1.49e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 62.53  E-value: 1.49e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966   2 DISKdIIERAARGEIPAFEEIYKSSSGFVYNVALRISASEHEASEITQDVFVKLFSGLKSFN-HKSSFNTWLYRVAVNEA 80
Cdd:PRK12514    5 DIEK-LIVRVSLGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAvSGLSPMTWLITIARNHA 83
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  81 LNR---RKKSNlensrrAEFDES---VEANPALREDPVGKSVNENIDkDKVAELlslvnEEHRVVLVLRE-MQGLNYEEM 153
Cdd:PRK12514   84 IDRlraRKAVA------VDIDEAhdlADPSPGPEAEVIAGDEGQRID-ACLEEL-----EKDRAAAVRRAyLEGLSYKEL 151
                         170
                  ....*....|....*...
gi 1085001966 154 SRVLGININTVRTRLKRA 171
Cdd:PRK12514  152 AERHDVPLNTMRTWLRRS 169
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
14-182 1.69e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 62.44  E-value: 1.69e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  14 GEIPAFEEIYKSSSGFVYNVALRISASEHEASEITQDVFVKLFSGLKSFNHKSSFNTWLYRVAVNEALNRRKKS-----N 88
Cdd:PRK12543    4 GDQEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNRPFRFWLIGLVIKQIHSWRRKRwrrfrI 83
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  89 LENSRRAEFDESVEANPALREDPVGKSVNENIDKdkvaellslVNEEHRVVLVLREMQGLNYEEMSRVLGININTVRTRL 168
Cdd:PRK12543   84 FEKAEEQRKPVSIDFSEDVLSKESNQELIELIHK---------LPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRI 154
                         170
                  ....*....|....
gi 1085001966 169 KRAreilIKKVKEN 182
Cdd:PRK12543  155 HAA----LKKLRQK 164
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
20-182 3.31e-12

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 61.43  E-value: 3.31e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  20 EEIYKSSSGFVYNVALRISASEHEASEITQDVFVKLFSGLKSFNHkSSFNTWLYRVAVNEALNRRKKSNLENSRRAEFDE 99
Cdd:PRK09644    4 EEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDN-QKVKPWLFKVAYHTFIDFVRKEKKVSFVGTDEIE 82
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966 100 SVEANPAlrEDPVgksVNENIdKDKVAELLSLVNEEHRVVLVLREMQGLNYEEMSRVLGININTVRTRLKRAREILIKKV 179
Cdd:PRK09644   83 AIQAEST--EEYV---VAKNS-YEKLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALL 156

                  ...
gi 1085001966 180 KEN 182
Cdd:PRK09644  157 KEE 159
PRK12533 PRK12533
RNA polymerase sigma factor; Provisional
31-175 4.26e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 237129 [Multi-domain]  Cd Length: 216  Bit Score: 62.05  E-value: 4.26e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  31 YNVALRISASEHEASEITQDVFVKLFSGLKSFnHKSSFNTWLYRVAVN---EALNRRKKSNlensRRAEFDEsVEANPAL 107
Cdd:PRK12533   32 YNLARWLCGNASDADDVVQEACMRALRFFDSF-RGDNARPWLLAIVRHtwySEWRRRANAH----EVAAPDT-LDDADSL 105
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1085001966 108 R------EDPVGKSVNENiDKDKVAELLSLVNEEHRVVLVLREMQGLNYEEMSRVLGININTVRTRLKRAREIL 175
Cdd:PRK12533  106 DdwqpagEDPLALLLRAE-DVRLVNAALAKLPVEYREVLVLRELEDMSYREIAAIADVPVGTVMSRLARARRRL 178
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
12-181 5.24e-12

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 61.47  E-value: 5.24e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  12 ARGEIPAFEEIYKSSSGFVYNVALRISASEHEASEITQDVFVKLFSGLKSFN-HKSSFNTWLYRVAVNEALNRRKksnle 90
Cdd:PRK13919   18 ARGEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDpRRGSARAWLLALAHHAAVDHVR----- 92
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  91 nsRRAEFDESVEanPALRE----DPVGKSVNE--NIDKDKVAELLSLVNEEHRVVLVLREMQGLNYEEMSRVLGININTV 164
Cdd:PRK13919   93 --RRAARPQPLE--PDEREpeafDLPGPGLDEegHLDRTRLGRALKALSPEERRVIEVLYYQGYTHREAAQLLGLPLGTL 168
                         170
                  ....*....|....*..
gi 1085001966 165 RTRLKRAREILIKKVKE 181
Cdd:PRK13919  169 KTRARRALSRLKEVLRE 185
PRK12517 PRK12517
RNA polymerase sigma factor; Provisional
3-177 1.42e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 183569 [Multi-domain]  Cd Length: 188  Bit Score: 60.09  E-value: 1.42e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966   3 ISKDIIERAARgeipaFEEIYKSSSGFVYNVALRISASEHEASEITQDVFVKLFSGLKSFNHKSSFNTWLYRVAvnealn 82
Cdd:PRK12517   14 VSSDMLSKQRR-----YEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDEKAAKAWLITIL------ 82
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  83 RRkksnlENSRRAE---FDeSVEANPALREDPVGKSVNENIDKDKVAELLSLVNEEHRVVLVLREMQGLNYEEMSRVLGI 159
Cdd:PRK12517   83 RR-----ENARRFErkqFD-LVDIEDDSIEDDASHSSEEEMEQEWLRRQIAKLDPEYREPLLLQVIGGFSGEEIAEILDL 156
                         170
                  ....*....|....*...
gi 1085001966 160 NINTVRTRLKRAREILIK 177
Cdd:PRK12517  157 NKNTVMTRLFRARNQLKE 174
PRK12534 PRK12534
RNA polymerase sigma factor; Provisional
2-171 2.04e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 183576 [Multi-domain]  Cd Length: 187  Bit Score: 59.68  E-value: 2.04e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966   2 DISKDIIERAARGEIPAFEEIYKSSSGFVYNVALRISASEHEASEITQDVFVKLFSGLKSFN-HKSSFNTWLYRVAVNEA 80
Cdd:PRK12534   10 DETGRLLTATAGGDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDpSRARGLTWLAMIARNKA 89
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  81 LNRRkKSNLENSRRAEFDESVEAnPALREDPVGK----SVNENIDKdKVAELLSLVNEEHRVVLvlreMQGLNYEEMSRV 156
Cdd:PRK12534   90 IDHL-RANAPQRRNVALDDAGEL-RAADASPLERteraSTRRRIDH-CLAELEPPRSELIRTAF----FEGITYEELAAR 162
                         170
                  ....*....|....*
gi 1085001966 157 LGININTVRTRLKRA 171
Cdd:PRK12534  163 TDTPIGTVKSWIRRG 177
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
36-175 3.58e-11

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 58.84  E-value: 3.58e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  36 RISASEhEASEITQDVFVKLFSGLKSFNHKSSFNTWLYRVAVNEALN-RRKKSnlensrRAEFDESVEANPalredpvGK 114
Cdd:PRK09637   21 RVSNEA-DVDDLLQEVLIKTHSNLHSLKDGSSIKSWLYQIANNTIIDfYRKKN------RSEELPDDLLFE-------DE 86
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1085001966 115 SVNENIDKDKVAELLSLVN---EEHRVVLVLREMQGLNYEEMSRVLGININTVRTRLKRAREIL 175
Cdd:PRK09637   87 EREENAKKELAPCLRPFIDalpEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRVKL 150
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
122-175 2.83e-10

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


Pssm-ID: 100119 [Multi-domain]  Cd Length: 55  Bit Score: 53.26  E-value: 2.83e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1085001966 122 KDKVAELLSLVNEEHRVVLVLREMQGLNYEEMSRVLGININTVRTRLKRAREIL 175
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
22-168 3.77e-10

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 56.24  E-value: 3.77e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  22 IYKSSSGFVYNVALRISASEHEASEITQDVFVKLFSGLKSFNHK-SSFNTWLYRVAVNEALNRRKksnlenSRRAEFDES 100
Cdd:PRK09645   14 LYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTgRSARAWLFTVARNLVIDERR------SARARPVEG 87
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1085001966 101 VEANPALREDPVGKSVNENIDKDKVAELLSLVNEEHRVVLVLREMQGLNYEEMSRVLGININTVRTRL 168
Cdd:PRK09645   88 GDDVLGVPEQSAPDEVDRALDRLLVADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRL 155
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
30-171 5.15e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 56.05  E-value: 5.15e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  30 VYNVALRISASEHEASEITQDVFVKLFSGLKSF-NHKSSFNTWLYRVAVNEALNRrkksnLENSRRAEFDESVEANPAlr 108
Cdd:PRK12524   39 ALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWrQGEARVSTWLYRVVCNLCTDR-----LRRRRRASVDLDDAPEPA-- 111
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1085001966 109 eDPVGKSVNENIDKDKVAEL---LSLVNEEHRVVLVLREMQGLNYEEMSRVLGININTVRT---RLKRA 171
Cdd:PRK12524  112 -DAAPGAEEALIEGDRMRALdaaLAALPERQRQAVVLRHIEGLSNPEIAEVMEIGVEAVESltaRGKRA 179
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
12-171 7.05e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 55.55  E-value: 7.05e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  12 ARGEIPAFEEIYKSSSGFVYNVALRISASEHEASEITQDVFVKLFSGLKSFN-HKSSFNTWLYRVAVNEALNrrkksNLE 90
Cdd:PRK12537   18 ARGDRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDpARGSARGWIYSVTRHLALN-----VLR 92
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  91 NSRRA----EFDESVEANPALREDPVGKSVNENidkdKVAELLSLVNEEHRVVLVLREMQGLNYEEMSRVLGININTVRT 166
Cdd:PRK12537   93 DTRREvvldDDAEETAQTLHEIIDDFDLWANSG----KIHRCLEQLEPARRNCILHAYVDGCSHAEIAQRLGAPLGTVKA 168

                  ....*
gi 1085001966 167 RLKRA 171
Cdd:PRK12537  169 WIKRS 173
PRK06811 PRK06811
RNA polymerase factor sigma-70; Validated
1-184 3.76e-09

RNA polymerase factor sigma-70; Validated


Pssm-ID: 180707 [Multi-domain]  Cd Length: 189  Bit Score: 53.40  E-value: 3.76e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966   1 MDIS-KDIIERAARGEIPAFEEIYKSSSGFVYNVALRI---SASEHEASEITQDVFVKLFSGLKSFN-HKSSFNTWLYRV 75
Cdd:PRK06811    1 MKINeDNFIKELKKKNEKALEFIVDTYGNLVKKIVHKVlgtVNYSQLIEECVNDIFLSIWNNIDKFDeEKGSFKKWIAAI 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  76 AVNEALNRRKKSNlENSRRAEFDESVEanpaLREDPVGKSVNENIDKDKVAELLSLVNEEHRVVLVLREMQGLNYEEMSR 155
Cdd:PRK06811   81 SKYKAIDYKRKLT-KNNEIDSIDEFIL----ISEESIENEIILKENKEEILKLINDLEKLDREIFIRRYLLGEKIEEIAK 155
                         170       180
                  ....*....|....*....|....*....
gi 1085001966 156 VLGININTVRTRLKRAREILIKKVKENGM 184
Cdd:PRK06811  156 KLGLTRSAIDNRLSRGRKKLQKNKLNISL 184
PRK12542 PRK12542
RNA polymerase sigma factor; Provisional
20-173 6.00e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 183581 [Multi-domain]  Cd Length: 185  Bit Score: 53.13  E-value: 6.00e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  20 EEIYKSSSGFVYNVALRISASEHEASEITQDVFVKLFSGLKSFNHKSS--FNTWLYRVAVNEALNRRKKSNLENSRRAEF 97
Cdd:PRK12542   12 EELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTqeLKRYILRVAKNKAIDSYRKNKRHETFLEEY 91
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  98 D-ESVEAnpalredpvgksVNENID---KDKVAE-----LLSLVNEEHRVVLVLREMQGLNYEEMSRVLGININTVRTRL 168
Cdd:PRK12542   92 ErESIEA------------VDENIEeweKRKMSEvqidtLLKELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQF 159

                  ....*
gi 1085001966 169 KRARE 173
Cdd:PRK12542  160 ERARK 164
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
122-175 1.16e-08

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: 48.99  E-value: 1.16e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1085001966 122 KDKVAELLSLVNEEHRVVLVLREMQGLNYEEMSRVLGININTVRTRLKRAREIL 175
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK09642 PRK09642
RNA polymerase sigma factor;
29-181 2.02e-08

RNA polymerase sigma factor;


Pssm-ID: 170031 [Multi-domain]  Cd Length: 160  Bit Score: 51.25  E-value: 2.02e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  29 FVYNVALRISASEHEASEITQDVFVKLFSGLKSFNHKsSFNTWLYRVAVNEALNRRKKSNLENSRRA---EFDESVEANP 105
Cdd:PRK09642    7 YIFQVIFSILRHEEDAKDVTQEVFVKIHASLPNYQFR-GLKTWMARIATNHAIDYKRKKARENEELSlckETEENIKSSH 85
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1085001966 106 ALREDPVGKSvneniDKDKVAELLSLVNEEHRVVLVLREMQGLNYEEMSRVLGININTVRTRLKRAREILIKKVKE 181
Cdd:PRK09642   86 NIEDLLLTKE-----QKLLIAQKLRELPENYRDVVLAHYLEEKSYQEIALQEKIEVKTVEMKLYRARKWIKKHWKE 156
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
41-175 2.12e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 51.32  E-value: 2.12e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  41 EHEASEITQDVFVKLFSGLKSFNHKSSFNTWLYRVAVNEALNRRKKSNLENSRRAEF-DESVEANPALREDPVGKSvnen 119
Cdd:PRK12511   28 SAEAEDLVHDALVRALERRASFRSGGNLRTWLMSILHNAFIDELRRRRVEARRADELaVLADASLPAAQEHAVRLA---- 103
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1085001966 120 idkdKVAELLSLVNEEHRVVLVLREMQGLNYEEMSRVLGININTVRTRLKRAREIL 175
Cdd:PRK12511  104 ----QIRDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAAL 155
PRK08241 PRK08241
RNA polymerase subunit sigma-70;
36-175 5.02e-08

RNA polymerase subunit sigma-70;


Pssm-ID: 236196 [Multi-domain]  Cd Length: 339  Bit Score: 51.48  E-value: 5.02e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  36 RISASEHEASEITQDVFVKLFSGLKSFNHKSSFNTWLYRVAVN---EALNRRkksnlenSRRA----EFDESVEANPALR 108
Cdd:PRK08241   38 RMLGSVHDAEDAVQETLLRAWRGYDRFEGRSSLRTWLYRIATNvclDALEGR-------ARRPlptdLGAPAADPVDELV 110
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966 109 ED---------PVGKSVNENIDKDKVAEL-----LSLVNE-EH-----RVVLVLREMQGLNYEEMSRVLGININTVRTRL 168
Cdd:PRK08241  111 ERpevpwlepyPDALLDPAAADPAARVVAresvrLAFVAAlQHlpprqRAVLILRDVLGWSAAEVAELLDTSVAAVNSAL 190

                  ....*..
gi 1085001966 169 KRAREIL 175
Cdd:PRK08241  191 QRARATL 197
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
18-181 5.41e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 49.93  E-value: 5.41e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  18 AFEEIYKSSSGFVYNVALRISASEHEASEITQDVFVKLFSGLKSFNHKSsFNTWLYRVAVNEALN-RRKKSNLENSRRAE 96
Cdd:PRK12541    6 SLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGEE-IRPWLFTIAYNAFIDwYRKEKKYKTTTIEE 84
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  97 FDESveanpalredPVGKSVNENIDKDKVAELLSLVNE---EHRVVLVLREMQGLNYEEMSRVLGININTVRTRLKRARE 173
Cdd:PRK12541   85 FHLP----------NVPSTEHEYFIKHEIASWLDSLSSlplERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRK 154

                  ....*...
gi 1085001966 174 ILiKKVKE 181
Cdd:PRK12541  155 ET-KSIKE 161
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
34-175 1.02e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 49.58  E-value: 1.02e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  34 ALRISASEHEASEITQDVFVKLFSGLKSFNHKSSFNTWLYRVAVNEALNRRKKSNLE-NSRRAEFDESVEANPalredpv 112
Cdd:PRK12516   27 AVSLIGRHDRADDLVQDTIMKAWAKQDHFEVGTNMKAWLFTILRNEFYSQMRKRGREvQDTDGMFTEQLAVHP------- 99
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1085001966 113 gkSVNENIDKDKVAELLSLVNEEHRVVLVLREMQGLNYEEMSRVLGININTVRTRLKRAREIL 175
Cdd:PRK12516  100 --SQYGTLDLQDFRAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQRL 160
PRK12547 PRK12547
RNA polymerase sigma factor; Provisional
34-172 1.34e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 139056 [Multi-domain]  Cd Length: 164  Bit Score: 49.10  E-value: 1.34e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  34 ALRISASEHEASEITQDVFVKLFSGLKSFNHKSSFNTWLYRVAVNEALNRRKKSNLE-NSRRAEFDESVEANPALredpv 112
Cdd:PRK12547   23 AVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGTNLKAWLFTILRNEFYSQMRKRGREvQDSDGVFTARVAVHPAQ----- 97
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966 113 gksvNENIDKDKVAELLSLVNEEHRVVLVLREMQGLNYEEMSRVLGININTVRTRLKRAR 172
Cdd:PRK12547   98 ----YGSLDLQDFKKALNLLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRAR 153
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
44-175 2.92e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 48.30  E-value: 2.92e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  44 ASEITQDVFVKLFSGLKSFNHKSSFNTWLYRVAVNEALNRRKKSNLEnsrRAEFDESVEANPALREDPVGKsvnenIDKD 123
Cdd:PRK12546   34 ADDLVQDTIVKAWTNFDKFQEGTNLRAWLFTILRNTFYSDRRKHKRE---VPDPEGVHAASLAVKPAHDGR-----LAMS 105
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1085001966 124 KVAELLSLVNEEHRVVLVLREMQGLNYEEMSRVLGININTVRTRLKRAREIL 175
Cdd:PRK12546  106 DFRAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARARL 157
PRK12532 PRK12532
RNA polymerase sigma factor; Provisional
35-175 3.31e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 171564 [Multi-domain]  Cd Length: 195  Bit Score: 48.39  E-value: 3.31e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  35 LRISASEHEASEITQDVFVKLFSGLKSFNHKSSFNTWLYRV-------AVNEALNRRKKSNLENSR--RAEFDESVEAN- 104
Cdd:PRK12532   24 LQLPDHPDLAEDLVQETLLSAYSAGDSFQGRALVNSWLFAIlknkiidALRQIGRQRKVFTLLDDEllDEAFESHFSQNg 103
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1085001966 105 -------PALREDPvGKSVNENIDKDKVAELLSLVNEEHRVVLVLREMQGLNYEEMSRVLGININTVRTRLKRAREIL 175
Cdd:PRK12532  104 hwtpegqPQHWNTP-EKSLNNNEFQKILQSCLYNLPENTARVFTLKEILGFSSDEIQQMCGISTSNYHTIMHRARESL 180
PRK12540 PRK12540
RNA polymerase sigma factor; Provisional
34-175 6.17e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183579 [Multi-domain]  Cd Length: 182  Bit Score: 47.27  E-value: 6.17e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  34 ALRISASEHEASEITQDVFVKLFSGLKSFNHKSSFNTWLYRVAVN--EALNRRKKSNLENSRrAEFDESVEANPalredp 111
Cdd:PRK12540   22 AISLSGNGDRADDLVQETLLRALANIDSFQPGSNLPAWLFTILRNlfRSDYRKRRREVEDAD-GSYAKTLKSQP------ 94
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1085001966 112 vgkSVNENIDKDKVAELLSLVNEEHRVVLVLREMQGLNYEEMSRVLGININTVRTRLKRAREIL 175
Cdd:PRK12540   95 ---GQNAHLEFEEFRAALDKLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARSKL 155
PRK06930 PRK06930
positive control sigma-like factor; Validated
121-181 9.32e-07

positive control sigma-like factor; Validated


Pssm-ID: 180757 [Multi-domain]  Cd Length: 170  Bit Score: 46.65  E-value: 9.32e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1085001966 121 DKDKVAELLSLVNEEHRVVLVLREMQGLNYEEMSRVLGININTVRTRLKRAREILIKKVKE 181
Cdd:PRK06930  104 DKIRIEDALSVLTEREKEVYLMHRGYGLSYSEIADYLNIKKSTVQSMIERAEKKIARQINE 164
sigI PRK09635
RNA polymerase sigma factor SigI; Provisional
21-172 8.22e-05

RNA polymerase sigma factor SigI; Provisional


Pssm-ID: 182008 [Multi-domain]  Cd Length: 290  Bit Score: 41.88  E-value: 8.22e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  21 EIYKSSSGFVYNVALRISASEHEASEITQDVFVKLFSGlkSFNHKSSFNTWLYRVAVNEALNRRKKSNLENSRRAEFDES 100
Cdd:PRK09635    9 AAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRA--PVGDIDDERGWLIVVTSRLCLDHIKSASTRRERPQDIAAW 86
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1085001966 101 VEANPAL-REDPVGKSVNENIDKDKVAELLSLVNEEHRVVLVLREMQGLNYEEMSRVLGININTVRTRLKRAR 172
Cdd:PRK09635   87 HDGDASVsSVDPADRVTLDDEVRLALLIMLERLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQLAHRAR 159
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
128-173 1.66e-04

Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. 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: 37.79  E-value: 1.66e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1085001966 128 LLSLVNEEHRVVLVLREMQGLNYEEMSRVLGININTVRTRLKRARE 173
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALR 46
HTH_30 pfam13556
PucR C-terminal helix-turn-helix domain; This helix-turn-helix domain is often found at the ...
147-175 6.46e-04

PucR C-terminal helix-turn-helix domain; This helix-turn-helix domain is often found at the C-terminus of PucR-like transcriptional regulators such as Swiss:O32138 and is likely to be DNA-binding.


Pssm-ID: 433305 [Multi-domain]  Cd Length: 56  Bit Score: 36.28  E-value: 6.46e-04
                          10        20
                  ....*....|....*....|....*....
gi 1085001966 147 GLNYEEMSRVLGININTVRTRLKRAREIL 175
Cdd:pfam13556   9 GGNISATARALHVHRNTLRYRLRRIEELL 37
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
116-175 2.13e-03

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 37.43  E-value: 2.13e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966 116 VNENIDKDKVAELLSLVNEEHRVVLVLreMQGLNYEEMSRVLGININTVRTRLKRAREIL 175
Cdd:COG2771   113 LLLAALARLLARAPGLTPREREVLRLL--AEGLTLKEIARILGISERTVRTHLKRIYRKL 170
PRK12531 PRK12531
RNA polymerase sigma factor; Provisional
18-175 2.21e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 105726 [Multi-domain]  Cd Length: 194  Bit Score: 37.22  E-value: 2.21e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  18 AFEEIYKSSSGFVYNVALRISASEHEASEITQDVFVKLFSGLKSFN-HKSSFNTWLYRVAVNEALN--RRKKSNLENSRR 94
Cdd:PRK12531   28 AFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDgQKSALSTWIYTIIRNLCFDllRKQKGKDLHIHA 107
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  95 AEFDESVEANPALREDpvgKSVNENIDKDKVAELLSLVNEEHRVVLVLREMQGLNYEEMSRVLGININTVRTRLKRAREI 174
Cdd:PRK12531  108 DDIWPSDYYPPDLVDH---YSPEQDMLKEQVMKFLDRLPKAQRDVLQAVYLEELPHQQVAEMFDIPLGTVKSRLRLAVEK 184

                  .
gi 1085001966 175 L 175
Cdd:PRK12531  185 L 185
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
32-159 2.66e-03

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 36.97  E-value: 2.66e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  32 NVALRISASEHEASEITQDVFVKLFSGLKSFNHKSSFNtWLYRVAVNEALNRRKKSNLENSRRAEFDESVEanpALREDP 111
Cdd:PRK07037   13 KIAARIVGCRSRAEDVVQDAFVKLVEAPNQDAVKQPVA-YLFRIVRNLAIDHYRRQALENKYHGDEEDGLD---VPSPEA 88
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1085001966 112 VGKSVNENIDK-DKVAELLSLVNEEHRVVLVLREMQGLNYEEMSRVLGI 159
Cdd:PRK07037   89 SPEAALINRDTlRHVADALSELPARTRYAFEMYRLHGETQKDIARELGV 137
PRK09648 PRK09648
RNA polymerase sigma factor ShbA;
6-171 4.87e-03

RNA polymerase sigma factor ShbA;


Pssm-ID: 236607 [Multi-domain]  Cd Length: 189  Bit Score: 36.10  E-value: 4.87e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966   6 DIIERAARGEIPAFEEIYKSssgfVYNVAL-----RISASEH---EASEITQDVFVKLFSGLKSF-NHKSSFNTWLYRVA 76
Cdd:PRK09648   13 ALVAEAVAGDRRALREVLEI----IRPLVVrycraRLGGVERpglSADDVAQEVCLAVITALPRYrDQGRPFLAFVYGIA 88
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085001966  77 ---VNEALNRRKKSNLENSRRAEFDESVEANP---ALREDpvgksvneniDKDKVAELLSLVNEEHRVVLVLREMQGLNY 150
Cdd:PRK09648   89 ahkVADAHRAAGRDKAVPTEEVPERPSDDAGPeerALRSE----------SSNRMRELLDTLPEKQREILILRVVVGLSA 158
                         170       180
                  ....*....|....*....|.
gi 1085001966 151 EEMSRVLGININTVRTRLKRA 171
Cdd:PRK09648  159 EETAEAVGSTPGAVRVAQHRA 179
PucR COG2508
DNA-binding transcriptional regulator, PucR/PutR family [Transcription];
147-175 6.07e-03

DNA-binding transcriptional regulator, PucR/PutR family [Transcription];


Pssm-ID: 441998 [Multi-domain]  Cd Length: 257  Bit Score: 36.13  E-value: 6.07e-03
                          10        20
                  ....*....|....*....|....*....
gi 1085001966 147 GLNYEEMSRVLGININTVRTRLKRAREIL 175
Cdd:COG2508   202 GGNVSATARALHVHRNTVRYRLRRIEELL 230
InsA COG3677
Transposase InsA [Mobilome: prophages, transposons];
145-181 6.29e-03

Transposase InsA [Mobilome: prophages, transposons];


Pssm-ID: 442893 [Multi-domain]  Cd Length: 241  Bit Score: 36.38  E-value: 6.29e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1085001966 145 MQGLNYEEMSRVLGININTVRTRLKRAREILIKKVKE 181
Cdd:COG3677    73 LNGISLRQIARVLGVSYKTVWRWLHRIREALDELVDE 109
 
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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