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Conserved domains on  [gi|1907616494|ref|WP_190223854|]
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RNA polymerase sigma factor [Streptomyces hydrogenans]

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]; ...
 53-216 5.47e-29

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: 106.62  E-value: 5.47e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494  53 DGRPPTLAELYRARRLDMVRLALFLVDDLHTAEDVVQDAFAAVCRAHGtSLAGLQDPAAYLHTAVVNAARSVL----RRR 128
Cdd:COG1595    13 AGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLD-SFRGRGSFRAWLYRIARNLAIDHLrkrrRRR 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494 129 RTARAYAPPHQGAGPPVDEALLLAEEHRDVLAALAELTHRQREVLVLRYWSELTEAQIADTLGLSRGTVKSTASRALDAL 208
Cdd:COG1595    92 ELLDELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKL 171


                  ....*...
gi 1907616494 209 EKRLEAAR 216
Cdd:COG1595   172 REALEEEG 179
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 53-216 5.47e-29

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: 106.62  E-value: 5.47e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494  53 DGRPPTLAELYRARRLDMVRLALFLVDDLHTAEDVVQDAFAAVCRAHGtSLAGLQDPAAYLHTAVVNAARSVL----RRR 128
Cdd:COG1595    13 AGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLD-SFRGRGSFRAWLYRIARNLAIDHLrkrrRRR 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494 129 RTARAYAPPHQGAGPPVDEALLLAEEHRDVLAALAELTHRQREVLVLRYWSELTEAQIADTLGLSRGTVKSTASRALDAL 208
Cdd:COG1595    92 ELLDELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKL 171


                  ....*...
gi 1907616494 209 EKRLEAAR 216
Cdd:COG1595   172 REALEEEG 179
SigE-fam_strep TIGR02983
RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors ...
 59-213 2.05e-27

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: 102.08  E-value: 2.05e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494  59 LAELYRARRLDMVRLALFLVDDLHTAEDVVQDAFAAVCRAHGtSLAGLQDPAAYLHTAVVNAARSVLRRRRTARAyaPPH 138
Cdd:TIGR02983   8 FTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWD-RIRDPDAPDAYVRRVLVNLARSRWRRRRLLEL--PTR 84

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907616494 139 QGAGPPVDEALLLAEEHRDVLAALAELTHRQREVLVLRYWSELTEAQIADTLGLSRGTVKSTASRALDALEKRLE 213
Cdd:TIGR02983  85 ELPDAAAPDPAPDVALRAALARALRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALARLRELLE 159
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 59-214 3.96e-19

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 80.79  E-value: 3.96e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494  59 LAELYRARRLDMVRLALFLVDDLHTAEDVVQDAFAAVCRaHGTSLAGLQDPAAYLHTAVVNAARSVL------RRRRTAR 132
Cdd:PRK11924   15 FSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWR-KADLFNGKGSARTWLLTIARNVCYDLLrrrrreKAVLSDD 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494 133 AYAPPHQGAGPPVDEALLLAEEHRDVLAALAELTHRQREVLVLRYWSELTEAQIADTLGLSRGTVKSTASRALDALEKRL 212
Cdd:PRK11924   94 ALEPEFAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQLLRECL 173


                  ..
gi 1907616494 213 EA 214
Cdd:PRK11924  174 EA 175
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 161-210 1.08e-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. 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: 57.82  E-value: 1.08e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1907616494 161 ALAELTHRQREVLVLRYWSELTEAQIADTLGLSRGTVKSTASRALDALEK 210
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 155-208 1.64e-11

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: 57.50  E-value: 1.64e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1907616494 155 HRDVLAALAELTHRQREVLVLRYWSELTEAQIADTLGLSRGTVKSTASRALDAL 208
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 162-216 6.18e-05

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 39.43  E-value: 6.18e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1907616494  162 LAELTHRQREVLvlRYWSE-LTEAQIADTLGLSRGTVKSTASRALDALE--KRLEAAR 216
Cdd:smart00421   1 LASLTPREREVL--RLLAEgLTNKEIAERLGISEKTVKTHLSNIMRKLGvrSRTQAVR 56
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 53-216 5.47e-29

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: 106.62  E-value: 5.47e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494  53 DGRPPTLAELYRARRLDMVRLALFLVDDLHTAEDVVQDAFAAVCRAHGtSLAGLQDPAAYLHTAVVNAARSVL----RRR 128
Cdd:COG1595    13 AGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLD-SFRGRGSFRAWLYRIARNLAIDHLrkrrRRR 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494 129 RTARAYAPPHQGAGPPVDEALLLAEEHRDVLAALAELTHRQREVLVLRYWSELTEAQIADTLGLSRGTVKSTASRALDAL 208
Cdd:COG1595    92 ELLDELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKL 171


                  ....*...
gi 1907616494 209 EKRLEAAR 216
Cdd:COG1595   172 REALEEEG 179
SigE-fam_strep TIGR02983
RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors ...
 59-213 2.05e-27

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: 102.08  E-value: 2.05e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494  59 LAELYRARRLDMVRLALFLVDDLHTAEDVVQDAFAAVCRAHGtSLAGLQDPAAYLHTAVVNAARSVLRRRRTARAyaPPH 138
Cdd:TIGR02983   8 FTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWD-RIRDPDAPDAYVRRVLVNLARSRWRRRRLLEL--PTR 84

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907616494 139 QGAGPPVDEALLLAEEHRDVLAALAELTHRQREVLVLRYWSELTEAQIADTLGLSRGTVKSTASRALDALEKRLE 213
Cdd:TIGR02983  85 ELPDAAAPDPAPDVALRAALARALRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALARLRELLE 159
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 59-212 2.60e-21

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: 86.25  E-value: 2.60e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494  59 LAELYRARRLDMVRLALFLVDDLHTAEDVVQDAFAAVCRAHGtSLAGLQDPAAYLHTAVVNAARSVLRRRRTARAYAPPH 138
Cdd:TIGR02937   3 FEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALD-RFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDLL 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907616494 139 QGAG---PPVDEALLLAEEHRDVLAALAELTHRQREVLVLRYWSELTEAQIADTLGLSRGTVKSTASRALDALEKRL 212
Cdd:TIGR02937  82 EELLdsdPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 59-214 3.96e-19

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 80.79  E-value: 3.96e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494  59 LAELYRARRLDMVRLALFLVDDLHTAEDVVQDAFAAVCRaHGTSLAGLQDPAAYLHTAVVNAARSVL------RRRRTAR 132
Cdd:PRK11924   15 FSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWR-KADLFNGKGSARTWLLTIARNVCYDLLrrrrreKAVLSDD 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494 133 AYAPPHQGAGPPVDEALLLAEEHRDVLAALAELTHRQREVLVLRYWSELTEAQIADTLGLSRGTVKSTASRALDALEKRL 212
Cdd:PRK11924   94 ALEPEFAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQLLRECL 173


                  ..
gi 1907616494 213 EA 214
Cdd:PRK11924  174 EA 175
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 61-212 9.89e-14

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: 66.05  E-value: 9.89e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494  61 ELYRARRLDMVRLALFLVDDLHTAEDVVQDAFAAVCRAHGTsLAGLQDPAAYLHTAVVNAA------RSVLRRRRTARAY 134
Cdd:TIGR02985   5 QLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRET-LEISESIKAYLFTIVKNRClnylrhKQVEEKYQEELAE 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907616494 135 APPHQGAGPPVDEALLLAEEHRDVLAALAELTHRQREVLVLRYWSELTEAQIADTLGLSRGTVKSTASRALDALEKRL 212
Cdd:TIGR02985  84 IEERELSEADPEEELEAKELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLRKEL 161
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 56-213 5.21e-13

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 64.20  E-value: 5.21e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494  56 PPTLAELYRARRLDMVRLALFLVDDLHTAEDVVQDAFAAVCRahgTSLAGLQDPAAYLHTAVVNAA----RSVLRRRRTA 131
Cdd:PRK09639    2 DETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYR---SDFKGIENEKGWLIKSARNVAynylRSEKRRRARI 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494 132 RAYAPPHQGAG-PPVDEALLLAEEHRDVLAALAELTHRQREVLVLRYwSELTEAQIADTLGLSRGTVKSTASRALDALEK 210
Cdd:PRK09639   79 LGEFQWQEVDNePSPEEIWIRKEEITKVQEVLAKMTERDRTVLLLRF-SGYSYKEIAEALGIKESSVGTTLARAKKKFRK 157


                  ...
gi 1907616494 211 RLE 213
Cdd:PRK09639  158 IYE 160
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 65-216 7.62e-12

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 61.59  E-value: 7.62e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494  65 ARRLD-MVRLALFLVDDLHTAEDVVQDAFAAVCRAHGTSLAGLQDPAAYLHTAVVNAARSVLRRRRTARAYAPPHQ-GAG 142
Cdd:PRK05602   27 ARKLPrLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPGEARFDTWLHRVVLNLCYDRLRRRREVPVEDAPDVpDPA 106

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907616494 143 PPVDEALLLAEEHRDVLAALAELTHRQREVLVLRYWSELTEAQIADTLGLSRGTVKSTASRALDALEKRLEAAR 216
Cdd:PRK05602  107 PGPDAGLEARQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALESLLARGRRALRAQLADLP 180
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 161-210 1.08e-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. 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: 57.82  E-value: 1.08e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1907616494 161 ALAELTHRQREVLVLRYWSELTEAQIADTLGLSRGTVKSTASRALDALEK 210
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 60-213 1.54e-11

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 60.59  E-value: 1.54e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494  60 AELYR--ARRLDmvRLALFLVDDLHTAEDVVQDAFAAVCRAhgtsLAGLQDPA---AYLHTAVVNAA-------RSVLRR 127
Cdd:PRK09652   13 ALLVRryQPRVK--RLLSRLTRDPADAEDLVQETFIKAYRA----LHSFRGGAafyTWLYRIARNTAinylrkqGRRPPA 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494 128 RRTARAYAPPHQGAG-----PPVDEALLLAEEHRDVLAALAELTHRQREVLVLRYWSELTEAQIADTLGLSRGTVKSTAS 202
Cdd:PRK09652   87 SDVDAEEAEDFDLADalrdiSTPENELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRIF 166

                         170
                  ....*....|.
gi 1907616494 203 RALDALEKRLE 213
Cdd:PRK09652  167 RAREALRAKLQ 177
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 155-208 1.64e-11

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: 57.50  E-value: 1.64e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1907616494 155 HRDVLAALAELTHRQREVLVLRYWSELTEAQIADTLGLSRGTVKSTASRALDAL 208
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 69-213 1.52e-10

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 57.84  E-value: 1.52e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494  69 DMVRLALFLVDDLHTAEDVVQDAFAAVCRAHGTsLAGLQDPAAYLHTAVVNAARSVLRR-----RRTARAYAPPHQGAGP 143
Cdd:PRK09415   28 EVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHT-YKGKSSLKTWLYRIAINHCKDYLKSwhnkkVIVTEDIFTYMESQKE 106

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494 144 PVDEALLLAEEHRDVLAALAELTHRQREVLVLRYWSELTEAQIADTLGLSRGTVKSTASRALDALEKRLE 213
Cdd:PRK09415  107 SVEEEVIQNAEDERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKELLKKGLE 176
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 155-208 2.12e-10

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: 54.38  E-value: 2.12e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1907616494 155 HRDVLAALAELTHRQREVLVLRYWSELTEAQIADTLGLSRGTVKSTASRALDAL 208
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK09047 PRK09047
RNA polymerase factor sigma-70; Validated
 146-214 4.49e-10

RNA polymerase factor sigma-70; Validated


Pssm-ID: 236367 [Multi-domain]  Cd Length: 161  Bit Score: 56.13  E-value: 4.49e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907616494 146 DEALLLAEEHRDVLAALAELTHRQREVLVLRYWSELTEAQIADTLGLSRGTVKSTASRALDALEKRLEA 214
Cdd:PRK09047   88 ADKLERAQVLQLIEEAIQKLPARQREAFLLRYWEDMDVAETAAAMGCSEGSVKTHCSRATHALAKALEA 156
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 46-214 6.98e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 56.24  E-value: 6.98e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494  46 ALPAWHGDGRPPTLAELYRARRLDMVRLALFLVDDLHTAEDVVQDAFAAVCRAHGTslaglQDPAAYLHTAVVNAARSVL 125
Cdd:PRK12513   15 ALMLRYRAGDAAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQ-----YQPRARFRTWLYQIARNLL 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494 126 RRRRTARAYAPPHQ-----------GAGPPVDEALLLAEEHRDVLAALAELTHRQREVLVLRYWSELTEAQIADTLGLSR 194
Cdd:PRK12513   90 IDHWRRHGARQAPSldadeqlhalaDDGAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREHGDLELEEIAELTGVPE 169

                         170       180
                  ....*....|....*....|
gi 1907616494 195 GTVKSTASRALDALEKRLEA 214
Cdd:PRK12513  170 ETVKSRLRYALQKLRELLAE 189
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 54-214 1.46e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 55.45  E-value: 1.46e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494  54 GRPPTLAELYRaRRLDMV-RLALFLVDDLHTAEDVVQDAFAAVCRaHGTSLAGLQDPAAYLHTAV----VNAARSVLRRR 128
Cdd:PRK12519   26 GQSAALGVLYD-RHAGLVyGLALKILGNSQEAEDLTQEIFLSLWR-KSSYDPKRGSLSSYLLTLTrsraIDRLRSRRSRQ 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494 129 RTARAYAPPHQG--AGPPVDEALLLAEEHRDVLAALAELTHRQREVLVLRYWSELTEAQIADTLGLSRGTVKSTASRALD 206
Cdd:PRK12519  104 RLLERWQQELLGeaSEDTPLEQASLAERSQRVQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKARARQGLL 183


                  ....*...
gi 1907616494 207 ALEKRLEA 214
Cdd:PRK12519  184 KLRELLQD 191
Sig70_famx3 TIGR02954
RNA polymerase sigma-70 factor, TIGR02954 family; This group of sigma factors are members of ...
 54-213 1.96e-09

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: 54.72  E-value: 1.96e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494  54 GRPPTLAELYRARRLDMVRLALFLVDDLHTAEDVVQDAfaaVCRAHgTSLAGLQDP---AAYLHTAVVNAARSVLRRRRT 130
Cdd:TIGR02954  13 GNKPAFESLIKKHKEKLYKTAFIYVKNEHDALDVIQET---VYKAY-LSIDKLKHPkyfNTWLTRILINECIDLLKKKKK 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494 131 ARAYAPPHQGAGppvDEALLLAEEHRDVLAALAELTHRQREVLVLRYWSELTEAQIADTLGLSRGTVKSTASRALDALEK 210
Cdd:TIGR02954  89 VIPFDPNTSIEK---GECETHADSRLDLYKAIDTLNDKYQTAIILRYYHDLTIKEIAEVMNKPEGTVKTYLHRALKKLKK 165


                  ...
gi 1907616494 211 RLE 213
Cdd:TIGR02954 166 RLE 168
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
58-213 2.55e-09

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 54.31  E-value: 2.55e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494  58 TLAELYRARRLDMVRLALFLVDDLHTAEDVVQDAFAAVCRaHGTSLAGLQDPA-AYLHTA----VVNAARSvlRRRRTAR 132
Cdd:PRK09645   10 LMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQ-HPEVLADTGRSArAWLFTVarnlVIDERRS--ARARPVE 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494 133 AYAPPHQGAGPPVDEALLLAEEHRDVLAALAELTHRQREVLVLRYWSELTEAQIADTLGLSRGTVKSTASRALDALEKRL 212
Cdd:PRK09645   87 GGDDVLGVPEQSAPDEVDRALDRLLVADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYALRALRLAL 166


                  .
gi 1907616494 213 E 213
Cdd:PRK09645  167 Q 167
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 46-216 4.72e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 54.13  E-value: 4.72e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494  46 ALPAWHGDGRPPTLAELYRARRLDMVRLALFLVDDLHTAEDVVQDAFAAVCRAHGTSLAGLQDPAAYLHTAVVNAARSVL 125
Cdd:PRK12524   15 ALLVLYANGDPAAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQGEARVSTWLYRVVCNLCTDRL 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494 126 RRRRTARAY---APPHQGAGPPVDEALLLAEEHRDVLAALAELTHRQREVLVLRYWSELTEAQIADTLGLSRGTVKSTAS 202
Cdd:PRK12524   95 RRRRRASVDlddAPEPADAAPGAEEALIEGDRMRALDAALAALPERQRQAVVLRHIEGLSNPEIAEVMEIGVEAVESLTA 174

                         170
                  ....*....|....
gi 1907616494 203 RALDALEKRLEAAR 216
Cdd:PRK12524  175 RGKRALAALLAGQR 188
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 146-213 2.94e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 51.66  E-value: 2.94e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907616494 146 DEALLLAEEHRDVLAALAELTHRQREVLVLRYWSELTEAQIADTLGLSRGTVKSTASRALDALEKRLE 213
Cdd:PRK12543   99 SEDVLSKESNQELIELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQ 166
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 142-213 1.58e-07

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 49.69  E-value: 1.58e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907616494 142 GPPVDEALLLAEEHRDVLAALAELTHRQREVLVLRYWSELTEAQIADTLGLSRGTVKSTASRALDALEKRLE 213
Cdd:PRK09641  114 DALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYIEDLSLKEISEILDLPVGTVKTRIHRGREALRKQLR 185
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 146-214 3.59e-07

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: 49.05  E-value: 3.59e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907616494 146 DEALLLAEEHRDVLAALAELTHRQREVLVLRYWSELTEAQIADTLGLSRGTVKSTASRALDALEKRLEA 214
Cdd:COG1191   168 EEELEHEELREALAEAIEQLPERERLVLSLYYFEELTLKEIAEVLGVSESRVSRLHKKALARLREYLKE 236
PRK09643 PRK09643
RNA polymerase sigma factor SigM; Reviewed
 47-216 2.30e-06

RNA polymerase sigma factor SigM; Reviewed


Pssm-ID: 236604 [Multi-domain]  Cd Length: 192  Bit Score: 46.24  E-value: 2.30e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494  47 LPAWHGDGRPPTLAELYRARRLDMVRLALFLVDDLHTAEDVVQDAFAAVCRAHGTsLAGLQDPAAYLHTAVVNAARSVLR 126
Cdd:PRK09643   17 LLAAHVAGDRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGS-FRGDAAVSSWLHRIVVNACLDRLR 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494 127 RRRTARAYapphqgagpPVDEALLLA----------EEHRDVLAALAELTHRQREVLVLRYWSELTEAQIADTLGLSRGT 196
Cdd:PRK09643   96 RAKARPTV---------PLDDVYPVAqlerdptarvETALAVQRALMRLPVEQRAALVAVDMQGYSVADAARMLGVAEGT 166

                         170       180
                  ....*....|....*....|
gi 1907616494 197 VKSTASRALDALEKRLEAAR 216
Cdd:PRK09643  167 VKSRCARGRARLAELLGYLR 186
PRK09646 PRK09646
ECF RNA polymerase sigma factor SigK;
28-199 3.13e-06

ECF RNA polymerase sigma factor SigK;


Pssm-ID: 182015 [Multi-domain]  Cd Length: 194  Bit Score: 45.82  E-value: 3.13e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494  28 ARVSRAEDVHVPRGRHLRALPAWHGDGRPPTLAELYRARRLDMVRLALFLVDDLHTAEDVVQDAFAAVCR-------AHG 100
Cdd:PRK09646    1 MKAAVPMTGPPAESPDLDALLRRVARGDQDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRtasrfdpARG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494 101 TSLAGLQDPAaylHTAVVNAARSVLRRRRT-ARAYAPPHQGAGPPVDEALLLAEEHRDVLAALAELTHRQREVLVLRYWS 179
Cdd:PRK09646   81 SALAWLLTLA---HRRAVDRVRSEQAASQReVRYGARNVDPAFDQVAEEVEARLERERVRDCLDALTDTQRESVTLAYYG 157

                         170       180
                  ....*....|....*....|
gi 1907616494 180 ELTEAQIADTLGLSRGTVKS 199
Cdd:PRK09646  158 GLTYREVAERLAVPLGTVKT 177
PRK06930 PRK06930
positive control sigma-like factor; Validated
 161-213 4.50e-06

positive control sigma-like factor; Validated


Pssm-ID: 180757 [Multi-domain]  Cd Length: 170  Bit Score: 45.11  E-value: 4.50e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1907616494 161 ALAELTHRQREVLVLRYWSELTEAQIADTLGLSRGTVKSTASRALDALEKRLE 213
Cdd:PRK06930  111 ALSVLTEREKEVYLMHRGYGLSYSEIADYLNIKKSTVQSMIERAEKKIARQIN 163
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 61-215 6.88e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 44.71  E-value: 6.88e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494  61 ELYRaRRLDMVRLALFLVDDLHTAEDVVQDAFAAVCRAhgtsLAGLQDPA---AYLHTAVVNAA---RSVLRRRRTARAY 134
Cdd:PRK12518   15 QLYR-RYQQKVRSTLYQLCGRELLDDLVQEVFLRVWKG----LPKLRNPAyfsTWLYRITWNVAtdaRRQFAQRPSRIQD 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494 135 APPHQGAGPPVDEALLLAEEHRD-VLAALAELTHRQREVLVLRYWSELTEAQIADTLGLSRGTVKSTASRALDALEKRLE 213
Cdd:PRK12518   90 DSLNDQPSRPSDTPDLMQLHYQDlVQQGLQTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQ 169


                  ..
gi 1907616494 214 AA 215
Cdd:PRK12518  170 QQ 171
PRK05949 PRK05949
RNA polymerase sigma factor; Validated
 157-211 1.18e-05

RNA polymerase sigma factor; Validated


Pssm-ID: 180321 [Multi-domain]  Cd Length: 327  Bit Score: 45.22  E-value: 1.18e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1907616494 157 DVLAALAELTHRQREVLVLRY----WSELTEAQIADTLGLSRGTVKSTASRALDALEKR 211
Cdd:PRK05949  259 DLNNLLAELTPQQREVLTLRFgledGKELSLAKVGERLNLSRERVRQLEHQALAHLRRR 317
PRK12533 PRK12533
RNA polymerase sigma factor; Provisional
 49-204 1.54e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 237129 [Multi-domain]  Cd Length: 216  Bit Score: 44.34  E-value: 1.54e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494  49 AWHGDGRPPTLAELYRARRLDMV---------RLALFLVDDLHTAEDVVQDAFAAVCRAHGTSLAGlqDPAAYLHTAVVN 119
Cdd:PRK12533    1 ADSDRTAGAAMDAAARGERFRQLvlphldaayNLARWLCGNASDADDVVQEACMRALRFFDSFRGD--NARPWLLAIVRH 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494 120 ----------AARSVLRRRRTARAYAPPHQGAGPPVDEALLL-AEEHRDVLAALAELTHRQREVLVLRYWSELTEAQIAD 188
Cdd:PRK12533   79 twysewrrraNAHEVAAPDTLDDADSLDDWQPAGEDPLALLLrAEDVRLVNAALAKLPVEYREVLVLRELEDMSYREIAA 158

                         170
                  ....*....|....*.
gi 1907616494 189 TLGLSRGTVKSTASRA 204
Cdd:PRK12533  159 IADVPVGTVMSRLARA 174
PRK07122 PRK07122
RNA polymerase sigma factor SigF; Reviewed
 145-213 1.75e-05

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 168831 [Multi-domain]  Cd Length: 264  Bit Score: 44.38  E-value: 1.75e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907616494 145 VDEALLLAEEHRDVLAALAELTHRQREVLVLRYWSELTEAQIADTLGLSRGTVKSTASRALDALEKRLE 213
Cdd:PRK07122  196 VDAGLDQIENREALRPLLAALPERERTVLVLRFFESMTQTQIAERVGISQMHVSRLLAKTLARLRDQLE 264
tfx PRK03975
putative transcriptional regulator; Provisional
 165-210 3.32e-05

putative transcriptional regulator; Provisional


Pssm-ID: 179690 [Multi-domain]  Cd Length: 141  Bit Score: 42.18  E-value: 3.32e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1907616494 165 LTHRQREVLVLRYwSELTEAQIADTLGLSRGTVKSTASRALDALEK 210
Cdd:PRK03975    7 LTERQIEVLRLRE-RGLTQQEIADILGTSRANVSSIEKRARENIEK 51
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 153-213 4.93e-05

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 42.31  E-value: 4.93e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907616494 153 EEHRDVLAALAELTHRQREVLVLRYWSELTEAQIADTLGLSRGTVKSTASRALDALEKRLE 213
Cdd:PRK09638  115 AEWSEMLDALSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRKEWG 175
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 46-216 5.32e-05

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 42.47  E-value: 5.32e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494  46 ALPAWHGDGRPPTLAELYRARRLDMVRLALFLVDDLHTAEDVVQDAFAAVCRahgtSLAGLQdPAAY---LHTAVVNAAR 122
Cdd:PRK09647   17 VFDATGDKATMPSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFR----SLQNYQ-PGTFegwLHRITTNLFL 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494 123 SVLRRRRTARAYAPPHQ-----GAGPPVDEALLLAEEHRDVLAALAELTHRQREVLVLRYWSELTEAQIADTLGLSRGTV 197
Cdd:PRK09647   92 DMVRRRARIRMEALPEDydrvpGDEPNPEQIYHDARLDPDLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTV 171

                         170
                  ....*....|....*....
gi 1907616494 198 KSTASRALDALEKRLEAAR 216
Cdd:PRK09647  172 RSRIHRGRQQLRAALAAHA 190
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 162-216 6.18e-05

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 39.43  E-value: 6.18e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1907616494  162 LAELTHRQREVLvlRYWSE-LTEAQIADTLGLSRGTVKSTASRALDALE--KRLEAAR 216
Cdd:smart00421   1 LASLTPREREVL--RLLAEgLTNKEIAERLGISEKTVKTHLSNIMRKLGvrSRTQAVR 56
PRK09649 PRK09649
RNA polymerase sigma factor SigC; Reviewed
 46-208 1.47e-04

RNA polymerase sigma factor SigC; Reviewed


Pssm-ID: 137458 [Multi-domain]  Cd Length: 185  Bit Score: 41.18  E-value: 1.47e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494  46 ALPAWHGDGRppTLAELYRARRLDMVRLALFLvDDLHTAEDVVQDAF----AAVCRAHGTSLAglqdpaaylHTAVVNAA 121
Cdd:PRK09649   15 ALSAAKGNGR--ALEAFIKATQQDVWRFVAYL-SDVGSADDLTQETFlraiGAIPRFSARSSA---------RTWLLAIA 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494 122 RSVLRRRRTARAYAPPHQGAGPPvdEALLLAEEHR-------DVLAALAELTHRQREVLVLRYWSELTEAQIADTLGLSR 194
Cdd:PRK09649   83 RHVVADHIRHVRSRPRTTRGARP--EHLIDGDRHArgfedlvEVTTMIADLTTDQREALLLTQLLGLSYADAAAVCGCPV 160

                         170
                  ....*....|....
gi 1907616494 195 GTVKSTASRALDAL 208
Cdd:PRK09649  161 GTIRSRVARARDAL 174
PRK12517 PRK12517
RNA polymerase sigma factor; Provisional
 62-214 1.47e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183569 [Multi-domain]  Cd Length: 188  Bit Score: 41.21  E-value: 1.47e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494  62 LYRARRLDMVRLALFLVDDLHTAEDVVQDAFAAVCRahgtSLAGLQDPAA---YLHTAV--VNAARSVLRRRRTARAYAP 136
Cdd:PRK12517   28 LVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWR----SLDSLKDEKAakaWLITILrrENARRFERKQFDLVDIEDD 103

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907616494 137 PHQGAGPPVDEALLlaeEHRDVLAALAELTHRQREVLVLRYWSELTEAQIADTLGLSRGTVKSTASRALDALEKRLEA 214
Cdd:PRK12517  104 SIEDDASHSSEEEM---EQEWLRRQIAKLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMTRLFRARNQLKEALEK 178
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 143-194 2.99e-04

DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 440334 [Multi-domain]  Cd Length: 268  Bit Score: 40.81  E-value: 2.99e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1907616494 143 PPVDEALLLAEEHRDVLAALAELTHRQREVLVLRYWSELTE----AQIADTLGLSR 194
Cdd:COG0568   185 PSPEEALEEELLREELREALDTLTEREREILRLRFGLDDGEphtlEEIGKEFGVSR 240
PRK09648 PRK09648
RNA polymerase sigma factor ShbA;
82-214 3.47e-04

RNA polymerase sigma factor ShbA;


Pssm-ID: 236607 [Multi-domain]  Cd Length: 189  Bit Score: 39.95  E-value: 3.47e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494  82 HTAEDVVQDafaaVCRAHGTSLAGLQDP----AAYLH----TAVVNAARSVLRRRRTARAYAP--PHQGAGPpvDEALLL 151
Cdd:PRK09648   53 LSADDVAQE----VCLAVITALPRYRDQgrpfLAFVYgiaaHKVADAHRAAGRDKAVPTEEVPerPSDDAGP--EERALR 126

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907616494 152 AEEHRDVLAALAELTHRQREVLVLRYWSELTEAQIADTLGLSRGTVKSTASRALDALEKRLEA 214
Cdd:PRK09648  127 SESSNRMRELLDTLPEKQREILILRVVVGLSAEETAEAVGSTPGAVRVAQHRALARLRAEIEA 189
PRK09636 PRK09636
RNA polymerase sigma factor SigJ; Provisional
 54-204 3.62e-04

RNA polymerase sigma factor SigJ; Provisional


Pssm-ID: 236600 [Multi-domain]  Cd Length: 293  Bit Score: 40.67  E-value: 3.62e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494  54 GRPPTLAELYRARRLDMVRLALFLVDDLHTAEDVVQDAFaavCRAHGTSLAGLQDPAAYLHTAVVNAARSVLRRRRTARA 133
Cdd:PRK09636    1 MTMADAAAEFEPLRPHLLSVAYRMLGSVADAEDIVQEAW---LRWNNADRAQIRDPRAWLTRVVTRLCLDRLRSARHRRE 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907616494 134 Y-------APPHQGAGPPvDEALLLAEEHR-DVLAALAELTHRQREVLVLRYWSELTEAQIADTLGLSRGTVKSTASRA 204
Cdd:PRK09636   78 TyvgpwlpEPVVEELDDP-LEAVVAAEDLSlALMLALERLSPLERAAFLLHDVFGVPFDEIASTLGRSPAACRQLASRA 155
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 82-214 7.14e-04

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 38.60  E-value: 7.14e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494  82 HTAEDVVQDAFAAVCRAhgTSLAGLQDPAAYLHTAVVNAA-----RSVLRRRRTARAYAPPHQGAGPPVDEALLLAEEHR 156
Cdd:PRK12527   20 QAAEDVAHDAYLRVLER--SSSAQIEHPRAFLYRTALNLVvdrhrRHRVRQAEPLEVLDEEERLHSPSPQTRLDLGQRLA 97

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1907616494 157 DVLAALAELTHRQREVLVLRYWSELTEAQIADTLGLSRGTVKSTASRALDALEKRLEA 214
Cdd:PRK12527   98 LLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMRQ 155
sigI PRK09635
RNA polymerase sigma factor SigI; Provisional
 59-204 7.29e-04

RNA polymerase sigma factor SigI; Provisional


Pssm-ID: 182008 [Multi-domain]  Cd Length: 290  Bit Score: 39.56  E-value: 7.29e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494  59 LAELYRARRLDMVRLALFLVDDLHTAEDVVQDAFAAVCRAHGTSlagLQDPAAYLHTAV----VNAARSVLRRRRTARAY 134
Cdd:PRK09635    7 VSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVGD---IDDERGWLIVVTsrlcLDHIKSASTRRERPQDI 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907616494 135 APPHQGAGP-----PVDEALLLAEEHRDVLAALAELTHRQREVLVLRYWSELTEAQIADTLGLSRGTVKSTASRA 204
Cdd:PRK09635   84 AAWHDGDASvssvdPADRVTLDDEVRLALLIMLERLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQLAHRA 158
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 146-216 7.76e-04

DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal transduction mechanisms, Transcription];


Pssm-ID: 441799 [Multi-domain]  Cd Length: 131  Bit Score: 38.33  E-value: 7.76e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494 146 DEALLLAEEHR-DVL-------------AALAELTHRQREVLvlRYWSE-LTEAQIADTLGLSRGTVKSTASRALDALE- 209
Cdd:COG2197    37 EEALELLEELRpDVVlldirmpgmdgleALRRLLTPREREVL--RLLAEgLSNKEIAERLGISERTVKTHVSNILRKLGv 114


                  ....*...
gi 1907616494 210 -KRLEAAR 216
Cdd:COG2197   115 rNRTELVL 122
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 62-122 9.87e-04

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: 36.41  E-value: 9.87e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907616494  62 LYRARRLDMVRLALFLVDDLHTAEDVVQDAFAAVCRAHGT-SLAGLQDPAAYLHTAVVNAAR 122
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERfDPERGVSFSTWLYTIIRNAII 62
COG2512 COG2512
Predicted transcriptional regulator, contains CW (cell wall-binding) repeats and an HTH domain ...
 158-211 1.43e-03

Predicted transcriptional regulator, contains CW (cell wall-binding) repeats and an HTH domain [General function prediction only];


Pssm-ID: 442002 [Multi-domain]  Cd Length: 80  Bit Score: 36.43  E-value: 1.43e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1907616494 158 VLAALAELTHRQREVL--VLRYWSELTEAQIADTLGLSrgtvKSTASRALDALEKR 211
Cdd:COG2512     6 ALLLYPELLEDERRVLelLRENGGRMTQSEIVKETGWS----KSKVSRLLSRLEER 57
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 59-208 1.49e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 38.22  E-value: 1.49e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494  59 LAELYRARRLDMVRLALFLVDDLHTAEDVVQDAFAAVCRAHGTSLAGLQDPAAYLHTAV----VNAARSVLRRRRTARAY 134
Cdd:PRK12537   25 LQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPARGSARGWIYSVTrhlaLNVLRDTRREVVLDDDA 104

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907616494 135 APPHQGAGPPVDEALLLAEEHRdVLAALAELTHRQREVLVLRYWSELTEAQIADTLGLSRGTVKSTASRALDAL 208
Cdd:PRK12537  105 EETAQTLHEIIDDFDLWANSGK-IHRCLEQLEPARRNCILHAYVDGCSHAEIAQRLGAPLGTVKAWIKRSLKAL 177
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 55-213 1.62e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 37.61  E-value: 1.62e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494  55 RPPTLAELYRARRLDMVRLALFLVDDLHTAEDVVQDAFAAVCrAHGTSLAGlQDPAAYLHTAVVNA------ARSVLRRR 128
Cdd:PRK12541    3 RKQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRML-VHIDYYKG-EEIRPWLFTIAYNAfidwyrKEKKYKTT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494 129 RTARAYAPPHqgagPPVDEALLLAEEHRDVLAALAELTHRQREVLVLRYWSELTEAQIADTLGLSRGTVKSTASRALDAL 208
Cdd:PRK12541   81 TIEEFHLPNV----PSTEHEYFIKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKET 156


                  ....*
gi 1907616494 209 EKRLE 213
Cdd:PRK12541  157 KSIKE 161
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
 65-214 1.94e-03

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 37.74  E-value: 1.94e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494  65 ARRLDMVRLALFLVDDLHTAEDVVQDAFAAVCRAHGTSlaGLQDPAAYLHTAVVNAA-----RSVLRRRRTARAYAP--- 136
Cdd:PRK07037    6 DNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQD--AVKQPVAYLFRIVRNLAidhyrRQALENKYHGDEEDGldv 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907616494 137 PHQGAGPpvdEALLLAEEH-RDVLAALAELTHRQREVLVLRYWSELTEAQIADTLGLSRGTVKSTASRALDALEKRLEA 214
Cdd:PRK07037   84 PSPEASP---EAALINRDTlRHVADALSELPARTRYAFEMYRLHGETQKDIARELGVSPTLVNFMIRDALVHCRKCLDA 159
GerE pfam00196
Bacterial regulatory proteins, luxR family;
169-205 2.32e-03

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 35.25  E-value: 2.32e-03
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1907616494 169 QREVLVLRYWSE-LTEAQIADTLGLSRGTVKSTASRAL 205
Cdd:pfam00196   5 PREREVLRWLAAgKSNKEIADELGISEKTVKVHRSNIM 42
PRK12526 PRK12526
RNA polymerase sigma factor; Provisional
 154-212 2.51e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237127 [Multi-domain]  Cd Length: 206  Bit Score: 37.47  E-value: 2.51e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1907616494 154 EHRDVLAALAELTHRQREVLVLRYWSELTEAQIADTLGLSRGTVKSTASRALDALEKRL 212
Cdd:PRK12526  143 MDKQILSYIEKLPEAQQTVVKGVYFQELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
 156-213 2.55e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 37.51  E-value: 2.55e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1907616494 156 RDVLAALAELTHRQREVLVLRYWSELTEAQIADTLGLSRGTVKSTASRALDALEKRLE 213
Cdd:PRK12546  105 SDFRAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARARLAELLQ 162
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 46-212 2.58e-03

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 37.59  E-value: 2.58e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494  46 ALPAWHGDGRPPTLAELYRARRLDMVRLALFLVDDLHTAEDVVQDAFAAVCRAHGTSLAGLQDPAAYL----HTAVVNAA 121
Cdd:PRK13919   12 ALLALVARGEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRRGSARAWLlalaHHAAVDHV 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494 122 RSVLRRRRTARAYAPPHQG---AGPPVDEalllaEEHRDVLA---ALAELTHRQREVLVLRYWSELTEAQIADTLGLSRG 195
Cdd:PRK13919   92 RRRAARPQPLEPDEREPEAfdlPGPGLDE-----EGHLDRTRlgrALKALSPEERRVIEVLYYQGYTHREAAQLLGLPLG 166

                         170
                  ....*....|....*..
gi 1907616494 196 TVKSTASRALDALEKRL 212
Cdd:PRK13919  167 TLKTRARRALSRLKEVL 183
PRK09651 PRK09651
RNA polymerase sigma factor FecI; Provisional
 84-213 2.69e-03

RNA polymerase sigma factor FecI; Provisional


Pssm-ID: 182018 [Multi-domain]  Cd Length: 172  Bit Score: 37.10  E-value: 2.69e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494  84 AEDVVQDAFAAVCRahGTSLAGLQDPAAYLHTAVVNAA-----RSVLRRRRTARAYAPPHQGAgPPVDEALLLAEEHRDV 158
Cdd:PRK09651   37 ADDIAQDTFLRVMV--SETLSTIRDPRSFLCTIAKRVMvdlfrRNALEKAYLEMLALMPEGGA-PSPEERESQLETLQLL 113

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1907616494 159 LAALAELTHRQREVLVLRYWSELTEAQIADTLGLSRGTVKSTASRALD-ALEKRLE 213
Cdd:PRK09651  114 DSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKATEhCLLFRLE 169
PRK07405 PRK07405
RNA polymerase sigma factor SigD; Validated
 156-211 2.79e-03

RNA polymerase sigma factor SigD; Validated


Pssm-ID: 180963 [Multi-domain]  Cd Length: 317  Bit Score: 37.82  E-value: 2.79e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907616494 156 RDVLAALAELTHRQREVLVLRYWSE----LTEAQIADTLGLSRGTVKSTASRALDALEKR 211
Cdd:PRK07405  248 LDLERLMEDLTPQQKEVIALRFGLEdgqpLTLAKIGERLNISRERVRQIEREALSKLRKR 307
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 144-215 3.25e-03

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 37.23  E-value: 3.25e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907616494 144 PVDEALLLAEEHRDVLAALAELTHRQREVLVLRYWSELTEAQIADTLGLSRGTVKSTASRALDALEKRLEAA 215
Cdd:PRK09640  114 ASEEKAPKPEERGGLDRWLVHVNPIDREILVLRFVAELEFQEIADIMHMGLSATKMRYKRALDKLREKFAGL 185
PRK07670 PRK07670
FliA/WhiG family RNA polymerase sigma factor;
147-213 4.10e-03

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 181075 [Multi-domain]  Cd Length: 251  Bit Score: 37.33  E-value: 4.10e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907616494 147 EALLLAEEHRDVLAA-LAELTHRQREVLVLRYWSELTEAQIADTLGLSRGTVKSTASRALDALEKRLE 213
Cdd:PRK07670  183 EEKLLKEELIEELAEkIKQLSEKEQLVISLFYKEELTLTEIGQVLNLSTSRISQIHSKALFKLKKLLE 250
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 165-199 4.49e-03

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


Pssm-ID: 99777 [Multi-domain]  Cd Length: 57  Bit Score: 34.43  E-value: 4.49e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1907616494 165 LTHRQREVLvlRYWSE-LTEAQIADTLGLSRGTVKS 199
Cdd:cd06170     1 LTPREREVL--RLLAEgKTNKEIADILGISEKTVKT 34
PRK07598 PRK07598
RNA polymerase sigma factor SigC; Validated
 146-208 7.05e-03

RNA polymerase sigma factor SigC; Validated


Pssm-ID: 236067 [Multi-domain]  Cd Length: 415  Bit Score: 36.77  E-value: 7.05e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907616494 146 DEALLLAEEHRDVLAALAELTHRQREVLVLRY----WSELTEAQIADTLGLSRGTVKSTASRALDAL 208
Cdd:PRK07598  332 EEMLMRESLQRDLQHLLADLTSRERDVIRMRFgladGHTYSLAEIGRALDLSRERVRQIESKALQKL 398
 
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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