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Conserved domains on  [gi|1080278075|gb|OFK70222|]
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RNA polymerase [Corynebacterium sp. HMSC074A09]

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]; ...
 11-158 1.21e-35

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: 122.03  E-value: 1.21e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  11 KREFSRLFREHYPAVLAYLRRRVPPSH-AEELAADVFERAWAGFDSLRGT--PLPWLYGIARNVMREFYRTR-RETENLD 86
Cdd:COG1595    16 EAAFEELYERYRPRLYRYARRLLGDRAdAEDLVQETFLRLWRKLDSFRGRgsFRAWLYRIARNLAIDHLRKRrRRRELLD 95

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1080278075  87 DHELESYAGYDAVDANL-------DITRALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRARTHLSEL 158
Cdd:COG1595    96 ELAEELPDEAADPEEALeaeelleALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREA 174
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 11-158 1.21e-35

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: 122.03  E-value: 1.21e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  11 KREFSRLFREHYPAVLAYLRRRVPPSH-AEELAADVFERAWAGFDSLRGT--PLPWLYGIARNVMREFYRTR-RETENLD 86
Cdd:COG1595    16 EAAFEELYERYRPRLYRYARRLLGDRAdAEDLVQETFLRLWRKLDSFRGRgsFRAWLYRIARNLAIDHLRKRrRRRELLD 95

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1080278075  87 DHELESYAGYDAVDANL-------DITRALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRARTHLSEL 158
Cdd:COG1595    96 ELAEELPDEAADPEEALeaeelleALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREA 174
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 12-158 2.18e-28

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: 102.81  E-value: 2.18e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  12 REFSRLFREHYPAVLAYLRRRVPPSH-AEELAADVFERAWAGFDSLR--GTPLPWLYGIARNVMREFYRTRR-------E 81
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDAdAEDLVQEAFLKLLEALDRFDpeGSFKAWLFRIARNLILDYLRRKRrlrreldL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1080278075  82 TENLDDHELESYAGYDAVDANLDITRALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRARTHLSEL 158
Cdd:TIGR02937  81 LEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLREL 157
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 10-157 9.03e-28

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 101.59  E-value: 9.03e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  10 RKREFSRLFREHYPAVLAYLRRRVP-PSHAEELAADVFERAWAGFDSLR--GTPLPWLYGIARNVMREFYR-TRRETENL 85
Cdd:PRK11924   11 DKEAFSELFRPHAPDLLRYARRQLGdRALAEDAVQEAFLRAWRKADLFNgkGSARTWLLTIARNVCYDLLRrRRREKAVL 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  86 DDHELESYAGY---------DAVDANLDITRALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRARTHLS 156
Cdd:PRK11924   91 SDDALEPEFAEtaetpeaalLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQLLR 170


                  .
gi 1080278075 157 E 157
Cdd:PRK11924  171 E 171
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 103-155 1.38e-13

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: 61.70  E-value: 1.38e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1080278075 103 LDITRALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRARTHL 155
Cdd:pfam08281   2 EALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 102-155 9.72e-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: 54.03  E-value: 9.72e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1080278075 102 NLDITRALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRARTHL 155
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 109-155 7.23e-05

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 38.66  E-value: 7.23e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1080278075  109 LMQLSHAEREILTLHAwEGLDHPDIAEVLGISRNNVRVRLHRARTHL 155
Cdd:smart00421   1 LASLTPREREVLRLLA-EGLTNKEIAERLGISEKTVKTHLSNIMRKL 46
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 11-158 1.21e-35

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: 122.03  E-value: 1.21e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  11 KREFSRLFREHYPAVLAYLRRRVPPSH-AEELAADVFERAWAGFDSLRGT--PLPWLYGIARNVMREFYRTR-RETENLD 86
Cdd:COG1595    16 EAAFEELYERYRPRLYRYARRLLGDRAdAEDLVQETFLRLWRKLDSFRGRgsFRAWLYRIARNLAIDHLRKRrRRRELLD 95

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1080278075  87 DHELESYAGYDAVDANL-------DITRALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRARTHLSEL 158
Cdd:COG1595    96 ELAEELPDEAADPEEALeaeelleALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREA 174
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 12-158 2.18e-28

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: 102.81  E-value: 2.18e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  12 REFSRLFREHYPAVLAYLRRRVPPSH-AEELAADVFERAWAGFDSLR--GTPLPWLYGIARNVMREFYRTRR-------E 81
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDAdAEDLVQEAFLKLLEALDRFDpeGSFKAWLFRIARNLILDYLRRKRrlrreldL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1080278075  82 TENLDDHELESYAGYDAVDANLDITRALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRARTHLSEL 158
Cdd:TIGR02937  81 LEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLREL 157
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 10-157 9.03e-28

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 101.59  E-value: 9.03e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  10 RKREFSRLFREHYPAVLAYLRRRVP-PSHAEELAADVFERAWAGFDSLR--GTPLPWLYGIARNVMREFYR-TRRETENL 85
Cdd:PRK11924   11 DKEAFSELFRPHAPDLLRYARRQLGdRALAEDAVQEAFLRAWRKADLFNgkGSARTWLLTIARNVCYDLLRrRRREKAVL 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  86 DDHELESYAGY---------DAVDANLDITRALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRARTHLS 156
Cdd:PRK11924   91 SDDALEPEFAEtaetpeaalLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQLLR 170


                  .
gi 1080278075 157 E 157
Cdd:PRK11924  171 E 171
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 10-157 4.51e-22

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 87.17  E-value: 4.51e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  10 RKREFSRLFREHYPAVLAYLRRRVP-PSHAEELAADVFERAWAGFDSLRG-----TplpWLYGIARNVMREFYRTRR--- 80
Cdd:PRK09652    8 DRAAFALLVRRYQPRVKRLLSRLTRdPADAEDLVQETFIKAYRALHSFRGgaafyT---WLYRIARNTAINYLRKQGrrp 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  81 ETENLDDHELESYAGYDAV------DANL-------DITRALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVR 147
Cdd:PRK09652   85 PASDVDAEEAEDFDLADALrdistpENELlsaeleqRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSR 164

                         170
                  ....*....|
gi 1080278075 148 LHRARTHLSE 157
Cdd:PRK09652  165 IFRAREALRA 174
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 14-157 8.14e-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: 80.68  E-value: 8.14e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  14 FSRLFREHYPAVLAYLRRRVP-PSHAEELAADVFERAWAGFDSLRG--TPLPWLYGIARN----------VMREFYRTRR 80
Cdd:TIGR02985   3 FEQLYRRYYPKLCAFARRYVKdEEDAEDIVQDVFLKLWENRETLEIseSIKAYLFTIVKNrclnylrhkqVEEKYQEELA 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1080278075  81 ETENLDDHELESYAGYDAVDANLDITRALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRARTHLSE 157
Cdd:TIGR02985  83 EIEERELSEADPEEELEAKELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLRK 159
SigZ TIGR02959
RNA polymerase sigma factor, SigZ family; This family of RNA polymerase sigma factors is a ...
 20-158 1.51e-17

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


Pssm-ID: 132004 [Multi-domain]  Cd Length: 170  Bit Score: 75.10  E-value: 1.51e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  20 EHYPAVLAYLRRRVP-PSHAEELAADVFERAWAGFDSLR-GTPL-PWLYGIARNVMREFYRTRRETENLDDHEL--ESYA 94
Cdd:TIGR02959   3 EFRSELKAFIKSRVSdASDVEDLLQEVFIKIHRNLPSLKdGQKIqSWLYQIARNTIIDFYRSKSRSVELPESLLaaDSAR 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1080278075  95 GYDAVDANLD-ITRALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRARTHLSEL 158
Cdd:TIGR02959  83 EETFVKELSQcIPPMIKELPDEYREAIRLTELEGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKEL 147
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 12-157 1.29e-14

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


Pssm-ID: 274379 [Multi-domain]  Cd Length: 159  Bit Score: 66.96  E-value: 1.29e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  12 REFSRLFREHYPAVLAYLRRRVPPSH-AEELAADVFERAWAGFDSLR-GTP-LPWLYGIARNVMREFYR-TRRETENLDD 87
Cdd:TIGR02989   1 KAFVRLLTRHERALRAFVRSLVADRDdVDDVLQETFVVAWRKFDQFDpGTNfVAWARGIARNKVLNYRRkLGRDRLVFDD 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1080278075  88 HELESYA--GYDAVDANL-DITRALM----QLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRARTHLSE 157
Cdd:TIGR02989  81 DLLEALAaeAEPTEAERLsDDRQALEgcleKLPERQRELLDLRYQRGQKATALAEQTGRTVNAVYKALQRIRVSLRE 157
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 20-158 8.40e-14

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 65.39  E-value: 8.40e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  20 EHYPAVL-AYLRRRVP-PSHAEELAADVFERAWAGFDSLR-GTPL-PWLYGIARNVMREFYRTRRETENLDDHELesYAG 95
Cdd:PRK09637    8 SEYKAQLkAFLHSRVSnEADVDDLLQEVLIKTHSNLHSLKdGSSIkSWLYQIANNTIIDFYRKKNRSEELPDDLL--FED 85

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1080278075  96 YDAV-DANLDITRALM----QLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRARTHLSEL 158
Cdd:PRK09637   86 EEREeNAKKELAPCLRpfidALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKEL 153
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
 20-158 9.79e-14

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 65.63  E-value: 9.79e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  20 EHYPAVLAY---LRRRvpPSHAEELAADVFERAWAGFDSLR-GTPL-PWLYGIARNVmreFY----RTRRETENLDDHEL 90
Cdd:PRK12546   15 EHLPALRAFaisLTRN--VAVADDLVQDTIVKAWTNFDKFQeGTNLrAWLFTILRNT---FYsdrrKHKREVPDPEGVHA 89

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1080278075  91 ESYAGYDAVDANL---DITRALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRARTHLSEL 158
Cdd:PRK12546   90 ASLAVKPAHDGRLamsDFRAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARARLAEL 160
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 103-155 1.38e-13

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: 61.70  E-value: 1.38e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1080278075 103 LDITRALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRARTHL 155
Cdd:pfam08281   2 EALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 4-163 1.85e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 64.60  E-value: 1.85e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075   4 LTLPG-SRKREFSRLFREHYPAVLAYLRRRVPPSH-AEELAADVFERAWAGFDSLR-GTPL-PWLYGIARNvmrEFY--- 76
Cdd:PRK12516    1 TTGPSvEGTPPFKRELLAALPSLRAFAVSLIGRHDrADDLVQDTIMKAWAKQDHFEvGTNMkAWLFTILRN---EFYsqm 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  77 RTR-RETENLDDHELESYA----GYDAVDANlDITRALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRA 151
Cdd:PRK12516   78 RKRgREVQDTDGMFTEQLAvhpsQYGTLDLQ-DFRAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRA 156

                         170
                  ....*....|....*
gi 1080278075 152 RTHLSEL---TGETD 163
Cdd:PRK12516  157 RQRLQEIlqiEGEAD 171
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
5-151 5.56e-13

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 63.17  E-value: 5.56e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075   5 TLPGSRKREFSRLFREHYPAVLAYLRRRV-PPSHAEELAADVFERAW---AGFDSLRGTPLPWLYGIARNVM---REFYR 77
Cdd:PRK09645    2 GMATAEAALMRALYDEHAAPLWRYALRLTgDRARAEDVVQETLLRAWqhpEVLADTGRSARAWLFTVARNLVideRRSAR 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1080278075  78 TRRETENLDDHELESYAGYDAVDANLD---ITRALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRA 151
Cdd:PRK09645   82 ARPVEGGDDVLGVPEQSAPDEVDRALDrllVADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYA 158
PRK12517 PRK12517
RNA polymerase sigma factor; Provisional
 35-164 5.75e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 183569 [Multi-domain]  Cd Length: 188  Bit Score: 63.55  E-value: 5.75e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  35 PSHAEELAADVFERAWAGFDSLRG--TPLPWLYGIAR--NVmREFYRTRRETENLDDHELESYAGYDAVD--ANLDITRA 108
Cdd:PRK12517   47 KHIAEDLVQETFLRAWRSLDSLKDekAAKAWLITILRreNA-RRFERKQFDLVDIEDDSIEDDASHSSEEemEQEWLRRQ 125

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1080278075 109 LMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRARTHLSELTGETDV 164
Cdd:PRK12517  126 IAKLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMTRLFRARNQLKEALEKPDV 181
PRK12547 PRK12547
RNA polymerase sigma factor; Provisional
 38-160 6.52e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 139056 [Multi-domain]  Cd Length: 164  Bit Score: 62.59  E-value: 6.52e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  38 AEELAADVFERAWAGFDSLR-GTPL-PWLYGIARNvmrEFY----RTRRETENLDDHELESYAGYDAVDANLDIT---RA 108
Cdd:PRK12547   33 AEDLVQDTLMKAWAKQDSFEmGTNLkAWLFTILRN---EFYsqmrKRGREVQDSDGVFTARVAVHPAQYGSLDLQdfkKA 109

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1080278075 109 LMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRARTHLSELTG 160
Cdd:PRK12547  110 LNLLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARNRLQELLK 161
PRK12540 PRK12540
RNA polymerase sigma factor; Provisional
 38-158 1.06e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 183579 [Multi-domain]  Cd Length: 182  Bit Score: 62.67  E-value: 1.06e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  38 AEELAADVFERAWAGFDSLR-GTPLP-WLYGIARNVMREFYRTRR-ETENLDDHELESYAGYDAVDANLDITR---ALMQ 111
Cdd:PRK12540   32 ADDLVQETLLRALANIDSFQpGSNLPaWLFTILRNLFRSDYRKRRrEVEDADGSYAKTLKSQPGQNAHLEFEEfraALDK 111

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1080278075 112 LSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRARTHLSEL 158
Cdd:PRK12540  112 LPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARSKLSAL 158
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 14-157 2.27e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 61.66  E-value: 2.27e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  14 FSRLFREHYPAVLAYLRRRVPPSHAEELAADVFERAWAGFDSLRGTPL--PWLYGIARNVM----REFYRTRRETENLDD 87
Cdd:PRK12518   13 FRQLYRRYQQKVRSTLYQLCGRELLDDLVQEVFLRVWKGLPKLRNPAYfsTWLYRITWNVAtdarRQFAQRPSRIQDDSL 92

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1080278075  88 HELESYAGYDAVDANLD----ITRALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRARTHLSE 157
Cdd:PRK12518   93 NDQPSRPSDTPDLMQLHyqdlVQQGLQTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRLFYARRQLRK 166
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 10-155 2.48e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 61.11  E-value: 2.48e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  10 RKREFSRLFREHYPAVLAYLRRRVPPSH-AEELAADVFERAWAGFDSLRGTPL-PWLYGIARNVMREFYRT--RRETENL 85
Cdd:PRK12541    3 RKQSLEEIYSEHMQDLFRYLLSLTGDSHfAEDLMQETFYRMLVHIDYYKGEEIrPWLFTIAYNAFIDWYRKekKYKTTTI 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1080278075  86 DDHEL-------ESYAGYDAVDANLDitrALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRARTHL 155
Cdd:PRK12541   83 EEFHLpnvpsteHEYFIKHEIASWLD---SLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKET 156
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 13-158 3.07e-12

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 61.12  E-value: 3.07e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  13 EFSRLFREHYPAV---LAYLRRRVppSHAEELAADVFER----AWAGFDSLRGtplpWLYGIARNVMREFYRT-----RR 80
Cdd:PRK09639    4 TFEDLFEQYYPDVvqqIFYIVKDR--TQAEDLAQEVFLRlyrsDFKGIENEKG----WLIKSARNVAYNYLRSekrrrAR 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  81 ETENLDDHELE-SYAGYDAVDANLDIT---RALMQLSHAEREILTLHaWEGLDHPDIAEVLGISRNNVRVRLHRARTHLS 156
Cdd:PRK09639   78 ILGEFQWQEVDnEPSPEEIWIRKEEITkvqEVLAKMTERDRTVLLLR-FSGYSYKEIAEALGIKESSVGTTLARAKKKFR 156


                  ..
gi 1080278075 157 EL 158
Cdd:PRK09639  157 KI 158
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 38-163 1.30e-11

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 59.76  E-value: 1.30e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  38 AEELAADVFERAWAGFDSLRG--TPLPWLYGIARNVMREFYR---TRR---ETENLDDHELESYAGYDAVDANLDITR-- 107
Cdd:PRK09415   43 AEDLTQEIFVKCYKSLHTYKGksSLKTWLYRIAINHCKDYLKswhNKKvivTEDIFTYMESQKESVEEEVIQNAEDERla 122

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1080278075 108 -ALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRARTHLSELTGETD 163
Cdd:PRK09415  123 sAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKELLKKGLEEEV 179
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 12-161 3.12e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 58.93  E-value: 3.12e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  12 REFSRLFREHYPAVLAYLRRRVPpshAEELAADVFERAWAGFDSLRGTPLP------WLYGIARNVMREFYRT---RRET 82
Cdd:PRK12513   26 AAFEALYARHRTGLYRFLLRLAR---DRALAEDIFQETWLRVIRARAQYQPrarfrtWLYQIARNLLIDHWRRhgaRQAP 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  83 ENLDDHELESYAGYD-AVDANLD-------ITRALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRARTH 154
Cdd:PRK12513  103 SLDADEQLHALADDGaAPEQQLSlfrdrrrLQAALETLPDEQREVFLLREHGDLELEEIAELTGVPEETVKSRLRYALQK 182


                  ....*..
gi 1080278075 155 LSELTGE 161
Cdd:PRK12513  183 LRELLAE 189
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 17-158 7.17e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 57.82  E-value: 7.17e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  17 LFREHYPAVLAYLRRRV-PPSHAEELAADVFERAW--AGFDSLRGTPLPWLYGIARNVMREFYRTRREtENLDDHELESY 93
Cdd:PRK12515   27 LYGRHHVRVYRFGLRLVrDEQTAEDLVSEVFLDVWrqAGQFEGRSQVSTWLLSIARFKALSALRRRKH-EEIDDEAAAAI 105

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1080278075  94 A-GYDAVDANLD------ITRA-LMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRARTHLSEL 158
Cdd:PRK12515  106 EdGADTPEVALQksdtsaALRAcLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKTRMFYARKKLAEL 178
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 102-155 9.72e-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: 54.03  E-value: 9.72e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1080278075 102 NLDITRALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRARTHL 155
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 11-160 7.29e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 54.78  E-value: 7.29e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  11 KREFSRLFREHYPAVLAYLRRRVPPSH-AEELAADVFERAW---AGFDSLRGTPLPWLYGIARNVMREFYRTRRETENLD 86
Cdd:PRK12537   22 RRALQALYQQESARLLGVARRIVRDRAlAEDIVHDAFIKIWtgaASFDPARGSARGWIYSVTRHLALNVLRDTRREVVLD 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  87 DHELESYAGYDAVDANLD-------ITRALMQLSHAEREILtLHAW-EGLDHPDIAEVLGISRNNVRVRLHRARTHLSEL 158
Cdd:PRK12537  102 DDAEETAQTLHEIIDDFDlwansgkIHRCLEQLEPARRNCI-LHAYvDGCSHAEIAQRLGAPLGTVKAWIKRSLKALREC 180


                  ..
gi 1080278075 159 TG 160
Cdd:PRK12537  181 MG 182
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 14-151 1.50e-09

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 53.87  E-value: 1.50e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  14 FSRLFREHYPAVLAY-LRRRVPPSHAEELAADVFERAWAGFDSLRGTPL--PWLYGIARNVMREFYRTRRETENLDDHEL 90
Cdd:PRK09638   20 LTTLFQQHYSFLYKYlLKLTLDPDLAEDLVQETMLKAIENLSSFQGRSKfsTWLISIASRLYKDHLRKQKREKLRLQRAK 99

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1080278075  91 ESYAGYDAVDANL------DITRALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRA 151
Cdd:PRK09638  100 EETLRKEKWEAAIkgaewsEMLDALSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTVKSRVHHG 166
PRK12512 PRK12512
RNA polymerase sigma factor; Provisional
 14-151 1.75e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 171551 [Multi-domain]  Cd Length: 184  Bit Score: 53.93  E-value: 1.75e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  14 FSRLFREHYPAVLAYLRRRV-----PPSHAEE------LAADVFERAWAgfdslRGTPL-PWLYGIARN----VMREfyR 77
Cdd:PRK12512   24 YRRLLKAVTPVLRAAARRGLaragqPADQAEDivqeilLAVHLKRHTWD-----PGAPFaPWLFAIARNklidALRR--R 96

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1080278075  78 TRRETENLDDHElESYAGYDAVDA--NLDITRALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRA 151
Cdd:PRK12512   97 GRRVFVDIDDFA-ETLPAEPATETlpAGDVGRHLETLPPRQRDVVQSISVEGASIKETAAKLSMSEGAVRVALHRG 171
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 14-161 2.26e-09

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 53.76  E-value: 2.26e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  14 FSRLFREHYPAVLAYLRRR-VPPSHAEELAADVFERAWAG---FDSLRGTPLPWLYGIARNVMREFYRTRR-ETENLDDH 88
Cdd:PRK13919   25 LRALFRRYAGAFLALARRMgLDGAAAEDVVQEVFIRVWKKakeFDPRRGSARAWLLALAHHAAVDHVRRRAaRPQPLEPD 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  89 ELESYAgYDAVDANLD---------ITRALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRARTHLSELT 159
Cdd:PRK13919  105 EREPEA-FDLPGPGLDeeghldrtrLGRALKALSPEERRVIEVLYYQGYTHREAAQLLGLPLGTLKTRARRALSRLKEVL 183


                  ..
gi 1080278075 160 GE 161
Cdd:PRK13919  184 RE 185
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 38-161 4.12e-09

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 52.57  E-value: 4.12e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  38 AEELAADVFERAWAGFDSLRGTPL-PWLYGIARNVMREFYRTRRETENLDDHEL--------ESYAgyDAVDANLDITRA 108
Cdd:PRK09644   28 AEDLLQETFYRAYIYLEDYDNQKVkPWLFKVAYHTFIDFVRKEKKVSFVGTDEIeaiqaestEEYV--VAKNSYEKLIQI 105

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1080278075 109 LMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRARTHLSELTGE 161
Cdd:PRK09644  106 IHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLKE 158
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 35-161 7.24e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 52.37  E-value: 7.24e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  35 PSHAEELAADVFERAW--AGFDSLRGTPLPWLYGIARN-------------VMREFYRTRRETENLDDHELESYAGYDAV 99
Cdd:PRK12519   53 SQEAEDLTQEIFLSLWrkSSYDPKRGSLSSYLLTLTRSraidrlrsrrsrqRLLERWQQELLGEASEDTPLEQASLAERS 132

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1080278075 100 DAnldITRALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRARTHLSELTGE 161
Cdd:PRK12519  133 QR---VQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKARARQGLLKLRELLQD 191
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 17-80 9.89e-09

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: 49.51  E-value: 9.89e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1080278075  17 LFREHYPAVLAYLRRRVPPSH-AEELAADVFERAWAG---FDSLRGT-PLPWLYGIARNVMREFYRTRR 80
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGAdAEDLVQEGFLGLWRAierFDPERGVsFSTWLYTIIRNAIIDYLRKQR 69
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 38-161 1.14e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 52.27  E-value: 1.14e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  38 AEELAADVFERAWAGFDSLRG--TPLPWLYGIARNVMREFYRTRRETENLDD-HELESYAGYDAVDANLDIT-------- 106
Cdd:PRK11922   57 AEDVVQEAYLRAFRALGTFRGdaSLSTWLSRIVLNEALGRLRRRRRLVNLAEmVMASTIAGGERTPLADPAEdperaaar 136

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1080278075 107 --------RALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRARTHLSELTGE 161
Cdd:PRK11922  137 reiralleRAIDALPDAFRAVFVLRVVEELSVEETAQALGLPEETVKTRLHRARRLLRESLAR 199
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 10-163 4.43e-08

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 50.04  E-value: 4.43e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  10 RKREFSRLFREHYPAVLAYLRRRV-PPSHAEELAADVFERAW---AGFDSLRGTPLPWLYGIARNvmREFYRTRRETENL 85
Cdd:PRK05602   18 DPAAFRVLVARKLPRLLALATRMLgDPAEAEDVAQETFLRIWkqaPSWRPGEARFDTWLHRVVLN--LCYDRLRRRREVP 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  86 DDHELE-------SYAGYDAVDANLDITRALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRAR----TH 154
Cdd:PRK05602   96 VEDAPDvpdpapgPDAGLEARQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALESLLARGRralrAQ 175


                  ....*....
gi 1080278075 155 LSELTGETD 163
Cdd:PRK05602  176 LADLPGSED 184
PRK12533 PRK12533
RNA polymerase sigma factor; Provisional
 35-162 9.97e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 237129 [Multi-domain]  Cd Length: 216  Bit Score: 49.34  E-value: 9.97e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  35 PSHAEELAADVFERAWAGFDSLRG-TPLPWLYGIARNVMREFYRTRR-------ETENLDDHELESYAGYDAVDANLDI- 105
Cdd:PRK12533   42 ASDADDVVQEACMRALRFFDSFRGdNARPWLLAIVRHTWYSEWRRRAnahevaaPDTLDDADSLDDWQPAGEDPLALLLr 121

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1080278075 106 -------TRALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRARTHLSELTGET 162
Cdd:PRK12533  122 aedvrlvNAALAKLPVEYREVLVLRELEDMSYREIAAIADVPVGTVMSRLARARRRLAALLGGA 185
PRK12536 PRK12536
RNA polymerase sigma factor; Provisional
 27-150 1.43e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 237131 [Multi-domain]  Cd Length: 181  Bit Score: 48.51  E-value: 1.43e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  27 AYLRRRVP--PSHAEELAADVF---ERAWAGFDSlrGTPL-PWLYGIARNVMREFYRTRRETENL-----DDHELESYAG 95
Cdd:PRK12536   36 GFLRRRLPqlPDEVEDLVQEILlavHNARHTYRA--DQPLtAWVHAIARYKLMDFLRSRARREALhdpldDESELFATSD 113

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1080278075  96 YDAVDANLDITRALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHR 150
Cdd:PRK12536  114 DEAAEARRDLGKLLEQLPDRQRLPIVHVKLEGLSVAETAQLTGLSESAVKVGIHR 168
algU PRK11923
RNA polymerase sigma factor AlgU; Provisional
 11-152 1.72e-07

RNA polymerase sigma factor AlgU; Provisional


Pssm-ID: 171347 [Multi-domain]  Cd Length: 193  Bit Score: 48.64  E-value: 1.72e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  11 KREFSRLFREHYPAVLAYLRRRVPPSH-AEELAADVFERAWAGFDSLRGTP--LPWLYGIARNVMREFY--RTRRETEN- 84
Cdd:PRK11923   19 KRAFDLLVLKYQHKILGLIVRFVHDTAeAQDVAQEAFIKAYRALGNFRGDSafYTWLYRIAINTAKNHLvsRGRRPPDSd 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  85 LDDHELESYAGYDAV-------------DANLDITRALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRA 151
Cdd:PRK11923   99 VSSEDAEFYDGDHALkdiesperallrdEIEGTVHRTIQQLPEDLRTALTLREFDGLSYEDIASVMQCPVGTVRSRIFRA 178


                  .
gi 1080278075 152 R 152
Cdd:PRK11923  179 R 179
PRK09646 PRK09646
ECF RNA polymerase sigma factor SigK;
14-160 1.98e-07

ECF RNA polymerase sigma factor SigK;


Pssm-ID: 182015 [Multi-domain]  Cd Length: 194  Bit Score: 48.51  E-value: 1.98e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  14 FSRLFREHYPAVLAYLRRRV-PPSHAEELAADVFERAW---AGFDSLRGTPLPWLYGIA--RNVMR----EFYRTRRETE 83
Cdd:PRK09646   32 FAELYDRTSSRVYGLVRRVLrDPGYSEETTQEVYLEVWrtaSRFDPARGSALAWLLTLAhrRAVDRvrseQAASQREVRY 111

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  84 NLDDHELESYAGYDAVDANLD---ITRALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRARTHLSELTG 160
Cdd:PRK09646  112 GARNVDPAFDQVAEEVEARLErerVRDCLDALTDTQRESVTLAYYGGLTYREVAERLAVPLGTVKTRMRDGLIRLRDCLG 191
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 17-155 2.54e-07

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 48.24  E-value: 2.54e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  17 LFREHYPAV--LAYlrRRVPPSH-AEELAADVFERAwagFDSLR----GTPLPWLYGIARNVMREFYRTRR--------- 80
Cdd:PRK09647   33 LVRQHADRVyrLAY--RLSGNQHdAEDLTQETFIRV---FRSLQnyqpGTFEGWLHRITTNLFLDMVRRRArirmealpe 107

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1080278075  81 ETENLDDHELESYAGYDavDANLD--ITRALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRARTHL 155
Cdd:PRK09647  108 DYDRVPGDEPNPEQIYH--DARLDpdLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQQL 182
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 108-157 3.61e-07

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: 44.73  E-value: 3.61e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1080278075 108 ALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRARTHLSE 157
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
PRK12525 PRK12525
RNA polymerase sigma factor; Provisional
 10-144 4.05e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 139037 [Multi-domain]  Cd Length: 168  Bit Score: 47.25  E-value: 4.05e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  10 RKREFSRLFREHYPAVLAYLRRRVPPSH-AEELAADVFERAWAGFD--SLRgTPLPWLYGIARNVMREFYRTrretENLD 86
Cdd:PRK12525    7 KNTLIGQMFQQDYDWLCKKLSRQLGCPHsAEDIASETFLQVLALPDpaSIR-EPRALLTTIARRLMYEGWRR----QDLE 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  87 DHELESYAG------------YDAVDANLDITRALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNV 144
Cdd:PRK12525   82 RAYLQSLAEapeavqpspeeqWMVIETLLAIDRLLDGLSGKARAAFLMSQLEGLTYVEIGERLGVSLSRI 151
PRK12523 PRK12523
RNA polymerase sigma factor; Reviewed
 17-145 7.96e-07

RNA polymerase sigma factor; Reviewed


Pssm-ID: 183572 [Multi-domain]  Cd Length: 172  Bit Score: 46.38  E-value: 7.96e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  17 LFREHYPAVLAYLRRRVP-PSHAEELAADVFERAwAGFDSLRG--TPLPWLYGIARNVMRE-FYRTRRETENLDDHELES 92
Cdd:PRK12523   15 LYRDHRGWLLAWLRRNVAcRQRAEDLSQDTFVRL-LGRPELPTprEPRAFLAAVAKGLMFDhFRRAALEQAYLAELALVP 93

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  93 YAGYDAVDANL-------DITRALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVR 145
Cdd:PRK12523   94 EAEQPSPEEQHliledlkAIDRLLGKLSSKARAAFLYNRLDGMGHAEIAERLGVSVSRVR 153
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 21-154 1.65e-06

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 45.54  E-value: 1.65e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  21 HYPAVLAYLRRRVPPSH-AEELAADVFERAWAGFDSLR-GTPLPWLYGIARNVMREFYRTR--RETENLDDHELESYAGY 96
Cdd:PRK12527    4 YYRELVRFLSARLGNRQaAEDVAHDAYLRVLERSSSAQiEHPRAFLYRTALNLVVDRHRRHrvRQAEPLEVLDEEERLHS 83

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1080278075  97 DAVDANLD-------ITRALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRARTH 154
Cdd:PRK12527   84 PSPQTRLDlgqrlalLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKH 148
PRK09649 PRK09649
RNA polymerase sigma factor SigC; Reviewed
 38-155 5.76e-06

RNA polymerase sigma factor SigC; Reviewed


Pssm-ID: 137458 [Multi-domain]  Cd Length: 185  Bit Score: 44.26  E-value: 5.76e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  38 AEELAADVFERAWAGFDSLRG--TPLPWLYGIARNVMREFYR---TRRETENLDDHELESYAGYDA--VDANLDITRALM 110
Cdd:PRK09649   50 ADDLTQETFLRAIGAIPRFSArsSARTWLLAIARHVVADHIRhvrSRPRTTRGARPEHLIDGDRHArgFEDLVEVTTMIA 129

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1080278075 111 QLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRARTHL 155
Cdd:PRK09649  130 DLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARARDAL 174
PRK12534 PRK12534
RNA polymerase sigma factor; Provisional
 3-87 5.80e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183576 [Multi-domain]  Cd Length: 187  Bit Score: 44.28  E-value: 5.80e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075   3 VLTLPGSRKREFSRLFREHYPAVLAYLRRRVPP-SHAEELAADVFERAW---AGFDSLRGTPLPWLYGIARNVMREFYRT 78
Cdd:PRK12534   16 LTATAGGDRHAFEALYRQTSPKLFGVCLRMIPQrAEAEEVLQDVFTLIWhkaGQFDPSRARGLTWLAMIARNKAIDHLRA 95

                          90
                  ....*....|..
gi 1080278075  79 R---RETENLDD 87
Cdd:PRK12534   96 NapqRRNVALDD 107
PRK12542 PRK12542
RNA polymerase sigma factor; Provisional
 67-160 1.46e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183581 [Multi-domain]  Cd Length: 185  Bit Score: 43.12  E-value: 1.46e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  67 IARNVMREFYRTRRETEN-LDDHELESYagyDAVDANLD-----------ITRALMQLSHAEREILTLHAWEGLDHPDIA 134
Cdd:PRK12542   69 VAKNKAIDSYRKNKRHETfLEEYERESI---EAVDENIEewekrkmsevqIDTLLKELNESNRQVFKYKVFYNLTYQEIS 145

                          90       100
                  ....*....|....*....|....*.
gi 1080278075 135 EVLGISRNNVRVRLHRARTHLSELTG 160
Cdd:PRK12542  146 SVMGITEANVRKQFERARKRVQNMIG 171
PRK12539 PRK12539
RNA polymerase sigma factor SigF;
58-162 1.82e-05

RNA polymerase sigma factor SigF;


Pssm-ID: 237132 [Multi-domain]  Cd Length: 184  Bit Score: 42.79  E-value: 1.82e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  58 GTPL-PWLYGIARNVMREFYR-TRRETENL---DDHELESYAGYDAVDANLDITRALMQLSHAEREILTLHAWEGLDHPD 132
Cdd:PRK12539   73 EQPLtPWVYAIARYKLIDHLRrTRASLADVpidDADELVAHDDHAAVESTLDLGRLLARLPEKMRLAIQAVKLEGLSVAE 152

                          90       100       110
                  ....*....|....*....|....*....|
gi 1080278075 133 IAEVLGISRNNVRVRLHRARTHLSELTGET 162
Cdd:PRK12539  153 AATRSGMSESAVKVSVHRGLKALAALIGRE 182
PRK06930 PRK06930
positive control sigma-like factor; Validated
 72-157 5.58e-05

positive control sigma-like factor; Validated


Pssm-ID: 180757 [Multi-domain]  Cd Length: 170  Bit Score: 41.25  E-value: 5.58e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  72 MREFYRTRRETENL--DDHELESYAG-YDAVDanldITRALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRL 148
Cdd:PRK06930   76 PLLIQRYFRSMEDLewDIEEPESVISeWDKIR----IEDALSVLTEREKEVYLMHRGYGLSYSEIADYLNIKKSTVQSMI 151


                  ....*....
gi 1080278075 149 HRARTHLSE 157
Cdd:PRK06930  152 ERAEKKIAR 160
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 109-155 7.23e-05

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 38.66  E-value: 7.23e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1080278075  109 LMQLSHAEREILTLHAwEGLDHPDIAEVLGISRNNVRVRLHRARTHL 155
Cdd:smart00421   1 LASLTPREREVLRLLA-EGLTNKEIAERLGISEKTVKTHLSNIMRKL 46
PRK12531 PRK12531
RNA polymerase sigma factor; Provisional
 11-151 7.77e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 105726 [Multi-domain]  Cd Length: 194  Bit Score: 41.07  E-value: 7.77e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  11 KREFSRLFREHYPAVLAYLRRRVPPSH-AEELAADVFERAWAG---FDSLRGTPLPWLYGIARNVMREFYRTRRETE--- 83
Cdd:PRK12531   26 KQAFALVFSYYAPKLKQFAMKHVGNEQvAMEMVQETMSTVWQKahlFDGQKSALSTWIYTIIRNLCFDLLRKQKGKDlhi 105

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1080278075  84 NLDDHELESYAGYDAVD--------ANLDITRALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRA 151
Cdd:PRK12531  106 HADDIWPSDYYPPDLVDhyspeqdmLKEQVMKFLDRLPKAQRDVLQAVYLEELPHQQVAEMFDIPLGTVKSRLRLA 181
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 14-157 8.89e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 40.96  E-value: 8.89e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  14 FSRLFREHYPAVLAY-LRRRVPPSHAEELAADVFERAWAGFDSLR---GTPLPWLYGIARNVMREFYRTRRE-TENLDD- 87
Cdd:PRK12514   21 FSSLYDATSAKLFGIcLRVLKDRSEAEEALQDVYVKIWTKADRFAvsgLSPMTWLITIARNHAIDRLRARKAvAVDIDEa 100

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1080278075  88 HEL-ESYAGYDAVDANLDITRalmQLSHAEREILTLHA-------WEGLDHPDIAEVLGISRNNVRVRLHRARTHLSE 157
Cdd:PRK12514  101 HDLaDPSPGPEAEVIAGDEGQ---RIDACLEELEKDRAaavrrayLEGLSYKELAERHDVPLNTMRTWLRRSLLKLRE 175
PRK09191 PRK09191
two-component response regulator; Provisional
 97-157 1.20e-04

two-component response regulator; Provisional


Pssm-ID: 236402 [Multi-domain]  Cd Length: 261  Bit Score: 40.99  E-value: 1.20e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1080278075  97 DAVDANLDITRALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRARTHLSE 157
Cdd:PRK09191   74 PGSPFEARAERRLAGLTPLPRQAFLLTALEGFSVEEAAEILGVDPAEAEALLDDARAEIAR 134
PRK12532 PRK12532
RNA polymerase sigma factor; Provisional
 20-157 1.57e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 171564 [Multi-domain]  Cd Length: 195  Bit Score: 40.30  E-value: 1.57e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  20 EHYPAVLAYLRRRVP--PSHAEELAADVFERAWAGFDSLRGTPL--PWLYGIARN----VMREFYRTRRETENLDDHEL- 90
Cdd:PRK12532   13 ESRKLLLHFARLQLPdhPDLAEDLVQETLLSAYSAGDSFQGRALvnSWLFAILKNkiidALRQIGRQRKVFTLLDDELLd 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  91 ESYAGYDAVDANL----------DITRALMQ-------------LSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVR 147
Cdd:PRK12532   93 EAFESHFSQNGHWtpegqpqhwnTPEKSLNNnefqkilqsclynLPENTARVFTLKEILGFSSDEIQQMCGISTSNYHTI 172

                         170
                  ....*....|
gi 1080278075 148 LHRARTHLSE 157
Cdd:PRK12532  173 MHRARESLRQ 182
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 35-157 1.88e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 39.77  E-value: 1.88e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  35 PSHAEELAADVFERAWAGFDSLR-GTPL-PWLYGIARNVM-----REFYRTRRETENLDDHELESYAGYDAVDANLDITR 107
Cdd:PRK12511   28 SAEAEDLVHDALVRALERRASFRsGGNLrTWLMSILHNAFidelrRRRVEARRADELAVLADASLPAAQEHAVRLAQIRD 107

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1080278075 108 ALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRARTHLSE 157
Cdd:PRK12511  108 AFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAALRA 157
PRK12522 PRK12522
RNA polymerase sigma factor; Provisional
 42-157 3.01e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183571 [Multi-domain]  Cd Length: 173  Bit Score: 39.47  E-value: 3.01e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  42 AADVFERAWAGFDSLR------GTPLPWLYGIARNVMREFYRTRRETENL--------DDHELEsyagyDAVDANLD--- 104
Cdd:PRK12522   30 AEDIFQETWIKVFSSRhqlsyvENYKKWITTICVRTFYDFYRKKKRWKDRildlfhkeDGGEIE-----FADDVNISeef 104

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1080278075 105 --------ITRALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRARTHLSE 157
Cdd:PRK12522  105 iqkveaemIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQMRE 165
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 38-155 3.03e-04

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 39.29  E-value: 3.03e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  38 AEELAADVFERAWAGFDSLRGTPL--PWLYGIARNVMREFYRTRRETENLDDhELESYAGYD-----AVDANL------- 103
Cdd:PRK09641   45 AEDAAQEAFIRAYVNIDSYDINRKfsTWLYRIATNLTIDRLRKRKPDYYLDA-EVAGTEGLTmysqlAADDALpeeqvvs 123

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1080278075 104 -----DITRALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRARTHL 155
Cdd:PRK09641  124 lelqeTIQEAILQLPEKYRTVIVLKYIEDLSLKEISEILDLPVGTVKTRIHRGREAL 180
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 12-157 5.12e-04

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 38.77  E-value: 5.12e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  12 REFSRLFREHYPAVLAYLRRRV-PPSHAEELAADVFERAWAGFDSLRGTPL--PWLYGIARNVMREFYRTRR------ET 82
Cdd:PRK09640   26 RAYEELMRRYQRTLFNVCARYLgNDRDADDVCQEVMLKVLYGLKNFEGKSKfkTWLYSITYNECITQYRKERrkrrlmDA 105

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1080278075  83 ENLDDHELESYAGYDAVDANLDITRALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRARTHLSE 157
Cdd:PRK09640  106 LSLDPLEEASEEKAPKPEERGGLDRWLVHVNPIDREILVLRFVAELEFQEIADIMHMGLSATKMRYKRALDKLRE 180
PRK06811 PRK06811
RNA polymerase factor sigma-70; Validated
 37-152 7.19e-04

RNA polymerase factor sigma-70; Validated


Pssm-ID: 180707 [Multi-domain]  Cd Length: 189  Bit Score: 38.38  E-value: 7.19e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  37 HAEELAADVFERAW---AGFDSLRGTPLPWLYGIARNVMREFYRTRRETENLDDHELESYAGYDAVDANL-------DIT 106
Cdd:PRK06811   47 LIEECVNDIFLSIWnniDKFDEEKGSFKKWIAAISKYKAIDYKRKLTKNNEIDSIDEFILISEESIENEIilkenkeEIL 126

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1080278075 107 RALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRAR 152
Cdd:PRK06811  127 KLINDLEKLDREIFIRRYLLGEKIEEIAKKLGLTRSAIDNRLSRGR 172
PRK08583 PRK08583
RNA polymerase sigma factor SigB; Validated
 95-150 7.92e-04

RNA polymerase sigma factor SigB; Validated


Pssm-ID: 236306 [Multi-domain]  Cd Length: 257  Bit Score: 38.52  E-value: 7.92e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1080278075  95 GYDAVDANLDITRALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRvRLHR 150
Cdd:PRK08583  189 GYELTEQRMILEKILPVLSDREKSIIQCTFIENLSQKETGERLGISQMHVS-RLQR 243
GerE pfam00196
Bacterial regulatory proteins, luxR family;
110-152 1.60e-03

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 35.25  E-value: 1.60e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1080278075 110 MQLSHAEREILTLHAwEGLDHPDIAEVLGISRNNVRVrlHRAR 152
Cdd:pfam00196   1 DSLSPREREVLRWLA-AGKSNKEIADELGISEKTVKV--HRSN 40
PRK09636 PRK09636
RNA polymerase sigma factor SigJ; Provisional
 91-157 2.18e-03

RNA polymerase sigma factor SigJ; Provisional


Pssm-ID: 236600 [Multi-domain]  Cd Length: 293  Bit Score: 37.21  E-value: 2.18e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1080278075  91 ESYAGYDAVDANLDITRALM----QLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRARTHLSE 157
Cdd:PRK09636   91 ELDDPLEAVVAAEDLSLALMlaleRLSPLERAAFLLHDVFGVPFDEIASTLGRSPAACRQLASRARKHVRA 161
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 36-140 2.29e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 36.79  E-value: 2.29e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  36 SHAEELAADVFERAW---AGFDSLRGTPLPWLYGIARNV-MREFYRTRRETENLDDHELESYAGYDAVDANLDITR---- 107
Cdd:PRK12524   51 AEAEDVTQEAMLRLWriaPDWRQGEARVSTWLYRVVCNLcTDRLRRRRRASVDLDDAPEPADAAPGAEEALIEGDRmral 130

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1080278075 108 --ALMQLSHAEREILTLHAWEGLDHPDIAEVLGIS 140
Cdd:PRK12524  131 daALAALPERQRQAVVLRHIEGLSNPEIAEVMEIG 165
PRK12528 PRK12528
RNA polymerase sigma factor; Provisional
 17-151 2.74e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 171561 [Multi-domain]  Cd Length: 161  Bit Score: 36.36  E-value: 2.74e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  17 LFREHYPAVLAYLRRRVP-PSHAEELAADVFERAWAGFDSLR-GTPLPWLYGIARNVMREFYRTrretENLDDHELESYA 94
Cdd:PRK12528    9 LYSAHHHWLTGWLRRRLGcPQSAADLAQDTFVKVLVARETAQiIEPRAFLTTIAKRVLCNHYRR----QDLERAYLEALA 84

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1080278075  95 GYDAVDANLDITRA-----LMQLSH-------AEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRA 151
Cdd:PRK12528   85 QLPERVAPSEEERAiiletLVELDQlldglppLVKRAFLLAQVDGLGYGEIATELGISLATVKRYLNKA 153
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 103-155 2.82e-03

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: 36.02  E-value: 2.82e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1080278075 103 LDITRALmqLSHAEREILTLHAwEGLDHPDIAEVLGISRNNVRVRLHRARTHL 155
Cdd:COG2197    63 LEALRRL--LTPREREVLRLLA-EGLSNKEIAERLGISERTVKTHVSNILRKL 112
PRK05911 PRK05911
RNA polymerase sigma factor sigma-28; Reviewed
 83-144 2.84e-03

RNA polymerase sigma factor sigma-28; Reviewed


Pssm-ID: 235644 [Multi-domain]  Cd Length: 257  Bit Score: 36.91  E-value: 2.84e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1080278075  83 ENLDDHELESyaGYDAVD---ANLDITRALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNV 144
Cdd:PRK05911  176 ERIADERAET--GYDVVDkkeFSSILAEAILALEEKERKVMALYYYEELVLKEIGKILGVSESRV 238
PRK09047 PRK09047
RNA polymerase factor sigma-70; Validated
 104-157 2.89e-03

RNA polymerase factor sigma-70; Validated


Pssm-ID: 236367 [Multi-domain]  Cd Length: 161  Bit Score: 36.49  E-value: 2.89e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1080278075 104 DITRALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRARTHLSE 157
Cdd:PRK09047   99 LIEEAIQKLPARQREAFLLRYWEDMDVAETAAAMGCSEGSVKTHCSRATHALAK 152
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
12-155 3.17e-03

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 36.66  E-value: 3.17e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  12 REFSRLFREHYPAVLAYLRRRVPPSHAEELAADVFERAWAGFDSLRGTPLPWLYGIARNVMREFYRTRRETENLDDHELE 91
Cdd:COG2771    28 LLAALLLLLALLLLAALLLLAAAAAALAAALAAALLLGLLLLLLIALLLLLLLLLALLLLLALLALLAALLARLAALLLA 107

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1080278075  92 SYAGYDAVDANLDITRALMQLSHAEREILTLHAwEGLDHPDIAEVLGISRNNVRVRLHRARTHL 155
Cdd:COG2771   108 LALAALLLAALARLLARAPGLTPREREVLRLLA-EGLTLKEIARILGISERTVRTHLKRIYRKL 170
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 94-150 3.42e-03

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: 36.73  E-value: 3.42e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1080278075  94 AGYDAVDANLDITRALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRnnVRV-RLHR 150
Cdd:COG1191   169 EELEHEELREALAEAIEQLPERERLVLSLYYFEELTLKEIAEVLGVSE--SRVsRLHK 224
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 112-152 3.47e-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: 34.05  E-value: 3.47e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1080278075 112 LSHAEREILTLHAwEGLDHPDIAEVLGISRNNVRVRLHRAR 152
Cdd:cd06170     1 LTPREREVLRLLA-EGKTNKEIADILGISEKTVKTHLRNIM 40
PRK09651 PRK09651
RNA polymerase sigma factor FecI; Provisional
 14-154 3.55e-03

RNA polymerase sigma factor FecI; Provisional


Pssm-ID: 182018 [Multi-domain]  Cd Length: 172  Bit Score: 36.33  E-value: 3.55e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  14 FSRLFREHYPAVLAYLRRRVPPS-HAEELAADVFERAWAGfDSLRGT--PLPWLYGIARNVMREFYRTRR-ETENLDDHE 89
Cdd:PRK09651   12 FESLYGTHHGWLKSWLTRKLQSAfDADDIAQDTFLRVMVS-ETLSTIrdPRSFLCTIAKRVMVDLFRRNAlEKAYLEMLA 90

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1080278075  90 LESYAGYDAVD---ANLD----ITRALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRARTH 154
Cdd:PRK09651   91 LMPEGGAPSPEereSQLEtlqlLDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKATEH 162
PRK06288 PRK06288
RNA polymerase sigma factor WhiG; Reviewed
 105-160 5.42e-03

RNA polymerase sigma factor WhiG; Reviewed


Pssm-ID: 235770 [Multi-domain]  Cd Length: 268  Bit Score: 36.20  E-value: 5.42e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1080278075 105 ITRALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRvRLH-----RARTHLSELTG 160
Cdd:PRK06288  206 IVEAIKTLPEREKKVLILYYYEDLTLKEIGKVLGVTESRIS-QLHtkavlQLRAKLAEIKK 265
PRK09648 PRK09648
RNA polymerase sigma factor ShbA;
11-155 5.89e-03

RNA polymerase sigma factor ShbA;


Pssm-ID: 236607 [Multi-domain]  Cd Length: 189  Bit Score: 35.72  E-value: 5.89e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  11 KREFSRLFREHYPAVLAYLRRRV-----PPSHAEELAADVferAWAGFDSL-----RGTP-LPWLYGIARNVMREFYR-- 77
Cdd:PRK09648   23 RRALREVLEIIRPLVVRYCRARLggverPGLSADDVAQEV---CLAVITALpryrdQGRPfLAFVYGIAAHKVADAHRaa 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  78 TRRE---TENLDDHELESyAG----YDAVDANLDITRALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHR 150
Cdd:PRK09648  100 GRDKavpTEEVPERPSDD-AGpeerALRSESSNRMRELLDTLPEKQREILILRVVVGLSAEETAEAVGSTPGAVRVAQHR 178


                  ....*
gi 1080278075 151 ARTHL 155
Cdd:PRK09648  179 ALARL 183
PRK12526 PRK12526
RNA polymerase sigma factor; Provisional
 11-161 9.56e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237127 [Multi-domain]  Cd Length: 206  Bit Score: 35.16  E-value: 9.56e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  11 KREFSRLFREHYPAVLAYLRRRVP-PSHAEELAADVFERAWAG---FDSLRGTPLPWLYGIARNV---MREFYRTRREtE 83
Cdd:PRK12526   37 KQAFTHLFQFFAPKIKRFGIKQLGnEAQANELVQETMSNVWRKahlYNGDKGAATTWVYTVMRNAafdMLRKIKAKKE-Q 115

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080278075  84 NL-------DDHELESYAGYDAVDANL---DITRALMQLSHAEREILTLHAWEGLDHPDIAEVLGISRNNVRVRLHRART 153
Cdd:PRK12526  116 NLgddiwpiEQALAESQSESEEFSDHLmdkQILSYIEKLPEAQQTVVKGVYFQELSQEQLAQQLNVPLGTVKSRLRLALA 195


                  ....*...
gi 1080278075 154 HLSELTGE 161
Cdd:PRK12526  196 KLKVQMGE 203
 
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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