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Conserved domains on  [gi|516129712|ref|WP_017560292|]
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MULTISPECIES: RNA polymerase sigma factor [Bacillus]

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]; ...
 10-175 1.52e-46

DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; DNA-directed RNA polymerase specialized sigma subunit, sigma24 family is part of the Pathway/BioSystem: RNA polymerase


:

Pssm-ID: 441203 [Multi-domain]  Cd Length: 181  Bit Score: 150.14  E-value: 1.52e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  10 NHDELDDVIKDYWQDVWNYSFIITKDPHLSDDITQDVFIKVFKNWNSFRRESSIKTWILKITRNTAINYLKSSYFKRISL 89
Cdd:COG1595   15 DEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRRELL 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  90 VGFFSD-DKQTLSAEQEFFKQEEMNDVWKVVLKLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRARSKVSKL 168
Cdd:COG1595   95 DELAEElPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREA 174


                 ....*..
gi 516129712 169 IGEGGSD 175
Cdd:COG1595  175 LEEEGAL 181
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 10-175 1.52e-46

DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; DNA-directed RNA polymerase specialized sigma subunit, sigma24 family is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 441203 [Multi-domain]  Cd Length: 181  Bit Score: 150.14  E-value: 1.52e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  10 NHDELDDVIKDYWQDVWNYSFIITKDPHLSDDITQDVFIKVFKNWNSFRRESSIKTWILKITRNTAINYLKSSYFKRISL 89
Cdd:COG1595   15 DEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRRELL 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  90 VGFFSD-DKQTLSAEQEFFKQEEMNDVWKVVLKLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRARSKVSKL 168
Cdd:COG1595   95 DELAEElPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREA 174


                 ....*..
gi 516129712 169 IGEGGSD 175
Cdd:COG1595  175 LEEEGAL 181
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 12-169 9.96e-41

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: 134.78  E-value: 9.96e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712   12 DELDDVIKDYWQDVWNYSFIITKDPHLSDDITQDVFIKVFKNWNSFRRESSIKTWILKITRNTAINYLKSSYFKRISLVG 91
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 516129712   92 FFSDDKQTLSAEQEFFKQEEMNDVWKVVLKLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRARSKVSKLI 169
Cdd:TIGR02937  81 LEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 33-171 6.14e-34

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 117.99  E-value: 6.14e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  33 TKDPHLSDDITQDVFIKVFKNWNSFRRESSIKTWILKITRNTAINYL-------KSSYFKRISLVGFFSDD--KQTLSAE 103
Cdd:PRK09652  31 TRDPADAEDLVQETFIKAYRALHSFRGGAAFYTWLYRIARNTAINYLrkqgrrpPASDVDAEEAEDFDLADalRDISTPE 110

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 516129712 104 QEFFKQEEMNDVWKVVLKLPKKHREIIILdAKYE-LSYEEMAETLGVSIGTVKSRLSRARSKVSKLIGE 171
Cdd:PRK09652 111 NELLSAELEQRVRAAIESLPEELRTAITL-REIEgLSYEEIAEIMGCPIGTVRSRIFRAREALRAKLQP 178
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 115-165 1.41e-12

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: 59.39  E-value: 1.41e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 516129712  115 VWKVVLKLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRARSKV 165
Cdd:pfam08281   4 LLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 117-165 2.49e-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: 55.96  E-value: 2.49e-11
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 516129712 117 KVVLKLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRARSKV 165
Cdd:cd06171    6 EALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 127-164 4.95e-04

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 36.74  E-value: 4.95e-04
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 516129712   127 REIIILDAKYE-LSYEEMAETLGVSIGTVKSRLSRARSK 164
Cdd:smart00421   7 REREVLRLLAEgLTNKEIAERLGISEKTVKTHLSNIMRK 45
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 10-175 1.52e-46

DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; DNA-directed RNA polymerase specialized sigma subunit, sigma24 family is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 441203 [Multi-domain]  Cd Length: 181  Bit Score: 150.14  E-value: 1.52e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  10 NHDELDDVIKDYWQDVWNYSFIITKDPHLSDDITQDVFIKVFKNWNSFRRESSIKTWILKITRNTAINYLKSSYFKRISL 89
Cdd:COG1595   15 DEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRRELL 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  90 VGFFSD-DKQTLSAEQEFFKQEEMNDVWKVVLKLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRARSKVSKL 168
Cdd:COG1595   95 DELAEElPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREA 174


                 ....*..
gi 516129712 169 IGEGGSD 175
Cdd:COG1595  175 LEEEGAL 181
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 12-169 9.96e-41

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: 134.78  E-value: 9.96e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712   12 DELDDVIKDYWQDVWNYSFIITKDPHLSDDITQDVFIKVFKNWNSFRRESSIKTWILKITRNTAINYLKSSYFKRISLVG 91
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 516129712   92 FFSDDKQTLSAEQEFFKQEEMNDVWKVVLKLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRARSKVSKLI 169
Cdd:TIGR02937  81 LEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 33-171 6.14e-34

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 117.99  E-value: 6.14e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  33 TKDPHLSDDITQDVFIKVFKNWNSFRRESSIKTWILKITRNTAINYL-------KSSYFKRISLVGFFSDD--KQTLSAE 103
Cdd:PRK09652  31 TRDPADAEDLVQETFIKAYRALHSFRGGAAFYTWLYRIARNTAINYLrkqgrrpPASDVDAEEAEDFDLADalRDISTPE 110

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 516129712 104 QEFFKQEEMNDVWKVVLKLPKKHREIIILdAKYE-LSYEEMAETLGVSIGTVKSRLSRARSKVSKLIGE 171
Cdd:PRK09652 111 NELLSAELEQRVRAAIESLPEELRTAITL-REIEgLSYEEIAEIMGCPIGTVRSRIFRAREALRAKLQP 178
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 1-173 8.35e-32

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 112.53  E-value: 8.35e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712   1 MEQTFIEKFNHDE----LDDVIKDYWQDVWNYSFIITKDPHLSDDITQDVFIKVFKNWNSFRRESSIKTWILKITRNTAI 76
Cdd:PRK09415   1 MEELTIEAFEIEDkedlIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGKSSLKTWLYRIAINHCK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  77 NYLKSSYFKRIslvgFFSDDK------QTLSAEQEFFKQEEMNDVWKVVLKLPKKHREIIILDAKYELSYEEMAETLGVS 150
Cdd:PRK09415  81 DYLKSWHNKKV----IVTEDIftymesQKESVEEEVIQNAEDERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVN 156

                        170       180
                 ....*....|....*....|...
gi 516129712 151 IGTVKSRLSRARSKVSKLIGEGG 173
Cdd:PRK09415 157 ENTVKTRLKKAKELLKKGLEEEV 179
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 10-164 9.54e-32

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 112.37  E-value: 9.54e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  10 NHDELDDVIKDYWQDVWNYSFIITKDPHLSDDITQDVFIKVFKNWNSFRRESSIKTWILKITRNTAINYLKSsyfKRISL 89
Cdd:PRK11924  11 DKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCYDLLRR---RRREK 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  90 VGFFSDDKQTLSA------EQEFFKQEEMNDVWKVVLKLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRARS 163
Cdd:PRK11924  88 AVLSDDALEPEFAetaetpEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQ 167


                 .
gi 516129712 164 K 164
Cdd:PRK11924 168 L 168
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 11-168 1.74e-26

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 98.48  E-value: 1.74e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  11 HDELDDVIKDYWQDVWNYSFIITKDPHLSDDITQDVFIKVFKnwNSFRRESSIKTWILKITRNTAINYLKSSYFKRISLV 90
Cdd:PRK09639   2 DETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYR--SDFKGIENEKGWLIKSARNVAYNYLRSEKRRRARIL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  91 GFF--SDDKQTLSAEQEFFKQEEMNDVWKVVLKLPKKHREIIILdaKYE-LSYEEMAETLGVSIGTVKSRLSRARSKVSK 167
Cdd:PRK09639  80 GEFqwQEVDNEPSPEEIWIRKEEITKVQEVLAKMTERDRTVLLL--RFSgYSYKEIAEALGIKESSVGTTLARAKKKFRK 157


                 .
gi 516129712 168 L 168
Cdd:PRK09639 158 I 158
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 19-167 1.91e-26

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: 98.40  E-value: 1.91e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712   19 KDYWQDVWNYSFIITKDPHLSDDITQDVFIKVFKNWNSFRRESSIKTWILKITRNTAINYLKSSYFKR---ISLVGFFSD 95
Cdd:TIGR02985   8 RRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETLEISESIKAYLFTIVKNRCLNYLRHKQVEEkyqEELAEIEER 87

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 516129712   96 DKQTLSAEQEFFKQEEMNDVWKVVLKLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRARSKVSK 167
Cdd:TIGR02985  88 ELSEADPEEELEAKELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLRK 159
SigM_subfam TIGR02950
RNA polymerase sigma factor, SigM family; This family of RNA polymerase sigma factors is a ...
 21-169 1.22e-24

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


Pssm-ID: 274361 [Multi-domain]  Cd Length: 154  Bit Score: 93.29  E-value: 1.22e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712   21 YWQDVWNYSFIITKDPHLSDDITQDVFIKVFKNWNSFRrESSIKTWILKITRNTAINYLKSSYFKRISLVGFFSDDKQT- 99
Cdd:TIGR02950   4 YMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFK-DSSIKPWLFRIARNAFIDWYRKDKKIQTIDDDAIGDLEQHp 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 516129712  100 -LSAEQEFFKQEEMNDVWKVVLKLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRARSKVSKLI 169
Cdd:TIGR02950  83 vESPEHHLLIKIEQEEITHHLSRLPENYRTVLILREFKEFSYKEIAELLNLSLAKVKSNLFRARKELKKLL 153
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 27-167 3.00e-23

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 90.46  E-value: 3.00e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  27 NYSFI------ITKDPHLSDDITQDVFIKVFKNWNSFRRESSIKTWILKITRNTAINYLKSSyfKRISLV-GFFSDDKQT 99
Cdd:PRK09638  27 HYSFLykyllkLTLDPDLAEDLVQETMLKAIENLSSFQGRSKFSTWLISIASRLYKDHLRKQ--KREKLRlQRAKEETLR 104

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 516129712 100 LSAEQEFFKQEEMNDVWKVVLKLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRARSKVSK 167
Cdd:PRK09638 105 KEKWEAAIKGAEWSEMLDALSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRK 172
SigE-fam_strep TIGR02983
RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors ...
 33-172 3.66e-21

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: 84.75  E-value: 3.66e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712   33 TKDPHLSDDITQDVFIKVFKNWNSFRRESSIKTWILKITRNTAInylksSYFKRISLVGFFSDDKQTLSAEQEFFKQEEM 112
Cdd:TIGR02983  27 TGDPHEAEDLVQEALVRTYVRWDRIRDPDAPDAYVRRVLVNLAR-----SRWRRRRLLELPTRELPDAAAPDPAPDVALR 101

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  113 NDVWKVVLKLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRARSKVSKLIGEG 172
Cdd:TIGR02983 102 AALARALRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALARLRELLEEP 161
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
 32-170 4.88e-21

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 84.89  E-value: 4.88e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  32 ITKDPHLSDDITQDVFIKVFKNWNSFRRESSIKTWILKITRNTainyLKSSYFKRISLVgffsDDKQTLSAEQEFFKQE- 110
Cdd:PRK12546  27 LTRNVAVADDLVQDTIVKAWTNFDKFQEGTNLRAWLFTILRNT----FYSDRRKHKREV----PDPEGVHAASLAVKPAh 98

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 516129712 111 ----EMNDVWKVVLKLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRARSKVSKLIG 170
Cdd:PRK12546  99 dgrlAMSDFRAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARARLAELLQ 162
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 37-175 4.31e-19

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 80.01  E-value: 4.31e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  37 HLSDDITQDVFIKVFKNWNSFRRESSIKTWILKITRNTAINYLKSSYFKRISLVGFFSddkQTLSAEQEFFKQEEMNDVW 116
Cdd:PRK12516  35 DRADDLVQDTIMKAWAKQDHFEVGTNMKAWLFTILRNEFYSQMRKRGREVQDTDGMFT---EQLAVHPSQYGTLDLQDFR 111

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712 117 KVVLKLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRARSKVSKLIG-EGGSD 175
Cdd:PRK12516 112 AALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQRLQEILQiEGEAD 171
PRK12540 PRK12540
RNA polymerase sigma factor; Provisional
 39-176 1.92e-18

RNA polymerase sigma factor; Provisional


Pssm-ID: 183579 [Multi-domain]  Cd Length: 182  Bit Score: 78.08  E-value: 1.92e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  39 SDDITQDVFIKVFKNWNSFRRESSIKTWILKITRNtainYLKSSYFKRISLV----GFFSddkQTLSAEQEFFKQEEMND 114
Cdd:PRK12540  32 ADDLVQETLLRALANIDSFQPGSNLPAWLFTILRN----LFRSDYRKRRREVedadGSYA---KTLKSQPGQNAHLEFEE 104

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 516129712 115 VWKVVLKLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRARSKVSKLIGEGGSDE 176
Cdd:PRK12540 105 FRAALDKLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARSKLSALLYVDGAED 166
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 35-173 3.02e-18

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 77.45  E-value: 3.02e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  35 DPHLSDDITQDVFIKVFKNWNSFRRESSIKTWILKITRNTAINYlKSSYFKRISLVGFFSDDKQTLSAEQE-FFKQEEMN 113
Cdd:PRK12518  33 GRELLDDLVQEVFLRVWKGLPKLRNPAYFSTWLYRITWNVATDA-RRQFAQRPSRIQDDSLNDQPSRPSDTpDLMQLHYQ 111

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 516129712 114 DVWKVVLK-LPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRARSKVSKLIGEGG 173
Cdd:PRK12518 112 DLVQQGLQtLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQQQG 172
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 29-169 4.23e-18

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 77.33  E-value: 4.23e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  29 SFIITK--DPHLSDDITQDVFIKVFKNWNSFRRESSIKTWILKITRNTAINYlkssYFKRISLVGFFSDDKQTLSAEQEF 106
Cdd:PRK09637  16 AFLHSRvsNEADVDDLLQEVLIKTHSNLHSLKDGSSIKSWLYQIANNTIIDF----YRKKNRSEELPDDLLFEDEEREEN 91

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 516129712 107 FKQEEMNDVWKVVLKLPKKHREIIILdAKYE-LSYEEMAETLGVSIGTVKSRLSRARSKVSKLI 169
Cdd:PRK09637  92 AKKELAPCLRPFIDALPEKYAEALRL-TELEgLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELL 154
algU PRK11923
RNA polymerase sigma factor AlgU; Provisional
 34-169 1.00e-17

RNA polymerase sigma factor AlgU; Provisional


Pssm-ID: 171347 [Multi-domain]  Cd Length: 193  Bit Score: 76.38  E-value: 1.00e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  34 KDPHLSDDITQDVFIKVFKNWNSFRRESSIKTWILKITRNTAINYLKSSYFK------RISLVGFFSDD---KQTLSAEQ 104
Cdd:PRK11923  42 HDTAEAQDVAQEAFIKAYRALGNFRGDSAFYTWLYRIAINTAKNHLVSRGRRppdsdvSSEDAEFYDGDhalKDIESPER 121

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 516129712 105 EFFKQEEMNDVWKVVLKLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRARSKVSKLI 169
Cdd:PRK11923 122 ALLRDEIEGTVHRTIQQLPEDLRTALTLREFDGLSYEDIASVMQCPVGTVRSRIFRAREAIDKAL 186
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 13-171 1.10e-17

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 75.69  E-value: 1.10e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  13 ELDDVIKDYWQDVWNYSFIITKDPHLSDDITQDVFIKVFKNWNSFRrESSIKTWILKITRNTAINYLKSSyfKRISLVGf 92
Cdd:PRK09644   2 EIEEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYD-NQKVKPWLFKVAYHTFIDFVRKE--KKVSFVG- 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  93 fSDDKQTLSAE--QEFFKQEEMNDVWKVVL-KLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRARSKVSKLI 169
Cdd:PRK09644  78 -TDEIEAIQAEstEEYVVAKNSYEKLIQIIhTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALL 156


                 ..
gi 516129712 170 GE 171
Cdd:PRK09644 157 KE 158
PRK12547 PRK12547
RNA polymerase sigma factor; Provisional
 39-173 1.75e-17

RNA polymerase sigma factor; Provisional


Pssm-ID: 139056 [Multi-domain]  Cd Length: 164  Bit Score: 75.30  E-value: 1.75e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  39 SDDITQDVFIKVFKNWNSFRRESSIKTWILKITRNTAINYLKSSYFKRISLVGFFSddkQTLSAEQEFFKQEEMNDVWKV 118
Cdd:PRK12547  33 AEDLVQDTLMKAWAKQDSFEMGTNLKAWLFTILRNEFYSQMRKRGREVQDSDGVFT---ARVAVHPAQYGSLDLQDFKKA 109

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 516129712 119 VLKLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRARSKVSKLIGEGG 173
Cdd:PRK12547 110 LNLLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARNRLQELLKVDG 164
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 28-163 1.87e-17

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 75.59  E-value: 1.87e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  28 YSFIITKDPHLSDDITQDVFIKVFKNWNSFRRESSIKTWILKITRNTAINYLKS--SYFKRISLVGFFSDDkqTLSAEQE 105
Cdd:PRK12511  20 YARSLTRDSAEAEDLVHDALVRALERRASFRSGGNLRTWLMSILHNAFIDELRRrrVEARRADELAVLADA--SLPAAQE 97

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 516129712 106 ffKQEEMNDVWKVVLKLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRARS 163
Cdd:PRK12511  98 --HAVRLAQIRDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARA 153
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 28-175 2.28e-17

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 75.54  E-value: 2.28e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  28 YSFI--ITKDPHLSDDITQDVFIKVFKNWNSFRRESSIKTWILKITRNTAINYLKSSYFKRI--SLVGFFSDDKQTlsAE 103
Cdd:PRK12515  36 YRFGlrLVRDEQTAEDLVSEVFLDVWRQAGQFEGRSQVSTWLLSIARFKALSALRRRKHEEIddEAAAAIEDGADT--PE 113

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 516129712 104 QEFFKQEEMNDVWKVVLKLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRARSKVSKLIGEGGSD 175
Cdd:PRK12515 114 VALQKSDTSAALRACLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKTRMFYARKKLAELLKAAGVE 185
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 6-170 3.18e-17

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 75.12  E-value: 3.18e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712   6 IEKFNHDELDDVIKDYWQDVWNYSFIITKDPHLSDDITQDVFIKVFKNWNSFRRESSIKTWILKITRNTAINYL---KSS 82
Cdd:PRK09641  12 VKKGDQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINRKFSTWLYRIATNLTIDRLrkrKPD 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  83 YFKRISLVG---------FFSDDKqtlSAEQEFFKQEEMNDVWKVVLKLPKKHREIIILDAKYELSYEEMAETLGVSIGT 153
Cdd:PRK09641  92 YYLDAEVAGtegltmysqLAADDA---LPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYIEDLSLKEISEILDLPVGT 168

                        170
                 ....*....|....*..
gi 516129712 154 VKSRLSRARSKVSKLIG 170
Cdd:PRK09641 169 VKTRIHRGREALRKQLR 185
PRK12522 PRK12522
RNA polymerase sigma factor; Provisional
 12-162 7.83e-17

RNA polymerase sigma factor; Provisional


Pssm-ID: 183571 [Multi-domain]  Cd Length: 173  Bit Score: 73.75  E-value: 7.83e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  12 DELDDVIKDYWQDVWNYSFIITKDPHLSDDITQDVFIKVFKNWNSFRRESSIKTWILKITRNTAIN-YLKSSYFKRISLV 90
Cdd:PRK12522   3 EKVEELIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVENYKKWITTICVRTFYDfYRKKKRWKDRILD 82

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 516129712  91 GFFSDDK------QTLSAEQEFFKQEEMNDVWKVVLKLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRAR 162
Cdd:PRK12522  83 LFHKEDGgeiefaDDVNISEEFIQKVEAEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAK 160
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 14-168 1.83e-16

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 72.28  E-value: 1.83e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  14 LDDVIKDYWQDVWNYSFIITKDPHLSDDITQDVFIKVFKNWNSFRRESsIKTWILKITRNTAIN-YLKSSYFKRISLVGF 92
Cdd:PRK12541   7 LEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGEE-IRPWLFTIAYNAFIDwYRKEKKYKTTTIEEF 85

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 516129712  93 FSDDKQtlSAEQEFFKQEEMNDVWKVVLKLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRARSKVSKL 168
Cdd:PRK12541  86 HLPNVP--STEHEYFIKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKETKSI 159
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 28-171 2.40e-16

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 72.80  E-value: 2.40e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  28 YSFII--TKDPHLSDDITQDVFIKVFKNWNSFRRESSIKTWILKITRNTAINYLKSSYFKRISlvGFFSDDKQTLSA--- 102
Cdd:PRK12513  40 YRFLLrlARDRALAEDIFQETWLRVIRARAQYQPRARFRTWLYQIARNLLIDHWRRHGARQAP--SLDADEQLHALAddg 117

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 516129712 103 ---EQEFFKQEEMNDVWKVVLKLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRARSKVSKLIGE 171
Cdd:PRK12513 118 aapEQQLSLFRDRRRLQAALETLPDEQREVFLLREHGDLELEEIAELTGVPEETVKSRLRYALQKLRELLAE 189
PRK09649 PRK09649
RNA polymerase sigma factor SigC; Reviewed
 14-162 3.16e-16

RNA polymerase sigma factor SigC; Reviewed


Pssm-ID: 137458 [Multi-domain]  Cd Length: 185  Bit Score: 72.38  E-value: 3.16e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  14 LDDVIKDYWQDVWNYSFIITkDPHLSDDITQDVFIKVFKNWNSFRRESSIKTWILKITRNTAINYLKSSYFKriSLVGFF 93
Cdd:PRK09649  26 LEAFIKATQQDVWRFVAYLS-DVGSADDLTQETFLRAIGAIPRFSARSSARTWLLAIARHVVADHIRHVRSR--PRTTRG 102

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 516129712  94 SDDKQTLSAEQEFFKQEEMNDVWKVVLKLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRAR 162
Cdd:PRK09649 103 ARPEHLIDGDRHARGFEDLVEVTTMIADLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARAR 171
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 41-175 5.37e-16

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 72.69  E-value: 5.37e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  41 DITQDVFIKVFKNWNSFRRESSIKTWILKITRNTAINYLKssyfKRISLVGFFSDDKQTLSAEQEFFKQEEMND------ 114
Cdd:PRK11922  59 DVVQEAYLRAFRALGTFRGDASLSTWLSRIVLNEALGRLR----RRRRLVNLAEMVMASTIAGGERTPLADPAEdperaa 134

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 516129712 115 --------VWKVVLKLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRARS----KVSKLIGEGGSD 175
Cdd:PRK11922 135 arreiralLERAIDALPDAFRAVFVLRVVEELSVEETAQALGLPEETVKTRLHRARRllreSLAREIGPALLD 207
PRK12535 PRK12535
RNA polymerase sigma factor; Provisional
 14-172 9.11e-16

RNA polymerase sigma factor; Provisional


Pssm-ID: 237130 [Multi-domain]  Cd Length: 196  Bit Score: 71.47  E-value: 9.11e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  14 LDDVIKDYWQDVWNYsFIITKDPHLSDDITQDVFIKVFKNWNSFRRESSIKTWILKITRNTAINYLKSSYFK-RISLVGF 92
Cdd:PRK12535  27 LTEFIRETQDDVWRL-LAHLGGHDIADDLTQETYLRVMSALPRFAARSSARTWLLSLARRVWVDNIRHDMARpRKSATEY 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  93 FSDDKQTLSAEQEFFKQEEMnDVWKVVLKLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRARSKVSKLIGEG 172
Cdd:PRK12535 106 EDAAATTASNETTGSWSEWI-DVRTLIDALPPERREALILTQVLGYTYEEAAKIADVRVGTIRSRVARARADLIAATATG 184
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 15-163 6.53e-15

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 69.43  E-value: 6.53e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  15 DDVIKDYWQDVWNYSFIITKDPHLSDDITQDVFIKVFKNWNSFRrESSIKTWILKITRNTAINYLKSSyfKRISLVGFfS 94
Cdd:PRK09647  31 EELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQ-PGTFEGWLHRITTNLFLDMVRRR--ARIRMEAL-P 106

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 516129712  95 DDKQTLSA-----EQEFFKQEEMNDVWKVVLKLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRARS 163
Cdd:PRK09647 107 EDYDRVPGdepnpEQIYHDARLDPDLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQ 180
PRK12517 PRK12517
RNA polymerase sigma factor; Provisional
 15-169 8.97e-15

RNA polymerase sigma factor; Provisional


Pssm-ID: 183569 [Multi-domain]  Cd Length: 188  Bit Score: 68.56  E-value: 8.97e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  15 DDVIKDYWQDVWNYSFIITKDPHLSDDITQDVFIKVFKNWNSFRRESSIKTWILKITRNTAINYLKSSYFKRISLVGFFS 94
Cdd:PRK12517  26 EALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDEKAAKAWLITILRRENARRFERKQFDLVDIEDDSI 105

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 516129712  95 DDKQTLSAEqeffkqEEMNDVW--KVVLKLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRARSKVSKLI 169
Cdd:PRK12517 106 EDDASHSSE------EEMEQEWlrRQIAKLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMTRLFRARNQLKEAL 176
PRK12533 PRK12533
RNA polymerase sigma factor; Provisional
 35-171 2.80e-14

RNA polymerase sigma factor; Provisional


Pssm-ID: 237129 [Multi-domain]  Cd Length: 216  Bit Score: 67.83  E-value: 2.80e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  35 DPHLSDDITQDVFIKVFKNWNSFRRESSiKTWILKITRNT---AINYLKSS----YFKRISLVGFFsDDKQTLSAEQE-- 105
Cdd:PRK12533  41 NASDADDVVQEACMRALRFFDSFRGDNA-RPWLLAIVRHTwysEWRRRANAhevaAPDTLDDADSL-DDWQPAGEDPLal 118

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 516129712 106 FFKQEEMNDVWKVVLKLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRARSKVSKLIGE 171
Cdd:PRK12533 119 LLRAEDVRLVNAALAKLPVEYREVLVLRELEDMSYREIAAIADVPVGTVMSRLARARRRLAALLGG 184
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 25-171 8.39e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 63.54  E-value: 8.39e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  25 VWNYSFIITKDPHLSDDITQDVFIKVFKNWNSFRRESSIKTWILKITRNTAINYLKSSYfKRISLVGFFSDDKQTLSAEQ 104
Cdd:PRK12519  42 VYGLALKILGNSQEAEDLTQEIFLSLWRKSSYDPKRGSLSSYLLTLTRSRAIDRLRSRR-SRQRLLERWQQELLGEASED 120

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 516129712 105 EFFKQ----EEMNDVWKVVLKLPKKHREIIILdAKYE-LSYEEMAETLGVSIGTVKSRLSRARSKVSKLIGE 171
Cdd:PRK12519 121 TPLEQaslaERSQRVQTALAQLPESQRQVLEL-AYYEgLSQSEIAKRLGIPLGTVKARARQGLLKLRELLQD 191
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 115-165 1.41e-12

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: 59.39  E-value: 1.41e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 516129712  115 VWKVVLKLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRARSKV 165
Cdd:pfam08281   4 LLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 32-166 8.63e-12

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: 60.03  E-value: 8.63e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712   32 ITKDPHLSDDITQDVFIKVFKNWNSFRRESSIKTWILKITRNTAINYLKSsyfKRISLVGFFSDDKQTLSAEQEFFKQEE 111
Cdd:TIGR02989  21 LVADRDDVDDVLQETFVVAWRKFDQFDPGTNFVAWARGIARNKVLNYRRK---LGRDRLVFDDDLLEALAAEAEPTEAER 97

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 516129712  112 MNDVWKVVL----KLPKKHREiiILDAKYE--LSYEEMAETLGVSIGTVKSRLSRARSKVS 166
Cdd:TIGR02989  98 LSDDRQALEgcleKLPERQRE--LLDLRYQrgQKATALAEQTGRTVNAVYKALQRIRVSLR 156
PRK12530 PRK12530
RNA polymerase sigma factor; Provisional
 34-162 2.00e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 237128 [Multi-domain]  Cd Length: 189  Bit Score: 59.78  E-value: 2.00e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  34 KDPHLSDDITQDVFIKVFKNWNSFRRESSIKTWILKITRNTAINYLKssYFKRISLVG----------FFSD-------- 95
Cdd:PRK12530  29 KDADLAEDVVQEALVSAYKNADSFKGQSALKTWIFAILKNKIIDLIR--YRKRFVNESelieedspnsFFDEkghwkpey 106

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 516129712  96 -DKQTLSAEQEFFKQEEMNDVWKVVL-KLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRAR 162
Cdd:PRK12530 107 yEPSEWQEVENTVYKEEFWLIFEACLnHLPAQQARVFMMREYLELSSEQICQECDISTSNLHVLLYRAR 175
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 117-165 2.49e-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: 55.96  E-value: 2.49e-11
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 516129712 117 KVVLKLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRARSKV 165
Cdd:cd06171    6 EALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 23-170 2.78e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 58.98  E-value: 2.78e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  23 QDVWNYSFIITKDPHLSDDITQDVFIKVFKNWNSFRRESSIKTWILKITRNTAINYLKSSYfKRISLVgffsDDKQTLSA 102
Cdd:PRK12543  18 QEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNRPFRFWLIGLVIKQIHSWRRKRW-RRFRIF----EKAEEQRK 92

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 516129712 103 EQEFFKQEEM------NDVWKVVLKLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRARSKVSKLIG 170
Cdd:PRK12543  93 PVSIDFSEDVlskesnQELIELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQ 166
PRK09643 PRK09643
RNA polymerase sigma factor SigM; Reviewed
 26-170 3.66e-11

RNA polymerase sigma factor SigM; Reviewed


Pssm-ID: 236604 [Multi-domain]  Cd Length: 192  Bit Score: 58.95  E-value: 3.66e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  26 WNYSFIITKDPHLSDDITQDVFIKVFKNWNSFRRESSIKTWILKITRNTAINYLKSSYFKRISLVgffSDDKQTLSAEQE 105
Cdd:PRK09643  41 WAVARRTSGTREDAADALQDAMLSAHRAAGSFRGDAAVSSWLHRIVVNACLDRLRRAKARPTVPL---DDVYPVAQLERD 117

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 516129712 106 FFKQEEMN-DVWKVVLKLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRARSKVSKLIG 170
Cdd:PRK09643 118 PTARVETAlAVQRALMRLPVEQRAALVAVDMQGYSVADAARMLGVAEGTVKSRCARGRARLAELLG 183
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 18-81 4.64e-11

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: 55.67  E-value: 4.64e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 516129712   18 IKDYWQDVWNYSFIITKDPHLSDDITQDVFIKVFKNWNSFR--RESSIKTWILKITRNTAINYLKS 81
Cdd:pfam04542   2 VERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDpeRGVSFSTWLYTIIRNAIIDYLRK 67
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 15-161 6.41e-11

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 58.41  E-value: 6.41e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  15 DDVIKDYWQDVWNYSFIITKDPHLSDDITQDVFIKVFKNWNSFRRESSIKTWILKITRNTAINYLKSSYFKRIsLVGFFS 94
Cdd:PRK09640  29 EELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGKSKFKTWLYSITYNECITQYRKERRKRR-LMDALS 107

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 516129712  95 DDKQTLSAEQEFFKQEEMNDVWKVVLKLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRA 161
Cdd:PRK09640 108 LDPLEEASEEKAPKPEERGGLDRWLVHVNPIDREILVLRFVAELEFQEIADIMHMGLSATKMRYKRA 174
PRK06811 PRK06811
RNA polymerase factor sigma-70; Validated
 37-171 6.57e-11

RNA polymerase factor sigma-70; Validated


Pssm-ID: 180707 [Multi-domain]  Cd Length: 189  Bit Score: 58.03  E-value: 6.57e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  37 HLSDDITQDVFIKVFKNWNSFRRE-SSIKTWILKITRNTAINYLKSSYFK----RISLVGFFSDDkqtlSAEQEFFKQEE 111
Cdd:PRK06811  46 QLIEECVNDIFLSIWNNIDKFDEEkGSFKKWIAAISKYKAIDYKRKLTKNneidSIDEFILISEE----SIENEIILKEN 121

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 516129712 112 MNDVWKVVLKLPKKHREIIILdaKYELSY--EEMAETLGVSIGTVKSRLSRARSKVSKLIGE 171
Cdd:PRK06811 122 KEEILKLINDLEKLDREIFIR--RYLLGEkiEEIAKKLGLTRSAIDNRLSRGRKKLQKNKLN 181
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
25-158 2.20e-10

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 56.63  E-value: 2.20e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  25 VWNYSFIITKDPHLSDDITQDVFIKVFKNWNSF-RRESSIKTWILKITRNTAINYLKSSYFKRISlVGFFSDDKQTLSAE 103
Cdd:PRK09645  22 LWRYALRLTGDRARAEDVVQETLLRAWQHPEVLaDTGRSARAWLFTVARNLVIDERRSARARPVE-GGDDVLGVPEQSAP 100

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 516129712 104 QEFFKQEEMNDVWKVVLKLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRL 158
Cdd:PRK09645 101 DEVDRALDRLLVADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRL 155
PRK12542 PRK12542
RNA polymerase sigma factor; Provisional
 10-176 8.11e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 183581 [Multi-domain]  Cd Length: 185  Bit Score: 55.06  E-value: 8.11e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  10 NHDELDDVIKDYWQDVWNYSFIITKDPHLSDDITQDVFIKVFKNWNSFRRESS--IKTWILKITRNTAINYLKSSYFKRI 87
Cdd:PRK12542   7 DYEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTqeLKRYILRVAKNKAIDSYRKNKRHET 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  88 SLVGFFSDDKQTLSAEQEFFKQEEMNDVW--KVVLKLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRARSKV 165
Cdd:PRK12542  87 FLEEYERESIEAVDENIEEWEKRKMSEVQidTLLKELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERARKRV 166

                        170
                 ....*....|.
gi 516129712 166 SKLIGEGGSDE 176
Cdd:PRK12542 167 QNMIGGIQHDE 177
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 35-176 1.87e-09

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 54.27  E-value: 1.87e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  35 DPHLSDDITQDVFIKVFKNWNSFR-RESSIKTWILKITRNTAINYLKSsyfKRISLVGFFSD--DKQTLSAEQEFFKQEE 111
Cdd:PRK05602  43 DPAEAEDVAQETFLRIWKQAPSWRpGEARFDTWLHRVVLNLCYDRLRR---RREVPVEDAPDvpDPAPGPDAGLEARQRA 119

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 516129712 112 mNDVWKVVLKLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRARSKVSKLIGEGGSDE 176
Cdd:PRK05602 120 -RRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALESLLARGRRALRAQLADLPGSE 183
PRK12534 PRK12534
RNA polymerase sigma factor; Provisional
 39-165 3.07e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 183576 [Multi-domain]  Cd Length: 187  Bit Score: 53.52  E-value: 3.07e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  39 SDDITQDVFIKVFKNWNSF--RRESSIkTWILKITRNTAINYLKSSYFKRISLV----GFFSDDKQTLSAEQEFFKQEEM 112
Cdd:PRK12534  52 AEEVLQDVFTLIWHKAGQFdpSRARGL-TWLAMIARNKAIDHLRANAPQRRNVAlddaGELRAADASPLERTERASTRRR 130

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 516129712 113 NDVWKVVLKLPkkhREIIILDAKYE-LSYEEMAETLGVSIGTVKSRLSRARSKV 165
Cdd:PRK12534 131 IDHCLAELEPP---RSELIRTAFFEgITYEELAARTDTPIGTVKSWIRRGLAKL 181
PRK12544 PRK12544
RNA polymerase factor sigma-70;
18-162 6.67e-09

RNA polymerase factor sigma-70;


Pssm-ID: 183583 [Multi-domain]  Cd Length: 206  Bit Score: 52.88  E-value: 6.67e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  18 IKDYWQDVWNYSFIITKDPHLSDDITQDVFIKVFKNWNSFRRESSIKTWILKITRNTAINYLKSSYfKRISLVGFFSDDK 97
Cdd:PRK12544  24 LEDLRKQMIKFATLQLSDLHLAEDAVQEALIGALKNADSFAGRAAFKTWVFAILKNKIIDLLRQKK-RHVSASSLLRDEE 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  98 QTLSAEQEFFKQ---------------EEM---NDVWKV----VLKLPKKHREIIILDAKYELSYEEMAETLGVSIGTVK 155
Cdd:PRK12544 103 EEEDFEELFDESghwqkderpqawgnpEESleqEQFWRIfeacLDGLPAKYARVFMMREFIELETNEICHAVDLSVSNLN 182


                 ....*..
gi 516129712 156 SRLSRAR 162
Cdd:PRK12544 183 VLLYRAR 189
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 121-167 2.04e-08

Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. 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: 48.19  E-value: 2.04e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 516129712  121 KLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRARSKVSK 167
Cdd:pfam04545   4 SLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
PRK09646 PRK09646
ECF RNA polymerase sigma factor SigK;
34-158 1.00e-07

ECF RNA polymerase sigma factor SigK;


Pssm-ID: 182015 [Multi-domain]  Cd Length: 194  Bit Score: 49.67  E-value: 1.00e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  34 KDPHLSDDITQDVFIKVFKNWNSFR-RESSIKTWILKITRNTAINYLKS--SYFKRISLVGFFSDDKQTLSAEQEFFKQE 110
Cdd:PRK09646  52 RDPGYSEETTQEVYLEVWRTASRFDpARGSALAWLLTLAHRRAVDRVRSeqAASQREVRYGARNVDPAFDQVAEEVEARL 131

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 516129712 111 EMNDVWKVVLKLPKKHREIIILdAKYE-LSYEEMAETLGVSIGTVKSRL 158
Cdd:PRK09646 132 ERERVRDCLDALTDTQRESVTL-AYYGgLTYREVAERLAVPLGTVKTRM 179
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 32-161 1.25e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 49.01  E-value: 1.25e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  32 ITKDPHLSDDITQDVFIKVFKNWNSFR-RESSIKTWILKITRNTAINYLKSSYfKRISLVGFFSDDKQTLSAEQEFFkqE 110
Cdd:PRK12537  43 IVRDRALAEDIVHDAFIKIWTGAASFDpARGSARGWIYSVTRHLALNVLRDTR-REVVLDDDAEETAQTLHEIIDDF--D 119

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 516129712 111 EMNDVWKV--VLKLPKKHREIIILDAKYE-LSYEEMAETLGVSIGTVKSRLSRA 161
Cdd:PRK12537 120 LWANSGKIhrCLEQLEPARRNCILHAYVDgCSHAEIAQRLGAPLGTVKAWIKRS 173
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 35-171 1.40e-07

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 49.14  E-value: 1.40e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  35 DPHLSDDITQDVFIKVFKNWNSFR-RESSIKTWILKITRNTAINYLKSSYFKRISLvgffsddkQTLSAEQEFF------ 107
Cdd:PRK13919  46 DGAAAEDVVQEVFIRVWKKAKEFDpRRGSARAWLLALAHHAAVDHVRRRAARPQPL--------EPDEREPEAFdlpgpg 117

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 516129712 108 -KQEEMND---VWKVVLKLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRARSKVSKLIGE 171
Cdd:PRK13919 118 lDEEGHLDrtrLGRALKALSPEERRVIEVLYYQGYTHREAAQLLGLPLGTLKTRARRALSRLKEVLRE 185
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 32-161 3.66e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 47.89  E-value: 3.66e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  32 ITKDPHLSDDITQDVFIKVFKNWNSFR-RESSIKTWILKITRNTAINYLKSSYFKRISL--VGFFSDDKQTlsAEQEFFK 108
Cdd:PRK12514  39 VLKDRSEAEEALQDVYVKIWTKADRFAvSGLSPMTWLITIARNHAIDRLRARKAVAVDIdeAHDLADPSPG--PEAEVIA 116

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 516129712 109 QEEMNDVWKVVLKLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRA 161
Cdd:PRK12514 117 GDEGQRIDACLEELEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMRTWLRRS 169
PRK12531 PRK12531
RNA polymerase sigma factor; Provisional
 59-165 8.73e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 105726 [Multi-domain]  Cd Length: 194  Bit Score: 46.85  E-value: 8.73e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  59 RESSIKTWILKITRNTAINYLKSSYFKRISLvgfFSDD-----------KQTLSAEQEFFKQEEMndvwKVVLKLPKKHR 127
Cdd:PRK12531  75 QKSALSTWIYTIIRNLCFDLLRKQKGKDLHI---HADDiwpsdyyppdlVDHYSPEQDMLKEQVM----KFLDRLPKAQR 147

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 516129712 128 EIiiLDAKY--ELSYEEMAETLGVSIGTVKSRLSRARSKV 165
Cdd:PRK12531 148 DV--LQAVYleELPHQQVAEMFDIPLGTVKSRLRLAVEKL 185
PRK09642 PRK09642
RNA polymerase sigma factor;
18-167 1.20e-06

RNA polymerase sigma factor;


Pssm-ID: 170031 [Multi-domain]  Cd Length: 160  Bit Score: 46.25  E-value: 1.20e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  18 IKDYWQDVWNYSFIITKDPHLSDDITQDVFIKVFKNWNSFRRESsIKTWILKITRNTAINYL--KSSYFKRISLVGFFSD 95
Cdd:PRK09642   1 MQTYRHYIFQVIFSILRHEEDAKDVTQEVFVKIHASLPNYQFRG-LKTWMARIATNHAIDYKrkKARENEELSLCKETEE 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 516129712  96 D-KQTLSAEQEFFKQEEMNDVWKVVLKLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRARSKVSK 167
Cdd:PRK09642  80 NiKSSHNIEDLLLTKEQKLLIAQKLRELPENYRDVVLAHYLEEKSYQEIALQEKIEVKTVEMKLYRARKWIKK 152
PRK06704 PRK06704
RNA polymerase subunit sigma-70;
10-173 1.93e-06

RNA polymerase subunit sigma-70;


Pssm-ID: 180663 [Multi-domain]  Cd Length: 228  Bit Score: 46.17  E-value: 1.93e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  10 NHDELDDVIKDYwQDVWNYSFIITKDPHLSDDITQDVFIKVFKNwnsFRRESSIKTWILKITRNTAINYLKS-SYFKRIS 88
Cdd:PRK06704  16 NHSNINFLIEQY-GELKRYCTFLTKNKWDGEDLAQETVCKVLQK---YSNKDICMTLVYKIARNRWLDQIKSkSVHEKIR 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  89 LVGFFSDDKQTLSAEQEFfkqeemndVWKVVLKLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRARSKVSKL 168
Cdd:PRK06704  92 DQITFEEPHEKIADLHEM--------VGKVLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRLKTV 163


                 ....*
gi 516129712 169 IGEGG 173
Cdd:PRK06704 164 SEEGI 168
PRK12526 PRK12526
RNA polymerase sigma factor; Provisional
 65-171 2.12e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 237127 [Multi-domain]  Cd Length: 206  Bit Score: 45.95  E-value: 2.12e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  65 TWILKITRNTAINYLKSSYFKRISLVGffsDD----KQTLSAEQEffKQEEMND------VWKVVLKLPKKHREIIILDA 134
Cdd:PRK12526  92 TWVYTVMRNAAFDMLRKIKAKKEQNLG---DDiwpiEQALAESQS--ESEEFSDhlmdkqILSYIEKLPEAQQTVVKGVY 166

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 516129712 135 KYELSYEEMAETLGVSIGTVKSRLSRARSKVSKLIGE 171
Cdd:PRK12526 167 FQELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQMGE 203
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 39-169 7.97e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 44.11  E-value: 7.97e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  39 SDDITQDVFIKVFKNWNSFRR-ESSIKTWILKITRNTAINYLKSSYFKRISLVGF--FSDDKQtlSAEQEFFKQEEMNDV 115
Cdd:PRK12524  53 AEDVTQEAMLRLWRIAPDWRQgEARVSTWLYRVVCNLCTDRLRRRRRASVDLDDApePADAAP--GAEEALIEGDRMRAL 130

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 516129712 116 WKVVLKLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRARSKVSKLI 169
Cdd:PRK12524 131 DAALAALPERQRQAVVLRHIEGLSNPEIAEVMEIGVEAVESLTARGKRALAALL 184
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
 39-169 2.07e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 43.31  E-value: 2.07e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  39 SDDITQDVFIKVFKN---WNSFRRESSikTWILKITRNTAINYLKSSYFKRISLVGFFSDDKQTLSAEQEffkQEEMNDV 115
Cdd:PRK12538  90 AEDVVQDTMLKVWTHrgrWQHGRAKFS--TWLYRVVSNRCIDLRRKPRTENVDAVPEVADGKPDAVSVIE---RNELSDL 164

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 516129712 116 WKVVL-KLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRARSKVSKLI 169
Cdd:PRK12538 165 LEAAMqRLPEQQRIAVILSYHENMSNGEIAEVMDTTVAAVESLLKRGRQQLRDLL 219
PRK09648 PRK09648
RNA polymerase sigma factor ShbA;
103-170 2.24e-05

RNA polymerase sigma factor ShbA;


Pssm-ID: 236607 [Multi-domain]  Cd Length: 189  Bit Score: 43.03  E-value: 2.24e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 516129712 103 EQEFFKQEEMNDVWKVVLKLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRARSKVSKLIG 170
Cdd:PRK09648 121 EERALRSESSNRMRELLDTLPEKQREILILRVVVGLSAEETAEAVGSTPGAVRVAQHRALARLRAEIE 188
PRK12532 PRK12532
RNA polymerase sigma factor; Provisional
 36-162 2.57e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 171564 [Multi-domain]  Cd Length: 195  Bit Score: 42.61  E-value: 2.57e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  36 PHLSDDITQDVFIKVFKNWNSFRRESSIKTWILKITRNTAINYLKSSYFKR--ISLVG----------FFS--------D 95
Cdd:PRK12532  30 PDLAEDLVQETLLSAYSAGDSFQGRALVNSWLFAILKNKIIDALRQIGRQRkvFTLLDdelldeafesHFSqnghwtpeG 109

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 516129712  96 DKQTLSAEQEFFKQEEMNDVWKVVL-KLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRAR 162
Cdd:PRK12532 110 QPQHWNTPEKSLNNNEFQKILQSCLyNLPENTARVFTLKEILGFSSDEIQQMCGISTSNYHTIMHRAR 177
PRK06930 PRK06930
positive control sigma-like factor; Validated
 122-171 5.99e-05

positive control sigma-like factor; Validated


Pssm-ID: 180757 [Multi-domain]  Cd Length: 170  Bit Score: 41.64  E-value: 5.99e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 516129712 122 LPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRARSKVSKLIGE 171
Cdd:PRK06930 115 LTEREKEVYLMHRGYGLSYSEIADYLNIKKSTVQSMIERAEKKIARQINE 164
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
126-164 1.48e-04

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 40.51  E-value: 1.48e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 516129712 126 HREIIILDAKYE-LSYEEMAETLGVSIGTVKSRLSRARSK 164
Cdd:COG2771  130 PREREVLRLLAEgLTLKEIARILGISERTVRTHLKRIYRK 169
PRK04217 PRK04217
hypothetical protein; Provisional
 137-172 3.25e-04

hypothetical protein; Provisional


Pssm-ID: 235258  Cd Length: 110  Bit Score: 38.32  E-value: 3.25e-04
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 516129712 137 ELSYEEMAETLGVSIGTVKSRLSRARSKVSKLIGEG 172
Cdd:PRK04217  58 GLTQEEAGKRMGVSRGTVWRALTSARKKVAQMLVEG 93
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 127-164 4.95e-04

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 36.74  E-value: 4.95e-04
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 516129712   127 REIIILDAKYE-LSYEEMAETLGVSIGTVKSRLSRARSK 164
Cdd:smart00421   7 REREVLRLLAEgLTNKEIAERLGISEKTVKTHLSNIMRK 45
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 127-164 5.44e-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: 5.44e-04
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 516129712 127 REIIILDAKyELSYEEMAETLGVSIGTVKSRLSRARSK 164
Cdd:COG2197   75 REVLRLLAE-GLSNKEIAERLGISERTVKTHVSNILRK 111
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
 32-150 5.45e-04

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 38.51  E-value: 5.45e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  32 ITKDPHLSDDITQDVFIKVfknwNSFRRESSIKT---WILKITRNTAINYLKSSYFKRIslvgFFSDDKQTL-------S 101
Cdd:PRK07037  18 IVGCRSRAEDVVQDAFVKL----VEAPNQDAVKQpvaYLFRIVRNLAIDHYRRQALENK----YHGDEEDGLdvpspeaS 89

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 516129712 102 AEQEFFKQEEMNDVWKVVLKLPKKHREIIILDAKYELSYEEMAETLGVS 150
Cdd:PRK07037  90 PEAALINRDTLRHVADALSELPARTRYAFEMYRLHGETQKDIARELGVS 138
PRK09651 PRK09651
RNA polymerase sigma factor FecI; Provisional
 39-161 7.08e-04

RNA polymerase sigma factor FecI; Provisional


Pssm-ID: 182018 [Multi-domain]  Cd Length: 172  Bit Score: 38.25  E-value: 7.08e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  39 SDDITQDVFIKVFKNwNSFRRESSIKTWILKITRNTAI-----NYLKSSYFKRISLVgffsDDKQTLSAEQEFFKQEEMN 113
Cdd:PRK09651  37 ADDIAQDTFLRVMVS-ETLSTIRDPRSFLCTIAKRVMVdlfrrNALEKAYLEMLALM----PEGGAPSPEERESQLETLQ 111

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 516129712 114 DVWKVVLKLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRA 161
Cdd:PRK09651 112 LLDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKA 159
PRK12536 PRK12536
RNA polymerase sigma factor; Provisional
 36-170 8.29e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 237131 [Multi-domain]  Cd Length: 181  Bit Score: 38.11  E-value: 8.29e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  36 PHLSD---DITQDVFIKVFKNWNSFRRESSIKTWILKITRNTAINYLKsSYFKRISLVGFFSDDKQTLSA-EQEFFkqEE 111
Cdd:PRK12536  43 PQLPDeveDLVQEILLAVHNARHTYRADQPLTAWVHAIARYKLMDFLR-SRARREALHDPLDDESELFATsDDEAA--EA 119

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712 112 MNDVWKVVLKLPKKHReIIILDAKYE-LSYEEMAETLGVSIGTVKSRLSRARSKVSKLIG 170
Cdd:PRK12536 120 RRDLGKLLEQLPDRQR-LPIVHVKLEgLSVAETAQLTGLSESAVKVGIHRGLKALAAKIR 178
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 93-164 1.66e-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: 37.88  E-value: 1.66e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 516129712  93 FSDDKQTLSAEQEFFKQEEMNDVWKVVLKLPKKHREIIILDAKYELSYEEMAETLGVSigtvKSRLSRARSK 164
Cdd:COG1191  158 LLDLLESGDPEEELEHEELREALAEAIEQLPERERLVLSLYYFEELTLKEIAEVLGVS----ESRVSRLHKK 225
MalT COG2909
ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];
138-164 1.99e-03

ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];


Pssm-ID: 442153 [Multi-domain]  Cd Length: 184  Bit Score: 37.38  E-value: 1.99e-03
                         10        20
                 ....*....|....*....|....*..
gi 516129712 138 LSYEEMAETLGVSIGTVKSRLSRARSK 164
Cdd:COG2909  138 LSNKEIAERLFISVNTVKTHLRNIYRK 164
PRK12512 PRK12512
RNA polymerase sigma factor; Provisional
 39-172 2.06e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 171551 [Multi-domain]  Cd Length: 184  Bit Score: 37.37  E-value: 2.06e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  39 SDDITQDVFIKVFKNWNSFRRESSIKTWILKITRNTAINYLKSSYfKRISLVgfFSDDKQTLSAEQEffkQEEMN--DVW 116
Cdd:PRK12512  53 AEDIVQEILLAVHLKRHTWDPGAPFAPWLFAIARNKLIDALRRRG-RRVFVD--IDDFAETLPAEPA---TETLPagDVG 126

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 516129712 117 KVVLKLPKKHREI---IILDAkyeLSYEEMAETLGVSIGTVKSRLSRARSKVSKLIGEG 172
Cdd:PRK12512 127 RHLETLPPRQRDVvqsISVEG---ASIKETAAKLSMSEGAVRVALHRGLAALAAKFRSE 182
PRK12539 PRK12539
RNA polymerase sigma factor SigF;
39-171 2.07e-03

RNA polymerase sigma factor SigF;


Pssm-ID: 237132 [Multi-domain]  Cd Length: 184  Bit Score: 37.02  E-value: 2.07e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  39 SDDITQDVFIKVFKNWNSFRRESSIKTWILKITRNTAINYLKSSyfkRISLVGFFSDDKQTLSAEQEFFKQEEMNDVWKV 118
Cdd:PRK12539  52 AEDLVQEALMAIHTRRHTYDPEQPLTPWVYAIARYKLIDHLRRT---RASLADVPIDDADELVAHDDHAAVESTLDLGRL 128

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 516129712 119 VLKLPKKHR---EIIILDAkyeLSYEEMAETLGVSIGTVKSRLSRARSKVSKLIGE 171
Cdd:PRK12539 129 LARLPEKMRlaiQAVKLEG---LSVAEAATRSGMSESAVKVSVHRGLKALAALIGR 181
PRK09047 PRK09047
RNA polymerase factor sigma-70; Validated
 33-173 2.46e-03

RNA polymerase factor sigma-70; Validated


Pssm-ID: 236367 [Multi-domain]  Cd Length: 161  Bit Score: 36.87  E-value: 2.46e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  33 TKDPHLSDDITQDVFIKVFKNWnsfrRESSIKTWIL---KITRNTAINYLKSSYFKR--ISLVGFFSDDKQ--------- 98
Cdd:PRK09047   1 VRDDDAALDIVQDAMIKLAEKY----GDRPAAEWPPlfqRILQNRIHDWFRRQKVRNtwVSLFSSFSDDDDdddfdplet 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516129712  99 -------TLSAEQEFFKQEEMNDVWKVVLKLPKKHREIIILDAKYELSYEEMAETLGVSIGTVKSRLSRARSKVSKLIGE 171
Cdd:PRK09047  77 ldsadegAESPADKLERAQVLQLIEEAIQKLPARQREAFLLRYWEDMDVAETAAAMGCSEGSVKTHCSRATHALAKALEA 156


                 ..
gi 516129712 172 GG 173
Cdd:PRK09047 157 KG 158
HTH_24 pfam13412
Winged helix-turn-helix DNA-binding;
124-160 9.07e-03

Winged helix-turn-helix DNA-binding;


Pssm-ID: 404317 [Multi-domain]  Cd Length: 45  Bit Score: 32.79  E-value: 9.07e-03
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 516129712  124 KKHREII-ILDAKYELSYEEMAETLGVSIGTVKSRLSR 160
Cdd:pfam13412   1 ETDRKILnLLQENPRISQRELAERLGLSPSTVNRRLKR 38
 
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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