NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|492654086|ref|WP_005912883|]
View 

MULTISPECIES: RNA polymerase sigma factor [Xanthomonas]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 1-165 4.73e-22

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: 86.97  E-value: 4.73e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492654086   1 MPLDTDLHTR--------FSALLQQHRAIVLKVAASYCRDRDDRDELAQEIATQLWRAFPGYDPSRRFSTWMYRIALNVA 72
Cdd:COG1595    1 MSSDEELLERlragdeaaFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492654086  73 ISDLRGRRAagEPIALDAVVERIADPCA---HDPVREQQVAALYAFIAHQLPLERAL-LLLYLDQHSYREIADVLGISET 148
Cdd:COG1595   81 IDHLRKRRR--RRELLDELAEELPDEAAdpeEALEAEELLEALLAALERLPPRQREVlVLRYLEGLSYAEIAEILGISEG 158

                        170
                 ....*....|....*..
gi 492654086 149 NVATKLSRLKSRIRAEL 165
Cdd:COG1595  159 TVKSRLSRARKKLREAL 175
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 1-165 4.73e-22

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: 86.97  E-value: 4.73e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492654086   1 MPLDTDLHTR--------FSALLQQHRAIVLKVAASYCRDRDDRDELAQEIATQLWRAFPGYDPSRRFSTWMYRIALNVA 72
Cdd:COG1595    1 MSSDEELLERlragdeaaFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492654086  73 ISDLRGRRAagEPIALDAVVERIADPCA---HDPVREQQVAALYAFIAHQLPLERAL-LLLYLDQHSYREIADVLGISET 148
Cdd:COG1595   81 IDHLRKRRR--RRELLDELAEELPDEAAdpeEALEAEELLEALLAALERLPPRQREVlVLRYLEGLSYAEIAEILGISEG 158

                        170
                 ....*....|....*..
gi 492654086 149 NVATKLSRLKSRIRAEL 165
Cdd:COG1595  159 TVKSRLSRARKKLREAL 175
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 11-165 1.08e-21

RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 85.48  E-value: 1.08e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492654086   11 FSALLQQHRAIVLKVAASYCRDRDDRDELAQEIATQLWRAFPGYDPSRRFSTWMYRIALNVAISDLRGRRAAGEPIALDA 90
Cdd:TIGR02937   3 FEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDLLE 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 492654086   91 VVERIADPCAHDPVREQQVAALYAFIAH-QLPLERALLLLYLDQHSYREIADVLGISETNVATKLSRLKSRIRAEL 165
Cdd:TIGR02937  83 ELLDSDPSPEEELEQEEEREALREALEKlPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 4-165 2.04e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 64.22  E-value: 2.04e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492654086   4 DTDLHTRFSALLQQHRAIVLKVAASYCRDRDDRDELAQEIATQLWRAFPGYDPSRRFSTWMYRIALNVAISDLRgRRAAG 83
Cdd:PRK11924   8 ATGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCYDLLR-RRRRE 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492654086  84 EPIALDAVVERIADPCAHDP----VREQQVAALYAFIAH-QLPLERALLLLYLDQHSYREIADVLGISETNVATKLSRLK 158
Cdd:PRK11924  87 KAVLSDDALEPEFAETAETPeaalLAKDDLARIDRCLDAlPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRAR 166


                 ....*..
gi 492654086 159 SRIRAEL 165
Cdd:PRK11924 167 QLLRECL 173
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 14-80 2.62e-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: 56.06  E-value: 2.62e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 492654086   14 LLQQHRAIVLKVAASYCRDRDDRDELAQEIATQLWRAFPGYDPSR--RFSTWMYRIALNVAISDLRGRR 80
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERgvSFSTWLYTIIRNAIIDYLRKQR 69
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 1-165 4.73e-22

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: 86.97  E-value: 4.73e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492654086   1 MPLDTDLHTR--------FSALLQQHRAIVLKVAASYCRDRDDRDELAQEIATQLWRAFPGYDPSRRFSTWMYRIALNVA 72
Cdd:COG1595    1 MSSDEELLERlragdeaaFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492654086  73 ISDLRGRRAagEPIALDAVVERIADPCA---HDPVREQQVAALYAFIAHQLPLERAL-LLLYLDQHSYREIADVLGISET 148
Cdd:COG1595   81 IDHLRKRRR--RRELLDELAEELPDEAAdpeEALEAEELLEALLAALERLPPRQREVlVLRYLEGLSYAEIAEILGISEG 158

                        170
                 ....*....|....*..
gi 492654086 149 NVATKLSRLKSRIRAEL 165
Cdd:COG1595  159 TVKSRLSRARKKLREAL 175
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 11-165 1.08e-21

RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 85.48  E-value: 1.08e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492654086   11 FSALLQQHRAIVLKVAASYCRDRDDRDELAQEIATQLWRAFPGYDPSRRFSTWMYRIALNVAISDLRGRRAAGEPIALDA 90
Cdd:TIGR02937   3 FEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDLLE 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 492654086   91 VVERIADPCAHDPVREQQVAALYAFIAH-QLPLERALLLLYLDQHSYREIADVLGISETNVATKLSRLKSRIRAEL 165
Cdd:TIGR02937  83 ELLDSDPSPEEELEQEEEREALREALEKlPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 4-165 2.04e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 64.22  E-value: 2.04e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492654086   4 DTDLHTRFSALLQQHRAIVLKVAASYCRDRDDRDELAQEIATQLWRAFPGYDPSRRFSTWMYRIALNVAISDLRgRRAAG 83
Cdd:PRK11924   8 ATGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCYDLLR-RRRRE 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492654086  84 EPIALDAVVERIADPCAHDP----VREQQVAALYAFIAH-QLPLERALLLLYLDQHSYREIADVLGISETNVATKLSRLK 158
Cdd:PRK11924  87 KAVLSDDALEPEFAETAETPeaalLAKDDLARIDRCLDAlPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRAR 166


                 ....*..
gi 492654086 159 SRIRAEL 165
Cdd:PRK11924 167 QLLRECL 173
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 14-80 2.62e-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: 56.06  E-value: 2.62e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 492654086   14 LLQQHRAIVLKVAASYCRDRDDRDELAQEIATQLWRAFPGYDPSR--RFSTWMYRIALNVAISDLRGRR 80
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERgvSFSTWLYTIIRNAIIDYLRKQR 69
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 10-165 1.61e-09

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 54.04  E-value: 1.61e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492654086  10 RFSALLQQHRAIVLKVAASYCRDRDDRDELAQEIATQLWRAFPGYDPSRRFSTWMYRIALNVAISDLR--GRRAAGEPI- 86
Cdd:PRK09652  11 AFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRGGAAFYTWLYRIARNTAINYLRkqGRRPPASDVd 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492654086  87 ALDAVVERIADPCAHDPVREQQvaALYAFIAHQLPLERAL---------LLLYLDQHSYREIADVLGISETNVATKLSRL 157
Cdd:PRK09652  91 AEEAEDFDLADALRDISTPENE--LLSAELEQRVRAAIESlpeelrtaiTLREIEGLSYEEIAEIMGCPIGTVRSRIFRA 168


                 ....*...
gi 492654086 158 KSRIRAEL 165
Cdd:PRK09652 169 REALRAKL 176
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 11-91 2.08e-09

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 53.89  E-value: 2.08e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492654086  11 FSALLQQHRAIVLKVAASYCRDRDDRDELAQEIATQLWRAFPGYDPSR-RFSTWMYRIALNVAISDLRGRRAAGEPIALD 89
Cdd:PRK05602  22 FRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPGEaRFDTWLHRVVLNLCYDRLRRRREVPVEDAPD 101


                 ..
gi 492654086  90 AV 91
Cdd:PRK05602 102 VP 103
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 11-165 2.13e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 53.92  E-value: 2.13e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492654086  11 FSALLQQHRAIVLKVAASYCRDRDDRDELAQEIATQLWRAFPGYDPSRRFSTWMYRIALNVAISDLRgRRAAGEPIALDA 90
Cdd:PRK12513  28 FEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPRARFRTWLYQIARNLLIDHWR-RHGARQAPSLDA 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492654086  91 VVERIADPCAH-DPVRE----QQVAALYAFIAHQLPLERALLLLYLDQH-SYREIADVLGISETNVATKLSRLKSRIRAE 164
Cdd:PRK12513 107 DEQLHALADDGaAPEQQlslfRDRRRLQAALETLPDEQREVFLLREHGDlELEEIAELTGVPEETVKSRLRYALQKLREL 186


                 .
gi 492654086 165 L 165
Cdd:PRK12513 187 L 187
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 10-111 2.32e-09

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


Pssm-ID: 274379 [Multi-domain]  Cd Length: 159  Bit Score: 53.09  E-value: 2.32e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492654086   10 RFSALLQQHRAIVLKVAASYCRDRDDRDELAQEIATQLWRAFPGYDPSRRFSTWMYRIALNVAISDLRGRRAAGEPIAlD 89
Cdd:TIGR02989   2 AFVRLLTRHERALRAFVRSLVADRDDVDDVLQETFVVAWRKFDQFDPGTNFVAWARGIARNKVLNYRRKLGRDRLVFD-D 80

                          90       100
                  ....*....|....*....|..
gi 492654086   90 AVVERIADpcAHDPVREQQVAA 111
Cdd:TIGR02989  81 DLLEALAA--EAEPTEAERLSD 100
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 11-162 3.49e-09

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 52.64  E-value: 3.49e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492654086  11 FSALLQQHRAIVLKVAASYCRDRDDRDELAQEIATQLWRAFPGYDPSrrFSTWMYRIALNVAISDLRG-----RRAAGEP 85
Cdd:PRK09639   5 FEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRSDFKGIEN--EKGWLIKSARNVAYNYLRSekrrrARILGEF 82

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 492654086  86 IALDAVVERIADPCAhdpVREQQVAALYAFIAHQLPLERALLLLYLDQHSYREIADVLGISETNVATKLSRLKSRIR 162
Cdd:PRK09639  83 QWQEVDNEPSPEEIW---IRKEEITKVQEVLAKMTERDRTVLLLRFSGYSYKEIAEALGIKESSVGTTLARAKKKFR 156
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 22-162 4.09e-09

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 52.83  E-value: 4.09e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492654086  22 VLKVAASYCRDRDDRDELAQEIATQLWRAFPGYDPSRRFSTWMYRIALNVAISDLRG-------------------RRAA 82
Cdd:PRK09415  29 VLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGKSSLKTWLYRIAINHCKDYLKSwhnkkvivtediftymesqKESV 108

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492654086  83 GEPIALDAVVERIADPCAHDPVREQQVAALYAFiahqlplerallllylDQHSYREIADVLGISETNVATKLSRLKSRIR 162
Cdd:PRK09415 109 EEEVIQNAEDERLASAVMSLPIKYREVIYLFYY----------------EELSIKEIAEVTGVNENTVKTRLKKAKELLK 172
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 11-80 3.12e-08

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 50.46  E-value: 3.12e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492654086  11 FSALLQQHRAIVLKVAASYCRDRDDRDELAQEIATQLWRAFPGYDPSRRFSTWMYRIALNVAISDLRGRR 80
Cdd:PRK09641  20 FAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINRKFSTWLYRIATNLTIDRLRKRK 89
SigW_bacill TIGR02948
RNA polymerase sigma-W factor; This sigma factor is restricted to certain lineages of the ...
 11-165 5.28e-08

RNA polymerase sigma-W factor; This sigma factor is restricted to certain lineages of the order Bacillales.


Pssm-ID: 131993 [Multi-domain]  Cd Length: 187  Bit Score: 49.89  E-value: 5.28e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492654086   11 FSALLQQHRAIVLKVAASYCRDRDDRDELAQEIATQLWRAFPGYDPSRRFSTWMYRIALNVAISDLRGRRA---AGEPIA 87
Cdd:TIGR02948  20 FADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIRAYTNIDTYDIQRKFSTWLYRIATNLTIDRLRKRKPdfyLDDEVQ 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492654086   88 LDAVVERIADPCAHDPVREQQVAAL-------YAFIAHQLPLERALLLLYLDQHSYREIADVLGISETNVATKLSRLKSR 160
Cdd:TIGR02948 100 GTDGLTMESQLAADEAPPEDQVISLelrdtiqQEIQALPPKYRMVIVLKYMEDLSLKEISEILDLPVGTVKTRIHRGREA 179


                  ....*
gi 492654086  161 IRAEL 165
Cdd:TIGR02948 180 LRKQL 184
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 22-165 5.48e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 49.89  E-value: 5.48e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492654086  22 VLKVAASYCRDRDDRDELAQEIATQLWRAFPGY-DPSRRFSTWMYRIALNVAISDLRGRRAAGepIALDAVVErIADPCA 100
Cdd:PRK12524  39 ALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWrQGEARVSTWLYRVVCNLCTDRLRRRRRAS--VDLDDAPE-PADAAP 115

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 492654086 101 hdPVREQ-----QVAALYAFIAH-QLPLERALLLLYLDQHSYREIADVLGISETNVATKLSRLKSRIRAEL 165
Cdd:PRK12524 116 --GAEEAliegdRMRALDAALAAlPERQRQAVVLRHIEGLSNPEIAEVMEIGVEAVESLTARGKRALAALL 184
PRK12534 PRK12534
RNA polymerase sigma factor; Provisional
 11-111 1.19e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183576 [Multi-domain]  Cd Length: 187  Bit Score: 48.90  E-value: 1.19e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492654086  11 FSALLQQHRAIVLKVAASYCRDRDDRDELAQEIATQLWRAFPGYDPSR-RFSTWMYRIALNVAISDLRGRRAAGEPIALD 89
Cdd:PRK12534  27 FEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRaRGLTWLAMIARNKAIDHLRANAPQRRNVALD 106

                         90       100
                 ....*....|....*....|..
gi 492654086  90 AVVERIADpcAHDPVREQQVAA 111
Cdd:PRK12534 107 DAGELRAA--DASPLERTERAS 126
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 11-81 1.90e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 48.18  E-value: 1.90e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 492654086  11 FSALLQQHRAIVLKVAASYCrDRDDRDELAQEIATQLWRAFPGYDPSRRFSTWMYRIALNVAIsDLRGRRA 81
Cdd:PRK12518  13 FRQLYRRYQQKVRSTLYQLC-GRELLDDLVQEVFLRVWKGLPKLRNPAYFSTWLYRITWNVAT-DARRQFA 81
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 9-165 2.03e-07

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: 47.94  E-value: 2.03e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492654086    9 TRFSALLQQHRAIVLKVAASYCRDRDDRDELAQEIATQLWRAFPGYDPSRRFSTWMYRIALNVAISDLRGRRaagepial 88
Cdd:TIGR02985   1 EAFEQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETLEISESIKAYLFTIVKNRCLNYLRHKQ-------- 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492654086   89 daVVERIADPCAHDPVREQQVA-ALYAFIAHQLPLERAL-------------LLLYLDQHSYREIADVLGISETNVATKL 154
Cdd:TIGR02985  73 --VEEKYQEELAEIEERELSEAdPEEELEAKELEEIIEEaieklpeqcreifILSRFEGLSNKEIAEELGISVKTVEYHI 150

                         170
                  ....*....|.
gi 492654086  155 SRLKSRIRAEL 165
Cdd:TIGR02985 151 TKALKFLRKEL 161
algU PRK11923
RNA polymerase sigma factor AlgU; Provisional
 11-89 3.66e-07

RNA polymerase sigma factor AlgU; Provisional


Pssm-ID: 171347 [Multi-domain]  Cd Length: 193  Bit Score: 47.87  E-value: 3.66e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492654086  11 FSALLQQHRAIVLKVAASYCRDRDDRDELAQEIATQLWRAFPGYDPSRRFSTWMYRIALNVAISDL--RGRRAAGEPIAL 88
Cdd:PRK11923  22 FDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDSAFYTWLYRIAINTAKNHLvsRGRRPPDSDVSS 101


                 .
gi 492654086  89 D 89
Cdd:PRK11923 102 E 102
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 11-80 7.14e-06

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 43.86  E-value: 7.14e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492654086  11 FSALLQQHRAIVLKVAASYCRDRDDRDELAQEIATQLWRAFPGYDPSRRFSTWMYRIALNVAISDLRGRR 80
Cdd:PRK09638  20 LTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGRSKFSTWLISIASRLYKDHLRKQK 89
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 11-165 1.03e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 43.80  E-value: 1.03e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492654086  11 FSALLQQHRAIVLKVAASYCRDRDDRDELAQEIATQLWRAFPGYDPSRRFSTWMYRIALNVAISDLRGRRAAGEPIALDA 90
Cdd:PRK11922  32 FEALMRRHNRRLYRTARAILRNDAEAEDVVQEAYLRAFRALGTFRGDASLSTWLSRIVLNEALGRLRRRRRLVNLAEMVM 111

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492654086  91 -------VVERIADPcAHDPVR-----------EQQVAAL-----YAFIAHqlplerallllYLDQHSYREIADVLGISE 147
Cdd:PRK11922 112 astiaggERTPLADP-AEDPERaaarreirallERAIDALpdafrAVFVLR-----------VVEELSVEETAQALGLPE 179

                        170
                 ....*....|....*...
gi 492654086 148 TNVATKLSRLKSRIRAEL 165
Cdd:PRK11922 180 ETVKTRLHRARRLLRESL 197
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 11-80 6.15e-05

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 41.46  E-value: 6.15e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492654086  11 FSALLQQHRAIVLKVAASYCRDRDDRDELAQEIATQLWRAFPGYDPSRRFSTWMYRIALNVAISDLRGRR 80
Cdd:PRK09640  28 YEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGKSKFKTWLYSITYNECITQYRKER 97
PRK08241 PRK08241
RNA polymerase subunit sigma-70;
11-80 7.85e-05

RNA polymerase subunit sigma-70;


Pssm-ID: 236196 [Multi-domain]  Cd Length: 339  Bit Score: 41.46  E-value: 7.85e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 492654086  11 FSALLQQHRAIVLkvaaSYCRdR-----DDRDELAQEIATQLWRAFPGYDPSRRFSTWMYRIALNVAISDLRGRR 80
Cdd:PRK08241  21 FAALVEPHRRELL----AHCY-RmlgsvHDAEDAVQETLLRAWRGYDRFEGRSSLRTWLYRIATNVCLDALEGRA 90
PRK09646 PRK09646
ECF RNA polymerase sigma factor SigK;
11-162 3.21e-04

ECF RNA polymerase sigma factor SigK;


Pssm-ID: 182015 [Multi-domain]  Cd Length: 194  Bit Score: 39.27  E-value: 3.21e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492654086  11 FSALLQQHRAIVLKVAASYCRDRDDRDELAQEIATQLWRAFPGYDPSR-RFSTWMYRIALNVAISDLRGRRAAGEPialD 89
Cdd:PRK09646  32 FAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDPARgSALAWLLTLAHRRAVDRVRSEQAASQR---E 108

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492654086  90 AVVERIADPCAHDPV---------REQQVAALYAFIAHQlplERALLLLYLDQHSYREIADVLGISetnvatkLSRLKSR 160
Cdd:PRK09646 109 VRYGARNVDPAFDQVaeevearleRERVRDCLDALTDTQ---RESVTLAYYGGLTYREVAERLAVP-------LGTVKTR 178


                 ..
gi 492654086 161 IR 162
Cdd:PRK09646 179 MR 180
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 11-80 3.51e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 39.33  E-value: 3.51e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492654086  11 FSALLQQHRAIVLKVAASYCRDRDDRDELAQEIATQLWRAFPGYDPSRRFSTWMYRIALNvAISDLRGRR 80
Cdd:PRK12543   9 FSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNRPFRFWLIGLVIK-QIHSWRRKR 77
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 14-154 5.03e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 38.94  E-value: 5.03e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492654086  14 LLQQHRAIVLKVAASYCRDRDDRDELAQEIATQLWRAFPGYDPSRRFSTWMYRIALNVAISDLRGRRAagEPIALDAVVE 93
Cdd:PRK12515  27 LYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGRSQVSTWLLSIARFKALSALRRRKH--EEIDDEAAAA 104

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 492654086  94 rIADPcAHDP----VREQQVAALYAFIAH-QLPLERALLLLYLDQHSYREIADVLGISETNVATKL 154
Cdd:PRK12515 105 -IEDG-ADTPevalQKSDTSAALRACLAKlSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKTRM 168
PRK09642 PRK09642
RNA polymerase sigma factor;
15-88 6.95e-04

RNA polymerase sigma factor;


Pssm-ID: 170031 [Multi-domain]  Cd Length: 160  Bit Score: 38.16  E-value: 6.95e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 492654086  15 LQQHRAIVLKVAASYCRDRDDRDELAQEIATQLWRAFPGYDpSRRFSTWMYRIALNVAISDLRGRRAAGEPIAL 88
Cdd:PRK09642   1 MQTYRHYIFQVIFSILRHEEDAKDVTQEVFVKIHASLPNYQ-FRGLKTWMARIATNHAIDYKRKKARENEELSL 73
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 11-111 1.26e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 37.49  E-value: 1.26e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492654086  11 FSALLQQHRAIVLKVAASYCRDRDDRDELAQEIATQLWR-----AFPGYDPSrrfsTWMYRIALNVAISDLRGRRAAGEP 85
Cdd:PRK12514  21 FSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTkadrfAVSGLSPM----TWLITIARNHAIDRLRARKAVAVD 96

                         90       100
                 ....*....|....*....|....*.
gi 492654086  86 IalDAVVErIADPCahdPVREQQVAA 111
Cdd:PRK12514  97 I--DEAHD-LADPS---PGPEAEVIA 116
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 132-161 1.72e-03

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: 34.74  E-value: 1.72e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 492654086  132 DQHSYREIADVLGISETNVATKLSRLKSRI 161
Cdd:pfam08281  25 EGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 26-165 3.51e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 36.30  E-value: 3.51e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492654086  26 AASYCRDRDDRDELAQEIATQLWRAFPGYDPSRRFSTWMYRIALNVAISDLRGRRAAGEPIALDAVVERIADPCAHD-PV 104
Cdd:PRK12511  21 ARSLTRDSAEAEDLVHDALVRALERRASFRSGGNLRTWLMSILHNAFIDELRRRRVEARRADELAVLADASLPAAQEhAV 100

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 492654086 105 REQQVAAlyAFIAHQLPLERALLLLYLDQHSYREIADVLGISetnVATKLSRLkSRIRAEL 165
Cdd:PRK12511 101 RLAQIRD--AFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIP---IGTLMSRI-GRARAAL 155
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 14-165 4.84e-03

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 35.92  E-value: 4.84e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492654086  14 LLQQHRAIVLKVAASYCRDRDDRDELAQEIATQLWRAFPGYDPSRrFSTWMYRIALNVAISDLRGR---RAAGEPIALDA 90
Cdd:PRK09647  33 LVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQPGT-FEGWLHRITTNLFLDMVRRRariRMEALPEDYDR 111

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492654086  91 VVERIADP-----CAH-DPVREQQVAALYA-FIAhqlplerALLLLYLDQHSYREIADVLGISETNVATKLSRLKSRIRA 163
Cdd:PRK09647 112 VPGDEPNPeqiyhDARlDPDLQAALDSLPPeFRA-------AVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQQLRA 184


                 ..
gi 492654086 164 EL 165
Cdd:PRK09647 185 AL 186
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 12-163 5.85e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 35.81  E-value: 5.85e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492654086  12 SALLQQHRAIVLKVAASYCRDRDDRDELAQEIATQLWRAfPGYDPSRR-FSTWMYRIALNVAISDLRGRRAAGEPI---- 86
Cdd:PRK12519  32 GVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRK-SSYDPKRGsLSSYLLTLTRSRAIDRLRSRRSRQRLLerwq 110

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492654086  87 ----------------ALDAVVERIADPCAHDPVREQQVAALYAFiahqlplerallllylDQHSYREIADVLGISETNV 150
Cdd:PRK12519 111 qellgeasedtpleqaSLAERSQRVQTALAQLPESQRQVLELAYY----------------EGLSQSEIAKRLGIPLGTV 174

                        170
                 ....*....|....*..
gi 492654086 151 ATK----LSRLKSRIRA 163
Cdd:PRK12519 175 KARarqgLLKLRELLQD 191
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH