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Conserved domains on  [gi|823321743|ref|WP_047075772|]
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MULTISPECIES: RNA polymerase sigma factor [Klebsiella]

Protein Classification

RNA polymerase sigma factor( domain architecture ID 11446377)

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 1-164 7.41e-33

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: 115.48  E-value: 7.41e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743   1 MNKDKNIANRIVDSQLAA-------HLSRLWRYGLVLSHNRDVAEELVQATCLRALEKSAQFTPGTRIDRWLFAILHSIW 73
Cdd:COG1595    1 MSSDEELLERLRAGDEAAfeelyerYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  74 ISELRARQVR--LGQGFVECEELAAPEPGEQDDTRWRYRQLMLRVNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTI 151
Cdd:COG1595   81 IDHLRKRRRRreLLDELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTV 160

                        170
                 ....*....|...
gi 823321743 152 MSRLAAARETLAK 164
Cdd:COG1595  161 KSRLSRARKKLRE 173
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 1-164 7.41e-33

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: 115.48  E-value: 7.41e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743   1 MNKDKNIANRIVDSQLAA-------HLSRLWRYGLVLSHNRDVAEELVQATCLRALEKSAQFTPGTRIDRWLFAILHSIW 73
Cdd:COG1595    1 MSSDEELLERLRAGDEAAfeelyerYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  74 ISELRARQVR--LGQGFVECEELAAPEPGEQDDTRWRYRQLMLRVNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTI 151
Cdd:COG1595   81 IDHLRKRRRRreLLDELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTV 160

                        170
                 ....*....|...
gi 823321743 152 MSRLAAARETLAK 164
Cdd:COG1595  161 KSRLSRARKKLRE 173
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 16-162 9.36e-31

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 109.88  E-value: 9.36e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  16 LAAHLSRLWRYGLVLSHNRDVAEELVQATCLRALEKSAQFTPGTRIDRWLFAILHSIWISELRARQV--RLGQGFVECEE 93
Cdd:PRK12511  10 VLDQLVPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRSGGNLRTWLMSILHNAFIDELRRRRVeaRRADELAVLAD 89

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 823321743  94 LAAPEPGEQddtRWRYRQLMLRVNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRLAAARETL 162
Cdd:PRK12511  90 ASLPAAQEH---AVRLAQIRDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAAL 155
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 16-164 5.42e-23

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: 89.33  E-value: 5.42e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743   16 LAAHLSRLWRYGLVLSHNRDVAEELVQATCLRALEKSAQFTPGTRIDRWLFAILHSIWISELRARQVRLGQGFVEcEELA 95
Cdd:TIGR02937   7 YERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDLL-EELL 85

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 823321743   96 APEPGEQDDTRWRYRQLMLR--VNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRLAAARETLAK 164
Cdd:TIGR02937  86 DSDPSPEEELEQEEEREALReaLEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRE 156
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 109-162 9.25e-11

Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif.


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 54.38  E-value: 9.25e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 823321743  109 YRQLMLRVNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRLAAARETL 162
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 117-162 3.20e-07

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: 45.17  E-value: 3.20e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 823321743 117 NQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRLAAARETL 162
Cdd:cd06171    9 DKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 1-164 7.41e-33

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: 115.48  E-value: 7.41e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743   1 MNKDKNIANRIVDSQLAA-------HLSRLWRYGLVLSHNRDVAEELVQATCLRALEKSAQFTPGTRIDRWLFAILHSIW 73
Cdd:COG1595    1 MSSDEELLERLRAGDEAAfeelyerYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  74 ISELRARQVR--LGQGFVECEELAAPEPGEQDDTRWRYRQLMLRVNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTI 151
Cdd:COG1595   81 IDHLRKRRRRreLLDELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTV 160

                        170
                 ....*....|...
gi 823321743 152 MSRLAAARETLAK 164
Cdd:COG1595  161 KSRLSRARKKLRE 173
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 16-162 9.36e-31

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 109.88  E-value: 9.36e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  16 LAAHLSRLWRYGLVLSHNRDVAEELVQATCLRALEKSAQFTPGTRIDRWLFAILHSIWISELRARQV--RLGQGFVECEE 93
Cdd:PRK12511  10 VLDQLVPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRSGGNLRTWLMSILHNAFIDELRRRRVeaRRADELAVLAD 89

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 823321743  94 LAAPEPGEQddtRWRYRQLMLRVNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRLAAARETL 162
Cdd:PRK12511  90 ASLPAAQEH---AVRLAQIRDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAAL 155
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 1-159 1.18e-25

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 96.58  E-value: 1.18e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743   1 MNKDKNIANRIVDSqlaaHLSRLWRYGLVLSHNRDVAEELVQATCLRALEKSAQFTPGTRIDRWLFAILHSIWISELRAR 80
Cdd:PRK11924   8 ATGDKEAFSELFRP----HAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCYDLLRRR 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  81 QVRLGQGFVECEE----LAAPEPGEQDDTRWRYRQLMLRVNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRLA 156
Cdd:PRK11924  84 RREKAVLSDDALEpefaETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLR 163


                 ...
gi 823321743 157 AAR 159
Cdd:PRK11924 164 RAR 166
PRK12547 PRK12547
RNA polymerase sigma factor; Provisional
 15-169 2.64e-23

RNA polymerase sigma factor; Provisional


Pssm-ID: 139056 [Multi-domain]  Cd Length: 164  Bit Score: 90.32  E-value: 2.64e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  15 QLAAHLSRLWRYGLVLSHNRDVAEELVQATCLRALEKSAQFTPGTRIDRWLFAILHSIWISELR--ARQVRLGQGfVECE 92
Cdd:PRK12547  11 ELLLALPALRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGTNLKAWLFTILRNEFYSQMRkrGREVQDSDG-VFTA 89

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 823321743  93 ELAAPEPGEQDDTRWRYRQLMlrvNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRLAAARETLAKTPAIS 169
Cdd:PRK12547  90 RVAVHPAQYGSLDLQDFKKAL---NLLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARNRLQELLKVD 163
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 16-164 5.42e-23

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: 89.33  E-value: 5.42e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743   16 LAAHLSRLWRYGLVLSHNRDVAEELVQATCLRALEKSAQFTPGTRIDRWLFAILHSIWISELRARQVRLGQGFVEcEELA 95
Cdd:TIGR02937   7 YERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDLL-EELL 85

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 823321743   96 APEPGEQDDTRWRYRQLMLR--VNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRLAAARETLAK 164
Cdd:TIGR02937  86 DSDPSPEEELEQEEEREALReaLEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRE 156
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 19-164 2.38e-22

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 88.33  E-value: 2.38e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  19 HLSRLWRYGLVLSHNRDVAEELVQATCLRALEKSAQFTPGTRIDRWLFAILHSIWISELRARQVRLGQGFVECEE----- 93
Cdd:PRK09652  19 YQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRGGAAFYTWLYRIARNTAINYLRKQGRRPPASDVDAEEaedfd 98

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 823321743  94 -----LAAPEPGEQDDTRWRYRQLMLRVNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRLAAARETLAK 164
Cdd:PRK09652  99 ladalRDISTPENELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRIFRAREALRA 174
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 15-169 1.05e-21

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 86.94  E-value: 1.05e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  15 QLAAHLSRLWRYGLVLSHNRDVAEELVQATCLRALEKSAQFTPGTRIDRWLFAILHSIWISELR--ARQVRLGQG-FVEC 91
Cdd:PRK12516  15 ELLAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVGTNMKAWLFTILRNEFYSQMRkrGREVQDTDGmFTEQ 94

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 823321743  92 EELAAPEPGEQDDTRWRYRqlmlrVNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRLAAARETLAKTPAIS 169
Cdd:PRK12516  95 LAVHPSQYGTLDLQDFRAA-----LDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQRLQEILQIE 167
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
 15-163 2.06e-21

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 86.05  E-value: 2.06e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  15 QLAAHLSRLWRYGLVLSHNRDVAEELVQATCLRALEKSAQFTPGTRIDRWLFAILHSIWISELR--ARQVRLGQGFVECE 92
Cdd:PRK12546  12 ELVEHLPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEGTNLRAWLFTILRNTFYSDRRkhKREVPDPEGVHAAS 91

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 823321743  93 ELAAPEpgeqDDTRWRYRQLMLRVNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRLAAARETLA 163
Cdd:PRK12546  92 LAVKPA----HDGRLAMSDFRAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARARLA 158
PRK12540 PRK12540
RNA polymerase sigma factor; Provisional
 15-163 2.23e-21

RNA polymerase sigma factor; Provisional


Pssm-ID: 183579 [Multi-domain]  Cd Length: 182  Bit Score: 85.79  E-value: 2.23e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  15 QLAAHLSRLWRYGLVLSHNRDVAEELVQATCLRALEKSAQFTPGTRIDRWLFAILHSIWISELRARQVRLGQGFVECEEL 94
Cdd:PRK12540  10 DILAAVPSLRAFAISLSGNGDRADDLVQETLLRALANIDSFQPGSNLPAWLFTILRNLFRSDYRKRRREVEDADGSYAKT 89

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 823321743  95 AAPEPGEqdDTRWRYRQLMLRVNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRLAAARETLA 163
Cdd:PRK12540  90 LKSQPGQ--NAHLEFEEFRAALDKLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARSKLS 156
SigH_actino TIGR02947
RNA polymerase sigma-70 factor, TIGR02947 family; This group of sigma factors are members of ...
 19-164 1.35e-20

RNA polymerase sigma-70 factor, TIGR02947 family; This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.


Pssm-ID: 131992 [Multi-domain]  Cd Length: 193  Bit Score: 84.25  E-value: 1.35e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743   19 HLSRLWRYGLVLSHNRDVAEELVQATCLRALEKSAQFTPGTRIDRWLFAILHSIWISELRARQVRLGQG---FVECEELA 95
Cdd:TIGR02947  20 YLDQLYGAALRMTRNPADAEDLVQEAYAKAFSSFHQFKPGTNLKAWLYRILTNTYINSYRKAQRRPQQSdddDIEDWQLA 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743   96 APEpgEQDDTRWRY-----------RQLMLRVNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRLAAARETLAK 164
Cdd:TIGR02947 100 KAA--SHTSNGLRSaelealdglpdQDIKDALQGLPEEFRQAVYLADVEGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRK 177
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 19-164 4.64e-17

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 74.29  E-value: 4.64e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  19 HLSRLWRYGLVLSHNRDVAEELVQATCLRALEKSAQFTPGTRIDRWLFAILHSIWISELRaRQVRlgqgfvecEELAAPE 98
Cdd:PRK09638  27 HYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGRSKFSTWLISIASRLYKDHLR-KQKR--------EKLRLQR 97

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 823321743  99 PGE--QDDTRWR-------YRQLMLRVNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRLAAARETLAK 164
Cdd:PRK09638  98 AKEetLRKEKWEaaikgaeWSEMLDALSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRK 172
SigM_subfam TIGR02950
RNA polymerase sigma factor, SigM family; This family of RNA polymerase sigma factors is a ...
 19-164 2.19e-16

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: 72.10  E-value: 2.19e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743   19 HLSRLWRYGLVLSHNRDVAEELVQATCLRALEKSAQFTpGTRIDRWLFAILHSIWISELRA---RQVRLGQGFVECEELA 95
Cdd:TIGR02950   4 YMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFK-DSSIKPWLFRIARNAFIDWYRKdkkIQTIDDDAIGDLEQHP 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 823321743   96 APEPGEQDDTRWRYRQLMLRVNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRLAAARETLAK 164
Cdd:TIGR02950  83 VESPEHHLLIKIEQEEITHHLSRLPENYRTVLILREFKEFSYKEIAELLNLSLAKVKSNLFRARKELKK 151
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
19-155 6.68e-16

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 71.26  E-value: 6.68e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  19 HLSRLWRYGLVLSHNRDVAEELVQATCLRALEKSAQFTPGTRIDR-WLFAILHSIWISELRARQVRlgQGFVECEELAAP 97
Cdd:PRK09645  18 HAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTGRSARaWLFTVARNLVIDERRSARAR--PVEGGDDVLGVP 95

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  98 EPGEQDDTRWRYRQLMLR--VNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRL 155
Cdd:PRK09645  96 EQSAPDEVDRALDRLLVAdaLAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRL 155
PRK12535 PRK12535
RNA polymerase sigma factor; Provisional
 23-162 1.80e-15

RNA polymerase sigma factor; Provisional


Pssm-ID: 237130 [Multi-domain]  Cd Length: 196  Bit Score: 70.70  E-value: 1.80e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  23 LWRyglVLSH--NRDVAEELVQATCLRALEKSAQFTPGTRIDRWLFAILHSIWISELRARQVRLGQGFVECEELAAPEPG 100
Cdd:PRK12535  38 VWR---LLAHlgGHDIADDLTQETYLRVMSALPRFAARSSARTWLLSLARRVWVDNIRHDMARPRKSATEYEDAAATTAS 114

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 823321743 101 EQDDTRW-RYRQLMLRVNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRLAAARETL 162
Cdd:PRK12535 115 NETTGSWsEWIDVRTLIDALPPERREALILTQVLGYTYEEAAKIADVRVGTIRSRVARARADL 177
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 17-177 4.05e-15

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 69.81  E-value: 4.05e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  17 AAHLSRLWRYGLVLSHNRDVAEELVQATCLRALEKSAQFTPGTrIDRWLFAILHSIWISELRARQ-VRLGQGFVECEELA 95
Cdd:PRK09647  35 RQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQPGT-FEGWLHRITTNLFLDMVRRRArIRMEALPEDYDRVP 113

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  96 APEPGEQD---DTRWRyRQLMLRVNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRLAAARETLAKTPAISPPA 172
Cdd:PRK09647 114 GDEPNPEQiyhDARLD-PDLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAALAAHAPH 192


                 ....*
gi 823321743 173 QEKRS 177
Cdd:PRK09647 193 AECAA 197
PRK09643 PRK09643
RNA polymerase sigma factor SigM; Reviewed
 19-163 8.54e-15

RNA polymerase sigma factor SigM; Reviewed


Pssm-ID: 236604 [Multi-domain]  Cd Length: 192  Bit Score: 68.58  E-value: 8.54e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  19 HLSRLWRYGLVLSHNRDVAEELVQATCLRALEKSAQFTPGTRIDRWLFAILHSIWISELRARQVRLGQGFVECEELA--A 96
Cdd:PRK09643  36 HHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGDAAVSSWLHRIVVNACLDRLRRAKARPTVPLDDVYPVAqlE 115

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 823321743  97 PEPGEQDDTRwryRQLMLRVNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRLAAARETLA 163
Cdd:PRK09643 116 RDPTARVETA---LAVQRALMRLPVEQRAALVAVDMQGYSVADAARMLGVAEGTVKSRCARGRARLA 179
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 16-162 6.53e-14

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 66.25  E-value: 6.53e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  16 LAAHLSRLWRYGLVLSHNRDVAEELVQATCLRALEKSAQFTPGTRIDRWLFAILHSIWISELR-ARQVRLGQGFVECEEL 94
Cdd:PRK12513  32 YARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPRARFRTWLYQIARNLLIDHWRrHGARQAPSLDADEQLH 111

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 823321743  95 AAPEPGEQDDTRWRYRQLMLR----VNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRLAAARETL 162
Cdd:PRK12513 112 ALADDGAAPEQQLSLFRDRRRlqaaLETLPDEQREVFLLREHGDLELEEIAELTGVPEETVKSRLRYALQKL 183
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 33-164 1.65e-12

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 62.41  E-value: 1.65e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  33 NRDVAEELVQATCLRALEKSAQFTPGTRIDRWLFAILHSIWISELRAR--------QVRLGQGFVECEELAA--PEPGEQ 102
Cdd:PRK09641  41 NRHEAEDAAQEAFIRAYVNIDSYDINRKFSTWLYRIATNLTIDRLRKRkpdyyldaEVAGTEGLTMYSQLAAddALPEEQ 120

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 823321743 103 DDTRWRYRQLMLRVNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRLAAARETLAK 164
Cdd:PRK09641 121 VVSLELQETIQEAILQLPEKYRTVIVLKYIEDLSLKEISEILDLPVGTVKTRIHRGREALRK 182
PRK12533 PRK12533
RNA polymerase sigma factor; Provisional
 30-163 3.46e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 237129 [Multi-domain]  Cd Length: 216  Bit Score: 62.05  E-value: 3.46e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  30 LSHNRDVAEELVQATCLRALeksaQFTPGTRIDR---WLFAILHSIWISELRARQVRLGQGFVECEELAAPEPGEQDDTR 106
Cdd:PRK12533  38 LCGNASDADDVVQEACMRAL----RFFDSFRGDNarpWLLAIVRHTWYSEWRRRANAHEVAAPDTLDDADSLDDWQPAGE 113

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 823321743 107 WRYRQLML-----RVN----QLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRLAAARETLA 163
Cdd:PRK12533 114 DPLALLLRaedvrLVNaalaKLPVEYREVLVLRELEDMSYREIAAIADVPVGTVMSRLARARRRLA 179
PRK12517 PRK12517
RNA polymerase sigma factor; Provisional
 2-162 1.21e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 183569 [Multi-domain]  Cd Length: 188  Bit Score: 60.09  E-value: 1.21e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743   2 NKDKNIANRIVDSQLAAHLSRLWRYGLVLSHNRDVAEELVQATCLRAL--------EKSAQftpgtridRWLFAILHsiw 73
Cdd:PRK12517  15 SSDMLSKQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWrsldslkdEKAAK--------AWLITILR--- 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  74 isELRARQVRLGQ-GFVECEEL-----AAPEPGEQDDTRWRYRQLMlrvnQLPEAQRNAVFLVYVEGFSYQEAAETLSVP 147
Cdd:PRK12517  84 --RENARRFERKQfDLVDIEDDsieddASHSSEEEMEQEWLRRQIA----KLDPEYREPLLLQVIGGFSGEEIAEILDLN 157

                        170
                 ....*....|....*
gi 823321743 148 IGTIMSRLAAARETL 162
Cdd:PRK12517 158 KNTVMTRLFRARNQL 172
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 22-164 1.28e-11

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: 59.50  E-value: 1.28e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743   22 RLWRYGLVLSHNRDVAEELVQATCLRALEKSAQFTPGTRIDRWLFAILHSIWISELRARQVRlgqgFVECEELAAPEPGE 101
Cdd:TIGR02985  13 KLCAFARRYVKDEEDAEDIVQDVFLKLWENRETLEISESIKAYLFTIVKNRCLNYLRHKQVE----EKYQEELAEIEERE 88

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 823321743  102 QDDT--------RWRYRQLMLRVNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRLAAARETLAK 164
Cdd:TIGR02985  89 LSEAdpeeeleaKELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLRK 159
PRK09649 PRK09649
RNA polymerase sigma factor SigC; Reviewed
 10-162 1.62e-11

RNA polymerase sigma factor SigC; Reviewed


Pssm-ID: 137458 [Multi-domain]  Cd Length: 185  Bit Score: 59.67  E-value: 1.62e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  10 RIVDSQLAAHLSRLWRYGLVLShNRDVAEELVQATCLRALEKSAQFTPGTRIDRWLFAILHSIWISELRARQVRLGQGFV 89
Cdd:PRK09649  24 RALEAFIKATQQDVWRFVAYLS-DVGSADDLTQETFLRAIGAIPRFSARSSARTWLLAIARHVVADHIRHVRSRPRTTRG 102

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 823321743  90 eceelAAPEPGEQDDTRWRYRQLMLRVN----QLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRLAAARETL 162
Cdd:PRK09649 103 -----ARPEHLIDGDRHARGFEDLVEVTtmiaDLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARARDAL 174
PRK09191 PRK09191
two-component response regulator; Provisional
 15-163 7.05e-11

two-component response regulator; Provisional


Pssm-ID: 236402 [Multi-domain]  Cd Length: 261  Bit Score: 59.09  E-value: 7.05e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  15 QLAAHLSRLWRYGLVLSHNRDVAEELVQATcLRALEKSAQFTPGTRIDRW-LFAILHSIWiselrarqvrlgqgfvecEE 93
Cdd:PRK09191   6 RIAPHLPYLRRYARALTGSQSSGDAYVAAT-LEALLADPSIFPEASSPRVgLYRLFHRLW------------------SS 66

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  94 LAAPEPGEQDDTRWRYRQlmlRVNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRLAAARETLA 163
Cdd:PRK09191  67 AGANDPEPGSPFEARAER---RLAGLTPLPRQAFLLTALEGFSVEEAAEILGVDPAEAEALLDDARAEIA 133
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 109-162 9.25e-11

Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif.


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 54.38  E-value: 9.25e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 823321743  109 YRQLMLRVNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRLAAARETL 162
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 17-163 2.40e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 56.66  E-value: 2.40e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  17 AAHLSRLWRYGLVLSHNRDVAEELVQATCLRALEKSAQFTPGTRIDRWLFAILHSIWISELRARQvrlgqgFVECEELAA 96
Cdd:PRK12515  29 GRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGRSQVSTWLLSIARFKALSALRRRK------HEEIDDEAA 102

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 823321743  97 PEPGEQDDT------RWRYRQLMLR-VNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRLAAARETLA 163
Cdd:PRK12515 103 AAIEDGADTpevalqKSDTSAALRAcLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKTRMFYARKKLA 176
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 16-176 3.58e-10

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 56.20  E-value: 3.58e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  16 LAAHLSRLWRYGLVLSHNRDVAEELVQATCLRALEKSAQFTPG-TRIDRWLFAILHSIWISELRARQvrlgqgFVECEEL 94
Cdd:PRK05602  26 VARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPGeARFDTWLHRVVLNLCYDRLRRRR------EVPVEDA 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  95 A-----APEPGEQDDTRWRYRQLMLRVNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRLAAARETLAKTPAIS 169
Cdd:PRK05602 100 PdvpdpAPGPDAGLEARQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALESLLARGRRALRAQLADL 179


                 ....*..
gi 823321743 170 PPAQEKR 176
Cdd:PRK05602 180 PGSEDDR 186
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 19-164 1.39e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 54.17  E-value: 1.39e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  19 HLSRLWRYGLVLSHNRDVAEELVQATCLRALeKSAQFTPGTRIDRWLFAILHSIWISELRARQVRLGQGFVECEELAAPE 98
Cdd:PRK12541  14 HMQDLFRYLLSLTGDSHFAEDLMQETFYRML-VHIDYYKGEEIRPWLFTIAYNAFIDWYRKEKKYKTTTIEEFHLPNVPS 92

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 823321743  99 PGEQDDTRWRYRQLMLRVNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRLAAARETLAK 164
Cdd:PRK12541  93 TEHEYFIKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKETKS 158
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 23-162 2.44e-09

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 53.73  E-value: 2.44e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  23 LWRYGLVLSHNRDVAEELVQATCLRALEKSAQFTpGTRIDRWLFAILHSIWISELRA--RQVRLGQGFVECEELAAPE-P 99
Cdd:PRK09644  14 VYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYD-NQKVKPWLFKVAYHTFIDFVRKekKVSFVGTDEIEAIQAESTEeY 92

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 823321743 100 GEQDDTrwrYRQLMLRVNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRLAAARETL 162
Cdd:PRK09644  93 VVAKNS---YEKLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRL 152
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 37-164 2.73e-09

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 53.76  E-value: 2.73e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  37 AEELVQATCLRALEKSAQFTPGTRIDR-WLFAILHSIWISELRARQVR---LGQGFVECEELAAPEPGEQDDTRWRYRQL 112
Cdd:PRK13919  50 AEDVVQEVFIRVWKKAKEFDPRRGSARaWLLALAHHAAVDHVRRRAARpqpLEPDEREPEAFDLPGPGLDEEGHLDRTRL 129

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 823321743 113 MLRVNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRlaaARETLAK 164
Cdd:PRK13919 130 GRALKALSPEERRVIEVLYYQGYTHREAAQLLGLPLGTLKTR---ARRALSR 178
PRK12531 PRK12531
RNA polymerase sigma factor; Provisional
 33-162 2.92e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 105726 [Multi-domain]  Cd Length: 194  Bit Score: 53.78  E-value: 2.92e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  33 NRDVAEELVQATCLRALEKSAQFTpGTR--IDRWLFAILHSIWISELR---ARQVRLGQGFVECEELAAPE-----PGEQ 102
Cdd:PRK12531  50 NEQVAMEMVQETMSTVWQKAHLFD-GQKsaLSTWIYTIIRNLCFDLLRkqkGKDLHIHADDIWPSDYYPPDlvdhySPEQ 128

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743 103 DDTRwryRQLMLRVNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRLAAARETL 162
Cdd:PRK12531 129 DMLK---EQVMKFLDRLPKAQRDVLQAVYLEELPHQQVAEMFDIPLGTVKSRLRLAVEKL 185
PRK12526 PRK12526
RNA polymerase sigma factor; Provisional
 25-164 1.04e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 237127 [Multi-domain]  Cd Length: 206  Bit Score: 52.50  E-value: 1.04e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  25 RYGLVLSHNRDVAEELVQATCLRALEKSAQFTPGT-RIDRWLFAILHSIWISELRARQVR----LGQGFVECEELAAPEP 99
Cdd:PRK12526  53 RFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKgAATTWVYTVMRNAAFDMLRKIKAKkeqnLGDDIWPIEQALAESQ 132

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 823321743 100 GEQD--DTRWRYRQLMLRVNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRLaaaRETLAK 164
Cdd:PRK12526 133 SESEefSDHLMDKQILSYIEKLPEAQQTVVKGVYFQELSQEQLAQQLNVPLGTVKSRL---RLALAK 196
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 15-164 1.56e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 51.60  E-value: 1.56e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  15 QLAAhLSRLWR------YGL---VLSHNRDvAEELVQATCLRaLEKSAQFTPGTR-IDRWLFAILHSIWISELRAR--QV 82
Cdd:PRK12519  27 QSAA-LGVLYDrhaglvYGLalkILGNSQE-AEDLTQEIFLS-LWRKSSYDPKRGsLSSYLLTLTRSRAIDRLRSRrsRQ 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  83 RLGQ--GFVECEELAAPEPGEQDDTRWRYRQLMLRVNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRlaaARE 160
Cdd:PRK12519 104 RLLErwQQELLGEASEDTPLEQASLAERSQRVQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKAR---ARQ 180


                 ....
gi 823321743 161 TLAK 164
Cdd:PRK12519 181 GLLK 184
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 21-162 2.93e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 50.93  E-value: 2.93e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  21 SRLWRYGLVLSHNRDVAEELVQATCLRALEKSAQFTPGTRIDR-WLFAILHSIWISELR--ARQVRLGQgfvECEELAAP 97
Cdd:PRK12537  34 ARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPARGSARgWIYSVTRHLALNVLRdtRREVVLDD---DAEETAQT 110

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 823321743  98 EPGEQDDTRWRYR--QLMLRVNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGT----IMSRLAAARETL 162
Cdd:PRK12537 111 LHEIIDDFDLWANsgKIHRCLEQLEPARRNCILHAYVDGCSHAEIAQRLGAPLGTvkawIKRSLKALRECM 181
PRK09646 PRK09646
ECF RNA polymerase sigma factor SigK;
26-155 3.15e-08

ECF RNA polymerase sigma factor SigK;


Pssm-ID: 182015 [Multi-domain]  Cd Length: 194  Bit Score: 50.82  E-value: 3.15e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  26 YGLVLSHNRDVA--EELVQATCLRALEKSAQFTP--GTRIDrWLFAILHSIWISELRA------RQVRLGQGFVECEELA 95
Cdd:PRK09646  44 YGLVRRVLRDPGysEETTQEVYLEVWRTASRFDParGSALA-WLLTLAHRRAVDRVRSeqaasqREVRYGARNVDPAFDQ 122

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  96 APEPGEQDDTRWRYRQLMlrvNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRL 155
Cdd:PRK09646 123 VAEEVEARLERERVRDCL---DALTDTQRESVTLAYYGGLTYREVAERLAVPLGTVKTRM 179
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 25-164 3.15e-08

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 50.90  E-value: 3.15e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  25 RYG-----LVLS--HNRDVAEELVQATCLRALEKSAQFTPGTRIDRWLFAI--------LHSIWISELRARQVRLGQGFV 89
Cdd:PRK09415  24 EYGqevlqLVYSyvKNKEVAEDLTQEIFVKCYKSLHTYKGKSSLKTWLYRIainhckdyLKSWHNKKVIVTEDIFTYMES 103

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 823321743  90 EcEELAAPEPGEQDDTRwryrQLMLRVNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRLAAARETLAK 164
Cdd:PRK09415 104 Q-KESVEEEVIQNAEDE----RLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKELLKK 173
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 33-163 1.34e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 49.12  E-value: 1.34e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  33 NRDVAEELVQATCLRALEKSAQFTPG-TRIDRWLFAILHSIWISELRaRQVRLGQGFVECEELAAPEPG--EQDDTRWRY 109
Cdd:PRK12524  49 DRAEAEDVTQEAMLRLWRIAPDWRQGeARVSTWLYRVVCNLCTDRLR-RRRRASVDLDDAPEPADAAPGaeEALIEGDRM 127

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 823321743 110 RQLMLRVNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRLAAARETLA 163
Cdd:PRK12524 128 RALDAALAALPERQRQAVVLRHIEGLSNPEIAEVMEIGVEAVESLTARGKRALA 181
algU PRK11923
RNA polymerase sigma factor AlgU; Provisional
 116-174 2.47e-07

RNA polymerase sigma factor AlgU; Provisional


Pssm-ID: 171347 [Multi-domain]  Cd Length: 193  Bit Score: 48.26  E-value: 2.47e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 823321743 116 VNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRLAAARETLAKtpAISPPAQE 174
Cdd:PRK11923 136 IQQLPEDLRTALTLREFDGLSYEDIASVMQCPVGTVRSRIFRAREAIDK--ALQPLLQE 192
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 117-162 3.20e-07

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: 45.17  E-value: 3.20e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 823321743 117 NQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRLAAARETL 162
Cdd:cd06171    9 DKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 33-162 4.23e-07

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 47.67  E-value: 4.23e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  33 NRDVAEELVQATCLRALEKSAQFTPGTRIDRWLFAILHSIWISELRARQvrlGQGFVECEELAAPEPGEQDDTRWRYRQL 112
Cdd:PRK09637  24 NEADVDDLLQEVLIKTHSNLHSLKDGSSIKSWLYQIANNTIIDFYRKKN---RSEELPDDLLFEDEEREENAKKELAPCL 100

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 823321743 113 MLRVNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRLAAARETL 162
Cdd:PRK09637 101 RPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRVKL 150
PRK12534 PRK12534
RNA polymerase sigma factor; Provisional
 22-167 1.80e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183576 [Multi-domain]  Cd Length: 187  Bit Score: 45.82  E-value: 1.80e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  22 RLWRYGLVLSHNRDVAEELVQATCLRALEKSAQFTPG-TRIDRWLFAILHSIWISELRARQ-VRLGQGFVECEELAAPEP 99
Cdd:PRK12534  37 KLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSrARGLTWLAMIARNKAIDHLRANApQRRNVALDDAGELRAADA 116

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743 100 GEQDDTRWRY--RQLMLRVNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRLaaaRETLAKTPA 167
Cdd:PRK12534 117 SPLERTERAStrRRIDHCLAELEPPRSELIRTAFFEGITYEELAARTDTPIGTVKSWI---RRGLAKLKA 183
PRK12512 PRK12512
RNA polymerase sigma factor; Provisional
 14-164 2.10e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 171551 [Multi-domain]  Cd Length: 184  Bit Score: 45.84  E-value: 2.10e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  14 SQLAAHLSRLWRYGLV-LSHNRDVAEELVQATCLRALEKSAQFTPGTRIDRWLFAILHSIWISELRARQVRLgqgFVECE 92
Cdd:PRK12512  29 KAVTPVLRAAARRGLArAGQPADQAEDIVQEILLAVHLKRHTWDPGAPFAPWLFAIARNKLIDALRRRGRRV---FVDID 105

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 823321743  93 E----LAAPEPGEQDDTRWRYRQLmlrvNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRLAAARETLAK 164
Cdd:PRK12512 106 DfaetLPAEPATETLPAGDVGRHL----ETLPPRQRDVVQSISVEGASIKETAAKLSMSEGAVRVALHRGLAALAA 177
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 18-164 2.10e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 46.11  E-value: 2.10e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  18 AHLSRLWRYGLVLSHNRDVAEELVQATCLRALEKSAQFTPGTRIDRWLFAILHSIWISELRARQVRLG----------QG 87
Cdd:PRK11922  38 RHNRRLYRTARAILRNDAEAEDVVQEAYLRAFRALGTFRGDASLSTWLSRIVLNEALGRLRRRRRLVNlaemvmastiAG 117

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  88 FVECEELAAPEPGEQDDTRWRYRQLMLR-VNQLPEAQRnAVF-LVYVEGFSYQEAAETLSVPIGTIMSRLAAAR----ET 161
Cdd:PRK11922 118 GERTPLADPAEDPERAAARREIRALLERaIDALPDAFR-AVFvLRVVEELSVEETAQALGLPEETVKTRLHRARrllrES 196


                 ...
gi 823321743 162 LAK 164
Cdd:PRK11922 197 LAR 199
PRK12522 PRK12522
RNA polymerase sigma factor; Provisional
 116-162 6.44e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183571 [Multi-domain]  Cd Length: 173  Bit Score: 44.09  E-value: 6.44e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 823321743 116 VNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRLAAARETL 162
Cdd:PRK12522 117 IQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQM 163
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 34-164 1.80e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 43.17  E-value: 1.80e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  34 RDVAEELVQATCLRA------LEKSAQFTPgtridrWLFAILHSIWISELR--ARQVRLGQGFVECEELAAPEpGEQDDT 105
Cdd:PRK12518  34 RELLDDLVQEVFLRVwkglpkLRNPAYFST------WLYRITWNVATDARRqfAQRPSRIQDDSLNDQPSRPS-DTPDLM 106

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743 106 RWRYRQLMLR-VNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRLAAARETLAK 164
Cdd:PRK12518 107 QLHYQDLVQQgLQTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRLFYARRQLRK 166
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 18-81 2.05e-05

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: 40.65  E-value: 2.05e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 823321743   18 AHLSRLWRYGLVLSHNRDVAEELVQATCLRALEKSAQFTP--GTRIDRWLFAILHSIWISELRARQ 81
Cdd:pfam04542   4 RYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPerGVSFSTWLYTIIRNAIIDYLRKQR 69
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 116-174 3.47e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 42.41  E-value: 3.47e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 823321743 116 VNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRLAAARETLAKTPAISPPAQE 174
Cdd:PRK12543 115 IHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQIEEIFLG 173
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 33-146 4.42e-05

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 41.68  E-value: 4.42e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  33 NRDVAEELVQATCLRALEKSAQftpgTRIDR---WLFAILHSIWISELRARQVRLGQGF---VECEELAAPEPGEQDDTR 106
Cdd:PRK12527  18 NRQAAEDVAHDAYLRVLERSSS----AQIEHpraFLYRTALNLVVDRHRRHRVRQAEPLevlDEEERLHSPSPQTRLDLG 93

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 823321743 107 WRYRQLMLRVNQLPEAQRNAVFLVYVEGFSYQEAAETLSV 146
Cdd:PRK12527  94 QRLALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGI 133
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 33-155 1.56e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 40.19  E-value: 1.56e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  33 NRDVAEELVQATCLRALEKSAQF-TPGTRIDRWLFAILHSIWISELRARQvRLGQGFVECEELAAPEPGEQD-----DTR 106
Cdd:PRK12514  42 DRSEAEEALQDVYVKIWTKADRFaVSGLSPMTWLITIARNHAIDRLRARK-AVAVDIDEAHDLADPSPGPEAeviagDEG 120

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 823321743 107 WRYRQLMlrvNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRL 155
Cdd:PRK12514 121 QRIDACL---EELEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMRTWL 166
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
 19-162 2.04e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 40.61  E-value: 2.04e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  19 HLSRLWRYGLVLSHNRDVAEELVQATCLRALEKSAQFTPG-TRIDRWLFAILHSIWIsELRaRQVRlgqgfVECEElAAP 97
Cdd:PRK12538  72 HIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGrAKFSTWLYRVVSNRCI-DLR-RKPR-----TENVD-AVP 143

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 823321743  98 EP--GEQDDTRWRYRQ-----LMLRVNQLPEAQRNAVFLVYVEGFSYQEAAETLSVPIGTIMSRLAAARETL 162
Cdd:PRK12538 144 EVadGKPDAVSVIERNelsdlLEAAMQRLPEQQRIAVILSYHENMSNGEIAEVMDTTVAAVESLLKRGRQQL 215
PRK12520 PRK12520
RNA polymerase sigma factor; Provisional
 11-104 2.18e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 237126 [Multi-domain]  Cd Length: 191  Bit Score: 40.10  E-value: 2.18e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  11 IVDSQLAAHLSRLWRYGLVLSHNRDVAEELVQATCLRALEKSAQFTPGTRIDRWLFAILHSIWISELR--ARQVRLgqgf 88
Cdd:PRK12520   3 IAPAQLEALRPHLLRFARLQLRDPALAEDAVSETLLAVLEHPERFAGQSSLKTYLVGILKHKIIDAIRsgRREVRL---- 78

                         90
                 ....*....|....*.
gi 823321743  89 veceELAAPEPGEQDD 104
Cdd:PRK12520  79 ----SLDDADEQSDDD 90
PRK12539 PRK12539
RNA polymerase sigma factor SigF;
7-141 2.75e-04

RNA polymerase sigma factor SigF;


Pssm-ID: 237132 [Multi-domain]  Cd Length: 184  Bit Score: 39.71  E-value: 2.75e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743   7 IANRIVDSQLAAHL-----SRLWRYGlvlsHNRDVAEELVQATCLRALEKSAQFTPGTRIDRWLFAILHSIWISELRA-- 79
Cdd:PRK12539  21 AAHRALLERLSGHLrayykGKLARIG----RGAEEAEDLVQEALMAIHTRRHTYDPEQPLTPWVYAIARYKLIDHLRRtr 96

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 823321743  80 ---RQVRLGqgfvECEELAAPEPGEQDDTRWRYRQLMLRvnqLPEAQRNAVFLVYVEGFSYQEAA 141
Cdd:PRK12539  97 aslADVPID----DADELVAHDDHAAVESTLDLGRLLAR---LPEKMRLAIQAVKLEGLSVAEAA 154
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 33-164 9.99e-04

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 38.01  E-value: 9.99e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  33 NRDVAEELVQATCLRALEksAQFTPGTRIDRWLF--AILHSI-WISELRARQVRLGQGFVECEELAAPEPgEQDDTRWRY 109
Cdd:PRK09639  26 DRTQAEDLAQEVFLRLYR--SDFKGIENEKGWLIksARNVAYnYLRSEKRRRARILGEFQWQEVDNEPSP-EEIWIRKEE 102

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 823321743 110 RQLMLRV-NQLPEAQRnAVFLVYVEGFSYQEAAETLSVPIGTIMSRLAAARETLAK 164
Cdd:PRK09639 103 ITKVQEVlAKMTERDR-TVLLLRFSGYSYKEIAEALGIKESSVGTTLARAKKKFRK 157
PRK12536 PRK12536
RNA polymerase sigma factor; Provisional
 14-141 1.70e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237131 [Multi-domain]  Cd Length: 181  Bit Score: 37.34  E-value: 1.70e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 823321743  14 SQLAAHLSRLWRYGLvlSHNRDVAEELVQATCLRALEKSAQFTPGTRIDRWLFAILHSIWISELRARQVR--LGQGFVEC 91
Cdd:PRK12536  28 SELAAHLRGFLRRRL--PQLPDEVEDLVQEILLAVHNARHTYRADQPLTAWVHAIARYKLMDFLRSRARReaLHDPLDDE 105

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 823321743  92 EELAAPEPGEQDDTRwryRQLMLRVNQLPEAQRNAVFLVYVEGFSYQEAA 141
Cdd:PRK12536 106 SELFATSDDEAAEAR---RDLGKLLEQLPDRQRLPIVHVKLEGLSVAETA 152
PRK12532 PRK12532
RNA polymerase sigma factor; Provisional
 13-80 6.54e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 171564 [Multi-domain]  Cd Length: 195  Bit Score: 35.68  E-value: 6.54e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 823321743  13 DSQLAAHLSRLWRYG-LVLSHNRDVAEELVQATCLRALEKSAQFTPGTRIDRWLFAILHSIWISELRAR 80
Cdd:PRK12532   8 DAELIESRKLLLHFArLQLPDHPDLAEDLVQETLLSAYSAGDSFQGRALVNSWLFAILKNKIIDALRQI 76
 
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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