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Conserved domains on  [gi|1525942823|ref|WP_124562585|]
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MULTISPECIES: RNA polymerase sigma factor [unclassified Pedobacter]

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]; ...
 5-166 5.43e-47

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: 151.30  E-value: 5.43e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823   5 EFNHLVNHHSVSLRSYALNFTKDAEDANDLVQDTMLKAITYYNKFKEGTNLKGWLFTIMKNTFINNYRRLVKTNTLItqS 84
Cdd:COG1595    18 AFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRRELL--D 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  85 EDISSANLSYSATKNQAESKFVLGDIDKALAQLPEEYYVPFI-RYFEGYKYHEIADMLEIPIGTVKTRIHVARGILKKYL 163
Cdd:COG1595    96 ELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVlRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREAL 175


                  ...
gi 1525942823 164 KTY 166
Cdd:COG1595   176 EEE 178
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 5-166 5.43e-47

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: 151.30  E-value: 5.43e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823   5 EFNHLVNHHSVSLRSYALNFTKDAEDANDLVQDTMLKAITYYNKFKEGTNLKGWLFTIMKNTFINNYRRLVKTNTLItqS 84
Cdd:COG1595    18 AFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRRELL--D 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  85 EDISSANLSYSATKNQAESKFVLGDIDKALAQLPEEYYVPFI-RYFEGYKYHEIADMLEIPIGTVKTRIHVARGILKKYL 163
Cdd:COG1595    96 ELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVlRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREAL 175


                  ...
gi 1525942823 164 KTY 166
Cdd:COG1595   176 EEE 178
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 6-169 3.89e-42

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 139.17  E-value: 3.89e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823   6 FNHLVNHHSVSLRSYALNFTKDAEDANDLVQDTMLKAITYYNKFKEGTNLKGWLFTIMKNTFINNYRRL------VKTNT 79
Cdd:PRK09652   12 FALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRGGAAFYTWLYRIARNTAINYLRKQgrrppaSDVDA 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  80 LITQSEDISSANLSYSATKNQAESKFVLGDIDKALAQLPEEYYVPFI-RYFEGYKYHEIADMLEIPIGTVKTRIHVARGI 158
Cdd:PRK09652   92 EEAEDFDLADALRDISTPENELLSAELEQRVRAAIESLPEELRTAITlREIEGLSYEEIAEIMGCPIGTVRSRIFRAREA 171

                         170
                  ....*....|.
gi 1525942823 159 LKKYLKTYSKE 169
Cdd:PRK09652  172 LRAKLQPLLDE 182
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 5-163 6.98e-36

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: 122.46  E-value: 6.98e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823   5 EFNHLVNHHSVSLRSYALNFTKDAEDANDLVQDTMLKAITYYNKFKEGTNLKGWLFTIMKNTFINNYRRlvkTNTLITQS 84
Cdd:TIGR02937   2 AFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRR---KRRLRREL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  85 EDISSANLSYSATKNQAESKFVLGDIDKALAQLPEEYYVPFI-RYFEGYKYHEIADMLEIPIGTVKTRIHVARGILKKYL 163
Cdd:TIGR02937  79 DLLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVlRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 9-77 4.98e-14

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: 63.38  E-value: 4.98e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1525942823   9 LVNHHSVSLRSYALNFTKDAEDANDLVQDTMLKAITYYNKFKE--GTNLKGWLFTIMKNTFINNYRRLVKT 77
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPerGVSFSTWLYTIIRNAIIDYLRKQRRT 71
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 109-160 4.32e-09

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: 50.18  E-value: 4.32e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1525942823 109 DIDKALAQLPEEYYVPFI-RYFEGYKYHEIADMLEIPIGTVKTRIHVARGILK 160
Cdd:cd06171     3 RLEEALDKLPEREREVILlRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 5-166 5.43e-47

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: 151.30  E-value: 5.43e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823   5 EFNHLVNHHSVSLRSYALNFTKDAEDANDLVQDTMLKAITYYNKFKEGTNLKGWLFTIMKNTFINNYRRLVKTNTLItqS 84
Cdd:COG1595    18 AFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRRELL--D 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  85 EDISSANLSYSATKNQAESKFVLGDIDKALAQLPEEYYVPFI-RYFEGYKYHEIADMLEIPIGTVKTRIHVARGILKKYL 163
Cdd:COG1595    96 ELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVlRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREAL 175


                  ...
gi 1525942823 164 KTY 166
Cdd:COG1595   176 EEE 178
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 6-169 3.89e-42

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 139.17  E-value: 3.89e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823   6 FNHLVNHHSVSLRSYALNFTKDAEDANDLVQDTMLKAITYYNKFKEGTNLKGWLFTIMKNTFINNYRRL------VKTNT 79
Cdd:PRK09652   12 FALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRGGAAFYTWLYRIARNTAINYLRKQgrrppaSDVDA 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  80 LITQSEDISSANLSYSATKNQAESKFVLGDIDKALAQLPEEYYVPFI-RYFEGYKYHEIADMLEIPIGTVKTRIHVARGI 158
Cdd:PRK09652   92 EEAEDFDLADALRDISTPENELLSAELEQRVRAAIESLPEELRTAITlREIEGLSYEEIAEIMGCPIGTVRSRIFRAREA 171

                         170
                  ....*....|.
gi 1525942823 159 LKKYLKTYSKE 169
Cdd:PRK09652  172 LRAKLQPLLDE 182
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 5-161 4.52e-37

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 125.85  E-value: 4.52e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823   5 EFNHLVNHHSVSLRSYALNFTKDAEDANDLVQDTMLKAITYYNKFKEGTNLKGWLFTIMKNTFINNYRRLVKTNTLITQS 84
Cdd:PRK11924   14 AFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCYDLLRRRRREKAVLSDD 93

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1525942823  85 EDISSANLSYSATKNQAESKFVLGDIDKALAQLPEEYYVPFI-RYFEGYKYHEIADMLEIPIGTVKTRIHVARGILKK 161
Cdd:PRK11924   94 ALEPEFAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLlRYVEGLSYREIAEILGVPVGTVKSRLRRARQLLRE 171
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 5-163 6.98e-36

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: 122.46  E-value: 6.98e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823   5 EFNHLVNHHSVSLRSYALNFTKDAEDANDLVQDTMLKAITYYNKFKEGTNLKGWLFTIMKNTFINNYRRlvkTNTLITQS 84
Cdd:TIGR02937   2 AFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRR---KRRLRREL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  85 EDISSANLSYSATKNQAESKFVLGDIDKALAQLPEEYYVPFI-RYFEGYKYHEIADMLEIPIGTVKTRIHVARGILKKYL 163
Cdd:TIGR02937  79 DLLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVlRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
SigH_actino TIGR02947
RNA polymerase sigma-70 factor, TIGR02947 family; This group of sigma factors are members of ...
 17-169 2.53e-33

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: 117.00  E-value: 2.53e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  17 LRSYALNFTKDAEDANDLVQDTMLKAITYYNKFKEGTNLKGWLFTIMKNTFINNYRRlVKTNTLITQSEDISSANLSYSA 96
Cdd:TIGR02947  24 LYGAALRMTRNPADAEDLVQEAYAKAFSSFHQFKPGTNLKAWLYRILTNTYINSYRK-AQRRPQQSDDDDIEDWQLAKAA 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  97 TKN-----QAESKFVLG----DIDKALAQLPEEY-YVPFIRYFEGYKYHEIADMLEIPIGTVKTRIHVARGILKKYLKTY 166
Cdd:TIGR02947 103 SHTsnglrSAELEALDGlpdqDIKDALQGLPEEFrQAVYLADVEGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLVDV 182


                  ...
gi 1525942823 167 SKE 169
Cdd:TIGR02947 183 AGE 185
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
 9-163 7.64e-31

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 110.31  E-value: 7.64e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823   9 LVNHHSvSLRSYALNFTKDAEDANDLVQDTMLKAITYYNKFKEGTNLKGWLFTIMKNTFINNYRRLVKtntlitQSEDIS 88
Cdd:PRK12546   13 LVEHLP-ALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEGTNLRAWLFTILRNTFYSDRRKHKR------EVPDPE 85

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1525942823  89 SANLSYSATKNQAESKFVLGDIDKALAQLPEEYYVPFIRY-FEGYKYHEIADMLEIPIGTVKTRIHVARGILKKYL 163
Cdd:PRK12546   86 GVHAASLAVKPAHDGRLAMSDFRAAFAQLPDEQREALILVgASGFSYEEAAEMCGVAVGTVKSRANRARARLAELL 161
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 6-163 3.27e-29

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: 105.34  E-value: 3.27e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823   6 FNHLVNHHSVSLRSYALNFTKDAEDANDLVQDTMLKAITYYNKFKEGTNLKGWLFTIMKNTFINNYRRLVKTNTLITQSE 85
Cdd:TIGR02985   3 FEQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETLEISESIKAYLFTIVKNRCLNYLRHKQVEEKYQEELA 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1525942823  86 DISSANLSYSATKNQAESKFVLGDIDKALAQLPEEYYVPFIR-YFEGYKYHEIADMLEIPIGTVKTRIHVARGILKKYL 163
Cdd:TIGR02985  83 EIEERELSEADPEEELEAKELEEIIEEAIEKLPEQCREIFILsRFEGLSNKEIAEELGISVKTVEYHITKALKFLRKEL 161
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 6-164 2.46e-27

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 100.86  E-value: 2.46e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823   6 FNHLVNHHSVSLRSYALNFTKDAEDANDLVQDTMLKAITYYNKFKEGTNLKGWLFTIMKNTFINNYRRLVKTNTLITQSE 85
Cdd:PRK09638   20 LTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGRSKFSTWLISIASRLYKDHLRKQKREKLRLQRAK 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  86 DISSANLSYSATKNQAESKfvlgDIDKALAQLPEEYYVPFI-RYFEGYKYHEIADMLEIPIGTVKTRIHVARGILKKYLK 164
Cdd:PRK09638  100 EETLRKEKWEAAIKGAEWS----EMLDALSKLDPEFRAPVIlKHYYGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRKEWG 175
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 15-162 2.97e-27

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 101.02  E-value: 2.97e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  15 VSLRSYALNFTKDAEDANDLVQDTMLKAITYYNKFKEGTNLKGWLFTIMKNTFINNYRRLVKTNTLITQSEDISSAnlsy 94
Cdd:PRK12511   15 VPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRSGGNLRTWLMSILHNAFIDELRRRRVEARRADELAVLADA---- 90

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1525942823  95 sATKNQAESKFVLGDIDKALAQLPEEYYVPF-IRYFEGYKYHEIADMLEIPIGTVKTRIHVARGILKKY 162
Cdd:PRK12511   91 -SLPAAQEHAVRLAQIRDAFFDLPEEQRAALhLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAALRAF 158
PRK12547 PRK12547
RNA polymerase sigma factor; Provisional
 16-164 3.32e-26

RNA polymerase sigma factor; Provisional


Pssm-ID: 139056 [Multi-domain]  Cd Length: 164  Bit Score: 97.64  E-value: 3.32e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  16 SLRSYALNFTKDAEDANDLVQDTMLKAITYYNKFKEGTNLKGWLFTIMKNTFinnYRRLVKTNTLITQSEDISSANLSYS 95
Cdd:PRK12547   18 ALRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGTNLKAWLFTILRNEF---YSQMRKRGREVQDSDGVFTARVAVH 94

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  96 ATKnqaESKFVLGDIDKALAQLPEEYYVPFIRY-FEGYKYHEIADMLEIPIGTVKTRIHVARGILKKYLK 164
Cdd:PRK12547   95 PAQ---YGSLDLQDFKKALNLLSADQREAIILIgASGFSYEDAAAICGCAVGTIKSRVSRARNRLQELLK 161
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 16-164 1.11e-23

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 91.95  E-value: 1.11e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  16 SLRSYALNFTKDAEDANDLVQDTMLKAITYYNKFKEGTNLKGWLFTIMKNTFinnYRRLVKTNTLITQSEDISSANLsys 95
Cdd:PRK12516   22 SLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVGTNMKAWLFTILRNEF---YSQMRKRGREVQDTDGMFTEQL--- 95

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  96 ATKNQAESKFVLGDIDKALAQLPEEYYVPFIRY-FEGYKYHEIADMLEIPIGTVKTRIHVARGILKKYLK 164
Cdd:PRK12516   96 AVHPSQYGTLDLQDFRAALDQLPDDQREAIILVgASGFAYEEAAEICGCAVGTIKSRVNRARQRLQEILQ 165
SigM_subfam TIGR02950
RNA polymerase sigma factor, SigM family; This family of RNA polymerase sigma factors is a ...
 13-163 9.08e-22

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: 85.97  E-value: 9.08e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  13 HSVSLRSYALNFTKDAEDANDLVQDTMLKAITYYNKFKeGTNLKGWLFTIMKNTFINNYRRLVKTNTliTQSEDISSANL 92
Cdd:TIGR02950   4 YMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFK-DSSIKPWLFRIARNAFIDWYRKDKKIQT--IDDDAIGDLEQ 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1525942823  93 S-YSATKNQAESKFVLGDIDKALAQLPEEYY-VPFIRYFEGYKYHEIADMLEIPIGTVKTRIHVARGILKKYL 163
Cdd:TIGR02950  81 HpVESPEHHLLIKIEQEEITHHLSRLPENYRtVLILREFKEFSYKEIAELLNLSLAKVKSNLFRARKELKKLL 153
PRK12540 PRK12540
RNA polymerase sigma factor; Provisional
 16-163 1.44e-21

RNA polymerase sigma factor; Provisional


Pssm-ID: 183579 [Multi-domain]  Cd Length: 182  Bit Score: 86.17  E-value: 1.44e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  16 SLRSYALNFTKDAEDANDLVQDTMLKAITYYNKFKEGTNLKGWLFTIMKNTFINNYRRlvktntlitQSEDISSANLSYS 95
Cdd:PRK12540   17 SLRAFAISLSGNGDRADDLVQETLLRALANIDSFQPGSNLPAWLFTILRNLFRSDYRK---------RRREVEDADGSYA 87

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1525942823  96 AT-KNQAE--SKFVLGDIDKALAQLPEEYYVPFIRY-FEGYKYHEIADMLEIPIGTVKTRIHVARGILKKYL 163
Cdd:PRK12540   88 KTlKSQPGqnAHLEFEEFRAALDKLPQDQREALILVgASGFSYEDAAAICGCAVGTIKSRVNRARSKLSALL 159
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 11-163 9.09e-20

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 81.57  E-value: 9.09e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  11 NHHSVSLRSYALNFTKDAEDANDLVQDTMLKAITYYNKFKEGTNLKGWLFTIMKNTFINNYRRlvktntliTQSEDISSA 90
Cdd:PRK09637    8 SEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDGSSIKSWLYQIANNTIIDFYRK--------KNRSEELPD 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1525942823  91 NLSYSATKNQAESKFVLGD-IDKALAQLPEEYYVPFIRY-FEGYKYHEIADMLEIPIGTVKTRIHVARGILKKYL 163
Cdd:PRK09637   80 DLLFEDEEREENAKKELAPcLRPFIDALPEKYAEALRLTeLEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELL 154
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
9-167 6.27e-18

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 76.66  E-value: 6.27e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823   9 LVNHHSVSLRSYALNFTKDAEDANDLVQDTMLKAITYYNKF-KEGTNLKGWLFTIMKNTFINNyRRLVKTNTLITQSEDI 87
Cdd:PRK09645   14 LYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLaDTGRSARAWLFTVARNLVIDE-RRSARARPVEGGDDVL 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  88 SSANLSYSATKNQAESKFVLGDidkALAQLPEEYYVPFIR-YFEGYKYHEIADMLEIPIGTVKTRIHVARGILKKYLKTY 166
Cdd:PRK09645   93 GVPEQSAPDEVDRALDRLLVAD---ALAQLSPEHRAVLVRsYYRGWSTAQIAADLGIPEGTVKSRLHYALRALRLALQER 169


                  .
gi 1525942823 167 S 167
Cdd:PRK09645  170 G 170
PRK12522 PRK12522
RNA polymerase sigma factor; Provisional
 17-164 1.00e-17

RNA polymerase sigma factor; Provisional


Pssm-ID: 183571 [Multi-domain]  Cd Length: 173  Bit Score: 76.06  E-value: 1.00e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  17 LRSYALNFTKDAEDANDLVQDTMLKAITYYNKFKEGTNLKGWLFTIMKNTFINNYRRLVKTNTLITQSEDISSANLSYSA 96
Cdd:PRK12522   16 IYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVENYKKWITTICVRTFYDFYRKKKRWKDRILDLFHKEDGGEIEFA 95

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1525942823  97 TKNQAESKFVLGD----IDKALAQLPEEYYVPFI-RYFEGYKYHEIADMLEIPIGTVKTRIHVARGILKKYLK 164
Cdd:PRK12522   96 DDVNISEEFIQKVeaemIREVIQLLNEKYKTVLVlYYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQMREHLE 168
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 9-176 1.51e-17

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 76.36  E-value: 1.51e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823   9 LVNHHSVSLRSYALNFTKDAEDANDLVQDTMLKAITYYNKFKEGTnLKGWLFTIMKNTFINNYRRL--VKTNTLITQSED 86
Cdd:PRK09647   33 LVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQPGT-FEGWLHRITTNLFLDMVRRRarIRMEALPEDYDR 111

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  87 ISSANLSYSATKNQAEskfvLG-DIDKALAQLPEEYYVPFIRY-FEGYKYHEIADMLEIPIGTVKTRIHVARGILKKYLK 164
Cdd:PRK09647  112 VPGDEPNPEQIYHDAR----LDpDLQAALDSLPPEFRAAVVLCdIEGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAALA 187

                         170
                  ....*....|..
gi 1525942823 165 TYSKEIASTEMA 176
Cdd:PRK09647  188 AHAPHAECAALL 199
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 3-161 2.96e-16

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 71.89  E-value: 2.96e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823   3 KFEFNHLVNHHSVSLRSYALNFTKDAEDANDLVQDTMLKAITYYNKFKeGTNLKGWLFTIMKNTFINNYRRLVKTNTliT 82
Cdd:PRK12541    4 KQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYK-GEEIRPWLFTIAYNAFIDWYRKEKKYKT--T 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  83 QSEDISSANLSysatkNQAESKFVLGDIDKALAQL----PEEYYVPFIRYFEGYKYHEIADMLEIPIGTVKTRIHVARGI 158
Cdd:PRK12541   81 TIEEFHLPNVP-----STEHEYFIKHEIASWLDSLsslpLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKE 155


                  ...
gi 1525942823 159 LKK 161
Cdd:PRK12541  156 TKS 158
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 6-165 5.24e-16

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 71.67  E-value: 5.24e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823   6 FNHLVNHHSVSLRS--YALNftkDAEDANDLVQDTMLKAITYYNKFKEGTNLKGWLFTIMKNTFINNYRRLVKTNTLITQ 83
Cdd:PRK12518   13 FRQLYRRYQQKVRStlYQLC---GRELLDDLVQEVFLRVWKGLPKLRNPAYFSTWLYRITWNVATDARRQFAQRPSRIQD 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  84 SedisSANLSYSATKNQAEskfvLGDID------KALAQLPEEYYVPFIRY-FEGYKYHEIADMLEIPIGTVKTRIHVAR 156
Cdd:PRK12518   90 D----SLNDQPSRPSDTPD----LMQLHyqdlvqQGLQTLSLEHRAVLVLHdLEDLPQKEIAEILNIPVGTVKSRLFYAR 161


                  ....*....
gi 1525942823 157 GILKKYLKT 165
Cdd:PRK12518  162 RQLRKFLQQ 170
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 27-163 5.57e-16

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 71.65  E-value: 5.57e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  27 DAEDANDLVQDTMLKAITYYNKFKEGTNLKGWLFTIMKNTFINNYRR----------LVKTNTLITQSEDISSANLSysa 96
Cdd:PRK09641   41 NRHEAEDAAQEAFIRAYVNIDSYDINRKFSTWLYRIATNLTIDRLRKrkpdyyldaeVAGTEGLTMYSQLAADDALP--- 117

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1525942823  97 tKNQAESKFVLGDIDKALAQLPEEYYVPFI-RYFEGYKYHEIADMLEIPIGTVKTRIHVARGILKKYL 163
Cdd:PRK09641  118 -EEQVVSLELQETIQEAILQLPEKYRTVIVlKYIEDLSLKEISEILDLPVGTVKTRIHRGREALRKQL 184
Sig70_famx3 TIGR02954
RNA polymerase sigma-70 factor, TIGR02954 family; This group of sigma factors are members of ...
 6-164 1.05e-15

RNA polymerase sigma-70 factor, TIGR02954 family; This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.


Pssm-ID: 213752 [Multi-domain]  Cd Length: 169  Bit Score: 70.51  E-value: 1.05e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823   6 FNHLVNHHSVSLRSYALNFTKDAEDANDLVQDTMLKAITYYNKFKEGTNLKGWLFTIMKNTFINnyrRLVKTNTLITQSE 85
Cdd:TIGR02954  18 FESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHPKYFNTWLTRILINECID---LLKKKKKVIPFDP 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  86 DISSANLSysaTKNQAESKFvlgDIDKALAQLPEEYYVPFI-RYFEGYKYHEIADMLEIPIGTVKTRIHVARGILKKYLK 164
Cdd:TIGR02954  95 NTSIEKGE---CETHADSRL---DLYKAIDTLNDKYQTAIIlRYYHDLTIKEIAEVMNKPEGTVKTYLHRALKKLKKRLE 168
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 6-167 3.57e-15

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 69.72  E-value: 3.57e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823   6 FNHLVNHHSVSLRSYALNFTKDAEDANDLVQDTMLKAITYYNKFKEGTNLKGWLFTIMKNTFINNYRRLVKTNTLITQSE 85
Cdd:PRK12513   28 FEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPRARFRTWLYQIARNLLIDHWRRHGARQAPSLDAD 107

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  86 DISSANLSYSATKNQAESKFVLGD-IDKALAQLPEEYYVPF-IRYFEGYKYHEIADMLEIPIGTVKTRIHVARGILKKYL 163
Cdd:PRK12513  108 EQLHALADDGAAPEQQLSLFRDRRrLQAALETLPDEQREVFlLREHGDLELEEIAELTGVPEETVKSRLRYALQKLRELL 187


                  ....
gi 1525942823 164 KTYS 167
Cdd:PRK12513  188 AEEV 191
PRK12533 PRK12533
RNA polymerase sigma factor; Provisional
 27-157 1.16e-14

RNA polymerase sigma factor; Provisional


Pssm-ID: 237129 [Multi-domain]  Cd Length: 216  Bit Score: 68.60  E-value: 1.16e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  27 DAEDANDLVQDTMLKAITYYNKFKeGTNLKGWLFTIMKNTFINNYRRLVKTNTLITQSEDISSANL-SYSATKNQAESKF 105
Cdd:PRK12533   41 NASDADDVVQEACMRALRFFDSFR-GDNARPWLLAIVRHTWYSEWRRRANAHEVAAPDTLDDADSLdDWQPAGEDPLALL 119

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1525942823 106 VLGD----IDKALAQLPEEYY-VPFIRYFEGYKYHEIADMLEIPIGTVKTRIhvARG 157
Cdd:PRK12533  120 LRAEdvrlVNAALAKLPVEYReVLVLRELEDMSYREIAAIADVPVGTVMSRL--ARA 174
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 9-77 4.98e-14

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: 63.38  E-value: 4.98e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1525942823   9 LVNHHSVSLRSYALNFTKDAEDANDLVQDTMLKAITYYNKFKE--GTNLKGWLFTIMKNTFINNYRRLVKT 77
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPerGVSFSTWLYTIIRNAIIDYLRKQRRT 71
SigE-fam_strep TIGR02983
RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors ...
 1-163 1.14e-13

RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.


Pssm-ID: 132028 [Multi-domain]  Cd Length: 162  Bit Score: 65.10  E-value: 1.14e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823   1 MTKFEFNHLVNHHSVSLRSYALNFTKDAEDANDLVQDTMLKAITYYNKFKEGTNLKGWLFTIMKNTFINNYRRlvktntl 80
Cdd:TIGR02983   3 ATEEEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRDPDAPDAYVRRVLVNLARSRWRR------- 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  81 iTQSEDISSANLSYSATKNQAESKFVLGDIDKALAQLPE-EYYVPFIRYFEGYKYHEIADMLEIPIGTVKTRIHVARGIL 159
Cdd:TIGR02983  76 -RRLLELPTRELPDAAAPDPAPDVALRAALARALRRLPArQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALARL 154


                  ....
gi 1525942823 160 KKYL 163
Cdd:TIGR02983 155 RELL 158
PRK12517 PRK12517
RNA polymerase sigma factor; Provisional
 6-163 6.66e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 183569 [Multi-domain]  Cd Length: 188  Bit Score: 63.55  E-value: 6.66e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823   6 FNHLVNHHSVSLRSYALNFTKDAEDANDLVQDTMLKAITYYNKFKEGTNLKGWLFTIMKNtfiNNYRRLVKTNTLITQSE 85
Cdd:PRK12517   25 YEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDEKAAKAWLITILRR---ENARRFERKQFDLVDIE 101

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1525942823  86 DISSANLSYSATKNQAESKFvlgdIDKALAQLPEEYYVP-FIRYFEGYKYHEIADMLEIPIGTVKTRIHVARGILKKYL 163
Cdd:PRK12517  102 DDSIEDDASHSSEEEMEQEW----LRRQIAKLDPEYREPlLLQVIGGFSGEEIAEILDLNKNTVMTRLFRARNQLKEAL 176
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 26-176 1.28e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 63.44  E-value: 1.28e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  26 KDAEDANDLVQDTMLKAITYYNKFKEGTNLKGWLFTIMKNTFINNYRRLVKTNTLITQSEDISSANLSYSATKNQAEskf 105
Cdd:PRK11922   52 RNDAEAEDVVQEAYLRAFRALGTFRGDASLSTWLSRIVLNEALGRLRRRRRLVNLAEMVMASTIAGGERTPLADPAE--- 128

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823 106 vlgDIDKALAQ-------------LPEEYYVPFI-RYFEGYKYHEIADMLEIPIGTVKTRIHVARGILKKYLktySKEIA 171
Cdd:PRK11922  129 ---DPERAAARreiralleraidaLPDAFRAVFVlRVVEELSVEETAQALGLPEETVKTRLHRARRLLRESL---AREIG 202


                  ....*
gi 1525942823 172 STEMA 176
Cdd:PRK11922  203 PALLD 207
algU PRK11923
RNA polymerase sigma factor AlgU; Provisional
 3-164 1.72e-12

RNA polymerase sigma factor AlgU; Provisional


Pssm-ID: 171347 [Multi-domain]  Cd Length: 193  Bit Score: 62.51  E-value: 1.72e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823   3 KFEFNHLVNHHSVSLRSYALNFTKDAEDANDLVQDTMLKAITYYNKFKEGTNLKGWLFTIMKNTFINNY----RRLVKTN 78
Cdd:PRK11923   19 KRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDSAFYTWLYRIAINTAKNHLvsrgRRPPDSD 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  79 TLITQSE--DISSANLSYSATKNQAESKFVLGDIDKALAQLPEEYYVPF-IRYFEGYKYHEIADMLEIPIGTVKTRIHVA 155
Cdd:PRK11923   99 VSSEDAEfyDGDHALKDIESPERALLRDEIEGTVHRTIQQLPEDLRTALtLREFDGLSYEDIASVMQCPVGTVRSRIFRA 178


                  ....*....
gi 1525942823 156 RGILKKYLK 164
Cdd:PRK11923  179 REAIDKALQ 187
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 8-164 4.53e-12

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 61.30  E-value: 4.53e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823   8 HLVNHHSVSLRSYALNFTKDAEDANDLVQDTMLKAITYYNKFKEGTNLKGWLFTIMkntfINNYRRLVKT--NTLITQSE 85
Cdd:PRK09415   20 EIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGKSSLKTWLYRIA----INHCKDYLKSwhNKKVIVTE 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  86 DISSANLSysaTKNQAESKFVLGDIDKALA----QLPEEYY-VPFIRYFEGYKYHEIADMLEIPIGTVKTRIHVARGILK 160
Cdd:PRK09415   96 DIFTYMES---QKESVEEEVIQNAEDERLAsavmSLPIKYReVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKELLK 172


                  ....
gi 1525942823 161 KYLK 164
Cdd:PRK09415  173 KGLE 176
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 26-164 1.00e-11

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 59.96  E-value: 1.00e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  26 KDAEDANDLVQDTMLKaiTYYNKFKEGTNLKGWLFTIMKNTFINNYRRLVKTNTLITQSEDISSANLSYSATKnQAESKF 105
Cdd:PRK09639   25 KDRTQAEDLAQEVFLR--LYRSDFKGIENEKGWLIKSARNVAYNYLRSEKRRRARILGEFQWQEVDNEPSPEE-IWIRKE 101

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1525942823 106 VLGDIDKALAQLPEEYYVPFIRYFEGYKYHEIADMLEIPIGTVKTRIHVARGILKKYLK 164
Cdd:PRK09639  102 EITKVQEVLAKMTERDRTVLLLRFSGYSYKEIAEALGIKESSVGTTLARAKKKFRKIYE 160
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 6-164 1.80e-11

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 59.57  E-value: 1.80e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823   6 FNHLVNHHSVSLRSYALNFTKDAEDANDLVQDTMLKAITYYNKFKEGTNLKGWLFTIMKNTFINNYRRLVKTNTLItqsE 85
Cdd:PRK09640   28 YEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGKSKFKTWLYSITYNECITQYRKERRKRRLM---D 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  86 DISSANLSySATKNQAESKFVLGDIDKALAQL-PEEYYVPFIRYFEGYKYHEIADMLEIPIGTVKTRIHVARGILKKYLK 164
Cdd:PRK09640  105 ALSLDPLE-EASEEKAPKPEERGGLDRWLVHVnPIDREILVLRFVAELEFQEIADIMHMGLSATKMRYKRALDKLREKFA 183
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 107-156 1.43e-10

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


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 54.00  E-value: 1.43e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1525942823 107 LGDIDKALAQLPEEYYVPFI-RYFEGYKYHEIADMLEIPIGTVKTRIHVAR 156
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLlRYLEGLSYAEIAELLGISEGTVKSRLSRAR 51
PRK09643 PRK09643
RNA polymerase sigma factor SigM; Reviewed
 6-163 1.99e-10

RNA polymerase sigma factor SigM; Reviewed


Pssm-ID: 236604 [Multi-domain]  Cd Length: 192  Bit Score: 57.03  E-value: 1.99e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823   6 FNHLVNHHSVSLRSYALNFTKDAEDANDLVQDTMLKAITYYNKFKEGTNLKGWLFTIMKNTFINNYRR-LVKTNTLITQS 84
Cdd:PRK09643   29 FGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGDAAVSSWLHRIVVNACLDRLRRaKARPTVPLDDV 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  85 EDISSANLSYSAtknQAESKFVlgdIDKALAQLPEEYYVPFIRY-FEGYKYHEIADMLEIPIGTVKTRIHVARGILKKYL 163
Cdd:PRK09643  109 YPVAQLERDPTA---RVETALA---VQRALMRLPVEQRAALVAVdMQGYSVADAARMLGVAEGTVKSRCARGRARLAELL 182
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 5-159 2.76e-10

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: 55.79  E-value: 2.76e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823   5 EFNHLVNHHSVSLRSYALNFTKDAEDANDLVQDTMLKAITYYNKFKEGTNLKGWLFTIMKNTfINNYRRLVKTNTLITqS 84
Cdd:TIGR02989   2 AFVRLLTRHERALRAFVRSLVADRDDVDDVLQETFVVAWRKFDQFDPGTNFVAWARGIARNK-VLNYRRKLGRDRLVF-D 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  85 EDISSAnLSYSATKNQAESkfvLGDIDKAL----AQLPEEYY-VPFIRYFEGYKYHEIADMLEIPIGTVKTRIHVARGIL 159
Cdd:TIGR02989  80 DDLLEA-LAAEAEPTEAER---LSDDRQALegclEKLPERQReLLDLRYQRGQKATALAEQTGRTVNAVYKALQRIRVSL 155
PRK09047 PRK09047
RNA polymerase factor sigma-70; Validated
 25-166 6.77e-10

RNA polymerase factor sigma-70; Validated


Pssm-ID: 236367 [Multi-domain]  Cd Length: 161  Bit Score: 54.97  E-value: 6.77e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  25 TKDAEDANDLVQDTMLKAITYYNKfKEGTNLKGWLFTIMKNTFINNYRRLVKTNTLIT---------------QSEDISS 89
Cdd:PRK09047    1 VRDDDAALDIVQDAMIKLAEKYGD-RPAAEWPPLFQRILQNRIHDWFRRQKVRNTWVSlfssfsdddddddfdPLETLDS 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1525942823  90 ANLSYSATKNQAESKFVLGDIDKALAQLPEEYYVPFI-RYFEGYKYHEIADMLEIPIGTVKTRIHVARGILKKYLKTY 166
Cdd:PRK09047   80 ADEGAESPADKLERAQVLQLIEEAIQKLPARQREAFLlRYWEDMDVAETAAAMGCSEGSVKTHCSRATHALAKALEAK 157
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
 6-170 8.65e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 55.63  E-value: 8.65e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823   6 FNHLVNHHSVSLRSYALNFTKDAEDANDLVQDTMLKAITYYNKFKEG-TNLKGWLFTIMKNTFInNYRRLVKTNTLITQS 84
Cdd:PRK12538   65 FRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGrAKFSTWLYRVVSNRCI-DLRRKPRTENVDAVP 143

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  85 EdISSANLSYSATKNQAESKFVLgdiDKALAQLPEEYYVPFI-RYFEGYKYHEIADMLEIPIGTVKTRIHVARGILKKYL 163
Cdd:PRK12538  144 E-VADGKPDAVSVIERNELSDLL---EAAMQRLPEQQRIAVIlSYHENMSNGEIAEVMDTTVAAVESLLKRGRQQLRDLL 219


                  ....*..
gi 1525942823 164 KTYSKEI 170
Cdd:PRK12538  220 RRHERDI 226
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 21-160 1.05e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 55.07  E-value: 1.05e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  21 ALNFTKDAEDANDLVQDTMLK--AITYYNKfKEGtNLKGWLFTIMKNTFINNYR------RLVK--TNTLITQ-SEDISS 89
Cdd:PRK12519   46 ALKILGNSQEAEDLTQEIFLSlwRKSSYDP-KRG-SLSSYLLTLTRSRAIDRLRsrrsrqRLLErwQQELLGEaSEDTPL 123

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1525942823  90 ANLSysatknQAEskfVLGDIDKALAQLPE-EYYVPFIRYFEGYKYHEIADMLEIPIGTVKTRihVARGILK 160
Cdd:PRK12519  124 EQAS------LAE---RSQRVQTALAQLPEsQRQVLELAYYEGLSQSEIAKRLGIPLGTVKAR--ARQGLLK 184
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 109-160 4.32e-09

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: 50.18  E-value: 4.32e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1525942823 109 DIDKALAQLPEEYYVPFI-RYFEGYKYHEIADMLEIPIGTVKTRIHVARGILK 160
Cdd:cd06171     3 RLEEALDKLPEREREVILlRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK12532 PRK12532
RNA polymerase sigma factor; Provisional
 17-164 4.70e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 171564 [Multi-domain]  Cd Length: 195  Bit Score: 53.39  E-value: 4.70e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  17 LRSYALNFTKDAEDANDLVQDTMLKAITYYNKFKEGTNLKGWLFTIMKNTFINNYR---RLVKTNTLItQSEDISSA--- 90
Cdd:PRK12532   19 LHFARLQLPDHPDLAEDLVQETLLSAYSAGDSFQGRALVNSWLFAILKNKIIDALRqigRQRKVFTLL-DDELLDEAfes 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  91 NLSYSATKNQAESKFVLGDIDKALAQ-------------LPEEYYVPF-IRYFEGYKYHEIADMLEIPIGTVKTRIHVAR 156
Cdd:PRK12532   98 HFSQNGHWTPEGQPQHWNTPEKSLNNnefqkilqsclynLPENTARVFtLKEILGFSSDEIQQMCGISTSNYHTIMHRAR 177


                  ....*...
gi 1525942823 157 GILKKYLK 164
Cdd:PRK12532  178 ESLRQCLQ 185
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 26-155 6.06e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 49.73  E-value: 6.06e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  26 KDAEDANDLVQDTMLKAITYYNKFKEGTNLKGWLFTIMKNTfINNYRRLVKTNTLITQSEDISSANLSYSaTKNQAESKF 105
Cdd:PRK12543   29 EDKQDVDDVVNEIYIQLWESLRKYDSNRPFRFWLIGLVIKQ-IHSWRRKRWRRFRIFEKAEEQRKPVSID-FSEDVLSKE 106

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1525942823 106 VLGDIDKALAQLPEEYYVPFI-RYFEGYKYHEIADMLEIPIGTVKTRIHVA 155
Cdd:PRK12543  107 SNQELIELIHKLPYKLRQVIIlRYLHDYSQEEIAQLLQIPIGTVKSRIHAA 157
PRK12526 PRK12526
RNA polymerase sigma factor; Provisional
 31-160 6.39e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 237127 [Multi-domain]  Cd Length: 206  Bit Score: 50.18  E-value: 6.39e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  31 ANDLVQDTM---LKAITYYNKFKEGTNLkgWLFTIMKNTFINNYRRlVKTNTLITQSEDISSANLSYSATKNQAE----- 102
Cdd:PRK12526   65 ANELVQETMsnvWRKAHLYNGDKGAATT--WVYTVMRNAAFDMLRK-IKAKKEQNLGDDIWPIEQALAESQSESEefsdh 141

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1525942823 103 --SKFVLGDIDKalaqLPE-EYYVPFIRYFEGYKYHEIADMLEIPIGTVKTRIHVARGILK 160
Cdd:PRK12526  142 lmDKQILSYIEK----LPEaQQTVVKGVYFQELSQEQLAQQLNVPLGTVKSRLRLALAKLK 198
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 27-164 6.75e-08

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 49.91  E-value: 6.75e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  27 DAEDANDLVQDTMLKAITYYNKF-KEGTNLKGWLFTIMKNTFINNYRRL-VKTNTLITQSEDISSANLSYSATKNqaESK 104
Cdd:PRK13919   46 DGAAAEDVVQEVFIRVWKKAKEFdPRRGSARAWLLALAHHAAVDHVRRRaARPQPLEPDEREPEAFDLPGPGLDE--EGH 123

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1525942823 105 FVLGDIDKALAQL-PEEYYVPFIRYFEGYKYHEIADMLEIPIGTVKTRIHVARGILKKYLK 164
Cdd:PRK13919  124 LDRTRLGRALKALsPEERRVIEVLYYQGYTHREAAQLLGLPLGTLKTRARRALSRLKEVLR 184
PRK12531 PRK12531
RNA polymerase sigma factor; Provisional
 6-155 1.23e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 105726 [Multi-domain]  Cd Length: 194  Bit Score: 49.16  E-value: 1.23e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823   6 FNHLVNHHSVSLRSYALNFTKDAEDANDLVQDTMLKAITYYNKFK-EGTNLKGWLFTIMKNTFINNYRRLvKTNTLITQS 84
Cdd:PRK12531   29 FALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDgQKSALSTWIYTIIRNLCFDLLRKQ-KGKDLHIHA 107

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1525942823  85 EDISSANL-------SYSATKNQAESKFVlgdidKALAQLPE-EYYVPFIRYFEGYKYHEIADMLEIPIGTVKTRIHVA 155
Cdd:PRK12531  108 DDIWPSDYyppdlvdHYSPEQDMLKEQVM-----KFLDRLPKaQRDVLQAVYLEELPHQQVAEMFDIPLGTVKSRLRLA 181
PRK12535 PRK12535
RNA polymerase sigma factor; Provisional
 27-156 2.01e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 237130 [Multi-domain]  Cd Length: 196  Bit Score: 48.74  E-value: 2.01e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  27 DAEDANDLVQDTMLKAITYYNKFKEGTNLKGWLFTIMKNTFINNYRR-LVKTNTLITQSEDISSANLSYSATKNQAEskF 105
Cdd:PRK12535   47 GHDIADDLTQETYLRVMSALPRFAARSSARTWLLSLARRVWVDNIRHdMARPRKSATEYEDAAATTASNETTGSWSE--W 124

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1525942823 106 VlgDIDKALAQLPEEYYVPFI-RYFEGYKYHEIADMLEIPIGTVKTRIHVAR 156
Cdd:PRK12535  125 I--DVRTLIDALPPERREALIlTQVLGYTYEEAAKIADVRVGTIRSRVARAR 174
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
 13-136 6.43e-07

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 46.99  E-value: 6.43e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  13 HSVSLRSYALNFTKDAEDANDLVQDTMLKAITYYNKFKEGTNLkGWLFTIMKNTFINNYRRLVKTNTLITQSED---ISS 89
Cdd:PRK07037    7 NRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQDAVKQPV-AYLFRIVRNLAIDHYRRQALENKYHGDEEDgldVPS 85

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1525942823  90 ANLSYSATKNQAESkfvLGDIDKALAQLPEEyyvpfIRY-FEGYKYHE 136
Cdd:PRK07037   86 PEASPEAALINRDT---LRHVADALSELPAR-----TRYaFEMYRLHG 125
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 9-152 1.06e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 46.69  E-value: 1.06e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823   9 LVNHHSVSLRSYALNFTKDAEDANDLVQDTMLKAITYYNKF--KEGTNlKGWLFTIMKNTFIN---NYRRLVKTNtlitq 83
Cdd:PRK12537   28 LYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFdpARGSA-RGWIYSVTRHLALNvlrDTRREVVLD----- 101

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  84 sEDISSANLSYSATKNQAESKFVLGDIDKALAQL-PEEYYVPFIRYFEGYKYHEIADMLEIPIGTVKTRI 152
Cdd:PRK12537  102 -DDAEETAQTLHEIIDDFDLWANSGKIHRCLEQLePARRNCILHAYVDGCSHAEIAQRLGAPLGTVKAWI 170
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 20-164 1.17e-06

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 46.03  E-value: 1.17e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  20 YALNFTKDAEDANDLVQDTMLKAITYYNKFkEGTNLKGWLFTIMKNTFINNYRRLVKTNTLITQSEDISSANlSYSATKN 99
Cdd:PRK09644   17 YLFSLTKSHHAAEDLLQETFYRAYIYLEDY-DNQKVKPWLFKVAYHTFIDFVRKEKKVSFVGTDEIEAIQAE-STEEYVV 94

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1525942823 100 QAESKFVLGDIdkaLAQLPEEY-YVPFIRYFEGYKYHEIADMLEIPIGTVKTRIHVARGILKKYLK 164
Cdd:PRK09644   95 AKNSYEKLIQI---IHTLPVIEaQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLK 157
PRK12539 PRK12539
RNA polymerase sigma factor SigF;
9-158 1.65e-06

RNA polymerase sigma factor SigF;


Pssm-ID: 237132 [Multi-domain]  Cd Length: 184  Bit Score: 45.88  E-value: 1.65e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823   9 LVNHHSVSLRSYALN----FTKDAEDANDLVQDTMLKAITYYNKFKEGTNLKGWLFTIMKNTFINNYRRlVKTNTLITQS 84
Cdd:PRK12539   26 LLERLSGHLRAYYKGklarIGRGAEEAEDLVQEALMAIHTRRHTYDPEQPLTPWVYAIARYKLIDHLRR-TRASLADVPI 104

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1525942823  85 EDISsaNLSYSATKNQAESKFvlgDIDKALAQLPEEYYVPfIRY--FEGYKYHEIADMLEIPIGTVKTRIHvaRGI 158
Cdd:PRK12539  105 DDAD--ELVAHDDHAAVESTL---DLGRLLARLPEKMRLA-IQAvkLEGLSVAEAATRSGMSESAVKVSVH--RGL 172
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 113-161 2.37e-06

Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.


Pssm-ID: 461347 [Multi-domain]  Cd Length: 50  Bit Score: 42.80  E-value: 2.37e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1525942823 113 ALAQLPE-EYYVPFIRYFEGYKYHEIADMLEIPIGTVKTRIHVARGILKK 161
Cdd:pfam04545   1 ALASLPPrERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
PRK12530 PRK12530
RNA polymerase sigma factor; Provisional
 4-85 2.97e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 237128 [Multi-domain]  Cd Length: 189  Bit Score: 45.53  E-value: 2.97e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823   4 FEFNHLVNHHSVSLRSYALNFT----KDAEDANDLVQDTMLKAITYYNKFKEGTNLKGWLFTIMKNTFIN--NYR-RLVK 76
Cdd:PRK12530    3 EQMNHISSLEIEEIRLQMLKFAtlqlKDADLAEDVVQEALVSAYKNADSFKGQSALKTWIFAILKNKIIDliRYRkRFVN 82


                  ....*....
gi 1525942823  77 TNTLITQSE 85
Cdd:PRK12530   83 ESELIEEDS 91
PRK09646 PRK09646
ECF RNA polymerase sigma factor SigK;
128-152 6.14e-06

ECF RNA polymerase sigma factor SigK;


Pssm-ID: 182015 [Multi-domain]  Cd Length: 194  Bit Score: 44.66  E-value: 6.14e-06
                          10        20
                  ....*....|....*....|....*
gi 1525942823 128 YFEGYKYHEIADMLEIPIGTVKTRI 152
Cdd:PRK09646  155 YYGGLTYREVAERLAVPLGTVKTRM 179
PRK09649 PRK09649
RNA polymerase sigma factor SigC; Reviewed
 24-159 1.14e-05

RNA polymerase sigma factor SigC; Reviewed


Pssm-ID: 137458 [Multi-domain]  Cd Length: 185  Bit Score: 43.88  E-value: 1.14e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  24 FTKDAEDANDLVQDTMLKAITYYNKFKEGTNLKGWLFTIMKNTFINNYRRLvktNTLITQSEDISSANLSYSATKNQAES 103
Cdd:PRK09649   43 YLSDVGSADDLTQETFLRAIGAIPRFSARSSARTWLLAIARHVVADHIRHV---RSRPRTTRGARPEHLIDGDRHARGFE 119

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1525942823 104 KFVlgDIDKALAQL-PEEYYVPFIRYFEGYKYHEIADMLEIPIGTVKTRIHVARGIL 159
Cdd:PRK09649  120 DLV--EVTTMIADLtTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARARDAL 174
PRK06811 PRK06811
RNA polymerase factor sigma-70; Validated
 47-169 1.66e-05

RNA polymerase factor sigma-70; Validated


Pssm-ID: 180707 [Multi-domain]  Cd Length: 189  Bit Score: 43.00  E-value: 1.66e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  47 NKFK-EGTNLKGWLFTIMKNTFINNYRRLVKTNTLITQSEDISSanlsysaTKNQAESKFVL----GDIDKALAQLPEEY 121
Cdd:PRK06811   64 DKFDeEKGSFKKWIAAISKYKAIDYKRKLTKNNEIDSIDEFILI-------SEESIENEIILkenkEEILKLINDLEKLD 136

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1525942823 122 YVPFI-RYFEGYKYHEIADMLEIPIGTVKTRIHVARGILKKYLKTYSKE 169
Cdd:PRK06811  137 REIFIrRYLLGEKIEEIAKKLGLTRSAIDNRLSRGRKKLQKNKLNISLG 185
PRK12544 PRK12544
RNA polymerase factor sigma-70;
17-169 2.68e-05

RNA polymerase factor sigma-70;


Pssm-ID: 183583 [Multi-domain]  Cd Length: 206  Bit Score: 42.87  E-value: 2.68e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  17 LRSYALNFTK----DAEDANDLVQDTMLKAITYYNKFKEGTNLKGWLFTIMKNTFINNYR---RLVKTNTLITQSEDISS 89
Cdd:PRK12544   27 LRKQMIKFATlqlsDLHLAEDAVQEALIGALKNADSFAGRAAFKTWVFAILKNKIIDLLRqkkRHVSASSLLRDEEEEED 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  90 ANLSYSAT----KNQAESKFVLGD-----------IDKALAQLPEEYYVPF-IRYFEGYKYHEIADMLEIPIGTVKTRIH 153
Cdd:PRK12544  107 FEELFDESghwqKDERPQAWGNPEesleqeqfwriFEACLDGLPAKYARVFmMREFIELETNEICHAVDLSVSNLNVLLY 186

                         170
                  ....*....|....*...
gi 1525942823 154 VARGILKKYL--KTYSKE 169
Cdd:PRK12544  187 RARLRLRECLenKWFLKE 204
PRK08241 PRK08241
RNA polymerase subunit sigma-70;
5-66 3.84e-05

RNA polymerase subunit sigma-70;


Pssm-ID: 236196 [Multi-domain]  Cd Length: 339  Bit Score: 42.62  E-value: 3.84e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1525942823   5 EFNHLVNHHSVSLRSYALNFTKDAEDANDLVQDTMLKAITYYNKFKEGTNLKGWLFTIMKNT 66
Cdd:PRK08241   20 AFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGYDRFEGRSSLRTWLYRIATNV 81
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 13-164 6.99e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 41.26  E-value: 6.99e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  13 HSVSLRSYALNFTKDAEDANDLVQDTMLKAITYYNKFKEGTNLKGWLFTIMKNTFINNYRRlvktntliTQSEDISSANL 92
Cdd:PRK12515   31 HHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGRSQVSTWLLSIARFKALSALRR--------RKHEEIDDEAA 102

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1525942823  93 SY----SATKNQAESKFVLGDIDKA-LAQLPEEYY-VPFIRYFEGYKYHEIADMLEIPIGTVKTRIHVARGILKKYLK 164
Cdd:PRK12515  103 AAiedgADTPEVALQKSDTSAALRAcLAKLSPAHReIIDLVYYHEKSVEEVGEIVGIPESTVKTRMFYARKKLAELLK 180
PRK09642 PRK09642
RNA polymerase sigma factor;
26-164 2.99e-04

RNA polymerase sigma factor;


Pssm-ID: 170031 [Multi-domain]  Cd Length: 160  Bit Score: 39.31  E-value: 2.99e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  26 KDAEDANDLVQDTMLKAITYYNKFkEGTNLKGWLFTIMKNTFINNYRRLVKTN---TLITQSEDISSANLSYSATKNQAE 102
Cdd:PRK09642   17 RHEEDAKDVTQEVFVKIHASLPNY-QFRGLKTWMARIATNHAIDYKRKKARENeelSLCKETEENIKSSHNIEDLLLTKE 95

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1525942823 103 SKFVlgdIDKALAQLPEEYY-VPFIRYFEGYKYHEIADMLEIPIGTVKTRIHVARGILKKYLK 164
Cdd:PRK09642   96 QKLL---IAQKLRELPENYRdVVLAHYLEEKSYQEIALQEKIEVKTVEMKLYRARKWIKKHWK 155
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 19-157 3.35e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 39.49  E-value: 3.35e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  19 SYALNFTKDAEDANDLVQDTMLKAITYYNKFKEG-TNLKGWLFTIMKNTFINNYRRLVKTNTLITQSEDISSANLSYSAT 97
Cdd:PRK12524   41 AVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQGeARVSTWLYRVVCNLCTDRLRRRRRASVDLDDAPEPADAAPGAEEA 120

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1525942823  98 KNQAESKFVLgdiDKALAQLPE-EYYVPFIRYFEGYKYHEIADMLEIPIGTVKTRihVARG 157
Cdd:PRK12524  121 LIEGDRMRAL---DAALAALPErQRQAVVLRHIEGLSNPEIAEVMEIGVEAVESL--TARG 176
Sig-70_X6 TIGR02999
RNA polymerase sigma factor, TIGR02999 family; This group of sigma factors are members of the ...
 109-164 1.02e-03

RNA polymerase sigma factor, TIGR02999 family; This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.


Pssm-ID: 132044 [Multi-domain]  Cd Length: 183  Bit Score: 38.07  E-value: 1.02e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823 109 DIDKALAQL----PEEYYVPFIRYFEGYKYHEIADMLEIPIGTVKTRIHVARGILKKYLK 164
Cdd:TIGR02999 124 DLDDALDKLaqvdPRQAEVVELRFFAGLTVEEIAELLGVSVRTVERDWRFARAWLADELS 183
PRK06930 PRK06930
positive control sigma-like factor; Validated
 71-160 2.78e-03

positive control sigma-like factor; Validated


Pssm-ID: 180757 [Multi-domain]  Cd Length: 170  Bit Score: 36.63  E-value: 2.78e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  71 YRRLVKTNTLITQSEDISSANLSYSATKNqaESKFVLGD---IDKALAQL-PEEYYVPFIRYFEGYKYHEIADMLEIPIG 146
Cdd:PRK06930   68 YQREVICDPLLIQRYFRSMEDLEWDIEEP--ESVISEWDkirIEDALSVLtEREKEVYLMHRGYGLSYSEIADYLNIKKS 145

                          90
                  ....*....|....
gi 1525942823 147 TVKTRIHvaRGILK 160
Cdd:PRK06930  146 TVQSMIE--RAEKK 157
PRK12520 PRK12520
RNA polymerase sigma factor; Provisional
 15-73 3.59e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237126 [Multi-domain]  Cd Length: 191  Bit Score: 36.63  E-value: 3.59e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1525942823  15 VSLRSYALNFT----KDAEDANDLVQDTMLKAITYYNKFKEGTNLKGWLFTIMKNTFINNYRR 73
Cdd:PRK12520    9 EALRPHLLRFArlqlRDPALAEDAVSETLLAVLEHPERFAGQSSLKTYLVGILKHKIIDAIRS 71
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 130-161 3.75e-03

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


Pssm-ID: 441799 [Multi-domain]  Cd Length: 131  Bit Score: 35.64  E-value: 3.75e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1525942823 130 EGYKYHEIADMLEIPIGTVKTriHVARgILKK 161
Cdd:COG2197    83 EGLSNKEIAERLGISERTVKT--HVSN-ILRK 111
Sigma70_ECF pfam07638
ECF sigma factor; These proteins are probably RNA polymerase sigma factors belonging to the ...
 109-156 4.34e-03

ECF sigma factor; These proteins are probably RNA polymerase sigma factors belonging to the extra-cytoplasmic function (ECF) subfamily and show sequence similarity to pfam04542 and pfam04545.


Pssm-ID: 254323 [Multi-domain]  Cd Length: 185  Bit Score: 36.24  E-value: 4.34e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1525942823 109 DIDKALAQL----PEEYYVPFIRYFEGYKYHEIADMLEIPIGTVKTRIHVAR 156
Cdd:pfam07638 125 DLDEALEQLfslsPRQARLVELRFFAGLSNDEIAERLGVSERTVERNWALAR 176
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
30-166 5.04e-03

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 36.04  E-value: 5.04e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  30 DANDLVQDTML---KAITYYNKFKEG---------------TNLKgwLFTIMKNTFINNYrrlVKTNTLI-------TQS 84
Cdd:PRK08295   50 DREDIVQEGMIglyKAIRDYDKDKLSsfksfaelcitrqiiTAIK--TANRQKHIPLNSY---VSLDKPIydeesdrTLL 124

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1525942823  85 EDISSANLSYSATK--NQAESKFVLGDIDKALAQLpeEYYVpFIRYFEGYKYHEIADMLEIPIGTVKTRIHVARGILKKY 162
Cdd:PRK08295  125 DVISEAKVTDPEELiiSKEELEDIEEKIEELLSEL--EKEV-LELYLDGKSYQEIAEELNRHVKSIDNALQRVKRKLEKY 201


                  ....
gi 1525942823 163 LKTY 166
Cdd:PRK08295  202 LENR 205
MalT COG2909
ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];
100-161 7.69e-03

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


Pssm-ID: 442153 [Multi-domain]  Cd Length: 184  Bit Score: 35.45  E-value: 7.69e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1525942823 100 QAESKFVLGDIDKALAQLPEEYYVpfiryfEGYKYHEIADMLEIPIGTVKTriHVaRGILKK 161
Cdd:COG2909   112 RALALRALGDREEALAALRRRLLA------EGLSNKEIAERLFISVNTVKT--HL-RNIYRK 164
 
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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