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Conserved domains on  [gi|518231705|ref|WP_019401913|]
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MULTISPECIES: sigma-70 family RNA polymerase sigma factor [Chelatococcus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK12546 super family cl31387
RNA polymerase sigma factor; Provisional
 12-155 9.29e-46

RNA polymerase sigma factor; Provisional


The actual alignment was detected with superfamily member PRK12546:

Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 149.22  E-value: 9.29e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  12 ASHQQSSSEIVALIPALRAFARTFCRNTSDADDLVQETLTKALAKIEQFEPGTSLKSWLFTIMRNTFYTQAKLARREAPG 91
Cdd:PRK12546   4 AKHRDPRDELVEHLPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEGTNLRAWLFTILRNTFYSDRRKHKREVPD 83

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 518231705  92 VSDCASTRLRVDATQEWSTRGRELHEAIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTVK 155
Cdd:PRK12546  84 PEGVHAASLAVKPAHDGRLAMSDFRAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVK 147
 
Name Accession Description Interval E-value
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
 12-155 9.29e-46

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 149.22  E-value: 9.29e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  12 ASHQQSSSEIVALIPALRAFARTFCRNTSDADDLVQETLTKALAKIEQFEPGTSLKSWLFTIMRNTFYTQAKLARREAPG 91
Cdd:PRK12546   4 AKHRDPRDELVEHLPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEGTNLRAWLFTILRNTFYSDRRKHKREVPD 83

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 518231705  92 VSDCASTRLRVDATQEWSTRGRELHEAIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTVK 155
Cdd:PRK12546  84 PEGVHAASLAVKPAHDGRLAMSDFRAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVK 147
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 1-157 2.25e-35

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


Pssm-ID: 441203 [Multi-domain]  Cd Length: 181  Bit Score: 122.41  E-value: 2.25e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705   1 MQPDRRL-EKGHASHQQSSSEIV-ALIPALRAFARTFCRNTSDADDLVQETLTKALAKIEQFEPGTSLKSWLFTIMRNTF 78
Cdd:COG1595    1 MSSDEELlERLRAGDEAAFEELYeRYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  79 YTQAKLARREAPGVSDC----ASTRLRVDATQEWSTRGRELHEAIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTV 154
Cdd:COG1595   81 IDHLRKRRRRRELLDELaeelPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTV 160


                 ...
gi 518231705 155 KSR 157
Cdd:COG1595  161 KSR 163
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 21-157 9.85e-28

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


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 102.04  E-value: 9.85e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705   21 IVALIPALRAFARTFCRNTSDADDLVQETLTKALAKIEQFEPGTSLKSWLFTIMRNTFYT---QAKLARREAPGVSDCAS 97
Cdd:TIGR02937   7 YERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDylrRKRRLRRELDLLEELLD 86

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705   98 TRLRVDATQEWSTRGRELHEAIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTVKSR 157
Cdd:TIGR02937  87 SDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRR 146
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 21-88 1.97e-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: 64.92  E-value: 1.97e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705   21 IVALIPALRAFARTFCRNTSDADDLVQETLTKALAKIEQFEP--GTSLKSWLFTIMRNTFYTQAKLARRE 88
Cdd:pfam04542   2 VERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPerGVSFSTWLYTIIRNAIIDYLRKQRRT 71
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 113-157 1.77e-06

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: 43.63  E-value: 1.77e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 518231705 113 RELHEAIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTVKSR 157
Cdd:cd06171    2 ERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQR 46
 
Name Accession Description Interval E-value
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
 12-155 9.29e-46

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 149.22  E-value: 9.29e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  12 ASHQQSSSEIVALIPALRAFARTFCRNTSDADDLVQETLTKALAKIEQFEPGTSLKSWLFTIMRNTFYTQAKLARREAPG 91
Cdd:PRK12546   4 AKHRDPRDELVEHLPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEGTNLRAWLFTILRNTFYSDRRKHKREVPD 83

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 518231705  92 VSDCASTRLRVDATQEWSTRGRELHEAIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTVK 155
Cdd:PRK12546  84 PEGVHAASLAVKPAHDGRLAMSDFRAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVK 147
PRK12547 PRK12547
RNA polymerase sigma factor; Provisional
 20-155 1.21e-43

RNA polymerase sigma factor; Provisional


Pssm-ID: 139056 [Multi-domain]  Cd Length: 164  Bit Score: 143.09  E-value: 1.21e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  20 EIVALIPALRAFARTFCRNTSDADDLVQETLTKALAKIEQFEPGTSLKSWLFTIMRNTFYTQAKLARREAPGVSDCASTR 99
Cdd:PRK12547  11 ELLLALPALRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGTNLKAWLFTILRNEFYSQMRKRGREVQDSDGVFTAR 90

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 518231705 100 LRVDATQEWSTRGRELHEAIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTVK 155
Cdd:PRK12547  91 VAVHPAQYGSLDLQDFKKALNLLSADQREAIILIGASGFSYEDAAAICGCAVGTIK 146
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 20-155 7.40e-43

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 142.03  E-value: 7.40e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  20 EIVALIPALRAFARTFCRNTSDADDLVQETLTKALAKIEQFEPGTSLKSWLFTIMRNTFYTQAKLARREAPGVSDCASTR 99
Cdd:PRK12516  15 ELLAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVGTNMKAWLFTILRNEFYSQMRKRGREVQDTDGMFTEQ 94

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 518231705 100 LRVDATQEWSTRGRELHEAIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTVK 155
Cdd:PRK12516  95 LAVHPSQYGTLDLQDFRAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIK 150
PRK12540 PRK12540
RNA polymerase sigma factor; Provisional
 20-155 6.86e-41

RNA polymerase sigma factor; Provisional


Pssm-ID: 183579 [Multi-domain]  Cd Length: 182  Bit Score: 136.63  E-value: 6.86e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  20 EIVALIPALRAFARTFCRNTSDADDLVQETLTKALAKIEQFEPGTSLKSWLFTIMRNTFYTQAKLARREAPGVSDCASTR 99
Cdd:PRK12540  10 DILAAVPSLRAFAISLSGNGDRADDLVQETLLRALANIDSFQPGSNLPAWLFTILRNLFRSDYRKRRREVEDADGSYAKT 89

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 518231705 100 LRVDATQEWSTRGRELHEAIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTVK 155
Cdd:PRK12540  90 LKSQPGQNAHLEFEEFRAALDKLPQDQREALILVGASGFSYEDAAAICGCAVGTIK 145
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 1-157 2.25e-35

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


Pssm-ID: 441203 [Multi-domain]  Cd Length: 181  Bit Score: 122.41  E-value: 2.25e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705   1 MQPDRRL-EKGHASHQQSSSEIV-ALIPALRAFARTFCRNTSDADDLVQETLTKALAKIEQFEPGTSLKSWLFTIMRNTF 78
Cdd:COG1595    1 MSSDEELlERLRAGDEAAFEELYeRYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  79 YTQAKLARREAPGVSDC----ASTRLRVDATQEWSTRGRELHEAIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTV 154
Cdd:COG1595   81 IDHLRKRRRRRELLDELaeelPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTV 160


                 ...
gi 518231705 155 KSR 157
Cdd:COG1595  161 KSR 163
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 21-157 9.85e-28

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


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 102.04  E-value: 9.85e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705   21 IVALIPALRAFARTFCRNTSDADDLVQETLTKALAKIEQFEPGTSLKSWLFTIMRNTFYT---QAKLARREAPGVSDCAS 97
Cdd:TIGR02937   7 YERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDylrRKRRLRRELDLLEELLD 86

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705   98 TRLRVDATQEWSTRGRELHEAIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTVKSR 157
Cdd:TIGR02937  87 SDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRR 146
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 26-155 8.55e-27

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 100.27  E-value: 8.55e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  26 PALRAFARTFCRNTSDADDLVQETLTKALAKIEQFEPGTSLKSWLFTIMRNTFYTQAKLARREAPGVSDCA--------S 97
Cdd:PRK09652  21 PRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRGGAAFYTWLYRIARNTAINYLRKQGRRPPASDVDAeeaedfdlA 100

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 518231705  98 TRLRVDATQEWSTRGRELHE----AIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTVK 155
Cdd:PRK09652 101 DALRDISTPENELLSAELEQrvraAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVR 162
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 19-153 1.01e-25

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 97.55  E-value: 1.01e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  19 SEIVALIPALRAFARTFCRNTSDADDLVQETLTKALAKIEQFEPGTSLKSWLFTIMRNTFYTQAK----LARREAPGVSd 94
Cdd:PRK12511   8 FDVLDQLVPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRSGGNLRTWLMSILHNAFIDELRrrrvEARRADELAV- 86

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 518231705  95 caSTRLRVDATQEWSTRGRELHEAIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGT 153
Cdd:PRK12511  87 --LADASLPAAQEHAVRLAQIRDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGT 143
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 26-157 2.01e-23

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 91.57  E-value: 2.01e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  26 PALRAFARTFCRNTSDADDLVQETLTKALAKIEQFEPGTSLKSWLFTIMRNTFYTqakLARREAPGVSDCASTRLRVDAT 105
Cdd:PRK11924  24 PDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCYD---LLRRRRREKAVLSDDALEPEFA 100

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 518231705 106 QEWST---------RGRELHEAIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTVKSR 157
Cdd:PRK11924 101 ETAETpeaallakdDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSR 161
SigH_actino TIGR02947
RNA polymerase sigma-70 factor, TIGR02947 family; This group of sigma factors are members of ...
 15-154 2.96e-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: 83.87  E-value: 2.96e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705   15 QQSSSEIVALIPALRAFARTFCRNTSDADDLVQETLTKALAKIEQFEPGTSLKSWLFTIMRNTFYTQAKLARREAPGVSD 94
Cdd:TIGR02947  11 QRFERDALEYLDQLYGAALRMTRNPADAEDLVQEAYAKAFSSFHQFKPGTNLKAWLYRILTNTYINSYRKAQRRPQQSDD 90

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 518231705   95 CASTRLRVDATQEWSTRG--------------RELHEAIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTV 154
Cdd:TIGR02947  91 DDIEDWQLAKAASHTSNGlrsaelealdglpdQDIKDALQGLPEEFRQAVYLADVEGFAYKEIAEIMGTPIGTV 164
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 42-155 2.25e-18

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 78.14  E-value: 2.25e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  42 ADDLVQETLTKALAKIEQFEPGTSLKSWLFTIMRNTFYTQAKLARRE---APGVSDCASTRLRVDATQ---EWStrgrEL 115
Cdd:PRK09638  45 AEDLVQETMLKAIENLSSFQGRSKFSTWLISIASRLYKDHLRKQKREklrLQRAKEETLRKEKWEAAIkgaEWS----EM 120

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 518231705 116 HEAIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTVK 155
Cdd:PRK09638 121 LDALSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTVK 160
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 26-154 5.78e-16

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: 71.58  E-value: 5.78e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705   26 PALRAFARTFCRNTSDADDLVQETLTKALAKIEQFEPGTSLKSWLFTIMRNTFYTQAKLARREAPGVSDCASTRLRVDAT 105
Cdd:TIGR02989  12 RALRAFVRSLVADRDDVDDVLQETFVVAWRKFDQFDPGTNFVAWARGIARNKVLNYRRKLGRDRLVFDDDLLEALAAEAE 91

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 518231705  106 ----QEWSTRGRELHEAIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTV 154
Cdd:TIGR02989  92 pteaERLSDDRQALEGCLEKLPERQRELLDLRYQRGQKATALAEQTGRTVNAV 144
PRK12533 PRK12533
RNA polymerase sigma factor; Provisional
 32-157 1.13e-14

RNA polymerase sigma factor; Provisional


Pssm-ID: 237129 [Multi-domain]  Cd Length: 216  Bit Score: 69.37  E-value: 1.13e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  32 ARTFCRNTSDADDLVQETLTKALAKIEQFEpGTSLKSWLFTIMRNTFYTQakLARREAPGVSDCASTRLRVDATQEWSTR 111
Cdd:PRK12533  35 ARWLCGNASDADDVVQEACMRALRFFDSFR-GDNARPWLLAIVRHTWYSE--WRRRANAHEVAAPDTLDDADSLDDWQPA 111

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 518231705 112 G-------------RELHEAIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTVKSR 157
Cdd:PRK12533 112 GedplalllraedvRLVNAALAKLPVEYREVLVLRELEDMSYREIAAIADVPVGTVMSR 170
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
26-155 1.70e-14

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 67.80  E-value: 1.70e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  26 PALRAFARTFCRNTSDADDLVQETLTKALAKIEQF-EPGTSLKSWLFTIMRNTFYTQAKLARREAPGVSDCASTRLRVDA 104
Cdd:PRK09645  20 APLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLaDTGRSARAWLFTVARNLVIDERRSARARPVEGGDDVLGVPEQSA 99

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 518231705 105 --TQEWSTRGRELHEAIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTVK 155
Cdd:PRK09645 100 pdEVDRALDRLLVADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVK 152
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 21-88 1.97e-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: 64.92  E-value: 1.97e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705   21 IVALIPALRAFARTFCRNTSDADDLVQETLTKALAKIEQFEP--GTSLKSWLFTIMRNTFYTQAKLARRE 88
Cdd:pfam04542   2 VERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPerGVSFSTWLYTIIRNAIIDYLRKQRRT 71
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 27-155 2.76e-14

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 67.70  E-value: 2.76e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  27 ALRAFARTFCRNTSDADDLVQETLTKALAKIEQFEPGTSLKSWLFTIMRNT---FYTqaKLARREAPGVSDCASTRLRV- 102
Cdd:PRK09637  13 QLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDGSSIKSWLYQIANNTiidFYR--KKNRSEELPDDLLFEDEEREe 90

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 518231705 103 DATQEWStrgRELHEAIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTVK 155
Cdd:PRK09637  91 NAKKELA---PCLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAK 140
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 26-142 1.18e-13

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: 65.28  E-value: 1.18e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705   26 PALRAFARTFCRNTSDADDLVQETLTKALAKIEQFEPGTSLKSWLFTIMRNTFYTQakLARREAPGVSDCASTRLRVDAT 105
Cdd:TIGR02985  12 PKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETLEISESIKAYLFTIVKNRCLNY--LRHKQVEEKYQEELAEIEEREL 89

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 518231705  106 QEWSTRG--------RELHEAIQRLPPQHREIIVLVGVLGMSYEE 142
Cdd:TIGR02985  90 SEADPEEeleakeleEIIEEAIEKLPEQCREIFILSRFEGLSNKE 134
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 5-157 2.37e-13

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 65.10  E-value: 2.37e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705   5 RRLEKGHASHQQSSSEIVALIP-ALRAFARTFCRNTSDADDLVQETLTKALAKIEQFEPGTSLKSWLFTIMRN------- 76
Cdd:PRK09641   7 RLIKQVKKGDQNAFAELVDLYKdKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINRKFSTWLYRIATNltidrlr 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  77 ----TFYTQAKLARREA-PGVSDCASTRLRVDATQEWSTRGRELHEAIQRLPPQHREIIVLVGVLGMSYEEAGEICGCAL 151
Cdd:PRK09641  87 krkpDYYLDAEVAGTEGlTMYSQLAADDALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYIEDLSLKEISEILDLPV 166


                 ....*.
gi 518231705 152 GTVKSR 157
Cdd:PRK09641 167 GTVKTR 172
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 38-157 2.61e-13

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 65.58  E-value: 2.61e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  38 NTSDADDLVQETLTKALAKIEQFEPGTsLKSWLFTIMRNTFYTQAklaRREApgvsdcastRLRVDATQEWSTR--GRE- 114
Cdd:PRK09647  51 NQHDAEDLTQETFIRVFRSLQNYQPGT-FEGWLHRITTNLFLDMV---RRRA---------RIRMEALPEDYDRvpGDEp 117

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 518231705 115 --------------LHEAIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTVKSR 157
Cdd:PRK09647 118 npeqiyhdarldpdLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSR 174
PRK09649 PRK09649
RNA polymerase sigma factor SigC; Reviewed
 35-155 2.67e-13

RNA polymerase sigma factor SigC; Reviewed


Pssm-ID: 137458 [Multi-domain]  Cd Length: 185  Bit Score: 65.06  E-value: 2.67e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  35 FCRNTSDADDLVQETLTKALAKIEQFEPGTSLKSWLFTIMRNTFYTQAKLARREAPGVSDCASTRLrVDATQEwsTRG-- 112
Cdd:PRK09649  43 YLSDVGSADDLTQETFLRAIGAIPRFSARSSARTWLLAIARHVVADHIRHVRSRPRTTRGARPEHL-IDGDRH--ARGfe 119

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 518231705 113 --RELHEAIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTVK 155
Cdd:PRK09649 120 dlVEVTTMIADLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIR 164
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 28-155 3.96e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 64.71  E-value: 3.96e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  28 LRAFARTFCRNTSDADDLVQETLTKALAKIEQFEPGTSLKSWLFTIMRNTFYTQA-KLARREAPgvSDCASTRLRVDAT- 105
Cdd:PRK12513  39 LYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPRARFRTWLYQIARNLLIDHWrRHGARQAP--SLDADEQLHALADd 116

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 518231705 106 -----QEWSTR--GRELHEAIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTVK 155
Cdd:PRK12513 117 gaapeQQLSLFrdRRRLQAALETLPDEQREVFLLREHGDLELEEIAELTGVPEETVK 173
SigM_subfam TIGR02950
RNA polymerase sigma factor, SigM family; This family of RNA polymerase sigma factors is a ...
 42-160 1.29e-12

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: 62.47  E-value: 1.29e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705   42 ADDLVQETLTKALAKIEQFEpGTSLKSWLFTIMRNTFYTQAKLARREAPgVSDCASTRLRVDATQ--EWSTRGRELHEAI 119
Cdd:TIGR02950  22 AEDLLQETFLKAYIHLHSFK-DSSIKPWLFRIARNAFIDWYRKDKKIQT-IDDDAIGDLEQHPVEspEHHLLIKIEQEEI 99

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 518231705  120 ----QRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTVKSRLSR 160
Cdd:TIGR02950 100 thhlSRLPENYRTVLILREFKEFSYKEIAELLNLSLAKVKSNLFR 144
SigE-fam_strep TIGR02983
RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors ...
 26-172 1.39e-12

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: 62.79  E-value: 1.39e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705   26 PALRAFARTFCRNTSDADDLVQETLTKALAKIEQFEPGTSLKSWLFTIMRNTFYTQAKLARREApgvsdcASTRLRVDAT 105
Cdd:TIGR02983  17 PRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRDPDAPDAYVRRVLVNLARSRWRRRRLLE------LPTRELPDAA 90

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 518231705  106 QEWSTRGRELH----EAIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTVKSRLSRARLRLLEELDER 172
Cdd:TIGR02983  91 APDPAPDVALRaalaRALRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALARLRELLEEP 161
PRK09643 PRK09643
RNA polymerase sigma factor SigM; Reviewed
 28-157 6.19e-12

RNA polymerase sigma factor SigM; Reviewed


Pssm-ID: 236604 [Multi-domain]  Cd Length: 192  Bit Score: 61.65  E-value: 6.19e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  28 LRAFARTFCRNTSDADDLVQETLTKALAKIEQFEPGTSLKSWLFTIMRNTFYTQAKLAR-REAPGVSDCAS-TRLRVDAT 105
Cdd:PRK09643  40 LWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGDAAVSSWLHRIVVNACLDRLRRAKaRPTVPLDDVYPvAQLERDPT 119

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 518231705 106 QEWSTRgRELHEAIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTVKSR 157
Cdd:PRK09643 120 ARVETA-LAVQRALMRLPVEQRAALVAVDMQGYSVADAARMLGVAEGTVKSR 170
PRK12535 PRK12535
RNA polymerase sigma factor; Provisional
 38-157 1.30e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 237130 [Multi-domain]  Cd Length: 196  Bit Score: 60.68  E-value: 1.30e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  38 NTSDADDLVQETLTKALAKIEQFEPGTSLKSWLFTIMR-----NTFYTQAKlARREAPGVSDCASTRLRVDATQEWStRG 112
Cdd:PRK12535  47 GHDIADDLTQETYLRVMSALPRFAARSSARTWLLSLARrvwvdNIRHDMAR-PRKSATEYEDAAATTASNETTGSWS-EW 124

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 518231705 113 RELHEAIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTVKSR 157
Cdd:PRK12535 125 IDVRTLIDALPPERREALILTQVLGYTYEEAAKIADVRVGTIRSR 169
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 26-155 1.46e-11

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 60.34  E-value: 1.46e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  26 PALRAFARTFCRNTSDADDLVQETLTKALAKIEQFEPGTSLKSWLFTIMRNTFYTQAKLARREAPgVSDCASTRLRVDAT 105
Cdd:PRK09640  37 RTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGKSKFKTWLYSITYNECITQYRKERRKRR-LMDALSLDPLEEAS 115

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 518231705 106 QEWSTRGRE---LHEAIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTVK 155
Cdd:PRK09640 116 EEKAPKPEErggLDRWLVHVNPIDREILVLRFVAELEFQEIADIMHMGLSATK 168
SigZ TIGR02959
RNA polymerase sigma factor, SigZ family; This family of RNA polymerase sigma factors is a ...
 28-155 1.89e-11

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


Pssm-ID: 132004 [Multi-domain]  Cd Length: 170  Bit Score: 59.69  E-value: 1.89e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705   28 LRAFARTFCRNTSDADDLVQETLTKALAKIEQFEPGTSLKSWLFTIMRNT---FYtQAKLARREAPGVSDCASTRLRVDA 104
Cdd:TIGR02959   8 LKAFIKSRVSDASDVEDLLQEVFIKIHRNLPSLKDGQKIQSWLYQIARNTiidFY-RSKSRSVELPESLLAADSAREETF 86

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 518231705  105 TQEWSTRGRELheaIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTVK 155
Cdd:TIGR02959  87 VKELSQCIPPM---IKELPDEYREAIRLTELEGLSQQEIAEKLGLSLSGAK 134
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 37-155 5.20e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 58.97  E-value: 5.20e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  37 RNTSDADDLVQETLTKALAKIEQFEPGTSLKSWLFTIMRntFYTQAKLARR--------EAPGVSDCASTRlrvDATQEW 108
Cdd:PRK12515  44 RDEQTAEDLVSEVFLDVWRQAGQFEGRSQVSTWLLSIAR--FKALSALRRRkheeiddeAAAAIEDGADTP---EVALQK 118

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 518231705 109 STRGRELHEAIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTVK 155
Cdd:PRK12515 119 SDTSAALRACLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVK 165
SigX5 TIGR02960
RNA polymerase sigma-70 factor, TIGR02960 family; This group of sigma factors are members of ...
 41-155 7.32e-11

RNA polymerase sigma-70 factor, TIGR02960 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.


Pssm-ID: 132005 [Multi-domain]  Cd Length: 324  Bit Score: 59.87  E-value: 7.32e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705   41 DADDLVQETLTKALAKIEQFEPGTSLKSWLFTIMRNTFY----------------------TQAKLARREAPGVSDCAST 98
Cdd:TIGR02960  31 EAEDLVQETLLRAWRARDRFEGRSSVRTWLYRIATNACLdalearqrrprpvglgapsadgTAAASEAAEVTWLEPLPDL 110

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 518231705   99 RLR--VDATQEWSTR--GRELHE-----AIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTVK 155
Cdd:TIGR02960 111 TLDldDPAAADPSVAagSRESVRlafvaAIQYLPPRQRAVLLLRDVLGWRAAETAELLGTSTASVN 176
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 37-160 2.57e-10

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 56.43  E-value: 2.57e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  37 RNTSDADDLVQETLTKALAKIEQFEpGTSLKSWLFTIMRNTFYTQAKLARREAPgVSDCASTRLRVDATQEWSTRgRELH 116
Cdd:PRK09644  23 KSHHAAEDLLQETFYRAYIYLEDYD-NQKVKPWLFKVAYHTFIDFVRKEKKVSF-VGTDEIEAIQAESTEEYVVA-KNSY 99

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 518231705 117 EA----IQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTVKSRLSR 160
Cdd:PRK09644 100 EKliqiIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFR 147
PRK12517 PRK12517
RNA polymerase sigma factor; Provisional
 23-157 3.44e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 183569 [Multi-domain]  Cd Length: 188  Bit Score: 56.62  E-value: 3.44e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  23 ALIPALRA----FARTFCRNTSDADDLVQETLTKALAKIEQFEPGTSLKSWLFTIMRNtfytqaKLARR----------- 87
Cdd:PRK12517  27 ALVKALHAdiyrYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDEKAAKAWLITILRR------ENARRferkqfdlvdi 100

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  88 EAPGVSDCASTRLRVDATQEWstrgreLHEAIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTVKSR 157
Cdd:PRK12517 101 EDDSIEDDASHSSEEEMEQEW------LRRQIAKLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMTR 164
Sig70_famx1 TIGR02943
RNA polymerase sigma-70 factor, TIGR02943 family; This group of sigma factors are members of ...
 17-148 3.68e-10

RNA polymerase sigma-70 factor, TIGR02943 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.


Pssm-ID: 274359 [Multi-domain]  Cd Length: 188  Bit Score: 56.70  E-value: 3.68e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705   17 SSSEIVALIPALRAFARTFCRNTSDADDLVQETLTKALAKIEQFEPGTSLKSWLFTIMRNTFYTQAKLARRE---APGVS 93
Cdd:TIGR02943   4 DPQELEQLRRDLLRFARLQLRDRDLAEDAVQETLLAALSHRDSFAGRSALKTWLFAILKNKIIDALRAKGREvkvSDLDD 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 518231705   94 DCASTRLRV-----------DATQEWSTRGRELH---------EAIQRLPPQHREIIVLVGVLGMSYEEAGEICG 148
Cdd:TIGR02943  84 ELDDEAFNAlftqnghwaqhGQPQHWNTPEKQLEnkefwevfeACLYHLPEQTARVFMMREVLGFESDEICQELE 158
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 37-155 6.59e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 55.33  E-value: 6.59e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  37 RNTSDADDLVQETLTKALAKIEQFEpGTSLKSWLFTIMRNTF---YTQAKlaRREAPGVSDCASTRlrVDATQEWSTRGR 113
Cdd:PRK12541  27 GDSHFAEDLMQETFYRMLVHIDYYK-GEEIRPWLFTIAYNAFidwYRKEK--KYKTTTIEEFHLPN--VPSTEHEYFIKH 101

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 518231705 114 ELH---EAIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTVK 155
Cdd:PRK12541 102 EIAswlDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVK 146
algU PRK11923
RNA polymerase sigma factor AlgU; Provisional
 35-157 6.62e-10

RNA polymerase sigma factor AlgU; Provisional


Pssm-ID: 171347 [Multi-domain]  Cd Length: 193  Bit Score: 55.96  E-value: 6.62e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  35 FCRNTSDADDLVQETLTKALAKIEQFEPGTSLKSWLFTIMRNTfytqAK---LARREAPGVSDCASTRLRV----DATQE 107
Cdd:PRK11923  40 FVHDTAEAQDVAQEAFIKAYRALGNFRGDSAFYTWLYRIAINT----AKnhlVSRGRRPPDSDVSSEDAEFydgdHALKD 115

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 518231705 108 WSTRGREL---------HEAIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTVKSR 157
Cdd:PRK11923 116 IESPERALlrdeiegtvHRTIQQLPEDLRTALTLREFDGLSYEDIASVMQCPVGTVRSR 174
PRK12522 PRK12522
RNA polymerase sigma factor; Provisional
 36-155 2.10e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 183571 [Multi-domain]  Cd Length: 173  Bit Score: 54.10  E-value: 2.10e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  36 CRNTSDADDLVQETLTKALAKIEQFEPGTSLKSWLFTIMRNTFYTQAKLARREAPGVSDCASTRLR----------VDAT 105
Cdd:PRK12522  24 AKTKEDAEDIFQETWIKVFSSRHQLSYVENYKKWITTICVRTFYDFYRKKKRWKDRILDLFHKEDGgeiefaddvnISEE 103

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 518231705 106 QEWSTRGRELHEAIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTVK 155
Cdd:PRK12522 104 FIQKVEAEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVK 153
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 25-146 4.25e-09

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 53.50  E-value: 4.25e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  25 IPALRAFARTFCRNTSDADDLVQETLTKALAKIEQFEPG-TSLKSWLFTIMRNTFYTQAKlARREAP--GVSDCASTRLR 101
Cdd:PRK05602  30 LPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPGeARFDTWLHRVVLNLCYDRLR-RRREVPveDAPDVPDPAPG 108

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 518231705 102 VDATQEWSTRGRELHEAIQRLPPQHREIIVLVGVLGMSYEEAGEI 146
Cdd:PRK05602 109 PDAGLEARQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAV 153
PRK12512 PRK12512
RNA polymerase sigma factor; Provisional
 21-155 7.92e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 171551 [Multi-domain]  Cd Length: 184  Bit Score: 52.78  E-value: 7.92e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  21 IVALIPALRAFARTFCRN----TSDADDLVQETLTKALAKIEQFEPGTSLKSWLFTIMRNtfytqaKL-------ARREA 89
Cdd:PRK12512  28 LKAVTPVLRAAARRGLARagqpADQAEDIVQEILLAVHLKRHTWDPGAPFAPWLFAIARN------KLidalrrrGRRVF 101

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 518231705  90 PGVSDCASTRLRVDATQewSTRGRELHEAIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTVK 155
Cdd:PRK12512 102 VDIDDFAETLPAEPATE--TLPAGDVGRHLETLPPRQRDVVQSISVEGASIKETAAKLSMSEGAVR 165
PRK12520 PRK12520
RNA polymerase sigma factor; Provisional
 18-88 1.26e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 237126 [Multi-domain]  Cd Length: 191  Bit Score: 52.43  E-value: 1.26e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 518231705  18 SSEIVALIPALRAFARTFCRNTSDADDLVQETLTKALAKIEQFEPGTSLKSWLFTIMRNTFYTQAKLARRE 88
Cdd:PRK12520   5 PAQLEALRPHLLRFARLQLRDPALAEDAVSETLLAVLEHPERFAGQSSLKTYLVGILKHKIIDAIRSGRRE 75
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 113-157 1.58e-08

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


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 48.99  E-value: 1.58e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 518231705  113 RELHEAIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTVKSR 157
Cdd:pfam08281   2 EALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSR 46
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 32-158 2.20e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 52.27  E-value: 2.20e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  32 ARTFCRNTSDADDLVQETLTKALAKIEQFEPGTSLKSWLFTIMRNTFYTQAKLARR--------EAPGVSDCASTRLRVD 103
Cdd:PRK11922  47 ARAILRNDAEAEDVVQEAYLRAFRALGTFRGDASLSTWLSRIVLNEALGRLRRRRRlvnlaemvMASTIAGGERTPLADP 126

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705 104 ATQEWSTRGRE-----LHEAIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTVKSRL 158
Cdd:PRK11922 127 AEDPERAAARReiralLERAIDALPDAFRAVFVLRVVEELSVEETAQALGLPEETVKTRL 186
PRK08241 PRK08241
RNA polymerase subunit sigma-70;
41-149 5.15e-08

RNA polymerase subunit sigma-70;


Pssm-ID: 236196 [Multi-domain]  Cd Length: 339  Bit Score: 51.48  E-value: 5.15e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  41 DADDLVQETLTKALAKIEQFEPGTSLKSWLFTIMRNTFYTQAKLARR---------EAPGVSDCASTRLRV-------DA 104
Cdd:PRK08241  45 DAEDAVQETLLRAWRGYDRFEGRSSLRTWLYRIATNVCLDALEGRARrplptdlgaPAADPVDELVERPEVpwlepypDA 124

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 518231705 105 TQEWSTRG-------RELHE-----AIQRLPPQHREIIVLVGVLGMSYEEAGEICGC 149
Cdd:PRK08241 125 LLDPAAADpaarvvaRESVRlafvaALQHLPPRQRAVLILRDVLGWSAAEVAELLDT 181
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 42-155 7.27e-08

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 50.13  E-value: 7.27e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  42 ADDLVQETLTKALAKIEQFEPGTSLKSWLFTIMRNTF--YTQAKLARREAPGVSDCASTRLRVDATQE---WSTRGRELH 116
Cdd:PRK09415  43 AEDLTQEIFVKCYKSLHTYKGKSSLKTWLYRIAINHCkdYLKSWHNKKVIVTEDIFTYMESQKESVEEeviQNAEDERLA 122

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 518231705 117 EAIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTVK 155
Cdd:PRK09415 123 SAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVK 161
PRK12534 PRK12534
RNA polymerase sigma factor; Provisional
 40-156 1.20e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183576 [Multi-domain]  Cd Length: 187  Bit Score: 49.67  E-value: 1.20e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  40 SDADDLVQETLTKALAKIEQFEPGTSLK-SWLFTIMRNTF--YTQAKLARREAPGVSDCAstRLRVD-----ATQEWSTR 111
Cdd:PRK12534  50 AEAEEVLQDVFTLIWHKAGQFDPSRARGlTWLAMIARNKAidHLRANAPQRRNVALDDAG--ELRAAdasplERTERAST 127

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 518231705 112 GRELHEAIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTVKS 156
Cdd:PRK12534 128 RRRIDHCLAELEPPRSELIRTAFFEGITYEELAARTDTPIGTVKS 172
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 26-171 2.48e-07

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 48.76  E-value: 2.48e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  26 PALRAFARTFCRNTSDADDLVQETLTKALAKIEQFEPG-TSLKSWLFTIMRNtfYTQAKLARREA------PGVSDCAST 98
Cdd:PRK13919  34 GAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRrGSARAWLLALAHH--AAVDHVRRRAArpqplePDEREPEAF 111

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 518231705  99 RLRVDATQEWSTRGR-ELHEAIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTVKSRLSRARLRLLEELDE 171
Cdd:PRK13919 112 DLPGPGLDEEGHLDRtRLGRALKALSPEERRVIEVLYYQGYTHREAAQLLGLPLGTLKTRARRALSRLKEVLRE 185
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 11-156 2.48e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 48.62  E-value: 2.48e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  11 HASHQQSSSEIVALipalrafARTFCRNTSDADDLVQETLTKALAKIEQFEPGT-SLKSWLFTIMRNTFYTQAKLARREA 89
Cdd:PRK12537  26 QALYQQESARLLGV-------ARRIVRDRALAEDIVHDAFIKIWTGAASFDPARgSARGWIYSVTRHLALNVLRDTRREV 98

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  90 P---GVSDCASTRLRVDATQEWSTRGRELHEAIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTVKS 156
Cdd:PRK12537  99 VlddDAEETAQTLHEIIDDFDLWANSGKIHRCLEQLEPARRNCILHAYVDGCSHAEIAQRLGAPLGTVKA 168
PRK12530 PRK12530
RNA polymerase sigma factor; Provisional
 31-76 5.37e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 237128 [Multi-domain]  Cd Length: 189  Bit Score: 47.84  E-value: 5.37e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 518231705  31 FARTFCRNTSDADDLVQETLTKALAKIEQFEPGTSLKSWLFTIMRN 76
Cdd:PRK12530  23 FATLQLKDADLAEDVVQEALVSAYKNADSFKGQSALKTWIFAILKN 68
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 113-157 1.77e-06

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: 43.63  E-value: 1.77e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 518231705 113 RELHEAIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTVKSR 157
Cdd:cd06171    2 ERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQR 46
PRK12532 PRK12532
RNA polymerase sigma factor; Provisional
 19-76 3.65e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 171564 [Multi-domain]  Cd Length: 195  Bit Score: 45.69  E-value: 3.65e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 518231705  19 SEIVALIPALRAFARTFCRNTSD-ADDLVQETLTKALAKIEQFEPGTSLKSWLFTIMRN 76
Cdd:PRK12532   9 AELIESRKLLLHFARLQLPDHPDlAEDLVQETLLSAYSAGDSFQGRALVNSWLFAILKN 67
PRK12531 PRK12531
RNA polymerase sigma factor; Provisional
 26-156 5.65e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 105726 [Multi-domain]  Cd Length: 194  Bit Score: 44.92  E-value: 5.65e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  26 PALRAFARTFCRNTSDADDLVQETLTKALAKIEQFE-PGTSLKSWLFTIMRNTFYTQAKLAR-REAPGVSD--CASTRLR 101
Cdd:PRK12531  38 PKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDgQKSALSTWIYTIIRNLCFDLLRKQKgKDLHIHADdiWPSDYYP 117

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 518231705 102 VDATQEWSTRGRELHEAIQR----LPPQHREIIVLVGVLGMSYEEAGEICGCALGTVKS 156
Cdd:PRK12531 118 PDLVDHYSPEQDMLKEQVMKfldrLPKAQRDVLQAVYLEELPHQQVAEMFDIPLGTVKS 176
PRK09191 PRK09191
two-component response regulator; Provisional
 18-154 4.00e-05

two-component response regulator; Provisional


Pssm-ID: 236402 [Multi-domain]  Cd Length: 261  Bit Score: 42.91  E-value: 4.00e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  18 SSEIVALIPALRAFARTFCRNTSDADDLVQETLTKALAKIEQFEPGTSLKSWLFTIMRNTFYTQAKLARREAPGVSDCAS 97
Cdd:PRK09191   4 SQRIAPHLPYLRRYARALTGSQSSGDAYVAATLEALLADPSIFPEASSPRVGLYRLFHRLWSSAGANDPEPGSPFEARAE 83

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 518231705  98 TRLrvdatqewstrgrelheaiQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTV 154
Cdd:PRK09191  84 RRL-------------------AGLTPLPRQAFLLTALEGFSVEEAAEILGVDPAEA 121
PRK12545 PRK12545
RNA polymerase factor sigma-70;
28-87 4.92e-05

RNA polymerase factor sigma-70;


Pssm-ID: 183584 [Multi-domain]  Cd Length: 201  Bit Score: 42.25  E-value: 4.92e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  28 LRAFARTFCRNTSDADDLVQETLTKALAKIEQFEPGTSLKSWLFTIMRNTFYTQAKLARR 87
Cdd:PRK12545  21 LLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQSAHKTWVFGILRNKLIDTLRARQR 80
PRK12536 PRK12536
RNA polymerase sigma factor; Provisional
 28-155 5.46e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 237131 [Multi-domain]  Cd Length: 181  Bit Score: 41.96  E-value: 5.46e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  28 LRAFART-FCRNTSDADDLVQETLTKALAKIEQFEPGTSLKSWLFTIMRntfYTQAKL----ARREAPGVSDCASTRLRV 102
Cdd:PRK12536  34 LRGFLRRrLPQLPDEVEDLVQEILLAVHNARHTYRADQPLTAWVHAIAR---YKLMDFlrsrARREALHDPLDDESELFA 110

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 518231705 103 DATQEWSTRGRELHEAIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTVK 155
Cdd:PRK12536 111 TSDDEAAEARRDLGKLLEQLPDRQRLPIVHVKLEGLSVAETAQLTGLSESAVK 163
PRK12539 PRK12539
RNA polymerase sigma factor SigF;
23-155 7.29e-05

RNA polymerase sigma factor SigF;


Pssm-ID: 237132 [Multi-domain]  Cd Length: 184  Bit Score: 41.64  E-value: 7.29e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  23 ALIPALRAFART----FCRNTSDADDLVQETLTKALAKIEQFEPGTSLKSWLFTIMRntfYTQAKLARREAPGVSDcast 98
Cdd:PRK12539  29 RLSGHLRAYYKGklarIGRGAEEAEDLVQEALMAIHTRRHTYDPEQPLTPWVYAIAR---YKLIDHLRRTRASLAD---- 101

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 518231705  99 rLRVDATQEWSTR--------GRELHEAIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTVK 155
Cdd:PRK12539 102 -VPIDDADELVAHddhaavesTLDLGRLLARLPEKMRLAIQAVKLEGLSVAEAATRSGMSESAVK 165
PRK09648 PRK09648
RNA polymerase sigma factor ShbA;
37-155 7.63e-05

RNA polymerase sigma factor ShbA;


Pssm-ID: 236607 [Multi-domain]  Cd Length: 189  Bit Score: 41.49  E-value: 7.63e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  37 RNTSDADDLVQETLTKALAKIEQFEP-GTSLKSWLFTI------------MRNTFYTQAKLARREAPGVSDcASTRLRVD 103
Cdd:PRK09648  50 RPGLSADDVAQEVCLAVITALPRYRDqGRPFLAFVYGIaahkvadahraaGRDKAVPTEEVPERPSDDAGP-EERALRSE 128

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 518231705 104 AtqewSTRGRELheaIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTVK 155
Cdd:PRK09648 129 S----SNRMREL---LDTLPEKQREILILRVVVGLSAEETAEAVGSTPGAVR 173
PRK12544 PRK12544
RNA polymerase factor sigma-70;
31-76 1.73e-04

RNA polymerase factor sigma-70;


Pssm-ID: 183583 [Multi-domain]  Cd Length: 206  Bit Score: 40.94  E-value: 1.73e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 518231705  31 FARTFCRNTSDADDLVQETLTKALAKIEQFEPGTSLKSWLFTIMRN 76
Cdd:PRK12544  34 FATLQLSDLHLAEDAVQEALIGALKNADSFAGRAAFKTWVFAILKN 79
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 118-155 2.99e-04

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: 37.41  E-value: 2.99e-04
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 518231705  118 AIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTVK 155
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVR 38
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 38-156 4.98e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 39.27  E-value: 4.98e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  38 NTSDADDLVQETLTKALAKiEQFEPGT-SLKSWLFTIMRN-------TFYTQAKLARR-------EAPGVSDCASTRLrv 102
Cdd:PRK12519  52 NSQEAEDLTQEIFLSLWRK-SSYDPKRgSLSSYLLTLTRSraidrlrSRRSRQRLLERwqqellgEASEDTPLEQASL-- 128

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 518231705 103 datqewSTRGRELHEAIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTVKS 156
Cdd:PRK12519 129 ------AERSQRVQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKA 176
PRK06704 PRK06704
RNA polymerase subunit sigma-70;
28-157 9.57e-04

RNA polymerase subunit sigma-70;


Pssm-ID: 180663 [Multi-domain]  Cd Length: 228  Bit Score: 38.85  E-value: 9.57e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  28 LRAFARTFCRNTSDADDLVQETLTKALAKIEQFEPGTSLkswLFTIMRNTFYTQAKlarreapgvSDCASTRLRVDAT-Q 106
Cdd:PRK06704  30 LKRYCTFLTKNKWDGEDLAQETVCKVLQKYSNKDICMTL---VYKIARNRWLDQIK---------SKSVHEKIRDQITfE 97

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 518231705 107 EWSTRGRELHEAIQR----LPPQHREIIVLVGVLGMSYEEAGEICGCALGTVKSR 157
Cdd:PRK06704  98 EPHEKIADLHEMVGKvlssLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKAS 152
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
 38-146 2.59e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 37.53  E-value: 2.59e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  38 NTSDADDLVQETLTKALAKIEQFEPGTS-LKSWLFTIMRNTFYTQAKLARRE-APGVSDCASTRLRVDATQEWSTRGREL 115
Cdd:PRK12538  86 NRADAEDVVQDTMLKVWTHRGRWQHGRAkFSTWLYRVVSNRCIDLRRKPRTEnVDAVPEVADGKPDAVSVIERNELSDLL 165

                         90       100       110
                 ....*....|....*....|....*....|.
gi 518231705 116 HEAIQRLPPQHREIIVLVGVLGMSYEEAGEI 146
Cdd:PRK12538 166 EAAMQRLPEQQRIAVILSYHENMSNGEIAEV 196
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 114-156 4.39e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 36.64  E-value: 4.39e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 518231705 114 ELHEAIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTVKS 156
Cdd:PRK12543 110 ELIELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKS 152
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 43-157 7.34e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 35.85  E-value: 7.34e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518231705  43 DDLVQETLTKALAKIEQFEPGTSLKSWLFTIMRNTfytqAKLARREApgvsdcASTRLRVDAT----QEWSTRG----RE 114
Cdd:PRK12518  38 DDLVQEVFLRVWKGLPKLRNPAYFSTWLYRITWNV----ATDARRQF------AQRPSRIQDDslndQPSRPSDtpdlMQ 107

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 518231705 115 LH------EAIQRLPPQHREIIVLVGVLGMSYEEAGEICGCALGTVKSR 157
Cdd:PRK12518 108 LHyqdlvqQGLQTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSR 156
 
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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