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Conserved domains on  [gi|446746728|ref|WP_000823984|]
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MULTISPECIES: RNA polymerase sigma factor [Bacillus]

Protein Classification

PRK12541 family protein( domain architecture ID 11485985)

PRK12541 family protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 1-161 4.14e-111

RNA polymerase sigma factor; Provisional


:

Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 312.64  E-value: 4.14e-111
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   1 MKRKQSLEDIYSEHMQDLFRYLLSLTGDSHYAEDLMQETFYRMLVHIDYYKGEEIRPWLFTIAYNAFIDWYRKEKRYKTT 80
Cdd:PRK12541   1 MKRKQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGEEIRPWLFTIAYNAFIDWYRKEKKYKTT 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728  81 TITEFHLPNVPSTEHSYFVKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKETQSIK 160
Cdd:PRK12541  81 TIEEFHLPNVPSTEHEYFIKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKETKSIK 160


                 .
gi 446746728 161 E 161
Cdd:PRK12541 161 E 161
 
Name Accession Description Interval E-value
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 1-161 4.14e-111

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 312.64  E-value: 4.14e-111
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   1 MKRKQSLEDIYSEHMQDLFRYLLSLTGDSHYAEDLMQETFYRMLVHIDYYKGEEIRPWLFTIAYNAFIDWYRKEKRYKTT 80
Cdd:PRK12541   1 MKRKQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGEEIRPWLFTIAYNAFIDWYRKEKKYKTT 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728  81 TITEFHLPNVPSTEHSYFVKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKETQSIK 160
Cdd:PRK12541  81 TIEEFHLPNVPSTEHEYFIKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKETKSIK 160


                 .
gi 446746728 161 E 161
Cdd:PRK12541 161 E 161
SigM_subfam TIGR02950
RNA polymerase sigma factor, SigM family; This family of RNA polymerase sigma factors is a ...
 11-161 7.37e-70

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: 208.08  E-value: 7.37e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   11 YSEHMQDLFRYLLSLTGDSHYAEDLMQETFYRMLVHIDYYKGEEIRPWLFTIAYNAFIDWYRKEKRYKTT---TITEFHL 87
Cdd:TIGR02950   1 YREYMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKDSSIKPWLFRIARNAFIDWYRKDKKIQTIdddAIGDLEQ 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446746728   88 PNVPSTEHSYFVKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKETQSIKE 161
Cdd:TIGR02950  81 HPVESPEHHLLIKIEQEEITHHLSRLPENYRTVLILREFKEFSYKEIAELLNLSLAKVKSNLFRARKELKKLLE 154
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 4-154 2.02e-40

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: 133.97  E-value: 2.02e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   4 KQSLEDIYSEHMQDLFRYLLSLTGDSHYAEDLMQETFYRMLVHIDYYKGEE-IRPWLFTIAYNAFIDWYRKEKRYKTTT- 81
Cdd:COG1595   16 EAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGsFRAWLYRIARNLAIDHLRKRRRRRELLd 95

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446746728  82 -ITEFHLPNVPSTEHSYFVKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRK 154
Cdd:COG1595   96 eLAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARK 169
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 10-76 2.75e-15

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: 66.46  E-value: 2.75e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   10 IYSEHMQDLFRYLLSLTGDSHYAEDLMQETFYRMLVHIDYY---KGEEIRPWLFTIAYNAFIDWYRKEKR 76
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFdpeRGVSFSTWLYTIIRNAIIDYLRKQRR 70
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 107-154 1.05e-08

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: 48.64  E-value: 1.05e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 446746728 107 LDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRK 154
Cdd:cd06171    5 EEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALK 52
 
Name Accession Description Interval E-value
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 1-161 4.14e-111

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 312.64  E-value: 4.14e-111
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   1 MKRKQSLEDIYSEHMQDLFRYLLSLTGDSHYAEDLMQETFYRMLVHIDYYKGEEIRPWLFTIAYNAFIDWYRKEKRYKTT 80
Cdd:PRK12541   1 MKRKQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGEEIRPWLFTIAYNAFIDWYRKEKKYKTT 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728  81 TITEFHLPNVPSTEHSYFVKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKETQSIK 160
Cdd:PRK12541  81 TIEEFHLPNVPSTEHEYFIKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKETKSIK 160


                 .
gi 446746728 161 E 161
Cdd:PRK12541 161 E 161
SigM_subfam TIGR02950
RNA polymerase sigma factor, SigM family; This family of RNA polymerase sigma factors is a ...
 11-161 7.37e-70

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: 208.08  E-value: 7.37e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   11 YSEHMQDLFRYLLSLTGDSHYAEDLMQETFYRMLVHIDYYKGEEIRPWLFTIAYNAFIDWYRKEKRYKTT---TITEFHL 87
Cdd:TIGR02950   1 YREYMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKDSSIKPWLFRIARNAFIDWYRKDKKIQTIdddAIGDLEQ 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446746728   88 PNVPSTEHSYFVKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKETQSIKE 161
Cdd:TIGR02950  81 HPVESPEHHLLIKIEQEEITHHLSRLPENYRTVLILREFKEFSYKEIAELLNLSLAKVKSNLFRARKELKKLLE 154
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 4-154 2.02e-40

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: 133.97  E-value: 2.02e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   4 KQSLEDIYSEHMQDLFRYLLSLTGDSHYAEDLMQETFYRMLVHIDYYKGEE-IRPWLFTIAYNAFIDWYRKEKRYKTTT- 81
Cdd:COG1595   16 EAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGsFRAWLYRIARNLAIDHLRKRRRRRELLd 95

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446746728  82 -ITEFHLPNVPSTEHSYFVKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRK 154
Cdd:COG1595   96 eLAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARK 169
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 5-154 2.76e-34

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: 117.83  E-value: 2.76e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728    5 QSLEDIYSEHMQDLFRYLLSLTGDSHYAEDLMQETFYRMLVHIDYYKGEE-IRPWLFTIAYNAFIDWYRKEKRYKTTTIT 83
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGsFKAWLFRIARNLILDYLRRKRRLRRELDL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446746728   84 EFHLPNVPSTEHSYFVKHEIASWL-DSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRK 154
Cdd:TIGR02937  81 LEELLDSDPSPEEELEQEEEREALrEALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARK 152
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 6-154 1.25e-30

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 108.81  E-value: 1.25e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   6 SLEDIYSEHMQDLFRYLLSLTGDSHYAEDLMQETFYRMLVHIDYYKGEEIRPWLFTIAYNAFIDWYRKEKRYKTTTITEF 85
Cdd:PRK09644   2 EIEEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDNQKVKPWLFKVAYHTFIDFVRKEKKVSFVGTDEI 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728  86 HLPNVPSTEhSYFVKHEIASWLDS-LSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRK 154
Cdd:PRK09644  82 EAIQAESTE-EYVVAKNSYEKLIQiIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRK 150
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 2-153 6.22e-29

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 104.67  E-value: 6.22e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   2 KRKQSLEDIYSEHMQDLFRYLLSLTGDSHYAEDLMQETFYRMLVHIDYYKGE-EIRPWLFTIAYNAFIDWYRKEKRYKTT 80
Cdd:PRK11924  10 GDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKgSARTWLLTIARNVCYDLLRRRRREKAV 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728  81 TITE-------FHLPNVPSTEHSyfvKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGR 153
Cdd:PRK11924  90 LSDDalepefaETAETPEAALLA---KDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRAR 166
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 4-155 2.15e-27

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 100.48  E-value: 2.15e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   4 KQSLEDIYSEHMQDLFRYLLSLTGDSHYAEDLMQETFYRMLVHIDYYKGE-EIRPWLFTIAYNAFIDWYRKEKRYKTTTI 82
Cdd:PRK09638  17 DAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGRsKFSTWLISIASRLYKDHLRKQKREKLRLQ 96

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446746728  83 TEFHLPNVPSTEHSYFVKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKE 155
Cdd:PRK09638  97 RAKEETLRKEKWEAAIKGAEWSEMLDALSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTVKSRVHHGIKQ 169
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 3-154 9.00e-27

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 99.11  E-value: 9.00e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   3 RKQSLEDIYSEHMQDLFRYLLSLTGDSHYAEDLMQETFYRMLVHIDYYKGEE-IRPWLFTIAYNAFIDWYRKEKR----- 76
Cdd:PRK09652   8 DRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRGGAaFYTWLYRIARNTAINYLRKQGRrppas 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728  77 -YKTTTITEF---HLPNVPSTEHSYFVKHEIASWL-DSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHR 151
Cdd:PRK09652  88 dVDAEEAEDFdlaDALRDISTPENELLSAELEQRVrAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRIFR 167


                 ...
gi 446746728 152 GRK 154
Cdd:PRK09652 168 ARE 170
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 6-155 2.04e-25

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 95.82  E-value: 2.04e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   6 SLEDIYSEHMQDLFRYLLSLTGDSHYAEDLMQETFYRMLVHIDYYK-GEEIRPWLFTIAYNAFIDWYRKEKRYKTTTITE 84
Cdd:PRK09637   2 KLESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKdGSSIKSWLYQIANNTIIDFYRKKNRSEELPDDL 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446746728  85 FHlpnvPSTEHSYFVKHEIASWLDS-LSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKE 155
Cdd:PRK09637  82 LF----EDEEREENAKKELAPCLRPfIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRVK 149
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
10-150 1.72e-24

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 93.22  E-value: 1.72e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728  10 IYSEHMQDLFRYLLSLTGDSHYAEDLMQETFYRMLVHIDYYKGEE--IRPWLFTIAYNAFIDWYRKEK-RYKTTTITEFH 86
Cdd:PRK09645  14 LYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTGrsARAWLFTVARNLVIDERRSARaRPVEGGDDVLG 93

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446746728  87 LPNVPSTEHsyfVKHEIASWL--DSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELH 150
Cdd:PRK09645  94 VPEQSAPDE---VDRALDRLLvaDALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLH 156
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 5-154 1.88e-24

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 92.70  E-value: 1.88e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   5 QSLEDIYSEHMQDLFRYLLSLTGDSHYAEDLMQETFYRMLvHIDYYKGEEIRPWLFTIAYNAFIDWYRKEKRYKTTTITE 84
Cdd:PRK09639   3 ETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLY-RSDFKGIENEKGWLIKSARNVAYNYLRSEKRRRARILGE 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446746728  85 FH---LPNVPSTEHSYFVKHEIASWLDSLSSLPLERRNVLLLRdYYGFSYKEIAEMTGLSLAKVKIELHRGRK 154
Cdd:PRK09639  82 FQwqeVDNEPSPEEIWIRKEEITKVQEVLAKMTERDRTVLLLR-FSGYSYKEIAEALGIKESSVGTTLARAKK 153
SigZ TIGR02959
RNA polymerase sigma factor, SigZ family; This family of RNA polymerase sigma factors is a ...
 11-154 2.81e-24

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: 92.43  E-value: 2.81e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   11 YSEHMQDLFRYLLSLTGDSHYAEDLMQETFYRMLVHIDYYKGEE-IRPWLFTIAYNAFIDWYRKEKRYKTTTITEFHlpn 89
Cdd:TIGR02959   1 WDEFRSELKAFIKSRVSDASDVEDLLQEVFIKIHRNLPSLKDGQkIQSWLYQIARNTIIDFYRSKSRSVELPESLLA--- 77

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446746728   90 VPSTEHSYFVKhEIASWLDS-LSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRK 154
Cdd:TIGR02959  78 ADSAREETFVK-ELSQCIPPmIKELPDEYREAIRLTELEGLSQQEIAEKLGLSLSGAKSRVQRGRK 142
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 8-161 6.21e-23

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 89.75  E-value: 6.21e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   8 EDIYSEHMQDLFRYLLSLTGDSHYAEDLMQETFYRMLVHIDYYKGE-EIRPWLFTIAYNAFIDWYRKEKRYKTTTI---T 83
Cdd:PRK12513  29 EALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPRaRFRTWLYQIARNLLIDHWRRHGARQAPSLdadE 108

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728  84 EFHLpnVPSTEHSyfVKHEIASWLDS------LSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKielHRGRKETQ 157
Cdd:PRK12513 109 QLHA--LADDGAA--PEQQLSLFRDRrrlqaaLETLPDEQREVFLLREHGDLELEEIAELTGVPEETVK---SRLRYALQ 181


                 ....
gi 446746728 158 SIKE 161
Cdd:PRK12513 182 KLRE 185
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 6-153 7.10e-23

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 89.85  E-value: 7.10e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   6 SLEDIYSEHMQDLFRYLLSLTGDSHYAEDLMQETFYRMLVHIDYYKGEEIRPWLFTIAYNAFIDWYRKEKRYKTTTITEF 85
Cdd:PRK09647  29 SWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQPGTFEGWLHRITTNLFLDMVRRRARIRMEALPED 108

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446746728  86 H--LP-NVPSTEHSYFVKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGR 153
Cdd:PRK09647 109 YdrVPgDEPNPEQIYHDARLDPDLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGR 179
SigH_actino TIGR02947
RNA polymerase sigma-70 factor, TIGR02947 family; This group of sigma factors are members of ...
 2-155 7.51e-22

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: 86.95  E-value: 7.51e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728    2 KRKQSLEDIYSEHMQDLFRYLLSLTGDSHYAEDLMQETFYRMLVHIDYYK-GEEIRPWLFTIAYNAFIDWYRKEKR---- 76
Cdd:TIGR02947   8 QRAQRFERDALEYLDQLYGAALRMTRNPADAEDLVQEAYAKAFSSFHQFKpGTNLKAWLYRILTNTYINSYRKAQRrpqq 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   77 YKTTTITEFHLPNVPSTEHSYFVKHEIASW--------LDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIE 148
Cdd:TIGR02947  88 SDDDDIEDWQLAKAASHTSNGLRSAELEALdglpdqdiKDALQGLPEEFRQAVYLADVEGFAYKEIAEIMGTPIGTVMSR 167


                  ....*..
gi 446746728  149 LHRGRKE 155
Cdd:TIGR02947 168 LHRGRKQ 174
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
 4-153 1.01e-20

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 83.74  E-value: 1.01e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   4 KQSLEDIYSEHMQDLFRYLLSLTGDSHYAEDLMQETFYRMLVHIDYYK-GEEIRPWLFTIAYNAFIDWYRKEKRykttti 82
Cdd:PRK12546   6 HRDPRDELVEHLPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQeGTNLRAWLFTILRNTFYSDRRKHKR------ 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728  83 tefhlpNVPSTE----HSYFVK--HE----IASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRG 152
Cdd:PRK12546  80 ------EVPDPEgvhaASLAVKpaHDgrlaMSDFRAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRA 153


                 .
gi 446746728 153 R 153
Cdd:PRK12546 154 R 154
SigE-fam_strep TIGR02983
RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors ...
 5-155 3.67e-19

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: 78.97  E-value: 3.67e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728    5 QSLEDIYSEHMQDLFRYLLSLTGDSHYAEDLMQETFYRMlvhidYYKGEEIR------PWLFTIAYNAFIDWYRKEKRyk 78
Cdd:TIGR02983   6 EEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRT-----YVRWDRIRdpdapdAYVRRVLVNLARSRWRRRRL-- 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446746728   79 tttiTEFHLPNVP--STEHSYFVKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKE 155
Cdd:TIGR02983  79 ----LELPTRELPdaAAPDPAPDVALRAALARALRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALAR 153
PRK12540 PRK12540
RNA polymerase sigma factor; Provisional
 1-155 1.57e-17

RNA polymerase sigma factor; Provisional


Pssm-ID: 183579 [Multi-domain]  Cd Length: 182  Bit Score: 75.39  E-value: 1.57e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   1 MKRKQSLEDIYSEHMQDLFRYLLSLTGDSHYAEDLMQETFYRMLVHIDYYK-GEEIRPWLFTIAYNAFIDWYRKEKR--- 76
Cdd:PRK12540   1 MPLTDSLRDDILAAVPSLRAFAISLSGNGDRADDLVQETLLRALANIDSFQpGSNLPAWLFTILRNLFRSDYRKRRReve 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728  77 -----YKTTTITEfhlPNvpSTEHSYFVKHEIAswldsLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHR 151
Cdd:PRK12540  81 dadgsYAKTLKSQ---PG--QNAHLEFEEFRAA-----LDKLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNR 150


                 ....
gi 446746728 152 GRKE 155
Cdd:PRK12540 151 ARSK 154
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 1-161 2.32e-17

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 74.82  E-value: 2.32e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   1 MKRKQSLEDIYSEhMQDLFRYLLSLTGDSHYAEDLMQETFYRMLVHIDYYK-GEEIRPWLFTIAYNAFIDWYRK---EKR 76
Cdd:PRK12511   1 MERKSKRFDVLDQ-LVPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRsGGNLRTWLMSILHNAFIDELRRrrvEAR 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728  77 YKTTTITEFHLPNVPSTEHSYfvkhEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKET 156
Cdd:PRK12511  80 RADELAVLADASLPAAQEHAV----RLAQIRDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAAL 155


                 ....*
gi 446746728 157 QSIKE 161
Cdd:PRK12511 156 RAFEE 160
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 4-153 1.21e-15

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 70.50  E-value: 1.21e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   4 KQSLEDIYSEHMQDLFRYLLSLTGDSHYAEDLMQETFYRMLVHIDYYKGE-EIRPWLFTIAYNAFIDWYRKEK--RYKTT 80
Cdd:PRK09641  17 QNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINrKFSTWLYRIATNLTIDRLRKRKpdYYLDA 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728  81 TIT-------EFHLPNVPSTEHSYFVKHEIASWL-DSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRG 152
Cdd:PRK09641  97 EVAgtegltmYSQLAADDALPEEQVVSLELQETIqEAILQLPEKYRTVIVLKYIEDLSLKEISEILDLPVGTVKTRIHRG 176


                 .
gi 446746728 153 R 153
Cdd:PRK09641 177 R 177
PRK12517 PRK12517
RNA polymerase sigma factor; Provisional
 1-153 1.76e-15

RNA polymerase sigma factor; Provisional


Pssm-ID: 183569 [Multi-domain]  Cd Length: 188  Bit Score: 70.10  E-value: 1.76e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   1 MKRKQS-LEDIYSEHMQDLFRYLLSLTGDSHYAEDLMQETFYRMLVHIDYYKGEEI-RPWLFTIaynafidwYRKE---- 74
Cdd:PRK12517  18 MLSKQRrYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDEKAaKAWLITI--------LRREnarr 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728  75 ---KRYKTTTITEFHLPNVPSTEHSYFVKHEiasWL-DSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELH 150
Cdd:PRK12517  90 ferKQFDLVDIEDDSIEDDASHSSEEEMEQE---WLrRQIAKLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMTRLF 166


                 ...
gi 446746728 151 RGR 153
Cdd:PRK12517 167 RAR 169
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 2-154 1.77e-15

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 69.78  E-value: 1.77e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   2 KRKQSLEDIYSEHMQDLFRYLLSLTGDSHYAEDLMQETFYRMLVHIDYYKGE-EIRPWLFTIAYNAFID----WYRKeKR 76
Cdd:PRK09415  13 DKEDLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGKsSLKTWLYRIAINHCKDylksWHNK-KV 91

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446746728  77 YKTTTITEFHLPNVPSTEHSYFVKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRK 154
Cdd:PRK09415  92 IVTEDIFTYMESQKESVEEEVIQNAEDERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKE 169
PRK12533 PRK12533
RNA polymerase sigma factor; Provisional
 25-154 1.83e-15

RNA polymerase sigma factor; Provisional


Pssm-ID: 237129 [Multi-domain]  Cd Length: 216  Bit Score: 70.53  E-value: 1.83e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728  25 LTGDSHYAEDLMQETFYRMLVHIDYYKGEEIRPWLFTIAYNA-FIDWYRKEKRYKTTTITEFHLPNVPSTEHSY------ 97
Cdd:PRK12533  38 LCGNASDADDVVQEACMRALRFFDSFRGDNARPWLLAIVRHTwYSEWRRRANAHEVAAPDTLDDADSLDDWQPAgedpla 117

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 446746728  98 -FVKHEIASWL-DSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRK 154
Cdd:PRK12533 118 lLLRAEDVRLVnAALAKLPVEYREVLVLRELEDMSYREIAAIADVPVGTVMSRLARARR 176
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 10-76 2.75e-15

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: 66.46  E-value: 2.75e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   10 IYSEHMQDLFRYLLSLTGDSHYAEDLMQETFYRMLVHIDYY---KGEEIRPWLFTIAYNAFIDWYRKEKR 76
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFdpeRGVSFSTWLYTIIRNAIIDYLRKQRR 70
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 21-159 2.78e-15

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 69.61  E-value: 2.78e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728  21 YLLSLTGDSHYAEDLMQETFYRMLVHIDYYK-GEEIRPWLFTIAYNAFIDWYRKekRYKTTTITEFHLPNVPSTEHSYFV 99
Cdd:PRK12516  26 FAVSLIGRHDRADDLVQDTIMKAWAKQDHFEvGTNMKAWLFTILRNEFYSQMRK--RGREVQDTDGMFTEQLAVHPSQYG 103

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728 100 KHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKETQSI 159
Cdd:PRK12516 104 TLDLQDFRAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQRLQEI 163
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 8-151 1.53e-14

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 67.66  E-value: 1.53e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   8 EDIYSEHMQDLFRYLLSLTGDSHYAEDLMQETFYRMLVHIDYYKGE-EIRPWLFTIAYNAFIDWYRKEKRyKTTTITEFH 86
Cdd:PRK09640  29 EELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGKsKFKTWLYSITYNECITQYRKERR-KRRLMDALS 107

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446746728  87 LPNVPSTEHSYFVKHEIASWLDS-LSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHR 151
Cdd:PRK09640 108 LDPLEEASEEKAPKPEERGGLDRwLVHVNPIDREILVLRFVAELEFQEIADIMHMGLSATKMRYKR 173
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 5-155 2.98e-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: 63.35  E-value: 2.98e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728    5 QSLEDIYSEHMQDLFRYLLSLTGDSHYAEDLMQETF-----YRMLVHIDyykgEEIRPWLFTIAYNAFIDWYRK---EKR 76
Cdd:TIGR02985   1 EAFEQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFlklweNRETLEIS----ESIKAYLFTIVKNRCLNYLRHkqvEEK 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   77 YKTT----TITEFHLPNvpsTEHSYFVKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRG 152
Cdd:TIGR02985  77 YQEElaeiEERELSEAD---PEEELEAKELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKA 153


                  ...
gi 446746728  153 RKE 155
Cdd:TIGR02985 154 LKF 156
PRK12535 PRK12535
RNA polymerase sigma factor; Provisional
 4-155 1.50e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 237130 [Multi-domain]  Cd Length: 196  Bit Score: 62.22  E-value: 1.50e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   4 KQSLEDIYSEHMQDLFRyLLSLTGDSHYAEDLMQETFYRMLVHIDYYKGEE-IRPWLFTIAYNAFIDWYRKEKRYKTTTI 82
Cdd:PRK12535  24 RAALTEFIRETQDDVWR-LLAHLGGHDIADDLTQETYLRVMSALPRFAARSsARTWLLSLARRVWVDNIRHDMARPRKSA 102

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446746728  83 TEFH--LPNVPSTEHSyfvkHEIASWLDS---LSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKE 155
Cdd:PRK12535 103 TEYEdaAATTASNETT----GSWSEWIDVrtlIDALPPERREALILTQVLGYTYEEAAKIADVRVGTIRSRVARARAD 176
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 7-154 2.03e-12

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


Pssm-ID: 274379 [Multi-domain]  Cd Length: 159  Bit Score: 61.18  E-value: 2.03e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728    7 LEDIYSEHMQDLFRYLLSLTGDSHYAEDLMQETFYRMLVHIDYYKGEE-IRPWLFTIAYNAFIDWYRKEKRYKTTTITEF 85
Cdd:TIGR02989   3 FVRLLTRHERALRAFVRSLVADRDDVDDVLQETFVVAWRKFDQFDPGTnFVAWARGIARNKVLNYRRKLGRDRLVFDDDL 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446746728   86 HlpNVPSTEHSYFVKHEIASWLDSL----SSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRK 154
Cdd:TIGR02989  83 L--EALAAEAEPTEAERLSDDRQALegclEKLPERQRELLDLRYQRGQKATALAEQTGRTVNAVYKALQRIRV 153
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 5-154 3.43e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 60.89  E-value: 3.43e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   5 QSLEDIYSEHMQDLFRYLLSLTGdSHYAEDLMQETFYRMLVHIDYYKGEE-IRPWLFTIAYNAFIDWYRK--EKRYKTTT 81
Cdd:PRK12518  11 QSFRQLYRRYQQKVRSTLYQLCG-RELLDDLVQEVFLRVWKGLPKLRNPAyFSTWLYRITWNVATDARRQfaQRPSRIQD 89

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446746728  82 ITEFHLPNVPSTEHSYFVKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRK 154
Cdd:PRK12518  90 DSLNDQPSRPSDTPDLMQLHYQDLVQQGLQTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRLFYARR 162
PRK12522 PRK12522
RNA polymerase sigma factor; Provisional
 4-154 3.75e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 183571 [Multi-domain]  Cd Length: 173  Bit Score: 61.04  E-value: 3.75e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   4 KQSLEDIYSEHMQDLFRYLLSLTGDSHYAEDLMQETFYRMLVHIDYYKGEE-IRPWLFTIAYNAFIDWYRKEKRYKTTTI 82
Cdd:PRK12522   2 EEKVEELIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVEnYKKWITTICVRTFYDFYRKKKRWKDRIL 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728  83 TEFH--------LPNVPSTEHSYFVKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRK 154
Cdd:PRK12522  82 DLFHkedggeieFADDVNISEEFIQKVEAEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKK 161
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 107-154 3.97e-12

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


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 57.85  E-value: 3.97e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 446746728  107 LDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRK 154
Cdd:pfam08281   5 LRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARK 52
PRK12547 PRK12547
RNA polymerase sigma factor; Provisional
 21-159 7.58e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 139056 [Multi-domain]  Cd Length: 164  Bit Score: 59.89  E-value: 7.58e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728  21 YLLSLTGDSHYAEDLMQETFYRMLVHIDYYK-GEEIRPWLFTIAYNAFIDWYRKEKRYKTTT---ITE---FHLPNVPST 93
Cdd:PRK12547  22 FAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEmGTNLKAWLFTILRNEFYSQMRKRGREVQDSdgvFTArvaVHPAQYGSL 101

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446746728  94 EHSYFVKheiaswldSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKETQSI 159
Cdd:PRK12547 102 DLQDFKK--------ALNLLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARNRLQEL 159
PRK12542 PRK12542
RNA polymerase sigma factor; Provisional
 5-159 8.31e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 183581 [Multi-domain]  Cd Length: 185  Bit Score: 60.07  E-value: 8.31e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   5 QSLEDIYSEHMQDLFRYLLSLTGDSHYAEDLMQETF---YRMLVHIDYYKGEEIRPWLFTIAYNAFIDWYRKEKRYKT-- 79
Cdd:PRK12542   9 EKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFitlYKNLEKLHSLNTQELKRYILRVAKNKAIDSYRKNKRHETfl 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728  80 ----TTITEFHLPNVPSTEHSYFVKHEIASWLDSLSSlplERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKE 155
Cdd:PRK12542  89 eeyeRESIEAVDENIEEWEKRKMSEVQIDTLLKELNE---SNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERARKR 165


                 ....
gi 446746728 156 TQSI 159
Cdd:PRK12542 166 VQNM 169
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 6-154 2.26e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 59.59  E-value: 2.26e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   6 SLEDIYSEHMQDLFRYLLSLTGDSHYAEDLMQETFYRMLVHIDYYKGE-EIRPWLFTIAYN-AFIdwyRKEKRYKTTTIT 83
Cdd:PRK11922  31 AFEALMRRHNRRLYRTARAILRNDAEAEDVVQEAYLRAFRALGTFRGDaSLSTWLSRIVLNeALG---RLRRRRRLVNLA 107

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728  84 E------------FHLPNVPSTEHSYFVKHEIASWLDS-LSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELH 150
Cdd:PRK11922 108 EmvmastiaggerTPLADPAEDPERAAARREIRALLERaIDALPDAFRAVFVLRVVEELSVEETAQALGLPEETVKTRLH 187


                 ....
gi 446746728 151 RGRK 154
Cdd:PRK11922 188 RARR 191
SigX4 TIGR02957
RNA polymerase sigma-70 factor, TIGR02957 family; This group of sigma factors are members of ...
 11-154 4.77e-11

RNA polymerase sigma-70 factor, TIGR02957 family; This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.


Pssm-ID: 132002 [Multi-domain]  Cd Length: 281  Bit Score: 59.29  E-value: 4.77e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   11 YSEHMQDLFRYLLSLTGDSHYAEDLMQETFYRmLVHIDYYKGEEIRPWLFTIAYNAFIDWYRKEKRYKTTTITEFhLPN- 89
Cdd:TIGR02957   3 FEALRPLLFSLAYRMLGSVADAEDIVQETFLR-WQEADRAQIENPKAYLTKVVTRRCIDVLRSARARREVYVGPW-LPEp 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446746728   90 VPSTEHSYFVKHEIAswlDSLSS---LPLER-----RNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRK 154
Cdd:TIGR02957  81 LLTTSADPAESVELA---ESLSMaylLLLERlspleRAVFVLREVFDYPYEEIASIVGKSEANCRQLVSRARR 150
PRK09643 PRK09643
RNA polymerase sigma factor SigM; Reviewed
 14-154 1.59e-10

RNA polymerase sigma factor SigM; Reviewed


Pssm-ID: 236604 [Multi-domain]  Cd Length: 192  Bit Score: 56.64  E-value: 1.59e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728  14 HMQDLFRYLLSLTGDSHYAEDLMQETFYRMLVHIDYYKGE-EIRPWLFTIAYNAFIDWYRKEKRYKTTTITEfhLPNVPS 92
Cdd:PRK09643  36 HHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGDaAVSSWLHRIVVNACLDRLRRAKARPTVPLDD--VYPVAQ 113

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446746728  93 TEHSYFVKHEIASWLD-SLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRK 154
Cdd:PRK09643 114 LERDPTARVETALAVQrALMRLPVEQRAALVAVDMQGYSVADAARMLGVAEGTVKSRCARGRA 176
PRK08241 PRK08241
RNA polymerase subunit sigma-70;
1-153 5.05e-10

RNA polymerase subunit sigma-70;


Pssm-ID: 236196 [Multi-domain]  Cd Length: 339  Bit Score: 56.48  E-value: 5.05e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   1 MKRKQSLEDIYSEHMQDLFRYLLS----LTGDSHYAEDLMQETFYRMLVHIDYYKGE-EIRPWLFTIAYNAFIDWYRKEK 75
Cdd:PRK08241  11 ARAAAGDRDAFAALVEPHRRELLAhcyrMLGSVHDAEDAVQETLLRAWRGYDRFEGRsSLRTWLYRIATNVCLDALEGRA 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728  76 RYKTTtiTEFHLPNVPSTEHSyfVKHEIASWL----DSLSS--------------------------LPLERRNVLLLRD 125
Cdd:PRK08241  91 RRPLP--TDLGAPAADPVDEL--VERPEVPWLepypDALLDpaaadpaarvvaresvrlafvaalqhLPPRQRAVLILRD 166

                        170       180
                 ....*....|....*....|....*...
gi 446746728 126 YYGFSYKEIAEMTGLSLAKVKIELHRGR 153
Cdd:PRK08241 167 VLGWSAAEVAELLDTSVAAVNSALQRAR 194
PRK12512 PRK12512
RNA polymerase sigma factor; Provisional
 32-152 7.17e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 171551 [Multi-domain]  Cd Length: 184  Bit Score: 54.70  E-value: 7.17e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728  32 AEDLMQETFyrMLVHID---YYKGEEIRPWLFTIAYNAFIDWYRKEKRYKTTTITEF--HLPNVPSTEHSyfVKHEIASW 106
Cdd:PRK12512  53 AEDIVQEIL--LAVHLKrhtWDPGAPFAPWLFAIARNKLIDALRRRGRRVFVDIDDFaeTLPAEPATETL--PAGDVGRH 128

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 446746728 107 LDslsSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRG 152
Cdd:PRK12512 129 LE---TLPPRQRDVVQSISVEGASIKETAAKLSMSEGAVRVALHRG 171
PRK12528 PRK12528
RNA polymerase sigma factor; Provisional
 6-151 7.38e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 171561 [Multi-domain]  Cd Length: 161  Bit Score: 54.47  E-value: 7.38e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   6 SLEDIYSEHMQDLFRYLLSLTGDSHYAEDLMQETFYRMLVHIDYYKGEEIRPWLFTIAYNAFIDWYRKEKRYKTTTITEF 85
Cdd:PRK12528   5 TVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQIIEPRAFLTTIAKRVLCNHYRRQDLERAYLEALA 84

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446746728  86 HLPN--VPSTEHSYFVKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHR 151
Cdd:PRK12528  85 QLPErvAPSEEERAIILETLVELDQLLDGLPPLVKRAFLLAQVDGLGYGEIATELGISLATVKRYLNK 152
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 4-154 9.64e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 54.35  E-value: 9.64e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   4 KQSLEDIYSEHMQDLFRYLLSLTGDSHYAEDLMQETFYRMLVHIDYYKGEE-IRPWLFTIAYNAFIDWYRKE-KRYKT-T 80
Cdd:PRK12543   6 QEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNRpFRFWLIGLVIKQIHSWRRKRwRRFRIfE 85

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446746728  81 TITEFHLPNVPSTEHSYFVKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRK 154
Cdd:PRK12543  86 KAEEQRKPVSIDFSEDVLSKESNQELIELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAALK 159
PRK12539 PRK12539
RNA polymerase sigma factor SigF;
32-154 1.78e-09

RNA polymerase sigma factor SigF;


Pssm-ID: 237132 [Multi-domain]  Cd Length: 184  Bit Score: 53.97  E-value: 1.78e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728  32 AEDLMQETFyrMLVHID---YYKGEEIRPWLFTIAYNAFIDWYRKEKRyktttitefHLPNVPSTEHSYFVKHEIASWLD 108
Cdd:PRK12539  52 AEDLVQEAL--MAIHTRrhtYDPEQPLTPWVYAIARYKLIDHLRRTRA---------SLADVPIDDADELVAHDDHAAVE 120

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 446746728 109 S-------LSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRK 154
Cdd:PRK12539 121 StldlgrlLARLPEKMRLAIQAVKLEGLSVAEAATRSGMSESAVKVSVHRGLK 173
PRK06704 PRK06704
RNA polymerase subunit sigma-70;
13-161 1.79e-09

RNA polymerase subunit sigma-70;


Pssm-ID: 180663 [Multi-domain]  Cd Length: 228  Bit Score: 54.26  E-value: 1.79e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728  13 EHMQDLFRYLLSLTGDSHYAEDLMQETFYRMLvhiDYYKGEEI-RPWLFTIAYNAFIDWYR----KEKRYKTTTITEFHl 87
Cdd:PRK06704  25 EQYGELKRYCTFLTKNKWDGEDLAQETVCKVL---QKYSNKDIcMTLVYKIARNRWLDQIKsksvHEKIRDQITFEEPH- 100

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446746728  88 PNVPSTehsyfvkHEIASWLdsLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKETQSIKE 161
Cdd:PRK06704 101 EKIADL-------HEMVGKV--LSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRLKTVSE 165
PRK09649 PRK09649
RNA polymerase sigma factor SigC; Reviewed
 4-153 2.99e-09

RNA polymerase sigma factor SigC; Reviewed


Pssm-ID: 137458 [Multi-domain]  Cd Length: 185  Bit Score: 53.12  E-value: 2.99e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   4 KQSLEDIYSEHMQDLFRYLLSLTgDSHYAEDLMQETFYRMLVHIDYYKGEE-IRPWLFTIAYNAFIDWYRKEKRYKTTTI 82
Cdd:PRK09649  23 GRALEAFIKATQQDVWRFVAYLS-DVGSADDLTQETFLRAIGAIPRFSARSsARTWLLAIARHVVADHIRHVRSRPRTTR 101

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446746728  83 TEFHLPNVPSTEHSYFVKH--EIASWLDSLSSlplERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGR 153
Cdd:PRK09649 102 GARPEHLIDGDRHARGFEDlvEVTTMIADLTT---DQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARAR 171
PRK12523 PRK12523
RNA polymerase sigma factor; Reviewed
 10-155 3.82e-09

RNA polymerase sigma factor; Reviewed


Pssm-ID: 183572 [Multi-domain]  Cd Length: 172  Bit Score: 52.93  E-value: 3.82e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728  10 IYSEHMQDLFRYLLSLTGDSHYAEDLMQETFYRMLVHIDYYKGEEIRPWLFTIAYNAFIDWYRK---EKRYktttITEFH 86
Cdd:PRK12523  15 LYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGRPELPTPREPRAFLAAVAKGLMFDHFRRaalEQAY----LAELA 90

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446746728  87 L-PNV--PSTEHSYFVKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKE 155
Cdd:PRK12523  91 LvPEAeqPSPEEQHLILEDLKAIDRLLGKLSSKARAAFLYNRLDGMGHAEIAERLGVSVSRVRQYLAQGLRQ 162
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 1-152 1.01e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 51.98  E-value: 1.01e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   1 MKRKQS--LEDIYSEHMQDLFRYLLSLTGDSHYAEDLMQETFYRMLVHIDY-YKGEEIRPWLFTIAYNAFID----WYRK 73
Cdd:PRK12519  23 LKAGQSaaLGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRKSSYdPKRGSLSSYLLTLTRSRAIDrlrsRRSR 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728  74 EK---RYKTTTITEfhLPNVPSTEHSYF--VKHEIAswlDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIE 148
Cdd:PRK12519 103 QRlleRWQQELLGE--ASEDTPLEQASLaeRSQRVQ---TALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKAR 177


                 ....
gi 446746728 149 LHRG 152
Cdd:PRK12519 178 ARQG 181
PRK12530 PRK12530
RNA polymerase sigma factor; Provisional
 6-157 1.03e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 237128 [Multi-domain]  Cd Length: 189  Bit Score: 51.69  E-value: 1.03e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   6 SLEDIYSEHMQDLFRYLLSLT----GDSHYAEDLMQETFYRMLVHIDYYKGEE-IRPWLFTIAYNAFIDWYRKEKRykTT 80
Cdd:PRK12530   4 QMNHISSLEIEEIRLQMLKFAtlqlKDADLAEDVVQEALVSAYKNADSFKGQSaLKTWIFAILKNKIIDLIRYRKR--FV 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728  81 TITEFHLPNVPST--------EHSYFVKHEIAS----------WL---DSLSSLPLERRNVLLLRDYYGFSYKEIAEMTG 139
Cdd:PRK12530  82 NESELIEEDSPNSffdekghwKPEYYEPSEWQEventvykeefWLifeACLNHLPAQQARVFMMREYLELSSEQICQECD 161

                        170
                 ....*....|....*...
gi 446746728 140 LSLAKVKIELHRGRKETQ 157
Cdd:PRK12530 162 ISTSNLHVLLYRARLQLQ 179
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 107-154 1.05e-08

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: 48.64  E-value: 1.05e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 446746728 107 LDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRK 154
Cdd:cd06171    5 EEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALK 52
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 1-151 3.62e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 50.20  E-value: 3.62e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   1 MKRKQSLEDIYSEHMQDLFRYLLSLTGDSHYAEDLMQETFYRMLVHIDYYKGEEIRP--WLFTIAYNAFIDWYRKeKRYK 78
Cdd:PRK12514  15 LGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSGLSPmtWLITIARNHAIDRLRA-RKAV 93

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446746728  79 TTTITEFH--LPNVPSTEHSYFVKHEIASWLDSLSSLPLERRNVllLRDYY--GFSYKEIAEMTGLSLAKVKIELHR 151
Cdd:PRK12514  94 AVDIDEAHdlADPSPGPEAEVIAGDEGQRIDACLEELEKDRAAA--VRRAYleGLSYKELAERHDVPLNTMRTWLRR 168
PRK12525 PRK12525
RNA polymerase sigma factor; Provisional
 26-145 4.84e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 139037 [Multi-domain]  Cd Length: 168  Bit Score: 49.56  E-value: 4.84e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728  26 TGDSHYAEDLMQETFYRMLVHIDYYKGEEIRPWLFTIAYNAFID-WYRKE-KRYKTTTITEFHLPNVPSTEHSYFVKHEI 103
Cdd:PRK12525  30 LGCPHSAEDIASETFLQVLALPDPASIREPRALLTTIARRLMYEgWRRQDlERAYLQSLAEAPEAVQPSPEEQWMVIETL 109

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 446746728 104 ASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKV 145
Cdd:PRK12525 110 LAIDRLLDGLSGKARAAFLMSQLEGLTYVEIGERLGVSLSRI 151
Sig70_famx1 TIGR02943
RNA polymerase sigma-70 factor, TIGR02943 family; This group of sigma factors are members of ...
 5-153 4.91e-08

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: 49.76  E-value: 4.91e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728    5 QSLEDIysehMQDLFRYLLSLTGDSHYAEDLMQETFYRMLVHIDYYKGEE-IRPWLFTIAYNAFIDWYRKEKRYKTTTIT 83
Cdd:TIGR02943   6 QELEQL----RRDLLRFARLQLRDRDLAEDAVQETLLAALSHRDSFAGRSaLKTWLFAILKNKIIDALRAKGREVKVSDL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   84 EFHL----PNVPSTEHSYFVKHEIAS-W------LDS----------LSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSL 142
Cdd:TIGR02943  82 DDELddeaFNALFTQNGHWAQHGQPQhWntpekqLENkefwevfeacLYHLPEQTARVFMMREVLGFESDEICQELEIST 161

                         170
                  ....*....|.
gi 446746728  143 AKVKIELHRGR 153
Cdd:TIGR02943 162 SNCHVLLYRAR 172
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 19-154 1.93e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 48.35  E-value: 1.93e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728  19 FRYLLSLTGDSHYAEDLMQETFYRML-VHIDYYKGE-EIRPWLFTIAYNAFIDWYRKEKRYKTTTITEFHLPN-VPSTEH 95
Cdd:PRK12524  40 LAVATRVLGDRAEAEDVTQEAMLRLWrIAPDWRQGEaRVSTWLYRVVCNLCTDRLRRRRRASVDLDDAPEPADaAPGAEE 119

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 446746728  96 SYFVKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRK 154
Cdd:PRK12524 120 ALIEGDRMRALDAALAALPERQRQAVVLRHIEGLSNPEIAEVMEIGVEAVESLTARGKR 178
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 14-145 2.38e-07

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 47.46  E-value: 2.38e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728  14 HMQDLFRYLLSLTGDSHYAEDLMQETFYRMLVHIDYYKGEEIRPWLFTIAYNAFIDWYRKEKRYKTTTI------TEFHl 87
Cdd:PRK12527   4 YYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQIEHPRAFLYRTALNLVVDRHRRHRVRQAEPLevldeeERLH- 82

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 446746728  88 pnVPSTEHSYFVKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKV 145
Cdd:PRK12527  83 --SPSPQTRLDLGQRLALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLV 138
PRK12536 PRK12536
RNA polymerase sigma factor; Provisional
 33-154 3.79e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 237131 [Multi-domain]  Cd Length: 181  Bit Score: 47.35  E-value: 3.79e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728  33 EDLMQETFyrMLVH---IDYYKGEEIRPWLFTIAYNAFIDWYRKEKRYKTTtitefhlpNVPSTEHsyfvkHEIASWLDS 109
Cdd:PRK12536  50 EDLVQEIL--LAVHnarHTYRADQPLTAWVHAIARYKLMDFLRSRARREAL--------HDPLDDE-----SELFATSDD 114

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 446746728 110 ------------LSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRK 154
Cdd:PRK12536 115 eaaearrdlgklLEQLPDRQRLPIVHVKLEGLSVAETAQLTGLSESAVKVGIHRGLK 171
PRK09651 PRK09651
RNA polymerase sigma factor FecI; Provisional
 6-146 5.55e-07

RNA polymerase sigma factor FecI; Provisional


Pssm-ID: 182018 [Multi-domain]  Cd Length: 172  Bit Score: 46.73  E-value: 5.55e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   6 SLEDIYSEHMQDLFRYLLSLTGDSHYAEDLMQETFYRMLVHIDYYKGEEIRPWLFTIAYNAFIDWYRK---EKRYKT--T 80
Cdd:PRK09651  11 TFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVSETLSTIRDPRSFLCTIAKRVMVDLFRRnalEKAYLEmlA 90

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446746728  81 TITEFHLPNVPSTEHSYFVKHEIASWLDSLSSlplERRNVLLLRDYYGFSYKEIAEMTGLSLAKVK 146
Cdd:PRK09651  91 LMPEGGAPSPEERESQLETLQLLDSMLDGLNG---KTREAFLLSQLDGLTYSEIAHKLGVSVSSVK 153
PRK06811 PRK06811
RNA polymerase factor sigma-70; Validated
 1-161 6.30e-07

RNA polymerase factor sigma-70; Validated


Pssm-ID: 180707 [Multi-domain]  Cd Length: 189  Bit Score: 46.86  E-value: 6.30e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   1 MKRK--QSLEDIYSEHMQDLF---RYLLSLTGDSHYAEDLMQETFYRMLVHIDYYKGEE--IRPWLFTIAYNAFIDWYRK 73
Cdd:PRK06811  12 LKKKneKALEFIVDTYGNLVKkivHKVLGTVNYSQLIEECVNDIFLSIWNNIDKFDEEKgsFKKWIAAISKYKAIDYKRK 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728  74 EKR-YKTTTITEFHLPNVPSTEHSYFVKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRG 152
Cdd:PRK06811  92 LTKnNEIDSIDEFILISEESIENEIILKENKEEILKLINDLEKLDREIFIRRYLLGEKIEEIAKKLGLTRSAIDNRLSRG 171


                 ....*....
gi 446746728 153 RKETQSIKE 161
Cdd:PRK06811 172 RKKLQKNKL 180
PRK12529 PRK12529
RNA polymerase sigma factor; Provisional
 32-152 6.58e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183574 [Multi-domain]  Cd Length: 178  Bit Score: 46.85  E-value: 6.58e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728  32 AEDLMQETFYRMLVHIDYYKGEEI---RPWLFTIAYNAFIDWYRKE--KRYKTTTITEFHLPNVPSTEHSYFVK---HEI 103
Cdd:PRK12529  42 ADDLAHDIFLRILASRDGGQREAIrqpRAYLARIANCVLVSWRRRQslELAWLEALATLPEPLHPSPEQQSVILetlHEI 121

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 446746728 104 ASWLDSLSslPLERRnVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRG 152
Cdd:PRK12529 122 DALLDTLR--PRVKQ-AFLMATLDGMKQKDIAQALDIALPTVKKYIHQA 167
sigI PRK09635
RNA polymerase sigma factor SigI; Provisional
 5-157 1.22e-06

RNA polymerase sigma factor SigI; Provisional


Pssm-ID: 182008 [Multi-domain]  Cd Length: 290  Bit Score: 46.88  E-value: 1.22e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   5 QSLEDIYSEHMQDLFRYLLSLT----GDSHYAEDLMQETFYRMLV----HIDyykgeEIRPWLFTIAYNAFIDWYR--KE 74
Cdd:PRK09635   1 MSQHDPVSAAWRAHRAYLVDLAfrmvGDIGVAEDMVQEAFSRLLRapvgDID-----DERGWLIVVTSRLCLDHIKsaST 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728  75 KRYKTTTITEFHL--PNVPSTEHSYFVK--HEI-ASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIEL 149
Cdd:PRK09635  76 RRERPQDIAAWHDgdASVSSVDPADRVTldDEVrLALLIMLERLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQLA 155


                 ....*...
gi 446746728 150 HRGRKETQ 157
Cdd:PRK09635 156 HRARRKIN 163
PRK09648 PRK09648
RNA polymerase sigma factor ShbA;
27-151 1.28e-06

RNA polymerase sigma factor ShbA;


Pssm-ID: 236607 [Multi-domain]  Cd Length: 189  Bit Score: 46.12  E-value: 1.28e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728  27 GDSHYAEDLMQETFYRMLVHIDYYKgEEIRPWL---FTIAYNAFIDWYRKEKRYKTTTITEfhLPNVPST----EHSYfV 99
Cdd:PRK09648  50 RPGLSADDVAQEVCLAVITALPRYR-DQGRPFLafvYGIAAHKVADAHRAAGRDKAVPTEE--VPERPSDdagpEERA-L 125

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 446746728 100 KHEIASWL-DSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHR 151
Cdd:PRK09648 126 RSESSNRMrELLDTLPEKQREILILRVVVGLSAEETAEAVGSTPGAVRVAQHR 178
PRK12544 PRK12544
RNA polymerase factor sigma-70;
1-153 1.70e-06

RNA polymerase factor sigma-70;


Pssm-ID: 183583 [Multi-domain]  Cd Length: 206  Bit Score: 45.95  E-value: 1.70e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   1 MKRKQSLEDIYSE--HMQDLFRYLLSLT----GDSHYAEDLMQETFYRMLVHIDYYKGEE-IRPWLFTIAYNAFIDWYRK 73
Cdd:PRK12544   8 AMDSSDLGNLLQDpvFLEDLRKQMIKFAtlqlSDLHLAEDAVQEALIGALKNADSFAGRAaFKTWVFAILKNKIIDLLRQ 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728  74 EKRYKTTTITEFHLPNVPSTEH-----SYFVKHEI-ASWLDS----------------LSSLPLERRNVLLLRDYYGFSY 131
Cdd:PRK12544  88 KKRHVSASSLLRDEEEEEDFEElfdesGHWQKDERpQAWGNPeesleqeqfwrifeacLDGLPAKYARVFMMREFIELET 167

                        170       180
                 ....*....|....*....|..
gi 446746728 132 KEIAEMTGLSLAKVKIELHRGR 153
Cdd:PRK12544 168 NEICHAVDLSVSNLNVLLYRAR 189
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 14-159 5.00e-06

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 44.26  E-value: 5.00e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728  14 HMQDLFRYLLSLTGDSHYAEDLMQETFYRMLVHIDYYKGEEIR--PWLFTIAYNAFIDwyRKEKRyktTTITEFHLPNVP 91
Cdd:PRK05602  29 KLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPGEARfdTWLHRVVLNLCYD--RLRRR---REVPVEDAPDVP 103

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446746728  92 STEHSYfVKHEIASWL-----DSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKETQSI 159
Cdd:PRK05602 104 DPAPGP-DAGLEARQRarrveQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALESLLARGRRALRAQ 175
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 10-155 9.22e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 43.57  E-value: 9.22e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728  10 IYSEHMQDLFRYLLSLTGDSHYAEDLMQETFYRMLVHIDYYKGE-EIRPWLFTIAYNAFIDWYRKEKRYKTTTITEFHLP 88
Cdd:PRK12515  27 LYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGRsQVSTWLLSIARFKALSALRRRKHEEIDDEAAAAIE 106

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446746728  89 NVPSTEHSYFVKHEIASWLDS-LSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKE 155
Cdd:PRK12515 107 DGADTPEVALQKSDTSAALRAcLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKTRMFYARKK 174
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 28-161 1.25e-05

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 43.36  E-value: 1.25e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728  28 DSHYAEDLMQETFYRMLVHIDYY--KGEEIRPWLFTIAYNAFIDWYRK-EKRYKTTTITE-----FHLPNVPSTEHSYFV 99
Cdd:PRK13919  46 DGAAAEDVVQEVFIRVWKKAKEFdpRRGSARAWLLALAHHAAVDHVRRrAARPQPLEPDErepeaFDLPGPGLDEEGHLD 125

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446746728 100 KHEIASWLDSLSslPLERRNVLLLRdYYGFSYKEIAEMTGLSLAKVKIelhRGRKETQSIKE 161
Cdd:PRK13919 126 RTRLGRALKALS--PEERRVIEVLY-YQGYTHREAAQLLGLPLGTLKT---RARRALSRLKE 181
PRK09636 PRK09636
RNA polymerase sigma factor SigJ; Provisional
 7-143 2.09e-05

RNA polymerase sigma factor SigJ; Provisional


Pssm-ID: 236600 [Multi-domain]  Cd Length: 293  Bit Score: 42.99  E-value: 2.09e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   7 LEDIYSEHMQDLFRYLLSLTGDSHYAEDLMQETFYRmLVHIDYYKGEEIRPWLFTIAYNAFIDWYRKEKRYKTTTITEFh 86
Cdd:PRK09636   6 AAAEFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLR-WNNADRAQIRDPRAWLTRVVTRLCLDRLRSARHRRETYVGPW- 83

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446746728  87 LPN-VPSTEH---SYFVKHEIASW-----LDSLSslPLERRnVLLLRDYYGFSYKEIAEMTGLSLA 143
Cdd:PRK09636  84 LPEpVVEELDdplEAVVAAEDLSLalmlaLERLS--PLERA-AFLLHDVFGVPFDEIASTLGRSPA 146
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 110-154 3.03e-05

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: 39.33  E-value: 3.03e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 446746728  110 LSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRK 154
Cdd:pfam04545   2 LASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALR 46
PRK09642 PRK09642
RNA polymerase sigma factor;
18-154 3.20e-05

RNA polymerase sigma factor;


Pssm-ID: 170031 [Multi-domain]  Cd Length: 160  Bit Score: 42.01  E-value: 3.20e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728  18 LFRYLLSLTGDSHYAEDLMQETFYRMLVHIDYYKGEEIRPWLFTIAYNAFIDWYRKEKR----YKTTTITEFHLPNVPST 93
Cdd:PRK09642   8 IFQVIFSILRHEEDAKDVTQEVFVKIHASLPNYQFRGLKTWMARIATNHAIDYKRKKAReneeLSLCKETEENIKSSHNI 87

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446746728  94 EHSYFVKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRK 154
Cdd:PRK09642  88 EDLLLTKEQKLLIAQKLRELPENYRDVVLAHYLEEKSYQEIALQEKIEVKTVEMKLYRARK 148
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
 14-159 6.78e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 41.38  E-value: 6.78e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728  14 HMQDLFRYLLSLTGDSHYAEDLMQETFYRMLVHIDYYKG--EEIRPWLFTIAYNAFIDWYRKEKRYKTTTITEFH--LPN 89
Cdd:PRK12538  72 HIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHgrAKFSTWLYRVVSNRCIDLRRKPRTENVDAVPEVAdgKPD 151

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446746728  90 VPSTehsyFVKHEIASWLDS-LSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKETQSI 159
Cdd:PRK12538 152 AVSV----IERNELSDLLEAaMQRLPEQQRIAVILSYHENMSNGEIAEVMDTTVAAVESLLKRGRQQLRDL 218
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
 9-141 3.90e-04

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 38.90  E-value: 3.90e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   9 DIYSEHMQDLFRYLLSLTGDSHYAEDLMQETFYRMlvhIDYYKGEEIR---PWLFTIAYNAFIDWYRK---EKRYKTTTI 82
Cdd:PRK07037   2 DVFVDNRSMLVKIAARIVGCRSRAEDVVQDAFVKL---VEAPNQDAVKqpvAYLFRIVRNLAIDHYRRqalENKYHGDEE 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728  83 TEFHLP-NVPSTEHSYFVKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLS 141
Cdd:PRK07037  79 DGLDVPsPEASPEAALINRDTLRHVADALSELPARTRYAFEMYRLHGETQKDIARELGVS 138
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 4-152 7.98e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 38.22  E-value: 7.98e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728   4 KQSLEDIYSEHMQDLFRYLLSLTGDSHYAEDLMQETFYRMLVH---IDYYKGEEiRPWLFTIAYNAFIDWYRKekRYKTT 80
Cdd:PRK12537  22 RRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGaasFDPARGSA-RGWIYSVTRHLALNVLRD--TRREV 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728  81 TITEfhlpnvpSTEHSYFVKHEIASWLDS----------LSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELH 150
Cdd:PRK12537  99 VLDD-------DAEETAQTLHEIIDDFDLwansgkihrcLEQLEPARRNCILHAYVDGCSHAEIAQRLGAPLGTVKAWIK 171


                 ..
gi 446746728 151 RG 152
Cdd:PRK12537 172 RS 173
PRK06930 PRK06930
positive control sigma-like factor; Validated
 101-157 1.40e-03

positive control sigma-like factor; Validated


Pssm-ID: 180757 [Multi-domain]  Cd Length: 170  Bit Score: 37.40  E-value: 1.40e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446746728 101 HEIASW-----LDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKETQ 157
Cdd:PRK06930  98 SVISEWdkiriEDALSVLTEREKEVYLMHRGYGLSYSEIADYLNIKKSTVQSMIERAEKKIA 159
algU PRK11923
RNA polymerase sigma factor AlgU; Provisional
 28-154 1.84e-03

RNA polymerase sigma factor AlgU; Provisional


Pssm-ID: 171347 [Multi-domain]  Cd Length: 193  Bit Score: 37.09  E-value: 1.84e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728  28 DSHYAEDLMQETFYRMLVHIDYYKGEE-IRPWLFTIAYNAFIDWY-RKEKRYKTTTIT----EFH-----LPNVPSTEHS 96
Cdd:PRK11923  43 DTAEAQDVAQEAFIKAYRALGNFRGDSaFYTWLYRIAINTAKNHLvSRGRRPPDSDVSsedaEFYdgdhaLKDIESPERA 122

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 446746728  97 YFVKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRK 154
Cdd:PRK11923 123 LLRDEIEGTVHRTIQQLPEDLRTALTLREFDGLSYEDIASVMQCPVGTVRSRIFRARE 180
PRK09646 PRK09646
ECF RNA polymerase sigma factor SigK;
28-146 2.15e-03

ECF RNA polymerase sigma factor SigK;


Pssm-ID: 182015 [Multi-domain]  Cd Length: 194  Bit Score: 36.96  E-value: 2.15e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446746728  28 DSHYAEDLMQETF---YRMLVHIDYYKGEEIRpWLFTIAYNAFIDWYR-------KEKRYKTTTITEFHlPNVPSTEHSY 97
Cdd:PRK09646  53 DPGYSEETTQEVYlevWRTASRFDPARGSALA-WLLTLAHRRAVDRVRseqaasqREVRYGARNVDPAF-DQVAEEVEAR 130

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 446746728  98 FVKHEIASWLDSLSslPLERRNVLLLrdYY-GFSYKEIAEMTGLSLAKVK 146
Cdd:PRK09646 131 LERERVRDCLDALT--DTQRESVTLA--YYgGLTYREVAERLAVPLGTVK 176
 
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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