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Conserved domains on  [gi|507080598|ref|WP_016151352|]
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MULTISPECIES: sigma-70 family RNA polymerase sigma factor [Enterobacteriaceae]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SigZ super family cl31278
RNA polymerase sigma factor, SigZ family; This family of RNA polymerase sigma factors is a ...
 15-176 7.27e-40

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).


The actual alignment was detected with superfamily member TIGR02959:

Pssm-ID: 132004 [Multi-domain]  Cd Length: 170  Bit Score: 133.26  E-value: 7.27e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598   15 WQQHEAELSRFLASRTGDREQAADLLQEVFLRARACADRFCEMENPRAWLYRTARNLLTDEYRAARDVVVLEDEIPLPDA 94
Cdd:TIGR02959   1 WDEFRSELKAFIKSRVSDASDVEDLLQEVFIKIHRNLPSLKDGQKIQSWLYQIARNTIIDFYRSKSRSVELPESLLAADS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598   95 FHDAVSTLEI--CLPETLQALPDEERWLIEEADLNRRPQQRLADELGITLTAFKSRLLRARKHLKETMTELCQVEADDAS 172
Cdd:TIGR02959  81 AREETFVKELsqCIPPMIKELPDEYREAIRLTELEGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLETCCHFEFDRVG 160


                  ....
gi 507080598  173 SVCC 176
Cdd:TIGR02959 161 NLID 164
 
Name Accession Description Interval E-value
SigZ TIGR02959
RNA polymerase sigma factor, SigZ family; This family of RNA polymerase sigma factors is a ...
 15-176 7.27e-40

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: 133.26  E-value: 7.27e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598   15 WQQHEAELSRFLASRTGDREQAADLLQEVFLRARACADRFCEMENPRAWLYRTARNLLTDEYRAARDVVVLEDEIPLPDA 94
Cdd:TIGR02959   1 WDEFRSELKAFIKSRVSDASDVEDLLQEVFIKIHRNLPSLKDGQKIQSWLYQIARNTIIDFYRSKSRSVELPESLLAADS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598   95 FHDAVSTLEI--CLPETLQALPDEERWLIEEADLNRRPQQRLADELGITLTAFKSRLLRARKHLKETMTELCQVEADDAS 172
Cdd:TIGR02959  81 AREETFVKELsqCIPPMIKELPDEYREAIRLTELEGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLETCCHFEFDRVG 160


                  ....
gi 507080598  173 SVCC 176
Cdd:TIGR02959 161 NLID 164
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 10-175 7.24e-33

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 115.47  E-value: 7.24e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  10 CMSVFWQQHEAELSRFLASRTGDREQAADLLQEVFLRARACADRFCEMENPRAWLYRTARNLLTDEYRAARDVVVLEDEI 89
Cdd:PRK09637   2 KLESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDGSSIKSWLYQIANNTIIDFYRKKNRSEELPDDL 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  90 PLPDAFHDAVSTLEI--CLPETLQALPDEERWLIEEADLNRRPQQRLADELGITLTAFKSRLLRARKHLKETMTELCQVE 167
Cdd:PRK09637  82 LFEDEEREENAKKELapCLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLEGCCDFE 161


                 ....*...
gi 507080598 168 ADDASSVC 175
Cdd:PRK09637 162 IDRQGNLI 169
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 14-162 1.23e-28

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: 104.69  E-value: 1.23e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  14 FWQQHEAELSRFLASRTGDREQAADLLQEVFLRARACADRFCEMENPRAWLYRTARNLLTDEYRAARDVVVLEDEIP--L 91
Cdd:COG1595   22 LYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRRELLDELAeeL 101

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 507080598  92 PDAFHDAVSTLE-----ICLPETLQALPDEERWLIEEADLNRRPQQRLADELGITLTAFKSRLLRARKHLKETMTE 162
Cdd:COG1595  102 PDEAADPEEALEaeellEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREALEE 177
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 14-80 2.32e-09

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: 51.43  E-value: 2.32e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598   14 FWQQHEAELSRFLASRTGDREQAADLLQEVFLRARACADRFcEME---NPRAWLYRTARNLLTDEYRAAR 80
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERF-DPErgvSFSTWLYTIIRNAIIDYLRKQR 69
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 104-157 1.24e-04

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: 38.24  E-value: 1.24e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 507080598 104 ICLPETLQALPDEERWLIEEADLNRRPQQRLADELGITLTAFKSRLLRARKHLK 157
Cdd:cd06171    2 ERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
SigZ TIGR02959
RNA polymerase sigma factor, SigZ family; This family of RNA polymerase sigma factors is a ...
 15-176 7.27e-40

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: 133.26  E-value: 7.27e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598   15 WQQHEAELSRFLASRTGDREQAADLLQEVFLRARACADRFCEMENPRAWLYRTARNLLTDEYRAARDVVVLEDEIPLPDA 94
Cdd:TIGR02959   1 WDEFRSELKAFIKSRVSDASDVEDLLQEVFIKIHRNLPSLKDGQKIQSWLYQIARNTIIDFYRSKSRSVELPESLLAADS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598   95 FHDAVSTLEI--CLPETLQALPDEERWLIEEADLNRRPQQRLADELGITLTAFKSRLLRARKHLKETMTELCQVEADDAS 172
Cdd:TIGR02959  81 AREETFVKELsqCIPPMIKELPDEYREAIRLTELEGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLETCCHFEFDRVG 160


                  ....
gi 507080598  173 SVCC 176
Cdd:TIGR02959 161 NLID 164
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 10-175 7.24e-33

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 115.47  E-value: 7.24e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  10 CMSVFWQQHEAELSRFLASRTGDREQAADLLQEVFLRARACADRFCEMENPRAWLYRTARNLLTDEYRAARDVVVLEDEI 89
Cdd:PRK09637   2 KLESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDGSSIKSWLYQIANNTIIDFYRKKNRSEELPDDL 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  90 PLPDAFHDAVSTLEI--CLPETLQALPDEERWLIEEADLNRRPQQRLADELGITLTAFKSRLLRARKHLKETMTELCQVE 167
Cdd:PRK09637  82 LFEDEEREENAKKELapCLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLEGCCDFE 161


                 ....*...
gi 507080598 168 ADDASSVC 175
Cdd:PRK09637 162 IDRQGNLI 169
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 14-162 1.23e-28

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: 104.69  E-value: 1.23e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  14 FWQQHEAELSRFLASRTGDREQAADLLQEVFLRARACADRFCEMENPRAWLYRTARNLLTDEYRAARDVVVLEDEIP--L 91
Cdd:COG1595   22 LYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRRELLDELAeeL 101

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 507080598  92 PDAFHDAVSTLE-----ICLPETLQALPDEERWLIEEADLNRRPQQRLADELGITLTAFKSRLLRARKHLKETMTE 162
Cdd:COG1595  102 PDEAADPEEALEaeellEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREALEE 177
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 14-160 1.63e-25

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: 95.88  E-value: 1.63e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598   14 FWQQHEAELSRFLASRTGDREQAADLLQEVFLRARACADRFCEMENPRAWLYRTARNLLTDEYRAARDVVVLEDEIP-LP 92
Cdd:TIGR02937   6 LYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDLLEeLL 85

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 507080598   93 DAFHDAVSTLE-----ICLPETLQALPDEERWLIEEADLNRRPQQRLADELGITLTAFKSRLLRARKHLKETM 160
Cdd:TIGR02937  86 DSDPSPEEELEqeeerEALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 12-160 1.01e-17

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 76.16  E-value: 1.01e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  12 SVFWQQHEAELSRFLASRTGDREQAADLLQEVFLRARACADRFCEMENPRAWLYRTARNLLTDEYRAARDVVVLEDEIPL 91
Cdd:PRK11924  16 SELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCYDLLRRRRREKAVLSDDAL 95

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 507080598  92 PDAFHDAVSTLEIC---------LPETLQALPDEERWLIEEADLNRRPQQRLADELGITLTAFKSRLLRARKHLKETM 160
Cdd:PRK11924  96 EPEFAETAETPEAAllakddlarIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQLLRECL 173
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 18-163 1.60e-17

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 75.61  E-value: 1.60e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  18 HEAELSRFLASRTGDREQAADLLQEVFLRARACADRFCEMENPRAWLYRTARNLLTDEYRAA-RDVVVLEDEIPLPDAFH 96
Cdd:PRK09652  19 YQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRGGAAFYTWLYRIARNTAINYLRKQgRRPPASDVDAEEAEDFD 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  97 DAVSTLEICLPE--------------TLQALPDEERWLIEEADLNRRPQQRLADELGITLTAFKSRLLRARKHLKETMTE 162
Cdd:PRK09652  99 LADALRDISTPEnellsaeleqrvraAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRIFRAREALRAKLQP 178


                 .
gi 507080598 163 L 163
Cdd:PRK09652 179 L 179
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
11-163 1.07e-16

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 73.57  E-value: 1.07e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  11 MSVFWQQHEAELSRFLASRTGDREQAADLLQEVFLRARACADRFCEMENP-RAWLYRTARNLLTDEYRAAR-------DV 82
Cdd:PRK09645  11 MRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTGRSaRAWLFTVARNLVIDERRSARarpveggDD 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  83 VVLEDEIPLPDAFHDAVSTLEIclPETLQALPDEERWLIEEADLNRRPQQRLADELGITLTAFKSRLLRARKHLKETMTE 162
Cdd:PRK09645  91 VLGVPEQSAPDEVDRALDRLLV--ADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYALRALRLALQE 168


                 .
gi 507080598 163 L 163
Cdd:PRK09645 169 R 169
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 15-157 1.18e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 65.34  E-value: 1.18e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  15 WQQHEAELSRFLASRTGDREQAADLLQEVFLRARACADRFcEMENPRAWLYRTARNLLTDEYRAARDVVVLEDE----IP 90
Cdd:PRK12541  11 YSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYY-KGEEIRPWLFTIAYNAFIDWYRKEKKYKTTTIEefhlPN 89

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 507080598  91 LPDAFHDAVSTLEIC-LPETLQALPDEERWLIEEADLNRRPQQRLADELGITLTAFKSRLLRARKHLK 157
Cdd:PRK12541  90 VPSTEHEYFIKHEIAsWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKETK 157
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 3-162 1.73e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 65.48  E-value: 1.73e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598   3 DVTAFNncmsVFWQQHEAELSRFLASRTGDREQAADLLQEVFLRARACADRFCEMENPRAWLYRTARNLLTDEYRAARDV 82
Cdd:PRK12513  24 DAAAFE----ALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPRARFRTWLYQIARNLLIDHWRRHGAR 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  83 VVLEDEI-----PLPDAFHDAVSTLEIC-----LPETLQALPDEER---WLIEEADLnrrPQQRLADELGITLTAFKSRL 149
Cdd:PRK12513 100 QAPSLDAdeqlhALADDGAAPEQQLSLFrdrrrLQAALETLPDEQRevfLLREHGDL---ELEEIAELTGVPEETVKSRL 176

                        170
                 ....*....|...
gi 507080598 150 LRARKHLKETMTE 162
Cdd:PRK12513 177 RYALQKLRELLAE 189
PRK09643 PRK09643
RNA polymerase sigma factor SigM; Reviewed
 18-163 1.76e-13

RNA polymerase sigma factor SigM; Reviewed


Pssm-ID: 236604 [Multi-domain]  Cd Length: 192  Bit Score: 65.12  E-value: 1.76e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  18 HEAELSRfLASRT-GDREQAADLLQEVFLRARACADRFCEMENPRAWLYRTARNLLTDEYR--AARDVVVLEDEIPLPDA 94
Cdd:PRK09643  36 HHRRLWA-VARRTsGTREDAADALQDAMLSAHRAAGSFRGDAAVSSWLHRIVVNACLDRLRraKARPTVPLDDVYPVAQL 114

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 507080598  95 FHDAVSTLE--ICLPETLQALPDEERWLIEEADLNRRPQQRLADELGITLTAFKSRLLRARKHLKETMTEL 163
Cdd:PRK09643 115 ERDPTARVEtaLAVQRALMRLPVEQRAALVAVDMQGYSVADAARMLGVAEGTVKSRCARGRARLAELLGYL 185
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 14-158 7.77e-13

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: 62.72  E-value: 7.77e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598   14 FWQQHEAELSRFLASRTGDREQAADLLQEVFLRARACADRFCEMENPRAWLYRTARNLLTDEYR-AARDVVVLEDEI--- 89
Cdd:TIGR02989   6 LLTRHERALRAFVRSLVADRDDVDDVLQETFVVAWRKFDQFDPGTNFVAWARGIARNKVLNYRRkLGRDRLVFDDDLlea 85

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 507080598   90 ---PLPDAFHDAVSTLEICLPETLQALPDEERWLIEEADLNRRPQQRLADELGITLTAFKSRLLRARKHLKE 158
Cdd:TIGR02989  86 laaEAEPTEAERLSDDRQALEGCLEKLPERQRELLDLRYQRGQKATALAEQTGRTVNAVYKALQRIRVSLRE 157
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 16-162 9.49e-13

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 62.49  E-value: 9.49e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  16 QQHEAELSRFLASRTGDREQAADLLQEVFLRARACADRfCEMENPRAWLYRTARNLLTDEYR--AARDVVVLED------ 87
Cdd:PRK12527   2 ENYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSS-AQIEHPRAFLYRTALNLVVDRHRrhRVRQAEPLEVldeeer 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 507080598  88 -EIPLPDAFHDAVSTLEIcLPETLQALPDEERWLIEEADLNRRPQQRLADELGITLTAFKSRLLRARKHLKETMTE 162
Cdd:PRK12527  81 lHSPSPQTRLDLGQRLAL-LQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMRQ 155
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 15-162 1.01e-11

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 59.89  E-value: 1.01e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  15 WQQHEAELSRFLASRTGDREQAADLLQEVFLRARACADRFcEMENPRAWLYRTARNLLTDEYRAARDVVVLEDEipLPDA 94
Cdd:PRK09644   7 YKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDY-DNQKVKPWLFKVAYHTFIDFVRKEKKVSFVGTD--EIEA 83

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 507080598  95 FHdAVSTLEIC--------LPETLQALPDEERWLIEEADLNRRPQQRLADELGITLTAFKSRLLRARKHLKETMTE 162
Cdd:PRK09644  84 IQ-AESTEEYVvaknsyekLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLKE 158
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 32-162 2.10e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 56.65  E-value: 2.10e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  32 DREQAADLLQEVFLRARACADRFCEMENPRAWLYRTARNLLTDEYR--AARDVVVLEDEIP-LPDAFHDAVSTLEI---- 104
Cdd:PRK12518  33 GRELLDDLVQEVFLRVWKGLPKLRNPAYFSTWLYRITWNVATDARRqfAQRPSRIQDDSLNdQPSRPSDTPDLMQLhyqd 112

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 507080598 105 CLPETLQALPDEERWLIEEADLNRRPQQRLADELGITLTAFKSRLLRARKHLKETMTE 162
Cdd:PRK12518 113 LVQQGLQTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQQ 170
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 16-163 2.13e-10

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 56.50  E-value: 2.13e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  16 QQHEAELSRFLASRTGDREQAADLLQEVFLRA-RAcadRFCEMENPRAWLYRTARNLLTDEYRAARDVVVLEDEIPLPDA 94
Cdd:PRK09639  10 EQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLyRS---DFKGIENEKGWLIKSARNVAYNYLRSEKRRRARILGEFQWQE 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  95 FHDAVSTLEIclpetlqALPDEERWLIEEADLNRRPQQRL--------------ADELGITLTAFKSRLLRARKHLKETM 160
Cdd:PRK09639  87 VDNEPSPEEI-------WIRKEEITKVQEVLAKMTERDRTvlllrfsgysykeiAEALGIKESSVGTTLARAKKKFRKIY 159


                 ...
gi 507080598 161 TEL 163
Cdd:PRK09639 160 EQM 162
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 31-163 6.22e-10

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 55.47  E-value: 6.22e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  31 GDREQAADLLQEVFLRARACADRFCEMENPRAWLYRTARNLLTDEYRAARDVVVLEDEI----------------PLPDa 94
Cdd:PRK09641  40 GNRHEAEDAAQEAFIRAYVNIDSYDINRKFSTWLYRIATNLTIDRLRKRKPDYYLDAEVagtegltmysqlaaddALPE- 118

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 507080598  95 fhDAVSTLEI--CLPETLQALPDEERWLI-----EEADLnrrpqQRLADELGITLTAFKSRLLRARKHLKETMTEL 163
Cdd:PRK09641 119 --EQVVSLELqeTIQEAILQLPEKYRTVIvlkyiEDLSL-----KEISEILDLPVGTVKTRIHRGREALRKQLRHL 187
SigH_actino TIGR02947
RNA polymerase sigma-70 factor, TIGR02947 family; This group of sigma factors are members of ...
 36-162 7.54e-10

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: 55.36  E-value: 7.54e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598   36 AADLLQEVFLRARACADRFCEMENPRAWLYRTARNLLTDEYRAAR------DVVVLEDEIPLPDAFHDA-------VSTL 102
Cdd:TIGR02947  38 AEDLVQEAYAKAFSSFHQFKPGTNLKAWLYRILTNTYINSYRKAQrrpqqsDDDDIEDWQLAKAASHTSnglrsaeLEAL 117

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 507080598  103 EiCLPET-----LQALPDEERWLIEEADLNRRPQQRLADELGITLTAFKSRLLRARKHLKETMTE 162
Cdd:TIGR02947 118 D-GLPDQdikdaLQGLPEEFRQAVYLADVEGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLVD 181
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 14-80 2.32e-09

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: 51.43  E-value: 2.32e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598   14 FWQQHEAELSRFLASRTGDREQAADLLQEVFLRARACADRFcEME---NPRAWLYRTARNLLTDEYRAAR 80
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERF-DPErgvSFSTWLYTIIRNAIIDYLRKQR 69
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 26-162 1.49e-08

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 51.84  E-value: 1.49e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  26 LASRTG-DREQAADLLQEVFLRARACADRFCEME-NPRAWLYRTARNLLTDEYR--AARDVVvLEDEIPLPDAFH----- 96
Cdd:PRK13919  39 LARRMGlDGAAAEDVVQEVFIRVWKKAKEFDPRRgSARAWLLALAHHAAVDHVRrrAARPQP-LEPDEREPEAFDlpgpg 117

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 507080598  97 -DAVSTLE-ICLPETLQALPDEERWLIEEADLNRRPQQRLADELGITLTAFKSRLLRARKHLKETMTE 162
Cdd:PRK13919 118 lDEEGHLDrTRLGRALKALSPEERRVIEVLYYQGYTHREAAQLLGLPLGTLKTRARRALSRLKEVLRE 185
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 14-158 1.89e-08

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: 51.02  E-value: 1.89e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598   14 FWQQHEAELSRFLASRTGDREQAADLLQEVFLRARACADRFCEMENPRAWLYRTARNLLTDEYRaaRDVVVledeiplpD 93
Cdd:TIGR02985   6 LYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETLEISESIKAYLFTIVKNRCLNYLR--HKQVE--------E 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598   94 AFHDAVSTL---EICLPETLQALPDEERWLIEEADLNRRPQQR----------------LADELGITLTAFKSRLLRARK 154
Cdd:TIGR02985  76 KYQEELAEIeerELSEADPEEELEAKELEEIIEEAIEKLPEQCreifilsrfeglsnkeIAEELGISVKTVEYHITKALK 155


                  ....
gi 507080598  155 HLKE 158
Cdd:TIGR02985 156 FLRK 159
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 21-162 4.49e-08

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 50.52  E-value: 4.49e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  21 ELSRFLASRTGDREQAADLLQEVFLRARACADRFCEMENPRAWLYRTARNLLTDEYRA--ARDVVVLEDEIP----LPDA 94
Cdd:PRK09415  28 EVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGKSSLKTWLYRIAINHCKDYLKSwhNKKVIVTEDIFTymesQKES 107

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 507080598  95 FHDAV--STLEICLPETLQALPDEERWLI-----EEADLnrrpqQRLADELGITLTAFKSRLLRARKHLKETMTE 162
Cdd:PRK09415 108 VEEEViqNAEDERLASAVMSLPIKYREVIylfyyEELSI-----KEIAEVTGVNENTVKTRLKKAKELLKKGLEE 177
PRK12540 PRK12540
RNA polymerase sigma factor; Provisional
 22-160 5.52e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 183579 [Multi-domain]  Cd Length: 182  Bit Score: 50.35  E-value: 5.52e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  22 LSRFLASRTGDREQAADLLQEVFLRARACADRFCEMENPRAWLYRTARNLLTDEYRAARDVVvledeiplPDAfhdavst 101
Cdd:PRK12540  18 LRAFAISLSGNGDRADDLVQETLLRALANIDSFQPGSNLPAWLFTILRNLFRSDYRKRRREV--------EDA------- 82

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 507080598 102 lEICLPETLQALPDEERWL-IEE--ADLNRRPQ-QR---------------LADELGITLTAFKSRLLRARKHLKETM 160
Cdd:PRK12540  83 -DGSYAKTLKSQPGQNAHLeFEEfrAALDKLPQdQRealilvgasgfsyedAAAICGCAVGTIKSRVNRARSKLSALL 159
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 26-163 2.54e-07

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 48.49  E-value: 2.54e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  26 LASRT-GDREQAADLLQEVFLRARACADRFCEMENP-RAWLYRTARNLLTDEYRAARDVVV-----LEDEIPLPDAfHDA 98
Cdd:PRK05602  36 LATRMlGDPAEAEDVAQETFLRIWKQAPSWRPGEARfDTWLHRVVLNLCYDRLRRRREVPVedapdVPDPAPGPDA-GLE 114

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 507080598  99 VSTLEICLPETLQALPDEERWLI----------EEAdlnrrpqqrlADELGITLTAFKSRLLRARKHLKETMTEL 163
Cdd:PRK05602 115 ARQRARRVEQALAALPERQREAIvlqyyqglsnIEA----------AAVMDISVDALESLLARGRRALRAQLADL 179
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
 18-143 4.58e-07

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 47.37  E-value: 4.58e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  18 HEAELSRFLASRTGDREQAADLLQEVFLRARACADRFcEMENPRAWLYRTARNLLTDEYR-AARDVVVLEDE-------- 88
Cdd:PRK07037   7 NRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQD-AVKQPVAYLFRIVRNLAIDHYRrQALENKYHGDEedgldvps 85

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 507080598  89 -IPLPDAFHDAVSTLEIcLPETLQALPDEERWLIEEADLNRRPQQRLADELGITLT 143
Cdd:PRK07037  86 pEASPEAALINRDTLRH-VADALSELPARTRYAFEMYRLHGETQKDIARELGVSPT 140
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 31-160 5.49e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 47.51  E-value: 5.49e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  31 GDREQAADLLQEVFLRARACADRFCEME-NPRAWLYRTARNLLTDEYRAARDVVV-------LEDEIPLPDAFHDAVST- 101
Cdd:PRK12514  41 KDRSEAEEALQDVYVKIWTKADRFAVSGlSPMTWLITIARNHAIDRLRARKAVAVdideahdLADPSPGPEAEVIAGDEg 120

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 507080598 102 --LEICLPEtlqaLPDEERWLIEEADLNRRPQQRLADELGITLTAFKSRLLRARKHLKETM 160
Cdd:PRK12514 121 qrIDACLEE----LEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMRTWLRRSLLKLRECL 177
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
 17-171 7.27e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 47.14  E-value: 7.27e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  17 QHEAELSRFLASRTGDREQAADLLQEVFLRARACADRFCEMENPRAWLYRTARN-LLTDEYRAARDVVVLEDEIPLPDAF 95
Cdd:PRK12546  15 EHLPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEGTNLRAWLFTILRNtFYSDRRKHKREVPDPEGVHAASLAV 94

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 507080598  96 ---HDAVSTLEIcLPETLQALPDEERWLIEEADLNRRPQQRLADELGITLTAFKSRLLRARKHLketmTELCQVEADDA 171
Cdd:PRK12546  95 kpaHDGRLAMSD-FRAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARARL----AELLQLEEGEE 168
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 17-158 7.84e-07

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 47.09  E-value: 7.84e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  17 QHEAELSRfLASR-TGDREQAADLLQEVFLRAracadrFCEMEN--P---RAWLYRTARNLLTDEYR---------AARD 81
Cdd:PRK09647  36 QHADRVYR-LAYRlSGNQHDAEDLTQETFIRV------FRSLQNyqPgtfEGWLHRITTNLFLDMVRrrarirmeaLPED 108

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 507080598  82 VVVLEDEIPLPD-AFHDAvsTLEICLPETLQALPDEERWLIEEADLNRRPQQRLADELGITLTAFKSRLLRARKHLKE 158
Cdd:PRK09647 109 YDRVPGDEPNPEqIYHDA--RLDPDLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQQLRA 184
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 11-158 9.26e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 47.03  E-value: 9.26e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  11 MSVFWQQHEAELSRFLASRTGDREQAADLLQEVFLRARACADRFCEMENPRAWLYRTAR-NLLT------DEYRAARDVV 83
Cdd:PRK12515  24 MQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGRSQVSTWLLSIARfKALSalrrrkHEEIDDEAAA 103

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 507080598  84 VLEDEIPLPDAFHDAVSTLEIcLPETLQALPDEERWLIEEADLNRRPQQRLADELGITLTAFKSRLLRARKHLKE 158
Cdd:PRK12515 104 AIEDGADTPEVALQKSDTSAA-LRACLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKTRMFYARKKLAE 177
PRK12531 PRK12531
RNA polymerase sigma factor; Provisional
 3-160 1.08e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 105726 [Multi-domain]  Cd Length: 194  Bit Score: 46.85  E-value: 1.08e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598   3 DVTAFnncmSVFWQQHEAELSRFLASRTGDREQAADLLQEVFLRARACADRF-CEMENPRAWLYRTARNLLTDEYRA--A 79
Cdd:PRK12531  25 DKQAF----ALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFdGQKSALSTWIYTIIRNLCFDLLRKqkG 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  80 RDVVVLEDEI--------PLPDAFHDAVSTLEICLPETLQALPDEERWLIEEADLNRRPQQRLADELGITLTAFKSRLLR 151
Cdd:PRK12531 101 KDLHIHADDIwpsdyyppDLVDHYSPEQDMLKEQVMKFLDRLPKAQRDVLQAVYLEELPHQQVAEMFDIPLGTVKSRLRL 180


                 ....*....
gi 507080598 152 ARKHLKETM 160
Cdd:PRK12531 181 AVEKLRHSM 189
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 22-158 2.17e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 45.93  E-value: 2.17e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  22 LSRFLASRTGDREQAADLLQEVFLRARACADRFCEMENPRAWLYRTARNLLTDEYRAAR------DVVVLEDEIPLPDAF 95
Cdd:PRK12511  17 LRRYARSLTRDSAEAEDLVHDALVRALERRASFRSGGNLRTWLMSILHNAFIDELRRRRvearraDELAVLADASLPAAQ 96

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 507080598  96 HDAVSTLEIclPETLQALPDEERWLIEEADLNRRPQQRLADELGITLTAFKSRLLRARKHLKE 158
Cdd:PRK12511  97 EHAVRLAQI--RDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAALRA 157
sigI PRK09635
RNA polymerase sigma factor SigI; Provisional
 15-159 2.35e-06

RNA polymerase sigma factor SigI; Provisional


Pssm-ID: 182008 [Multi-domain]  Cd Length: 290  Bit Score: 46.50  E-value: 2.35e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  15 WQQHEAELSRFLASRTGDREQAADLLQEVFLR-ARACADrfcEMENPRAWLYRTARNLLTDEYRAAR-------DVVVLE 86
Cdd:PRK09635  11 WRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRlLRAPVG---DIDDERGWLIVVTSRLCLDHIKSAStrrerpqDIAAWH 87

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 507080598  87 DEIPLPDAFHDAVS-TLE----ICLPETLQALPDEERWLIEEADLNRRPQQRLADELGITLTAFKSRLLRARKHLKET 159
Cdd:PRK09635  88 DGDASVSSVDPADRvTLDdevrLALLIMLERLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQLAHRARRKINES 165
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 22-173 2.62e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 45.73  E-value: 2.62e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  22 LSRFLASRTGDREQAADLLQEVFLRARACADRFCEMENPRAWLYRTARNLLTDEYR-AARDVVVLEDEIPLPDAFH-DAV 99
Cdd:PRK12516  23 LRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVGTNMKAWLFTILRNEFYSQMRkRGREVQDTDGMFTEQLAVHpSQY 102

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 507080598 100 STLEIC-LPETLQALPDEERWLIEEADLNRRPQQRLADELGITLTAFKSRLLRARKHLKETMTelCQVEAD---DASS 173
Cdd:PRK12516 103 GTLDLQdFRAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQRLQEILQ--IEGEADygpDADS 178
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 26-157 3.29e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 45.27  E-value: 3.29e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  26 LASRT-GDREQAADLLQEVFLRA-RACADRFCEMENPRAWLYRTARNLLTDEYRAARDVVVLEDEIP-LPDAFHDAVSTL 102
Cdd:PRK12524  42 VATRVlGDRAEAEDVTQEAMLRLwRIAPDWRQGEARVSTWLYRVVCNLCTDRLRRRRRASVDLDDAPePADAAPGAEEAL 121

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598 103 E-----ICLPETLQALPDEERWLIEEADLNRRPQQRLADELGITLTAFKSRLLRARKHLK 157
Cdd:PRK12524 122 IegdrmRALDAALAALPERQRQAVVLRHIEGLSNPEIAEVMEIGVEAVESLTARGKRALA 181
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 105-156 3.85e-06

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


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 42.44  E-value: 3.85e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 507080598  105 CLPETLQALPDEERWLIEEADLNRRPQQRLADELGITLTAFKSRLLRARKHL 156
Cdd:pfam08281   3 ALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK09636 PRK09636
RNA polymerase sigma factor SigJ; Provisional
 26-159 2.39e-05

RNA polymerase sigma factor SigJ; Provisional


Pssm-ID: 236600 [Multi-domain]  Cd Length: 293  Bit Score: 43.37  E-value: 2.39e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  26 LASR-TGDREQAADLLQEVFLRARAcADRfCEMENPRAWLYRTARNLLTDEYRAAR------------DVVVLEDEIPLP 92
Cdd:PRK09636  20 VAYRmLGSVADAEDIVQEAWLRWNN-ADR-AQIRDPRAWLTRVVTRLCLDRLRSARhrretyvgpwlpEPVVEELDDPLE 97

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 507080598  93 D--AFHDAVSTLEIclpeTLQALPDEERWLIEEADLNRRPQQRLADELGITLTAFKSRLLRARKHLKET 159
Cdd:PRK09636  98 AvvAAEDLSLALML----ALERLSPLERAAFLLHDVFGVPFDEIASTLGRSPAACRQLASRARKHVRAA 162
PRK12547 PRK12547
RNA polymerase sigma factor; Provisional
 22-160 7.36e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 139056 [Multi-domain]  Cd Length: 164  Bit Score: 41.40  E-value: 7.36e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  22 LSRFLASRTGDREQAADLLQEVFLRARACADRFCEMENPRAWLYRTARNLLTDEYRAARDVV-----VLEDEIPLPDAFH 96
Cdd:PRK12547  19 LRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGTNLKAWLFTILRNEFYSQMRKRGREVqdsdgVFTARVAVHPAQY 98

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 507080598  97 DAVSTLEicLPETLQALPDEERWLIEEADLNRRPQQRLADELGITLTAFKSRLLRARKHLKETM 160
Cdd:PRK12547  99 GSLDLQD--FKKALNLLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARNRLQELL 160
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 104-157 1.24e-04

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: 38.24  E-value: 1.24e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 507080598 104 ICLPETLQALPDEERWLIEEADLNRRPQQRLADELGITLTAFKSRLLRARKHLK 157
Cdd:cd06171    2 ERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK09649 PRK09649
RNA polymerase sigma factor SigC; Reviewed
 11-80 1.57e-04

RNA polymerase sigma factor SigC; Reviewed


Pssm-ID: 137458 [Multi-domain]  Cd Length: 185  Bit Score: 40.41  E-value: 1.57e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  11 MSVFWQQHEAELSRFLASRTgDREQAADLLQEVFLRARACADRFCEMENPRAWLYRTARNLLTDEYRAAR 80
Cdd:PRK09649  26 LEAFIKATQQDVWRFVAYLS-DVGSADDLTQETFLRAIGAIPRFSARSSARTWLLAIARHVVADHIRHVR 94
PRK12533 PRK12533
RNA polymerase sigma factor; Provisional
 22-169 2.61e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 237129 [Multi-domain]  Cd Length: 216  Bit Score: 40.10  E-value: 2.61e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  22 LSRFLasrTGDREQAADLLQEVFLRARacadRF---CEMENPRAWLYRTARNLLTDEY--RAARDVVVLEDEI---PLPD 93
Cdd:PRK12533  34 LARWL---CGNASDADDVVQEACMRAL----RFfdsFRGDNARPWLLAIVRHTWYSEWrrRANAHEVAAPDTLddaDSLD 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  94 AFHDAVSTLEICL---------PETLQALPDEERWLI---EEADLNRRPQQRLADelgITLTAFKSRLLRARKHLKETMT 161
Cdd:PRK12533 107 DWQPAGEDPLALLlraedvrlvNAALAKLPVEYREVLvlrELEDMSYREIAAIAD---VPVGTVMSRLARARRRLAALLG 183


                 ....*...
gi 507080598 162 ELCQVEAD 169
Cdd:PRK12533 184 GASAAQAA 191
PRK08241 PRK08241
RNA polymerase subunit sigma-70;
36-158 2.65e-04

RNA polymerase subunit sigma-70;


Pssm-ID: 236196 [Multi-domain]  Cd Length: 339  Bit Score: 40.31  E-value: 2.65e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  36 AADLLQEVFLRARACADRFCEMENPRAWLYRTARN-------------LLTDEYRAARDVVVLEDEI-------PLPDAF 95
Cdd:PRK08241  46 AEDAVQETLLRAWRGYDRFEGRSSLRTWLYRIATNvcldalegrarrpLPTDLGAPAADPVDELVERpevpwlePYPDAL 125

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 507080598  96 HDAVS-----------TLEICLPETLQALPDEERWLIEEADLNRRPQQRLADELGITLTAFKSRLLRARKHLKE 158
Cdd:PRK08241 126 LDPAAadpaarvvareSVRLAFVAALQHLPPRQRAVLILRDVLGWSAAEVAELLDTSVAAVNSALQRARATLAE 199
PRK12529 PRK12529
RNA polymerase sigma factor; Provisional
 10-146 3.61e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183574 [Multi-domain]  Cd Length: 178  Bit Score: 39.53  E-value: 3.61e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  10 CMSVFWQQHEAELSRFLASR--TGDREQAADLLQEVFLRARAC--ADRFCEMENPRAWLYRTARNLLTD-EYRAARDVVV 84
Cdd:PRK12529  14 KVATLYRENHAWLRNWLAYRlrSWGRGVADDLAHDIFLRILASrdGGQREAIRQPRAYLARIANCVLVSwRRRQSLELAW 93

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 507080598  85 LEDEIPLPDAFHDAVSTLEICLpETLQ---ALPDEERWLIEE----ADLNRRPQQRLADELGITLTAFK 146
Cdd:PRK12529  94 LEALATLPEPLHPSPEQQSVIL-ETLHeidALLDTLRPRVKQaflmATLDGMKQKDIAQALDIALPTVK 161
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 110-158 8.95e-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: 35.87  E-value: 8.95e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 507080598  110 LQALPDEERWLIEEADLNRRPQQRLADELGITLTAFKSRLLRARKHLKE 158
Cdd:pfam04545   2 LASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
PRK12545 PRK12545
RNA polymerase factor sigma-70;
13-162 1.37e-03

RNA polymerase factor sigma-70;


Pssm-ID: 183584 [Multi-domain]  Cd Length: 201  Bit Score: 38.01  E-value: 1.37e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  13 VFWQQHEAELSRFLASRTGDREQAADLLQEVFLRARACADRFCEMENPRAWLYRTARNLLTDEYRAARDVV--------- 83
Cdd:PRK12545  12 AYLAQLRHDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQSAHKTWVFGILRNKLIDTLRARQRTVnlsaldael 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  84 ----VLEDEIpLPDAFHDAVSTLEICLPETLQALPDEERWLIEEADLNRRPQQ----------------RLADELGITLT 143
Cdd:PRK12545  92 dgeaLLDREL-FKDNGHWAAHAKPRPWPKPETILQQQQFWTLFETCLDHLPEQigrvfmmrefldfeidDICTELTLTAN 170

                        170
                 ....*....|....*....
gi 507080598 144 AFKSRLLRARKHLKETMTE 162
Cdd:PRK12545 171 HCSVLLYRARTRLRTCLSE 189
PRK12530 PRK12530
RNA polymerase sigma factor; Provisional
 32-165 2.25e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237128 [Multi-domain]  Cd Length: 189  Bit Score: 37.05  E-value: 2.25e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  32 DREQAADLLQEVFLRARACADRFCEMENPRAWLYRTARNLLTDEYRA-ARDVVVLE-DEIPLPDAFHDAVS--TLEICLP 107
Cdd:PRK12530  30 DADLAEDVVQEALVSAYKNADSFKGQSALKTWIFAILKNKIIDLIRYrKRFVNESElIEEDSPNSFFDEKGhwKPEYYEP 109

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 507080598 108 ETLQ----ALPDEERWLIEEADLNRRPQQrladelgitltafKSRLLRARKHLKETMTELCQ 165
Cdd:PRK12530 110 SEWQevenTVYKEEFWLIFEACLNHLPAQ-------------QARVFMMREYLELSSEQICQ 158
PRK12528 PRK12528
RNA polymerase sigma factor; Provisional
 9-152 3.32e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 171561 [Multi-domain]  Cd Length: 161  Bit Score: 36.36  E-value: 3.32e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598   9 NCMSVFWQQHEAELSRFLASRTGDREQAADLLQEVFLR---ARACAdrfcEMENPRAWLYRTARNLLTDEYR------AA 79
Cdd:PRK12528   4 ATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKvlvARETA----QIIEPRAFLTTIAKRVLCNHYRrqdlerAY 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 507080598  80 RDVVVLEDEIPLPDAFHDAV--STLeICLPETLQALPDEERWLIEEADLNRRPQQRLADELGITLTAFKSRLLRA 152
Cdd:PRK12528  80 LEALAQLPERVAPSEEERAIilETL-VELDQLLDGLPPLVKRAFLLAQVDGLGYGEIATELGISLATVKRYLNKA 153
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 11-118 3.77e-03

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 36.54  E-value: 3.77e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  11 MSVFWQQHEAELSRFLASRTGDREQAADLLQEVFLRARACADRFcemeNPRA----WLYRTARNLLTDEYRAARDVVVLE 86
Cdd:PRK09638  20 LTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSF----QGRSkfstWLISIASRLYKDHLRKQKREKLRL 95

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 507080598  87 DEIP--LPDAF--HDAVSTLE---IClpETLQALPDEER 118
Cdd:PRK09638  96 QRAKeeTLRKEkwEAAIKGAEwseML--DALSKLDPEFR 132
PRK12526 PRK12526
RNA polymerase sigma factor; Provisional
 24-162 4.39e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237127 [Multi-domain]  Cd Length: 206  Bit Score: 36.32  E-value: 4.39e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  24 RFLASRTGDREQAADLLQEVFLRARACADRFCEMENP-RAWLYRTARNLLTDEYR--AARDVVVLEDEI-PLPDAFHDAV 99
Cdd:PRK12526  53 RFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKGAaTTWVYTVMRNAAFDMLRkiKAKKEQNLGDDIwPIEQALAESQ 132

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 507080598 100 STLEIC--------LPETLQALPDEERWLIEEADLNRRPQQRLADELGITLTAFKSRLLRARKHLKETMTE 162
Cdd:PRK12526 133 SESEEFsdhlmdkqILSYIEKLPEAQQTVVKGVYFQELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQMGE 203
PRK12525 PRK12525
RNA polymerase sigma factor; Provisional
 8-124 5.04e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 139037 [Multi-domain]  Cd Length: 168  Bit Score: 36.08  E-value: 5.04e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598   8 NNCMSVFWQQHEAELSRFLASRTGDREQAADLLQEVFLRARACADRfCEMENPRAWLYRTARNLLTDEYRAArdvvvled 87
Cdd:PRK12525   8 NTLIGQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDP-ASIREPRALLTTIARRLMYEGWRRQ-------- 78

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 507080598  88 eiPLPDAFHDAVSTleicLPETLQALPdEERWLIEEA 124
Cdd:PRK12525  79 --DLERAYLQSLAE----APEAVQPSP-EEQWMVIET 108
PRK12535 PRK12535
RNA polymerase sigma factor; Provisional
 24-77 6.98e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237130 [Multi-domain]  Cd Length: 196  Bit Score: 35.64  E-value: 6.98e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 507080598  24 RFLAsRTGDREQAADLLQEVFLRARACADRFCEMENPRAWLYRTARNLLTDEYR 77
Cdd:PRK12535  40 RLLA-HLGGHDIADDLTQETYLRVMSALPRFAARSSARTWLLSLARRVWVDNIR 92
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
 31-158 9.48e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 35.60  E-value: 9.48e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 507080598  31 GDREQAADLLQEVFLRARACADRFcemENPRA----WLYRTARNLLTDEYRAARDVVVleDEIPLP-DAFHDAVSTLE-- 103
Cdd:PRK12538  85 GNRADAEDVVQDTMLKVWTHRGRW---QHGRAkfstWLYRVVSNRCIDLRRKPRTENV--DAVPEVaDGKPDAVSVIErn 159

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 507080598 104 ---ICLPETLQALPDEERWLIEEADLNRRPQQRLADELGITLTAFKSRLLRARKHLKE 158
Cdd:PRK12538 160 elsDLLEAAMQRLPEQQRIAVILSYHENMSNGEIAEVMDTTVAAVESLLKRGRQQLRD 217
 
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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