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Conserved domains on  [gi|1002292766|ref|XP_015650731|]
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RNA polymerase sigma factor sigF, chloroplastic [Oryza sativa Japonica Group]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Sig70-cyanoRpoD super family cl37206
RNA polymerase sigma factor, cyanobacterial RpoD-like family; This family includes a number of ...
 274-556 6.39e-89

RNA polymerase sigma factor, cyanobacterial RpoD-like family; This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).


The actual alignment was detected with superfamily member TIGR02997:

Pssm-ID: 274382 [Multi-domain]  Cd Length: 298  Bit Score: 276.43  E-value: 6.39e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 274 LTAKEERHLFSKIQILMKIEEAHRKLEVQCGREPTLAEWAEAVGMSSKELQSSIRTGRRCREKMARSNFRLVIHVARKYE 353
Cdd:TIGR02997  16 LTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKMIKANLRLVVSVAKKYQ 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 354 GYGLDIQDLVQDGCSGLMKTFEKFNPSKGCRFPTYAYWWIRQSIKKSIFKNSRLIRLPESVYALLRKVGKARMECIME-G 432
Cdd:TIGR02997  96 NRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKLNKIKKVQRELSQKlG 175

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 433 EQPTNANVARRAGITIEKLAKLRAKTRKPRSMQDHVWSDEGVTFQEITEDPNVEpPDLSVDRMMMRQQVRDFLGILSPRE 512
Cdd:TIGR02997 176 RTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLEDDGES-PEEQVERESLRQDLESLLAELTPRE 254

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....
gi 1002292766 513 KEIIEHRFGIHDGEPKTLHVIGDMFGLSKERIRQLQNRALEKLK 556
Cdd:TIGR02997 255 RQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR 298
 
Name Accession Description Interval E-value
Sig70-cyanoRpoD TIGR02997
RNA polymerase sigma factor, cyanobacterial RpoD-like family; This family includes a number of ...
 274-556 6.39e-89

RNA polymerase sigma factor, cyanobacterial RpoD-like family; This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).


Pssm-ID: 274382 [Multi-domain]  Cd Length: 298  Bit Score: 276.43  E-value: 6.39e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 274 LTAKEERHLFSKIQILMKIEEAHRKLEVQCGREPTLAEWAEAVGMSSKELQSSIRTGRRCREKMARSNFRLVIHVARKYE 353
Cdd:TIGR02997  16 LTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKMIKANLRLVVSVAKKYQ 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 354 GYGLDIQDLVQDGCSGLMKTFEKFNPSKGCRFPTYAYWWIRQSIKKSIFKNSRLIRLPESVYALLRKVGKARMECIME-G 432
Cdd:TIGR02997  96 NRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKLNKIKKVQRELSQKlG 175

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 433 EQPTNANVARRAGITIEKLAKLRAKTRKPRSMQDHVWSDEGVTFQEITEDPNVEpPDLSVDRMMMRQQVRDFLGILSPRE 512
Cdd:TIGR02997 176 RTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLEDDGES-PEEQVERESLRQDLESLLAELTPRE 254

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....
gi 1002292766 513 KEIIEHRFGIHDGEPKTLHVIGDMFGLSKERIRQLQNRALEKLK 556
Cdd:TIGR02997 255 RQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR 298
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 330-569 3.20e-84

DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 440334 [Multi-domain]  Cd Length: 268  Bit Score: 263.07  E-value: 3.20e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 330 GRRCREKMARSNFRLVIHVARKYEGYGLDIQDLVQDGCSGLMKTFEKFNPSKGCRFPTYAYWWIRQSIKKSIFKNSRLIR 409
Cdd:COG0568    28 DEEAKRKLVEANLRLVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDPERGFRFSTYATWWIRQAITRAIADQWRTIR 107

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 410 LPESVYALLRKVGKARMECIME-GEQPTNANVARRAGITIEKLAKLRAKTRKPRSMQDHVWSDEGVTFQEITEDPNVEPP 488
Cdd:COG0568   108 LPVHMAETLNKLRRAKRQLLQElGREPTPEEIAEELGVPEEKVREMLRLAREPVSLDAPVGDDEDSELGDLLEDEEAPSP 187

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 489 DLSVDRMMMRQQVRDFLGILSPREKEIIEHRFGIHDGEPKTLHVIGDMFGLSKERIRQLQNRALEKLKRSASLQGFDVYF 568
Cdd:COG0568   188 EEALEEELLREELREALDTLTEREREILRLRFGLDDGEPHTLEEIGKEFGVSRERVRQIEAKALRKLRHPLRSRKLRDYL 267


                  .
gi 1002292766 569 D 569
Cdd:COG0568   268 D 268
PRK07406 PRK07406
RNA polymerase sigma factor RpoD; Validated
 174-556 4.91e-68

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236012 [Multi-domain]  Cd Length: 373  Bit Score: 224.66  E-value: 4.91e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 174 ALLAEETDILATQLKASQLYSVDSSKSNEELQSKGQVFVRSTRLLERRSKRRYAPRASIADVScsadnskkkekskkygr 253
Cdd:PRK07406    2 PELEDELLLLEEDRQPAATDDLDSDEDEESSSENADELSEKEAKAKALARIKIGPKKVYTEDS----------------- 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 254 vlepdepFKLFLRDRETTEFLTAKEERHLFSKIQILMKIEEAHRKLEVQCGREPTLAEWAEAVGMSSKELQSSIRTGRRC 333
Cdd:PRK07406   65 -------IRVYLQEIGRIRLLRPDEEIELARKIADLLELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRA 137

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 334 REKMARSNFRLVIHVARKYEGYGLDIQDLVQDGCSGLMKTFEKFNPSKGCRFPTYAYWWIRQSIKKSIFKNSRLIRLPES 413
Cdd:PRK07406  138 KEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH 217

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 414 VYALLRKVGKARMECIME-GEQPTNANVARRAGITIEKLAKLRAKTRKPRSMQDHVWSDEGVTFQEITEdPNVEPPDLSV 492
Cdd:PRK07406  218 LYETISRIKKTTKVLSQEfGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADGETPEDDV 296

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1002292766 493 DRMMMRQQVRDFLGILSPREKEIIEHRFGIHDGEPKTLHVIGDMFGLSKERIRQLQNRALEKLK 556
Cdd:PRK07406  297 AKNLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLR 360
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 337-406 5.10e-19

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: 81.09  E-value: 5.10e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 337 MARSNFRLVIHVARKYEGYGLDIQDLVQDGCSGLMKTFEKFNPSKGCRFPTYAYWWIRQSIKKSIFKNSR 406
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRR 70
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 498-556 9.36e-10

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: 54.42  E-value: 9.36e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1002292766 498 RQQVRDFLGILSPREKEIIEHRFGihdgEPKTLHVIGDMFGLSKERIRQLQNRALEKLK 556
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFG----EGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
Sig70-cyanoRpoD TIGR02997
RNA polymerase sigma factor, cyanobacterial RpoD-like family; This family includes a number of ...
 274-556 6.39e-89

RNA polymerase sigma factor, cyanobacterial RpoD-like family; This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).


Pssm-ID: 274382 [Multi-domain]  Cd Length: 298  Bit Score: 276.43  E-value: 6.39e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 274 LTAKEERHLFSKIQILMKIEEAHRKLEVQCGREPTLAEWAEAVGMSSKELQSSIRTGRRCREKMARSNFRLVIHVARKYE 353
Cdd:TIGR02997  16 LTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKMIKANLRLVVSVAKKYQ 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 354 GYGLDIQDLVQDGCSGLMKTFEKFNPSKGCRFPTYAYWWIRQSIKKSIFKNSRLIRLPESVYALLRKVGKARMECIME-G 432
Cdd:TIGR02997  96 NRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKLNKIKKVQRELSQKlG 175

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 433 EQPTNANVARRAGITIEKLAKLRAKTRKPRSMQDHVWSDEGVTFQEITEDPNVEpPDLSVDRMMMRQQVRDFLGILSPRE 512
Cdd:TIGR02997 176 RTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLEDDGES-PEEQVERESLRQDLESLLAELTPRE 254

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....
gi 1002292766 513 KEIIEHRFGIHDGEPKTLHVIGDMFGLSKERIRQLQNRALEKLK 556
Cdd:TIGR02997 255 RQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR 298
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 330-569 3.20e-84

DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 440334 [Multi-domain]  Cd Length: 268  Bit Score: 263.07  E-value: 3.20e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 330 GRRCREKMARSNFRLVIHVARKYEGYGLDIQDLVQDGCSGLMKTFEKFNPSKGCRFPTYAYWWIRQSIKKSIFKNSRLIR 409
Cdd:COG0568    28 DEEAKRKLVEANLRLVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDPERGFRFSTYATWWIRQAITRAIADQWRTIR 107

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 410 LPESVYALLRKVGKARMECIME-GEQPTNANVARRAGITIEKLAKLRAKTRKPRSMQDHVWSDEGVTFQEITEDPNVEPP 488
Cdd:COG0568   108 LPVHMAETLNKLRRAKRQLLQElGREPTPEEIAEELGVPEEKVREMLRLAREPVSLDAPVGDDEDSELGDLLEDEEAPSP 187

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 489 DLSVDRMMMRQQVRDFLGILSPREKEIIEHRFGIHDGEPKTLHVIGDMFGLSKERIRQLQNRALEKLKRSASLQGFDVYF 568
Cdd:COG0568   188 EEALEEELLREELREALDTLTEREREILRLRFGLDDGEPHTLEEIGKEFGVSRERVRQIEAKALRKLRHPLRSRKLRDYL 267


                  .
gi 1002292766 569 D 569
Cdd:COG0568   268 D 268
PRK07406 PRK07406
RNA polymerase sigma factor RpoD; Validated
 174-556 4.91e-68

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236012 [Multi-domain]  Cd Length: 373  Bit Score: 224.66  E-value: 4.91e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 174 ALLAEETDILATQLKASQLYSVDSSKSNEELQSKGQVFVRSTRLLERRSKRRYAPRASIADVScsadnskkkekskkygr 253
Cdd:PRK07406    2 PELEDELLLLEEDRQPAATDDLDSDEDEESSSENADELSEKEAKAKALARIKIGPKKVYTEDS----------------- 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 254 vlepdepFKLFLRDRETTEFLTAKEERHLFSKIQILMKIEEAHRKLEVQCGREPTLAEWAEAVGMSSKELQSSIRTGRRC 333
Cdd:PRK07406   65 -------IRVYLQEIGRIRLLRPDEEIELARKIADLLELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRA 137

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 334 REKMARSNFRLVIHVARKYEGYGLDIQDLVQDGCSGLMKTFEKFNPSKGCRFPTYAYWWIRQSIKKSIFKNSRLIRLPES 413
Cdd:PRK07406  138 KEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH 217

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 414 VYALLRKVGKARMECIME-GEQPTNANVARRAGITIEKLAKLRAKTRKPRSMQDHVWSDEGVTFQEITEdPNVEPPDLSV 492
Cdd:PRK07406  218 LYETISRIKKTTKVLSQEfGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADGETPEDDV 296

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1002292766 493 DRMMMRQQVRDFLGILSPREKEIIEHRFGIHDGEPKTLHVIGDMFGLSKERIRQLQNRALEKLK 556
Cdd:PRK07406  297 AKNLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLR 360
PRK07405 PRK07405
RNA polymerase sigma factor SigD; Validated
 257-562 9.26e-65

RNA polymerase sigma factor SigD; Validated


Pssm-ID: 180963 [Multi-domain]  Cd Length: 317  Bit Score: 214.24  E-value: 9.26e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 257 PDEPFKLFLRDRETTEFLTAKEERHLFSKIQILMKIEEAHRKLEVQCGREPTLAEWAEAVGMSSKELQSSIRTGRRCREK 336
Cdd:PRK07405    6 STDLVRTYLREIGRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAKRK 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 337 MARSNFRLVIHVARKYEGYGLDIQDLVQDGCSGLMKTFEKFNPSKGCRFPTYAYWWIRQSIKKSIFKNSRLIRLPESVYA 416
Cdd:PRK07405   86 MVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITE 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 417 LLRKVGKARMECIME-GEQPTNANVARRAGITIEKLAKLRAKTRKPRSMQDHVWSDEGVTFQEITEDPNVEPPDLSVdRM 495
Cdd:PRK07405  166 KLNKIKKAQRQLSQQlGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDTGASPEDFAT-QS 244

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1002292766 496 MMRQQVRDFLGILSPREKEIIEHRFGIHDGEPKTLHVIGDMFGLSKERIRQLQNRALEKL-KRSASLQ 562
Cdd:PRK07405  245 SLQLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLrKRKANIQ 312
PRK05949 PRK05949
RNA polymerase sigma factor; Validated
 274-557 1.33e-64

RNA polymerase sigma factor; Validated


Pssm-ID: 180321 [Multi-domain]  Cd Length: 327  Bit Score: 214.32  E-value: 1.33e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 274 LTAKEERHLFSKIQILMKIEEAHRKLEVQCGREPTLAEWAEAVGMSSKELQSSIRTGRRCREKMARSNFRLVIHVARKYE 353
Cdd:PRK05949   33 LTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAKQKMIEANLRLVVAIAKKYQ 112

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 354 GYGLDIQDLVQDGCSGLMKTFEKFNPSKGCRFPTYAYWWIRQSIKKSIFKNSRLIRLPESVYALLRKVGKARMECIME-G 432
Cdd:PRK05949  113 KRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEKLNKIKKTQRELSQKlG 192

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 433 EQPTNANVARRAGITIEKLAKLRAKTRKPRSMQDHVWSDEGVTFQEITEDPNVEpPDLSVDRMMMRQQVRDFLGILSPRE 512
Cdd:PRK05949  193 RSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTELSELLEDEGPS-PDQYITQELLRQDLNNLLAELTPQQ 271

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 1002292766 513 KEIIEHRFGIHDGEPKTLHVIGDMFGLSKERIRQLQNRALEKLKR 557
Cdd:PRK05949  272 REVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRR 316
PRK07598 PRK07598
RNA polymerase sigma factor SigC; Validated
 262-556 3.56e-54

RNA polymerase sigma factor SigC; Validated


Pssm-ID: 236067 [Multi-domain]  Cd Length: 415  Bit Score: 189.31  E-value: 3.56e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 262 KLFLRDRETTEFLTAKEERHLFSKIQILMKIE--------------------EAHRKLEVQCGREPTLAEWA-------- 313
Cdd:PRK07598   63 RLYLQEIGRVRLLGRDEEVSEAQKVQRYMKLIvlanaakegdevikpylrliEVRERLTSELGHRPSLERWAktadisla 142

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 314 --------------EAVGMSSKELQSSIRTGRRCREKMARSNFRLVIHVARKYEGYGLDIQDLVQDGCSGLMKTFEKFNP 379
Cdd:PRK07598  143 dlkptlaegkrrwaEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDP 222

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 380 SKGCRFPTYAYWWIRQSIKKSIFKNSRLIRLPESVYALLRKVGKARMECIME-GEQPTNANVARRAGITIEKLAKLRAKT 458
Cdd:PRK07598  223 TKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEkGRTPTIEDIAQELEMTPTQVREVLLRV 302

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 459 RKPRSMQDHVWSDEGVTFQEITEDPNVEPPDLSVdRMMMRQQVRDFLGILSPREKEIIEHRFGIHDGEPKTLHVIGDMFG 538
Cdd:PRK07598  303 PRSVSLETKVGKDKDTELGDLLETDDISPEEMLM-RESLQRDLQHLLADLTSRERDVIRMRFGLADGHTYSLAEIGRALD 381

                         330
                  ....*....|....*...
gi 1002292766 539 LSKERIRQLQNRALEKLK 556
Cdd:PRK07598  382 LSRERVRQIESKALQKLR 399
PRK07921 PRK07921
RNA polymerase sigma factor SigB; Reviewed
 321-556 8.80e-53

RNA polymerase sigma factor SigB; Reviewed


Pssm-ID: 181169 [Multi-domain]  Cd Length: 324  Bit Score: 183.01  E-value: 8.80e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 321 KELQSSIRTGRRCREKMARSNFRLVIHVARKYEGYGLDIQDLVQDGCSGLMKTFEKFNPSKGCRFPTYAYWWIRQSIKKS 400
Cdd:PRK07921   75 RDLAAVVRDGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRG 154

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 401 IFKNSRLIRLPESVYALLRKVGKARMECIME-GEQPTNANVARRAGITIEKLAKLRAKTRKPRSMQDHVWSDEGVTFQEI 479
Cdd:PRK07921  155 MADQSRTIRLPVHLVEQVNKLARIKRELHQQlGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDF 234

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1002292766 480 TEDPNVEPPDLSVDRMMMRQQVRDFLGILSPREKEIIEHRFGIHDGEPKTLHVIGDMFGLSKERIRQLQNRALEKLK 556
Cdd:PRK07921  235 IEDSEATSAENAVIAGLLHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLR 311
PRK05901 PRK05901
RNA polymerase sigma factor; Provisional
 274-564 1.29e-47

RNA polymerase sigma factor; Provisional


Pssm-ID: 235640 [Multi-domain]  Cd Length: 509  Bit Score: 173.64  E-value: 1.29e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 274 LTAKEERHLfSKiqilmKIEEAHRKLEvqcgrepTLAEWAEAVGMSSKELQSSIRTGRRCREKMARSNFRLVIHVARKYE 353
Cdd:PRK05901  226 LNAEEEVEL-AK-----RIEAGLYAEE-------LLAEGEKLDPELRRDLQWIGRDGKRAKNHLLEANLRLVVSLAKRYT 292

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 354 GYGLDIQDLVQDGCSGLMKTFEKFNPSKGCRFPTYAYWWIRQSIKKSIFKNSRLIRLPESVYALLRKVGKARMECIME-G 432
Cdd:PRK05901  293 NRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVETINKLGRIERELLQElG 372

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 433 EQPTNANVARRAGITIEKLAKLRAKTRKPRSMQDHVWSDEGVTFQEITEDPNVEPPDLSVDRMMMRQQVRDFLGILSPRE 512
Cdd:PRK05901  373 REPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGDSQFGDFIEDSEAVSPVDAVSFTLLQDQLQEVLETLSERE 452

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1002292766 513 KEIIEHRFGIHDGEPKTLHVIGDMFGLSKERIRQLQNRALEKLK---RSASLQGF 564
Cdd:PRK05901  453 AGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRhpsRSQVLRDF 507
PRK05657 PRK05657
RNA polymerase sigma factor RpoS; Validated
 334-563 1.39e-40

RNA polymerase sigma factor RpoS; Validated


Pssm-ID: 235548 [Multi-domain]  Cd Length: 325  Bit Score: 149.72  E-value: 1.39e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 334 REKMARSNFRLVIHVARKYEGYGLDIQDLVQDGCSGLMKTFEKFNPSKGCRFPTYAYWWIRQSIKKSIFKNSRLIRLPES 413
Cdd:PRK05657   88 RQRMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPVH 167

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 414 VYALLRKVGKARMECIM-EGEQPTNANVARRAGITIEKLAKLRAKTRKPRSMQDHVWSDEGVTFQEITEDPNVEPPDLSV 492
Cdd:PRK05657  168 VVKELNVYLRAARELEHkLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLGGDPEKSLLDILADEQENGPEDTT 247

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1002292766 493 DRMMMRQQVRDFLGILSPREKEIIEHRFGIHDGEPKTLHVIGDMFGLSKERIRQLQNRALEKLKRSASLQG 563
Cdd:PRK05657  248 QDDDMKQSIVKWLFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREILQTQG 318
PRK09210 PRK09210
RNA polymerase sigma factor RpoD; Validated
 334-564 1.17e-39

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 148.59  E-value: 1.17e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 334 REKMARSNFRLVIHVARKYEGYGLDIQDLVQDGCSGLMKTFEKFNPSKGCRFPTYAYWWIRQSIKKSIFKNSRLIRLP-- 411
Cdd:PRK09210  131 KQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPvh 210

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 412 --ESVYALLRKVGKARMECimeGEQPTNANVARRAGITIEKLAKLRAKTRKPRSMQDHVWSDEGVTFQEITEDPNVEPPD 489
Cdd:PRK09210  211 mvETINKLIRVQRQLLQEL---GREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPA 287

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1002292766 490 LSVDRMMMRQQVRDFLGILSPREKEIIEHRFGIHDGEPKTLHVIGDMFGLSKERIRQLQNRALEKLK---RSASLQGF 564
Cdd:PRK09210  288 DHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRhpsRSKQLKDF 365
rpoH_proteo TIGR02392
alternative sigma factor RpoH; A sigma factor is a DNA-binding protein protein that binds to ...
 340-557 6.11e-35

alternative sigma factor RpoH; A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors. [Cellular processes, Adaptations to atypical conditions, Transcription, Transcription factors]


Pssm-ID: 274107 [Multi-domain]  Cd Length: 270  Bit Score: 132.79  E-value: 6.11e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 340 SNFRLVIHVARKYEGYGLDIQDLVQDGCSGLMKTFEKFNPSKGCRFPTYAYWWIRQSIKKSIFKNSRLIRLPES-----V 414
Cdd:TIGR02392  43 SHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYILRNWRLVKVATTkaqrkL 122

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 415 YALLRKVGKARMECIMEGEQptnANVARRAGITIEKLAKLRAKTRKPR---SMQDHVWSDEGVTFQEITEDPNVEPPDLS 491
Cdd:TIGR02392 123 FFNLRKMKKRLQGWLNPEEV---EAIAEELGVSEREVREMESRLSGQDmslNASIDDDEDDGGAPIAYLVDKRSDPEDTL 199

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1002292766 492 VDR---MMMRQQVRDFLGILSPREKEIIEHRFgiHDGEPKTLHVIGDMFGLSKERIRQLQNRALEKLKR 557
Cdd:TIGR02392 200 EEEqweELQRQALANALGSLDARSRRIIEARW--LDDDKLTLQELAAEYGVSAERIRQIEKNAMKKLKA 266
PRK05658 PRK05658
RNA polymerase sigma factor RpoD; Validated
 308-556 5.79e-33

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 235549 [Multi-domain]  Cd Length: 619  Bit Score: 133.38  E-value: 5.79e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 308 TLAEWAEAVGMSSKELQS---SIRTG----RRCREKMARSNFRLVIHVARKYEGYGLDIQDLVQDGCSGLMKTFEKFNPS 380
Cdd:PRK05658  349 ELEAIEEETGLTIEELKEinrQISKGeakaRRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 428

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 381 KGCRFPTYAYWWIRQSIKKSIFKNSRLIRLP----ESVYALLRkvgkarmecIM------EGEQPTNANVARRAGITIEK 450
Cdd:PRK05658  429 RGYKFSTYATWWIRQAITRSIADQARTIRIPvhmiETINKLNR---------ISrqmlqeIGREPTPEELAERLGMPEDK 499

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 451 LAKLRAKTRKPRSMQDHVWSDEGVTFQEITEDPNVEPPdlsVDRMM---MRQQVRDFLGILSPREKEIIEHRFGIHDGEP 527
Cdd:PRK05658  500 VRKVLKIAKEPISLETPIGDDEDSHLGDFIEDKNAELP---IDAAIqesLREATTDVLASLTPREAKVLRMRFGIDMNTD 576

                         250       260
                  ....*....|....*....|....*....
gi 1002292766 528 KTLHVIGDMFGLSKERIRQLQNRALEKLK 556
Cdd:PRK05658  577 HTLEEVGKQFDVTRERIRQIEAKALRKLR 605
PRK06596 PRK06596
RNA polymerase factor sigma-32; Reviewed
 336-556 3.81e-32

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 235838 [Multi-domain]  Cd Length: 284  Bit Score: 125.29  E-value: 3.81e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 336 KMARSNFRLVIHVARKYEGYGLDIQDLVQDGCSGLMKTFEKFNPSKGCRFPTYAYWWIRQSIKKSIFKNSRLIRLpesvy 415
Cdd:PRK06596   52 QLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKV----- 126

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 416 AL----------LRKVgKARMECIMEGEQptnANVARRAGITIEKLaklraktrkpRSM------QDH-----VWSDEGV 474
Cdd:PRK06596  127 ATtkaqrklffnLRKA-KKRLGWLNPEEV---EMVAEELGVSEEEV----------REMesrlsgQDAsldapIDDDDEE 192

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 475 TFQEIT--EDPNVEPPDLSVDR---MMMRQQVRDFLGILSPREKEIIEHRFgIHDgEPKTLHVIGDMFGLSKERIRQLQN 549
Cdd:PRK06596  193 SGAPQDylEDKSSDPADVLEEDnweDQRRALLADALEGLDERSRDIIEARW-LDD-DKSTLQELAAEYGVSAERVRQIEK 270


                  ....*..
gi 1002292766 550 RALEKLK 556
Cdd:PRK06596  271 NAMKKLK 277
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 323-557 9.38e-32

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


Pssm-ID: 440804 [Multi-domain]  Cd Length: 236  Bit Score: 122.62  E-value: 9.38e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 323 LQSSIRTGRRCREKMARSNFRLVIHVARKY-EGYGLDIQDLVQDGCSGLMKTFEKFNPSKGCRFPTYAYWWIRQSIKKSI 401
Cdd:COG1191     6 LRRYQEGDEEAREELIEEYLPLVKKIASRLaGRLPAELDDLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRGAILDYL 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 402 FKNSrliRLPESVYALLRKVGKARMECIME-GEQPTNANVARRAGITIEKLAKLR--AKTRKPRSMQDHVwsDEGVTFQE 478
Cdd:COG1191    86 RDED---WVPRSVRELARKIEEAIEELEQElGREPTDEEIAEELGISLEEVQEALeaANAYQLLSLDEPL--EDGDDLLD 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1002292766 479 ITEDPNvepPDLSVDRMMMRQQVRDFLGILSPREKEIIEHRFgihdGEPKTLHVIGDMFGLSKERIRQLQNRALEKLKR 557
Cdd:COG1191   161 LLESGD---PEEELEHEELREALAEAIEQLPERERLVLSLYY----FEELTLKEIAEVLGVSESRVSRLHKKALARLRE 232
rpoH2 PRK07500
RNA polymerase factor sigma-32; Reviewed
 331-558 3.44e-31

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 236033 [Multi-domain]  Cd Length: 289  Bit Score: 122.84  E-value: 3.44e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 331 RRCREKMARSNFRLVIHVARKYEGYGLDIQDLVQDGCSGLMKTFEKFNPSKGCRFPTYAYWWIRQSIKKSIFKNSRLIR- 409
Cdd:PRK07500   39 EDALHRIISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVRg 118

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 410 -LPESVYAL---LRKVgKARmecIMEGEQPTNAN-----VARRAGITIEKLAKLRAKTRKP-RSMQDHVWSDE--GVTFQ 477
Cdd:PRK07500  119 gTSSAQKALffnLRRL-RAR---LAQADEELTKQeihreIATALGVSLSDVEMMDARLSGPdASLNAPQSEEDegRSERM 194

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 478 EITEDPNVEPPDL---SVDRMMMRQQVRDFLGILSPREKEIIEHRFGIHDGEpkTLHVIGDMFGLSKERIRQLQNRALEK 554
Cdd:PRK07500  195 DFLVDDSPLPDEQvesSIDGERRRRWLTQALQTLNERELRIIRERRLREDGA--TLEALGEELGISKERVRQIEARALEK 272


                  ....
gi 1002292766 555 LKRS 558
Cdd:PRK07500  273 LRRA 276
PRK05803 PRK05803
RNA polymerase sporulation sigma factor SigK;
334-557 5.69e-23

RNA polymerase sporulation sigma factor SigK;


Pssm-ID: 180266 [Multi-domain]  Cd Length: 233  Bit Score: 97.71  E-value: 5.69e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 334 REKMARSNFRLVIHVARKYEGYGLDIQDLVQDGCSGLMKTFEKFNPSKGCRFPTYAywwirqsikksifknsrlirlpes 413
Cdd:PRK05803   51 RNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYA------------------------ 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 414 vyallrkvgkARmeCImegeqpTNanvarragitiEKLAKLRA--KTRKPRSMQDHVWSD-EG--VTFQEITEDPNVEPP 488
Cdd:PRK05803  107 ----------AR--CI------EN-----------EILMHLRNlkKTKKEVSLQDPIGVDkEGneISLIDILGSEEDDVI 157

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1002292766 489 DLsVDRMMMRQQVRDFLGILSPREKEIIEHRFGIHDGEPKTLHVIGDMFGLSKERIRQLQNRALEKLKR 557
Cdd:PRK05803  158 EQ-VELKMEVEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFK 225
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 337-406 5.10e-19

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: 81.09  E-value: 5.10e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 337 MARSNFRLVIHVARKYEGYGLDIQDLVQDGCSGLMKTFEKFNPSKGCRFPTYAYWWIRQSIKKSIFKNSR 406
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRR 70
FliA_WhiG TIGR02479
RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar ...
 358-557 8.55e-19

RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.


Pssm-ID: 274153 [Multi-domain]  Cd Length: 224  Bit Score: 85.40  E-value: 8.55e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 358 DIQDLVQDGCSGLMKTFEKFNPSKGCRFPTYAYWWIRQSIkksIFKNSRLIRLPESVYALLRKVGKARMECIME-GEQPT 436
Cdd:TIGR02479  25 ELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAM---LDELRRLDWVPRSLRQKARKLERAIRELEARlGREPT 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 437 NANVARRAGITIEKLAKLRAKTRKPR--SMqDHVW--SDEGVTFQEITEDPNVEPPDLSVDRMMMRQQVRDFLGILSPRE 512
Cdd:TIGR02479 102 EEEIAEELGMDLKEYRQALNEINALSlvSL-DELLesGDDGGSLIDRIEDDKSEDPEEELEREELREALAEAIESLSERE 180

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1002292766 513 KEIIEHRFgihdGEPKTLHVIGDMFGLSKERIRQLQNRALEKLKR 557
Cdd:TIGR02479 181 QLVLSLYY----YEELNLKEIGEVLGLTESRVSQIHSQALKKLRA 221
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 332-557 1.14e-16

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: 77.39  E-value: 1.14e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 332 RCREKMARSNFRLVIHVARKYEGYGLDIQDLVQDGCSGLMKTFEKFNPSKgcRFPTYAYWWIRQSIKKSIFKNSRLIRLP 411
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEG--SFKAWLFRIARNLILDYLRRKRRLRREL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 412 ESVYALLRkvgkarmecimegeqptnanvarragitieklaklraktrkprsmqdhvwsdegvtfqeitedpNVEPPDLS 491
Cdd:TIGR02937  79 DLLEELLD----------------------------------------------------------------SDPSPEEE 94

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1002292766 492 VDRMMMRQQVRDFLGILSPREKEIIEHRFgihdGEPKTLHVIGDMFGLSKERIRQLQNRALEKLKR 557
Cdd:TIGR02937  95 LEQEEEREALREALEKLPEREREVLVLRY----LEGLSYKEIAEILGISVGTVKRRLKRARKKLRE 156
PRK05572 PRK05572
RNA polymerase sporulation sigma factor, SigF/SigG family;
334-557 2.87e-16

RNA polymerase sporulation sigma factor, SigF/SigG family;


Pssm-ID: 180137 [Multi-domain]  Cd Length: 252  Bit Score: 78.86  E-value: 2.87e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 334 REKMARSNFRLVIHVARKYEGYGLDIQDLVQDGCSGLMKTFEKFNPSKGCRFPTYAYWWIRQSIKKSIfKNSRLIRLPES 413
Cdd:PRK05572   34 RDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRFL-RDDGTVKVSRS 112

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 414 VYALLRKVGKARMECIME-GEQPTNANVARRAGITIEKLAKLRAKTRKPRSMQDHVWSDEG--VTF-QEITEDpnveppd 489
Cdd:PRK05572  113 LKETANKIRKDKDELSKElGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVHENDGdpITLlDQIADQ------- 185

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1002292766 490 lSVDRMMMRQQVRDFLGILSPREKEIIEHRFgIHDgepKTLHVIGDMFGLSKERIRQLQNRALEKLKR 557
Cdd:PRK05572  186 -SEEDWFDKIALKEAIRELDERERLIVYLRY-FKD---KTQSEVAKRLGISQVQVSRLEKKILKQMKE 248
PRK08215 PRK08215
RNA polymerase sporulation sigma factor SigG;
321-557 1.45e-15

RNA polymerase sporulation sigma factor SigG;


Pssm-ID: 181296 [Multi-domain]  Cd Length: 258  Bit Score: 76.91  E-value: 1.45e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 321 KELQSSIRTG-RRCREKMARSNFRLVIHVARKYEGYGLDIQDLVQDGCSGLMKTFEKFNPSKGCRFPTYAYWWIRQSIKK 399
Cdd:PRK08215   25 RELFERMQNGdKEAREKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRR 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 400 SIFKNSRlIRLPESVYALLRKVGKARMECIME-GEQPTNANVARRAGITIEKLAKLRAKTRKPRSMQDHVWSDEGVT--- 475
Cdd:PRK08215  105 YLRDNNP-IRVSRSLRDIAYKALQVREKLINEnSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIYHDGGDPiyv 183

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 476 FQEITEDPNVEppDLSVDRMMMRQQVRDflgiLSPREKEIIEHRFgiHDGepKTLHVIGDMFGLSKERIRQLQNRALEKL 555
Cdd:PRK08215  184 MDQISDEKNKD--ENWLEEIALKEAMKK----LNDREKLILNLRF--FQG--KTQMEVAEEIGISQAQVSRLEKAALKHM 253


                  ..
gi 1002292766 556 KR 557
Cdd:PRK08215  254 RK 255
PRK08301 PRK08301
RNA polymerase sporulation sigma factor SigE;
341-557 1.55e-15

RNA polymerase sporulation sigma factor SigE;


Pssm-ID: 236228 [Multi-domain]  Cd Length: 234  Bit Score: 76.05  E-value: 1.55e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 341 NFRLVIHVARKYEGYGLDIQDLVQDGCSGLMKTFEKFNPSKGCRFPTYAywwirqsikksifknSRLIRLPESVYalLRK 420
Cdd:PRK08301   61 NLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYA---------------SRCIENEILMY--LRR 123

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 421 VGKARMEciMEGEQPTN----ANvarragitiEKLaklraktrkprsMQDHVWSDEGVTFQEITEDpnveppdlsVDRMM 496
Cdd:PRK08301  124 NNKVKAE--VSFDEPLNidwdGN---------ELL------------LSDVLGTDNDIIYKDIEDE---------VDRKL 171

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1002292766 497 MRQQvrdfLGILSPREKEIIEHRFGIHDGEPKTLHVIGDMFGLSKERIRQLQNRALEKLKR 557
Cdd:PRK08301  172 LKKA----LKKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKK 228
PRK06288 PRK06288
RNA polymerase sigma factor WhiG; Reviewed
 344-560 1.61e-15

RNA polymerase sigma factor WhiG; Reviewed


Pssm-ID: 235770 [Multi-domain]  Cd Length: 268  Bit Score: 77.03  E-value: 1.61e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 344 LVIHVARKYeGYGL----DIQDLVQDGCSGLMKTFEKFNPSKGCRFPTYAYwwirQSIKKSIFKNSRLI-RLPESVYALL 418
Cdd:PRK06288   43 LVKYVAGRI-AVGMpqnvEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAV----TRIRGAIFDELRSIdWIPRSVRQKA 117

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 419 RKVGKARmeCIME---GEQPTNANVARRAGITIEKLAKLRAKTR--KPRSMQDhVWS--DEG--VTFQEITEDPNVEPPD 489
Cdd:PRK06288  118 RQIERAI--AMLEarlGRTPSDEEIADELGISLEEYNSLLSKLSgtSVVSLND-LWFggDEGdeVSLMDTLESPAALNPD 194

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1002292766 490 LSVDRMMMRQQVRDFLGILSPREKEIIEhrfgIHDGEPKTLHVIGDMFGLSKERIRQLQNRALEKLKRSAS 560
Cdd:PRK06288  195 EIAEREEIKRVIVEAIKTLPEREKKVLI----LYYYEDLTLKEIGKVLGVTESRISQLHTKAVLQLRAKLA 261
PRK07408 PRK07408
RNA polymerase sigma factor SigF; Reviewed
 334-524 3.96e-12

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 180965 [Multi-domain]  Cd Length: 256  Bit Score: 66.48  E-value: 3.96e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 334 REKMARSNFRLVIHVARKY-----EGYgldiQDLVQDGCSGLMKTFEKFNPSKGCRFPTYAYWWIRQSIKKSIFKNSRLI 408
Cdd:PRK07408   27 RNQLVELNLGLVRKEAHRWsnqcsEPY----EDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPTV 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 409 RLPESVYALLRKVGKARMECIME-GEQPTNANVARRAGITIEKL--AKLRAKTRKPRSMQDHVWSDEG--VTFQEITEDP 483
Cdd:PRK07408  103 RIPRRWQELQRQAKKVRQELRQElGRQPTDQEIAQALDISLEEWqeIKLALQNRTPLSLDAPVNQDEDgsTSLGDLLPDP 182

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1002292766 484 NVEPPDLSVDRmmmRQQVRDFLGILSPREKEIIEHRFgIHD 524
Cdd:PRK07408  183 RYRSFQLAQED---RIRLQQALAQLEERTREVLEFVF-LHD 219
PRK07670 PRK07670
FliA/WhiG family RNA polymerase sigma factor;
360-557 1.61e-11

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 181075 [Multi-domain]  Cd Length: 251  Bit Score: 64.68  E-value: 1.61e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 360 QDLVQDGCSGLMKTFEKFNPSKGCRFPTYAYWWIRQSIKKSIFKNSrliRLPESVYALLRKVGkarmECIMEGEQ----- 434
Cdd:PRK07670   53 DDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRKED---WLPRSMREKTKKVE----AAIEKLEQrymrn 125

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 435 PTNANVARRAGITIEKLAklraktrkpRSMQDHVWS------------DEGVTFQEITEDPNVEPPDLSVDRMMMRQQVR 502
Cdd:PRK07670  126 VTPKEVAAELGMTEEEVE---------ATMNEGFFAnllsidekthdqDDGENVSVTIRDDKTPTPEEKLLKEELIEELA 196

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1002292766 503 DFLGILSPREKEIIehrfGIHDGEPKTLHVIGDMFGLSKERIRQLQNRALEKLKR 557
Cdd:PRK07670  197 EKIKQLSEKEQLVI----SLFYKEELTLTEIGQVLNLSTSRISQIHSKALFKLKK 247
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 505-557 2.71e-11

Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. 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: 58.59  E-value: 2.71e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1002292766 505 LGILSPREKEIIEHRFGihdgEPKTLHVIGDMFGLSKERIRQLQNRALEKLKR 557
Cdd:pfam04545   2 LASLPPRERQVLVLRYG----EGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
PRK05911 PRK05911
RNA polymerase sigma factor sigma-28; Reviewed
 360-564 6.06e-11

RNA polymerase sigma factor sigma-28; Reviewed


Pssm-ID: 235644 [Multi-domain]  Cd Length: 257  Bit Score: 63.10  E-value: 6.06e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 360 QDLVQDGCSGLMKTFEKFNPSKGCRFPTYAYWWIRQSIKKSIFKNSrliRLPESVYALLRKVGKArMECIME--GEQPTN 437
Cdd:PRK05911   54 EDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRKQD---WVPRSVHQKANKLADA-MDSLRQslGKEPTD 129

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 438 ANVARRAGITIEKLAKLRAKTR--------KPRSMQDHvwSDEGVTFQEITEDPNVEPPDLSVDrmmmRQQVRDFL--GI 507
Cdd:PRK05911  130 GELCEYLNISQQELSGWFSSARpalilslnEEFPCQSD--DEAGLALEERIADERAETGYDVVD----KKEFSSILaeAI 203

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1002292766 508 LSPREKEiiEHRFGIHDGEPKTLHVIGDMFGLSKERIRQLQNRALEKLKrsASLQGF 564
Cdd:PRK05911  204 LALEEKE--RKVMALYYYEELVLKEIGKILGVSESRVSQIHSKALLKLR--ATLSAF 256
PRK08583 PRK08583
RNA polymerase sigma factor SigB; Validated
 344-562 9.31e-10

RNA polymerase sigma factor SigB; Validated


Pssm-ID: 236306 [Multi-domain]  Cd Length: 257  Bit Score: 59.32  E-value: 9.31e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 344 LVIHVARKYEGYGLDIQDLVQDGCSGLMKTFEKFNPSKGCRFPTYAYWWIRQSIKKSIFKNSRLIRLPESVYALLRKVGK 423
Cdd:PRK08583   41 LVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKK 120

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 424 ARMECIMEGEQ-PTNANVARRAGITIEKL--AKLRAKTRKPRSMQDHVWSD-EG--VTFQEI--TEDPNVEppdlSVDRM 495
Cdd:PRK08583  121 AVDELTTELQRsPKISEIADRLGVSEEEVleAMEMGKSYQALSVDHSIEADsDGstVTLLDIvgQQEDGYE----LTEQR 196

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1002292766 496 MMRQQVrdfLGILSPREKEIIEHRFGIHDGEPKTlhviGDMFGLSKERIRQLQNRALEKLKRSASLQ 562
Cdd:PRK08583  197 MILEKI---LPVLSDREKSIIQCTFIENLSQKET----GERLGISQMHVSRLQRQAIKKLREAAFLD 256
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 498-556 9.36e-10

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: 54.42  E-value: 9.36e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1002292766 498 RQQVRDFLGILSPREKEIIEHRFGihdgEPKTLHVIGDMFGLSKERIRQLQNRALEKLK 556
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFG----EGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK07122 PRK07122
RNA polymerase sigma factor SigF; Reviewed
 331-556 2.06e-08

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 168831 [Multi-domain]  Cd Length: 264  Bit Score: 55.55  E-value: 2.06e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 331 RRCREKMARSNFRLVIHVARKYEGYGLDIQDLVQDGCSGLMKTFEKFNPSKGCRFPTYAYWWIRQSIKKSIFKNSRLIRL 410
Cdd:PRK07122   39 QRQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWSVKV 118

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 411 PESVYALLRKVGKARMECIME-GEQPTNANVARRAGITIEKLAK--LRAKTRKPRSMqDHVWSDEGVTFQEITEdpNVEP 487
Cdd:PRK07122  119 PRRLKELHLRLGRATAELSQRlGRAPTASELAAELGMDREEVVEglVAGSAYNTLSI-DSGGGSGDDDARAIAD--TLGD 195

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1002292766 488 PDLSVDRMMMRQQVRDFLGILSPREKEIIEHRFgihdGEPKTLHVIGDMFGLSKERIRQLQNRALEKLK 556
Cdd:PRK07122  196 VDAGLDQIENREALRPLLAALPERERTVLVLRF----FESMTQTQIAERVGISQMHVSRLLAKTLARLR 260
Sigma70_r3 pfam04539
Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the ...
 417-492 4.79e-08

Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but as some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme.


Pssm-ID: 427997 [Multi-domain]  Cd Length: 78  Bit Score: 50.30  E-value: 4.79e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1002292766 417 LLRKVGKARMECIME-GEQPTNANVARRAGITIEKLAKLRAKTRKPRSMQDHVWSDEGVTFQEITEDPNVEPPDLSV 492
Cdd:pfam04539   2 LLNKIKRAQRELEQElGREPTPEEIAEELGLSPEKVREVLEAAREPVSLDTPVGEEEDGELGDLLEDDDIESPEEAV 78
fliA PRK06986
flagellar biosynthesis sigma factor; Validated
 357-563 2.58e-06

flagellar biosynthesis sigma factor; Validated


Pssm-ID: 235901 [Multi-domain]  Cd Length: 236  Bit Score: 48.69  E-value: 2.58e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 357 LDIQDLVQDGCSGLMKTFEKFNPSKGCRFPTYAYWWIRQSI----------KKSIFKNSRLIRlpESVYALLRKVGKArm 426
Cdd:PRK06986   36 VDLDDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMldelrsldwvPRSVRRNAREVA--QAIRQLEQELGRE-- 111

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 427 ecimegeqPTNANVARRAGITIEKLAKLRAKTR--KPRSMQD-HVWSDEGVTFQEITEDPNvepPDLSVDRMMMRQQVRD 503
Cdd:PRK06986  112 --------PTDTEVAEKLGLSLEEYREMLLDTNisQLFSIDElRGEHGDSILVTEDHQDED---PLQQLEDEELREALVE 180

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 504 FLGILSPREKEIIehrfGIHDGEPKTLHVIGDMFGLSKERIRQLQNRALEKLKrsASLQG 563
Cdd:PRK06986  181 AIESLPEREQLVL----SLYYQEELNLKEIGAVLGVSESRVSQIHSQAIKRLR--ARLGE 234
PRK06930 PRK06930
positive control sigma-like factor; Validated
 426-557 2.33e-04

positive control sigma-like factor; Validated


Pssm-ID: 180757 [Multi-domain]  Cd Length: 170  Bit Score: 42.02  E-value: 2.33e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 426 MECIMEGEQPTNAN-VARRAGITIEKLAKLRAKTRKPRSMQDHVWSDEgVTFQEITEDpnveppdlsvDRMMMRqqvrDF 504
Cdd:PRK06930   47 IEWMEKGRQPGNRRgIDRRAAYQREVICDPLLIQRYFRSMEDLEWDIE-EPESVISEW----------DKIRIE----DA 111

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1002292766 505 LGILSPREKEIiehrFGIHDGEPKTLHVIGDMFGLSKERIRQLQNRALEKLKR 557
Cdd:PRK06930  112 LSVLTEREKEV----YLMHRGYGLSYSEIADYLNIKKSTVQSMIERAEKKIAR 160
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 318-557 1.08e-03

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: 40.36  E-value: 1.08e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 318 MSS-KELQSSIRTG-RRCREKMARSNFRLVIHVARKYEGYGLDIQDLVQDgcsglmkTFEKfnpskgcrfptyaywwirq 395
Cdd:COG1595     1 MSSdEELLERLRAGdEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQE-------TFLR------------------- 54

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 396 sikksIFKNSRLIRLPESVYALLRKVgkARMECIMEgeqptnanvarragitieklakLRAKTRKPRSMQDHvwsdegvt 475
Cdd:COG1595    55 -----LWRKLDSFRGRGSFRAWLYRI--ARNLAIDH----------------------LRKRRRRRELLDEL-------- 97

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 476 fqEITEDPNVEPPDLSVDRMMMRQQVRDFLGILSPREKEIIEHRFgIHDgepKTLHVIGDMFGLSKERIRQLQNRALEKL 555
Cdd:COG1595    98 --AEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRY-LEG---LSYAEIAEILGISEGTVKSRLSRARKKL 171


                  ..
gi 1002292766 556 KR 557
Cdd:COG1595   172 RE 173
PRK06759 PRK06759
RNA polymerase factor sigma-70; Validated
 500-559 2.69e-03

RNA polymerase factor sigma-70; Validated


Pssm-ID: 235857 [Multi-domain]  Cd Length: 154  Bit Score: 38.65  E-value: 2.69e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002292766 500 QVRDFLGILSPREKEIIEHRFgihdGEPKTLHVIGDMFGLSKERIRQLQNRALEKLKRSA 559
Cdd:PRK06759   99 KVKDFMSVLDEKEKYIIFERF----FVGKTMGEIALETEMTYYQVRWIYRQALEKMRNSV 154
Sigma70_r3 pfam04539
Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the ...
 291-332 3.67e-03

Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but as some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme.


Pssm-ID: 427997 [Multi-domain]  Cd Length: 78  Bit Score: 36.43  E-value: 3.67e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1002292766 291 KIEEAHRKLEVQCGREPTLAEWAEAVGMSSKELQSSIRTGRR 332
Cdd:pfam04539   5 KIKRAQRELEQELGREPTPEEIAEELGLSPEKVREVLEAARE 46
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 291-367 4.39e-03

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


Pssm-ID: 440804 [Multi-domain]  Cd Length: 236  Bit Score: 39.04  E-value: 4.39e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1002292766 291 KIEEAHRKLEVQCGREPTLAEWAEAVGMSSKELQssirtgrrcrEKMARSNFRLVIHVARKYEgYGLDIQDLVQDGC 367
Cdd:COG1191   101 KIEEAIEELEQELGREPTDEEIAEELGISLEEVQ----------EALEAANAYQLLSLDEPLE-DGDDLLDLLESGD 166
 
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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