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Conserved domains on  [gi|15232364|ref|NP_190960|]
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RNApolymerase sigma-subunit C [Arabidopsis thaliana]

Protein Classification

RNA polymerase sigma factor RpoD/SigA( domain architecture ID 11426268)

RNA polymerase sigma factor RpoD/SigA is the primary sigma factor during exponential growth

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
333-570 8.64e-68

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: 220.31  E-value: 8.64e-68
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 333 RDELVKS-TRsLVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSTMVSRHARGVHIPS 411
Cdd:COG0568  32 KRKLVEAnLR-LVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDPERGFRFSTYATWWIRQAITRAIADQWRTIRLPV 110
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 412 SIIRTINHIQKARKTLKTSHGIKyAADEEIAKLTGHSVKKIRAANQCLKVVGSIDKKVGDCFTTKFLEFTPDTTMESPEE 491
Cdd:COG0568 111 HMAETLNKLRRAKRQLLQELGRE-PTPEEIAEELGVPEEKVREMLRLAREPVSLDAPVGDDEDSELGDLLEDEEAPSPEE 189
                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15232364 492 AVMRQSARRDIHDLLEGLEPREKQVMVLRYGLQDYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLRDQPNAEDLRYYLN 570
Cdd:COG0568 190 ALEEELLREELREALDTLTEREREILRLRFGLDDGEPHTLEEIGKEFGVSRERVRQIEAKALRKLRHPLRSRKLRDYLD 268
PRTases_typeI super family cl00309
Phosphoribosyl transferase (PRT)-type I domain; Phosphoribosyl transferase (PRT) domain. The ...
46-72 1.85e-08

Phosphoribosyl transferase (PRT)-type I domain; Phosphoribosyl transferase (PRT) domain. The type I PRTases are identified by a conserved PRPP binding motif which features two adjacent acidic residues surrounded by one or more hydrophobic residue. PRTases catalyze the displacement of the alpha-1'-pyrophosphate of 5-phosphoribosyl-alpha1-pyrophosphate (PRPP) by a nitrogen-containing nucleophile. The reaction products are an alpha-1 substituted ribose-5'-phosphate and a free pyrophosphate (PP). PRPP, an activated form of ribose-5-phosphate, is a key metabolite connecting nucleotide synthesis and salvage pathways. The type I PRTase family includes a range of diverse phosphoribosyl transferase enzymes and regulatory proteins of the nucleotide synthesis and salvage pathways, including adenine phosphoribosyltransferase EC:2.4.2.7., hypoxanthine-guanine-xanthine phosphoribosyltransferase, hypoxanthine phosphoribosyltransferase EC:2.4.2.8., ribose-phosphate pyrophosphokinase EC:2.7.6.1., amidophosphoribosyltransferase EC:2.4.2.14., orotate phosphoribosyltransferase EC:2.4.2.10., uracil phosphoribosyltransferase EC:2.4.2.9., and xanthine-guanine phosphoribosyltransferase EC:2.4.2.22.


The actual alignment was detected with superfamily member PLN02541:

Pssm-ID: 444823  Cd Length: 244  Bit Score: 55.56  E-value: 1.85e-08
                         10        20
                 ....*....|....*....|....*..
gi 15232364   46 LVFVHPHPLIKHWLSLLRSDQTSFPIF 72
Cdd:PLN02541  33 LVFVPPHPLIKHWLSVLRNEQTPPPIF 59
 
Name Accession Description Interval E-value
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
333-570 8.64e-68

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: 220.31  E-value: 8.64e-68
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 333 RDELVKS-TRsLVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSTMVSRHARGVHIPS 411
Cdd:COG0568  32 KRKLVEAnLR-LVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDPERGFRFSTYATWWIRQAITRAIADQWRTIRLPV 110
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 412 SIIRTINHIQKARKTLKTSHGIKyAADEEIAKLTGHSVKKIRAANQCLKVVGSIDKKVGDCFTTKFLEFTPDTTMESPEE 491
Cdd:COG0568 111 HMAETLNKLRRAKRQLLQELGRE-PTPEEIAEELGVPEEKVREMLRLAREPVSLDAPVGDDEDSELGDLLEDEEAPSPEE 189
                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15232364 492 AVMRQSARRDIHDLLEGLEPREKQVMVLRYGLQDYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLRDQPNAEDLRYYLN 570
Cdd:COG0568 190 ALEEELLREELREALDTLTEREREILRLRFGLDDGEPHTLEEIGKEFGVSRERVRQIEAKALRKLRHPLRSRKLRDYLD 268
Sig70-cyanoRpoD TIGR02997
RNA polymerase sigma factor, cyanobacterial RpoD-like family; This family includes a number of ...
278-557 5.46e-62

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: 206.33  E-value: 5.46e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364   278 ETEMSTGVKIVADMERIRTQLEEESGKVASLSCWAAAAGMNEKLLMRNLHYGWYCRDELVKSTRSLVLFLARNYRGLGIA 357
Cdd:TIGR02997  21 EIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKMIKANLRLVVSVAKKYQNRGLE 100
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364   358 HEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSTMVSRHARGVHIPSSIIRTINHIQKARKTLktSHGIKYAA 437
Cdd:TIGR02997 101 LLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKLNKIKKVQREL--SQKLGRTP 178
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364   438 DE-EIAKLTGHSVKKIR----AANQCLkvvgSIDKKVGDCFTTKFLEFTPDTTmESPEEAVMRQSARRDIHDLLEGLEPR 512
Cdd:TIGR02997 179 SEaEIAEALELEPEQVRellqRARQPV----SLDAPVGDEEDTELGDLLEDDG-ESPEEQVERESLRQDLESLLAELTPR 253
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 15232364   513 EKQVMVLRYGLQDYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLR 557
Cdd:TIGR02997 254 ERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR 298
PRK07406 PRK07406
RNA polymerase sigma factor RpoD; Validated
271-561 1.71e-58

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236012 [Multi-domain]  Cd Length: 373  Bit Score: 199.62  E-value: 1.71e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  271 RERISRNETEMSTGVKIvAD---MERIRTQLEEESGKVASLSCWAAAAGMNEKLLMRNLHYGWYCRDELVKSTRSLVLFL 347
Cdd:PRK07406  74 RIRLLRPDEEIELARKI-ADlleLEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKEKMVQSNLRLVVSI 152
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  348 ARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSTMVSRHARGVHIPSSIIRTINHIQKARKTL 427
Cdd:PRK07406 153 AKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVL 232
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  428 KTSHGIKyAADEEIAKLTGHSVKKIRAANQCLKVVGSIDKKVG---DCFTTKFLEftpdTTMESPEEAVMRQSARRDIHD 504
Cdd:PRK07406 233 SQEFGRK-PTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGkeeDSRLGDFIE----ADGETPEDDVAKNLLREDLEG 307
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 15232364  505 LLEGLEPREKQVMVLRYGLQDYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLRdQPN 561
Cdd:PRK07406 308 VLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLR-HPN 363
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
336-405 5.80e-14

Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime. The aromatic residues of the recognition helix, found at the C-terminus of this domain are though to mediate strand separation, thereby allowing transcription initiation.


Pssm-ID: 427998 [Multi-domain]  Cd Length: 71  Bit Score: 66.84  E-value: 5.80e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364   336 LVKSTRSLVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSTMVSRHAR 405
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRR 70
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
499-557 6.10e-11

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: 57.88  E-value: 6.10e-11
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 15232364 499 RRDIHDLLEGLEPREKQVMVLRYglqdYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLR 557
Cdd:cd06171   1 RERLEEALDKLPEREREVILLRF----GEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PLN02541 PLN02541
uracil phosphoribosyltransferase
46-72 1.85e-08

uracil phosphoribosyltransferase


Pssm-ID: 215297  Cd Length: 244  Bit Score: 55.56  E-value: 1.85e-08
                         10        20
                 ....*....|....*....|....*..
gi 15232364   46 LVFVHPHPLIKHWLSLLRSDQTSFPIF 72
Cdd:PLN02541  33 LVFVPPHPLIKHWLSVLRNEQTPPPIF 59
Upp COG0035
Uracil phosphoribosyltransferase [Nucleotide transport and metabolism]; Uracil ...
47-74 5.75e-04

Uracil phosphoribosyltransferase [Nucleotide transport and metabolism]; Uracil phosphoribosyltransferase is part of the Pathway/BioSystem: Pyrimidine salvage


Pssm-ID: 439805  Cd Length: 209  Bit Score: 41.59  E-value: 5.75e-04
                        10        20
                ....*....|....*....|....*...
gi 15232364  47 VFVHPHPLIKHWLSLLRSDQTSFPIFVR 74
Cdd:COG0035   4 VHVVDHPLIQHKLTLLRDKNTDTKEFRR 31
 
Name Accession Description Interval E-value
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
333-570 8.64e-68

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: 220.31  E-value: 8.64e-68
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 333 RDELVKS-TRsLVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSTMVSRHARGVHIPS 411
Cdd:COG0568  32 KRKLVEAnLR-LVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDPERGFRFSTYATWWIRQAITRAIADQWRTIRLPV 110
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 412 SIIRTINHIQKARKTLKTSHGIKyAADEEIAKLTGHSVKKIRAANQCLKVVGSIDKKVGDCFTTKFLEFTPDTTMESPEE 491
Cdd:COG0568 111 HMAETLNKLRRAKRQLLQELGRE-PTPEEIAEELGVPEEKVREMLRLAREPVSLDAPVGDDEDSELGDLLEDEEAPSPEE 189
                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15232364 492 AVMRQSARRDIHDLLEGLEPREKQVMVLRYGLQDYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLRDQPNAEDLRYYLN 570
Cdd:COG0568 190 ALEEELLREELREALDTLTEREREILRLRFGLDDGEPHTLEEIGKEFGVSRERVRQIEAKALRKLRHPLRSRKLRDYLD 268
Sig70-cyanoRpoD TIGR02997
RNA polymerase sigma factor, cyanobacterial RpoD-like family; This family includes a number of ...
278-557 5.46e-62

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: 206.33  E-value: 5.46e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364   278 ETEMSTGVKIVADMERIRTQLEEESGKVASLSCWAAAAGMNEKLLMRNLHYGWYCRDELVKSTRSLVLFLARNYRGLGIA 357
Cdd:TIGR02997  21 EIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKMIKANLRLVVSVAKKYQNRGLE 100
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364   358 HEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSTMVSRHARGVHIPSSIIRTINHIQKARKTLktSHGIKYAA 437
Cdd:TIGR02997 101 LLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKLNKIKKVQREL--SQKLGRTP 178
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364   438 DE-EIAKLTGHSVKKIR----AANQCLkvvgSIDKKVGDCFTTKFLEFTPDTTmESPEEAVMRQSARRDIHDLLEGLEPR 512
Cdd:TIGR02997 179 SEaEIAEALELEPEQVRellqRARQPV----SLDAPVGDEEDTELGDLLEDDG-ESPEEQVERESLRQDLESLLAELTPR 253
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 15232364   513 EKQVMVLRYGLQDYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLR 557
Cdd:TIGR02997 254 ERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR 298
PRK07406 PRK07406
RNA polymerase sigma factor RpoD; Validated
271-561 1.71e-58

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236012 [Multi-domain]  Cd Length: 373  Bit Score: 199.62  E-value: 1.71e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  271 RERISRNETEMSTGVKIvAD---MERIRTQLEEESGKVASLSCWAAAAGMNEKLLMRNLHYGWYCRDELVKSTRSLVLFL 347
Cdd:PRK07406  74 RIRLLRPDEEIELARKI-ADlleLEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKEKMVQSNLRLVVSI 152
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  348 ARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSTMVSRHARGVHIPSSIIRTINHIQKARKTL 427
Cdd:PRK07406 153 AKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVL 232
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  428 KTSHGIKyAADEEIAKLTGHSVKKIRAANQCLKVVGSIDKKVG---DCFTTKFLEftpdTTMESPEEAVMRQSARRDIHD 504
Cdd:PRK07406 233 SQEFGRK-PTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGkeeDSRLGDFIE----ADGETPEDDVAKNLLREDLEG 307
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 15232364  505 LLEGLEPREKQVMVLRYGLQDYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLRdQPN 561
Cdd:PRK07406 308 VLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLR-HPN 363
PRK07405 PRK07405
RNA polymerase sigma factor SigD; Validated
285-557 9.46e-48

RNA polymerase sigma factor SigD; Validated


Pssm-ID: 180963 [Multi-domain]  Cd Length: 317  Bit Score: 169.17  E-value: 9.46e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  285 VKIVADMERIRTQLEEESGKVASLSCWAAAAGMNEKLLMRNLHYGWYCRDELVKSTRSLVLFLARNYRGLGIAHEDLIQA 364
Cdd:PRK07405  35 VQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAKRKMVEANLRLVVSVAKKYLKRNVDLLDLIQE 114
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  365 GYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSTMVSRHARGVHIPSSIIRTINHIQKARKTLKTSHGiKYAADEEIAKL 444
Cdd:PRK07405 115 GTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKLNKIKKAQRQLSQQLG-RAATIGELAEE 193
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  445 TGHSVKKIRA----ANQCLkvvgSIDKKVGDCFTTKFLEFTPDTTmESPEEAVMRQSARRDIHDLLEGLEPREKQVMVLR 520
Cdd:PRK07405 194 LELTPKQVREylerARQPL----SLDLRVGDNQDTELGELLEDTG-ASPEDFATQSSLQLDLERLMEDLTPQQKEVIALR 268
                        250       260       270
                 ....*....|....*....|....*....|....*..
gi 15232364  521 YGLQDYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLR 557
Cdd:PRK07405 269 FGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLR 305
PRK05949 PRK05949
RNA polymerase sigma factor; Validated
278-557 2.05e-47

RNA polymerase sigma factor; Validated


Pssm-ID: 180321 [Multi-domain]  Cd Length: 327  Bit Score: 168.48  E-value: 2.05e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  278 ETEMSTGVKIVADME--RIRTQLEEESGKVASLSCWAAAAGMNEKLLMRNLHYGWYCRDELVKSTRSLVLFLARNYRGLG 355
Cdd:PRK05949  36 EQEIVYGKQVQQMMSllEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAKQKMIEANLRLVVAIAKKYQKRN 115
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  356 IAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSTMVSRHARGVHIPSSIIRTINHIQKARKTLKTSHGiKY 435
Cdd:PRK05949 116 MEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEKLNKIKKTQRELSQKLG-RS 194
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  436 AADEEIAKLTGHSVKKIRAANQCLKVVGSIDKKVGDCFTTKFLEFTPDTTMeSPEEAVMRQSARRDIHDLLEGLEPREKQ 515
Cdd:PRK05949 195 ATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTELSELLEDEGP-SPDQYITQELLRQDLNNLLAELTPQQRE 273
                        250       260       270       280
                 ....*....|....*....|....*....|....*....|..
gi 15232364  516 VMVLRYGLQDYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLR 557
Cdd:PRK05949 274 VLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLR 315
PRK07921 PRK07921
RNA polymerase sigma factor SigB; Reviewed
333-568 5.12e-47

RNA polymerase sigma factor SigB; Reviewed


Pssm-ID: 181169 [Multi-domain]  Cd Length: 324  Bit Score: 167.22  E-value: 5.12e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  333 RDELVKSTRSLVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSTMVSRHARGVHIPSS 412
Cdd:PRK07921  88 RRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVH 167
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  413 IIRTINHIQKARKTLKTSHGiKYAADEEIAKLTGHSVKKIRAANQCLKVVGSIDKKVGDCFTTKFLEFTPDTTMESPEEA 492
Cdd:PRK07921 168 LVEQVNKLARIKRELHQQLG-REATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEATSAENA 246
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15232364  493 VMRQSARRDIHDLLEGLEPREKQVMVLRYGLQDYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLRDQPNAEDLRYY 568
Cdd:PRK07921 247 VIAGLLHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGERADRLRSY 322
PRK05901 PRK05901
RNA polymerase sigma factor; Provisional
319-569 6.76e-44

RNA polymerase sigma factor; Provisional


Pssm-ID: 235640 [Multi-domain]  Cd Length: 509  Bit Score: 163.24  E-value: 6.76e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  319 EKLLMRNLHYGWYCRDELVKSTRSLVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMST 398
Cdd:PRK05901 259 RRDLQWIGRDGKRAKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITR 338
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  399 MVSRHARGVHIPSSIIRTINHIQKARKTLKTSHGiKYAADEEIAKLTGHSVKKIRAANQclkvVG----SIDKKVGDCFT 474
Cdd:PRK05901 339 AMADQARTIRIPVHMVETINKLGRIERELLQELG-REPTPEELAKEMGFTPEKVREIQK----YNrepiSLDKTIGKEGD 413
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  475 TKFLEFTPDTTMESPEEAVMRQSARRDIHDLLEGLEPREKQVMVLRYGLQDYRPKSLEEIGKLLKVSKEWIRKIERRAMA 554
Cdd:PRK05901 414 SQFGDFIEDSEAVSPVDAVSFTLLQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLR 493
                        250
                 ....*....|....*
gi 15232364  555 KLRDQPNAEDLRYYL 569
Cdd:PRK05901 494 KLRHPSRSQVLRDFL 508
PRK07598 PRK07598
RNA polymerase sigma factor SigC; Validated
260-569 3.94e-43

RNA polymerase sigma factor SigC; Validated


Pssm-ID: 236067 [Multi-domain]  Cd Length: 415  Bit Score: 159.26  E-value: 3.94e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  260 RVRRPPKYRKKRERISRNETEMSTGVKIVADMERIRTQLeeesGKVASLSCWAAAAGMNEKLLMRNLHYG---WY----- 331
Cdd:PRK07598  86 KVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSEL----GHRPSLERWAKTADISLADLKPTLAEGkrrWAeiakl 161
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  332 --------------CRDELVKSTRSLVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMS 397
Cdd:PRK07598 162 tveeleqiqkqglrAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGIT 241
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  398 TMVSRHARGVHIPSSIIRTINHIQKARKTLKTSHGiKYAADEEIAKLTGHSVKKIRAANQCLKVVGSIDKKVGDCFTTKF 477
Cdd:PRK07598 242 RAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKG-RTPTIEDIAQELEMTPTQVREVLLRVPRSVSLETKVGKDKDTEL 320
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  478 LEFTpDTTMESPEEAVMRQSARRDIHDLLEGLEPREKQVMVLRYGLQDYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLR 557
Cdd:PRK07598 321 GDLL-ETDDISPEEMLMRESLQRDLQHLLADLTSRERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQKLR 399
                        330
                 ....*....|...
gi 15232364  558 dQPNAEDL-RYYL 569
Cdd:PRK07598 400 -QPKRRNRiRDYL 411
PRK09210 PRK09210
RNA polymerase sigma factor RpoD; Validated
343-569 1.27e-37

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 142.82  E-value: 1.27e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  343 LVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSTMVSRHARGVHIPSSIIRTINHIQK 422
Cdd:PRK09210 141 LVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIR 220
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  423 ARKTLKTSHGiKYAADEEIAKLTGHSVKKIRaanQCLKVVG---SIDKKVGDCFTTKFLEFTPDTTMESPEEAVMRQSAR 499
Cdd:PRK09210 221 VQRQLLQELG-REPTPEEIAEEMDMPPEKVR---EILKIAQepvSLETPIGEEDDSHLGDFIEDQDATSPADHAAYELLK 296
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  500 RDIHDLLEGLEPREKQVMVLRYGLQDYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLRDQPNAEDLRYYL 569
Cdd:PRK09210 297 EQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFL 366
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
333-558 1.92e-34

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: 130.33  E-value: 1.92e-34
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 333 RDELVKSTRSLVLFLARNYRGLGIA-HEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSM------STMVSRHAR 405
Cdd:COG1191  17 REELIEEYLPLVKKIASRLAGRLPAeLDDLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRGAIldylrdEDWVPRSVR 96
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 406 gvhipssiiRTINHIQKARKTLKTSHGIKYaADEEIAKLTGHSVKKIRAANQCLKV--VGSIDKKVGDcfttkFLEFTPD 483
Cdd:COG1191  97 ---------ELARKIEEAIEELEQELGREP-TDEEIAEELGISLEEVQEALEAANAyqLLSLDEPLED-----GDDLLDL 161
                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15232364 484 TTMESPEEAVMRQSARRDIHDLLEGLEPREKQVMVLRYglqdYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLRD 558
Cdd:COG1191 162 LESGDPEEELEHEELREALAEAIEQLPERERLVLSLYY----FEELTLKEIAEVLGVSESRVSRLHKKALARLRE 232
PRK05658 PRK05658
RNA polymerase sigma factor RpoD; Validated
334-569 2.33e-30

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 235549 [Multi-domain]  Cd Length: 619  Bit Score: 125.68  E-value: 2.33e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  334 DELVKSTRSLVLFLARNY--RGLGIAheDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSTMVSRHARGVHIPS 411
Cdd:PRK05658 383 KEMVEANLRLVISIAKKYtnRGLQFL--DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 460
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  412 SIIRTINHIQK-ARKTLktsHGI-KYAADEEIAKLTGHSVKKIRaanQCLKVVG---SIDKKVGDCFTTKFLEFTPDTTM 486
Cdd:PRK05658 461 HMIETINKLNRiSRQML---QEIgREPTPEELAERLGMPEDKVR---KVLKIAKepiSLETPIGDDEDSHLGDFIEDKNA 534
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  487 ESPEEAVMRQSARRDIHDLLEGLEPREKQVMVLRYGLQDYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLRDQPNAEDLR 566
Cdd:PRK05658 535 ELPIDAAIQESLREATTDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSRKLR 614

                 ...
gi 15232364  567 YYL 569
Cdd:PRK05658 615 SFL 617
PRK05657 PRK05657
RNA polymerase sigma factor RpoS; Validated
343-558 2.60e-26

RNA polymerase sigma factor RpoS; Validated


Pssm-ID: 235548 [Multi-domain]  Cd Length: 325  Bit Score: 109.66  E-value: 2.60e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  343 LVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSTMVSRHARGVHIPSSIIRTINHIQK 422
Cdd:PRK05657  98 LVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPVHVVKELNVYLR 177
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  423 ARKTLkTSHGIKYAADEEIAKLTGHS---VKKIRAANQclkVVGSIDKKVGDCFTTKFLEFTPDTTMESPEEAVMRQSAR 499
Cdd:PRK05657 178 AAREL-EHKLDHEPSAEEIAELLDKPvddVSRMLALNE---RITSLDTPLGGDPEKSLLDILADEQENGPEDTTQDDDMK 253
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 15232364  500 RDIHDLLEGLEPREKQVMVLRYGLQDYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLRD 558
Cdd:PRK05657 254 QSIVKWLFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLRE 312
SigBFG TIGR02980
RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; This group of similar sigma-70 factors ...
333-559 1.80e-23

RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.


Pssm-ID: 274373 [Multi-domain]  Cd Length: 227  Bit Score: 98.84  E-value: 1.80e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364   333 RDELVKSTRSLVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYvqywirkSMSTMVS---RHAR---- 405
Cdd:TIGR02980   5 REKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTF-------AVPTIMGeikRFFRddtw 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364   406 GVHIPSSIIRTINHIQKARKTLKTSHGIKYAAdEEIAKLTGHSVKKIRAANQCLK--VVGSIDKKVGDCfttkflEFTPD 483
Cdd:TIGR02980  78 AVRVPRRLKELGVKINKATEELTQRLGRSPTI-AEIAERLGVSEEEVVEALEAGNayQALSLDASIEDD------DGDPI 150
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15232364   484 TTMES---PEEAVMRQSARRDIHDLLEGLEPREKQVMVLRYglqdYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLRDQ 559
Cdd:TIGR02980 151 ALLDTlgdEDDALETVEDRLALKPLLAALPERERRILLLRF----FEDKTQSEIAERLGISQMHVSRLLRRALKKLREQ 225
FliA_WhiG TIGR02479
RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar ...
336-557 8.45e-22

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: 94.26  E-value: 8.45e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364   336 LVKSTRSLVLFLARNYRGLGIAH---EDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSTMVSRHArgvHIPSS 412
Cdd:TIGR02479   1 LIRRYLPLVKRIAGRLSVGLPSSvelDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMLDELRRLD---WVPRS 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364   413 IIRTINHIQKARKTLKTSHGiKYAADEEIAKLTGHSVKKIRAANQ---CLKVVgSIDKKVGDCF-TTKFLEFTPDTTMES 488
Cdd:TIGR02479  78 LRQKARKLERAIRELEARLG-REPTEEEIAEELGMDLKEYRQALNeinALSLV-SLDELLESGDdGGSLIDRIEDDKSED 155
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15232364   489 PEEAVMRQSARRDIHDLLEGLEPREKQVMVLRYglqdYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLR 557
Cdd:TIGR02479 156 PEEELEREELREALAEAIESLSEREQLVLSLYY----YEELNLKEIGEVLGLTESRVSQIHSQALKKLR 220
rpoH2 PRK07500
RNA polymerase factor sigma-32; Reviewed
343-557 5.19e-19

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 236033 [Multi-domain]  Cd Length: 289  Bit Score: 87.40  E-value: 5.19e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  343 LVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSTMVSRHArgvhipsSIIRT-INHIQ 421
Cdd:PRK07500  52 LVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNW-------SIVRGgTSSAQ 124
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  422 KA--------RKTLK------TSHGIKyaadEEIAKLTGHSVK-------KIRAANQCLKVVGSIDKKvGDCFTTKFLEF 480
Cdd:PRK07500 125 KAlffnlrrlRARLAqadeelTKQEIH----REIATALGVSLSdvemmdaRLSGPDASLNAPQSEEDE-GRSERMDFLVD 199
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15232364  481 TPDTTMESPEEAVMRQSARRDIHDLLEGLEPREKQVMVLRYGLQDyrPKSLEEIGKLLKVSKEWIRKIERRAMAKLR 557
Cdd:PRK07500 200 DSPLPDEQVESSIDGERRRRWLTQALQTLNERELRIIRERRLRED--GATLEALGEELGISKERVRQIEARALEKLR 274
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
333-559 7.23e-18

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: 80.85  E-value: 7.23e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364   333 RDELVKSTRSLVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHtrGYKFSTYVQYWIRKSMstmvsrhargvhipss 412
Cdd:TIGR02937   3 FEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDP--EGSFKAWLFRIARNLI---------------- 64
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364   413 iirtINHIQKARKTLKTSHGIKYAADEEiakltghsvkkiraanqclkvvgsidkkvgdcfttkfleftpdttmESPEEA 492
Cdd:TIGR02937  65 ----LDYLRRKRRLRRELDLLEELLDSD----------------------------------------------PSPEEE 94
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15232364   493 VMRQSARRDIHDLLEGLEPREKQVMVLRYglqdYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLRDQ 559
Cdd:TIGR02937  95 LEQEEEREALREALEKLPEREREVLVLRY----LEGLSYKEIAEILGISVGTVKRRLKRARKKLREL 157
PRK06596 PRK06596
RNA polymerase factor sigma-32; Reviewed
319-558 3.22e-16

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 235838 [Multi-domain]  Cd Length: 284  Bit Score: 79.06  E-value: 3.22e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  319 EKLLMRNLHYGwycRD-----ELVKSTRSLVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIR 393
Cdd:PRK06596  34 EYMLAKRLREH---GDleaakQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIK 110
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  394 KSMSTMVSRHARGVHIPSSiirtinhiqKARKTL-----KTSHGIKYAADEE---IAKLTGHSVKKIRAANQCLKVV--- 462
Cdd:PRK06596 111 AEIHEYILRNWRIVKVATT---------KAQRKLffnlrKAKKRLGWLNPEEvemVAEELGVSEEEVREMESRLSGQdas 181
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  463 --GSIDKKVGDCFTTK-FLE---FTPDTTMESPEEAVMRQSArrdIHDLLEGLEPREKQVMVLRYgLQDyRPKSLEEIGK 536
Cdd:PRK06596 182 ldAPIDDDDEESGAPQdYLEdksSDPADVLEEDNWEDQRRAL---LADALEGLDERSRDIIEARW-LDD-DKSTLQELAA 256
                        250       260
                 ....*....|....*....|..
gi 15232364  537 LLKVSKEWIRKIERRAMAKLRD 558
Cdd:PRK06596 257 EYGVSAERVRQIEKNAMKKLKA 278
fliA PRK06986
flagellar biosynthesis sigma factor; Validated
359-557 4.80e-16

flagellar biosynthesis sigma factor; Validated


Pssm-ID: 235901 [Multi-domain]  Cd Length: 236  Bit Score: 77.58  E-value: 4.80e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  359 EDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSTMVSRH---ARGVHipsSIIRTINH-IQKarktLKTSHGiK 434
Cdd:PRK06986  39 DDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDELRSLdwvPRSVR---RNAREVAQaIRQ----LEQELG-R 110
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  435 YAADEEIAKLTGHSVKKIRA---ANQCLKVVgSIDKKVGDCftTKFLEFTPDTTMESPEEAVMRQSARRDIHDLLEGLEP 511
Cdd:PRK06986 111 EPTDTEVAEKLGLSLEEYREmllDTNISQLF-SIDELRGEH--GDSILVTEDHQDEDPLQQLEDEELREALVEAIESLPE 187
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 15232364  512 REKQVMVLRYglqdYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLR 557
Cdd:PRK06986 188 REQLVLSLYY----QEELNLKEIGAVLGVSESRVSQIHSQAIKRLR 229
PRK06288 PRK06288
RNA polymerase sigma factor WhiG; Reviewed
356-557 7.07e-15

RNA polymerase sigma factor WhiG; Reviewed


Pssm-ID: 235770 [Multi-domain]  Cd Length: 268  Bit Score: 75.11  E-value: 7.07e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  356 IAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSTMVsrhaRGVH-IPSSIIRTINHIQKARKTLKTSHGiK 434
Cdd:PRK06288  59 VEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDEL----RSIDwIPRSVRQKARQIERAIAMLEARLG-R 133
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  435 YAADEEIAKLTGHSVKKIRAAnqCLKVVG----SID--KKVGD-CFTTKFLEFTPDTTMESPEEAVMRQSARRDIHDLLE 507
Cdd:PRK06288 134 TPSDEEIADELGISLEEYNSL--LSKLSGtsvvSLNdlWFGGDeGDEVSLMDTLESPAALNPDEIAEREEIKRVIVEAIK 211
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 15232364  508 GLEPREKQVMVLRYglqdYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLR 557
Cdd:PRK06288 212 TLPEREKKVLILYY----YEDLTLKEIGKVLGVTESRISQLHTKAVLQLR 257
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
336-405 5.80e-14

Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime. The aromatic residues of the recognition helix, found at the C-terminus of this domain are though to mediate strand separation, thereby allowing transcription initiation.


Pssm-ID: 427998 [Multi-domain]  Cd Length: 71  Bit Score: 66.84  E-value: 5.80e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364   336 LVKSTRSLVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSTMVSRHAR 405
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRR 70
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
505-558 9.77e-13

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: 62.83  E-value: 9.77e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 15232364   505 LLEGLEPREKQVMVLRYglqdYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLRD 558
Cdd:pfam04545   1 ALASLPPRERQVLVLRY----GEGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
PRK05572 PRK05572
RNA polymerase sporulation sigma factor, SigF/SigG family;
333-559 2.33e-12

RNA polymerase sporulation sigma factor, SigF/SigG family;


Pssm-ID: 180137 [Multi-domain]  Cd Length: 252  Bit Score: 67.30  E-value: 2.33e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  333 RDELVKSTRSLVL-----FLARNYRglgiaHEDLIQAGYVGVLQGAERFDHTRGYKFSTY--------VQYWIRKSMSTM 399
Cdd:PRK05572  34 RDTLVEKNLRLVWsvvqrFLNRGYE-----PDDLFQIGCIGLLKAVDKFDLSYDVKFSTYavpmiigeIQRFLRDDGTVK 108
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  400 VSRhargvhipsSIIRTINHIQKARKTLKTSHGiKYAADEEIAKLTGHSVKKIRAANQCLKVVGSIDKKV----GDCFTT 475
Cdd:PRK05572 109 VSR---------SLKETANKIRKDKDELSKELG-REPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVhendGDPITL 178
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  476 KfleftpDTTMESPEEAVMRQSARRDIhdlLEGLEPREKQVMVLRYglqdYRPKSLEEIGKLLKVSKEWIRKIERRAMAK 555
Cdd:PRK05572 179 L------DQIADQSEEDWFDKIALKEA---IRELDERERLIVYLRY----FKDKTQSEVAKRLGISQVQVSRLEKKILKQ 245

                 ....
gi 15232364  556 LRDQ 559
Cdd:PRK05572 246 MKEK 249
PRK08583 PRK08583
RNA polymerase sigma factor SigB; Validated
334-558 4.56e-12

RNA polymerase sigma factor SigB; Validated


Pssm-ID: 236306 [Multi-domain]  Cd Length: 257  Bit Score: 66.26  E-value: 4.56e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  334 DELVKSTRSLVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYvqywirkSMSTMV---SRHAR----G 406
Cdd:PRK08583  32 EKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAF-------AVPTIIgeiKRYLRdktwS 104
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  407 VHIPSSIIRTINHIQKARKTLkTSHGIKYAADEEIAKLTGHSVKKIRAA------NQCLKVVGSI--DKkvgDCFTTKFL 478
Cdd:PRK08583 105 VHVPRRIKELGPKIKKAVDEL-TTELQRSPKISEIADRLGVSEEEVLEAmemgksYQALSVDHSIeaDS---DGSTVTLL 180
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  479 EFtpdttMESPEEAVMRQSARRDIHDLLEGLEPREKQVMVLRYglqdYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLRD 558
Cdd:PRK08583 181 DI-----VGQQEDGYELTEQRMILEKILPVLSDREKSIIQCTF----IENLSQKETGERLGISQMHVSRLQRQAIKKLRE 251
PRK07670 PRK07670
FliA/WhiG family RNA polymerase sigma factor;
334-557 7.99e-12

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 181075 [Multi-domain]  Cd Length: 251  Bit Score: 65.45  E-value: 7.99e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  334 DELVKSTRSLVLF-LARNYRGL--GIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSTMVSRHARgvhIP 410
Cdd:PRK07670  25 DELIRRYMPLVHYhVQRISVGLpkSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRKEDW---LP 101
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  411 SSIIRTINHIQKARKTLKTSHGiKYAADEEIAKLTGHSVKKIRAA--NQCLKVVGSIDKKVGDCFTTKFLEFT-PDTTME 487
Cdd:PRK07670 102 RSMREKTKKVEAAIEKLEQRYM-RNVTPKEVAAELGMTEEEVEATmnEGFFANLLSIDEKTHDQDDGENVSVTiRDDKTP 180
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  488 SPEEAVMRQSARRDIHDLLEGLEPREKQVMVLRYglqdYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLR 557
Cdd:PRK07670 181 TPEEKLLKEELIEELAEKIKQLSEKEQLVISLFY----KEELTLTEIGQVLNLSTSRISQIHSKALFKLK 246
PRK05911 PRK05911
RNA polymerase sigma factor sigma-28; Reviewed
333-557 2.16e-11

RNA polymerase sigma factor sigma-28; Reviewed


Pssm-ID: 235644 [Multi-domain]  Cd Length: 257  Bit Score: 64.25  E-value: 2.16e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  333 RDELVKSTRSLVLFLA-RNYRGL--GIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSTMVSRHArgvHI 409
Cdd:PRK05911  25 RDVLIEFYLPLVKNVAhRLISGMpsHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRKQD---WV 101
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  410 PSSIIRTINHIQKARKTLKTSHGiKYAADEEIAKLTGHSVKKIR----AANQCLKVVGSIDKKV--GDCFTTKFLEFTPD 483
Cdd:PRK05911 102 PRSVHQKANKLADAMDSLRQSLG-KEPTDGELCEYLNISQQELSgwfsSARPALILSLNEEFPCqsDDEAGLALEERIAD 180
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15232364  484 TTMESPEEAVMRQSARRDIHDLLEGLEPREKQVMVLRYglqdYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLR 557
Cdd:PRK05911 181 ERAETGYDVVDKKEFSSILAEAILALEEKERKVMALYY----YEELVLKEIGKILGVSESRVSQIHSKALLKLR 250
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
499-557 6.10e-11

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: 57.88  E-value: 6.10e-11
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 15232364 499 RRDIHDLLEGLEPREKQVMVLRYglqdYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLR 557
Cdd:cd06171   1 RERLEEALDKLPEREREVILLRF----GEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK05803 PRK05803
RNA polymerase sporulation sigma factor SigK;
333-556 6.77e-11

RNA polymerase sporulation sigma factor SigK;


Pssm-ID: 180266 [Multi-domain]  Cd Length: 233  Bit Score: 62.66  E-value: 6.77e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  333 RDELVKSTRSLVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVqywirksmstmvsrhARGvhIPSS 412
Cdd:PRK05803  51 RNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYA---------------ARC--IENE 113
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  413 IIRTINHIQKARKTLKTSHGIKYAAD-EEIakltghSVKKIRAANQclkvvGSIDKKVgdcfttkfleftpDTTMEspee 491
Cdd:PRK05803 114 ILMHLRNLKKTKKEVSLQDPIGVDKEgNEI------SLIDILGSEE-----DDVIEQV-------------ELKME---- 165
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15232364  492 avmrqsaRRDIHDLLEGLEPREKQVMVLRYGLQDYRPKSLEEIGKLLKVSKEWIRKIERRAMAKL 556
Cdd:PRK05803 166 -------VEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKL 223
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
487-559 1.12e-09

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: 57.70  E-value: 1.12e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15232364 487 ESPEEAVMRQSARRDIHDLLEGLEPREKQVMVLRYgLQDYrpkSLEEIGKLLKVSKEWIRKIERRAMAKLRDQ 559
Cdd:COG1595 106 ADPEEALEAEELLEALLAALERLPPRQREVLVLRY-LEGL---SYAEIAEILGISEGTVKSRLSRARKKLREA 174
PLN02541 PLN02541
uracil phosphoribosyltransferase
46-72 1.85e-08

uracil phosphoribosyltransferase


Pssm-ID: 215297  Cd Length: 244  Bit Score: 55.56  E-value: 1.85e-08
                         10        20
                 ....*....|....*....|....*..
gi 15232364   46 LVFVHPHPLIKHWLSLLRSDQTSFPIF 72
Cdd:PLN02541  33 LVFVPPHPLIKHWLSVLRNEQTPPPIF 59
PRK07408 PRK07408
RNA polymerase sigma factor SigF; Reviewed
359-516 1.10e-07

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 180965 [Multi-domain]  Cd Length: 256  Bit Score: 53.39  E-value: 1.10e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  359 EDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSTMVSRHARGVHIPSSIIRTINHIQKARKTLKTSHGiKYAAD 438
Cdd:PRK07408  54 EDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPTVRIPRRWQELQRQAKKVRQELRQELG-RQPTD 132
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  439 EEIAKLTGHSVK---KIRAANQCLKVVgSIDKKVG---DCFTTkFLEFTPDTTMESpeeavmRQSARRDIHDL---LEGL 509
Cdd:PRK07408 133 QEIAQALDISLEewqEIKLALQNRTPL-SLDAPVNqdeDGSTS-LGDLLPDPRYRS------FQLAQEDRIRLqqaLAQL 204

                 ....*..
gi 15232364  510 EPREKQV 516
Cdd:PRK07408 205 EERTREV 211
PRK07122 PRK07122
RNA polymerase sigma factor SigF; Reviewed
333-559 1.46e-07

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 168831 [Multi-domain]  Cd Length: 264  Bit Score: 52.86  E-value: 1.46e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  333 RDELVKSTRSLVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYvqywirkSMSTM---VSRHAR---- 405
Cdd:PRK07122  42 RDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSF-------AVPTImgeVRRHFRdnsw 114
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  406 GVHIPSSIIRTinHIQKARKTLKTSHGIKYA--ADEEIAKLTGHSVKKIraanQCLkVVG------SIDKKVGDCFT-TK 476
Cdd:PRK07122 115 SVKVPRRLKEL--HLRLGRATAELSQRLGRAptASELAAELGMDREEVV----EGL-VAGsayntlSIDSGGGSGDDdAR 187
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  477 FLEFT---PDTTMESPEEavmRQSARrdihDLLEGLEPREKQVMVLRYglqdYRPKSLEEIGKLLKVSKEWIRKIERRAM 553
Cdd:PRK07122 188 AIADTlgdVDAGLDQIEN---REALR----PLLAALPERERTVLVLRF----FESMTQTQIAERVGISQMHVSRLLAKTL 256

                 ....*.
gi 15232364  554 AKLRDQ 559
Cdd:PRK07122 257 ARLRDQ 262
Sigma70_r3 pfam04539
Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the ...
416-493 3.56e-07

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: 47.98  E-value: 3.56e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15232364   416 TINHIQKARKTLKTSHGIKyAADEEIAKLTGHSVKKIRAANQCLKVVGSIDKKVGDCFTTKFLEFTPDTTMESPEEAV 493
Cdd:pfam04539   2 LLNKIKRAQRELEQELGRE-PTPEEIAEELGLSPEKVREVLEAAREPVSLDTPVGEEEDGELGDLLEDDDIESPEEAV 78
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
483-557 2.52e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 48.04  E-value: 2.52e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15232364  483 DTTMESPEEAVMRQSARRDIHDLLEGLEPREKQVMVLRYglqdYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLR 557
Cdd:PRK11924 100 AETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRY----VEGLSYREIAEILGVPVGTVKSRLRRARQLLR 170
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
487-559 2.46e-05

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 44.94  E-value: 2.46e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15232364  487 ESPEEAVMRQSARRDIHDLLEGLEPREKQVMVLRYglQDYrpkSLEEIGKLLKVSKEWIRKIERRAMAKLRDQ 559
Cdd:PRK09639  91 PSPEEIWIRKEEITKVQEVLAKMTERDRTVLLLRF--SGY---SYKEIAEALGIKESSVGTTLARAKKKFRKI 158
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
334-550 4.90e-05

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 44.51  E-value: 4.90e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  334 DELVKSTRSLVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSTMVSRHARGVHIPssi 413
Cdd:PRK08295  27 EYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCITRQIITAIKTANRQKHIP--- 103
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  414 irtinhiqkarktLKTSHgikyaadeeiakltghsvkkiraanqclkvvgSIDKKVGDCFTTKFLEFT-PDTTMESPEEA 492
Cdd:PRK08295 104 -------------LNSYV--------------------------------SLDKPIYDEESDRTLLDViSEAKVTDPEEL 138
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15232364  493 VMRQSARRDIHD-LLEGLEPREKQvmVLRYGLQDYrpkSLEEIGKLLKVSKEWI--------RKIER 550
Cdd:PRK08295 139 IISKEELEDIEEkIEELLSELEKE--VLELYLDGK---SYQEIAEELNRHVKSIdnalqrvkRKLEK 200
PRK08301 PRK08301
RNA polymerase sporulation sigma factor SigE;
499-557 5.51e-05

RNA polymerase sporulation sigma factor SigE;


Pssm-ID: 236228 [Multi-domain]  Cd Length: 234  Bit Score: 44.85  E-value: 5.51e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 15232364  499 RRDIHDLLEGLEPREKQVMVLRYGLQDYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLR 557
Cdd:PRK08301 169 RKLLKKALKKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLK 227
Upp COG0035
Uracil phosphoribosyltransferase [Nucleotide transport and metabolism]; Uracil ...
47-74 5.75e-04

Uracil phosphoribosyltransferase [Nucleotide transport and metabolism]; Uracil phosphoribosyltransferase is part of the Pathway/BioSystem: Pyrimidine salvage


Pssm-ID: 439805  Cd Length: 209  Bit Score: 41.59  E-value: 5.75e-04
                        10        20
                ....*....|....*....|....*...
gi 15232364  47 VFVHPHPLIKHWLSLLRSDQTSFPIFVR 74
Cdd:COG0035   4 VHVVDHPLIQHKLTLLRDKNTDTKEFRR 31
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
351-538 1.62e-03

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 39.68  E-value: 1.62e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  351 YRGLGIAHE--DLIQAGYVGVLQGAERFDHTRgyKFSTyvqyWIRKsMSTMVsrhargvhipssiirTINHIQKaRKTlk 428
Cdd:PRK09641  36 YRMLGNRHEaeDAAQEAFIRAYVNIDSYDINR--KFST----WLYR-IATNL---------------TIDRLRK-RKP-- 90
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  429 tshgiKYAADEEIAK---LTGHSvkKIRAanqclkvvgsidkkvgdcfttkfleftpdtTMESPEEAVMRQSARRDIHDL 505
Cdd:PRK09641  91 -----DYYLDAEVAGtegLTMYS--QLAA------------------------------DDALPEEQVVSLELQETIQEA 133
                        170       180       190
                 ....*....|....*....|....*....|...
gi 15232364  506 LEGLEPREKQVMVLRYgLQDyrpKSLEEIGKLL 538
Cdd:PRK09641 134 ILQLPEKYRTVIVLKY-IED---LSLKEISEIL 162
upp PRK00129
uracil phosphoribosyltransferase; Reviewed
47-72 1.91e-03

uracil phosphoribosyltransferase; Reviewed


Pssm-ID: 234653  Cd Length: 209  Bit Score: 39.69  E-value: 1.91e-03
                         10        20
                 ....*....|....*....|....*.
gi 15232364   47 VFVHPHPLIKHWLSLLRSDQTSFPIF 72
Cdd:PRK00129   4 VHVVDHPLIQHKLTLLRDKNTSTKRF 29
PRK09648 PRK09648
RNA polymerase sigma factor ShbA;
488-559 2.20e-03

RNA polymerase sigma factor ShbA;


Pssm-ID: 236607 [Multi-domain]  Cd Length: 189  Bit Score: 39.57  E-value: 2.20e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15232364  488 SPEEAVMRQSARRDIHDLLEGLEPREKQVMVLR--YGLqdyrpkSLEEIGKLLKVSKEWIRKIERRAMAKLRDQ 559
Cdd:PRK09648 119 GPEERALRSESSNRMRELLDTLPEKQREILILRvvVGL------SAEETAEAVGSTPGAVRVAQHRALARLRAE 186
PRK08215 PRK08215
RNA polymerase sporulation sigma factor SigG;
320-405 9.61e-03

RNA polymerase sporulation sigma factor SigG;


Pssm-ID: 181296 [Multi-domain]  Cd Length: 258  Bit Score: 38.00  E-value: 9.61e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364  320 KLLMRNLHYG-WYCRDELVKSTRSLVLFLAR--NYRGLGIahEDLIQAGYVGVLQGAERFDHTRGYKFSTY--------V 388
Cdd:PRK08215  25 RELFERMQNGdKEAREKLINGNLRLVLSVIQrfNNRGENV--DDLFQVGCIGLMKAIDNFDLSQNVKFSTYavpmiigeI 102
                         90
                 ....*....|....*..
gi 15232364  389 QYWIRKSMSTMVSRHAR 405
Cdd:PRK08215 103 RRYLRDNNPIRVSRSLR 119
 
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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