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Conserved domains on  [gi|1589200337|gb|TCU63462|]
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RNA polymerase RpoD-like sigma 70 subunit [Longicatena caecimuris]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK09210 super family cl35786
RNA polymerase sigma factor RpoD; Validated
 6-394 0e+00

RNA polymerase sigma factor RpoD; Validated


The actual alignment was detected with superfamily member PRK09210:

Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 565.77  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337   6 AKAQLQEYKTLDEIKDELQEAYQVNKVLYQKDIMDAVEHLDMSDADFDELLQWFSDNGIAVKDDEDDVDLLDDDALVgdd 85
Cdd:PRK09210    1 KKTKKKETTTLEQVVKELIEKGKKRGTLTYDEIAEKLIPFELDSDQIDDLYERLEDAGISIVDEEGNPSSAQVVEEE--- 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337  86 ddidflddedeeedslaaEIESLEQSFANSSHTKINDPVKMYLKEIGRVELLDPKEEPEIARRIQAGDEEAKKKLISANL 165
Cdd:PRK09210   78 ------------------EEEELDNDLSVPPGVKINDPVRMYLKEIGRVPLLTAEEEIELAKRIEEGDEEAKQRLAEANL 139

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 166 RLVVSIAKKYVGRGMLFLDLIQEGNMGLVKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLT 245
Cdd:PRK09210  140 RLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 219

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 246 RIQRQLVQDLGRDPSAEEIAAKMEnISPEKVREIQKIALEPVSLETPIGEEDDSHLGDFIEDKEALSPDEYANNQLLKDE 325
Cdd:PRK09210  220 RVQRQLLQELGREPTPEEIAEEMD-MPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAAYELLKEQ 298

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1589200337 326 INTVLQGLTEREEKVLRLRFGLYDGRTRTLEEVGKEFNVTRERIRQIEAKALRKLKHPTRSKRLKDFVD 394
Cdd:PRK09210  299 LEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 367
 
Name Accession Description Interval E-value
PRK09210 PRK09210
RNA polymerase sigma factor RpoD; Validated
 6-394 0e+00

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 565.77  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337   6 AKAQLQEYKTLDEIKDELQEAYQVNKVLYQKDIMDAVEHLDMSDADFDELLQWFSDNGIAVKDDEDDVDLLDDDALVgdd 85
Cdd:PRK09210    1 KKTKKKETTTLEQVVKELIEKGKKRGTLTYDEIAEKLIPFELDSDQIDDLYERLEDAGISIVDEEGNPSSAQVVEEE--- 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337  86 ddidflddedeeedslaaEIESLEQSFANSSHTKINDPVKMYLKEIGRVELLDPKEEPEIARRIQAGDEEAKKKLISANL 165
Cdd:PRK09210   78 ------------------EEEELDNDLSVPPGVKINDPVRMYLKEIGRVPLLTAEEEIELAKRIEEGDEEAKQRLAEANL 139

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 166 RLVVSIAKKYVGRGMLFLDLIQEGNMGLVKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLT 245
Cdd:PRK09210  140 RLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 219

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 246 RIQRQLVQDLGRDPSAEEIAAKMEnISPEKVREIQKIALEPVSLETPIGEEDDSHLGDFIEDKEALSPDEYANNQLLKDE 325
Cdd:PRK09210  220 RVQRQLLQELGREPTPEEIAEEMD-MPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAAYELLKEQ 298

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1589200337 326 INTVLQGLTEREEKVLRLRFGLYDGRTRTLEEVGKEFNVTRERIRQIEAKALRKLKHPTRSKRLKDFVD 394
Cdd:PRK09210  299 LEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 367
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 126-394 2.97e-168

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: 471.08  E-value: 2.97e-168
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 126 MYLKEIGRVELLDPKEEPEIARRIQAGDEEAKKKLISANLRLVVSIAKKYVGRGMLFLDLIQEGNMGLVKAVEKFDYTKG 205
Cdd:COG0568     1 AYLREIGRVPLLTAEEEVELARRIQAGDEEAKRKLVEANLRLVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDPERG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 206 FKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLTRIQRQLVQDLGRDPSAEEIAAKMeNISPEKVREIQKIALE 285
Cdd:COG0568    81 FRFSTYATWWIRQAITRAIADQWRTIRLPVHMAETLNKLRRAKRQLLQELGREPTPEEIAEEL-GVPEEKVREMLRLARE 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 286 PVSLETPIGEEDDSHLGDFIEDKEALSPDEYANNQLLKDEINTVLQGLTEREEKVLRLRFGLYDGRTRTLEEVGKEFNVT 365
Cdd:COG0568   160 PVSLDAPVGDDEDSELGDLLEDEEAPSPEEALEEELLREELREALDTLTEREREILRLRFGLDDGEPHTLEEIGKEFGVS 239

                         250       260
                  ....*....|....*....|....*....
gi 1589200337 366 RERIRQIEAKALRKLKHPTRSKRLKDFVD 394
Cdd:COG0568   240 RERVRQIEAKALRKLRHPLRSRKLRDYLD 268
RpoD_Cterm TIGR02393
RNA polymerase sigma factor RpoD, C-terminal domain; This model represents the well-conserved ...
 156-394 2.64e-158

RNA polymerase sigma factor RpoD, C-terminal domain; This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc. [Transcription, Transcription factors]


Pssm-ID: 274108 [Multi-domain]  Cd Length: 238  Bit Score: 444.82  E-value: 2.64e-158
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 156 AKKKLISANLRLVVSIAKKYVGRGMLFLDLIQEGNMGLVKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPV 235
Cdd:TIGR02393   1 AKKKLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 236 HMVETINKLTRIQRQLVQDLGRDPSAEEIAAKMeNISPEKVREIQKIALEPVSLETPIGEEDDSHLGDFIEDKEALSPDE 315
Cdd:TIGR02393  81 HMVETINKLIKAERQLTQELGREPTDEELAERM-GMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDESIESPDD 159

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1589200337 316 YANNQLLKDEINTVLQGLTEREEKVLRLRFGLYDGRTRTLEEVGKEFNVTRERIRQIEAKALRKLKHPTRSKRLKDFVD 394
Cdd:TIGR02393 160 AAAKELLREQLDEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLKDFLD 238
Sigma70_r3 pfam04539
Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the ...
 239-317 2.58e-28

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: 106.15  E-value: 2.58e-28
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1589200337 239 ETINKLTRIQRQLVQDLGRDPSAEEIAAKMeNISPEKVREIQKIALEPVSLETPIGEEDDSHLGDFIEDKEALSPDEYA 317
Cdd:pfam04539   1 ELLNKIKRAQRELEQELGREPTPEEIAEEL-GLSPEKVREVLEAAREPVSLDTPVGEEEDGELGDLLEDDDIESPEEAV 78
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 323-381 2.77e-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: 58.27  E-value: 2.77e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1589200337 323 KDEINTVLQGLTEREEKVLRLRFGlydgRTRTLEEVGKEFNVTRERIRQIEAKALRKLK 381
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFG----EGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
PRK09210 PRK09210
RNA polymerase sigma factor RpoD; Validated
 6-394 0e+00

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 565.77  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337   6 AKAQLQEYKTLDEIKDELQEAYQVNKVLYQKDIMDAVEHLDMSDADFDELLQWFSDNGIAVKDDEDDVDLLDDDALVgdd 85
Cdd:PRK09210    1 KKTKKKETTTLEQVVKELIEKGKKRGTLTYDEIAEKLIPFELDSDQIDDLYERLEDAGISIVDEEGNPSSAQVVEEE--- 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337  86 ddidflddedeeedslaaEIESLEQSFANSSHTKINDPVKMYLKEIGRVELLDPKEEPEIARRIQAGDEEAKKKLISANL 165
Cdd:PRK09210   78 ------------------EEEELDNDLSVPPGVKINDPVRMYLKEIGRVPLLTAEEEIELAKRIEEGDEEAKQRLAEANL 139

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 166 RLVVSIAKKYVGRGMLFLDLIQEGNMGLVKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLT 245
Cdd:PRK09210  140 RLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 219

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 246 RIQRQLVQDLGRDPSAEEIAAKMEnISPEKVREIQKIALEPVSLETPIGEEDDSHLGDFIEDKEALSPDEYANNQLLKDE 325
Cdd:PRK09210  220 RVQRQLLQELGREPTPEEIAEEMD-MPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAAYELLKEQ 298

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1589200337 326 INTVLQGLTEREEKVLRLRFGLYDGRTRTLEEVGKEFNVTRERIRQIEAKALRKLKHPTRSKRLKDFVD 394
Cdd:PRK09210  299 LEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 367
PRK05901 PRK05901
RNA polymerase sigma factor; Provisional
 2-394 1.34e-169

RNA polymerase sigma factor; Provisional


Pssm-ID: 235640 [Multi-domain]  Cd Length: 509  Bit Score: 484.11  E-value: 1.34e-169
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337   2 KKTKAKAQlQEYKTLDEIKDELQEAyqVNKVLYQKDIMDAVEHLDMSDADFDELLqwFSDNGIAVKDDEDDVDLLDDDAL 81
Cdd:PRK05901   84 KAAAAKAP-AKKKLKDELDSSKKAE--KKNALDKDDDLNYVKDIDVLNQADDDDD--DDDDDDLDDDDIDDDDDDEDDDE 158

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337  82 VGDDDDIDF------------LDDEDEEEDSLAAEIESLEQSFANSSHTKINDPVKMYLKEIGRVELLDPKEEPEIARRI 149
Cdd:PRK05901  159 DDDDDDVDDedeekkeakeleKLSDDDDFVWDEDDSEALRQARKDAKLTATADPVKAYLKQIGKVKLLNAEEEVELAKRI 238

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 150 QAG---------------------------DEEAKKKLISANLRLVVSIAKKYVGRGMLFLDLIQEGNMGLVKAVEKFDY 202
Cdd:PRK05901  239 EAGlyaeellaegekldpelrrdlqwigrdGKRAKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDY 318

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 203 TKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLTRIQRQLVQDLGRDPSAEEIAAKMeNISPEKVREIQKI 282
Cdd:PRK05901  319 TKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVETINKLGRIERELLQELGREPTPEELAKEM-GFTPEKVREIQKY 397

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 283 ALEPVSLETPIGEEDDSHLGDFIEDKEALSPDEYANNQLLKDEINTVLQGLTEREEKVLRLRFGLYDGRTRTLEEVGKEF 362
Cdd:PRK05901  398 NREPISLDKTIGKEGDSQFGDFIEDSEAVSPVDAVSFTLLQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVY 477

                         410       420       430
                  ....*....|....*....|....*....|..
gi 1589200337 363 NVTRERIRQIEAKALRKLKHPTRSKRLKDFVD 394
Cdd:PRK05901  478 GVTRERIRQIESKTLRKLRHPSRSQVLRDFLD 509
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 126-394 2.97e-168

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: 471.08  E-value: 2.97e-168
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 126 MYLKEIGRVELLDPKEEPEIARRIQAGDEEAKKKLISANLRLVVSIAKKYVGRGMLFLDLIQEGNMGLVKAVEKFDYTKG 205
Cdd:COG0568     1 AYLREIGRVPLLTAEEEVELARRIQAGDEEAKRKLVEANLRLVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDPERG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 206 FKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLTRIQRQLVQDLGRDPSAEEIAAKMeNISPEKVREIQKIALE 285
Cdd:COG0568    81 FRFSTYATWWIRQAITRAIADQWRTIRLPVHMAETLNKLRRAKRQLLQELGREPTPEEIAEEL-GVPEEKVREMLRLARE 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 286 PVSLETPIGEEDDSHLGDFIEDKEALSPDEYANNQLLKDEINTVLQGLTEREEKVLRLRFGLYDGRTRTLEEVGKEFNVT 365
Cdd:COG0568   160 PVSLDAPVGDDEDSELGDLLEDEEAPSPEEALEEELLREELREALDTLTEREREILRLRFGLDDGEPHTLEEIGKEFGVS 239

                         250       260
                  ....*....|....*....|....*....
gi 1589200337 366 RERIRQIEAKALRKLKHPTRSKRLKDFVD 394
Cdd:COG0568   240 RERVRQIEAKALRKLRHPLRSRKLRDYLD 268
RpoD_Cterm TIGR02393
RNA polymerase sigma factor RpoD, C-terminal domain; This model represents the well-conserved ...
 156-394 2.64e-158

RNA polymerase sigma factor RpoD, C-terminal domain; This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc. [Transcription, Transcription factors]


Pssm-ID: 274108 [Multi-domain]  Cd Length: 238  Bit Score: 444.82  E-value: 2.64e-158
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 156 AKKKLISANLRLVVSIAKKYVGRGMLFLDLIQEGNMGLVKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPV 235
Cdd:TIGR02393   1 AKKKLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 236 HMVETINKLTRIQRQLVQDLGRDPSAEEIAAKMeNISPEKVREIQKIALEPVSLETPIGEEDDSHLGDFIEDKEALSPDE 315
Cdd:TIGR02393  81 HMVETINKLIKAERQLTQELGREPTDEELAERM-GMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDESIESPDD 159

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1589200337 316 YANNQLLKDEINTVLQGLTEREEKVLRLRFGLYDGRTRTLEEVGKEFNVTRERIRQIEAKALRKLKHPTRSKRLKDFVD 394
Cdd:TIGR02393 160 AAAKELLREQLDEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLKDFLD 238
PRK05658 PRK05658
RNA polymerase sigma factor RpoD; Validated
 118-394 7.35e-154

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 235549 [Multi-domain]  Cd Length: 619  Bit Score: 447.70  E-value: 7.35e-154
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 118 TKINDPVKMYLKEIGRVEL---LDPKEEPEIARRIQAGD---EEAKKKLISANLRLVVSIAKKYVGRGMLFLDLIQEGNM 191
Cdd:PRK05658  337 VRVYDEIKKLQQELEAIEEetgLTIEELKEINRQISKGEakaRRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI 416

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 192 GLVKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLTRIQRQLVQDLGRDPSAEEIAAKMEnI 271
Cdd:PRK05658  417 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEIGREPTPEELAERLG-M 495

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 272 SPEKVREIQKIALEPVSLETPIGEEDDSHLGDFIEDKEALSPDEYANNQLLKDEINTVLQGLTEREEKVLRLRFGLYDGR 351
Cdd:PRK05658  496 PEDKVRKVLKIAKEPISLETPIGDDEDSHLGDFIEDKNAELPIDAAIQESLREATTDVLASLTPREAKVLRMRFGIDMNT 575

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|...
gi 1589200337 352 TRTLEEVGKEFNVTRERIRQIEAKALRKLKHPTRSKRLKDFVD 394
Cdd:PRK05658  576 DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSRKLRSFLD 618
Sig70-cyanoRpoD TIGR02997
RNA polymerase sigma factor, cyanobacterial RpoD-like family; This family includes a number of ...
 122-381 3.15e-128

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: 370.81  E-value: 3.15e-128
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 122 DPVKMYLKEIGRVELLDPKEEPEIARRIQ-------AGDEE---------------------------------AKKKLI 161
Cdd:TIGR02997   1 DLVRLYLQEIGRVPLLTPEEEIELARQVQqmmvleeLREELeeqlgrepskeewaaaaglseaelrqrlrqgqrAKEKMI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 162 SANLRLVVSIAKKYVGRGMLFLDLIQEGNMGLVKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETI 241
Cdd:TIGR02997  81 KANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 242 NKLTRIQRQLVQDLGRDPSAEEIAAKMEnISPEKVREIQKIALEPVSLETPIGEEDDSHLGDFIEDkEALSPDEYANNQL 321
Cdd:TIGR02997 161 NKIKKVQRELSQKLGRTPSEAEIAEALE-LEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLED-DGESPEEQVERES 238

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 322 LKDEINTVLQGLTEREEKVLRLRFGLYDGRTRTLEEVGKEFNVTRERIRQIEAKALRKLK 381
Cdd:TIGR02997 239 LRQDLESLLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR 298
PRK07921 PRK07921
RNA polymerase sigma factor SigB; Reviewed
 122-392 9.16e-127

RNA polymerase sigma factor SigB; Reviewed


Pssm-ID: 181169 [Multi-domain]  Cd Length: 324  Bit Score: 368.29  E-value: 9.16e-127
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 122 DPVKMYLKEIGRVELLDPKEEPEIARRIQAG---------------------------DEEAKKKLISANLRLVVSIAKK 174
Cdd:PRK07921   26 DLVRVYLNGIGKTALLTAADEVELAKRIEAGlyaehlletrkrlsearkrdlaavvrdGEAARRHLLEANLRLVVSLAKR 105

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 175 YVGRGMLFLDLIQEGNMGLVKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLTRIQRQLVQD 254
Cdd:PRK07921  106 YTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKRELHQQ 185

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 255 LGRDPSAEEIAAKMEnISPEKVREIQKIALEPVSLETPIGEEDDSHLGDFIEDKEALSPDEYANNQLLKDEINTVLQGLT 334
Cdd:PRK07921  186 LGREATDEELAEESG-IPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEATSAENAVIAGLLHTDIRSVLATLD 264

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1589200337 335 EREEKVLRLRFGLYDGRTRTLEEVGKEFNVTRERIRQIEAKALRKLKHPTRSKRLKDF 392
Cdd:PRK07921  265 EREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGERADRLRSY 322
PRK07406 PRK07406
RNA polymerase sigma factor RpoD; Validated
 122-393 2.41e-125

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236012 [Multi-domain]  Cd Length: 373  Bit Score: 366.42  E-value: 2.41e-125
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 122 DPVKMYLKEIGRVELLDPKEEPEIARRI--------------QAGDEE--------------------------AKKKLI 161
Cdd:PRK07406   63 DSIRVYLQEIGRIRLLRPDEEIELARKIadlleleelreqfeSELGREpsdkewaelvdmplpkfrrrlmlgrrAKEKMV 142

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 162 SANLRLVVSIAKKYVGRGMLFLDLIQEGNMGLVKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETI 241
Cdd:PRK07406  143 QSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETI 222

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 242 NKLTRIQRQLVQDLGRDPSAEEIAAKMEnISPEKVREIQKIALEPVSLETPIGEEDDSHLGDFIEDKEALSPDEYANNqL 321
Cdd:PRK07406  223 SRIKKTTKVLSQEFGRKPTEEEIAESME-MTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEADGETPEDDVAKN-L 300

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1589200337 322 LKDEINTVLQGLTEREEKVLRLRFGLYDGRTRTLEEVGKEFNVTRERIRQIEAKALRKLKHPTRSKRLKDFV 393
Cdd:PRK07406  301 LREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVLKEYI 372
rpoS_proteo TIGR02394
RNA polymerase sigma factor RpoS; A sigma factor is a DNA-binding protein protein that binds ...
 118-382 2.74e-101

RNA polymerase sigma factor RpoS; 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 RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393). [Cellular processes, Adaptations to atypical conditions, Transcription, Transcription factors]


Pssm-ID: 131447 [Multi-domain]  Cd Length: 285  Bit Score: 302.03  E-value: 2.74e-101
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 118 TKINDPVKMYLKEIGRVELLDPKEEPEIARRIQAGDEEAKKKLISANLRLVVSIAKKYVGRGMLFLDLIQEGNMGLVKAV 197
Cdd:TIGR02394   9 TRVADVTQLYLREIGFKPLLTAEEEIAYARRALAGDFEARKVMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAV 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 198 EKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLTRIQRQLVQDLGRDPSAEEIAAKMENiSPEKVR 277
Cdd:TIGR02394  89 EKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPVHVIKELNVYLRAARQLEKKLGREPSVEEIAELLDK-PVEDVS 167

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 278 EIQKIALEPVSLETPIGEEDDSHLGDFIEDKEALSPDEYANNQLLKDEINTVLQGLTEREEKVLRLRFGLYDGRTRTLEE 357
Cdd:TIGR02394 168 RVLALNERITSLDAPLDDDSSKSLLDTIADEQSIDPESLVQNDDLKQLIEAWLAELNERQREVLARRFGLLGYEPATLEE 247

                         250       260
                  ....*....|....*....|....*
gi 1589200337 358 VGKEFNVTRERIRQIEAKALRKLKH 382
Cdd:TIGR02394 248 VAAEVGLTRERVRQIQVEALKKLRR 272
PRK05657 PRK05657
RNA polymerase sigma factor RpoS; Validated
 109-381 1.08e-92

RNA polymerase sigma factor RpoS; Validated


Pssm-ID: 235548 [Multi-domain]  Cd Length: 325  Bit Score: 281.46  E-value: 1.08e-92
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 109 EQSFANSSHTKINDPVKMYLKEIGRVELLDPKEEPEIARRIQAGDEEAKKKLISANLRLVVSIAKKYVGRGMLFLDLIQE 188
Cdd:PRK05657   40 EELLSQGATQRVLDATQLYLNEIGYSPLLTAEEEVYFARRALRGDFAARQRMIESNLRLVVKIAKRYLNRGLALLDLIEE 119

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 189 GNMGLVKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLTRIQRQLVQDLGRDPSAEEIAAKM 268
Cdd:PRK05657  120 GNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPVHVVKELNVYLRAARELEHKLDHEPSAEEIAELL 199

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 269 ENiSPEKVREIQKIALEPVSLETPIGEEDDSHLGDFIEDKEALSPDEYANNQLLKDEINTVLQGLTEREEKVLRLRFGLY 348
Cdd:PRK05657  200 DK-PVDDVSRMLALNERITSLDTPLGGDPEKSLLDILADEQENGPEDTTQDDDMKQSIVKWLFELNDKQREVLARRFGLL 278

                         250       260       270
                  ....*....|....*....|....*....|...
gi 1589200337 349 DGRTRTLEEVGKEFNVTRERIRQIEAKALRKLK 381
Cdd:PRK05657  279 GYEAATLEDVAREIGLTRERVRQIQVEALRRLR 311
PRK05949 PRK05949
RNA polymerase sigma factor; Validated
 114-393 6.00e-89

RNA polymerase sigma factor; Validated


Pssm-ID: 180321 [Multi-domain]  Cd Length: 327  Bit Score: 271.72  E-value: 6.00e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 114 NSSHTKINDPVKMYLKEIGRV-------------------ELLDPKE----------------------EPEIARRIQAG 152
Cdd:PRK05949   10 TKQPTFSADMVRTYLHEIGRVplltheqeivygkqvqqmmSLLEAKEalakklgrepslpewaeavnlsETELKQTLKQG 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 153 dEEAKKKLISANLRLVVSIAKKYVGRGMLFLDLIQEGNMGLVKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIR 232
Cdd:PRK05949   90 -KRAKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIR 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 233 IPVHMVETINKLTRIQRQLVQDLGRDPSAEEIAAKMEnISPEKVREIQKIALEPVSLETPIGEEDDSHLGDFIEDkEALS 312
Cdd:PRK05949  169 LPIHITEKLNKIKKTQRELSQKLGRSATPAEIAKELE-LEPSQIREYLSMARQPISLDVRVGDNQDTELSELLED-EGPS 246

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 313 PDEYANNQLLKDEINTVLQGLTEREEKVLRLRFGLYDGRTRTLEEVGKEFNVTRERIRQIEAKALRKLKHptRSKRLKDF 392
Cdd:PRK05949  247 PDQYITQELLRQDLNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRR--RRANVKEY 324


                  .
gi 1589200337 393 V 393
Cdd:PRK05949  325 L 325
PRK07598 PRK07598
RNA polymerase sigma factor SigC; Validated
 143-394 1.60e-87

RNA polymerase sigma factor SigC; Validated


Pssm-ID: 236067 [Multi-domain]  Cd Length: 415  Bit Score: 271.36  E-value: 1.60e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 143 PEIARRIQAGDEEAKKKLISANLRLVVSIAKKYVGRGMLFLDLIQEGNMGLVKAVEKFDYTKGFKFSTYATWWIRQAITR 222
Cdd:PRK07598  163 VEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITR 242

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 223 AIADQARTIRIPVHMVETINKLTRIQRQLVQDLGRDPSAEEIAAKMEnISPEKVREIQKIALEPVSLETPIGEEDDSHLG 302
Cdd:PRK07598  243 AIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELE-MTPTQVREVLLRVPRSVSLETKVGKDKDTELG 321

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 303 DFIEdKEALSPDEYANNQLLKDEINTVLQGLTEREEKVLRLRFGLYDGRTRTLEEVGKEFNVTRERIRQIEAKALRKLKH 382
Cdd:PRK07598  322 DLLE-TDDISPEEMLMRESLQRDLQHLLADLTSRERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQKLRQ 400

                         250
                  ....*....|..
gi 1589200337 383 PTRSKRLKDFVD 394
Cdd:PRK07598  401 PKRRNRIRDYLE 412
PRK07405 PRK07405
RNA polymerase sigma factor SigD; Validated
 122-381 1.87e-83

RNA polymerase sigma factor SigD; Validated


Pssm-ID: 180963 [Multi-domain]  Cd Length: 317  Bit Score: 257.38  E-value: 1.87e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 122 DPVKMYLKEIGRVELLDPKEEPEIARRIQ----------------------------------------AGDEEAKKKLI 161
Cdd:PRK07405    8 DLVRTYLREIGRVPLLTHEEEILYGKQVQrlvalqeireelaeelgreptdaewakaaklseeelrsaiAEGEAAKRKMV 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 162 SANLRLVVSIAKKYVGRGMLFLDLIQEGNMGLVKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETI 241
Cdd:PRK07405   88 EANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKL 167

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 242 NKLTRIQRQLVQDLGRDPSAEEIAAKMEnISPEKVREIQKIALEPVSLETPIGEEDDSHLGDFIEDkEALSPDEYANNQL 321
Cdd:PRK07405  168 NKIKKAQRQLSQQLGRAATIGELAEELE-LTPKQVREYLERARQPLSLDLRVGDNQDTELGELLED-TGASPEDFATQSS 245

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 322 LKDEINTVLQGLTEREEKVLRLRFGLYDGRTRTLEEVGKEFNVTRERIRQIEAKALRKLK 381
Cdd:PRK07405  246 LQLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLR 305
PRK06596 PRK06596
RNA polymerase factor sigma-32; Reviewed
 127-381 1.71e-48

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 235838 [Multi-domain]  Cd Length: 284  Bit Score: 166.12  E-value: 1.71e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 127 YLKEIGRVELLDPKEEPEIARRIQA-GDEEAKKKLISANLRLVVSIAKKYVGRGMLFLDLIQEGNMGLVKAVEKFDYTKG 205
Cdd:PRK06596   19 YIQAVNKIPMLTAEEEYMLAKRLREhGDLEAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVG 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 206 FKFSTYATWWIRQAITRAIadqARTIRIpVHMVETIN--KLTRIQRQLVQDLG--RDPSAEEIAAKMeNISPEKVREI-Q 280
Cdd:PRK06596   99 VRLVSFAVHWIKAEIHEYI---LRNWRI-VKVATTKAqrKLFFNLRKAKKRLGwlNPEEVEMVAEEL-GVSEEEVREMeS 173

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 281 KIALEPVSLETPIGEEDDSH--LGDFIEDKEALSPDEYANNQLL---KDEINTVLQGLTEREEKVLRLRFgLYDGRTrTL 355
Cdd:PRK06596  174 RLSGQDASLDAPIDDDDEESgaPQDYLEDKSSDPADVLEEDNWEdqrRALLADALEGLDERSRDIIEARW-LDDDKS-TL 251

                         250       260
                  ....*....|....*....|....*.
gi 1589200337 356 EEVGKEFNVTRERIRQIEAKALRKLK 381
Cdd:PRK06596  252 QELAAEYGVSAERVRQIEKNAMKKLK 277
rpoH_proteo TIGR02392
alternative sigma factor RpoH; A sigma factor is a DNA-binding protein protein that binds to ...
 127-381 4.92e-48

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: 164.38  E-value: 4.92e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 127 YLKEIGRVELLDPKEEPEIARRIQ-AGDEEAKKKLISANLRLVVSIAKKYVGRGMLFLDLIQEGNMGLVKAVEKFDYTKG 205
Cdd:TIGR02392   6 YIRAVNRIPMLTPEEEYQLAKRLReHGDLDAAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERG 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 206 FKFSTYATWWIRQAITRAIADQARTIRIPVhmvetinklTRIQRQLV-------QDLGRDPSAEEIA--AKMENISPEKV 276
Cdd:TIGR02392  86 VRLVSFAVHWIKAEIHEYILRNWRLVKVAT---------TKAQRKLFfnlrkmkKRLQGWLNPEEVEaiAEELGVSEREV 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 277 REI-QKIALEPVSLETPIGEEDDSHLG--DFIEDKEALSPDEYANNQ---LLKDEINTVLQGLTEREEKVLRLRFgLYDG 350
Cdd:TIGR02392 157 REMeSRLSGQDMSLNASIDDDEDDGGApiAYLVDKRSDPEDTLEEEQweeLQRQALANALGSLDARSRRIIEARW-LDDD 235

                         250       260       270
                  ....*....|....*....|....*....|.
gi 1589200337 351 RTrTLEEVGKEFNVTRERIRQIEAKALRKLK 381
Cdd:TIGR02392 236 KL-TLQELAAEYGVSAERIRQIEKNAMKKLK 265
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 141-381 1.52e-47

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: 161.92  E-value: 1.52e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 141 EEPEIARRIQAGDEEAKKKLISANLRLVVSIAKKYVGRGMLFL-DLIQEGNMGLVKAVEKFDYTKGFKFSTYATWWIRQA 219
Cdd:COG1191     1 DLEELLRRYQEGDEEAREELIEEYLPLVKKIASRLAGRLPAELdDLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRGA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 220 ITRAIADQArtiRIPVHMVETINKLTRIQRQLVQDLGRDPSAEEIAAKMeNISPEKVREIQK--IALEPVSLETPIGEED 297
Cdd:COG1191    81 ILDYLRDED---WVPRSVRELARKIEEAIEELEQELGREPTDEEIAEEL-GISLEEVQEALEaaNAYQLLSLDEPLEDGD 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 298 DshLGDFIedkEALSPDEYANNQLLKDEINTVLQGLTEREEKVLRLRFglYDGrtRTLEEVGKEFNVTRERIRQIEAKAL 377
Cdd:COG1191   157 D--LLDLL---ESGDPEEELEHEELREALAEAIEQLPERERLVLSLYY--FEE--LTLKEIAEVLGVSESRVSRLHKKAL 227


                  ....
gi 1589200337 378 RKLK 381
Cdd:COG1191   228 ARLR 231
SigBFG TIGR02980
RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; This group of similar sigma-70 factors ...
 153-381 7.92e-41

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: 143.91  E-value: 7.92e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 153 DEEAKKKLISANLRLVVSIAKKYVGRGMLFLDLIQEGNMGLVKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIR 232
Cdd:TIGR02980   1 DKEAREKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIMGEIKRFFRDDTWAVR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 233 IPVHMVETINKLTRIQRQLVQDLGRDPSAEEIAAKMEnISPEKVREIQ--KIALEPVSLETPIGEEDDS--HLGDFIEDK 308
Cdd:TIGR02980  81 VPRRLKELGVKINKATEELTQRLGRSPTIAEIAERLG-VSEEEVVEALeaGNAYQALSLDASIEDDDGDpiALLDTLGDE 159

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1589200337 309 EAlSPDEYANNQLLKDeintVLQGLTEREEKVLRLRFglYDGRTRTleEVGKEFNVTRERIRQIEAKALRKLK 381
Cdd:TIGR02980 160 DD-ALETVEDRLALKP----LLAALPERERRILLLRF--FEDKTQS--EIAERLGISQMHVSRLLRRALKKLR 223
rpoH2 PRK07500
RNA polymerase factor sigma-32; Reviewed
 133-381 9.30e-38

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 236033 [Multi-domain]  Cd Length: 289  Bit Score: 137.86  E-value: 9.30e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 133 RVELLDPKEEPEIARRI-QAGDEEAKKKLISANLRLVVSIAKKYVGRGMLFLDLIQEGNMGLVKAVEKFDYTKGFKFSTY 211
Cdd:PRK07500   17 KAPYLEREEEHALAYRWkDHRDEDALHRIISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTY 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 212 ATWWIRQAItraiadQARTIRiPVHMVET----------INkLTRIQRQLVQD---LGRDPSAEEIAAKMeNISPEKVRE 278
Cdd:PRK07500   97 ATWWIRASI------QDYILR-NWSIVRGgtssaqkalfFN-LRRLRARLAQAdeeLTKQEIHREIATAL-GVSLSDVEM 167

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 279 IQ-KIALEPVSLETPIGEEDDSHLG--DFIEDKEALsPDEYANN----QLLKDEINTVLQGLTEREEKVLRLRFGLYDGr 351
Cdd:PRK07500  168 MDaRLSGPDASLNAPQSEEDEGRSErmDFLVDDSPL-PDEQVESsidgERRRRWLTQALQTLNERELRIIRERRLREDG- 245

                         250       260       270
                  ....*....|....*....|....*....|
gi 1589200337 352 tRTLEEVGKEFNVTRERIRQIEAKALRKLK 381
Cdd:PRK07500  246 -ATLEALGEELGISKERVRQIEARALEKLR 274
PRK08215 PRK08215
RNA polymerase sporulation sigma factor SigG;
136-381 1.24e-32

RNA polymerase sporulation sigma factor SigG;


Pssm-ID: 181296 [Multi-domain]  Cd Length: 258  Bit Score: 123.13  E-value: 1.24e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 136 LLDPKEEPEIARRIQAGDEEAKKKLISANLRLVVSIAKKYVGRGMLFLDLIQEGNMGLVKAVEKFDYTKGFKFSTYATWW 215
Cdd:PRK08215   18 VLKNEEMRELFERMQNGDKEAREKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPM 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 216 IRQAITRAIADQaRTIRIPVHMVETINKLTRIQRQLVQDLGRDPSAEEIaAKMENISPEKVRE----IQkialEPVSLET 291
Cdd:PRK08215   98 IIGEIRRYLRDN-NPIRVSRSLRDIAYKALQVREKLINENSKEPTVEEI-AKELEVPREEVVFaldaIQ----DPVSLFE 171

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 292 PIGEEDdshlGDFIEDKEALSPDEYANNQLLKD-EINTVLQGLTEREEKVLRLRFglYDGRTRTleEVGKEFNVTRERIR 370
Cdd:PRK08215  172 PIYHDG----GDPIYVMDQISDEKNKDENWLEEiALKEAMKKLNDREKLILNLRF--FQGKTQM--EVAEEIGISQAQVS 243

                         250
                  ....*....|.
gi 1589200337 371 QIEAKALRKLK 381
Cdd:PRK08215  244 RLEKAALKHMR 254
FliA_WhiG TIGR02479
RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar ...
 184-381 1.91e-30

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: 116.22  E-value: 1.91e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 184 DLIQEGNMGLVKAVEKFDYTKGFKFSTYATWWIRQAI---TRAIADQARTIRIPVHMVEtinkltRIQRQLVQDLGRDPS 260
Cdd:TIGR02479  28 DLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMldeLRRLDWVPRSLRQKARKLE------RAIRELEARLGREPT 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 261 AEEIAAKMeNISPEKVREIQK--IALEPVSLETPIGEEDDS-HLGDFIEDKEALSPDEYANNQLLKDEINTVLQGLTERE 337
Cdd:TIGR02479 102 EEEIAEEL-GMDLKEYRQALNeiNALSLVSLDELLESGDDGgSLIDRIEDDKSEDPEEELEREELREALAEAIESLSERE 180

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1589200337 338 EKVLRLRFglYDGrtRTLEEVGKEFNVTRERIRQIEAKALRKLK 381
Cdd:TIGR02479 181 QLVLSLYY--YEE--LNLKEIGEVLGLTESRVSQIHSQALKKLR 220
spore_sigF TIGR02885
RNA polymerase sigma-F factor; Members of this protein family are the RNA polymerase sigma ...
 150-381 3.10e-30

RNA polymerase sigma-F factor; Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore. [Transcription, Transcription factors, Cellular processes, Sporulation and germination]


Pssm-ID: 131931 [Multi-domain]  Cd Length: 231  Bit Score: 115.97  E-value: 3.10e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 150 QAGDEEAKKKLISANLRLVVSIAKKYVGRGMLFLDLIQEGNMGLVKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQAr 229
Cdd:TIGR02885   6 QNGDKEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFLRDDG- 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 230 TIRIPVHMVETINKLTRIQRQLVQDLGRDPSAEEIAAKMEnISPEKVREIQKIALEPVSLETPIGEEDdshlGDFIEDKE 309
Cdd:TIGR02885  85 IIKVSRSLKELARKIRYMKEELSKELGREPTINELAEALG-VSPEEIVMALESARSPQSLYDTVHQDD----GDPIYLLD 159

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1589200337 310 ALSpDEYANNQLLKDEI--NTVLQGLTEREEKVLRLRFglYDGRTRTleEVGKEFNVTRERIRQIEAKALRKLK 381
Cdd:TIGR02885 160 QIA-DKGSEDSDWLEKIalKEAISKLDERERQIIMLRY--FKDKTQT--EVANMLGISQVQVSRLEKKVLKKMK 228
PRK05572 PRK05572
RNA polymerase sporulation sigma factor, SigF/SigG family;
137-381 3.15e-30

RNA polymerase sporulation sigma factor, SigF/SigG family;


Pssm-ID: 180137 [Multi-domain]  Cd Length: 252  Bit Score: 116.61  E-value: 3.15e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 137 LDPKEEPEIARRIQAGDEEAKKKLISANLRLVVSIAKKYVGRGMLFLDLIQEGNMGLVKAVEKFDYTKGFKFSTYATWWI 216
Cdd:PRK05572   14 LKDEENKELIKKSQDGDQEARDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMI 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 217 RQAITRAIADQArTIRIPVHMVETINKLTRIQRQLVQDLGRDPSAEEIAAKMEnISPEKVREIQKIALEPVSLETPIGEE 296
Cdd:PRK05572   94 IGEIQRFLRDDG-TVKVSRSLKETANKIRKDKDELSKELGREPTIEELAEYLG-VTPEEVVLAQEASRSPQSIHETVHEN 171

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 297 DDS--HLGDFIEDKEAlspDEYANNQLLKDEINtvlqGLTEREEKVLRLRFglYDGRTRTleEVGKEFNVTRERIRQIEA 374
Cdd:PRK05572  172 DGDpiTLLDQIADQSE---EDWFDKIALKEAIR----ELDERERLIVYLRY--FKDKTQS--EVAKRLGISQVQVSRLEK 240


                  ....*..
gi 1589200337 375 KALRKLK 381
Cdd:PRK05572  241 KILKQMK 247
PRK05803 PRK05803
RNA polymerase sporulation sigma factor SigK;
137-382 1.27e-29

RNA polymerase sporulation sigma factor SigK;


Pssm-ID: 180266 [Multi-domain]  Cd Length: 233  Bit Score: 114.27  E-value: 1.27e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 137 LDPKEEPEIARRIQAGDEEAKKKLISANLRLVVSIAKKYVGRGMLFLDLIQEGNMGLVKAVEKFDYTKGFKFSTYAtwwi 216
Cdd:PRK05803   31 LSEEEERKYLELMKEGDEEARNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYA---- 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 217 rqaitraiadqARTIRIPVHMVETINKLTRIQrqlvqdlgrdpsaeeiaakmenispekvreiqkialepVSLETPIGEE 296
Cdd:PRK05803  107 -----------ARCIENEILMHLRNLKKTKKE--------------------------------------VSLQDPIGVD 137

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 297 DDSH---LGDFIEDkEALSPDEYANNQLLKDEINTVLQGLTEREEKVLRLRFGLYDGRTRTLEEVGKEFNVTRERIRQIE 373
Cdd:PRK05803  138 KEGNeisLIDILGS-EEDDVIEQVELKMEVEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIE 216


                  ....*....
gi 1589200337 374 AKALRKLKH 382
Cdd:PRK05803  217 KRALKKLFK 225
Sigma70_r3 pfam04539
Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the ...
 239-317 2.58e-28

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: 106.15  E-value: 2.58e-28
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1589200337 239 ETINKLTRIQRQLVQDLGRDPSAEEIAAKMeNISPEKVREIQKIALEPVSLETPIGEEDDSHLGDFIEDKEALSPDEYA 317
Cdd:pfam04539   1 ELLNKIKRAQRELEQELGREPTPEEIAEEL-GLSPEKVREVLEAAREPVSLDTPVGEEEDGELGDLLEDDDIESPEEAV 78
PRK06288 PRK06288
RNA polymerase sigma factor WhiG; Reviewed
 129-381 2.68e-26

RNA polymerase sigma factor WhiG; Reviewed


Pssm-ID: 235770 [Multi-domain]  Cd Length: 268  Bit Score: 106.31  E-value: 2.68e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 129 KEIGRVELLDPKEEPEIARRIQA-GDEEAKKKLISANLRLVVSIAKKyVGRGML----FLDLIQEGNMGLVKAVEKFDYT 203
Cdd:PRK06288    4 KMSGKIPKYAQQDETELWREYKKtGDPKIREYLILKYSPLVKYVAGR-IAVGMPqnveFDDLVSYGVFGLIDAIEKFDPE 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 204 KGFKFSTYATWWIRQAI---TRAIADQARTIRIPVHMVEtinkltRIQRQLVQDLGRDPSAEEIAAKMeNISPEKVREI- 279
Cdd:PRK06288   83 REIKFKTYAVTRIRGAIfdeLRSIDWIPRSVRQKARQIE------RAIAMLEARLGRTPSDEEIADEL-GISLEEYNSLl 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 280 -QKIALEPVSLET--PIGEEDDS-HLGDFIEDKEALSPDEYANNQLLKDEINTVLQGLTEREEKVLRLRFglYDGrtRTL 355
Cdd:PRK06288  156 sKLSGTSVVSLNDlwFGGDEGDEvSLMDTLESPAALNPDEIAEREEIKRVIVEAIKTLPEREKKVLILYY--YED--LTL 231

                         250       260
                  ....*....|....*....|....*.
gi 1589200337 356 EEVGKEFNVTRERIRQIEAKALRKLK 381
Cdd:PRK06288  232 KEIGKVLGVTESRISQLHTKAVLQLR 257
PRK07670 PRK07670
FliA/WhiG family RNA polymerase sigma factor;
184-382 3.54e-24

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 181075 [Multi-domain]  Cd Length: 251  Bit Score: 100.12  E-value: 3.54e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 184 DLIQEGNMGLVKAVEKFDYTKGFKFSTYATWWIRQAITraiaDQARTI-RIPVHMVETINKLTRIQRQLVQDLGRDPSAE 262
Cdd:PRK07670   54 DLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAII----DGLRKEdWLPRSMREKTKKVEAAIEKLEQRYMRNVTPK 129

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 263 EIAAKMeNISPEKVREIQKIALEPVSL---ETPIGEEDDSHLGDFIEDKEALSPDEYANNQLLKDEINTVLQGLTEREEK 339
Cdd:PRK07670  130 EVAAEL-GMTEEEVEATMNEGFFANLLsidEKTHDQDDGENVSVTIRDDKTPTPEEKLLKEELIEELAEKIKQLSEKEQL 208

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1589200337 340 VLrlrfGLYDGRTRTLEEVGKEFNVTRERIRQIEAKALRKLKH 382
Cdd:PRK07670  209 VI----SLFYKEELTLTEIGQVLNLSTSRISQIHSKALFKLKK 247
PRK07408 PRK07408
RNA polymerase sigma factor SigF; Reviewed
 150-349 2.00e-23

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 180965 [Multi-domain]  Cd Length: 256  Bit Score: 98.07  E-value: 2.00e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 150 QAGDEEAKKKLISANLRLVVSIAKKYVGR-GMLFLDLIQEGNMGLVKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQA 228
Cdd:PRK07408   20 QNPSIALRNQLVELNLGLVRKEAHRWSNQcSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKS 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 229 RTIRIPVHMVETINKLTRIQRQLVQDLGRDPSAEEIAAKMeNISPEKVREIqKIAL---EPVSLETPIGEEDDSH--LGD 303
Cdd:PRK07408  100 PTVRIPRRWQELQRQAKKVRQELRQELGRQPTDQEIAQAL-DISLEEWQEI-KLALqnrTPLSLDAPVNQDEDGStsLGD 177

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 1589200337 304 fiedkeaLSPD-EYANNQLLKDE---INTVLQGLTEREEKVLRLRFgLYD 349
Cdd:PRK07408  178 -------LLPDpRYRSFQLAQEDrirLQQALAQLEERTREVLEFVF-LHD 219
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 160-230 2.18e-23

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: 92.27  E-value: 2.18e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1589200337 160 LISANLRLVVSIAKKYVGRGMLFLDLIQEGNMGLVKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQART 230
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRRT 71
PRK07122 PRK07122
RNA polymerase sigma factor SigF; Reviewed
 143-381 2.25e-23

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 168831 [Multi-domain]  Cd Length: 264  Bit Score: 98.31  E-value: 2.25e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 143 PEIARRIQAGDEEA------KKKLISANLRLVVSIAKKYVGRGMLFLDLIQEGNMGLVKAVEKFDYTKGFKFSTYATWWI 216
Cdd:PRK07122   22 PEMFRELAGLPAGSpefqrqRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTI 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 217 RQAITRAIADQARTIRIPVHMVETINKLTRIQRQLVQDLGRDPSAEEIAAKMEnISPEKVRE--IQKIALEPVSLETPIG 294
Cdd:PRK07122  102 MGEVRRHFRDNSWSVKVPRRLKELHLRLGRATAELSQRLGRAPTASELAAELG-MDREEVVEglVAGSAYNTLSIDSGGG 180

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 295 EEDDSH------LGDF------IEDKEALSPdeyannqllkdeintVLQGLTEREEKVLRLRFglYDGRTRT--LEEVGk 360
Cdd:PRK07122  181 SGDDDAraiadtLGDVdagldqIENREALRP---------------LLAALPERERTVLVLRF--FESMTQTqiAERVG- 242

                         250       260
                  ....*....|....*....|.
gi 1589200337 361 efnVTRERIRQIEAKALRKLK 381
Cdd:PRK07122  243 ---ISQMHVSRLLAKTLARLR 260
fliA PRK06986
flagellar biosynthesis sigma factor; Validated
 184-381 2.97e-17

flagellar biosynthesis sigma factor; Validated


Pssm-ID: 235901 [Multi-domain]  Cd Length: 236  Bit Score: 80.28  E-value: 2.97e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 184 DLIQEGNMGLVKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQ---ARTIRIPVHMVETinkltrIQRQLVQDLGRDPS 260
Cdd:PRK06986   40 DLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDELRSLdwvPRSVRRNAREVAQ------AIRQLEQELGREPT 113

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 261 AEEIAAKMeNISPEKVREIqkiaLEPVSLETPIGEED-DSHLGDFIEDKEALSPDEyANNQLLKDE----INTVLQGLTE 335
Cdd:PRK06986  114 DTEVAEKL-GLSLEEYREM----LLDTNISQLFSIDElRGEHGDSILVTEDHQDED-PLQQLEDEElreaLVEAIESLPE 187

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1589200337 336 REEKVLrlrfGLYDGRTRTLEEVGKEFNVTRERIRQIEAKALRKLK 381
Cdd:PRK06986  188 REQLVL----SLYYQEELNLKEIGAVLGVSESRVSQIHSQAIKRLR 229
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 155-381 2.71e-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: 75.46  E-value: 2.71e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 155 EAKKKLISANLRLVVSIAKKYVGRGMLFLDLIQEGNMGLVKAVEKFDYTKgfKFSTYATWWIRQAITRAIADQARtirip 234
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEG--SFKAWLFRIARNLILDYLRRKRR----- 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 235 vhmvetinkLTRIQRQLVQDLGRDPSAEEIAAKMEnispekvreiqkialepvsletpigeeddshlgdfiedkealspd 314
Cdd:TIGR02937  74 ---------LRRELDLLEELLDSDPSPEEELEQEE--------------------------------------------- 99

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1589200337 315 eyannqlLKDEINTVLQGLTEREEKVLRLRFglYDGrtRTLEEVGKEFNVTRERIRQIEAKALRKLK 381
Cdd:TIGR02937 100 -------EREALREALEKLPEREREVLVLRY--LEG--LSYKEIAEILGISVGTVKRRLKRARKKLR 155
PRK08583 PRK08583
RNA polymerase sigma factor SigB; Validated
 145-381 4.35e-16

RNA polymerase sigma factor SigB; Validated


Pssm-ID: 236306 [Multi-domain]  Cd Length: 257  Bit Score: 77.43  E-value: 4.35e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 145 IARRIQAGDEEAKKKLISANLRLVVSIAKKYVGRGMLFLDLIQEGNMGLVKAVEKFDYTKGFKFSTYATWWIRQAITRAI 224
Cdd:PRK08583   19 IAEYQENQDEEAQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYL 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 225 ADQARTIRIPVHMVETINKLTRIQRQLVQDLGRDPSAEEIAAKMEnISPEKVREIQKI--ALEPVSLETPIGEEDDSH-- 300
Cdd:PRK08583   99 RDKTWSVHVPRRIKELGPKIKKAVDELTTELQRSPKISEIADRLG-VSEEEVLEAMEMgkSYQALSVDHSIEADSDGStv 177

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 301 -LGDFIEDKEalSPDEYANNQLLkdeINTVLQGLTEREEKVLRLRFglYDGRTRtlEEVGKEFNVTRERIRQIEAKALRK 379
Cdd:PRK08583  178 tLLDIVGQQE--DGYELTEQRMI---LEKILPVLSDREKSIIQCTF--IENLSQ--KETGERLGISQMHVSRLQRQAIKK 248


                  ..
gi 1589200337 380 LK 381
Cdd:PRK08583  249 LR 250
PRK08301 PRK08301
RNA polymerase sporulation sigma factor SigE;
137-381 3.32e-15

RNA polymerase sporulation sigma factor SigE;


Pssm-ID: 236228 [Multi-domain]  Cd Length: 234  Bit Score: 74.51  E-value: 3.32e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 137 LDPKEEPEIARRIQAGDEEAKKKLISANLRLVVSIAKKYVGRGMLFLDLIQEGNMGLVKAVEKFDYTKGFKFSTYATwwi 216
Cdd:PRK08301   34 LSKEEEEYLLNKLPKGDEAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYAS--- 110

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 217 rqaitraiadqaRTIRIPVHMVETINKLTRIQRQLVQDLGRDPSAEEIAakmenispekvreiqkialepvsLETPIGEE 296
Cdd:PRK08301  111 ------------RCIENEILMYLRRNNKVKAEVSFDEPLNIDWDGNELL-----------------------LSDVLGTD 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 297 DDShLGDFIEDKealspdeyANNQLLKdeinTVLQGLTEREEKVLRLRFGLYDGRTRTLEEVGKEFNVTRERIRQIEAKA 376
Cdd:PRK08301  156 NDI-IYKDIEDE--------VDRKLLK----KALKKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRI 222


                  ....*
gi 1589200337 377 LRKLK 381
Cdd:PRK08301  223 IKRLK 227
PRK05911 PRK05911
RNA polymerase sigma factor sigma-28; Reviewed
 155-381 3.42e-15

RNA polymerase sigma factor sigma-28; Reviewed


Pssm-ID: 235644 [Multi-domain]  Cd Length: 257  Bit Score: 74.65  E-value: 3.42e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 155 EAKKKLISANLRLVVSIAKKYVGrGM----LFLDLIQEGNMGLVKAVEKFDYTKGFKFSTYATWWIRQAItraIADQART 230
Cdd:PRK05911   23 EYRDVLIEFYLPLVKNVAHRLIS-GMpshvKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAI---IDDLRKQ 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 231 IRIPVHMVETINKLTRIQRQLVQDLGRDPSAEEIAAKMeNISPEKVR---EIQKIALePVSLETPIGEEDDSHLGDFIED 307
Cdd:PRK05911   99 DWVPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYL-NISQQELSgwfSSARPAL-ILSLNEEFPCQSDDEAGLALEE 176

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1589200337 308 KEALSPDEYANNQLLKDEINTVL----QGLTEREEKVLrlrfGLYDGRTRTLEEVGKEFNVTRERIRQIEAKALRKLK 381
Cdd:PRK05911  177 RIADERAETGYDVVDKKEFSSILaeaiLALEEKERKVM----ALYYYEELVLKEIGKILGVSESRVSQIHSKALLKLR 250
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 329-382 1.28e-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: 64.76  E-value: 1.28e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1589200337 329 VLQGLTEREEKVLRLRFGlydgRTRTLEEVGKEFNVTRERIRQIEAKALRKLKH 382
Cdd:pfam04545   1 ALASLPPRERQVLVLRYG----EGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 323-381 2.77e-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: 58.27  E-value: 2.77e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1589200337 323 KDEINTVLQGLTEREEKVLRLRFGlydgRTRTLEEVGKEFNVTRERIRQIEAKALRKLK 381
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFG----EGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
Sigma70_r1_2 pfam00140
Sigma-70 factor, region 1.2;
122-155 4.25e-11

Sigma-70 factor, region 1.2;


Pssm-ID: 425482 [Multi-domain]  Cd Length: 34  Bit Score: 57.32  E-value: 4.25e-11
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1589200337 122 DPVKMYLKEIGRVELLDPKEEPEIARRIQAGDEE 155
Cdd:pfam00140   1 DSVRLYLKEIGRIPLLTAEEEVELAKRIEAGDEA 34
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
137-364 8.60e-11

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 61.08  E-value: 8.60e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 137 LDPKEEPEIARRIQAGDEEAKKKLISANLRLVVSIAKKYVGRGMLFLDLIQEGNMGLVKAVEKFDYTKGFKFSTYAtwwi 216
Cdd:PRK08295    6 YDELEDEELVELARSGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFA---- 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 217 RQAITRAIadqartiripvhmvetINKLTRIQRQlvqdlgrdpsaeeiaakmenispekvreiQKIAL-EPVSLETPIGE 295
Cdd:PRK08295   82 ELCITRQI----------------ITAIKTANRQ-----------------------------KHIPLnSYVSLDKPIYD 116

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1589200337 296 EDDSH-LGDFIEDKEALSPDE-YANNQLLKDEINTVLQGLTEREEKVLRLrfgLYDGrtRTLEEVGKEFNV 364
Cdd:PRK08295  117 EESDRtLLDVISEAKVTDPEElIISKEELEDIEEKIEELLSELEKEVLEL---YLDG--KSYQEIAEELNR 182
PRK05658 PRK05658
RNA polymerase sigma factor RpoD; Validated
 122-155 9.50e-07

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 235549 [Multi-domain]  Cd Length: 619  Bit Score: 50.95  E-value: 9.50e-07
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1589200337 122 DPVKMYLKEIGRVELLDPKEEPEIARRIQAGDEE 155
Cdd:PRK05658  104 DPVRMYLREMGTVELLTREGEIEIAKRIEAGENI 137
PRK12427 PRK12427
FliA/WhiG family RNA polymerase sigma factor;
184-381 3.17e-06

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 183523 [Multi-domain]  Cd Length: 231  Bit Score: 47.93  E-value: 3.17e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 184 DLIQEGNMGLVKAVEKFDYTKGfKFSTYATWWIRQAIT---RAIADQARTIRIPVHmvetinKLTRIQRQLVQDLGRDPS 260
Cdd:PRK12427   47 DMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILdelRELDWRPRRLRQKTH------KTNDAIREIAKRLGHEPN 119

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 261 AEEIAAKMeNISPEKVREIQKI--ALEPVSLETPIGeeDDSHlGDFIEDKEAlsPDEYANNQLLKDeintVLQGLTEREE 338
Cdd:PRK12427  120 FEEISAEL-NLTAEEYQEYLLLenAGTLESLDELLA--LEAH-NDILQSRDL--EENIIIEDNLKQ----ALSQLDEREQ 189

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1589200337 339 KVLRlrfgLYDGRTRTLEEVGKEFNVTRERIRQIEAKALRKLK 381
Cdd:PRK12427  190 LILH----LYYQHEMSLKEIALVLDLTEARICQLNKKIAQKIK 228
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 140-381 1.58e-05

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: 44.99  E-value: 1.58e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 140 KEEPEIARRIQAGDEEAKKKLISANLRLVVSIAKKYVGRGMLFLDLIQEGNMGLVKAVEKFDYTKGFKFstyatwWIRQA 219
Cdd:COG1595     2 SSDEELLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRA------WLYRI 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 220 ITRAIADQARtiripvhmvetinKLTRIQRQLvqdlgrdpsaeeiaakmenispekvreiqkialepvsletpigEEDDS 299
Cdd:COG1595    76 ARNLAIDHLR-------------KRRRRRELL-------------------------------------------DELAE 99

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1589200337 300 HLGDfiedkEALSPDEYANNQLLKDEINTVLQGLTEREEKVLRLRFglYDGrtRTLEEVGKEFNVTRERIRQIEAKALRK 379
Cdd:COG1595   100 ELPD-----EAADPEEALEAEELLEALLAALERLPPRQREVLVLRY--LEG--LSYAEIAEILGISEGTVKSRLSRARKK 170


                  ..
gi 1589200337 380 LK 381
Cdd:COG1595   171 LR 172
PRK08311 PRK08311
RNA polymerase sigma factor SigI;
144-217 1.28e-03

RNA polymerase sigma factor SigI;


Pssm-ID: 236233 [Multi-domain]  Cd Length: 237  Bit Score: 39.85  E-value: 1.28e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1589200337 144 EIARRIQAGDEEAKKKLISANLRLVVSIAKKYVGRgmlFLDLIQE-----GNMGLVKAVEKFDYTKGFKFSTYATWWIR 217
Cdd:PRK08311    7 DILEKIKNGDEELREELIEEYKPFIAKVVSSVCGR---YIDWENDdelsiGLIAFNEAIDSYDEEKGKSFLSFAELVIK 82
 
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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