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Conserved domains on  [gi|1325806947|ref|WP_101688158|]
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RNA polymerase sigma factor [Corynebacterium amycolatum]

Protein Classification

RNA polymerase sigma factor( domain architecture ID 11481872)

RNA polymerase sigma factor similar to Streptomyces coelicolor RNA polymerase principal sigma factor HrdA and HrdB/SigA; sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released

CATH:  1.10.10.10|1.20.120.1810
Gene Ontology:  GO:0016987|GO:0006352|GO:0003677
PubMed:  12540296|16285916

Graphical summary

 Zoom to residue level

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List of domain hits

 Name Accession Description Interval E-value
PRK05901 PRK05901
RNA polymerase sigma factor; Provisional
 198-520 0e+00

RNA polymerase sigma factor; Provisional


:

Pssm-ID: 235640 [Multi-domain]  Cd Length: 509  Bit Score: 704.06  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 198 EDESARLRQARKDAALTASADSVRAYLKQIGKVALLTAEEEVSLAKRIEAGLYAQYKIDEakesGERIAYAQKRDLREIS 277
Cdd:PRK05901  191 EDDSEALRQARKDAKLTATADPVKAYLKQIGKVKLLNAEEEVELAKRIEAGLYAEELLAE----GEKLDPELRRDLQWIG 266

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 278 RDGQRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQART 357
Cdd:PRK05901  267 RDGKRAKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQART 346

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 358 IRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITEEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAV 437
Cdd:PRK05901  347 IRIPVHMVETINKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGDSQFGDFIEDSEAV 426

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 438 IAVDAVSFTLLQDQLGDVLETLSEREAGVVRLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRD 517
Cdd:PRK05901  427 SPVDAVSFTLLQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRHPSRSQVLRD 506


                  ...
gi 1325806947 518 YLE 520
Cdd:PRK05901  507 FLD 509
 
Name Accession Description Interval E-value
PRK05901 PRK05901
RNA polymerase sigma factor; Provisional
 198-520 0e+00

RNA polymerase sigma factor; Provisional


Pssm-ID: 235640 [Multi-domain]  Cd Length: 509  Bit Score: 704.06  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 198 EDESARLRQARKDAALTASADSVRAYLKQIGKVALLTAEEEVSLAKRIEAGLYAQYKIDEakesGERIAYAQKRDLREIS 277
Cdd:PRK05901  191 EDDSEALRQARKDAKLTATADPVKAYLKQIGKVKLLNAEEEVELAKRIEAGLYAEELLAE----GEKLDPELRRDLQWIG 266

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 278 RDGQRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQART 357
Cdd:PRK05901  267 RDGKRAKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQART 346

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 358 IRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITEEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAV 437
Cdd:PRK05901  347 IRIPVHMVETINKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGDSQFGDFIEDSEAV 426

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 438 IAVDAVSFTLLQDQLGDVLETLSEREAGVVRLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRD 517
Cdd:PRK05901  427 SPVDAVSFTLLQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRHPSRSQVLRD 506


                  ...
gi 1325806947 518 YLE 520
Cdd:PRK05901  507 FLD 509
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 222-520 5.52e-153

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: 437.18  E-value: 5.52e-153
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 222 AYLKQIGKVALLTAEEEVSLAKRIEAGlyaqykideakesgeriayaqkrdlreisrdGQRAKNHLLEANLRLVVSLAKR 301
Cdd:COG0568     1 AYLREIGRVPLLTAEEEVELARRIQAG-------------------------------DEEAKRKLVEANLRLVVSIAKK 49

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 302 YTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQD 381
Cdd:COG0568    50 YQGRGLPLLDLIQEGNLGLMKAVEKFDPERGFRFSTYATWWIRQAITRAIADQWRTIRLPVHMAETLNKLRRAKRQLLQE 129

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 382 LGREPTPEELAKEMDITEEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVIAVDAVSFTLLQDQLGDVLETLSE 461
Cdd:COG0568   130 LGREPTPEEIAEELGVPEEKVREMLRLAREPVSLDAPVGDDEDSELGDLLEDEEAPSPEEALEEELLREELREALDTLTE 209

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1325806947 462 REAGVVRLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLE 520
Cdd:COG0568   210 REREILRLRFGLDDGEPHTLEEIGKEFGVSRERVRQIEAKALRKLRHPLRSRKLRDYLD 268
RpoD_Cterm TIGR02393
RNA polymerase sigma factor RpoD, C-terminal domain; This model represents the well-conserved ...
 283-520 5.98e-145

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: 415.93  E-value: 5.98e-145
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 283 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPV 362
Cdd:TIGR02393   1 AKKKLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 363 HMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITEEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVIAVDA 442
Cdd:TIGR02393  81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDESIESPDDA 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1325806947 443 VSFTLLQDQLGDVLETLSEREAGVVRLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLE 520
Cdd:TIGR02393 161 AAKELLREQLDEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLKDFLD 238
Sigma70_r3 pfam04539
Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the ...
 366-443 2.51e-27

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: 104.61  E-value: 2.51e-27
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1325806947 366 EVINKLGRIQRELLQDLGREPTPEELAKEMDITEEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVIAVDAV 443
Cdd:pfam04539   1 ELLNKIKRAQRELEQELGREPTPEEIAEELGLSPEKVREVLEAAREPVSLDTPVGEEEDGELGDLLEDDDIESPEEAV 78
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 449-507 3.76e-09

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: 52.49  E-value: 3.76e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1325806947 449 QDQLGDVLETLSEREAGVVRLRFGltdgMPRTLDEIGQVYGVTRERIRQIESKTMSKLR 507
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFG----EGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
PRK05901 PRK05901
RNA polymerase sigma factor; Provisional
 198-520 0e+00

RNA polymerase sigma factor; Provisional


Pssm-ID: 235640 [Multi-domain]  Cd Length: 509  Bit Score: 704.06  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 198 EDESARLRQARKDAALTASADSVRAYLKQIGKVALLTAEEEVSLAKRIEAGLYAQYKIDEakesGERIAYAQKRDLREIS 277
Cdd:PRK05901  191 EDDSEALRQARKDAKLTATADPVKAYLKQIGKVKLLNAEEEVELAKRIEAGLYAEELLAE----GEKLDPELRRDLQWIG 266

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 278 RDGQRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQART 357
Cdd:PRK05901  267 RDGKRAKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQART 346

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 358 IRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITEEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAV 437
Cdd:PRK05901  347 IRIPVHMVETINKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGDSQFGDFIEDSEAV 426

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 438 IAVDAVSFTLLQDQLGDVLETLSEREAGVVRLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRD 517
Cdd:PRK05901  427 SPVDAVSFTLLQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRHPSRSQVLRD 506


                  ...
gi 1325806947 518 YLE 520
Cdd:PRK05901  507 FLD 509
PRK07921 PRK07921
RNA polymerase sigma factor SigB; Reviewed
 197-518 4.28e-172

RNA polymerase sigma factor SigB; Reviewed


Pssm-ID: 181169 [Multi-domain]  Cd Length: 324  Bit Score: 488.09  E-value: 4.28e-172
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 197 NEDESARLRQARKDAALTA---SADSVRAYLKQIGKVALLTAEEEVSLAKRIEAGLYAQYKIdeakESGERIAYAQKRDL 273
Cdd:PRK07921    2 MADATARATTSRVDSDLDAqspAADLVRVYLNGIGKTALLTAADEVELAKRIEAGLYAEHLL----ETRKRLSEARKRDL 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 274 REISRDGQRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMAD 353
Cdd:PRK07921   78 AAVVRDGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMAD 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 354 QARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITEEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIED 433
Cdd:PRK07921  158 QSRTIRLPVHLVEQVNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIED 237

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 434 SEAVIAVDAVSFTLLQDQLGDVLETLSEREAGVVRLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQ 513
Cdd:PRK07921  238 SEATSAENAVIAGLLHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGERAD 317


                  ....*
gi 1325806947 514 VLRDY 518
Cdd:PRK07921  318 RLRSY 322
PRK09210 PRK09210
RNA polymerase sigma factor RpoD; Validated
 218-520 1.54e-164

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 470.62  E-value: 1.54e-164
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 218 DSVRAYLKQIGKVALLTAEEEVSLAKRIEAGlyaqykiDEAkesgeriayaqkrdlreisrdgqrAKNHLLEANLRLVVS 297
Cdd:PRK09210   96 DPVRMYLKEIGRVPLLTAEEEIELAKRIEEG-------DEE------------------------AKQRLAEANLRLVVS 144

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 298 LAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRE 377
Cdd:PRK09210  145 IAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQ 224

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 378 LLQDLGREPTPEELAKEMDITEEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVIAVDAVSFTLLQDQLGDVLE 457
Cdd:PRK09210  225 LLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAAYELLKEQLEDVLD 304

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1325806947 458 TLSEREAGVVRLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLE 520
Cdd:PRK09210  305 TLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 367
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 222-520 5.52e-153

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: 437.18  E-value: 5.52e-153
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 222 AYLKQIGKVALLTAEEEVSLAKRIEAGlyaqykideakesgeriayaqkrdlreisrdGQRAKNHLLEANLRLVVSLAKR 301
Cdd:COG0568     1 AYLREIGRVPLLTAEEEVELARRIQAG-------------------------------DEEAKRKLVEANLRLVVSIAKK 49

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 302 YTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQD 381
Cdd:COG0568    50 YQGRGLPLLDLIQEGNLGLMKAVEKFDPERGFRFSTYATWWIRQAITRAIADQWRTIRLPVHMAETLNKLRRAKRQLLQE 129

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 382 LGREPTPEELAKEMDITEEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVIAVDAVSFTLLQDQLGDVLETLSE 461
Cdd:COG0568   130 LGREPTPEEIAEELGVPEEKVREMLRLAREPVSLDAPVGDDEDSELGDLLEDEEAPSPEEALEEELLREELREALDTLTE 209

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1325806947 462 REAGVVRLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLE 520
Cdd:COG0568   210 REREILRLRFGLDDGEPHTLEEIGKEFGVSRERVRQIEAKALRKLRHPLRSRKLRDYLD 268
RpoD_Cterm TIGR02393
RNA polymerase sigma factor RpoD, C-terminal domain; This model represents the well-conserved ...
 283-520 5.98e-145

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: 415.93  E-value: 5.98e-145
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 283 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPV 362
Cdd:TIGR02393   1 AKKKLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 363 HMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITEEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVIAVDA 442
Cdd:TIGR02393  81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDESIESPDDA 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1325806947 443 VSFTLLQDQLGDVLETLSEREAGVVRLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLE 520
Cdd:TIGR02393 161 AAKELLREQLDEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLKDFLD 238
PRK05658 PRK05658
RNA polymerase sigma factor RpoD; Validated
 250-520 1.20e-136

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 235549 [Multi-domain]  Cd Length: 619  Bit Score: 408.80  E-value: 1.20e-136
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 250 YAQYKIDEAKESGERIAYAQKrdlreISRdgqRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDY 329
Cdd:PRK05658  356 ETGLTIEELKEINRQISKGEA-----KAR---RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 427

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 330 TKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITEEKVLEIQQYA 409
Cdd:PRK05658  428 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIA 507

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 410 REPISLDQTIGDEGDSQLGDFIEDSEAVIAVDAVSFTLLQDQLGDVLETLSEREAGVVRLRFGLTDGMPRTLDEIGQVYG 489
Cdd:PRK05658  508 KEPISLETPIGDDEDSHLGDFIEDKNAELPIDAAIQESLREATTDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFD 587

                         250       260       270
                  ....*....|....*....|....*....|.
gi 1325806947 490 VTRERIRQIESKTMSKLRHPSRSQVLRDYLE 520
Cdd:PRK05658  588 VTRERIRQIEAKALRKLRHPSRSRKLRSFLD 618
Sig70-cyanoRpoD TIGR02997
RNA polymerase sigma factor, cyanobacterial RpoD-like family; This family includes a number of ...
 218-507 3.75e-124

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: 365.03  E-value: 3.75e-124
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 218 DSVRAYLKQIGKVALLTAEEEVSLAKRIEAGLYAQYKIDEAKESGER-------IAYAQK--RDLREISRDGQRAKNHLL 288
Cdd:TIGR02997   1 DLVRLYLQEIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGRepskeewAAAAGLseAELRQRLRQGQRAKEKMI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 289 EANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVI 368
Cdd:TIGR02997  81 KANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 369 NKLGRIQRELLQDLGREPTPEELAKEMDITEEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDsEAVIAVDAVSFTLL 448
Cdd:TIGR02997 161 NKIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLED-DGESPEEQVERESL 239

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1325806947 449 QDQLGDVLETLSEREAGVVRLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLR 507
Cdd:TIGR02997 240 RQDLESLLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR 298
PRK07406 PRK07406
RNA polymerase sigma factor RpoD; Validated
 198-520 5.20e-122

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236012 [Multi-domain]  Cd Length: 373  Bit Score: 362.56  E-value: 5.20e-122
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 198 EDESARLRQARKDAALTASADSVRAYLKQIGKVALLTAEEEVSLAKRIEAGLYAQYKIDEAKESGERI----AYAQKRDL 273
Cdd:PRK07406   43 EAKAKALARIKIGPKKVYTEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLELEELREQFESELGREpsdkEWAELVDM 122

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 274 -----REISRDGQRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAIT 348
Cdd:PRK07406  123 plpkfRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAIT 202

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 349 RAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITEEKVLEIQQYAREPISLDQTIGDEGDSQLG 428
Cdd:PRK07406  203 RAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLG 282

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 429 DFIE-DSEAviAVDAVSFTLLQDQLGDVLETLSEREAGVVRLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLR 507
Cdd:PRK07406  283 DFIEaDGET--PEDDVAKNLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLR 360

                         330
                  ....*....|...
gi 1325806947 508 HPSRSQVLRDYLE 520
Cdd:PRK07406  361 HPNRNSVLKEYIR 373
PRK05949 PRK05949
RNA polymerase sigma factor; Validated
 214-519 1.03e-90

RNA polymerase sigma factor; Validated


Pssm-ID: 180321 [Multi-domain]  Cd Length: 327  Bit Score: 280.58  E-value: 1.03e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 214 TASADSVRAYLKQIGKVALLTAEEEVSLAKRIEAGLYAQYKIDEAKESGERIAYAQK---------RDLREISRDGQRAK 284
Cdd:PRK05949   14 TFSADMVRTYLHEIGRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEwaeavnlseTELKQTLKQGKRAK 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 285 NHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHM 364
Cdd:PRK05949   94 QKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHI 173

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 365 VEVINKLGRIQRELLQDLGREPTPEELAKEMDITEEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDsEAVIAVDAVS 444
Cdd:PRK05949  174 TEKLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTELSELLED-EGPSPDQYIT 252

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1325806947 445 FTLLQDQLGDVLETLSEREAGVVRLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHpsRSQVLRDYL 519
Cdd:PRK05949  253 QELLRQDLNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRR--RRANVKEYL 325
PRK07405 PRK07405
RNA polymerase sigma factor SigD; Validated
 216-519 4.11e-90

RNA polymerase sigma factor SigD; Validated


Pssm-ID: 180963 [Multi-domain]  Cd Length: 317  Bit Score: 278.57  E-value: 4.11e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 216 SADSVRAYLKQIGKVALLTAEEEVSLAKRIEAgLYAQYKIDE--AKESGERIAYAQ--------KRDLREISRDGQRAKN 285
Cdd:PRK07405    6 STDLVRTYLREIGRVPLLTHEEEILYGKQVQR-LVALQEIREelAEELGREPTDAEwakaaklsEEELRSAIAEGEAAKR 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 286 HLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMV 365
Cdd:PRK07405   85 KMVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHIT 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 366 EVINKLGRIQRELLQDLGREPTPEELAKEMDITEEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAViAVDAVSF 445
Cdd:PRK07405  165 EKLNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDTGAS-PEDFATQ 243

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1325806947 446 TLLQDQLGDVLETLSEREAGVVRLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRhpSRSQVLRDYL 519
Cdd:PRK07405  244 SSLQLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLR--KRKANIQEYL 315
PRK07598 PRK07598
RNA polymerase sigma factor SigC; Validated
 216-520 5.20e-88

RNA polymerase sigma factor SigC; Validated


Pssm-ID: 236067 [Multi-domain]  Cd Length: 415  Bit Score: 276.75  E-value: 5.20e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 216 SADSVRAYLKQIGKVALLTAEEEVSLAKRIEAGLYAQYKIDEAKESGERIAYAQK------------------------- 270
Cdd:PRK07598   58 STDLVRLYLQEIGRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRlievrerltselghrpslerwakta 137

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 271 --------------------------RDLREISRDGQRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAV 324
Cdd:PRK07598  138 disladlkptlaegkrrwaeiakltvEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAV 217

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 325 EKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITEEKVLE 404
Cdd:PRK07598  218 EKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVRE 297

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 405 IQQYAREPISLDQTIGDEGDSQLGDFIEdSEAVIAVDAVSFTLLQDQLGDVLETLSEREAGVVRLRFGLTDGMPRTLDEI 484
Cdd:PRK07598  298 VLLRVPRSVSLETKVGKDKDTELGDLLE-TDDISPEEMLMRESLQRDLQHLLADLTSRERDVIRMRFGLADGHTYSLAEI 376

                         330       340       350
                  ....*....|....*....|....*....|....*.
gi 1325806947 485 GQVYGVTRERIRQIESKTMSKLRHPSRSQVLRDYLE 520
Cdd:PRK07598  377 GRALDLSRERVRQIESKALQKLRQPKRRNRIRDYLE 412
rpoS_proteo TIGR02394
RNA polymerase sigma factor RpoS; A sigma factor is a DNA-binding protein protein that binds ...
 214-508 1.09e-80

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: 253.11  E-value: 1.09e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 214 TASADSVRAYLKQIGKVALLTAEEEVSLAKRIEAGLYAqykideakesgeriayaqkrdlreisrdgqrAKNHLLEANLR 293
Cdd:TIGR02394   9 TRVADVTQLYLREIGFKPLLTAEEEIAYARRALAGDFE-------------------------------ARKVMIESNLR 57

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 294 LVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGR 373
Cdd:TIGR02394  58 LVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPVHVIKELNVYLR 137

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 374 IQRELLQDLGREPTPEELAKEMDITEEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVIAVDAVSFTLLQDQLG 453
Cdd:TIGR02394 138 AARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPLDDDSSKSLLDTIADEQSIDPESLVQNDDLKQLIE 217

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1325806947 454 DVLETLSEREAGVVRLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRH 508
Cdd:TIGR02394 218 AWLAELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRR 272
PRK05657 PRK05657
RNA polymerase sigma factor RpoS; Validated
 198-516 1.38e-71

RNA polymerase sigma factor RpoS; Validated


Pssm-ID: 235548 [Multi-domain]  Cd Length: 325  Bit Score: 231.00  E-value: 1.38e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 198 EDESARLRQARKDAALTASADSVRAYLKQIGKVALLTAEEEVSLAKRIEAGLYAqykideakesgeriayAQKRdlreis 277
Cdd:PRK05657   33 SDNDLAEEELLSQGATQRVLDATQLYLNEIGYSPLLTAEEEVYFARRALRGDFA----------------ARQR------ 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 278 rdgqraknhLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQART 357
Cdd:PRK05657   91 ---------MIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRT 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 358 IRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITEEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAV 437
Cdd:PRK05657  162 IRLPVHVVKELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLGGDPEKSLLDILADEQEN 241

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1325806947 438 IAVDAVSFTLLQDQLGDVLETLSEREAGVVRLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQVLR 516
Cdd:PRK05657  242 GPEDTTQDDDMKQSIVKWLFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREILQTQGLS 320
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 273-507 5.04e-46

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: 160.76  E-value: 5.04e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 273 LREISRDGQRAKNHLLEANLRLVVSLAKRYTGRGMAFL-DLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRqaitRAM 351
Cdd:COG1191     6 LRRYQEGDEEAREELIEEYLPLVKKIASRLAGRLPAELdDLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIR----GAI 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 352 ADQARTI-RIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITEEKVLEIQQ--YAREPISLDQTIGDEGDsqLG 428
Cdd:COG1191    82 LDYLRDEdWVPRSVRELARKIEEAIEELEQELGREPTDEEIAEELGISLEEVQEALEaaNAYQLLSLDEPLEDGDD--LL 159

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1325806947 429 DFIEDSEAVIAVDAVsftLLQDQLGDVLETLSEREAGVVRLRFGltDGMprTLDEIGQVYGVTRERIRQIESKTMSKLR 507
Cdd:COG1191   160 DLLESGDPEEELEHE---ELREALAEAIEQLPERERLVLSLYYF--EEL--TLKEIAEVLGVSESRVSRLHKKALARLR 231
SigBFG TIGR02980
RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; This group of similar sigma-70 factors ...
 281-507 1.15e-39

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: 143.52  E-value: 1.15e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 281 QRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRI 360
Cdd:TIGR02980   2 KEAREKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIMGEIKRFFRDDTWAVRV 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 361 PVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITEEKVLEIQQYAR--EPISLDQTIG--DEGDSQLGDFIEDSEa 436
Cdd:TIGR02980  82 PRRLKELGVKINKATEELTQRLGRSPTIAEIAERLGVSEEEVVEALEAGNayQALSLDASIEddDGDPIALLDTLGDED- 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1325806947 437 viavDAVSFTLLQDQLGDVLETLSEREAGVVRLRFglTDGMprTLDEIGQVYGVTRERIRQIESKTMSKLR 507
Cdd:TIGR02980 161 ----DALETVEDRLALKPLLAALPERERRILLLRF--FEDK--TQSEIAERLGISQMHVSRLLRRALKKLR 223
rpoH_proteo TIGR02392
alternative sigma factor RpoH; A sigma factor is a DNA-binding protein protein that binds to ...
 218-507 1.14e-38

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: 142.03  E-value: 1.14e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 218 DSVRAYLKQIGKVALLTAEEEVSLAKRieaglyaqykideakesgeriaYAQKRDLReisrdgqrAKNHLLEANLRLVVS 297
Cdd:TIGR02392   1 GSLDAYIRAVNRIPMLTPEEEYQLAKR----------------------LREHGDLD--------AAKKLVLSHLRFVVK 50

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 298 LAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAItramadqartiripvHmvEVINKLGRI--- 374
Cdd:TIGR02392  51 IARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEI---------------H--EYILRNWRLvkv 113

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 375 -----QRELL-------QDLGREPTPEE---LAKEMDITEEKVLEIQQYAREP-ISLDQTIGDEGDSQ------LGDFIE 432
Cdd:TIGR02392 114 attkaQRKLFfnlrkmkKRLQGWLNPEEveaIAEELGVSEREVREMESRLSGQdMSLNASIDDDEDDGgapiayLVDKRS 193

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1325806947 433 DSEAVIAVDAVSfTLLQDQLGDVLETLSEREAGVVRLRFgLTDGmPRTLDEIGQVYGVTRERIRQIESKTMSKLR 507
Cdd:TIGR02392 194 DPEDTLEEEQWE-ELQRQALANALGSLDARSRRIIEARW-LDDD-KLTLQELAAEYGVSAERIRQIEKNAMKKLK 265
PRK06596 PRK06596
RNA polymerase factor sigma-32; Reviewed
 222-507 6.49e-37

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 235838 [Multi-domain]  Cd Length: 284  Bit Score: 137.61  E-value: 6.49e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 222 AYLKQIGKVALLTAEEEVSLAKRieaglyaqykideakesgeriaYAQKRDLReisrdgqrAKNHLLEANLRLVVSLAKR 301
Cdd:PRK06596   18 AYIQAVNKIPMLTAEEEYMLAKR----------------------LREHGDLE--------AAKQLVLSHLRFVVHIARG 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 302 YTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAItramadqartiripvHmvEVINKLGRI------- 374
Cdd:PRK06596   68 YRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEI---------------H--EYILRNWRIvkvattk 130

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 375 -QRELLQDLGREP------TPEE---LAKEMDITEEKVLEIQQ-YAREPISLDQTIGDEGDS--QLGDFIEDSE---AVI 438
Cdd:PRK06596  131 aQRKLFFNLRKAKkrlgwlNPEEvemVAEELGVSEEEVREMESrLSGQDASLDAPIDDDDEEsgAPQDYLEDKSsdpADV 210

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1325806947 439 AVDAVSFTLLQDQLGDVLETLSEREAGVVRLRFgLTDGmPRTLDEIGQVYGVTRERIRQIESKTMSKLR 507
Cdd:PRK06596  211 LEEDNWEDQRRALLADALEGLDERSRDIIEARW-LDDD-KSTLQELAAEYGVSAERVRQIEKNAMKKLK 277
FliA_WhiG TIGR02479
RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar ...
 311-507 1.33e-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: 118.53  E-value: 1.33e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 311 DLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAI---TRAMADQARTIRIPVHMVEvinklgRIQRELLQDLGREPT 387
Cdd:TIGR02479  28 DLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMldeLRRLDWVPRSLRQKARKLE------RAIRELEARLGREPT 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 388 PEELAKEMDITEEKVLEIQQY--AREPISLDQTIGDEGDS-QLGDFIEDSEAVIAVDAVSFTLLQDQLGDVLETLSEREA 464
Cdd:TIGR02479 102 EEEIAEELGMDLKEYRQALNEinALSLVSLDELLESGDDGgSLIDRIEDDKSEDPEEELEREELREALAEAIESLSEREQ 181

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1325806947 465 GVVRLRF--GLtdgmprTLDEIGQVYGVTRERIRQIESKTMSKLR 507
Cdd:TIGR02479 182 LVLSLYYyeEL------NLKEIGEVLGLTESRVSQIHSQALKKLR 220
PRK05572 PRK05572
RNA polymerase sporulation sigma factor, SigF/SigG family;
257-507 1.90e-30

RNA polymerase sporulation sigma factor, SigF/SigG family;


Pssm-ID: 180137 [Multi-domain]  Cd Length: 252  Bit Score: 118.92  E-value: 1.90e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 257 EAKESGERIAYAQKRDLREISRDG-QRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKF 335
Cdd:PRK05572    6 KNKKKKPQLKDEENKELIKKSQDGdQEARDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKF 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 336 STYATWWIRQAITRAMADQArTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITEEKVLEIQQYAREPISL 415
Cdd:PRK05572   86 STYAVPMIIGEIQRFLRDDG-TVKVSRSLKETANKIRKDKDELSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSI 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 416 DQTI-GDEGDS-QLGDFIEDSEAVIAVDAVSftllqdqLGDVLETLSEREAGVVRLRFgLTDgmpRTLDEIGQVYGVTRE 493
Cdd:PRK05572  165 HETVhENDGDPiTLLDQIADQSEEDWFDKIA-------LKEAIRELDERERLIVYLRY-FKD---KTQSEVAKRLGISQV 233

                         250
                  ....*....|....
gi 1325806947 494 RIRQIESKTMSKLR 507
Cdd:PRK05572  234 QVSRLEKKILKQMK 247
PRK07408 PRK07408
RNA polymerase sigma factor SigF; Reviewed
 265-471 2.34e-28

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 180965 [Multi-domain]  Cd Length: 256  Bit Score: 113.48  E-value: 2.34e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 265 IAYAQKRDLReisrdgqrAKNHLLEANLRLVVSLAKRYTGR-GMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWI 343
Cdd:PRK07408   16 RAYQQNPSIA--------LRNQLVELNLGLVRKEAHRWSNQcSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYI 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 344 RQAITRAMADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITEEKVLEIQ--QYAREPISLDQTIGD 421
Cdd:PRK07408   88 RGEIQHYLRDKSPTVRIPRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKlaLQNRTPLSLDAPVNQ 167

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1325806947 422 EGDSQ--LGDFIEDSEaviavdAVSFTLLQD---QLGDVLETLSEREAGVVRLRF 471
Cdd:PRK07408  168 DEDGStsLGDLLPDPR------YRSFQLAQEdriRLQQALAQLEERTREVLEFVF 216
spore_sigF TIGR02885
RNA polymerase sigma-F factor; Members of this protein family are the RNA polymerase sigma ...
 273-507 2.64e-28

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: 112.50  E-value: 2.64e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 273 LREISRDG-QRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAM 351
Cdd:TIGR02885   1 LIKLAQNGdKEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 352 ADQArTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITEEKVLEIQQYAREPISLDQTIG-DEGDS-QLGD 429
Cdd:TIGR02885  81 RDDG-IIKVSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLYDTVHqDDGDPiYLLD 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 430 FIED--SEAVIAVDAVSftllqdqLGDVLETLSEREAGVVRLRFgLTDgmpRTLDEIGQVYGVTRERIRQIESKTMSKLR 507
Cdd:TIGR02885 160 QIADkgSEDSDWLEKIA-------LKEAISKLDERERQIIMLRY-FKD---KTQTEVANMLGISQVQVSRLEKKVLKKMK 228
Sigma70_r3 pfam04539
Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the ...
 366-443 2.51e-27

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: 104.61  E-value: 2.51e-27
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1325806947 366 EVINKLGRIQRELLQDLGREPTPEELAKEMDITEEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDSEAVIAVDAV 443
Cdd:pfam04539   1 ELLNKIKRAQRELEQELGREPTPEEIAEELGLSPEKVREVLEAAREPVSLDTPVGEEEDGELGDLLEDDDIESPEEAV 78
rpoH2 PRK07500
RNA polymerase factor sigma-32; Reviewed
 212-507 4.38e-27

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 236033 [Multi-domain]  Cd Length: 289  Bit Score: 110.51  E-value: 4.38e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 212 ALTASADsvRAYLKQIGKVALLTAEEEVSLAkrieaglyaqykideakesgerIAYAQKRDlreisrdgQRAKNHLLEAN 291
Cdd:PRK07500    2 AADASAD--RSMIRSAMKAPYLEREEEHALA----------------------YRWKDHRD--------EDALHRIISAH 49

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 292 LRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAItramadQARTIRiPVHMVE----- 366
Cdd:PRK07500   50 MRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASI------QDYILR-NWSIVRggtss 122

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 367 ----VINKLGRIQRELLQD---LGREPTPEELAKEMDITEEKVLEIQ-QYAREPISLDQTI--GDEGDSQLGDFIEDSEA 436
Cdd:PRK07500  123 aqkaLFFNLRRLRARLAQAdeeLTKQEIHREIATALGVSLSDVEMMDaRLSGPDASLNAPQseEDEGRSERMDFLVDDSP 202

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1325806947 437 V---IAVDAVSFTLLQDQLGDVLETLSEREAGVVRLRfGLTDGmPRTLDEIGQVYGVTRERIRQIESKTMSKLR 507
Cdd:PRK07500  203 LpdeQVESSIDGERRRRWLTQALQTLNERELRIIRER-RLRED-GATLEALGEELGISKERVRQIEARALEKLR 274
PRK07670 PRK07670
FliA/WhiG family RNA polymerase sigma factor;
311-508 1.27e-26

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 181075 [Multi-domain]  Cd Length: 251  Bit Score: 108.21  E-value: 1.27e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 311 DLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITramaDQARTI-RIPVHMVEVINKLGRIQRELLQDLGREPTPE 389
Cdd:PRK07670   54 DLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAII----DGLRKEdWLPRSMREKTKKVEAAIEKLEQRYMRNVTPK 129

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 390 ELAKEMDITEEKVLEI--QQYAREPISLDQTIGDEGDSQLGDF-IEDSEAVIAVDAVSFTLLQDQLGDVLETLSEREAGV 466
Cdd:PRK07670  130 EVAAELGMTEEEVEATmnEGFFANLLSIDEKTHDQDDGENVSVtIRDDKTPTPEEKLLKEELIEELAEKIKQLSEKEQLV 209

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1325806947 467 VRLRFglTDGMprTLDEIGQVYGVTRERIRQIESKTMSKLRH 508
Cdd:PRK07670  210 ISLFY--KEEL--TLTEIGQVLNLSTSRISQIHSKALFKLKK 247
PRK07122 PRK07122
RNA polymerase sigma factor SigF; Reviewed
 271-507 2.56e-25

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 168831 [Multi-domain]  Cd Length: 264  Bit Score: 104.86  E-value: 2.56e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 271 RDLREISRDGQRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRA 350
Cdd:PRK07122   29 AGLPAGSPEFQRQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRH 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 351 MADQARTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITEEKVLE--IQQYAREPISLDQTIG--DEGDSQ 426
Cdd:PRK07122  109 FRDNSWSVKVPRRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEglVAGSAYNTLSIDSGGGsgDDDARA 188

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 427 LGDFIEDSEAviAVDAVSFtllQDQLGDVLETLSEREAGVVRLRFglTDGMPRTldEIGQVYGVTRERIRQIESKTMSKL 506
Cdd:PRK07122  189 IADTLGDVDA--GLDQIEN---REALRPLLAALPERERTVLVLRF--FESMTQT--QIAERVGISQMHVSRLLAKTLARL 259


                  .
gi 1325806947 507 R 507
Cdd:PRK07122  260 R 260
PRK06288 PRK06288
RNA polymerase sigma factor WhiG; Reviewed
 309-507 1.40e-24

RNA polymerase sigma factor WhiG; Reviewed


Pssm-ID: 235770 [Multi-domain]  Cd Length: 268  Bit Score: 102.84  E-value: 1.40e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 309 FLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAI---TRAMADQARTIRIPVHMVEvinklgRIQRELLQDLGRE 385
Cdd:PRK06288   61 FDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIfdeLRSIDWIPRSVRQKARQIE------RAIAMLEARLGRT 134

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 386 PTPEELAKEMDITEEKVLEIQQYARE--PISLDQTI--GDEGDS-QLGDFIEDSEAVIAVDAVSFTLLQDQLGDVLETLS 460
Cdd:PRK06288  135 PSDEEIADELGISLEEYNSLLSKLSGtsVVSLNDLWfgGDEGDEvSLMDTLESPAALNPDEIAEREEIKRVIVEAIKTLP 214

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1325806947 461 EREAGVVRLRFglTDGMprTLDEIGQVYGVTRERIRQIESKTMSKLR 507
Cdd:PRK06288  215 EREKKVLILYY--YEDL--TLKEIGKVLGVTESRISQLHTKAVLQLR 257
PRK08215 PRK08215
RNA polymerase sporulation sigma factor SigG;
268-471 2.98e-24

RNA polymerase sporulation sigma factor SigG;


Pssm-ID: 181296 [Multi-domain]  Cd Length: 258  Bit Score: 101.95  E-value: 2.98e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 268 AQKRDLREISRDGQR-AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQA 346
Cdd:PRK08215   22 EEMRELFERMQNGDKeAREKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGE 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 347 ITRAMADQaRTIRIPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITEEKVLEIQQYAREPISLDQTI-GDEGDS 425
Cdd:PRK08215  102 IRRYLRDN-NPIRVSRSLRDIAYKALQVREKLINENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIyHDGGDP 180

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1325806947 426 -----QLGDfiEDSEAVIAVDAVSftllqdqLGDVLETLSEREAGVVRLRF 471
Cdd:PRK08215  181 iyvmdQISD--EKNKDENWLEEIA-------LKEAMKKLNDREKLILNLRF 222
PRK05803 PRK05803
RNA polymerase sporulation sigma factor SigK;
283-508 1.77e-23

RNA polymerase sporulation sigma factor SigK;


Pssm-ID: 180266 [Multi-domain]  Cd Length: 233  Bit Score: 98.86  E-value: 1.77e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 283 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYAtwwirqaitramadqARTiripv 362
Cdd:PRK05803   50 ARNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYA---------------ARC----- 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 363 hmvevinklgrIQRELLqdlgreptpeelakeMDITEEKVLEIQQYAREPISLDQtigdEGDS-QLGDFI-EDSEAVIav 440
Cdd:PRK05803  110 -----------IENEIL---------------MHLRNLKKTKKEVSLQDPIGVDK----EGNEiSLIDILgSEEDDVI-- 157

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1325806947 441 DAVSFTLLQDQLGDVLETLSEREAGVVRLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRH 508
Cdd:PRK05803  158 EQVELKMEVEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFK 225
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 287-357 6.41e-22

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: 89.18  E-value: 6.41e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1325806947 287 LLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQART 357
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRRT 71
fliA PRK06986
flagellar biosynthesis sigma factor; Validated
 277-507 3.00e-19

flagellar biosynthesis sigma factor; Validated


Pssm-ID: 235901 [Multi-domain]  Cd Length: 236  Bit Score: 86.83  E-value: 3.00e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 277 SRDGQRAKNHLLEANLRLVVSLAKRYTGR---GMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYAtwwiRQAITRAMAD 353
Cdd:PRK06986    3 TAEGKMDQDELVEQYAPLVKRIALRLKARlpaSVDLDDLIQAGMIGLLEAARRYDGEQGASFETYA----GQRIRGAMLD 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 354 Q-------ARTIRIPVHMVEVinklgrIQRELLQDLGREPTPEELAKEMDITEEKVLEIQQ--YAREPISLDQTIGDEGD 424
Cdd:PRK06986   79 ElrsldwvPRSVRRNAREVAQ------AIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLdtNISQLFSIDELRGEHGD 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 425 SQLGDFIEDSEAVIavDAVSFTLLQDQLGDVLETLSEREAGVVRL--RFGLtdgmprTLDEIGQVYGVTRERIRQIESKT 502
Cdd:PRK06986  153 SILVTEDHQDEDPL--QQLEDEELREALVEAIESLPEREQLVLSLyyQEEL------NLKEIGAVLGVSESRVSQIHSQA 224


                  ....*
gi 1325806947 503 MSKLR 507
Cdd:PRK06986  225 IKRLR 229
PRK05911 PRK05911
RNA polymerase sigma factor sigma-28; Reviewed
 284-507 1.30e-18

RNA polymerase sigma factor sigma-28; Reviewed


Pssm-ID: 235644 [Multi-domain]  Cd Length: 257  Bit Score: 85.44  E-value: 1.30e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 284 KNHLLEANLRLVVSLAKRYTGrGM----AFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQArtiR 359
Cdd:PRK05911   25 RDVLIEFYLPLVKNVAHRLIS-GMpshvKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRKQD---W 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 360 IPVHMVEVINKLGRIQRELLQDLGREPTPEELAKEMDITEEKVLEIQQYAREP--ISLDQTIGDEGDSQLG----DFIED 433
Cdd:PRK05911  101 VPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPAliLSLNEEFPCQSDDEAGlaleERIAD 180

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1325806947 434 SEAVIAVDAVSFTLLQDQLGDVLETLSEREAGVVRLRFglTDGMprTLDEIGQVYGVTRERIRQIESKTMSKLR 507
Cdd:PRK05911  181 ERAETGYDVVDKKEFSSILAEAILALEEKERKVMALYY--YEEL--VLKEIGKILGVSESRVSQIHSKALLKLR 250
PRK08583 PRK08583
RNA polymerase sigma factor SigB; Validated
 294-507 3.85e-16

RNA polymerase sigma factor SigB; Validated


Pssm-ID: 236306 [Multi-domain]  Cd Length: 257  Bit Score: 78.20  E-value: 3.85e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 294 LVVSLAKRYTgRGMAFL-DLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLG 372
Cdd:PRK08583   41 LVESLAYKYS-KGQSHHeDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIK 119

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 373 RIQRELLQDLGREPTPEELAKEMDITEEKVLEIQQYAR--EPISLDQTIgdEGDSqlgdfieDSEAVIAVDAV-----SF 445
Cdd:PRK08583  120 KAVDELTTELQRSPKISEIADRLGVSEEEVLEAMEMGKsyQALSVDHSI--EADS-------DGSTVTLLDIVgqqedGY 190

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1325806947 446 TLLQDQ--LGDVLETLSEREAGVVRLRFglTDGMPRTldEIGQVYGVTRERIRQIESKTMSKLR 507
Cdd:PRK08583  191 ELTEQRmiLEKILPVLSDREKSIIQCTF--IENLSQK--ETGERLGISQMHVSRLQRQAIKKLR 250
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 282-507 2.22e-14

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: 70.84  E-value: 2.22e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 282 RAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKgyKFSTYATWWIRQAITRAMADQARtirip 361
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEG--SFKAWLFRIARNLILDYLRRKRR----- 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 362 vhmvevinkLGRIQRELLQDLGREPTPEELAkemdITEEKVLEIQQyarepisldqtigdegdsqlgdfiedseaviavd 441
Cdd:TIGR02937  74 ---------LRRELDLLEELLDSDPSPEEEL----EQEEEREALRE---------------------------------- 106

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1325806947 442 avsftllqdqlgdVLETLSEREAGVVRLRFGltDGMprTLDEIGQVYGVTRERIRQIESKTMSKLR 507
Cdd:TIGR02937 107 -------------ALEKLPEREREVLVLRYL--EGL--SYKEIAEILGISVGTVKRRLKRARKKLR 155
Sigma70_r1_2 pfam00140
Sigma-70 factor, region 1.2;
218-251 5.47e-12

Sigma-70 factor, region 1.2;


Pssm-ID: 425482 [Multi-domain]  Cd Length: 34  Bit Score: 60.02  E-value: 5.47e-12
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1325806947 218 DSVRAYLKQIGKVALLTAEEEVSLAKRIEAGLYA 251
Cdd:pfam00140   1 DSVRLYLKEIGRIPLLTAEEEVELAKRIEAGDEA 34
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 455-508 6.59e-12

Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. 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: 60.13  E-value: 6.59e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1325806947 455 VLETLSEREAGVVRLRFGltdgMPRTLDEIGQVYGVTRERIRQIESKTMSKLRH 508
Cdd:pfam04545   1 ALASLPPRERQVLVLRYG----EGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
PRK08301 PRK08301
RNA polymerase sporulation sigma factor SigE;
233-507 2.45e-11

RNA polymerase sporulation sigma factor SigE;


Pssm-ID: 236228 [Multi-domain]  Cd Length: 234  Bit Score: 63.72  E-value: 2.45e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 233 LTAEEEVSLAKRIEAGlyaqykiDEAkesgeriayaqkrdlreisrdgqrAKNHLLEANLRLVVSLAKRYTGRGMAFLDL 312
Cdd:PRK08301   34 LSKEEEEYLLNKLPKG-------DEA------------------------VRSLLIERNLRLVVYIARKFENTGINIEDL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 313 IQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTiRIPVHMVEVI------NKLgriqreLLQDLgrep 386
Cdd:PRK08301   83 ISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMYLRRNNKV-KAEVSFDEPLnidwdgNEL------LLSDV---- 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 387 tpeeLAKEMDITeekvleiqqYarepisldQTIGDEGDSQLgdfiedseaviavdavsftllqdqLGDVLETLSEREAGV 466
Cdd:PRK08301  152 ----LGTDNDII---------Y--------KDIEDEVDRKL------------------------LKKALKKLSDREKQI 186

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|.
gi 1325806947 467 VRLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLR 507
Cdd:PRK08301  187 MELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLK 227
PRK12427 PRK12427
FliA/WhiG family RNA polymerase sigma factor;
311-507 2.16e-10

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 183523 [Multi-domain]  Cd Length: 231  Bit Score: 60.65  E-value: 2.16e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 311 DLIQEGNLGLIRAVEKFDYTKGyKFSTYATWWIRQAIT---RAMADQARTIRIPVHmvevinKLGRIQRELLQDLGREPT 387
Cdd:PRK12427   47 DMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILdelRELDWRPRRLRQKTH------KTNDAIREIAKRLGHEPN 119

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 388 PEELAKEMDITEEKVLEIQQY--AREPISLDQTIGDEGDSQLGDFIEDSEAVIavdavsftlLQDQLGDVLETLSEREAG 465
Cdd:PRK12427  120 FEEISAELNLTAEEYQEYLLLenAGTLESLDELLALEAHNDILQSRDLEENII---------IEDNLKQALSQLDEREQL 190

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1325806947 466 VVRLRFgltdGMPRTLDEIGQVYGVTRERIRQIESKTMSKLR 507
Cdd:PRK12427  191 ILHLYY----QHEMSLKEIALVLDLTEARICQLNKKIAQKIK 228
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 449-507 3.76e-09

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: 52.49  E-value: 3.76e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1325806947 449 QDQLGDVLETLSEREAGVVRLRFGltdgMPRTLDEIGQVYGVTRERIRQIESKTMSKLR 507
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFG----EGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
257-405 2.76e-06

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 48.37  E-value: 2.76e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1325806947 257 EAKESGERIAYAQKRDlreisrdgQRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFS 336
Cdd:PRK08295    7 DELEDEELVELARSGD--------KEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFK 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1325806947 337 TYATWWI-RQAITrAMADQARTIRIPVHMVEVINKL------GRIQRELLQDlGREPTPEEL---AKEMDITEEKVLEI 405
Cdd:PRK08295   79 SFAELCItRQIIT-AIKTANRQKHIPLNSYVSLDKPiydeesDRTLLDVISE-AKVTDPEELiisKEELEDIEEKIEEL 155
 
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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