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Conserved domains on  [gi|488973340|ref|WP_002884252|]
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MULTISPECIES: RNA polymerase sigma factor RpoD [Streptococcus]

Protein Classification

RNA polymerase sigma factor RpoD/SigA( domain architecture ID 11483650)

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK09210 PRK09210
RNA polymerase sigma factor RpoD; Validated
 1-368 0e+00

RNA polymerase sigma factor RpoD; Validated


:

Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 703.28  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340   1 MAKKKQNTAFNVQVADFIRNHKKAGTAIDDEVTEKLvIPFVLDADGIDDLLERLTDGGISITDKDGNPSSKYVVEAPKPE 80
Cdd:PRK09210   2 KTKKKETTTLEQVVKELIEKGKKRGTLTYDEIAEKL-IPFELDSDQIDDLYERLEDAGISIVDEEGNPSSAQVVEEEEEE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340  81 ELtDEELLGSNSAKVNDPVRMYLKEIGVVPLLSNEEEKELAIAVENGDLEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160
Cdd:PRK09210  81 EL-DNDLSVPPGVKINDPVRMYLKEIGRVPLLTAEEEIELAKRIEEGDEEAKQRLAEANLRLVVSIAKRYVGRGMLFLDL 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 161 IQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQIA 240
Cdd:PRK09210 160 IQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGREPTPEEIA 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 241 ERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFG 320
Cdd:PRK09210 240 EEMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFG 319

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|....*...
gi 488973340 321 LDDGKMRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSKQLKDFIE 368
Cdd:PRK09210 320 LDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 367
 
Name Accession Description Interval E-value
PRK09210 PRK09210
RNA polymerase sigma factor RpoD; Validated
 1-368 0e+00

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 703.28  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340   1 MAKKKQNTAFNVQVADFIRNHKKAGTAIDDEVTEKLvIPFVLDADGIDDLLERLTDGGISITDKDGNPSSKYVVEAPKPE 80
Cdd:PRK09210   2 KTKKKETTTLEQVVKELIEKGKKRGTLTYDEIAEKL-IPFELDSDQIDDLYERLEDAGISIVDEEGNPSSAQVVEEEEEE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340  81 ELtDEELLGSNSAKVNDPVRMYLKEIGVVPLLSNEEEKELAIAVENGDLEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160
Cdd:PRK09210  81 EL-DNDLSVPPGVKINDPVRMYLKEIGRVPLLTAEEEIELAKRIEEGDEEAKQRLAEANLRLVVSIAKRYVGRGMLFLDL 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 161 IQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQIA 240
Cdd:PRK09210 160 IQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGREPTPEEIA 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 241 ERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFG 320
Cdd:PRK09210 240 EEMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFG 319

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|....*...
gi 488973340 321 LDDGKMRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSKQLKDFIE 368
Cdd:PRK09210 320 LDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 367
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 101-368 4.70e-173

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: 482.25  E-value: 4.70e-173
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 101 MYLKEIGVVPLLSNEEEKELAIAVENGDLEAKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKG 180
Cdd:COG0568    1 AYLREIGRVPLLTAEEEVELARRIQAGDEEAKRKLVEANLRLVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDPERG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 181 FKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEP 260
Cdd:COG0568   81 FRFSTYATWWIRQAITRAIADQWRTIRLPVHMAETLNKLRRAKRQLLQELGREPTPEEIAEELGVPEEKVREMLRLAREP 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 261 VSLETPIGEEDDSHLGDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKVFNVTR 340
Cdd:COG0568  161 VSLDAPVGDDEDSELGDLLEDEEAPSPEEALEEELLREELREALDTLTEREREILRLRFGLDDGEPHTLEEIGKEFGVSR 240

                        250       260
                 ....*....|....*....|....*...
gi 488973340 341 ERIRQIEAKALRKLRHPSRSKQLKDFIE 368
Cdd:COG0568  241 ERVRQIEAKALRKLRHPLRSRKLRDYLD 268
RpoD_Cterm TIGR02393
RNA polymerase sigma factor RpoD, C-terminal domain; This model represents the well-conserved ...
 131-368 2.87e-170

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: 474.09  E-value: 2.87e-170
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340  131 AKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPV 210
Cdd:TIGR02393   1 AKKKLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340  211 HMVETINKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDY 290
Cdd:TIGR02393  81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDESIESPDDA 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488973340  291 TTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSKQLKDFIE 368
Cdd:TIGR02393 161 AAKELLREQLDEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLKDFLD 238
Sigma70_r3 pfam04539
Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the ...
 214-291 5.55e-31

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: 112.70  E-value: 5.55e-31
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488973340  214 ETINKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYT 291
Cdd:pfam04539   1 ELLNKIKRAQRELEQELGREPTPEEIAEELGLSPEKVREVLEAAREPVSLDTPVGEEEDGELGDLLEDDDIESPEEAV 78
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 297-355 5.77e-13

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: 62.89  E-value: 5.77e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 488973340 297 REQLDEVLDTLTDREENVLRLRFGLDdgkmRTLEDVGKVFNVTRERIRQIEAKALRKLR 355
Cdd:cd06171    1 RERLEEALDKLPEREREVILLRFGEG----LSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
PRK09210 PRK09210
RNA polymerase sigma factor RpoD; Validated
 1-368 0e+00

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 703.28  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340   1 MAKKKQNTAFNVQVADFIRNHKKAGTAIDDEVTEKLvIPFVLDADGIDDLLERLTDGGISITDKDGNPSSKYVVEAPKPE 80
Cdd:PRK09210   2 KTKKKETTTLEQVVKELIEKGKKRGTLTYDEIAEKL-IPFELDSDQIDDLYERLEDAGISIVDEEGNPSSAQVVEEEEEE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340  81 ELtDEELLGSNSAKVNDPVRMYLKEIGVVPLLSNEEEKELAIAVENGDLEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160
Cdd:PRK09210  81 EL-DNDLSVPPGVKINDPVRMYLKEIGRVPLLTAEEEIELAKRIEEGDEEAKQRLAEANLRLVVSIAKRYVGRGMLFLDL 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 161 IQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQIA 240
Cdd:PRK09210 160 IQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGREPTPEEIA 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 241 ERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFG 320
Cdd:PRK09210 240 EEMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFG 319

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|....*...
gi 488973340 321 LDDGKMRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSKQLKDFIE 368
Cdd:PRK09210 320 LDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 367
PRK05901 PRK05901
RNA polymerase sigma factor; Provisional
 1-368 9.80e-177

RNA polymerase sigma factor; Provisional


Pssm-ID: 235640 [Multi-domain]  Cd Length: 509  Bit Score: 501.06  E-value: 9.80e-177
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340   1 MAKKKQNTAFNVQVADFIRNHKKAGTAIDD--EVTEKLVIPFVLDADGIDDLLERLTDGGISITDKDGNPSSKYVVEAPK 78
Cdd:PRK05901  87 AAKAPAKKKLKDELDSSKKAEKKNALDKDDdlNYVKDIDVLNQADDDDDDDDDDDLDDDDIDDDDDDEDDDEDDDDDDVD 166

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340  79 PEELTDEELLGSNSAK--------------------------VNDPVRMYLKEIGVVPLLSNEEEKELAIAVENG----- 127
Cdd:PRK05901 167 DEDEEKKEAKELEKLSddddfvwdeddsealrqarkdakltaTADPVKAYLKQIGKVKLLNAEEEVELAKRIEAGlyaee 246

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 128 --------------DLE--------AKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFKFST 185
Cdd:PRK05901 247 llaegekldpelrrDLQwigrdgkrAKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFST 326

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 186 YATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLET 265
Cdd:PRK05901 327 YATWWIRQAITRAMADQARTIRIPVHMVETINKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDK 406

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 266 PIGEEDDSHLGDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKVFNVTRERIRQ 345
Cdd:PRK05901 407 TIGKEGDSQFGDFIEDSEAVSPVDAVSFTLLQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQ 486

                        410       420
                 ....*....|....*....|...
gi 488973340 346 IEAKALRKLRHPSRSKQLKDFIE 368
Cdd:PRK05901 487 IESKTLRKLRHPSRSQVLRDFLD 509
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 101-368 4.70e-173

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: 482.25  E-value: 4.70e-173
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 101 MYLKEIGVVPLLSNEEEKELAIAVENGDLEAKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKG 180
Cdd:COG0568    1 AYLREIGRVPLLTAEEEVELARRIQAGDEEAKRKLVEANLRLVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDPERG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 181 FKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEP 260
Cdd:COG0568   81 FRFSTYATWWIRQAITRAIADQWRTIRLPVHMAETLNKLRRAKRQLLQELGREPTPEEIAEELGVPEEKVREMLRLAREP 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 261 VSLETPIGEEDDSHLGDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKVFNVTR 340
Cdd:COG0568  161 VSLDAPVGDDEDSELGDLLEDEEAPSPEEALEEELLREELREALDTLTEREREILRLRFGLDDGEPHTLEEIGKEFGVSR 240

                        250       260
                 ....*....|....*....|....*...
gi 488973340 341 ERIRQIEAKALRKLRHPSRSKQLKDFIE 368
Cdd:COG0568  241 ERVRQIEAKALRKLRHPLRSRKLRDYLD 268
RpoD_Cterm TIGR02393
RNA polymerase sigma factor RpoD, C-terminal domain; This model represents the well-conserved ...
 131-368 2.87e-170

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: 474.09  E-value: 2.87e-170
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340  131 AKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPV 210
Cdd:TIGR02393   1 AKKKLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340  211 HMVETINKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDY 290
Cdd:TIGR02393  81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDESIESPDDA 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488973340  291 TTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSKQLKDFIE 368
Cdd:TIGR02393 161 AAKELLREQLDEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLKDFLD 238
PRK05658 PRK05658
RNA polymerase sigma factor RpoD; Validated
 130-369 1.98e-167

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 235549 [Multi-domain]  Cd Length: 619  Bit Score: 481.22  E-value: 1.98e-167
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 130 EAKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIP 209
Cdd:PRK05658 380 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 459

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 210 VHMVETINKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVD 289
Cdd:PRK05658 460 VHMIETINKLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDDEDSHLGDFIEDKNAELPID 539

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 290 YTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSKQLKDFIED 369
Cdd:PRK05658 540 AAIQESLREATTDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSRKLRSFLDN 619
PRK07406 PRK07406
RNA polymerase sigma factor RpoD; Validated
 97-368 6.63e-134

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236012 [Multi-domain]  Cd Length: 373  Bit Score: 387.22  E-value: 6.63e-134
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340  97 DPVRMYLKEIGVVPLLSNEEEKELA--IA-------------VENGDL-------------------------EAKQRLA 136
Cdd:PRK07406  63 DSIRVYLQEIGRIRLLRPDEEIELArkIAdlleleelreqfeSELGREpsdkewaelvdmplpkfrrrlmlgrRAKEKMV 142

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 137 EANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETI 216
Cdd:PRK07406 143 QSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETI 222

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 217 NKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEvIENPVDYTTRVVL 296
Cdd:PRK07406 223 SRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEAD-GETPEDDVAKNLL 301

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 488973340 297 REQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSKQLKDFIE 368
Cdd:PRK07406 302 REDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVLKEYIR 373
Sig70-cyanoRpoD TIGR02997
RNA polymerase sigma factor, cyanobacterial RpoD-like family; This family includes a number of ...
 97-355 1.21e-126

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: 365.80  E-value: 1.21e-126
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340   97 DPVRMYLKEIGVVPLLSNEEE------------------------------KELAIAVENGDLE----------AKQRLA 136
Cdd:TIGR02997   1 DLVRLYLQEIGRVPLLTPEEEielarqvqqmmvleelreeleeqlgrepskEEWAAAAGLSEAElrqrlrqgqrAKEKMI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340  137 EANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETI 216
Cdd:TIGR02997  81 KANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340  217 NKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEViENPVDYTTRVVL 296
Cdd:TIGR02997 161 NKIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLEDDG-ESPEEQVERESL 239

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 488973340  297 REQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKVFNVTRERIRQIEAKALRKLR 355
Cdd:TIGR02997 240 RQDLESLLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR 298
PRK07921 PRK07921
RNA polymerase sigma factor SigB; Reviewed
 97-366 2.96e-121

RNA polymerase sigma factor SigB; Reviewed


Pssm-ID: 181169 [Multi-domain]  Cd Length: 324  Bit Score: 353.27  E-value: 2.96e-121
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340  97 DPVRMYLKEIGVVPLLSNEEEKELAIAVENG-------------------DLE--------AKQRLAEANLRLVVSIAKR 149
Cdd:PRK07921  26 DLVRVYLNGIGKTALLTAADEVELAKRIEAGlyaehlletrkrlsearkrDLAavvrdgeaARRHLLEANLRLVVSLAKR 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 150 YVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQE 229
Cdd:PRK07921 106 YTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKRELHQQ 185

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 230 LGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTD 309
Cdd:PRK07921 186 LGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEATSAENAVIAGLLHTDIRSVLATLDE 265

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 488973340 310 REENVLRLRFGLDDGKMRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSKQLKDF 366
Cdd:PRK07921 266 REQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGERADRLRSY 322
rpoS_proteo TIGR02394
RNA polymerase sigma factor RpoS; A sigma factor is a DNA-binding protein protein that binds ...
 85-356 4.73e-104

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: 307.81  E-value: 4.73e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340   85 EELLGSNSAKVNDPVRMYLKEIGVVPLLSNEEEKELAIAVENGDLEAKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEG 164
Cdd:TIGR02394   1 EFKKAETETRVADVTQLYLREIGFKPLLTAEEEIAYARRALAGDFEARKVMIESNLRLVVSIAKHYVNRGLPLLDLIEEG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340  165 NMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQIAERMD 244
Cdd:TIGR02394  81 NLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPVHVIKELNVYLRAARQLEKKLGREPSVEEIAELLD 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340  245 MTPDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDG 324
Cdd:TIGR02394 161 KPVEDVSRVLALNERITSLDAPLDDDSSKSLLDTIADEQSIDPESLVQNDDLKQLIEAWLAELNERQREVLARRFGLLGY 240

                         250       260       270
                  ....*....|....*....|....*....|..
gi 488973340  325 KMRTLEDVGKVFNVTRERIRQIEAKALRKLRH 356
Cdd:TIGR02394 241 EPATLEEVAAEVGLTRERVRQIQVEALKKLRR 272
PRK05657 PRK05657
RNA polymerase sigma factor RpoS; Validated
 75-355 5.58e-96

RNA polymerase sigma factor RpoS; Validated


Pssm-ID: 235548 [Multi-domain]  Cd Length: 325  Bit Score: 288.78  E-value: 5.58e-96
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340  75 EAPKPEELTDEELLGSNSAKVNDPVRMYLKEIGVVPLLSNEEEKELAIAVENGDLEAKQRLAEANLRLVVSIAKRYVGRG 154
Cdd:PRK05657  31 EPSDNDLAEEELLSQGATQRVLDATQLYLNEIGYSPLLTAEEEVYFARRALRGDFAARQRMIESNLRLVVKIAKRYLNRG 110

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 155 MQFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDP 234
Cdd:PRK05657 111 LALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPVHVVKELNVYLRAARELEHKLDHEP 190

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 235 TPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENV 314
Cdd:PRK05657 191 SAEEIAELLDKPVDDVSRMLALNERITSLDTPLGGDPEKSLLDILADEQENGPEDTTQDDDMKQSIVKWLFELNDKQREV 270

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|.
gi 488973340 315 LRLRFGLDDGKMRTLEDVGKVFNVTRERIRQIEAKALRKLR 355
Cdd:PRK05657 271 LARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLR 311
PRK05949 PRK05949
RNA polymerase sigma factor; Validated
 97-367 9.23e-94

RNA polymerase sigma factor; Validated


Pssm-ID: 180321 [Multi-domain]  Cd Length: 327  Bit Score: 283.27  E-value: 9.23e-94
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340  97 DPVRMYLKEIGVVPLLSNEEE-----------------------------------------KELAIAVENGDlEAKQRL 135
Cdd:PRK05949  18 DMVRTYLHEIGRVPLLTHEQEivygkqvqqmmslleakealakklgrepslpewaeavnlseTELKQTLKQGK-RAKQKM 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 136 AEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215
Cdd:PRK05949  97 IEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEK 176

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIeNPVDYTTRVV 295
Cdd:PRK05949 177 LNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTELSELLEDEGP-SPDQYITQEL 255

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 488973340 296 LREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKVFNVTRERIRQIEAKALRKLRHpsRSKQLKDFI 367
Cdd:PRK05949 256 LRQDLNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRR--RRANVKEYL 325
PRK07598 PRK07598
RNA polymerase sigma factor SigC; Validated
 112-368 4.44e-92

RNA polymerase sigma factor SigC; Validated


Pssm-ID: 236067 [Multi-domain]  Cd Length: 415  Bit Score: 281.76  E-value: 4.44e-92
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 112 LSNEEEKElaiaVENGDLEAKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWI 191
Cdd:PRK07598 161 LTVEELEQ----IQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWI 236

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 192 RQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEED 271
Cdd:PRK07598 237 RQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLLRVPRSVSLETKVGKDK 316

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 272 DSHLGDFIEDEVIeNPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKVFNVTRERIRQIEAKAL 351
Cdd:PRK07598 317 DTELGDLLETDDI-SPEEMLMRESLQRDLQHLLADLTSRERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKAL 395

                        250
                 ....*....|....*..
gi 488973340 352 RKLRHPSRSKQLKDFIE 368
Cdd:PRK07598 396 QKLRQPKRRNRIRDYLE 412
PRK07405 PRK07405
RNA polymerase sigma factor SigD; Validated
 97-355 4.51e-90

RNA polymerase sigma factor SigD; Validated


Pssm-ID: 180963 [Multi-domain]  Cd Length: 317  Bit Score: 273.56  E-value: 4.51e-90
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340  97 DPVRMYLKEIGVVPLLSNEEE-----------------------------------------KELAIAVENGDLeAKQRL 135
Cdd:PRK07405   8 DLVRTYLREIGRVPLLTHEEEilygkqvqrlvalqeireelaeelgreptdaewakaaklseEELRSAIAEGEA-AKRKM 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 136 AEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 215
Cdd:PRK07405  87 VEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEK 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 216 INKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEViENPVDYTTRVV 295
Cdd:PRK07405 167 LNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDTG-ASPEDFATQSS 245

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 296 LREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKVFNVTRERIRQIEAKALRKLR 355
Cdd:PRK07405 246 LQLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLR 305
PRK06596 PRK06596
RNA polymerase factor sigma-32; Reviewed
 102-355 7.28e-56

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 235838 [Multi-domain]  Cd Length: 284  Bit Score: 184.22  E-value: 7.28e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 102 YLKEIGVVPLLSNEEEKELAIA-VENGDLEAKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKG 180
Cdd:PRK06596  19 YIQAVNKIPMLTAEEEYMLAKRlREHGDLEAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVG 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 181 FKFSTYATWWIRQAITRAIadqARTIRIpVHMVETIN--KL---VREQRNLLQELGQDPTpEQIAERMDMTPDKVREI-L 254
Cdd:PRK06596  99 VRLVSFAVHWIKAEIHEYI---LRNWRI-VKVATTKAqrKLffnLRKAKKRLGWLNPEEV-EMVAEELGVSEEEVREMeS 173

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 255 KIAQEPVSLETPIGEEDDSH--LGDFIEDE------VIENPVDYTTRvvlREQLDEVLDTLTDREENVLRLRFgLDDGKM 326
Cdd:PRK06596 174 RLSGQDASLDAPIDDDDEESgaPQDYLEDKssdpadVLEEDNWEDQR---RALLADALEGLDERSRDIIEARW-LDDDKS 249

                        250       260
                 ....*....|....*....|....*....
gi 488973340 327 rTLEDVGKVFNVTRERIRQIEAKALRKLR 355
Cdd:PRK06596 250 -TLQELAAEYGVSAERVRQIEKNAMKKLK 277
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 116-355 2.21e-51

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: 171.16  E-value: 2.21e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 116 EEKELAIAVENGDLEAKQRLAEANLRLVVSIAKRYVGRGMQFL-DLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQA 194
Cdd:COG1191    1 DLEELLRRYQEGDEEAREELIEEYLPLVKKIASRLAGRLPAELdDLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRGA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 195 ITRAIADQArtiRIPVHMVETINKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQ--EPVSLETPIGEEDD 272
Cdd:COG1191   81 ILDYLRDED---WVPRSVRELARKIEEAIEELEQELGREPTDEEIAEELGISLEEVQEALEAANayQLLSLDEPLEDGDD 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 273 shLGDFIEDeviENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDdgkmRTLEDVGKVFNVTRERIRQIEAKALR 352
Cdd:COG1191  158 --LLDLLES---GDPEEELEHEELREALAEAIEQLPERERLVLSLYYFEE----LTLKEIAEVLGVSESRVSRLHKKALA 228


                 ...
gi 488973340 353 KLR 355
Cdd:COG1191  229 RLR 231
rpoH_proteo TIGR02392
alternative sigma factor RpoH; A sigma factor is a DNA-binding protein protein that binds to ...
 102-355 5.08e-49

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: 166.30  E-value: 5.08e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340  102 YLKEIGVVPLLSNEEEKELAIAV-ENGDLEAKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKG 180
Cdd:TIGR02392   6 YIRAVNRIPMLTPEEEYQLAKRLrEHGDLDAAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERG 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340  181 FKFSTYATWWIRQAITRAIadqARTIRIpVHMVETIN--KLVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREI-L 254
Cdd:TIGR02392  86 VRLVSFAVHWIKAEIHEYI---LRNWRL-VKVATTKAqrKLFFNLRKMKKRLQGWLNPEEveaIAEELGVSEREVREMeS 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340  255 KIAQEPVSLETPIGEEDDS------HLGDFIED--EVIENPVDYTTRvvlREQLDEVLDTLTDREENVLRLRFgLDDGKM 326
Cdd:TIGR02392 162 RLSGQDMSLNASIDDDEDDggapiaYLVDKRSDpeDTLEEEQWEELQ---RQALANALGSLDARSRRIIEARW-LDDDKL 237

                         250       260
                  ....*....|....*....|....*....
gi 488973340  327 rTLEDVGKVFNVTRERIRQIEAKALRKLR 355
Cdd:TIGR02392 238 -TLQELAAEYGVSAERIRQIEKNAMKKLK 265
rpoH2 PRK07500
RNA polymerase factor sigma-32; Reviewed
 110-355 1.12e-38

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 236033 [Multi-domain]  Cd Length: 289  Bit Score: 139.40  E-value: 1.12e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 110 PLLSNEEEKELAIAVENG-DLEAKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYAT 188
Cdd:PRK07500  19 PYLEREEEHALAYRWKDHrDEDALHRIISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYAT 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 189 WWIRQAITRAI-------------ADQA-----RtiRIPVHMVETINKLVREQ--RNLLQELGqdpTPEQIAERMDMtpd 248
Cdd:PRK07500  99 WWIRASIQDYIlrnwsivrggtssAQKAlffnlR--RLRARLAQADEELTKQEihREIATALG---VSLSDVEMMDA--- 170

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 249 kvreilKIAQEPVSLETPIGEEDDSHLG--DFIE------DEVIENPVDYTTRvvlREQLDEVLDTLTDREENVLRLRFG 320
Cdd:PRK07500 171 ------RLSGPDASLNAPQSEEDEGRSErmDFLVddsplpDEQVESSIDGERR---RRWLTQALQTLNERELRIIRERRL 241

                        250       260       270
                 ....*....|....*....|....*....|....*
gi 488973340 321 LDDGkmRTLEDVGKVFNVTRERIRQIEAKALRKLR 355
Cdd:PRK07500 242 REDG--ATLEALGEELGISKERVRQIEARALEKLR 274
PRK08215 PRK08215
RNA polymerase sporulation sigma factor SigG;
110-355 1.88e-36

RNA polymerase sporulation sigma factor SigG;


Pssm-ID: 181296 [Multi-domain]  Cd Length: 258  Bit Score: 132.76  E-value: 1.88e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 110 PLLSNEEEKELAIAVENGDLEAKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATW 189
Cdd:PRK08215  17 PVLKNEEMRELFERMQNGDKEAREKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVP 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 190 WIRQAITRAIADQaRTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGE 269
Cdd:PRK08215  97 MIIGEIRRYLRDN-NPIRVSRSLRDIAYKALQVREKLINENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIYH 175

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 270 E--DDSHLGDFIEDE--VIENPVDYTTrvvlreqLDEVLDTLTDREENVLRLRFGldDGKmrTLEDVGKVFNVTRERIRQ 345
Cdd:PRK08215 176 DggDPIYVMDQISDEknKDENWLEEIA-------LKEAMKKLNDREKLILNLRFF--QGK--TQMEVAEEIGISQAQVSR 244

                        250
                 ....*....|
gi 488973340 346 IEAKALRKLR 355
Cdd:PRK08215 245 LEKAALKHMR 254
FliA_WhiG TIGR02479
RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar ...
 142-355 1.95e-35

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: 128.93  E-value: 1.95e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340  142 LVVSIAKRYVGR---GMQFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAI---TRAIADQARTIRIPVHMVEt 215
Cdd:TIGR02479   8 LVKRIAGRLSVGlpsSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMldeLRRLDWVPRSLRQKARKLE- 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340  216 inklvREQRNLLQELGQDPTPEQIAERMDMTPDKVREILK--IAQEPVSLETPIGEEDDS-HLGDFIEDEVIENPVDYTT 292
Cdd:TIGR02479  87 -----RAIRELEARLGREPTEEEIAEELGMDLKEYRQALNeiNALSLVSLDELLESGDDGgSLIDRIEDDKSEDPEEELE 161

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488973340  293 RVVLREQLDEVLDTLTDREENVLRLRF--GLddgkmrTLEDVGKVFNVTRERIRQIEAKALRKLR 355
Cdd:TIGR02479 162 REELREALAEAIESLSEREQLVLSLYYyeEL------NLKEIGEVLGLTESRVSQIHSQALKKLR 220
spore_sigF TIGR02885
RNA polymerase sigma-F factor; Members of this protein family are the RNA polymerase sigma ...
 124-355 2.29e-34

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: 126.37  E-value: 2.29e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340  124 VENGDLEAKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQA 203
Cdd:TIGR02885   5 AQNGDKEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFLRDDG 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340  204 rTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDS--HLGDFIED 281
Cdd:TIGR02885  85 -IIKVSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLYDTVHQDDGDpiYLLDQIAD 163

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488973340  282 EVIENpVDYTTRVVLReqldEVLDTLTDREENVLRLRFGLDdgkmRTLEDVGKVFNVTRERIRQIEAKALRKLR 355
Cdd:TIGR02885 164 KGSED-SDWLEKIALK----EAISKLDERERQIIMLRYFKD----KTQTEVANMLGISQVQVSRLEKKVLKKMK 228
PRK05572 PRK05572
RNA polymerase sporulation sigma factor, SigF/SigG family;
112-355 6.19e-34

RNA polymerase sporulation sigma factor, SigF/SigG family;


Pssm-ID: 180137 [Multi-domain]  Cd Length: 252  Bit Score: 125.85  E-value: 6.19e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 112 LSNEEEKELAIAVENGDLEAKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWI 191
Cdd:PRK05572  14 LKDEENKELIKKSQDGDQEARDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMI 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 192 RQAITRAIADQArTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEED 271
Cdd:PRK05572  94 IGEIQRFLRDDG-TVKVSRSLKETANKIRKDKDELSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVHEND 172

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 272 DS--HLGDFIEDEVIENPVDyttRVVLREQLDEvldtLTDREENVLRLRFGLDdgkmRTLEDVGKVFNVTRERIRQIEAK 349
Cdd:PRK05572 173 GDpiTLLDQIADQSEEDWFD---KIALKEAIRE----LDERERLIVYLRYFKD----KTQSEVAKRLGISQVQVSRLEKK 241


                 ....*.
gi 488973340 350 ALRKLR 355
Cdd:PRK05572 242 ILKQMK 247
PRK05803 PRK05803
RNA polymerase sporulation sigma factor SigK;
112-356 1.44e-31

RNA polymerase sporulation sigma factor SigK;


Pssm-ID: 180266 [Multi-domain]  Cd Length: 233  Bit Score: 119.28  E-value: 1.44e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 112 LSNEEEKELAIAVENGDLEAKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYAtwwi 191
Cdd:PRK05803  31 LSEEEERKYLELMKEGDEEARNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYA---- 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 192 rqaitraiadqARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQIaERMDmtpdkvreILKIAQEPVsletpigeed 271
Cdd:PRK05803 107 -----------ARCIENEILMHLRNLKKTKKEVSLQDPIGVDKEGNEI-SLID--------ILGSEEDDV---------- 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 272 dshlgdfieDEVIENPVDyttrvvlREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKVFNVTRERIRQIEAKAL 351
Cdd:PRK05803 157 ---------IEQVELKME-------VEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRAL 220


                 ....*
gi 488973340 352 RKLRH 356
Cdd:PRK05803 221 KKLFK 225
Sigma70_r3 pfam04539
Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the ...
 214-291 5.55e-31

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: 112.70  E-value: 5.55e-31
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488973340  214 ETINKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYT 291
Cdd:pfam04539   1 ELLNKIKRAQRELEQELGREPTPEEIAEELGLSPEKVREVLEAAREPVSLDTPVGEEEDGELGDLLEDDDIESPEEAV 78
PRK06288 PRK06288
RNA polymerase sigma factor WhiG; Reviewed
 104-355 2.82e-27

RNA polymerase sigma factor WhiG; Reviewed


Pssm-ID: 235770 [Multi-domain]  Cd Length: 268  Bit Score: 108.62  E-value: 2.82e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 104 KEIGVVPLLSNEEEKELAIA-VENGDLEAKQRLAEANLRLVVSIAKRyVGRGM----QFLDLIQEGNMGLMKAVDKFDYS 178
Cdd:PRK06288   4 KMSGKIPKYAQQDETELWREyKKTGDPKIREYLILKYSPLVKYVAGR-IAVGMpqnvEFDDLVSYGVFGLIDAIEKFDPE 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 179 KGFKFSTYATWWIRQAI----------TRAIADQARTIRIPVHMVETinklvreqrnllqELGQDPTPEQIAERMDMTPD 248
Cdd:PRK06288  83 REIKFKTYAVTRIRGAIfdelrsidwiPRSVRQKARQIERAIAMLEA-------------RLGRTPSDEEIADELGISLE 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 249 KVREILK--IAQEPVSLET--PIGEEDDS-HLGDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRF--GL 321
Cdd:PRK06288 150 EYNSLLSklSGTSVVSLNDlwFGGDEGDEvSLMDTLESPAALNPDEIAEREEIKRVIVEAIKTLPEREKKVLILYYyeDL 229

                        250       260       270
                 ....*....|....*....|....*....|....
gi 488973340 322 ddgkmrTLEDVGKVFNVTRERIRQIEAKALRKLR 355
Cdd:PRK06288 230 ------TLKEIGKVLGVTESRISQLHTKAVLQLR 257
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 135-205 4.23e-25

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: 96.50  E-value: 4.23e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488973340  135 LAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQART 205
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRRT 71
PRK07122 PRK07122
RNA polymerase sigma factor SigF; Reviewed
 118-355 4.11e-23

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 168831 [Multi-domain]  Cd Length: 264  Bit Score: 97.15  E-value: 4.11e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 118 KELAIAVENGDLEAKQR--LAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAI 195
Cdd:PRK07122  26 RELAGLPAGSPEFQRQRdrIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEV 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 196 TRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKI--AQEPVSLETPIG--EED 271
Cdd:PRK07122 106 RRHFRDNSWSVKVPRRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAgsAYNTLSIDSGGGsgDDD 185

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 272 DSHLGDFIED-----EVIENpvdyttrvvlREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGkvfnVTRERIRQI 346
Cdd:PRK07122 186 ARAIADTLGDvdaglDQIEN----------REALRPLLAALPERERTVLVLRFFESMTQTQIAERVG----ISQMHVSRL 251


                 ....*....
gi 488973340 347 EAKALRKLR 355
Cdd:PRK07122 252 LAKTLARLR 260
PRK07670 PRK07670
FliA/WhiG family RNA polymerase sigma factor;
159-356 7.58e-23

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 181075 [Multi-domain]  Cd Length: 251  Bit Score: 95.88  E-value: 7.58e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 159 DLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITraiaDQARTI-RIPVHMVETINKLVREQRNLLQELGQDPTPE 237
Cdd:PRK07670  54 DLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAII----DGLRKEdWLPRSMREKTKKVEAAIEKLEQRYMRNVTPK 129

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 238 QIAERMDMTPDKVREILK--IAQEPVSL-ETPIGEEDDSHLGDFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENV 314
Cdd:PRK07670 130 EVAAELGMTEEEVEATMNegFFANLLSIdEKTHDQDDGENVSVTIRDDKTPTPEEKLLKEELIEELAEKIKQLSEKEQLV 209

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 488973340 315 LRLrFGLDDgkmRTLEDVGKVFNVTRERIRQIEAKALRKLRH 356
Cdd:PRK07670 210 ISL-FYKEE---LTLTEIGQVLNLSTSRISQIHSKALFKLKK 247
PRK07408 PRK07408
RNA polymerase sigma factor SigF; Reviewed
 125-281 3.90e-22

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 180965 [Multi-domain]  Cd Length: 256  Bit Score: 94.22  E-value: 3.90e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 125 ENGDLEAKQRLAEANLRLVVSIAKRYVGRGMQ-FLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQA 203
Cdd:PRK07408  20 QNPSIALRNQLVELNLGLVRKEAHRWSNQCSEpYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKS 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 204 RTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREIlKIAQ---EPVSLETPIGEEDDSH--LGDF 278
Cdd:PRK07408 100 PTVRIPRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEI-KLALqnrTPLSLDAPVNQDEDGStsLGDL 178


                 ...
gi 488973340 279 IED 281
Cdd:PRK07408 179 LPD 181
fliA PRK06986
flagellar biosynthesis sigma factor; Validated
 131-355 3.60e-21

flagellar biosynthesis sigma factor; Validated


Pssm-ID: 235901 [Multi-domain]  Cd Length: 236  Bit Score: 91.06  E-value: 3.60e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 131 AKQRLAEANLRLVVSIAKRYVGR---GMQFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAI--ADQA-R 204
Cdd:PRK06986   9 DQDELVEQYAPLVKRIALRLKARlpaSVDLDDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDELrsLDWVpR 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 205 TIRIPVHMVETinklvrEQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQ--EPVSLETPIGEEDDSHLGDFIEDE 282
Cdd:PRK06986  89 SVRRNAREVAQ------AIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNisQLFSIDELRGEHGDSILVTEDHQD 162

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488973340 283 viENPVDYTTRVVLREQLDEVLDTLTDREENVLRL--RFGLDdgkmrtLEDVGKVFNVTRERIRQIEAKALRKLR 355
Cdd:PRK06986 163 --EDPLQQLEDEELREALVEAIESLPEREQLVLSLyyQEELN------LKEIGAVLGVSESRVSQIHSQAIKRLR 229
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 130-355 1.36e-20

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: 87.40  E-value: 1.36e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340  130 EAKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKgfKFSTYATWWIRQAITRAIADQARtirip 209
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEG--SFKAWLFRIARNLILDYLRRKRR----- 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340  210 vhmvetinkLVREQRNLLQELGQDPTPEQIAERMDmtpdkvreilkiaqepvsletpigeeddshlgdfiedevienpvd 289
Cdd:TIGR02937  74 ---------LRRELDLLEELLDSDPSPEEELEQEE--------------------------------------------- 99

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 488973340  290 yttrvvLREQLDEVLDTLTDREENVLRLRFGLDdgkmRTLEDVGKVFNVTRERIRQIEAKALRKLR 355
Cdd:TIGR02937 100 ------EREALREALEKLPEREREVLVLRYLEG----LSYKEIAEILGISVGTVKRRLKRARKKLR 155
PRK08301 PRK08301
RNA polymerase sporulation sigma factor SigE;
110-355 3.95e-18

RNA polymerase sporulation sigma factor SigE;


Pssm-ID: 236228 [Multi-domain]  Cd Length: 234  Bit Score: 82.60  E-value: 3.95e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 110 PLLSNEEEKELAIAVENGDLEAKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATW 189
Cdd:PRK08301  32 PPLSKEEEEYLLNKLPKGDEAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASR 111

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 190 WIRQAItraiadqartiripvhmvetinkLVREQRNllqelgqdptpeqiaermdmtpdkvreiLKIAQEpVSLETPIGE 269
Cdd:PRK08301 112 CIENEI-----------------------LMYLRRN----------------------------NKVKAE-VSFDEPLNI 139

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 270 EDDSH---LGDFI---EDEV---IENPVDyttrvvlREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKVFNVTR 340
Cdd:PRK08301 140 DWDGNellLSDVLgtdNDIIykdIEDEVD-------RKLLKKALKKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQ 212

                        250
                 ....*....|....*
gi 488973340 341 ERIRQIEAKALRKLR 355
Cdd:PRK08301 213 SYISRLEKRIIKRLK 227
PRK05911 PRK05911
RNA polymerase sigma factor sigma-28; Reviewed
 125-355 2.94e-17

RNA polymerase sigma factor sigma-28; Reviewed


Pssm-ID: 235644 [Multi-domain]  Cd Length: 257  Bit Score: 80.43  E-value: 2.94e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 125 ENGDLEAKQRLAEANLRLVVSIAKRYVGrGM----QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAItraIA 200
Cdd:PRK05911  18 STQEIEYRDVLIEFYLPLVKNVAHRLIS-GMpshvKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAI---ID 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 201 DQARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEP--VSLETPIGEEDDSHLG-- 276
Cdd:PRK05911  94 DLRKQDWVPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPAliLSLNEEFPCQSDDEAGla 173

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 277 --DFIEDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDdgkmRTLEDVGKVFNVTRERIRQIEAKALRKL 354
Cdd:PRK05911 174 leERIADERAETGYDVVDKKEFSSILAEAILALEEKERKVMALYYYEE----LVLKEIGKILGVSESRVSQIHSKALLKL 249


                 .
gi 488973340 355 R 355
Cdd:PRK05911 250 R 250
PRK08583 PRK08583
RNA polymerase sigma factor SigB; Validated
 125-355 9.00e-16

RNA polymerase sigma factor SigB; Validated


Pssm-ID: 236306 [Multi-domain]  Cd Length: 257  Bit Score: 76.27  E-value: 9.00e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 125 ENGDLEAKQRLAEANLRLVVSIAKRYvGRGMQFL-DLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQA 203
Cdd:PRK08583  24 ENQDEEAQEKLVKHYKNLVESLAYKY-SKGQSHHeDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRDKT 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 204 RTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQ--EPVSLETPIgeEDDSHLGDFIED 281
Cdd:PRK08583 103 WSVHVPRRIKELGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEVLEAMEMGKsyQALSVDHSI--EADSDGSTVTLL 180

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488973340 282 EVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFglddGKMRTLEDVGKVFNVTRERIRQIEAKALRKLR 355
Cdd:PRK08583 181 DIVGQQEDGYELTEQRMILEKILPVLSDREKSIIQCTF----IENLSQKETGERLGISQMHVSRLQRQAIKKLR 250
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 303-356 8.43e-14

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: 65.14  E-value: 8.43e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 488973340  303 VLDTLTDREENVLRLRFGlddgKMRTLEDVGKVFNVTRERIRQIEAKALRKLRH 356
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 ...
 297-355 5.77e-13

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: 62.89  E-value: 5.77e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 488973340 297 REQLDEVLDTLTDREENVLRLRFGLDdgkmRTLEDVGKVFNVTRERIRQIEAKALRKLR 355
Cdd:cd06171    1 RERLEEALDKLPEREREVILLRFGEG----LSYEEIAEILGISRSTVRQRLHRALKKLR 55
Sigma70_r1_2 pfam00140
Sigma-70 factor, region 1.2;
97-130 2.29e-10

Sigma-70 factor, region 1.2;


Pssm-ID: 425482 [Multi-domain]  Cd Length: 34  Bit Score: 55.01  E-value: 2.29e-10
                          10        20        30
                  ....*....|....*....|....*....|....
gi 488973340   97 DPVRMYLKEIGVVPLLSNEEEKELAIAVENGDLE 130
Cdd:pfam00140   1 DSVRLYLKEIGRIPLLTAEEEVELAKRIEAGDEA 34
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
116-317 2.58e-08

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 53.76  E-value: 2.58e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 116 EEKELAIAVENGDLEAKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWI-RQA 194
Cdd:PRK08295  10 EDEELVELARSGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCItRQI 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 195 ITrAIADQARTIRIPVHmvetinklvreqrnllqelgqdptpeqiaermdmtpdkvreilkiaqEPVSLETPIGEEDDSH 274
Cdd:PRK08295  90 IT-AIKTANRQKHIPLN-----------------------------------------------SYVSLDKPIYDEESDR 121

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 488973340 275 -LGDFIEDEVIENPvdyTTRVVLREQLDEVLDT----LTDREENVLRL 317
Cdd:PRK08295 122 tLLDVISEAKVTDP---EELIISKEELEDIEEKieelLSELEKEVLEL 166
PRK05658 PRK05658
RNA polymerase sigma factor RpoD; Validated
 41-127 9.83e-08

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 235549 [Multi-domain]  Cd Length: 619  Bit Score: 53.64  E-value: 9.83e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340  41 VLDADGIDDLLERLTDGGISITDKDGNPSSKYVVEAPKPEELTDEELLGSNSAKVN---------DPVRMYLKEIGVVPL 111
Cdd:PRK05658  39 IVDSEQIEDIIAMLNDMGIQVVEEAPDADDLLLAENEADAQTDEDAEEEAAAALSSveseigrtdDPVRMYLREMGTVEL 118

                         90
                 ....*....|....*.
gi 488973340 112 LSNEEEKELAIAVENG 127
Cdd:PRK05658 119 LTREGEIEIAKRIEAG 134
PRK12427 PRK12427
FliA/WhiG family RNA polymerase sigma factor;
159-355 5.60e-07

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 183523 [Multi-domain]  Cd Length: 231  Bit Score: 49.86  E-value: 5.60e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 159 DLIQEGNMGLMKAVDKFDYSKGfKFSTYATWWIRQAIT---RAIADQARTIRIPVHmveTINKLVREQRnllQELGQDPT 235
Cdd:PRK12427  47 DMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILdelRELDWRPRRLRQKTH---KTNDAIREIA---KRLGHEPN 119

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 236 PEQIAERMDMTPDKVREILKI--AQEPVSLETPIGeeDDSHlGDFIEDEVIENpvdyttRVVLREQLDEVLDTLTDREEN 313
Cdd:PRK12427 120 FEEISAELNLTAEEYQEYLLLenAGTLESLDELLA--LEAH-NDILQSRDLEE------NIIIEDNLKQALSQLDEREQL 190

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 488973340 314 VLRLRFGLDdgkmRTLEDVGKVFNVTRERIRQIEAKALRKLR 355
Cdd:PRK12427 191 ILHLYYQHE----MSLKEIALVLDLTEARICQLNKKIAQKIK 228
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 115-254 1.38e-04

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: 42.29  E-value: 1.38e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488973340 115 EEEKELAIAVENGDLEAKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFKFstyatwWIRQA 194
Cdd:COG1595    2 SSDEELLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRA------WLYRI 75

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488973340 195 ITRAIADQART-IRIPVHMVETINKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREIL 254
Cdd:COG1595   76 ARNLAIDHLRKrRRRRELLDELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVL 136
 
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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