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Conserved domains on  [gi|501135355|ref|WP_012183988|]
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RNA polymerase sigma factor RpoD/SigA [Salinispora arenicola]

Protein Classification

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 38-329 1.54e-133

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: 380.55  E-value: 1.54e-133
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355  38 YLHEISRTPLLDAATEVDLSKAIEAGlyaehlldedrvpagveraelqrlvaeGERAKDLFIRANLRLVVSIARRYVRSG 117
Cdd:COG0568    2 YLREIGRVPLLTAEEEVELARRIQAG---------------------------DEEAKRKLVEANLRLVVSIAKKYQGRG 54

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 118 MPMLDLIQEGNTGLVRAVEKFDYERGFKFSTYATWWIRQAISRAIAQQERTVRLPVHLVEDVNRMRNVARQLTRELGSDP 197
Cdd:COG0568   55 LPLLDLIQEGNLGLMKAVEKFDPERGFRFSTYATWWIRQAITRAIADQWRTIRLPVHMAETLNKLRRAKRQLLQELGREP 134

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 198 EPEQIATALGVSVERVNELVRWSQDTVSLDTPVGDDGDTNLGDLVADSDAPSPEEIVLTGLERQRIEGLLSHLDDRSAGI 277
Cdd:COG0568  135 TPEEIAEELGVPEEKVREMLRLAREPVSLDAPVGDDEDSELGDLLEDEEAPSPEEALEEELLREELREALDTLTEREREI 214

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|..
gi 501135355 278 MRARYGLEDGREHSLTEVASRFSLSRERIRQLEIQALGRLRELARAEGLQAA 329
Cdd:COG0568  215 LRLRFGLDDGEPHTLEEIGKEFGVSRERVRQIEAKALRKLRHPLRSRKLRDY 266
 
Name Accession Description Interval E-value
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 38-329 1.54e-133

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: 380.55  E-value: 1.54e-133
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355  38 YLHEISRTPLLDAATEVDLSKAIEAGlyaehlldedrvpagveraelqrlvaeGERAKDLFIRANLRLVVSIARRYVRSG 117
Cdd:COG0568    2 YLREIGRVPLLTAEEEVELARRIQAG---------------------------DEEAKRKLVEANLRLVVSIAKKYQGRG 54

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 118 MPMLDLIQEGNTGLVRAVEKFDYERGFKFSTYATWWIRQAISRAIAQQERTVRLPVHLVEDVNRMRNVARQLTRELGSDP 197
Cdd:COG0568   55 LPLLDLIQEGNLGLMKAVEKFDPERGFRFSTYATWWIRQAITRAIADQWRTIRLPVHMAETLNKLRRAKRQLLQELGREP 134

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 198 EPEQIATALGVSVERVNELVRWSQDTVSLDTPVGDDGDTNLGDLVADSDAPSPEEIVLTGLERQRIEGLLSHLDDRSAGI 277
Cdd:COG0568  135 TPEEIAEELGVPEEKVREMLRLAREPVSLDAPVGDDEDSELGDLLEDEEAPSPEEALEEELLREELREALDTLTEREREI 214

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|..
gi 501135355 278 MRARYGLEDGREHSLTEVASRFSLSRERIRQLEIQALGRLRELARAEGLQAA 329
Cdd:COG0568  215 LRLRFGLDDGEPHTLEEIGKEFGVSRERVRQIEAKALRKLRHPLRSRKLRDY 266
PRK07921 PRK07921
RNA polymerase sigma factor SigB; Reviewed
 33-328 2.26e-124

RNA polymerase sigma factor SigB; Reviewed


Pssm-ID: 181169 [Multi-domain]  Cd Length: 324  Bit Score: 359.43  E-value: 2.26e-124
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355  33 DLVGVYLHEISRTPLLDAATEVDLSKAIEAGLYAEHLLDEDRVPAGVERAELQRLVAEGERAKDLFIRANLRLVVSIARR 112
Cdd:PRK07921  26 DLVRVYLNGIGKTALLTAADEVELAKRIEAGLYAEHLLETRKRLSEARKRDLAAVVRDGEAARRHLLEANLRLVVSLAKR 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 113 YVRSGMPMLDLIQEGNTGLVRAVEKFDYERGFKFSTYATWWIRQAISRAIAQQERTVRLPVHLVEDVNRMRNVARQLTRE 192
Cdd:PRK07921 106 YTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKRELHQQ 185

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 193 LGSDPEPEQIATALGVSVERVNELVRWSQDTVSLDTPVGDDGDTNLGDLVADSDAPSPEEIVLTGLERQRIEGLLSHLDD 272
Cdd:PRK07921 186 LGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEATSAENAVIAGLLHTDIRSVLATLDE 265

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 501135355 273 RSAGIMRARYGLEDGREHSLTEVASRFSLSRERIRQLEIQALGRLRELARAEGLQA 328
Cdd:PRK07921 266 REQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGERADRLRS 321
Sig70-cyanoRpoD TIGR02997
RNA polymerase sigma factor, cyanobacterial RpoD-like family; This family includes a number of ...
 33-318 5.33e-112

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: 326.90  E-value: 5.33e-112
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355   33 DLVGVYLHEISRTPLLDAATEVDLSKAIEAGLYAEHLLDEDR-------------VPAGVERAELQRLVAEGERAKDLFI 99
Cdd:TIGR02997   1 DLVRLYLQEIGRVPLLTPEEEIELARQVQQMMVLEELREELEeqlgrepskeewaAAAGLSEAELRQRLRQGQRAKEKMI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355  100 RANLRLVVSIARRYVRSGMPMLDLIQEGNTGLVRAVEKFDYERGFKFSTYATWWIRQAISRAIAQQERTVRLPVHLVEDV 179
Cdd:TIGR02997  81 KANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355  180 NRMRNVARQLTRELGSDPEPEQIATALGVSVERVNELVRWSQDTVSLDTPVGDDGDTNLGDLVADsDAPSPEEIVLTGLE 259
Cdd:TIGR02997 161 NKIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLED-DGESPEEQVERESL 239

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 501135355  260 RQRIEGLLSHLDDRSAGIMRARYGLEDGREHSLTEVASRFSLSRERIRQLEIQALGRLR 318
Cdd:TIGR02997 240 RQDLESLLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR 298
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 98-168 2.22e-21

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: 86.10  E-value: 2.22e-21
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 501135355   98 FIRANLRLVVSIARRYVRSGMPMLDLIQEGNTGLVRAVEKFDYERGFKFSTYATWWIRQAISRAIAQQERT 168
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRRT 71
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 260-318 1.69e-05

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: 41.71  E-value: 1.69e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 501135355 260 RQRIEGLLSHLDDRSAGIMRARYGledgREHSLTEVASRFSLSRERIRQLEIQALGRLR 318
Cdd:cd06171    1 RERLEEALDKLPEREREVILLRFG----EGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 38-329 1.54e-133

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: 380.55  E-value: 1.54e-133
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355  38 YLHEISRTPLLDAATEVDLSKAIEAGlyaehlldedrvpagveraelqrlvaeGERAKDLFIRANLRLVVSIARRYVRSG 117
Cdd:COG0568    2 YLREIGRVPLLTAEEEVELARRIQAG---------------------------DEEAKRKLVEANLRLVVSIAKKYQGRG 54

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 118 MPMLDLIQEGNTGLVRAVEKFDYERGFKFSTYATWWIRQAISRAIAQQERTVRLPVHLVEDVNRMRNVARQLTRELGSDP 197
Cdd:COG0568   55 LPLLDLIQEGNLGLMKAVEKFDPERGFRFSTYATWWIRQAITRAIADQWRTIRLPVHMAETLNKLRRAKRQLLQELGREP 134

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 198 EPEQIATALGVSVERVNELVRWSQDTVSLDTPVGDDGDTNLGDLVADSDAPSPEEIVLTGLERQRIEGLLSHLDDRSAGI 277
Cdd:COG0568  135 TPEEIAEELGVPEEKVREMLRLAREPVSLDAPVGDDEDSELGDLLEDEEAPSPEEALEEELLREELREALDTLTEREREI 214

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|..
gi 501135355 278 MRARYGLEDGREHSLTEVASRFSLSRERIRQLEIQALGRLRELARAEGLQAA 329
Cdd:COG0568  215 LRLRFGLDDGEPHTLEEIGKEFGVSRERVRQIEAKALRKLRHPLRSRKLRDY 266
PRK07921 PRK07921
RNA polymerase sigma factor SigB; Reviewed
 33-328 2.26e-124

RNA polymerase sigma factor SigB; Reviewed


Pssm-ID: 181169 [Multi-domain]  Cd Length: 324  Bit Score: 359.43  E-value: 2.26e-124
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355  33 DLVGVYLHEISRTPLLDAATEVDLSKAIEAGLYAEHLLDEDRVPAGVERAELQRLVAEGERAKDLFIRANLRLVVSIARR 112
Cdd:PRK07921  26 DLVRVYLNGIGKTALLTAADEVELAKRIEAGLYAEHLLETRKRLSEARKRDLAAVVRDGEAARRHLLEANLRLVVSLAKR 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 113 YVRSGMPMLDLIQEGNTGLVRAVEKFDYERGFKFSTYATWWIRQAISRAIAQQERTVRLPVHLVEDVNRMRNVARQLTRE 192
Cdd:PRK07921 106 YTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKRELHQQ 185

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 193 LGSDPEPEQIATALGVSVERVNELVRWSQDTVSLDTPVGDDGDTNLGDLVADSDAPSPEEIVLTGLERQRIEGLLSHLDD 272
Cdd:PRK07921 186 LGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEATSAENAVIAGLLHTDIRSVLATLDE 265

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 501135355 273 RSAGIMRARYGLEDGREHSLTEVASRFSLSRERIRQLEIQALGRLRELARAEGLQA 328
Cdd:PRK07921 266 REQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGERADRLRS 321
PRK05901 PRK05901
RNA polymerase sigma factor; Provisional
 33-318 1.27e-116

RNA polymerase sigma factor; Provisional


Pssm-ID: 235640 [Multi-domain]  Cd Length: 509  Bit Score: 346.21  E-value: 1.27e-116
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355  33 DLVGVYLHEISRTPLLDAATEVDLSKAIEAGLYAEHLLDEDRVPAGVERAELQRLVAEGERAKDLFIRANLRLVVSIARR 112
Cdd:PRK05901 211 DPVKAYLKQIGKVKLLNAEEEVELAKRIEAGLYAEELLAEGEKLDPELRRDLQWIGRDGKRAKNHLLEANLRLVVSLAKR 290

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 113 YVRSGMPMLDLIQEGNTGLVRAVEKFDYERGFKFSTYATWWIRQAISRAIAQQERTVRLPVHLVEDVNRMRNVARQLTRE 192
Cdd:PRK05901 291 YTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVETINKLGRIERELLQE 370

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 193 LGSDPEPEQIATALGVSVERVNELVRWSQDTVSLDTPVGDDGDTNLGDLVADSDAPSPEEIVLTGLERQRIEGLLSHLDD 272
Cdd:PRK05901 371 LGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGDSQFGDFIEDSEAVSPVDAVSFTLLQDQLQEVLETLSE 450

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*.
gi 501135355 273 RSAGIMRARYGLEDGREHSLTEVASRFSLSRERIRQLEIQALGRLR 318
Cdd:PRK05901 451 REAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLR 496
Sig70-cyanoRpoD TIGR02997
RNA polymerase sigma factor, cyanobacterial RpoD-like family; This family includes a number of ...
 33-318 5.33e-112

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: 326.90  E-value: 5.33e-112
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355   33 DLVGVYLHEISRTPLLDAATEVDLSKAIEAGLYAEHLLDEDR-------------VPAGVERAELQRLVAEGERAKDLFI 99
Cdd:TIGR02997   1 DLVRLYLQEIGRVPLLTPEEEIELARQVQQMMVLEELREELEeqlgrepskeewaAAAGLSEAELRQRLRQGQRAKEKMI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355  100 RANLRLVVSIARRYVRSGMPMLDLIQEGNTGLVRAVEKFDYERGFKFSTYATWWIRQAISRAIAQQERTVRLPVHLVEDV 179
Cdd:TIGR02997  81 KANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355  180 NRMRNVARQLTRELGSDPEPEQIATALGVSVERVNELVRWSQDTVSLDTPVGDDGDTNLGDLVADsDAPSPEEIVLTGLE 259
Cdd:TIGR02997 161 NKIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLED-DGESPEEQVERESL 239

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 501135355  260 RQRIEGLLSHLDDRSAGIMRARYGLEDGREHSLTEVASRFSLSRERIRQLEIQALGRLR 318
Cdd:TIGR02997 240 RQDLESLLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR 298
RpoD_Cterm TIGR02393
RNA polymerase sigma factor RpoD, C-terminal domain; This model represents the well-conserved ...
 94-326 1.82e-109

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: 318.47  E-value: 1.82e-109
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355   94 AKDLFIRANLRLVVSIARRYVRSGMPMLDLIQEGNTGLVRAVEKFDYERGFKFSTYATWWIRQAISRAIAQQERTVRLPV 173
Cdd:TIGR02393   1 AKKKLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355  174 HLVEDVNRMRNVARQLTRELGSDPEPEQIATALGVSVERVNELVRWSQDTVSLDTPVGDDGDTNLGDLVADSDAPSPEEI 253
Cdd:TIGR02393  81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDESIESPDDA 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 501135355  254 VLTGLERQRIEGLLSHLDDRSAGIMRARYGLEDGREHSLTEVASRFSLSRERIRQLEIQALGRLRELARAEGL 326
Cdd:TIGR02393 161 AAKELLREQLDEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKL 233
PRK09210 PRK09210
RNA polymerase sigma factor RpoD; Validated
 33-326 5.67e-105

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 311.53  E-value: 5.67e-105
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355  33 DLVGVYLHEISRTPLLDAATEVDLSKAIEAGlyaehllDEdrvpagveraELQRLVAEgerakdlfirANLRLVVSIARR 112
Cdd:PRK09210  96 DPVRMYLKEIGRVPLLTAEEEIELAKRIEEG-------DE----------EAKQRLAE----------ANLRLVVSIAKR 148

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 113 YVRSGMPMLDLIQEGNTGLVRAVEKFDYERGFKFSTYATWWIRQAISRAIAQQERTVRLPVHLVEDVNRMRNVARQLTRE 192
Cdd:PRK09210 149 YVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQE 228

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 193 LGSDPEPEQIATALGVSVERVNELVRWSQDTVSLDTPVGDDGDTNLGDLVADSDAPSPEEIVLTGLERQRIEGLLSHLDD 272
Cdd:PRK09210 229 LGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAAYELLKEQLEDVLDTLTD 308

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....
gi 501135355 273 RSAGIMRARYGLEDGREHSLTEVASRFSLSRERIRQLEIQALGRLRELARAEGL 326
Cdd:PRK09210 309 REENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQL 362
PRK07406 PRK07406
RNA polymerase sigma factor RpoD; Validated
 33-318 1.28e-95

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236012 [Multi-domain]  Cd Length: 373  Bit Score: 287.83  E-value: 1.28e-95
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355  33 DLVGVYLHEISRTPLLDAATEVDLSKAIEAGLYAEHLLDE-----DRVPAGVERAEL--------QRLVAEGERAKDLFI 99
Cdd:PRK07406  63 DSIRVYLQEIGRIRLLRPDEEIELARKIADLLELEELREQfeselGREPSDKEWAELvdmplpkfRRRLMLGRRAKEKMV 142

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 100 RANLRLVVSIARRYVRSGMPMLDLIQEGNTGLVRAVEKFDYERGFKFSTYATWWIRQAISRAIAQQERTVRLPVHLVEDV 179
Cdd:PRK07406 143 QSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETI 222

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 180 NRMRNVARQLTRELGSDPEPEQIATALGVSVERVNELVRWSQDTVSLDTPVGDDGDTNLGDLVaDSDAPSPEEIVLTGLE 259
Cdd:PRK07406 223 SRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFI-EADGETPEDDVAKNLL 301

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 501135355 260 RQRIEGLLSHLDDRSAGIMRARYGLEDGREHSLTEVASRFSLSRERIRQLEIQALGRLR 318
Cdd:PRK07406 302 REDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLR 360
PRK05949 PRK05949
RNA polymerase sigma factor; Validated
 33-318 2.12e-87

RNA polymerase sigma factor; Validated


Pssm-ID: 180321 [Multi-domain]  Cd Length: 327  Bit Score: 265.55  E-value: 2.12e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355  33 DLVGVYLHEISRTPLLDAATEV-------------DLSKAIEAGLYAEHLLDEDRVPAGVERAELQRLVAEGERAKDLFI 99
Cdd:PRK05949  18 DMVRTYLHEIGRVPLLTHEQEIvygkqvqqmmsllEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAKQKMI 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 100 RANLRLVVSIARRYVRSGMPMLDLIQEGNTGLVRAVEKFDYERGFKFSTYATWWIRQAISRAIAQQERTVRLPVHLVEDV 179
Cdd:PRK05949  98 EANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEKL 177

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 180 NRMRNVARQLTRELGSDPEPEQIATALGVSVERVNELVRWSQDTVSLDTPVGDDGDTNLGDLVADsDAPSPEEIVLTGLE 259
Cdd:PRK05949 178 NKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTELSELLED-EGPSPDQYITQELL 256

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 501135355 260 RQRIEGLLSHLDDRSAGIMRARYGLEDGREHSLTEVASRFSLSRERIRQLEIQALGRLR 318
Cdd:PRK05949 257 RQDLNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLR 315
rpoS_proteo TIGR02394
RNA polymerase sigma factor RpoS; A sigma factor is a DNA-binding protein protein that binds ...
 33-326 9.45e-84

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: 254.65  E-value: 9.45e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355   33 DLVGVYLHEISRTPLLDAATEVDLSKAIEAGLYAehlldedrvpagveraelqrlvaegerAKDLFIRANLRLVVSIARR 112
Cdd:TIGR02394  13 DVTQLYLREIGFKPLLTAEEEIAYARRALAGDFE---------------------------ARKVMIESNLRLVVSIAKH 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355  113 YVRSGMPMLDLIQEGNTGLVRAVEKFDYERGFKFSTYATWWIRQAISRAIAQQERTVRLPVHLVEDVNRMRNVARQLTRE 192
Cdd:TIGR02394  66 YVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPVHVIKELNVYLRAARQLEKK 145

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355  193 LGSDPEPEQIATALGVSVERVNELVRWSQDTVSLDTPVGDDGDTNLGDLVADSDAPSPEEIVLTGLERQRIEGLLSHLDD 272
Cdd:TIGR02394 146 LGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPLDDDSSKSLLDTIADEQSIDPESLVQNDDLKQLIEAWLAELNE 225

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 501135355  273 RSAGIMRARYGLEDGREHSLTEVASRFSLSRERIRQLEIQALGRLRELARAEGL 326
Cdd:TIGR02394 226 RQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRILERDGV 279
PRK05658 PRK05658
RNA polymerase sigma factor RpoD; Validated
 56-318 5.14e-81

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 235549 [Multi-domain]  Cd Length: 619  Bit Score: 257.80  E-value: 5.14e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355  56 LSKAIEAGLYAEHLLDEDRVPAGVERAELQRL-----------------VAEGER----AKDLFIRANLRLVVSIARRYV 114
Cdd:PRK05658 322 LEKEIASGKPWSEFLVRVYDEIKKLQQELEAIeeetgltieelkeinrqISKGEAkarrAKKEMVEANLRLVISIAKKYT 401

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 115 RSGMPMLDLIQEGNTGLVRAVEKFDYERGFKFSTYATWWIRQAISRAIAQQERTVRLPVHLVEDVNRMRNVARQLTRELG 194
Cdd:PRK05658 402 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEIG 481

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 195 SDPEPEQIATALGVSVERVNELVRWSQDTVSLDTPVGDDGDTNLGDLVADSDAPSPEEIVLTGLERQRIEGLLSHLDDRS 274
Cdd:PRK05658 482 REPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDDEDSHLGDFIEDKNAELPIDAAIQESLREATTDVLASLTPRE 561

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....
gi 501135355 275 AGIMRARYGLEDGREHSLTEVASRFSLSRERIRQLEIQALGRLR 318
Cdd:PRK05658 562 AKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 605
PRK05657 PRK05657
RNA polymerase sigma factor RpoS; Validated
 33-326 1.79e-77

RNA polymerase sigma factor RpoS; Validated


Pssm-ID: 235548 [Multi-domain]  Cd Length: 325  Bit Score: 239.86  E-value: 1.79e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355  33 DLVGVYLHEISRTPLLDAATEVDLSkaieaglyaehlldedrvpagveraelqRLVAEGE-RAKDLFIRANLRLVVSIAR 111
Cdd:PRK05657  53 DATQLYLNEIGYSPLLTAEEEVYFA----------------------------RRALRGDfAARQRMIESNLRLVVKIAK 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 112 RYVRSGMPMLDLIQEGNTGLVRAVEKFDYERGFKFSTYATWWIRQAISRAIAQQERTVRLPVHLVEDVNRMRNVARQLTR 191
Cdd:PRK05657 105 RYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPVHVVKELNVYLRAARELEH 184

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 192 ELGSDPEPEQIATALGVSVERVNELVRWSQDTVSLDTPVGDDGDTNLGDLVADSDAPSPEEIVLTGLERQRIEGLLSHLD 271
Cdd:PRK05657 185 KLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLGGDPEKSLLDILADEQENGPEDTTQDDDMKQSIVKWLFELN 264

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 501135355 272 DRSAGIMRARYGLeDGREHS-LTEVASRFSLSRERIRQLEIQALGRLRELARAEGL 326
Cdd:PRK05657 265 DKQREVLARRFGL-LGYEAAtLEDVAREIGLTRERVRQIQVEALRRLREILQTQGL 319
PRK07405 PRK07405
RNA polymerase sigma factor SigD; Validated
 33-319 4.32e-77

RNA polymerase sigma factor SigD; Validated


Pssm-ID: 180963 [Multi-domain]  Cd Length: 317  Bit Score: 238.89  E-value: 4.32e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355  33 DLVGVYLHEISRTPLLDAATEVDLSKAIEAGLYAEHLLDE-----DRVP--------AGVERAELQRLVAEGERAKDLFI 99
Cdd:PRK07405   8 DLVRTYLREIGRVPLLTHEEEILYGKQVQRLVALQEIREElaeelGREPtdaewakaAKLSEEELRSAIAEGEAAKRKMV 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 100 RANLRLVVSIARRYVRSGMPMLDLIQEGNTGLVRAVEKFDYERGFKFSTYATWWIRQAISRAIAQQERTVRLPVHLVEDV 179
Cdd:PRK07405  88 EANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKL 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 180 NRMRNVARQLTRELGSDPEPEQIATALGVSVERVNELVRWSQDTVSLDTPVGDDGDTNLGDLVADsDAPSPEEIVLTGLE 259
Cdd:PRK07405 168 NKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLED-TGASPEDFATQSSL 246

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 260 RQRIEGLLSHLDDRSAGIMRARYGLEDGREHSLTEVASRFSLSRERIRQLEIQALGRLRE 319
Cdd:PRK07405 247 QLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRK 306
PRK07598 PRK07598
RNA polymerase sigma factor SigC; Validated
 77-322 7.51e-74

RNA polymerase sigma factor SigC; Validated


Pssm-ID: 236067 [Multi-domain]  Cd Length: 415  Bit Score: 233.61  E-value: 7.51e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355  77 AGVERAELQRLVAEGERAKDLFIRANLRLVVSIARRYVRSGMPMLDLIQEGNTGLVRAVEKFDYERGFKFSTYATWWIRQ 156
Cdd:PRK07598 159 AKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQ 238

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 157 AISRAIAQQERTVRLPVHLVEDVNRMRNVARQLTRELGSDPEPEQIATALGVSVERVNELVRWSQDTVSLDTPVGDDGDT 236
Cdd:PRK07598 239 GITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLLRVPRSVSLETKVGKDKDT 318

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 237 NLGDLVaDSDAPSPEEIVLTGLERQRIEGLLSHLDDRSAGIMRARYGLEDGREHSLTEVASRFSLSRERIRQLEIQALGR 316
Cdd:PRK07598 319 ELGDLL-ETDDISPEEMLMRESLQRDLQHLLADLTSRERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQK 397


                 ....*.
gi 501135355 317 LRELAR 322
Cdd:PRK07598 398 LRQPKR 403
rpoH_proteo TIGR02392
alternative sigma factor RpoH; A sigma factor is a DNA-binding protein protein that binds to ...
 37-318 4.18e-43

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: 149.35  E-value: 4.18e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355   37 VYLHEISRTPLLDAATEVDLskaieaglyAEHLLDEDRVPAgveraelqrlvaegerAKDLfIRANLRLVVSIARRYVRS 116
Cdd:TIGR02392   5 AYIRAVNRIPMLTPEEEYQL---------AKRLREHGDLDA----------------AKKL-VLSHLRFVVKIARGYRGY 58

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355  117 GMPMLDLIQEGNTGLVRAVEKFDYERGFKFSTYATWWIRQAISRAIAQQERTVRLPV-----HLVEDVNRMRNvarQLTR 191
Cdd:TIGR02392  59 GLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYILRNWRLVKVATtkaqrKLFFNLRKMKK---RLQG 135

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355  192 ELgSDPEPEQIATALGVSVERVNEL-VRWSQDTVSLDTPVGDDGD--TNLGDLVADSDaPSPEEIV----LTGLERQRIE 264
Cdd:TIGR02392 136 WL-NPEEVEAIAEELGVSEREVREMeSRLSGQDMSLNASIDDDEDdgGAPIAYLVDKR-SDPEDTLeeeqWEELQRQALA 213

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 501135355  265 GLLSHLDDRSAGIMRARYGLEDGRehSLTEVASRFSLSRERIRQLEIQALGRLR 318
Cdd:TIGR02392 214 NALGSLDARSRRIIEARWLDDDKL--TLQELAAEYGVSAERIRQIEKNAMKKLK 265
PRK06596 PRK06596
RNA polymerase factor sigma-32; Reviewed
 38-324 2.79e-41

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 235838 [Multi-domain]  Cd Length: 284  Bit Score: 145.32  E-value: 2.79e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355  38 YLHEISRTPLLDAATEVDLSKAieaglYAEHlldEDRvpagveraelqrlvaegERAKDLfIRANLRLVVSIARRYVRSG 117
Cdd:PRK06596  19 YIQAVNKIPMLTAEEEYMLAKR-----LREH---GDL-----------------EAAKQL-VLSHLRFVVHIARGYRGYG 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 118 MPMLDLIQEGNTGLVRAVEKFDYERGFKFSTYATWWIRQAISRAIAQQERTVRLPV-----HLVEDVNRMRNVARQLTRE 192
Cdd:PRK06596  73 LPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKVATtkaqrKLFFNLRKAKKRLGWLNPE 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 193 lgsdpEPEQIATALGVSVERVNEL-VRWSQDTVSLDTPVGDDGD--TNLGDLVADsDAPSPEEIV----LTGLERQRIEG 265
Cdd:PRK06596 153 -----EVEMVAEELGVSEEEVREMeSRLSGQDASLDAPIDDDDEesGAPQDYLED-KSSDPADVLeednWEDQRRALLAD 226

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 501135355 266 LLSHLDDRSAGIMRARYGLEDGRehSLTEVASRFSLSRERIRQLEIQALGRLRELARAE 324
Cdd:PRK06596 227 ALEGLDERSRDIIEARWLDDDKS--TLQELAAEYGVSAERVRQIEKNAMKKLKAAIEAA 283
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 84-319 3.43e-40

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: 140.73  E-value: 3.43e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355  84 LQRLVAEGERAKDLFIRANLRLVVSIARRYVRSGMPML-DLIQEGNTGLVRAVEKFDYERGFKFSTYATWWIRQAISRAI 162
Cdd:COG1191    6 LRRYQEGDEEAREELIEEYLPLVKKIASRLAGRLPAELdDLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRGAILDYL 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 163 aqqERTVRLPVHLVEDVNRMRNVARQLTRELGSDPEPEQIATALGVSVERVNELVRWSQ--DTVSLDTPVGDDGDtnLGD 240
Cdd:COG1191   86 ---RDEDWVPRSVRELARKIEEAIEELEQELGREPTDEEIAEELGISLEEVQEALEAANayQLLSLDEPLEDGDD--LLD 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 501135355 241 LVadsDAPSPEEIVLTGLERQRIEGLLSHLDDRSAGIMRARYgledGREHSLTEVASRFSLSRERIRQLEIQALGRLRE 319
Cdd:COG1191  161 LL---ESGDPEEELEHEELREALAEAIEQLPERERLVLSLYY----FEELTLKEIAEVLGVSESRVSRLHKKALARLRE 232
rpoH2 PRK07500
RNA polymerase factor sigma-32; Reviewed
 92-318 1.13e-35

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 236033 [Multi-domain]  Cd Length: 289  Bit Score: 130.54  E-value: 1.13e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355  92 ERAKDLFIRANLRLVVSIARRYVRSGMPMLDLIQEGNTGLVRAVEKFDYERGFKFSTYATWWIRQAISRAIAQQERTVRL 171
Cdd:PRK07500  39 EDALHRIISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVRG 118

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 172 PVH-----LVEDVNRMRNVARQLTRELGSDPEPEQIATALGVSVERVNEL-VRWSQDTVSLDTPV--GDDGDTNLGDLVA 243
Cdd:PRK07500 119 GTSsaqkaLFFNLRRLRARLAQADEELTKQEIHREIATALGVSLSDVEMMdARLSGPDASLNAPQseEDEGRSERMDFLV 198

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 501135355 244 DsDAPSPEEIVLTGLERQR----IEGLLSHLDDRSAGIMRARYGLEDGRehSLTEVASRFSLSRERIRQLEIQALGRLR 318
Cdd:PRK07500 199 D-DSPLPDEQVESSIDGERrrrwLTQALQTLNERELRIIRERRLREDGA--TLEALGEELGISKERVRQIEARALEKLR 274
PRK07408 PRK07408
RNA polymerase sigma factor SigF; Reviewed
 102-302 1.89e-26

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 180965 [Multi-domain]  Cd Length: 256  Bit Score: 105.00  E-value: 1.89e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 102 NLRLVVSIARRYVR-SGMPMLDLIQEGNTGLVRAVEKFDYERGFKFSTYATWWIRQAISRAIAQQERTVRLPVHLVEDVN 180
Cdd:PRK07408  34 NLGLVRKEAHRWSNqCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPTVRIPRRWQELQR 113

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 181 RMRNVARQLTRELGSDPEPEQIATALGVSVERVNE--LVRWSQDTVSLDTPVGDDGD--TNLGDLVADSDAPSPEeivLT 256
Cdd:PRK07408 114 QAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEikLALQNRTPLSLDAPVNQDEDgsTSLGDLLPDPRYRSFQ---LA 190

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 501135355 257 GLERQRIEGLLSHLDDrsagimRARYGLEDGREHSLT--EVASRFSLS 302
Cdd:PRK07408 191 QEDRIRLQQALAQLEE------RTREVLEFVFLHDLTqkEAAERLGIS 232
spore_sigF TIGR02885
RNA polymerase sigma-F factor; Members of this protein family are the RNA polymerase sigma ...
 84-319 4.51e-24

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: 98.25  E-value: 4.51e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355   84 LQRLVAEGER-AKDLFIRANLRLVVSIARRYVRSGMPMLDLIQEGNTGLVRAVEKFDYERGFKFSTYATWWIRQAISRAI 162
Cdd:TIGR02885   1 LIKLAQNGDKeARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355  163 aQQERTVRLPVHLVEDVNRMRNVARQLTRELGSDPEPEQIATALGVSVERVNELVRWSQDTVSL-DTPVGDDGD-TNLGD 240
Cdd:TIGR02885  81 -RDDGIIKVSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLyDTVHQDDGDpIYLLD 159

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 501135355  241 LVADsdaPSPEEIVLtgLERQRIEGLLSHLDDRSAGIMRARYgledGREHSLTEVASRFSLSRERIRQLEIQALGRLRE 319
Cdd:TIGR02885 160 QIAD---KGSEDSDW--LEKIALKEAISKLDERERQIIMLRY----FKDKTQTEVANMLGISQVQVSRLEKKVLKKMKE 229
FliA_WhiG TIGR02479
RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar ...
 98-320 1.16e-23

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: 96.96  E-value: 1.16e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355   98 FIRANLRLVVSIARRyVRSGMP----MLDLIQEGNTGLVRAVEKFDYERGFKFSTYATWWIRQAI---SRAIAQQERTVR 170
Cdd:TIGR02479   1 LIRRYLPLVKRIAGR-LSVGLPssveLDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMldeLRRLDWVPRSLR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355  171 LPVHLVEDvnrmrnVARQLTRELGSDPEPEQIATALGVSVErvnELVRWSQDT-----VSLDTPVGDDGD-TNLGDLVAD 244
Cdd:TIGR02479  80 QKARKLER------AIRELEARLGREPTEEEIAEELGMDLK---EYRQALNEInalslVSLDELLESGDDgGSLIDRIED 150

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 501135355  245 SDAPSPEEIVLTGLERQRIEGLLSHLDDRSAGIMRARYgledGREHSLTEVASRFSLSRERIRQLEIQALGRLREL 320
Cdd:TIGR02479 151 DKSEDPEEELEREELREALAEAIESLSEREQLVLSLYY----YEELNLKEIGEVLGLTESRVSQIHSQALKKLRAK 222
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 98-168 2.22e-21

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: 86.10  E-value: 2.22e-21
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 501135355   98 FIRANLRLVVSIARRYVRSGMPMLDLIQEGNTGLVRAVEKFDYERGFKFSTYATWWIRQAISRAIAQQERT 168
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRRT 71
PRK05803 PRK05803
RNA polymerase sporulation sigma factor SigK;
80-324 3.23e-21

RNA polymerase sporulation sigma factor SigK;


Pssm-ID: 180266 [Multi-domain]  Cd Length: 233  Bit Score: 90.39  E-value: 3.23e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355  80 ERAELQRLVAEGERAKDLFIRANLRLVVSIARRYVRSGMPMLDLIQEGNTGLVRAVEKFDYERGFKFSTYAtwwirqaiS 159
Cdd:PRK05803  36 ERKYLELMKEGDEEARNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYA--------A 107

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 160 RAIaQQErtvrLPVHLvedvnrmrnvaRQLTRELGsdpepeqiatalgvsvervnelvrwsqdTVSLDTPVGDDGDTN-- 237
Cdd:PRK05803 108 RCI-ENE----ILMHL-----------RNLKKTKK----------------------------EVSLQDPIGVDKEGNei 143

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 238 -LGDLVAdSDAPSPEEIVLTGLERQRIEGLLSHLDDRSAGIMRARYGLEDGREHSLTEVASRFSLSRERIRQLEIQALGR 316
Cdd:PRK05803 144 sLIDILG-SEEDDVIEQVELKMEVEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKK 222


                 ....*....
gi 501135355 317 L-RELARAE 324
Cdd:PRK05803 223 LfKELYRAE 231
PRK05572 PRK05572
RNA polymerase sporulation sigma factor, SigF/SigG family;
83-319 4.04e-21

RNA polymerase sporulation sigma factor, SigF/SigG family;


Pssm-ID: 180137 [Multi-domain]  Cd Length: 252  Bit Score: 90.42  E-value: 4.04e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355  83 ELQRLVAEGER-AKDLFIRANLRLVVSIARRYVRSGMPMLDLIQEGNTGLVRAVEKFDYERGFKFSTYATWWIRQAISRA 161
Cdd:PRK05572  21 ELIKKSQDGDQeARDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRF 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 162 IaQQERTVRLPVHLVEDVNRMRNVARQLTRELGSDPEPEQIATALGVSVERV---NELVRWSQdtvSL-DTPVGDDGD-T 236
Cdd:PRK05572 101 L-RDDGTVKVSRSLKETANKIRKDKDELSKELGREPTIEELAEYLGVTPEEVvlaQEASRSPQ---SIhETVHENDGDpI 176

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 237 NLGDLVADSDapspEEIVLTGLERQRIeglLSHLDDRSAGIMRARYgledGREHSLTEVASRFSLSRERIRQLEIQALGR 316
Cdd:PRK05572 177 TLLDQIADQS----EEDWFDKIALKEA---IRELDERERLIVYLRY----FKDKTQSEVAKRLGISQVQVSRLEKKILKQ 245


                 ...
gi 501135355 317 LRE 319
Cdd:PRK05572 246 MKE 248
PRK08215 PRK08215
RNA polymerase sporulation sigma factor SigG;
80-318 1.03e-20

RNA polymerase sporulation sigma factor SigG;


Pssm-ID: 181296 [Multi-domain]  Cd Length: 258  Bit Score: 89.62  E-value: 1.03e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355  80 ERAELQRLVAEGER-AKDLFIRANLRLVVSIARRYVRSGMPMLDLIQEGNTGLVRAVEKFDYERGFKFSTYATWWIrqai 158
Cdd:PRK08215  23 EMRELFERMQNGDKeAREKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMI---- 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 159 sraIAQQERTVRlpvhlveDVNRMRnVAR--------------QLTRELGSDPEPEQIATALGVSVERVNELVRWSQDTV 224
Cdd:PRK08215  99 ---IGEIRRYLR-------DNNPIR-VSRslrdiaykalqvreKLINENSKEPTVEEIAKELEVPREEVVFALDAIQDPV 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 225 SLDTPVGDDGdtnlGD--LVAD--SDAPSPEEivlTGLERQRIEGLLSHLDDRSAGIMRARYglEDGREHslTEVASRFS 300
Cdd:PRK08215 168 SLFEPIYHDG----GDpiYVMDqiSDEKNKDE---NWLEEIALKEAMKKLNDREKLILNLRF--FQGKTQ--MEVAEEIG 236

                        250
                 ....*....|....*...
gi 501135355 301 LSRERIRQLEIQALGRLR 318
Cdd:PRK08215 237 ISQAQVSRLEKAALKHMR 254
Sigma70_r3 pfam04539
Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the ...
 177-254 8.03e-20

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: 82.27  E-value: 8.03e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 501135355  177 EDVNRMRNVARQLTRELGSDPEPEQIATALGVSVERVNELVRWSQDTVSLDTPVGDDGDTNLGDLVADSDAPSPEEIV 254
Cdd:pfam04539   1 ELLNKIKRAQRELEQELGREPTPEEIAEELGLSPEKVREVLEAAREPVSLDTPVGEEEDGELGDLLEDDDIESPEEAV 78
PRK07670 PRK07670
FliA/WhiG family RNA polymerase sigma factor;
122-320 2.06e-18

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 181075 [Multi-domain]  Cd Length: 251  Bit Score: 83.17  E-value: 2.06e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 122 DLIQEGNTGLVRAVEKFDYERGFKFSTYATWWIRQAISRAIAQQErtvRLPVHLVEDVNRMRNVARQLTRELGSDPEPEQ 201
Cdd:PRK07670  54 DLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRKED---WLPRSMREKTKKVEAAIEKLEQRYMRNVTPKE 130

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 202 IATALGVSVERVNELVRWS--QDTVSLD-TPVGDDGDTNLGDLVADSDAPSPEEIVltgLERQRIEGL---LSHLDDRSA 275
Cdd:PRK07670 131 VAAELGMTEEEVEATMNEGffANLLSIDeKTHDQDDGENVSVTIRDDKTPTPEEKL---LKEELIEELaekIKQLSEKEQ 207

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 501135355 276 GIMRARYgledGREHSLTEVASRFSLSRERIRQLEIQALGRLREL 320
Cdd:PRK07670 208 LVISLFY----KEELTLTEIGQVLNLSTSRISQIHSKALFKLKKL 248
PRK06288 PRK06288
RNA polymerase sigma factor WhiG; Reviewed
 80-318 3.50e-18

RNA polymerase sigma factor WhiG; Reviewed


Pssm-ID: 235770 [Multi-domain]  Cd Length: 268  Bit Score: 82.81  E-value: 3.50e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355  80 ERAELQRLVAEGERAKDLFIRANLRLVVSIARRYVRS----GMP----MLDLIQEGNTGLVRAVEKFDYERGFKFSTYAT 151
Cdd:PRK06288  13 AQQDETELWREYKKTGDPKIREYLILKYSPLVKYVAGriavGMPqnveFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAV 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 152 WWIRQAIS---RAIAQQERTVRLPVHLVEdvnrmRNVARqLTRELGSDPEPEQIATALGVSVERVNELVRWSQDT--VSL 226
Cdd:PRK06288  93 TRIRGAIFdelRSIDWIPRSVRQKARQIE-----RAIAM-LEARLGRTPSDEEIADELGISLEEYNSLLSKLSGTsvVSL 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 227 DT--PVGDDGDT-NLGDLVADSDAPSPEEIVLTGLERQRIEGLLSHLDDRSAGIMRARYgLEDgreHSLTEVASRFSLSR 303
Cdd:PRK06288 167 NDlwFGGDEGDEvSLMDTLESPAALNPDEIAEREEIKRVIVEAIKTLPEREKKVLILYY-YED---LTLKEIGKVLGVTE 242

                        250
                 ....*....|....*
gi 501135355 304 ERIRQLEIQALGRLR 318
Cdd:PRK06288 243 SRISQLHTKAVLQLR 257
PRK08583 PRK08583
RNA polymerase sigma factor SigB; Validated
 92-324 1.42e-16

RNA polymerase sigma factor SigB; Validated


Pssm-ID: 236306 [Multi-domain]  Cd Length: 257  Bit Score: 78.20  E-value: 1.42e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355  92 ERAKDLFIRANLRLVVSIARRYVRSGMPMLDLIQEGNTGLVRAVEKFDYERGFKFSTYATWWIRQAISRAIAQQERTVRL 171
Cdd:PRK08583  28 EEAQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRDKTWSVHV 107

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 172 PVHLVEDVNRMRNVARQLTRELGSDPEPEQIATALGVSVERVNELVRWSQ--DTVSLDTPVGDDGD---TNLGDLVADSD 246
Cdd:PRK08583 108 PRRIKELGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEVLEAMEMGKsyQALSVDHSIEADSDgstVTLLDIVGQQE 187

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 247 ApspeeivltGLER--QR--IEGLLSHLDDRSAGIMRARYglEDGRehSLTEVASRFSLSRERIRQLEIQALGRLRELAR 322
Cdd:PRK08583 188 D---------GYELteQRmiLEKILPVLSDREKSIIQCTF--IENL--SQKETGERLGISQMHVSRLQRQAIKKLREAAF 254


                 ..
gi 501135355 323 AE 324
Cdd:PRK08583 255 LD 256
PRK05911 PRK05911
RNA polymerase sigma factor sigma-28; Reviewed
 95-318 9.71e-15

RNA polymerase sigma factor sigma-28; Reviewed


Pssm-ID: 235644 [Multi-domain]  Cd Length: 257  Bit Score: 72.73  E-value: 9.71e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355  95 KDLFIRANLRLVVSIARRYVrSGMP----MLDLIQEGNTGLVRAVEKFDYERGFKFSTYATWWIRQAISRAIAQQERTVR 170
Cdd:PRK05911  25 RDVLIEFYLPLVKNVAHRLI-SGMPshvkTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRKQDWVPR 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 171 lPVHlvEDVNRMRNVARQLTRELGSDPEPEQIATALGVSVErvnELVRWSQDT-----VSL--DTPVGDDGDTNLG--DL 241
Cdd:PRK05911 104 -SVH--QKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQ---ELSGWFSSArpaliLSLneEFPCQSDDEAGLAleER 177

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 242 VADSDAPSPEEIVltglERQRIEGLLSH----LDDRSAGIMrARYGLEdgrEHSLTEVASRFSLSRERIRQLEIQALGRL 317
Cdd:PRK05911 178 IADERAETGYDVV----DKKEFSSILAEailaLEEKERKVM-ALYYYE---ELVLKEIGKILGVSESRVSQIHSKALLKL 249


                 .
gi 501135355 318 R 318
Cdd:PRK05911 250 R 250
PRK07122 PRK07122
RNA polymerase sigma factor SigF; Reviewed
 72-319 2.91e-14

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 168831 [Multi-domain]  Cd Length: 264  Bit Score: 71.73  E-value: 2.91e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355  72 EDRVPAGVERAELQRLVAEGERAKDLFIRANLRLVVSIARRYVRSGMPMLDLIQEGNTGLVRAVEKFDYERGFKFSTYAT 151
Cdd:PRK07122  19 ADVPEMFRELAGLPAGSPEFQRQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAV 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 152 WWIRQAISRAIAQQERTVRLPVHLVEDVNRMRNVARQLTRELGSDPEPEQIATALGVSVERVNE--LVRWSQDTVSLDTP 229
Cdd:PRK07122  99 PTIMGEVRRHFRDNSWSVKVPRRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEglVAGSAYNTLSIDSG 178

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 230 VG--DDGDTNLGDLVADSDaPSPEEIVltglERQRIEGLLSHLDDRSAGIMRARYgledGREHSLTEVASRFSLSRERIR 307
Cdd:PRK07122 179 GGsgDDDARAIADTLGDVD-AGLDQIE----NREALRPLLAALPERERTVLVLRF----FESMTQTQIAERVGISQMHVS 249

                        250
                 ....*....|..
gi 501135355 308 QLEIQALGRLRE 319
Cdd:PRK07122 250 RLLAKTLARLRD 261
fliA PRK06986
flagellar biosynthesis sigma factor; Validated
 122-319 2.15e-13

flagellar biosynthesis sigma factor; Validated


Pssm-ID: 235901 [Multi-domain]  Cd Length: 236  Bit Score: 68.72  E-value: 2.15e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 122 DLIQEGNTGLVRAVEKFDYERGFKFSTYATWWIRQAISRAIAQQE---RTVRLPVHLVEDvnrmrnVARQLTRELGSDPE 198
Cdd:PRK06986  40 DLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDELRSLDwvpRSVRRNAREVAQ------AIRQLEQELGREPT 113

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 199 PEQIATALGVSVERVNELVRWSQ--DTVSLDTPVGDDGDTNLGDLVADSDapSPEEIVLTGLERQRIEGLLSHLDDRSAG 276
Cdd:PRK06986 114 DTEVAEKLGLSLEEYREMLLDTNisQLFSIDELRGEHGDSILVTEDHQDE--DPLQQLEDEELREALVEAIESLPEREQL 191

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 501135355 277 IMRARYgledGREHSLTEVASRFSLSRERIRQLEIQALGRLRE 319
Cdd:PRK06986 192 VLSLYY----QEELNLKEIGAVLGVSESRVSQIHSQAIKRLRA 230
PRK08301 PRK08301
RNA polymerase sporulation sigma factor SigE;
80-324 7.17e-13

RNA polymerase sporulation sigma factor SigE;


Pssm-ID: 236228 [Multi-domain]  Cd Length: 234  Bit Score: 67.19  E-value: 7.17e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355  80 ERAELQRLVAEGERAKDLFIRANLRLVVSIARRYVRSGMPMLDLIQEGNTGLVRAVEKFDYERGFKFSTYAtwwirqaiS 159
Cdd:PRK08301  39 EEYLLNKLPKGDEAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYA--------S 110

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 160 RAIaqqertvrlpvhlvedvnrmrnvarqltrelgsdpEPEqIATALgvsveRVNELVRwsqDTVSLDTPVGDDGDTN-- 237
Cdd:PRK08301 111 RCI-----------------------------------ENE-ILMYL-----RRNNKVK---AEVSFDEPLNIDWDGNel 146

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 238 -LGD-LVADSDapspeeIVLTGLE----RQRIEGLLSHLDDRSAGIMRARYGLEDGREHSLTEVASRFSLSRERIRQLEI 311
Cdd:PRK08301 147 lLSDvLGTDND------IIYKDIEdevdRKLLKKALKKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEK 220

                        250
                 ....*....|....
gi 501135355 312 QALGRLR-ELARAE 324
Cdd:PRK08301 221 RIIKRLKkEINKMV 234
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 93-320 3.59e-12

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: 63.52  E-value: 3.59e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355   93 RAKDLFIRANLRLVVSIARRYVRSGMPMLDLIQEGNTGLVRAVEKFDYERgfKFSTYATWWIRqaisraiaqqertvrlp 172
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEG--SFKAWLFRIAR----------------- 61

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355  173 vhlvedvNRMRNVARQLTRELGSDPEPEQIAtalgvsvervnelvrwsqdtvsldtpvgddgdtnlgdlvadSDAPSPEE 252
Cdd:TIGR02937  62 -------NLILDYLRRKRRLRRELDLLEELL-----------------------------------------DSDPSPEE 93

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 501135355  253 IVLTGLERQRIEGLLSHLDDRSAGIMRARYgledGREHSLTEVASRFSLSRERIRQLEIQALGRLREL 320
Cdd:TIGR02937  94 ELEQEEEREALREALEKLPEREREVLVLRY----LEGLSYKEIAEILGISVGTVKRRLKRARKKLREL 157
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 266-319 6.11e-08

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: 48.58  E-value: 6.11e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 501135355  266 LLSHLDDRSAGIMRARYGledgREHSLTEVASRFSLSRERIRQLEIQALGRLRE 319
Cdd:pfam04545   1 ALASLPPRERQVLVLRYG----EGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
Sigma70_r1_2 pfam00140
Sigma-70 factor, region 1.2;
33-66 2.87e-07

Sigma-70 factor, region 1.2;


Pssm-ID: 425482 [Multi-domain]  Cd Length: 34  Bit Score: 46.15  E-value: 2.87e-07
                          10        20        30
                  ....*....|....*....|....*....|....
gi 501135355   33 DLVGVYLHEISRTPLLDAATEVDLSKAIEAGLYA 66
Cdd:pfam00140   1 DSVRLYLKEIGRIPLLTAEEEVELAKRIEAGDEA 34
PRK12427 PRK12427
FliA/WhiG family RNA polymerase sigma factor;
122-319 1.13e-05

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 183523 [Multi-domain]  Cd Length: 231  Bit Score: 46.01  E-value: 1.13e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 122 DLIQEGNTGLVRAVEKFDYERGfKFSTYATWWIRQAIS---RAIAQQERTVRLPVHlvedvnRMRNVARQLTRELGSDPE 198
Cdd:PRK12427  47 DMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILdelRELDWRPRRLRQKTH------KTNDAIREIAKRLGHEPN 119

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 199 PEQIATALGVSVERVNE--LVRWSQDTVSLDTPVGDDGDtnlGDLVADSDApsPEEIVLtgleRQRIEGLLSHLDDRSAG 276
Cdd:PRK12427 120 FEEISAELNLTAEEYQEylLLENAGTLESLDELLALEAH---NDILQSRDL--EENIII----EDNLKQALSQLDEREQL 190

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 501135355 277 IMRARYgledGREHSLTEVASRFSLSRERIRQLEIQALGRLRE 319
Cdd:PRK12427 191 ILHLYY----QHEMSLKEIALVLDLTEARICQLNKKIAQKIKS 229
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 260-318 1.69e-05

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: 41.71  E-value: 1.69e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 501135355 260 RQRIEGLLSHLDDRSAGIMRARYGledgREHSLTEVASRFSLSRERIRQLEIQALGRLR 318
Cdd:cd06171    1 RERLEEALDKLPEREREVILLRFG----EGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
83-274 1.98e-05

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 44.90  E-value: 1.98e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355  83 ELQRLVAEG-ERAKDLFIRANLRLVVSIARRYVRSGMPMLDLIQEGNTGLVRAVEKFDYERGFKFSTYATWWI-RQAISr 160
Cdd:PRK08295  13 ELVELARSGdKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCItRQIIT- 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501135355 161 AIaqqeRTvrlpvhlvedVNRMRNvaRQLTrelgsdpepeqiatalgvsvervnelvrwsqDTVSLDTPVGDDG-DTNLG 239
Cdd:PRK08295  92 AI----KT----------ANRQKH--IPLN-------------------------------SYVSLDKPIYDEEsDRTLL 124

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 501135355 240 DLVADSDAPSPEEIV----------------LTGLERqriEGLLSHLDDRS 274
Cdd:PRK08295 125 DVISEAKVTDPEELIiskeeledieekieelLSELEK---EVLELYLDGKS 172
 
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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