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Conserved domains on  [gi|55274894|gb|AAV49249|]
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RNA polymerase subunit sigma-38, partial [Shigella boydii]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK05657 super family cl35357
RNA polymerase sigma factor RpoS; Validated
 1-195 1.84e-136

RNA polymerase sigma factor RpoS; Validated


The actual alignment was detected with superfamily member PRK05657:

Pssm-ID: 235548 [Multi-domain]  Cd Length: 325  Bit Score: 384.31  E-value: 1.84e-136
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894    1 LRLVVKIARRYGNRGLALLALIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVY 80
Cdd:PRK05657  96 LRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPVHVVKELNVY 175

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894   81 LRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQS 160
Cdd:PRK05657 176 LRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLGGDPEKSLLDILADEQENGPEDTTQDDDMKQS 255

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 55274894  161 IVKWLFELNAKQREVLARRFGLLGYEAATLEDVGR 195
Cdd:PRK05657 256 IVKWLFELNDKQREVLARRFGLLGYEAATLEDVAR 290
 
Name Accession Description Interval E-value
PRK05657 PRK05657
RNA polymerase sigma factor RpoS; Validated
 1-195 1.84e-136

RNA polymerase sigma factor RpoS; Validated


Pssm-ID: 235548 [Multi-domain]  Cd Length: 325  Bit Score: 384.31  E-value: 1.84e-136
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894    1 LRLVVKIARRYGNRGLALLALIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVY 80
Cdd:PRK05657  96 LRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPVHVVKELNVY 175

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894   81 LRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQS 160
Cdd:PRK05657 176 LRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLGGDPEKSLLDILADEQENGPEDTTQDDDMKQS 255

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 55274894  161 IVKWLFELNAKQREVLARRFGLLGYEAATLEDVGR 195
Cdd:PRK05657 256 IVKWLFELNDKQREVLARRFGLLGYEAATLEDVAR 290
rpoS_proteo TIGR02394
RNA polymerase sigma factor RpoS; A sigma factor is a DNA-binding protein protein that binds ...
 1-195 1.08e-125

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: 355.57  E-value: 1.08e-125
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894     1 LRLVVKIARRYGNRGLALLALIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVY 80
Cdd:TIGR02394  56 LRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPVHVIKELNVY 135

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894    81 LRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQS 160
Cdd:TIGR02394 136 LRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPLDDDSSKSLLDTIADEQSIDPESLVQNDDLKQL 215

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 55274894   161 IVKWLFELNAKQREVLARRFGLLGYEAATLEDVGR 195
Cdd:TIGR02394 216 IEAWLAELNERQREVLARRFGLLGYEPATLEEVAA 250
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 1-195 9.62e-102

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: 294.27  E-value: 9.62e-102
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894   1 LRLVVKIARRYGNRGLALLALIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVY 80
Cdd:COG0568  40 LRLVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDPERGFRFSTYATWWIRQAITRAIADQWRTIRLPVHMAETLNKL 119

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894  81 LRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQS 160
Cdd:COG0568 120 RRAKRQLLQELGREPTPEEIAEELGVPEEKVREMLRLAREPVSLDAPVGDDEDSELGDLLEDEEAPSPEEALEEELLREE 199

                       170       180       190
                ....*....|....*....|....*....|....*
gi 55274894 161 IVKWLFELNAKQREVLARRFGLLGYEAATLEDVGR 195
Cdd:COG0568 200 LREALDTLTEREREILRLRFGLDDGEPHTLEEIGK 234
Sigma70_r3 pfam04539
Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the ...
 75-150 1.01e-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: 81.50  E-value: 1.01e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 55274894    75 KELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPED 150
Cdd:pfam04539   1 ELLNKIKRAQRELEQELGREPTPEEIAEELGLSPEKVREVLEAAREPVSLDTPVGEEEDGELGDLLEDDDIESPEE 76
 
Name Accession Description Interval E-value
PRK05657 PRK05657
RNA polymerase sigma factor RpoS; Validated
 1-195 1.84e-136

RNA polymerase sigma factor RpoS; Validated


Pssm-ID: 235548 [Multi-domain]  Cd Length: 325  Bit Score: 384.31  E-value: 1.84e-136
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894    1 LRLVVKIARRYGNRGLALLALIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVY 80
Cdd:PRK05657  96 LRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPVHVVKELNVY 175

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894   81 LRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQS 160
Cdd:PRK05657 176 LRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLGGDPEKSLLDILADEQENGPEDTTQDDDMKQS 255

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 55274894  161 IVKWLFELNAKQREVLARRFGLLGYEAATLEDVGR 195
Cdd:PRK05657 256 IVKWLFELNDKQREVLARRFGLLGYEAATLEDVAR 290
rpoS_proteo TIGR02394
RNA polymerase sigma factor RpoS; A sigma factor is a DNA-binding protein protein that binds ...
 1-195 1.08e-125

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: 355.57  E-value: 1.08e-125
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894     1 LRLVVKIARRYGNRGLALLALIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVY 80
Cdd:TIGR02394  56 LRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPVHVIKELNVY 135

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894    81 LRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQS 160
Cdd:TIGR02394 136 LRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPLDDDSSKSLLDTIADEQSIDPESLVQNDDLKQL 215

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 55274894   161 IVKWLFELNAKQREVLARRFGLLGYEAATLEDVGR 195
Cdd:TIGR02394 216 IEAWLAELNERQREVLARRFGLLGYEPATLEEVAA 250
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 1-195 9.62e-102

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: 294.27  E-value: 9.62e-102
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894   1 LRLVVKIARRYGNRGLALLALIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVY 80
Cdd:COG0568  40 LRLVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDPERGFRFSTYATWWIRQAITRAIADQWRTIRLPVHMAETLNKL 119

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894  81 LRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQS 160
Cdd:COG0568 120 RRAKRQLLQELGREPTPEEIAEELGVPEEKVREMLRLAREPVSLDAPVGDDEDSELGDLLEDEEAPSPEEALEEELLREE 199

                       170       180       190
                ....*....|....*....|....*....|....*
gi 55274894 161 IVKWLFELNAKQREVLARRFGLLGYEAATLEDVGR 195
Cdd:COG0568 200 LREALDTLTEREREILRLRFGLDDGEPHTLEEIGK 234
Sig70-cyanoRpoD TIGR02997
RNA polymerase sigma factor, cyanobacterial RpoD-like family; This family includes a number of ...
 1-195 6.30e-76

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: 229.82  E-value: 6.30e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894     1 LRLVVKIARRYGNRGLALLALIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVY 80
Cdd:TIGR02997  84 LRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKLNKI 163

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894    81 LRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKALLDILADEKENgPEDTTQDDDMKQS 160
Cdd:TIGR02997 164 KKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLEDDGES-PEEQVERESLRQD 242

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 55274894   161 IVKWLFELNAKQREVLARRFGLLGYEAATLEDVGR 195
Cdd:TIGR02997 243 LESLLAELTPRERQVLRLRFGLDGGEPLTLAEIGR 277
RpoD_Cterm TIGR02393
RNA polymerase sigma factor RpoD, C-terminal domain; This model represents the well-conserved ...
 1-194 1.17e-71

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: 216.78  E-value: 1.17e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894     1 LRLVVKIARRYGNRGLALLALIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVY 80
Cdd:TIGR02393  10 LRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKL 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894    81 LRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQS 160
Cdd:TIGR02393  90 IKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDESIESPDDAAAKELLREQ 169

                         170       180       190
                  ....*....|....*....|....*....|....
gi 55274894   161 IVKWLFELNAKQREVLARRFGLLGYEAATLEDVG 194
Cdd:TIGR02393 170 LDEVLETLTERERKVLRMRYGLLDGRPHTLEEVG 203
PRK07921 PRK07921
RNA polymerase sigma factor SigB; Reviewed
 1-195 3.48e-60

RNA polymerase sigma factor SigB; Reviewed


Pssm-ID: 181169 [Multi-domain]  Cd Length: 324  Bit Score: 190.33  E-value: 3.48e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894    1 LRLVVKIARRYGNRGLALLALIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVY 80
Cdd:PRK07921  96 LRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKL 175

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894   81 LRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQS 160
Cdd:PRK07921 176 ARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEATSAENAVIAGLLHTD 255

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 55274894  161 IVKWLFELNAKQREVLARRFGLLGYEAATLEDVGR 195
Cdd:PRK07921 256 IRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGK 290
PRK09210 PRK09210
RNA polymerase sigma factor RpoD; Validated
 1-195 7.39e-59

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 188.27  E-value: 7.39e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894    1 LRLVVKIARRYGNRGLALLALIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVY 80
Cdd:PRK09210 139 LRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKL 218

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894   81 LRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQS 160
Cdd:PRK09210 219 IRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAAYELLKEQ 298

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 55274894  161 IVKWLFELNAKQREVLARRFGLLGYEAATLEDVGR 195
Cdd:PRK09210 299 LEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGK 333
PRK05901 PRK05901
RNA polymerase sigma factor; Provisional
 1-195 2.35e-56

RNA polymerase sigma factor; Provisional


Pssm-ID: 235640 [Multi-domain]  Cd Length: 509  Bit Score: 185.58  E-value: 2.35e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894    1 LRLVVKIARRYGNRGLALLALIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVY 80
Cdd:PRK05901 281 LRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVETINKL 360

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894   81 LRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN-ERItSVDTPLG--GDSEkaLLDILADEKENGPEDTTqDDDM 157
Cdd:PRK05901 361 GRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNrEPI-SLDKTIGkeGDSQ--FGDFIEDSEAVSPVDAV-SFTL 436

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 55274894  158 KQSIVKWLFE-LNAKQREVLARRFGLLGYEAATLEDVGR 195
Cdd:PRK05901 437 LQDQLQEVLEtLSEREAGVIRMRFGLTDGQPKTLDEIGQ 475
PRK05949 PRK05949
RNA polymerase sigma factor; Validated
 1-195 3.53e-54

RNA polymerase sigma factor; Validated


Pssm-ID: 180321 [Multi-domain]  Cd Length: 327  Bit Score: 175.03  E-value: 3.53e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894    1 LRLVVKIARRYGNRGLALLALIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVY 80
Cdd:PRK05949 101 LRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEKLNKI 180

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894   81 LRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKALLDILADEkENGPEDTTQDDDMKQS 160
Cdd:PRK05949 181 KKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTELSELLEDE-GPSPDQYITQELLRQD 259

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 55274894  161 IVKWLFELNAKQREVLARRFGLLGYEAATLEDVGR 195
Cdd:PRK05949 260 LNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGE 294
PRK07406 PRK07406
RNA polymerase sigma factor RpoD; Validated
 1-194 4.45e-53

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236012 [Multi-domain]  Cd Length: 373  Bit Score: 173.43  E-value: 4.45e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894    1 LRLVVKIARRYGNRGLALLALIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVY 80
Cdd:PRK07406 146 LRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRI 225

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894   81 LRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKALLDILADEKENgPEDTTQDDDMKQS 160
Cdd:PRK07406 226 KKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEADGET-PEDDVAKNLLRED 304

                        170       180       190
                 ....*....|....*....|....*....|....
gi 55274894  161 IVKWLFELNAKQREVLARRFGLLGYEAATLEDVG 194
Cdd:PRK07406 305 LEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIG 338
PRK07598 PRK07598
RNA polymerase sigma factor SigC; Validated
 1-195 5.32e-53

RNA polymerase sigma factor SigC; Validated


Pssm-ID: 236067 [Multi-domain]  Cd Length: 415  Bit Score: 174.67  E-value: 5.32e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894    1 LRLVVKIARRYGNRGLALLALIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVY 80
Cdd:PRK07598 185 LRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKI 264

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894   81 LRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKALLDILADEkENGPEDTTQDDDMKQS 160
Cdd:PRK07598 265 KKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLLRVPRSVSLETKVGKDKDTELGDLLETD-DISPEEMLMRESLQRD 343

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 55274894  161 IVKWLFELNAKQREVLARRFGLLGYEAATLEDVGR 195
Cdd:PRK07598 344 LQHLLADLTSRERDVIRMRFGLADGHTYSLAEIGR 378
PRK05658 PRK05658
RNA polymerase sigma factor RpoD; Validated
 1-194 1.11e-47

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 235549 [Multi-domain]  Cd Length: 619  Bit Score: 164.20  E-value: 1.11e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894    1 LRLVVKIARRYGNRGLALLALIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVY 80
Cdd:PRK05658 390 LRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKL 469

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894   81 LRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRL-NERItSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQ 159
Cdd:PRK05658 470 NRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIaKEPI-SLETPIGDDEDSHLGDFIEDKNAELPIDAAIQESLRE 548

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 55274894  160 SIVKWLFELNAKQREVLARRFGLLGYEAATLEDVG 194
Cdd:PRK05658 549 ATTDVLASLTPREAKVLRMRFGIDMNTDHTLEEVG 583
PRK07405 PRK07405
RNA polymerase sigma factor SigD; Validated
 1-194 2.77e-47

RNA polymerase sigma factor SigD; Validated


Pssm-ID: 180963 [Multi-domain]  Cd Length: 317  Bit Score: 157.23  E-value: 2.77e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894    1 LRLVVKIARRYGNRGLALLALIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVY 80
Cdd:PRK07405  91 LRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKLNKI 170

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894   81 LRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKALLDILADEKENgPEDTTQDDDMKQS 160
Cdd:PRK07405 171 KKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDTGAS-PEDFATQSSLQLD 249

                        170       180       190
                 ....*....|....*....|....*....|....
gi 55274894  161 IVKWLFELNAKQREVLARRFGLLGYEAATLEDVG 194
Cdd:PRK07405 250 LERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIG 283
rpoH_proteo TIGR02392
alternative sigma factor RpoH; A sigma factor is a DNA-binding protein protein that binds to ...
 1-195 2.53e-27

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: 103.90  E-value: 2.53e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894     1 LRLVVKIARRYGNRGLALLALIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRtirlpihIVK----- 75
Cdd:TIGR02392  45 LRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYILRNWR-------LVKvattk 117

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894    76 ---ELNVYLRTARelsHKLDHEPSAEE---IAEQLDKPVDDVSRM-LRLNERITSVDTPLGGDSEK--ALLDILADEKEN 146
Cdd:TIGR02392 118 aqrKLFFNLRKMK---KRLQGWLNPEEveaIAEELGVSEREVREMeSRLSGQDMSLNASIDDDEDDggAPIAYLVDKRSD 194

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 55274894   147 gPEDT----TQDDDMKQSIVKWLFELNAKQREVLARRFglLGYEAATLEDVGR 195
Cdd:TIGR02392 195 -PEDTleeeQWEELQRQALANALGSLDARSRRIIEARW--LDDDKLTLQELAA 244
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 1-180 3.19e-27

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: 102.98  E-value: 3.19e-27
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894   1 LRLVVKIARRYGNRGLALLA-LIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRqtieRAIMNQTRTI-RLPIHIVKELN 78
Cdd:COG1191  25 LPLVKKIASRLAGRLPAELDdLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIR----GAILDYLRDEdWVPRSVRELAR 100

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894  79 VYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLR--LNERITSVDTPLGGDSEkaLLDILadeKENGPEDTTQDDD 156
Cdd:COG1191 101 KIEEAIEELEQELGREPTDEEIAEELGISLEEVQEALEaaNAYQLLSLDEPLEDGDD--LLDLL---ESGDPEEELEHEE 175

                       170       180
                ....*....|....*....|....
gi 55274894 157 MKQSIVKWLFELNAKQREVLARRF 180
Cdd:COG1191 176 LREALAEAIEQLPERERLVLSLYY 199
PRK06596 PRK06596
RNA polymerase factor sigma-32; Reviewed
 1-192 5.62e-27

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 235838 [Multi-domain]  Cd Length: 284  Bit Score: 103.33  E-value: 5.62e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894    1 LRLVVKIARRYGNRGLALLALIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRtirlpihIVK----- 75
Cdd:PRK06596  58 LRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWR-------IVKvattk 130

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894   76 ---ELNVYLRTARELSHKLDHEpSAEEIAEQLDKPVDDVSRM-LRLNERITSVDTPLGGDSEK--ALLDILADEKENgPE 149
Cdd:PRK06596 131 aqrKLFFNLRKAKKRLGWLNPE-EVEMVAEELGVSEEEVREMeSRLSGQDASLDAPIDDDDEEsgAPQDYLEDKSSD-PA 208

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 55274894  150 DT---TQDDDMKQSIVKW-LFELNAKQREVLARRFglLGYEAATLED 192
Cdd:PRK06596 209 DVleeDNWEDQRRALLADaLEGLDERSRDIIEARW--LDDDKSTLQE 253
SigBFG TIGR02980
RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; This group of similar sigma-70 factors ...
 1-180 1.67e-26

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


Pssm-ID: 274373 [Multi-domain]  Cd Length: 227  Bit Score: 100.76  E-value: 1.67e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894     1 LRLVVKIARRYGNRGLALLALIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIvKELNVY 80
Cdd:TIGR02980  13 LPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIMGEIKRFFRDDTWAVRVPRRL-KELGVK 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894    81 LRTARE-LSHKLDHEPSAEEIAEQLDKPVDDVSRML--RLNERITSVDTPLG--GDSEKALLDILADEKENgpEDTTQDd 155
Cdd:TIGR02980  92 INKATEeLTQRLGRSPTIAEIAERLGVSEEEVVEALeaGNAYQALSLDASIEddDGDPIALLDTLGDEDDA--LETVED- 168

                         170       180
                  ....*....|....*....|....*
gi 55274894   156 dmKQSIVKWLFELNAKQREVLARRF 180
Cdd:TIGR02980 169 --RLALKPLLAALPERERRILLLRF 191
rpoH2 PRK07500
RNA polymerase factor sigma-32; Reviewed
 1-194 1.27e-25

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 236033 [Multi-domain]  Cd Length: 289  Bit Score: 100.11  E-value: 1.27e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894    1 LRLVVKIARRYGNRGLALLALIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRL-PIHIVKELNV 79
Cdd:PRK07500  50 MRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVRGgTSSAQKALFF 129

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894   80 YLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRM-LRLNERITSVDTPLGGDSEKAL--LDILADEKENGPEDTT 152
Cdd:PRK07500 130 NLRRLRarlaQADEELTKQEIHREIATALGVSLSDVEMMdARLSGPDASLNAPQSEEDEGRSerMDFLVDDSPLPDEQVE 209

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 55274894  153 QDDDMKQSIVkWLFE----LNAKQREVL-ARRfglLGYEAATLEDVG 194
Cdd:PRK07500 210 SSIDGERRRR-WLTQalqtLNERELRIIrERR---LREDGATLEALG 252
FliA_WhiG TIGR02479
RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar ...
 21-195 2.28e-21

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: 87.33  E-value: 2.28e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894    21 LIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQtierAIMNQTRTI----RLPIHIVKELNvylRTARELSHKLDHEPS 96
Cdd:TIGR02479  29 LIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRG----AMLDELRRLdwvpRSLRQKARKLE---RAIRELEARLGREPT 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894    97 AEEIAEQLDKPVDDVSRMLR--LNERITSVDTPL-GGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQR 173
Cdd:TIGR02479 102 EEEIAEELGMDLKEYRQALNeiNALSLVSLDELLeSGDDGGSLIDRIEDDKSEDPEEELEREELREALAEAIESLSEREQ 181

                         170       180
                  ....*....|....*....|..
gi 55274894   174 EVLARRFgllgYEAATLEDVGR 195
Cdd:TIGR02479 182 LVLSLYY----YEELNLKEIGE 199
Sigma70_r3 pfam04539
Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the ...
 75-150 1.01e-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: 81.50  E-value: 1.01e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 55274894    75 KELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKALLDILADEKENGPED 150
Cdd:pfam04539   1 ELLNKIKRAQRELEQELGREPTPEEIAEELGLSPEKVREVLEAAREPVSLDTPVGEEEDGELGDLLEDDDIESPEE 76
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 1-66 7.85e-18

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: 73.78  E-value: 7.85e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 55274894     1 LRLVVKIARRYGNRGLALLALIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRT 66
Cdd:pfam04542   6 LPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRRT 71
PRK06288 PRK06288
RNA polymerase sigma factor WhiG; Reviewed
 21-195 1.32e-17

RNA polymerase sigma factor WhiG; Reviewed


Pssm-ID: 235770 [Multi-domain]  Cd Length: 268  Bit Score: 78.19  E-value: 1.32e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894   21 LIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQtierAIMNQTRTI-RLPIHIVKELNVYLRTARELSHKLDHEPSAEE 99
Cdd:PRK06288  64 LVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRG----AIFDELRSIdWIPRSVRQKARQIERAIAMLEARLGRTPSDEE 139

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894  100 IAEQLDKPVDDV-SRMLRLNEriTSV----DTPLGGD--SEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQ 172
Cdd:PRK06288 140 IADELGISLEEYnSLLSKLSG--TSVvslnDLWFGGDegDEVSLMDTLESPAALNPDEIAEREEIKRVIVEAIKTLPERE 217

                        170       180
                 ....*....|....*....|...
gi 55274894  173 REVLArrfgLLGYEAATLEDVGR 195
Cdd:PRK06288 218 KKVLI----LYYYEDLTLKEIGK 236
PRK07122 PRK07122
RNA polymerase sigma factor SigF; Reviewed
 1-180 1.79e-16

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 168831 [Multi-domain]  Cd Length: 264  Bit Score: 75.20  E-value: 1.79e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894    1 LRLVVKIARRYGNRGLALLALIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIvKELNVY 80
Cdd:PRK07122  50 LPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWSVKVPRRL-KELHLR 128

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894   81 LRTAR-ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNE--RITSVDTPLGGDSE--KALLDILADekengpEDTTQDD 155
Cdd:PRK07122 129 LGRATaELSQRLGRAPTASELAAELGMDREEVVEGLVAGSayNTLSIDSGGGSGDDdaRAIADTLGD------VDAGLDQ 202

                        170       180
                 ....*....|....*....|....*.
gi 55274894  156 DMKQSIVKWLFE-LNAKQREVLARRF 180
Cdd:PRK07122 203 IENREALRPLLAaLPERERTVLVLRF 228
PRK07670 PRK07670
FliA/WhiG family RNA polymerase sigma factor;
21-195 4.44e-15

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 181075 [Multi-domain]  Cd Length: 251  Bit Score: 70.84  E-value: 4.44e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894   21 LIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQtierAIMNQTRTI-RLPihivkelnvylRTARELSHKLDH------ 93
Cdd:PRK07670  55 LKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRG----AIIDGLRKEdWLP-----------RSMREKTKKVEAaiekle 119

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894   94 -----EPSAEEIAEQLDKPVDDV---------SRMLRLNERITsvdtplGGDSEKALLDILADEKENGPEDTTQDDDMKQ 159
Cdd:PRK07670 120 qrymrNVTPKEVAAELGMTEEEVeatmnegffANLLSIDEKTH------DQDDGENVSVTIRDDKTPTPEEKLLKEELIE 193

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 55274894  160 SIVKWLFELNAKQREVLarrfGLLGYEAATLEDVGR 195
Cdd:PRK07670 194 ELAEKIKQLSEKEQLVI----SLFYKEELTLTEIGQ 225
PRK08215 PRK08215
RNA polymerase sporulation sigma factor SigG;
1-180 9.62e-15

RNA polymerase sporulation sigma factor SigG;


Pssm-ID: 181296 [Multi-domain]  Cd Length: 258  Bit Score: 70.36  E-value: 9.62e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894    1 LRLVVKIARRYGNRGLALLALIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTrtirlPIHIVKELN-- 78
Cdd:PRK08215  47 LRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-----PIRVSRSLRdi 121

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894   79 VY--LRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKAL--LDILADEK---ENGPEDT 151
Cdd:PRK08215 122 AYkaLQVREKLINENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIYHDGGDPIyvMDQISDEKnkdENWLEEI 201

                        170       180
                 ....*....|....*....|....*....
gi 55274894  152 TQDDDMKQsivkwlfeLNAKQREVLARRF 180
Cdd:PRK08215 202 ALKEAMKK--------LNDREKLILNLRF 222
PRK07408 PRK07408
RNA polymerase sigma factor SigF; Reviewed
 21-176 1.18e-14

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 180965 [Multi-domain]  Cd Length: 256  Bit Score: 69.95  E-value: 1.18e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894   21 LIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEI 100
Cdd:PRK07408  56 LVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPTVRIPRRWQELQRQAKKVRQELRQELGRQPTDQEI 135

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894  101 AEQLDKPVDD--VSRMLRLNERITSVDTPLGGDSEKA--LLDILADEKENGPEDTTQDddmKQSIVKWLFELNAKQREVL 176
Cdd:PRK07408 136 AQALDISLEEwqEIKLALQNRTPLSLDAPVNQDEDGStsLGDLLPDPRYRSFQLAQED---RIRLQQALAQLEERTREVL 212
spore_sigF TIGR02885
RNA polymerase sigma-F factor; Members of this protein family are the RNA polymerase sigma ...
 1-180 3.46e-13

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: 65.51  E-value: 3.46e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894     1 LRLVVKIARRYGNRGLALLALIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIER-----AIMNQTRTirlpihiVK 75
Cdd:TIGR02885  21 LRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRflrddGIIKVSRS-------LK 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894    76 ELNVYLRTARE-LSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSV-DTPLGGDSEKA-LLDILADEkenGPEDTT 152
Cdd:TIGR02885  94 ELARKIRYMKEeLSKELGREPTINELAEALGVSPEEIVMALESARSPQSLyDTVHQDDGDPIyLLDQIADK---GSEDSD 170

                         170       180
                  ....*....|....*....|....*...
gi 55274894   153 QDDdmKQSIVKWLFELNAKQREVLARRF 180
Cdd:TIGR02885 171 WLE--KIALKEAISKLDERERQIIMLRY 196
PRK08583 PRK08583
RNA polymerase sigma factor SigB; Validated
 3-174 4.90e-12

RNA polymerase sigma factor SigB; Validated


Pssm-ID: 236306 [Multi-domain]  Cd Length: 257  Bit Score: 62.79  E-value: 4.90e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894    3 LVVKIARRYGNRGLALLALIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIvKELNVYLR 82
Cdd:PRK08583  41 LVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRDKTWSVHVPRRI-KELGPKIK 119

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894   83 TA-RELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRL--NERITSVDTPLGGDSEK---ALLDILAdEKENGPEDTTQD-- 154
Cdd:PRK08583 120 KAvDELTTELQRSPKISEIADRLGVSEEEVLEAMEMgkSYQALSVDHSIEADSDGstvTLLDIVG-QQEDGYELTEQRmi 198

                        170       180
                 ....*....|....*....|....*...
gi 55274894  155 --------DDMKQSIVKWLFELNAKQRE 174
Cdd:PRK08583 199 lekilpvlSDREKSIIQCTFIENLSQKE 226
PRK05572 PRK05572
RNA polymerase sporulation sigma factor, SigF/SigG family;
1-111 2.74e-11

RNA polymerase sporulation sigma factor, SigF/SigG family;


Pssm-ID: 180137 [Multi-domain]  Cd Length: 252  Bit Score: 60.37  E-value: 2.74e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894    1 LRLVVKIARRYGNRGLALLALIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIER-----AIMNQTRTIrlpihivK 75
Cdd:PRK05572  42 LRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRflrddGTVKVSRSL-------K 114

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 55274894   76 ELNVYLRTAR-ELSHKLDHEPSAEEIAEQLDKPVDDV 111
Cdd:PRK05572 115 ETANKIRKDKdELSKELGREPTIEELAEYLGVTPEEV 151
PRK05803 PRK05803
RNA polymerase sporulation sigma factor SigK;
1-195 9.81e-11

RNA polymerase sporulation sigma factor SigK;


Pssm-ID: 180266 [Multi-domain]  Cd Length: 233  Bit Score: 58.80  E-value: 9.81e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894    1 LRLVVKIARRYGNRGLALLALIEEGNLGLIRAVEKFDPERGFRFSTYATwwirqtieRAIMNqtrtirlpihivkELNVY 80
Cdd:PRK05803  59 LRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYAA--------RCIEN-------------EILMH 117

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894   81 LRtarelshkldhepsaeeiaeQLDKPVDDVSrmlrLNEritsvdtPLGGD---SEKALLDILADEKENGPEDTTQDDDM 157
Cdd:PRK05803 118 LR--------------------NLKKTKKEVS----LQD-------PIGVDkegNEISLIDILGSEEDDVIEQVELKMEV 166

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 55274894  158 KQsIVKWLFELNAKQREVLARRFGLLGYEAATLEDVGR 195
Cdd:PRK05803 167 EK-LYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAK 203
PRK05911 PRK05911
RNA polymerase sigma factor sigma-28; Reviewed
 21-195 3.00e-10

RNA polymerase sigma factor sigma-28; Reviewed


Pssm-ID: 235644 [Multi-domain]  Cd Length: 257  Bit Score: 57.71  E-value: 3.00e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894   21 LIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTrtiRLPIHIVKELNVYLRTARELSHKLDHEPSAEEI 100
Cdd:PRK05911  56 LYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRKQD---WVPRSVHQKANKLADAMDSLRQSLGKEPTDGEL 132

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894  101 AEQLDKPVDDVSR---------MLRLNERITSVDTplgGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 171
Cdd:PRK05911 133 CEYLNISQQELSGwfssarpalILSLNEEFPCQSD---DEAGLALEERIADERAETGYDVVDKKEFSSILAEAILALEEK 209

                        170       180
                 ....*....|....*....|....
gi 55274894  172 QREVLArrfgLLGYEAATLEDVGR 195
Cdd:PRK05911 210 ERKVMA----LYYYEELVLKEIGK 229
PRK08301 PRK08301
RNA polymerase sporulation sigma factor SigE;
1-48 7.03e-08

RNA polymerase sporulation sigma factor SigE;


Pssm-ID: 236228 [Multi-domain]  Cd Length: 234  Bit Score: 50.62  E-value: 7.03e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 55274894    1 LRLVVKIARRYGNRGLALLALIEEGNLGLIRAVEKFDPERGFRFSTYA 48
Cdd:PRK08301  62 LRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYA 109
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 1-116 7.10e-08

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: 49.65  E-value: 7.10e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894     1 LRLVVKIARRYGNRGLALLALIEEGNLGLIRAVEKFDPERgfRFSTYATWWIRQTIERAImNQTRTIRLPIHIVKELNVY 80
Cdd:TIGR02937  11 LPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEG--SFKAWLFRIARNLILDYL-RRKRRLRRELDLLEELLDS 87

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 55274894    81 LRTARE-------------------------LSHKLDHEPSAEEIAEQLDKPVDDVSRMLR 116
Cdd:TIGR02937  88 DPSPEEeleqeeerealrealeklpererevLVLRYLEGLSYKEIAEILGISVGTVKRRLK 148
fliA PRK06986
flagellar biosynthesis sigma factor; Validated
 21-176 8.21e-08

flagellar biosynthesis sigma factor; Validated


Pssm-ID: 235901 [Multi-domain]  Cd Length: 236  Bit Score: 50.62  E-value: 8.21e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894   21 LIEEGNLGLIRAVEKFDPERGFRFSTYAtwwiRQTIERAIMNQ-------TRTIRLPIHIVKElnvylrTARELSHKLDH 93
Cdd:PRK06986  41 LIQAGMIGLLEAARRYDGEQGASFETYA----GQRIRGAMLDElrsldwvPRSVRRNAREVAQ------AIRQLEQELGR 110

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894   94 EPSAEEIAEQLDKPVDDVSRMLR--LNERITSVDTpLGGDSEKALLDILADEKENgPEDTTQDDDMKQSIVKWLFELNAK 171
Cdd:PRK06986 111 EPTDTEVAEKLGLSLEEYREMLLdtNISQLFSIDE-LRGEHGDSILVTEDHQDED-PLQQLEDEELREALVEAIESLPER 188


                 ....*
gi 55274894  172 QREVL 176
Cdd:PRK06986 189 EQLVL 193
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
3-176 2.10e-04

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 40.66  E-value: 2.10e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894    3 LVVKIARRYGNRGLALLALIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPihivkeLNVYLr 82
Cdd:PRK08295  36 FVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCITRQIITAIKTANRQKHIP------LNSYV- 108

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894   83 tarelshkldhepsaeeiaeQLDKPVDDvsrmlrlneritsvdtplgGDSEKALLDILADEKENGPE----DTTQDDDMK 158
Cdd:PRK08295 109 --------------------SLDKPIYD-------------------EESDRTLLDVISEAKVTDPEeliiSKEELEDIE 149

                        170
                 ....*....|....*...
gi 55274894  159 QSIVKWLFELnakQREVL 176
Cdd:PRK08295 150 EKIEELLSEL---EKEVL 164
PRK12427 PRK12427
FliA/WhiG family RNA polymerase sigma factor;
27-138 4.05e-04

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 183523 [Multi-domain]  Cd Length: 231  Bit Score: 39.84  E-value: 4.05e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55274894   27 LGLIRAVEKFD-PERGFrfSTYATWWIRQTIE---RAIMNQTRTIRLPIHIVKELnvylrtARELSHKLDHEPSAEEIAE 102
Cdd:PRK12427  54 MGLLEALRRYGhPDEQF--AAYAVHRIRGAILdelRELDWRPRRLRQKTHKTNDA------IREIAKRLGHEPNFEEISA 125

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 55274894  103 QLDKPVDDVSRMLRLN--ERITSVDTPLGGDSEKALLD 138
Cdd:PRK12427 126 ELNLTAEEYQEYLLLEnaGTLESLDELLALEAHNDILQ 163
 
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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