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Conserved domains on  [gi|499635672|ref|WP_011316406|]
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MULTISPECIES: RpoD/SigA family RNA polymerase sigma factor [Nostocaceae]

Protein Classification

RpoD/SigA family RNA polymerase sigma factor( domain architecture ID 11496295)

RpoD/SigA family RNA polymerase sigma factor similar to Synechococcus elongatus RNA polymerase sigma factor SigA2, which is a component of the biological clock pathway that affects the circadian expression of a subset of genes in this bacterium

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Sig70-cyanoRpoD TIGR02997
RNA polymerase sigma factor, cyanobacterial RpoD-like family; This family includes a number of ...
 6-303 2.18e-167

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: 466.72  E-value: 2.18e-167
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672    6 DSVGIYLREISKYPMLTPEQEITLARQVKQMTVVQQHKQVLEEQLHQQLNIQQLAADMGKSETEVFQILRLGQKAKEKMI 85
Cdd:TIGR02997   1 DLVRLYLQEIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKMI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672   86 AANLRLVVAIAKKYRWSQLEFLDLVQEGSIGLQKAVERFDPNRGYKFSTCAYWWIRQEITKAIANKSTTIRTPSHMNDRL 165
Cdd:TIGR02997  81 KANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672  166 IKLKKVQRELVKILGREPNIAEIAEFAELEPNQVRECLIAFRHPLSLDRPMGQEDEVDFLEILPADGTSPNEYLDEGFLR 245
Cdd:TIGR02997 161 NKIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLEDDGESPEEQVERESLR 240

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 499635672  246 QDLANCLITLKPLQKQVLMLRFGLGSVDKLSTKQIAERLNIKQAKVGTTQKQAIKVLH 303
Cdd:TIGR02997 241 QDLESLLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR 298
 
Name Accession Description Interval E-value
Sig70-cyanoRpoD TIGR02997
RNA polymerase sigma factor, cyanobacterial RpoD-like family; This family includes a number of ...
 6-303 2.18e-167

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: 466.72  E-value: 2.18e-167
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672    6 DSVGIYLREISKYPMLTPEQEITLARQVKQMTVVQQHKQVLEEQLHQQLNIQQLAADMGKSETEVFQILRLGQKAKEKMI 85
Cdd:TIGR02997   1 DLVRLYLQEIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKMI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672   86 AANLRLVVAIAKKYRWSQLEFLDLVQEGSIGLQKAVERFDPNRGYKFSTCAYWWIRQEITKAIANKSTTIRTPSHMNDRL 165
Cdd:TIGR02997  81 KANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672  166 IKLKKVQRELVKILGREPNIAEIAEFAELEPNQVRECLIAFRHPLSLDRPMGQEDEVDFLEILPADGTSPNEYLDEGFLR 245
Cdd:TIGR02997 161 NKIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLEDDGESPEEQVERESLR 240

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 499635672  246 QDLANCLITLKPLQKQVLMLRFGLGSVDKLSTKQIAERLNIKQAKVGTTQKQAIKVLH 303
Cdd:TIGR02997 241 QDLESLLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR 298
PRK05949 PRK05949
RNA polymerase sigma factor; Validated
 2-314 2.96e-108

RNA polymerase sigma factor; Validated


Pssm-ID: 180321 [Multi-domain]  Cd Length: 327  Bit Score: 317.94  E-value: 2.96e-108
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672   2 SPQPDSVGIYLREISKYPMLTPEQEITLARQVKQMTVVQQHKQVLEEQLHQQLNIQQLAADMGKSETEVFQILRLGQKAK 81
Cdd:PRK05949  14 TFSADMVRTYLHEIGRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAK 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672  82 EKMIAANLRLVVAIAKKYRWSQLEFLDLVQEGSIGLQKAVERFDPNRGYKFSTCAYWWIRQEITKAIANKSTTIRTPSHM 161
Cdd:PRK05949  94 QKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHI 173

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672 162 NDRLIKLKKVQRELVKILGREPNIAEIAEFAELEPNQVRECLIAFRHPLSLDRPMGQEDEVDFLEILPADGTSPNEYLDE 241
Cdd:PRK05949 174 TEKLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTELSELLEDEGPSPDQYITQ 253

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 499635672 242 GFLRQDLANCLITLKPLQKQVLMLRFGLGSVDKLSTKQIAERLNIKQAKVGTTQKQAIKVLHRQQPQMREYLA 314
Cdd:PRK05949 254 ELLRQDLNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRRRRANVKEYLA 326
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 11-314 2.91e-95

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: 282.71  E-value: 2.91e-95
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672  11 YLREISKYPMLTPEQEITLARQVKQMtvvqqhkqvleeqlhqqlniqqlaadmgksetevfqilrlGQKAKEKMIAANLR 90
Cdd:COG0568    2 YLREIGRVPLLTAEEEVELARRIQAG----------------------------------------DEEAKRKLVEANLR 41

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672  91 LVVAIAKKYRWSQLEFLDLVQEGSIGLQKAVERFDPNRGYKFSTCAYWWIRQEITKAIANKSTTIRTPSHMNDRLIKLKK 170
Cdd:COG0568   42 LVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDPERGFRFSTYATWWIRQAITRAIADQWRTIRLPVHMAETLNKLRR 121

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672 171 VQRELVKILGREPNIAEIAEFAELEPNQVRECLIAFRHPLSLDRPMGQEDEVDFLEILPADGT-SPNEYLDEGFLRQDLA 249
Cdd:COG0568  122 AKRQLLQELGREPTPEEIAEELGVPEEKVREMLRLAREPVSLDAPVGDDEDSELGDLLEDEEApSPEEALEEELLREELR 201

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 499635672 250 NCLITLKPLQKQVLMLRFGLGSVDKLSTKQIAERLNIKQAKVGTTQKQAIKVL--HRQQPQMREYLA 314
Cdd:COG0568  202 EALDTLTEREREILRLRFGLDDGEPHTLEEIGKEFGVSRERVRQIEAKALRKLrhPLRSRKLRDYLD 268
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 84-152 1.63e-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: 78.01  E-value: 1.63e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 499635672   84 MIAANLRLVVAIAKKYRWSQLEFLDLVQEGSIGLQKAVERFDPNRGYKFSTCAYWWIRQEITKAIANKS 152
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQR 69
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 245-302 6.53e-06

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: 42.86  E-value: 6.53e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 499635672 245 RQDLANCLITLKPLQKQVLMLRFGLGsvdkLSTKQIAERLNIKQAKVGTTQKQAIKVL 302
Cdd:cd06171    1 RERLEEALDKLPEREREVILLRFGEG----LSYEEIAEILGISRSTVRQRLHRALKKL 54
 
Name Accession Description Interval E-value
Sig70-cyanoRpoD TIGR02997
RNA polymerase sigma factor, cyanobacterial RpoD-like family; This family includes a number of ...
 6-303 2.18e-167

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: 466.72  E-value: 2.18e-167
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672    6 DSVGIYLREISKYPMLTPEQEITLARQVKQMTVVQQHKQVLEEQLHQQLNIQQLAADMGKSETEVFQILRLGQKAKEKMI 85
Cdd:TIGR02997   1 DLVRLYLQEIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKMI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672   86 AANLRLVVAIAKKYRWSQLEFLDLVQEGSIGLQKAVERFDPNRGYKFSTCAYWWIRQEITKAIANKSTTIRTPSHMNDRL 165
Cdd:TIGR02997  81 KANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672  166 IKLKKVQRELVKILGREPNIAEIAEFAELEPNQVRECLIAFRHPLSLDRPMGQEDEVDFLEILPADGTSPNEYLDEGFLR 245
Cdd:TIGR02997 161 NKIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLEDDGESPEEQVERESLR 240

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 499635672  246 QDLANCLITLKPLQKQVLMLRFGLGSVDKLSTKQIAERLNIKQAKVGTTQKQAIKVLH 303
Cdd:TIGR02997 241 QDLESLLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR 298
PRK05949 PRK05949
RNA polymerase sigma factor; Validated
 2-314 2.96e-108

RNA polymerase sigma factor; Validated


Pssm-ID: 180321 [Multi-domain]  Cd Length: 327  Bit Score: 317.94  E-value: 2.96e-108
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672   2 SPQPDSVGIYLREISKYPMLTPEQEITLARQVKQMTVVQQHKQVLEEQLHQQLNIQQLAADMGKSETEVFQILRLGQKAK 81
Cdd:PRK05949  14 TFSADMVRTYLHEIGRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAK 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672  82 EKMIAANLRLVVAIAKKYRWSQLEFLDLVQEGSIGLQKAVERFDPNRGYKFSTCAYWWIRQEITKAIANKSTTIRTPSHM 161
Cdd:PRK05949  94 QKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHI 173

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672 162 NDRLIKLKKVQRELVKILGREPNIAEIAEFAELEPNQVRECLIAFRHPLSLDRPMGQEDEVDFLEILPADGTSPNEYLDE 241
Cdd:PRK05949 174 TEKLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTELSELLEDEGPSPDQYITQ 253

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 499635672 242 GFLRQDLANCLITLKPLQKQVLMLRFGLGSVDKLSTKQIAERLNIKQAKVGTTQKQAIKVLHRQQPQMREYLA 314
Cdd:PRK05949 254 ELLRQDLNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRRRRANVKEYLA 326
PRK07405 PRK07405
RNA polymerase sigma factor SigD; Validated
 1-314 2.57e-99

RNA polymerase sigma factor SigD; Validated


Pssm-ID: 180963 [Multi-domain]  Cd Length: 317  Bit Score: 294.74  E-value: 2.57e-99
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672   1 MSPQPDSVGIYLREISKYPMLTPEQEITLARQVKQMTVVQQHKQVLEEQLHQQLNIQQLAADMGKSETEVFQILRLGQKA 80
Cdd:PRK07405   3 AKTSTDLVRTYLREIGRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAA 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672  81 KEKMIAANLRLVVAIAKKYRWSQLEFLDLVQEGSIGLQKAVERFDPNRGYKFSTCAYWWIRQEITKAIANKSTTIRTPSH 160
Cdd:PRK07405  83 KRKMVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIH 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672 161 MNDRLIKLKKVQRELVKILGREPNIAEIAEFAELEPNQVRECLIAFRHPLSLDRPMGQEDEVDFLEILPADGTSPNEYLD 240
Cdd:PRK07405 163 ITEKLNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDTGASPEDFAT 242

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 499635672 241 EGFLRQDLANCLITLKPLQKQVLMLRFGLGSVDKLSTKQIAERLNIKQAKVGTTQKQAIKVLHRQQPQMREYLA 314
Cdd:PRK07405 243 QSSLQLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRKRKANIQEYLA 316
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 11-314 2.91e-95

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: 282.71  E-value: 2.91e-95
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672  11 YLREISKYPMLTPEQEITLARQVKQMtvvqqhkqvleeqlhqqlniqqlaadmgksetevfqilrlGQKAKEKMIAANLR 90
Cdd:COG0568    2 YLREIGRVPLLTAEEEVELARRIQAG----------------------------------------DEEAKRKLVEANLR 41

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672  91 LVVAIAKKYRWSQLEFLDLVQEGSIGLQKAVERFDPNRGYKFSTCAYWWIRQEITKAIANKSTTIRTPSHMNDRLIKLKK 170
Cdd:COG0568   42 LVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDPERGFRFSTYATWWIRQAITRAIADQWRTIRLPVHMAETLNKLRR 121

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672 171 VQRELVKILGREPNIAEIAEFAELEPNQVRECLIAFRHPLSLDRPMGQEDEVDFLEILPADGT-SPNEYLDEGFLRQDLA 249
Cdd:COG0568  122 AKRQLLQELGREPTPEEIAEELGVPEEKVREMLRLAREPVSLDAPVGDDEDSELGDLLEDEEApSPEEALEEELLREELR 201

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 499635672 250 NCLITLKPLQKQVLMLRFGLGSVDKLSTKQIAERLNIKQAKVGTTQKQAIKVL--HRQQPQMREYLA 314
Cdd:COG0568  202 EALDTLTEREREILRLRFGLDDGEPHTLEEIGKEFGVSRERVRQIEAKALRKLrhPLRSRKLRDYLD 268
PRK07406 PRK07406
RNA polymerase sigma factor RpoD; Validated
 6-269 1.20e-72

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236012 [Multi-domain]  Cd Length: 373  Bit Score: 228.51  E-value: 1.20e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672   6 DSVGIYLREISKYPMLTPEQEITLARQVKQMTVVQQHKQVLEEQLHQQLNIQQLAADMGKSETEVFQILRLGQKAKEKMI 85
Cdd:PRK07406  63 DSIRVYLQEIGRIRLLRPDEEIELARKIADLLELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKEKMV 142

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672  86 AANLRLVVAIAKKYRWSQLEFLDLVQEGSIGLQKAVERFDPNRGYKFSTCAYWWIRQEITKAIANKSTTIRTPSHMNDRL 165
Cdd:PRK07406 143 QSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETI 222

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672 166 IKLKKVQRELVKILGREPNIAEIAEFAELEPNQVRECLIAFRHPLSLDRPMGQEDEV---DFLEilpADGTSPNEYLDEG 242
Cdd:PRK07406 223 SRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSrlgDFIE---ADGETPEDDVAKN 299

                        250       260
                 ....*....|....*....|....*..
gi 499635672 243 FLRQDLANCLITLKPLQKQVLMLRFGL 269
Cdd:PRK07406 300 LLREDLEGVLATLSPRERDVLRLRYGL 326
PRK07598 PRK07598
RNA polymerase sigma factor SigC; Validated
 6-313 9.55e-72

RNA polymerase sigma factor SigC; Validated


Pssm-ID: 236067 [Multi-domain]  Cd Length: 415  Bit Score: 227.44  E-value: 9.55e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672   6 DSVGIYLREISKYPMLTPEQEITLARQVK---QMTVVQ-------------QHKQVLEEQLHQQL----NIQQLAADMGK 65
Cdd:PRK07598  60 DLVRLYLQEIGRVRLLGRDEEVSEAQKVQrymKLIVLAnaakegdevikpyLRLIEVRERLTSELghrpSLERWAKTADI 139

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672  66 SET----------------------EVFQILRLGQKAKEKMIAANLRLVVAIAKKYRWSQLEFLDLVQEGSIGLQKAVER 123
Cdd:PRK07598 140 SLAdlkptlaegkrrwaeiakltveELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEK 219

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672 124 FDPNRGYKFSTCAYWWIRQEITKAIANKSTTIRTPSHMNDRLIKLKKVQRELVKILGREPNIAEIAEFAELEPNQVRECL 203
Cdd:PRK07598 220 FDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVL 299

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672 204 IAFRHPLSLDRPMGQEDEVDFLEILPADGTSPNEYLDEGFLRQDLANCLITLKPLQKQVLMLRFGLGSVDKLSTKQIAER 283
Cdd:PRK07598 300 LRVPRSVSLETKVGKDKDTELGDLLETDDISPEEMLMRESLQRDLQHLLADLTSRERDVIRMRFGLADGHTYSLAEIGRA 379

                        330       340       350
                 ....*....|....*....|....*....|..
gi 499635672 284 LNIKQAKVGTTQKQAIKVLH--RQQPQMREYL 313
Cdd:PRK07598 380 LDLSRERVRQIESKALQKLRqpKRRNRIRDYL 411
PRK09210 PRK09210
RNA polymerase sigma factor RpoD; Validated
 6-269 9.41e-68

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 215.62  E-value: 9.41e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672   6 DSVGIYLREISKYPMLTPEQEITLARQVKQmtvvqqhkqvleeqlhqqlniqqlaadmGKSEtevfqilrlgqkAKEKMI 85
Cdd:PRK09210  96 DPVRMYLKEIGRVPLLTAEEEIELAKRIEE----------------------------GDEE------------AKQRLA 135

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672  86 AANLRLVVAIAKKYRWSQLEFLDLVQEGSIGLQKAVERFDPNRGYKFSTCAYWWIRQEITKAIANKSTTIRTPSHMNDRL 165
Cdd:PRK09210 136 EANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETI 215

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672 166 IKLKKVQRELVKILGREPNIAEIAEFAELEPNQVRECLIAFRHPLSLDRPMGQEDEV---DFLEilPADGTSPNEYLDEG 242
Cdd:PRK09210 216 NKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDShlgDFIE--DQDATSPADHAAYE 293

                        250       260
                 ....*....|....*....|....*..
gi 499635672 243 FLRQDLANCLITLKPLQKQVLMLRFGL 269
Cdd:PRK09210 294 LLKEQLEDVLDTLTDREENVLRLRFGL 320
PRK07921 PRK07921
RNA polymerase sigma factor SigB; Reviewed
 2-269 9.41e-67

RNA polymerase sigma factor SigB; Reviewed


Pssm-ID: 181169 [Multi-domain]  Cd Length: 324  Bit Score: 211.90  E-value: 9.41e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672   2 SPQPDSVGIYLREISKYPMLTPEQEITLARQVkQMTVVQQHKQVLEEQLHQQLniqqlaadmgKSETEVfqILRLGQKAK 81
Cdd:PRK07921  22 SPAADLVRVYLNGIGKTALLTAADEVELAKRI-EAGLYAEHLLETRKRLSEAR----------KRDLAA--VVRDGEAAR 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672  82 EKMIAANLRLVVAIAKKYRWSQLEFLDLVQEGSIGLQKAVERFDPNRGYKFSTCAYWWIRQEITKAIANKSTTIRTPSHM 161
Cdd:PRK07921  89 RHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHL 168

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672 162 NDRLIKLKKVQRELVKILGREPNIAEIAEFAELEPNQVRECLIAFRHPLSLDRPMGQEDEV---DFLEilPADGTSPNEY 238
Cdd:PRK07921 169 VEQVNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAplgDFIE--DSEATSAENA 246

                        250       260       270
                 ....*....|....*....|....*....|.
gi 499635672 239 LDEGFLRQDLANCLITLKPLQKQVLMLRFGL 269
Cdd:PRK07921 247 VIAGLLHTDIRSVLATLDEREQQVIRLRFGL 277
PRK05901 PRK05901
RNA polymerase sigma factor; Provisional
 6-270 7.62e-66

RNA polymerase sigma factor; Provisional


Pssm-ID: 235640 [Multi-domain]  Cd Length: 509  Bit Score: 214.86  E-value: 7.62e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672   6 DSVGIYLREISKYPMLTPEQEITLArqvKQMtvvqqhkqvlEEQLHQQLNIQQLAADMGKSETEVFQILRLGQKAKEKMI 85
Cdd:PRK05901 211 DPVKAYLKQIGKVKLLNAEEEVELA---KRI----------EAGLYAEELLAEGEKLDPELRRDLQWIGRDGKRAKNHLL 277

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672  86 AANLRLVVAIAKKYRWSQLEFLDLVQEGSIGLQKAVERFDPNRGYKFSTCAYWWIRQEITKAIANKSTTIRTPSHMNDRL 165
Cdd:PRK05901 278 EANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVETI 357

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672 166 IKLKKVQRELVKILGREPNIAEIAEFAELEPNQVRECL-IAfRHPLSLDRPMGQEDE---VDFLE----ILPADGTSPNE 237
Cdd:PRK05901 358 NKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQkYN-REPISLDKTIGKEGDsqfGDFIEdseaVSPVDAVSFTL 436

                        250       260       270
                 ....*....|....*....|....*....|...
gi 499635672 238 yldegfLRQDLANCLITLKPLQKQVLMLRFGLG 270
Cdd:PRK05901 437 ------LQDQLQEVLETLSEREAGVIRMRFGLT 463
rpoS_proteo TIGR02394
RNA polymerase sigma factor RpoS; A sigma factor is a DNA-binding protein protein that binds ...
 6-304 7.03e-58

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: 187.62  E-value: 7.03e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672    6 DSVGIYLREISKYPMLTPEQEITLARQVkqmtvvqqhkqvleeqlhqqlniqqLAADMgksetevfqilrlgqKAKEKMI 85
Cdd:TIGR02394  13 DVTQLYLREIGFKPLLTAEEEIAYARRA-------------------------LAGDF---------------EARKVMI 52

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672   86 AANLRLVVAIAKKYRWSQLEFLDLVQEGSIGLQKAVERFDPNRGYKFSTCAYWWIRQEITKAIANKSTTIRTPSHMNDRL 165
Cdd:TIGR02394  53 ESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPVHVIKEL 132

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672  166 IKLKKVQRELVKILGREPNIAEIAEFAELEPNQVRECLIAFRHPLSLDRPMGQEDEVDFLEILPADGT-SPNEYLDEGFL 244
Cdd:TIGR02394 133 NVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPLDDDSSKSLLDTIADEQSiDPESLVQNDDL 212

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672  245 RQDLANCLITLKPLQKQVLMLRFGLGSVDKLSTKQIAERLNIKQAKVGTTQKQAIKVLHR 304
Cdd:TIGR02394 213 KQLIEAWLAELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRR 272
PRK05658 PRK05658
RNA polymerase sigma factor RpoD; Validated
 26-270 1.60e-50

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 235549 [Multi-domain]  Cd Length: 619  Bit Score: 176.52  E-value: 1.60e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672  26 EITLARQVKQMTVVQQHKQVLEEQLhqqlNIQQLAADMGKSETEVFQILRLGQK-------AKEKMIAANLRLVVAIAKK 98
Cdd:PRK05658 324 KEIASGKPWSEFLVRVYDEIKKLQQ----ELEAIEEETGLTIEELKEINRQISKgeakarrAKKEMVEANLRLVISIAKK 399

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672  99 YRWSQLEFLDLVQEGSIGLQKAVERFDPNRGYKFSTCAYWWIRQEITKAIANKSTTIRTPSHMNDRLIKLKKVQRELVKI 178
Cdd:PRK05658 400 YTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQE 479

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672 179 LGREPNIAEIAEFAELEPNQVRECL-IAfRHPLSLDRPMGQEDEV---DFLE----ILPADGTSpneyldEGFLRQDLAN 250
Cdd:PRK05658 480 IGREPTPEELAERLGMPEDKVRKVLkIA-KEPISLETPIGDDEDShlgDFIEdknaELPIDAAI------QESLREATTD 552

                        250       260
                 ....*....|....*....|
gi 499635672 251 CLITLKPLQKQVLMLRFGLG 270
Cdd:PRK05658 553 VLASLTPREAKVLRMRFGID 572
PRK05657 PRK05657
RNA polymerase sigma factor RpoS; Validated
 6-304 6.57e-49

RNA polymerase sigma factor RpoS; Validated


Pssm-ID: 235548 [Multi-domain]  Cd Length: 325  Bit Score: 165.90  E-value: 6.57e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672   6 DSVGIYLREISKYPMLTPEQEITLARQVKQmtvvqqhkqvleeqlhqqlniqqlaadmGKSEtevfqilrlgqkAKEKMI 85
Cdd:PRK05657  53 DATQLYLNEIGYSPLLTAEEEVYFARRALR----------------------------GDFA------------ARQRMI 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672  86 AANLRLVVAIAKKYRWSQLEFLDLVQEGSIGLQKAVERFDPNRGYKFSTCAYWWIRQEITKAIANKSTTIRTPSHMNDRL 165
Cdd:PRK05657  93 ESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPVHVVKEL 172

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672 166 IKLKKVQRELVKILGREPNIAEIAEFAELEPNQVRECLIAFRHPLSLDRPMGQEDEVDFLEILPAD-GTSPNEYLDEGFL 244
Cdd:PRK05657 173 NVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLGGDPEKSLLDILADEqENGPEDTTQDDDM 252

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672 245 RQDLANCLITLKPLQKQVLMLRFGLGSVDKLSTKQIAERLNIKQAKVGTTQKQAIKVLHR 304
Cdd:PRK05657 253 KQSIVKWLFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLRE 312
SigBFG TIGR02980
RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; This group of similar sigma-70 factors ...
 78-313 1.34e-43

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: 148.91  E-value: 1.34e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672   78 QKAKEKMIAANLRLVVAIAKKYRWSQLEFLDLVQEGSIGLQKAVERFDPNRGYKFSTCAYWWIRQEITKAIANKSTTIRT 157
Cdd:TIGR02980   2 KEAREKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIMGEIKRFFRDDTWAVRV 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672  158 PSHMNDRLIKLKKVQRELVKILGREPNIAEIAEFAELEPNQVRECLIAFR--HPLSLDRPMGQ--EDEVDFLEILPADGT 233
Cdd:TIGR02980  82 PRRLKELGVKINKATEELTQRLGRSPTIAEIAERLGVSEEEVVEALEAGNayQALSLDASIEDddGDPIALLDTLGDEDD 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672  234 SPNEYLDEGFLRQDLAncliTLKPLQKQVLMLRFglgsVDKLSTKQIAERLNIKQAKVGTTQKQAIKvlhrqqpQMREYL 313
Cdd:TIGR02980 162 ALETVEDRLALKPLLA----ALPERERRILLLRF----FEDKTQSEIAERLGISQMHVSRLLRRALK-------KLREQL 226
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 78-314 3.75e-36

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: 129.94  E-value: 3.75e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672  78 QKAKEKMIAANLRLVVAIAKKYR---WSQLEflDLVQEGSIGLQKAVERFDPNRGYKFSTCAYWWIRQEITKAIANKStt 154
Cdd:COG1191   14 EEAREELIEEYLPLVKKIASRLAgrlPAELD--DLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRGAILDYLRDED-- 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672 155 iRTPSHMNDRLIKLKKVQRELVKILGREPNIAEIAEFAELEPNQVRECL--IAFRHPLSLDRPMGQEDevDFLEILpaDG 232
Cdd:COG1191   90 -WVPRSVRELARKIEEAIEELEQELGREPTDEEIAEELGISLEEVQEALeaANAYQLLSLDEPLEDGD--DLLDLL--ES 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672 233 TSPNEYLDEGFLRQDLANCLITLKPLQKQVLMLRFglgsVDKLSTKQIAERLNIKQAKVGTTQKQAIKVLhrqqpqmREY 312
Cdd:COG1191  165 GDPEEELEHEELREALAEAIEQLPERERLVLSLYY----FEELTLKEIAEVLGVSESRVSRLHKKALARL-------REY 233


                 ..
gi 499635672 313 LA 314
Cdd:COG1191  234 LK 235
rpoH_proteo TIGR02392
alternative sigma factor RpoH; A sigma factor is a DNA-binding protein protein that binds to ...
 6-283 1.59e-25

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: 102.74  E-value: 1.59e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672    6 DSVGIYLREISKYPMLTPEQEITLARQvkqmtvvqqhkqvleeqLHQQLNIQqlaadmgksetevfqilrlgqkAKEKMI 85
Cdd:TIGR02392   1 GSLDAYIRAVNRIPMLTPEEEYQLAKR-----------------LREHGDLD----------------------AAKKLV 41

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672   86 AANLRLVVAIAKKYRWSQLEFLDLVQEGSIGLQKAVERFDPNRGYKFSTCAYWWIRQEITKAIanksttIRtpshmNDRL 165
Cdd:TIGR02392  42 LSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYI------LR-----NWRL 110

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672  166 IKL--KKVQRELV--------KILG--REPNIAEIAEFAELEPNQVRECLIAFRHP-LSLDRPMGQEDEvdfleilpaDG 232
Cdd:TIGR02392 111 VKVatTKAQRKLFfnlrkmkkRLQGwlNPEEVEAIAEELGVSEREVREMESRLSGQdMSLNASIDDDED---------DG 181

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 499635672  233 TSPNEYLDEGflRQDLANCLITLKPLQKQVLMLRFGLGSVDKLSTKQIAER 283
Cdd:TIGR02392 182 GAPIAYLVDK--RSDPEDTLEEEQWEELQRQALANALGSLDARSRRIIEAR 230
PRK07408 PRK07408
RNA polymerase sigma factor SigF; Reviewed
 88-303 2.28e-24

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 180965 [Multi-domain]  Cd Length: 256  Bit Score: 99.22  E-value: 2.28e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672  88 NLRLVVAIAkkYRWSQL---EFLDLVQEGSIGLQKAVERFDPNRGYKFSTCAYWWIRQEITKAIANKSTTIRTPSHMNDR 164
Cdd:PRK07408  34 NLGLVRKEA--HRWSNQcsePYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPTVRIPRRWQEL 111

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672 165 LIKLKKVQRELVKILGREPNIAEIAEFAELEPNQVRECLIAFRH--PLSLDRPMGQ--EDEVDFLEILPADGTSPNEYLD 240
Cdd:PRK07408 112 QRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNrtPLSLDAPVNQdeDGSTSLGDLLPDPRYRSFQLAQ 191

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 499635672 241 EGflRQDLANCLITLKPLQKQVLMLRFglgsVDKLSTKQIAERLNIKQAKVGTTQKQAIKVLH 303
Cdd:PRK07408 192 ED--RIRLQQALAQLEERTREVLEFVF----LHDLTQKEAAERLGISPVTVSRRVKKGLDQLK 248
PRK06596 PRK06596
RNA polymerase factor sigma-32; Reviewed
 11-144 3.39e-24

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 235838 [Multi-domain]  Cd Length: 284  Bit Score: 99.48  E-value: 3.39e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672  11 YLREISKYPMLTPEQEITLArqvkqmtvvqqhkqvleEQLHQQLNIQqlaadmgksetevfqilrlgqkAKEKMIAANLR 90
Cdd:PRK06596  19 YIQAVNKIPMLTAEEEYMLA-----------------KRLREHGDLE----------------------AAKQLVLSHLR 59

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 499635672  91 LVVAIAKKYRWSQLEFLDLVQEGSIGLQKAVERFDPNRGYKFSTCAYWWIRQEI 144
Cdd:PRK06596  60 FVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEI 113
PRK05572 PRK05572
RNA polymerase sporulation sigma factor, SigF/SigG family;
78-314 3.43e-23

RNA polymerase sporulation sigma factor, SigF/SigG family;


Pssm-ID: 180137 [Multi-domain]  Cd Length: 252  Bit Score: 95.81  E-value: 3.43e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672  78 QKAKEKMIAANLRLVVAIAKKYRWSQLEFLDLVQEGSIGLQKAVERFDPNRGYKFSTCAYWWIRQEITKAIANKStTIRT 157
Cdd:PRK05572  31 QEARDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKV 109

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672 158 PSHMNDRLIKLKKVQRELVKILGREPNIAEIAEFAELEPNQVRECLIAFRHPLSLDRPMGQEDEVDFLEILPADGTSPNE 237
Cdd:PRK05572 110 SRSLKETANKIRKDKDELSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVHENDGDPITLLDQIADQSEED 189

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 499635672 238 YLDEGFLRQDLANclitLKPLQKQVLMLRFglgSVDKLSTkQIAERLNIKQAKVGTTQKQAIKvlhrqqpQMREYLA 314
Cdd:PRK05572 190 WFDKIALKEAIRE----LDERERLIVYLRY---FKDKTQS-EVAKRLGISQVQVSRLEKKILK-------QMKEKLD 251
PRK08215 PRK08215
RNA polymerase sporulation sigma factor SigG;
69-313 3.68e-22

RNA polymerase sporulation sigma factor SigG;


Pssm-ID: 181296 [Multi-domain]  Cd Length: 258  Bit Score: 93.09  E-value: 3.68e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672  69 EVFQILRLGQK-AKEKMIAANLRLVVAIAKKYRwSQLEFLD-LVQEGSIGLQKAVERFDPNRGYKFSTCAYWWIRQEITK 146
Cdd:PRK08215  26 ELFERMQNGDKeAREKLINGNLRLVLSVIQRFN-NRGENVDdLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRR 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672 147 AIANKStTIRTPSHMNDRLIKLKKVQRELVKILGREPNIAEIAEFAELEPNQVRECLIAFRHPLSLDRPMGQeDEVDflE 226
Cdd:PRK08215 105 YLRDNN-PIRVSRSLRDIAYKALQVREKLINENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIYH-DGGD--P 180

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672 227 ILPADGTSPNEYLDEGFLRQ-DLANCLITLKPLQKQVLMLRFGLGSvdklSTKQIAERLNIKQAKVGTTQKQAIKvlhrq 305
Cdd:PRK08215 181 IYVMDQISDEKNKDENWLEEiALKEAMKKLNDREKLILNLRFFQGK----TQMEVAEEIGISQAQVSRLEKAALK----- 251


                 ....*...
gi 499635672 306 qpQMREYL 313
Cdd:PRK08215 252 --HMRKYI 257
PRK08583 PRK08583
RNA polymerase sigma factor SigB; Validated
 65-302 3.14e-21

RNA polymerase sigma factor SigB; Validated


Pssm-ID: 236306 [Multi-domain]  Cd Length: 257  Bit Score: 90.52  E-value: 3.14e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672  65 KSETEVFQILRLGQK-----AKEKMIAANLRLVVAIAKKYRWSQLEFLDLVQEGSIGLQKAVERFDPNRGYKFSTCAYWW 139
Cdd:PRK08583  10 LTKEEVNKWIAEYQEnqdeeAQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPT 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672 140 IRQEITKAIANKSTTIRTPSHMNDRLIKLKKVQRELVKILGREPNIAEIAEFAELEPNQVRECLIAFR--HPLSLDRPMG 217
Cdd:PRK08583  90 IIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEVLEAMEMGKsyQALSVDHSIE 169

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672 218 QEDEVDFLEILPADGTSpneylDEGFLRQD----LANCLITLKPLQKQVLMLRFglgsVDKLSTKQIAERLNIKQAKVGT 293
Cdd:PRK08583 170 ADSDGSTVTLLDIVGQQ-----EDGYELTEqrmiLEKILPVLSDREKSIIQCTF----IENLSQKETGERLGISQMHVSR 240


                 ....*....
gi 499635672 294 TQKQAIKVL 302
Cdd:PRK08583 241 LQRQAIKKL 249
PRK07122 PRK07122
RNA polymerase sigma factor SigF; Reviewed
 78-291 1.17e-20

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 168831 [Multi-domain]  Cd Length: 264  Bit Score: 89.45  E-value: 1.17e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672  78 QKAKEKMIAANLRLVVAIAKKY--RWSQLEflDLVQEGSIGLQKAVERFDPNRGYKFSTCAYWWIRQEITKAIANKSTTI 155
Cdd:PRK07122  39 QRQRDRIVTRCLPLADHIARRFdgRGEPRD--DLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWSV 116

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672 156 RTPSHMNDRLIKLKKVQRELVKILGREPNIAEIAEFAELEPNQVRECLIAFR--HPLSLDRPMGQEDE-----VDFL-EI 227
Cdd:PRK07122 117 KVPRRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAGSayNTLSIDSGGGSGDDdaraiADTLgDV 196

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 499635672 228 LPAdgtspneyLDEGFLRQDLANCLITLKPLQKQVLMLRFglgsVDKLSTKQIAERLNIKQAKV 291
Cdd:PRK07122 197 DAG--------LDQIENREALRPLLAALPERERTVLVLRF----FESMTQTQIAERVGISQMHV 248
rpoH2 PRK07500
RNA polymerase factor sigma-32; Reviewed
 78-144 1.27e-18

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 236033 [Multi-domain]  Cd Length: 289  Bit Score: 83.93  E-value: 1.27e-18
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 499635672  78 QKAKEKMIAANLRLVVAIAKKYRWSQLEFLDLVQEGSIGLQKAVERFDPNRGYKFSTCAYWWIRQEI 144
Cdd:PRK07500  39 EDALHRIISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASI 105
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 84-152 1.63e-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: 78.01  E-value: 1.63e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 499635672   84 MIAANLRLVVAIAKKYRWSQLEFLDLVQEGSIGLQKAVERFDPNRGYKFSTCAYWWIRQEITKAIANKS 152
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQR 69
PRK05803 PRK05803
RNA polymerase sporulation sigma factor SigK;
67-305 2.93e-18

RNA polymerase sporulation sigma factor SigK;


Pssm-ID: 180266 [Multi-domain]  Cd Length: 233  Bit Score: 81.92  E-value: 2.93e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672  67 ETEVFQILRLGQK-AKEKMIAANLRLVVAIAKKYRWSQLEFLDLVQEGSIGLQKAVERFDPNRGYKFSTCAYWWIRQEIT 145
Cdd:PRK05803  36 ERKYLELMKEGDEeARNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYAARCIENEIL 115

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672 146 kaianksttirtpshMNDRliKLKKVQRElvkilgrepniaeiaefaelepnqvrecliafrhpLSLDRPMGQE---DEV 222
Cdd:PRK05803 116 ---------------MHLR--NLKKTKKE-----------------------------------VSLQDPIGVDkegNEI 143

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672 223 DFLEILPADGTSPNEYLDEGFLRQDLANCLITLKPLQKQVLMLRFGLGSVDKLSTKQIAERLNIKQAKVGTTQKQAIKVL 302
Cdd:PRK05803 144 SLIDILGSEEDDVIEQVELKMEVEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKL 223


                 ...
gi 499635672 303 HRQ 305
Cdd:PRK05803 224 FKE 226
Sigma70_r3 pfam04539
Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the ...
 163-239 6.07e-17

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: 74.18  E-value: 6.07e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 499635672  163 DRLIKLKKVQRELVKILGREPNIAEIAEFAELEPNQVRECLIAFRHPLSLDRPMGQEDEVDFLEILPAD-GTSPNEYL 239
Cdd:pfam04539   1 ELLNKIKRAQRELEQELGREPTPEEIAEELGLSPEKVREVLEAAREPVSLDTPVGEEEDGELGDLLEDDdIESPEEAV 78
FliA_WhiG TIGR02479
RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar ...
 102-302 3.15e-15

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: 73.46  E-value: 3.15e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672  102 SQLEFLDLVQEGSIGLQKAVERFDPNRGYKFSTCAYWWIRQEI---TKAIANKSTTIRTPSHmndrliKLKKVQRELVKI 178
Cdd:TIGR02479  22 SSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMldeLRRLDWVPRSLRQKAR------KLERAIRELEAR 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672  179 LGREPNIAEIAEFAELEPNQVRECL--IAFRHPLSLDRPMGQEDEVDFLEILPADGTS--PNEYLDEGFLRQDLANCLIT 254
Cdd:TIGR02479  96 LGREPTEEEIAEELGMDLKEYRQALneINALSLVSLDELLESGDDGGSLIDRIEDDKSedPEEELEREELREALAEAIES 175

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 499635672  255 LKPLQKQVLMLRFglgsVDKLSTKQIAERLNIKQAKVGTTQKQAIKVL 302
Cdd:TIGR02479 176 LSEREQLVLSLYY----YEELNLKEIGEVLGLTESRVSQIHSQALKKL 219
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 79-305 8.27e-14

RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 67.76  E-value: 8.27e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672   79 KAKEKMIAANLRLVVAIAKKYRWSQLEFLDLVQEGSIGLQKAVERFDPNrgYKFSTCAYWWIRQEITkaianksttirtp 158
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLIL------------- 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672  159 shmnDRLIKLKKVQRelvkilgrepniaeiaefaelepnqvrecliafrhplsldrpmgqedEVDFLEILPADGTSPNEY 238
Cdd:TIGR02937  66 ----DYLRRKRRLRR-----------------------------------------------ELDLLEELLDSDPSPEEE 94

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 499635672  239 LDEGFLRQDLANCLITLKPLQKQVLMLRFglgsVDKLSTKQIAERLNIKQAKVGTTQKQAIKVLHRQ 305
Cdd:TIGR02937  95 LEQEEEREALREALEKLPEREREVLVLRY----LEGLSYKEIAEILGISVGTVKRRLKRARKKLREL 157
Sigma70_r1_2 pfam00140
Sigma-70 factor, region 1.2;
6-36 1.23e-09

Sigma-70 factor, region 1.2;


Pssm-ID: 425482 [Multi-domain]  Cd Length: 34  Bit Score: 52.70  E-value: 1.23e-09
                          10        20        30
                  ....*....|....*....|....*....|.
gi 499635672    6 DSVGIYLREISKYPMLTPEQEITLARQVKQM 36
Cdd:pfam00140   1 DSVRLYLKEIGRIPLLTAEEEVELAKRIEAG 31
PRK05911 PRK05911
RNA polymerase sigma factor sigma-28; Reviewed
 102-299 1.82e-09

RNA polymerase sigma factor sigma-28; Reviewed


Pssm-ID: 235644 [Multi-domain]  Cd Length: 257  Bit Score: 57.32  E-value: 1.82e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672 102 SQLEFLDLVQEGSIGLQKAVERFDPNRGYKFSTCAYWWIRQEITKAIANKSTtirTPSHMNDRLIKLKKVQRELVKILGR 181
Cdd:PRK05911  49 SHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRKQDW---VPRSVHQKANKLADAMDSLRQSLGK 125

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672 182 EPNIAEIAEFAELEPNQVRECLIAFRHPLSL----DRPMGQEDEVDF-LEILPADGTSPNEY--LDEGFLRQDLANCLIT 254
Cdd:PRK05911 126 EPTDGELCEYLNISQQELSGWFSSARPALILslneEFPCQSDDEAGLaLEERIADERAETGYdvVDKKEFSSILAEAILA 205

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 499635672 255 LKPLQKQVLMLRFglgsVDKLSTKQIAERLNIKQAKVGTTQKQAI 299
Cdd:PRK05911 206 LEEKERKVMALYY----YEELVLKEIGKILGVSESRVSQIHSKAL 246
PRK08301 PRK08301
RNA polymerase sporulation sigma factor SigE;
66-144 7.76e-09

RNA polymerase sporulation sigma factor SigE;


Pssm-ID: 236228 [Multi-domain]  Cd Length: 234  Bit Score: 55.25  E-value: 7.76e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672  66 SETEVFQILRLGQ---KAKEKMIAANLRLVVAIAKKYRWSQLEFLDLVQEGSIGLQKAVERFDPNRGYKFSTCAYWWIRQ 142
Cdd:PRK08301  36 KEEEEYLLNKLPKgdeAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIEN 115


                 ..
gi 499635672 143 EI 144
Cdd:PRK08301 116 EI 117
fliA PRK06986
flagellar biosynthesis sigma factor; Validated
 77-302 1.20e-08

flagellar biosynthesis sigma factor; Validated


Pssm-ID: 235901 [Multi-domain]  Cd Length: 236  Bit Score: 54.47  E-value: 1.20e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672  77 GQKAKEKMIAANLRLVVAIAkkYRW-----SQLEFLDLVQEGSIGLQKAVERFDPNRGYKFSTCAywwiRQEITKAIANK 151
Cdd:PRK06986   6 GKMDQDELVEQYAPLVKRIA--LRLkarlpASVDLDDLIQAGMIGLLEAARRYDGEQGASFETYA----GQRIRGAMLDE 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672 152 sttIRT------PSHMNDRLIklKKVQRELVKILGREPNIAEIAEFAELEPNQVRECLIAFR--HPLSLDRPMGQEDEVd 223
Cdd:PRK06986  80 ---LRSldwvprSVRRNAREV--AQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNisQLFSIDELRGEHGDS- 153

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 499635672 224 FLEILPADGTSPNEYLDEGFLRQDLANCLITLKPLQKQVLMLRFGlgsvDKLSTKQIAERLNIKQAKVGTTQKQAIKVL 302
Cdd:PRK06986 154 ILVTEDHQDEDPLQQLEDEELREALVEAIESLPEREQLVLSLYYQ----EELNLKEIGAVLGVSESRVSQIHSQAIKRL 228
PRK07670 PRK07670
FliA/WhiG family RNA polymerase sigma factor;
108-282 1.29e-08

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 181075 [Multi-domain]  Cd Length: 251  Bit Score: 54.67  E-value: 1.29e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672 108 DLVQEGSIGLQKAVERFDPNRGYKFSTCAYWWIRQEITKAIANKSttiRTPSHMNDRLIKLKKVQRELVKILGREPNIAE 187
Cdd:PRK07670  54 DLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRKED---WLPRSMREKTKKVEAAIEKLEQRYMRNVTPKE 130

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672 188 IAEFAELEPNQV----RECLiaFRHPLSLDRPMGQEDEVDF--LEILPADGTSPNEYLDEGFLRQDLANCLITLKPLQKQ 261
Cdd:PRK07670 131 VAAELGMTEEEVeatmNEGF--FANLLSIDEKTHDQDDGENvsVTIRDDKTPTPEEKLLKEELIEELAEKIKQLSEKEQL 208

                        170       180
                 ....*....|....*....|....*...
gi 499635672 262 VLMLRFG-------LGSVDKLSTKQIAE 282
Cdd:PRK07670 209 VISLFYKeeltlteIGQVLNLSTSRISQ 236
PRK06288 PRK06288
RNA polymerase sigma factor WhiG; Reviewed
 105-291 1.66e-08

RNA polymerase sigma factor WhiG; Reviewed


Pssm-ID: 235770 [Multi-domain]  Cd Length: 268  Bit Score: 54.69  E-value: 1.66e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672 105 EFLDLVQEGSIGLQKAVERFDPNRGYKFSTCAYWWIRQEI---TKAIANKSTTIRTpshmndrliKLKKVQR---ELVKI 178
Cdd:PRK06288  60 EFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIfdeLRSIDWIPRSVRQ---------KARQIERaiaMLEAR 130

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672 179 LGREPNIAEIAEFAELEPNQVRECL--IAFRHPLSLD--RPMGQE-DEVDFLEILPA-DGTSPNEYLDEGFLRQDLANCL 252
Cdd:PRK06288 131 LGRTPSDEEIADELGISLEEYNSLLskLSGTSVVSLNdlWFGGDEgDEVSLMDTLESpAALNPDEIAEREEIKRVIVEAI 210

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 499635672 253 ITLKPLQKQVLMLRFglgsVDKLSTKQIAERLNIKQAKV 291
Cdd:PRK06288 211 KTLPEREKKVLILYY----YEDLTLKEIGKVLGVTESRI 245
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
91-148 2.45e-08

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 53.37  E-value: 2.45e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 499635672  91 LVVAIAKKYRWSQLEFLDLVQEGSIGLQKAVERFDPNRGYKFSTCAYWWIRQEITKAI 148
Cdd:PRK08295  36 FVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCITRQIITAI 93
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 218-305 3.07e-07

DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; DNA-directed RNA polymerase specialized sigma subunit, sigma24 family is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 441203 [Multi-domain]  Cd Length: 181  Bit Score: 49.61  E-value: 3.07e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672 218 QEDEVDFLEILPADGTSPNEYLDEGFLRQDLANCLITLKPLQKQVLMLRFglgsVDKLSTKQIAERLNIKQAKVGTTQKQ 297
Cdd:COG1595   91 RELLDELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRY----LEGLSYAEIAEILGISEGTVKSRLSR 166


                 ....*...
gi 499635672 298 AIKVLHRQ 305
Cdd:COG1595  167 ARKKLREA 174
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 218-313 1.55e-06

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 47.25  E-value: 1.55e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672 218 QEDEVDFLEilpadgtSPNEYLDEGFLRQDLANCLITLKPLQKQVLMLRFglgsvDKLSTKQIAERLNIKQAKVGTTQKQ 297
Cdd:PRK09639  83 QWQEVDNEP-------SPEEIWIRKEEITKVQEVLAKMTERDRTVLLLRF-----SGYSYKEIAEALGIKESSVGTTLAR 150

                         90
                 ....*....|....*.
gi 499635672 298 AIKVLHRQQPQMREYL 313
Cdd:PRK09639 151 AKKKFRKIYEQMEEEE 166
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 245-302 6.53e-06

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: 42.86  E-value: 6.53e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 499635672 245 RQDLANCLITLKPLQKQVLMLRFGLGsvdkLSTKQIAERLNIKQAKVGTTQKQAIKVL 302
Cdd:cd06171    1 RERLEEALDKLPEREREVILLRFGEG----LSYEEIAEILGISRSTVRQRLHRALKKL 54
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 245-302 1.18e-03

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.


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 36.28  E-value: 1.18e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 499635672  245 RQDLANCLITLKPLQKQVLMLRFGLGsvdkLSTKQIAERLNIKQAKVGTTQKQAIKVL 302
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLRYLEG----LSYAEIAELLGISEGTVKSRLSRARKKL 54
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 251-302 4.18e-03

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: 34.71  E-value: 4.18e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 499635672  251 CLITLKPLQKQVLMLRFGlgsvDKLSTKQIAERLNIKQAKVGTTQKQAIKVL 302
Cdd:pfam04545   1 ALASLPPRERQVLVLRYG----EGLTLEEIGERLGISRERVRQIEKRALRKL 48
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 108-313 9.03e-03

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 36.60  E-value: 9.03e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672 108 DLVQEGSIGLQKAVERFDPNRgyKFSTcayWWIRQEITKAIanksttirtpshmnDRLIKlkkvqrelvkilgREPNIae 187
Cdd:PRK09641  47 DAAQEAFIRAYVNIDSYDINR--KFST---WLYRIATNLTI--------------DRLRK-------------RKPDY-- 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499635672 188 iaefaelepnqvrecliafrhplSLDRPMGQEDEVDFLEILPADGTSPNEYLDEGFLRQDLANCLITLKPLQKQVLMLRF 267
Cdd:PRK09641  93 -----------------------YLDAEVAGTEGLTMYSQLAADDALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKY 149

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 499635672 268 glgsVDKLSTKQIAERLNIKQAKVGTTqkqaikvLHRQQPQMREYL 313
Cdd:PRK09641 150 ----IEDLSLKEISEILDLPVGTVKTR-------IHRGREALRKQL 184
 
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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