|
Name |
Accession |
Description |
Interval |
E-value |
| PRK08583 |
PRK08583 |
RNA polymerase sigma factor SigB; Validated |
2-256 |
1.41e-167 |
|
RNA polymerase sigma factor SigB; Validated
Pssm-ID: 236306 [Multi-domain] Cd Length: 257 Bit Score: 463.01 E-value: 1.41e-167
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 2 AKESKSANEVSPEQINQWIKEHQENKNTDAQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDMSFER 81
Cdd:PRK08583 1 MKESSQPTKLTKEEVNKWIAEYQENQDEEAQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 82 KFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTAELERSPSISEIADRLEVSEEEVLEAMEMGQSYN 161
Cdd:PRK08583 81 SFEAFAVPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEVLEAMEMGKSYQ 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 162 ALSVDHSIEADKDGSTVTLLDIMGQQDDHYDLTEKRMILEKILPILSDREREIIQCTFIEGLSQKETGERIGLSQMHVSR 241
Cdd:PRK08583 161 ALSVDHSIEADSDGSTVTLLDIVGQQEDGYELTEQRMILEKILPVLSDREKSIIQCTFIENLSQKETGERLGISQMHVSR 240
|
250
....*....|....*
gi 446963851 242 LQRTAIKKLQEAAHK 256
Cdd:PRK08583 241 LQRQAIKKLREAAFL 255
|
|
| Sigma_B |
TIGR02941 |
RNA polymerase sigma-B factor; This sigma factor is restricted to certain lineages of the ... |
2-256 |
3.60e-153 |
|
RNA polymerase sigma-B factor; This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria, and Bacillus.
Pssm-ID: 131987 [Multi-domain] Cd Length: 255 Bit Score: 426.62 E-value: 3.60e-153
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 2 AKESKSANEVSPEQINQWIKEHQENKNTDAQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDMSFER 81
Cdd:TIGR02941 1 MEIQSQPTNLTKEDVIQWIAEFQQNQNGEAQEKLVDHYQNLVYSIAYKYSKGGPMHEDLVQVGMLGLLGAIRRYDYSIGN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 82 KFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTAELERSPSISEIADRLEVSEEEVLEAMEMGQSYN 161
Cdd:TIGR02941 81 AFEPFAIPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAIDELTDHLQRSPKIIEIADHLGLSEEEVLEIMEMGQSYR 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 162 ALSVDHSIEADKDGSTVTLLDIMGQQDDHYDLTEKRMILEKILPILSDREREIIQCTFIEGLSQKETGERIGLSQMHVSR 241
Cdd:TIGR02941 161 ALSVDDVIEADSDGSTVARLDSVGEVEDGYDQTERRMVLEKILPILSEREKSIIHCTFEENLSQKETGERLGISQMHVSR 240
|
250
....*....|....*
gi 446963851 242 LQRTAIKKLQEAAHK 256
Cdd:TIGR02941 241 LQRQAISKLKEAAFL 255
|
|
| FliA |
COG1191 |
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ... |
15-253 |
1.17e-64 |
|
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: 201.21 E-value: 1.17e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 15 QINQWIKEHQENkNTDAQDKLVKHYQKLIESLAYKYS-KGQSHHEDLVQVGMVGLIGAINRFDMSFERKFEAFLVPTVIG 93
Cdd:COG1191 1 DLEELLRRYQEG-DEEAREELIEEYLPLVKKIASRLAgRLPAELDDLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRG 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 94 EIKRYLRDKTWsvhVPRRIKEIGPRIKKVSDELTAELERSPSISEIADRLEVSEEEVLEAMEMGQSYNALSVDHSIEADK 173
Cdd:COG1191 80 AILDYLRDEDW---VPRSVRELARKIEEAIEELEQELGREPTDEEIAEELGISLEEVQEALEAANAYQLLSLDEPLEDGD 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 174 DgstvtLLDIM--GQQDDHYDLTEKRMILEKILPILSDREREIIQCTFIEGLSQKETGERIGLSQMHVSRLQRTAIKKLQ 251
Cdd:COG1191 157 D-----LLDLLesGDPEEELEHEELREALAEAIEQLPERERLVLSLYYFEELTLKEIAEVLGVSESRVSRLHKKALARLR 231
|
..
gi 446963851 252 EA 253
Cdd:COG1191 232 EY 233
|
|
| Sigma70_r2 |
pfam04542 |
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ... |
35-104 |
1.01e-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: 77.63 E-value: 1.01e-18
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 35 LVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDMSFERKFEAFLVPTVIGEIKRYLRDKTW 104
Cdd:pfam04542 1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRR 70
|
|
| Sigma70_r4 |
cd06171 |
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ... |
200-251 |
2.48e-10 |
|
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: 54.80 E-value: 2.48e-10
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|..
gi 446963851 200 LEKILPILSDREREIIQCTFIEGLSQKETGERIGLSQMHVSRLQRTAIKKLQ 251
Cdd:cd06171 4 LEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
|
|
| HTH_LUXR |
smart00421 |
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon |
204-256 |
2.31e-03 |
|
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
Pssm-ID: 197715 [Multi-domain] Cd Length: 58 Bit Score: 35.58 E-value: 2.31e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*...
gi 446963851 204 LPILSDREREIIQCTfIEGLSQKETGERIGLS----QMHVSRLQR-TAIKKLQEAAHK 256
Cdd:smart00421 1 LASLTPREREVLRLL-AEGLTNKEIAERLGISektvKTHLSNIMRkLGVRSRTQAVRL 57
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PRK08583 |
PRK08583 |
RNA polymerase sigma factor SigB; Validated |
2-256 |
1.41e-167 |
|
RNA polymerase sigma factor SigB; Validated
Pssm-ID: 236306 [Multi-domain] Cd Length: 257 Bit Score: 463.01 E-value: 1.41e-167
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 2 AKESKSANEVSPEQINQWIKEHQENKNTDAQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDMSFER 81
Cdd:PRK08583 1 MKESSQPTKLTKEEVNKWIAEYQENQDEEAQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 82 KFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTAELERSPSISEIADRLEVSEEEVLEAMEMGQSYN 161
Cdd:PRK08583 81 SFEAFAVPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEVLEAMEMGKSYQ 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 162 ALSVDHSIEADKDGSTVTLLDIMGQQDDHYDLTEKRMILEKILPILSDREREIIQCTFIEGLSQKETGERIGLSQMHVSR 241
Cdd:PRK08583 161 ALSVDHSIEADSDGSTVTLLDIVGQQEDGYELTEQRMILEKILPVLSDREKSIIQCTFIENLSQKETGERLGISQMHVSR 240
|
250
....*....|....*
gi 446963851 242 LQRTAIKKLQEAAHK 256
Cdd:PRK08583 241 LQRQAIKKLREAAFL 255
|
|
| Sigma_B |
TIGR02941 |
RNA polymerase sigma-B factor; This sigma factor is restricted to certain lineages of the ... |
2-256 |
3.60e-153 |
|
RNA polymerase sigma-B factor; This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria, and Bacillus.
Pssm-ID: 131987 [Multi-domain] Cd Length: 255 Bit Score: 426.62 E-value: 3.60e-153
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 2 AKESKSANEVSPEQINQWIKEHQENKNTDAQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDMSFER 81
Cdd:TIGR02941 1 MEIQSQPTNLTKEDVIQWIAEFQQNQNGEAQEKLVDHYQNLVYSIAYKYSKGGPMHEDLVQVGMLGLLGAIRRYDYSIGN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 82 KFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTAELERSPSISEIADRLEVSEEEVLEAMEMGQSYN 161
Cdd:TIGR02941 81 AFEPFAIPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAIDELTDHLQRSPKIIEIADHLGLSEEEVLEIMEMGQSYR 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 162 ALSVDHSIEADKDGSTVTLLDIMGQQDDHYDLTEKRMILEKILPILSDREREIIQCTFIEGLSQKETGERIGLSQMHVSR 241
Cdd:TIGR02941 161 ALSVDDVIEADSDGSTVARLDSVGEVEDGYDQTERRMVLEKILPILSEREKSIIHCTFEENLSQKETGERLGISQMHVSR 240
|
250
....*....|....*
gi 446963851 242 LQRTAIKKLQEAAHK 256
Cdd:TIGR02941 241 LQRQAISKLKEAAFL 255
|
|
| SigBFG |
TIGR02980 |
RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; This group of similar sigma-70 factors ... |
30-254 |
3.22e-109 |
|
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: 314.16 E-value: 3.22e-109
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 30 DAQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDMSFERKFEAFLVPTVIGEIKRYLRDKTWSVHVP 109
Cdd:TIGR02980 3 EAREKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIMGEIKRFFRDDTWAVRVP 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 110 RRIKEIGPRIKKVSDELTAELERSPSISEIADRLEVSEEEVLEAMEMGQSYNALSVDHSIEADkDGSTVTLLDIMGQQDD 189
Cdd:TIGR02980 83 RRLKELGVKINKATEELTQRLGRSPTIAEIAERLGVSEEEVVEALEAGNAYQALSLDASIEDD-DGDPIALLDTLGDEDD 161
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446963851 190 HYDLTEKRMILEKILPILSDREREIIQCTFIEGLSQKETGERIGLSQMHVSRLQRTAIKKLQEAA 254
Cdd:TIGR02980 162 ALETVEDRLALKPLLAALPERERRILLLRFFEDKTQSEIAERLGISQMHVSRLLRRALKKLREQL 226
|
|
| FliA |
COG1191 |
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ... |
15-253 |
1.17e-64 |
|
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: 201.21 E-value: 1.17e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 15 QINQWIKEHQENkNTDAQDKLVKHYQKLIESLAYKYS-KGQSHHEDLVQVGMVGLIGAINRFDMSFERKFEAFLVPTVIG 93
Cdd:COG1191 1 DLEELLRRYQEG-DEEAREELIEEYLPLVKKIASRLAgRLPAELDDLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRG 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 94 EIKRYLRDKTWsvhVPRRIKEIGPRIKKVSDELTAELERSPSISEIADRLEVSEEEVLEAMEMGQSYNALSVDHSIEADK 173
Cdd:COG1191 80 AILDYLRDEDW---VPRSVRELARKIEEAIEELEQELGREPTDEEIAEELGISLEEVQEALEAANAYQLLSLDEPLEDGD 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 174 DgstvtLLDIM--GQQDDHYDLTEKRMILEKILPILSDREREIIQCTFIEGLSQKETGERIGLSQMHVSRLQRTAIKKLQ 251
Cdd:COG1191 157 D-----LLDLLesGDPEEELEHEELREALAEAIEQLPERERLVLSLYYFEELTLKEIAEVLGVSESRVSRLHKKALARLR 231
|
..
gi 446963851 252 EA 253
Cdd:COG1191 232 EY 233
|
|
| PRK07122 |
PRK07122 |
RNA polymerase sigma factor SigF; Reviewed |
32-252 |
1.10e-50 |
|
RNA polymerase sigma factor SigF; Reviewed
Pssm-ID: 168831 [Multi-domain] Cd Length: 264 Bit Score: 166.49 E-value: 1.10e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 32 QDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDMSFERKFEAFLVPTVIGEIKRYLRDKTWSVHVPRR 111
Cdd:PRK07122 42 RDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWSVKVPRR 121
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 112 IKEIGPRIKKVSDELTAELERSPSISEIADRLEVSEEEVLEAMEMGQSYNALSVDHSIEADKDGsTVTLLDIMGQQDDHY 191
Cdd:PRK07122 122 LKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAGSAYNTLSIDSGGGSGDDD-ARAIADTLGDVDAGL 200
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446963851 192 DLTEKRMILEKILPILSDREREIIQCTFIEGLSQKETGERIGLSQMHVSRLQRTAIKKLQE 252
Cdd:PRK07122 201 DQIENREALRPLLAALPERERTVLVLRFFESMTQTQIAERVGISQMHVSRLLAKTLARLRD 261
|
|
| spore_sigF |
TIGR02885 |
RNA polymerase sigma-F factor; Members of this protein family are the RNA polymerase sigma ... |
20-252 |
9.54e-44 |
|
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: 147.55 E-value: 9.54e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 20 IKEHQENkNTDAQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDMSFERKFEAFLVPTVIGEIKRYL 99
Cdd:TIGR02885 2 IKLAQNG-DKEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 100 RDKTwSVHVPRRIKEIGPRIKKVSDELTAELERSPSISEIADRLEVSEEEVLEAMEMGQSYNALsvdHSIEADKDGSTVT 179
Cdd:TIGR02885 81 RDDG-IIKVSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSL---YDTVHQDDGDPIY 156
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446963851 180 LLDIMGQQDDHYDLTEKRMILEKILPILSDREREIIQCTFIEGLSQKETGERIGLSQMHVSRLQRTAIKKLQE 252
Cdd:TIGR02885 157 LLDQIADKGSEDSDWLEKIALKEAISKLDERERQIIMLRYFKDKTQTEVANMLGISQVQVSRLEKKVLKKMKE 229
|
|
| PRK05572 |
PRK05572 |
RNA polymerase sporulation sigma factor, SigF/SigG family; |
3-252 |
9.81e-42 |
|
RNA polymerase sporulation sigma factor, SigF/SigG family;
Pssm-ID: 180137 [Multi-domain] Cd Length: 252 Bit Score: 143.19 E-value: 9.81e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 3 KESKSANEVSPEQINQWIKEHQENkNTDAQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDMSFERK 82
Cdd:PRK05572 6 KNKKKKPQLKDEENKELIKKSQDG-DQEARDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVK 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 83 FEAFLVPTVIGEIKRYLRDKTwSVHVPRRIKEIGPRIKKVSDELTAELERSPSISEIADRLEVSEEEVLEAMEmgqSYNA 162
Cdd:PRK05572 85 FSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKETANKIRKDKDELSKELGREPTIEELAEYLGVTPEEVVLAQE---ASRS 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 163 LSVDHSIEADKDGSTVTLLDIMGQQDDHyDLTEKrMILEKILPILSDREREIIQCTFIEGLSQKETGERIGLSQMHVSRL 242
Cdd:PRK05572 161 PQSIHETVHENDGDPITLLDQIADQSEE-DWFDK-IALKEAIRELDERERLIVYLRYFKDKTQSEVAKRLGISQVQVSRL 238
|
250
....*....|
gi 446963851 243 QRTAIKKLQE 252
Cdd:PRK05572 239 EKKILKQMKE 248
|
|
| PRK07408 |
PRK07408 |
RNA polymerase sigma factor SigF; Reviewed |
15-252 |
2.17e-40 |
|
RNA polymerase sigma factor SigF; Reviewed
Pssm-ID: 180965 [Multi-domain] Cd Length: 256 Bit Score: 139.67 E-value: 2.17e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 15 QINQWIKEHQENKNTDAQDKLVKHYQKLIESLAYKYSkGQSH--HEDLVQVGMVGLIGAINRFDMSFERKFEAFLVPTVI 92
Cdd:PRK07408 10 ETMELLRAYQQNPSIALRNQLVELNLGLVRKEAHRWS-NQCSepYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIR 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 93 GEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTAELERSPSISEIADRLEVSEEEVLEAMEMGQSYNALSVDHSIEAD 172
Cdd:PRK07408 89 GEIQHYLRDKSPTVRIPRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRTPLSLDAPVNQD 168
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 173 KDGSTvTLLDIMgqQDDHYDL----TEKRMILEKILPILSDREREIIQCTFIEGLSQKETGERIGLSQMHVSRLQRTAIK 248
Cdd:PRK07408 169 EDGST-SLGDLL--PDPRYRSfqlaQEDRIRLQQALAQLEERTREVLEFVFLHDLTQKEAAERLGISPVTVSRRVKKGLD 245
|
....
gi 446963851 249 KLQE 252
Cdd:PRK07408 246 QLKK 249
|
|
| PRK08215 |
PRK08215 |
RNA polymerase sporulation sigma factor SigG; |
25-251 |
1.08e-32 |
|
RNA polymerase sporulation sigma factor SigG;
Pssm-ID: 181296 [Multi-domain] Cd Length: 258 Bit Score: 119.67 E-value: 1.08e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 25 ENKNTDAQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDMSFERKFEAFLVPTVIGEIKRYLRDKTw 104
Cdd:PRK08215 32 QNGDKEAREKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN- 110
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 105 SVHVPRRIKEIGPRIKKVSDELTAELERSPSISEIADRLEVSEEEVLEAMEMGQSynALSVDHSIEADkDGSTVTLLDIM 184
Cdd:PRK08215 111 PIRVSRSLRDIAYKALQVREKLINENSKEPTVEEIAKELEVPREEVVFALDAIQD--PVSLFEPIYHD-GGDPIYVMDQI 187
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446963851 185 GQQDDHYDLTEKRMILEKILPILSDREREIIQCTFIEGLSQKETGERIGLSQMHVSRLQRTAIKKLQ 251
Cdd:PRK08215 188 SDEKNKDENWLEEIALKEAMKKLNDREKLILNLRFFQGKTQMEVAEEIGISQAQVSRLEKAALKHMR 254
|
|
| FliA_WhiG |
TIGR02479 |
RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar ... |
35-252 |
3.25e-27 |
|
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: 104.66 E-value: 3.25e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 35 LVKHYQKLIESLAYKYSKGQSHH---EDLVQVGMVGLIGAINRFDMSFERKFEAFLVPTVIGEIKRYLRDKTWsvhVPRR 111
Cdd:TIGR02479 1 LIRRYLPLVKRIAGRLSVGLPSSvelDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMLDELRRLDW---VPRS 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 112 IKEIGPRIKKVSDELTAELERSPSISEIADRLEVSEEEVLEAMEMGQSYNALSVDHSIEADKDGSTVTLL---DIMGQQD 188
Cdd:TIGR02479 78 LRQKARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELLESGDDGGSLIDRiedDKSEDPE 157
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446963851 189 DHYDLTEKRMILEKILPILSDREREIIQCTFIEGLSQKETGERIGLSQMHVSRLQRTAIKKLQE 252
Cdd:TIGR02479 158 EELEREELREALAEAIESLSEREQLVLSLYYYEELNLKEIGEVLGLTESRVSQIHSQALKKLRA 221
|
|
| sigma70-ECF |
TIGR02937 |
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ... |
30-253 |
2.25e-23 |
|
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: 92.41 E-value: 2.25e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 30 DAQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDMsfERKFEAFLVPTVIGEIKRYLRDKTWsvhvp 109
Cdd:TIGR02937 1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDP--EGSFKAWLFRIARNLILDYLRRKRR----- 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 110 rrikeigprIKKVSDELTAELERSPSIseiadrlevseeevleamemgqsynalsvdhsieadkdgstvtlldimgqqDD 189
Cdd:TIGR02937 74 ---------LRRELDLLEELLDSDPSP---------------------------------------------------EE 93
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446963851 190 HYDLTEKRMILEKILPILSDREREIIQCTFIEGLSQKETGERIGLSQMHVSRLQRTAIKKLQEA 253
Cdd:TIGR02937 94 ELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLREL 157
|
|
| PRK06288 |
PRK06288 |
RNA polymerase sigma factor WhiG; Reviewed |
2-250 |
9.02e-20 |
|
RNA polymerase sigma factor WhiG; Reviewed
Pssm-ID: 235770 [Multi-domain] Cd Length: 268 Bit Score: 85.51 E-value: 9.02e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 2 AKESKSANEVSPEQINQWIKEHQENKNTDAQDKLVKHYQKLIESLAYKYSKGQSHH---EDLVQVGMVGLIGAINRFDMS 78
Cdd:PRK06288 3 KKMSGKIPKYAQQDETELWREYKKTGDPKIREYLILKYSPLVKYVAGRIAVGMPQNvefDDLVSYGVFGLIDAIEKFDPE 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 79 FERKFEAFLVPTVIGEIKRYLRDKTWsvhVPRRIKEIGPRIKKVSDELTAELERSPSISEIADRLEVSEEEVLEAMEMGQ 158
Cdd:PRK06288 83 REIKFKTYAVTRIRGAIFDELRSIDW---IPRSVRQKARQIERAIAMLEARLGRTPSDEEIADELGISLEEYNSLLSKLS 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 159 SYNALSVDHSIEADKDGSTVTLLDIM--GQQDDHYDLTEKRMILEKI---LPILSDREREIIQCTFIEGLSQKETGERIG 233
Cdd:PRK06288 160 GTSVVSLNDLWFGGDEGDEVSLMDTLesPAALNPDEIAEREEIKRVIveaIKTLPEREKKVLILYYYEDLTLKEIGKVLG 239
|
250
....*....|....*..
gi 446963851 234 LSQMHVSRLQRTAIKKL 250
Cdd:PRK06288 240 VTESRISQLHTKAVLQL 256
|
|
| PRK07670 |
PRK07670 |
FliA/WhiG family RNA polymerase sigma factor; |
17-256 |
4.47e-19 |
|
FliA/WhiG family RNA polymerase sigma factor;
Pssm-ID: 181075 [Multi-domain] Cd Length: 251 Bit Score: 83.56 E-value: 4.47e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 17 NQWIKEHQEnkntDAQDKLVKHYQKLIESLAYKYSKG---QSHHEDLVQVGMVGLIGAINRFDMSFERKFEAFLVPTVIG 93
Cdd:PRK07670 13 DRWKEERDP----DAADELIRRYMPLVHYHVQRISVGlpkSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRG 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 94 EIKRYLRDKTWsvhVPRRIKEIGPRIKKVSDELTAELERSPSISEIADRLEVSEEEVLEAMEMGQSYNALSVDHSIEADK 173
Cdd:PRK07670 89 AIIDGLRKEDW---LPRSMREKTKKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGFFANLLSIDEKTHDQD 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 174 DGSTVTLLDImgqqDDHYDLTEKRMI-------LEKILPILSDREREIIQCTFIEGLSQKETGERIGLSQMHVSRLQRTA 246
Cdd:PRK07670 166 DGENVSVTIR----DDKTPTPEEKLLkeelieeLAEKIKQLSEKEQLVISLFYKEELTLTEIGQVLNLSTSRISQIHSKA 241
|
250
....*....|
gi 446963851 247 IKKLQEAAHK 256
Cdd:PRK07670 242 LFKLKKLLEK 251
|
|
| Sigma70_r2 |
pfam04542 |
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ... |
35-104 |
1.01e-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: 77.63 E-value: 1.01e-18
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 35 LVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDMSFERKFEAFLVPTVIGEIKRYLRDKTW 104
Cdd:pfam04542 1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRR 70
|
|
| fliA |
PRK06986 |
flagellar biosynthesis sigma factor; Validated |
58-252 |
5.40e-17 |
|
flagellar biosynthesis sigma factor; Validated
Pssm-ID: 235901 [Multi-domain] Cd Length: 236 Bit Score: 77.58 E-value: 5.40e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 58 EDLVQVGMVGLIGAINRFDMSFERKFEAFLVPTVIGEIKRYLRDKTWsvhVPRRIKEIGPRIKKVSDELTAELERSPSIS 137
Cdd:PRK06986 39 DDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDELRSLDW---VPRSVRRNAREVAQAIRQLEQELGREPTDT 115
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 138 EIADRLEVSEEEVLEAMEMGQSYNALSVDHSIEADKDGSTVTLLDimgQQDDHYDLTEK---RMILEKILPILSDREREI 214
Cdd:PRK06986 116 EVAEKLGLSLEEYREMLLDTNISQLFSIDELRGEHGDSILVTEDH---QDEDPLQQLEDeelREALVEAIESLPEREQLV 192
|
170 180 190
....*....|....*....|....*....|....*...
gi 446963851 215 IQCTFIEGLSQKETGERIGLSQMHVSRLQRTAIKKLQE 252
Cdd:PRK06986 193 LSLYYQEELNLKEIGAVLGVSESRVSQIHSQAIKRLRA 230
|
|
| RpoD |
COG0568 |
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ... |
25-256 |
1.78e-16 |
|
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: 76.63 E-value: 1.78e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 25 ENKNTDAQDKLVKHYQKLIESLAYKYS-KGQSHhEDLVQVGMVGLIGAINRFDMSFERKF--------EAflvptvigEI 95
Cdd:COG0568 25 QAGDEEAKRKLVEANLRLVVSIAKKYQgRGLPL-LDLIQEGNLGLMKAVEKFDPERGFRFstyatwwiRQ--------AI 95
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 96 KRYLRDKtWS-----VHVPRRIKeigpRIKKVSDELTAELERSPSISEIADRLEVSEEEVLEAMEMGQsyNALSVDHSIE 170
Cdd:COG0568 96 TRAIADQ-WRtirlpVHMAETLN----KLRRAKRQLLQELGREPTPEEIAEELGVPEEKVREMLRLAR--EPVSLDAPVG 168
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 171 ADKDGstvTLLDI-----MGQQDDHYDLTEKRMILEKILPILSDREREIIQCTFIEGLSQKETGERIGlSQMHVSR---- 241
Cdd:COG0568 169 DDEDS---ELGDLledeeAPSPEEALEEELLREELREALDTLTEREREILRLRFGLDDGEPHTLEEIG-KEFGVSRervr 244
|
250
....*....|....*.
gi 446963851 242 -LQRTAIKKLQEAAHK 256
Cdd:COG0568 245 qIEAKALRKLRHPLRS 260
|
|
| PRK05911 |
PRK05911 |
RNA polymerase sigma factor sigma-28; Reviewed |
25-253 |
1.58e-15 |
|
RNA polymerase sigma factor sigma-28; Reviewed
Pssm-ID: 235644 [Multi-domain] Cd Length: 257 Bit Score: 73.88 E-value: 1.58e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 25 ENKNTDAQDKLVKHYQKLIESLAYKYSKGQSHH---EDLVQVGMVGLIGAINRFDMSFERKFEAFLVPTVIGEIKRYLRD 101
Cdd:PRK05911 18 STQEIEYRDVLIEFYLPLVKNVAHRLISGMPSHvktEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRK 97
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 102 KTWsvhVPRRIKEIGPRIKKVSDELTAELERSPSISEIADRLEVSEEEVLEAMEMGQSYNALSVDHSIEA-DKDGSTVTL 180
Cdd:PRK05911 98 QDW---VPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILSLNEEFPCqSDDEAGLAL 174
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446963851 181 LDIMGQQ--DDHYDLTEKR---MILEKILPILSDREREIIQCTFIEGLSQKETGERIGLSQMHVSRLQRTAIKKLQEA 253
Cdd:PRK05911 175 EERIADEraETGYDVVDKKefsSILAEAILALEEKERKVMALYYYEELVLKEIGKILGVSESRVSQIHSKALLKLRAT 252
|
|
| PRK05803 |
PRK05803 |
RNA polymerase sporulation sigma factor SigK; |
31-250 |
6.36e-15 |
|
RNA polymerase sporulation sigma factor SigK;
Pssm-ID: 180266 [Multi-domain] Cd Length: 233 Bit Score: 71.90 E-value: 6.36e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 31 AQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDMSFERKFEAFLVPTVIGEIKRYLRDktwsvhvpr 110
Cdd:PRK05803 50 ARNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYAARCIENEILMHLRN--------- 120
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 111 rikeigprIKKVSDELtaelerspsiseiadrlevseeevleamemgqsynalSVDHSIEADKDGSTVTLLDIMG-QQDD 189
Cdd:PRK05803 121 --------LKKTKKEV-------------------------------------SLQDPIGVDKEGNEISLIDILGsEEDD 155
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 190 HYDLTEKRMILEKI---LPILSDREREIIQCTFieGL------SQKETGERIGLSQMHVSRLQRTAIKKL 250
Cdd:PRK05803 156 VIEQVELKMEVEKLykkIDILDEREKEVIEMRY--GLgngkekTQREIAKALGISRSYVSRIEKRALKKL 223
|
|
| PRK05949 |
PRK05949 |
RNA polymerase sigma factor; Validated |
3-251 |
9.74e-13 |
|
RNA polymerase sigma factor; Validated
Pssm-ID: 180321 [Multi-domain] Cd Length: 327 Bit Score: 66.79 E-value: 9.74e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 3 KESKSANEVSPEQINQWIKEHQEnkntdAQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDMSFERK 82
Cdd:PRK05949 69 PEWAEAVNLSETELKQTLKQGKR-----AKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYK 143
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 83 FEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTAELERSPSISEIADRLEVSEEEVLEAMEMGQsyNA 162
Cdd:PRK05949 144 FSTYAYWWIRQAITRAIAQQARTIRLPIHITEKLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMAR--QP 221
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 163 LSVDHSIEADKDGSTVTLLDIMGQQDDHYDLTEK-RMILEKILPILSDREREIIQCTF----IEGLSQKETGERIGLSQM 237
Cdd:PRK05949 222 ISLDVRVGDNQDTELSELLEDEGPSPDQYITQELlRQDLNNLLAELTPQQREVLTLRFgledGKELSLAKVGERLNLSRE 301
|
250
....*....|....
gi 446963851 238 HVSRLQRTAIKKLQ 251
Cdd:PRK05949 302 RVRQLEHQALAHLR 315
|
|
| Sigma70_r4 |
pfam04545 |
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ... |
204-252 |
3.65e-12 |
|
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.
Pssm-ID: 461347 [Multi-domain] Cd Length: 50 Bit Score: 59.36 E-value: 3.65e-12
10 20 30 40
....*....|....*....|....*....|....*....|....*....
gi 446963851 204 LPILSDREREIIQCTFIEGLSQKETGERIGLSQMHVSRLQRTAIKKLQE 252
Cdd:pfam04545 2 LASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
|
|
| PRK07405 |
PRK07405 |
RNA polymerase sigma factor SigD; Validated |
4-253 |
2.42e-11 |
|
RNA polymerase sigma factor SigD; Validated
Pssm-ID: 180963 [Multi-domain] Cd Length: 317 Bit Score: 62.47 E-value: 2.42e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 4 ESKSANEVSPEQINQWIKEHQEnkntdAQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDMSFERKF 83
Cdd:PRK07405 60 EWAKAAKLSEEELRSAIAEGEA-----AKRKMVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRF 134
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 84 EAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTAELERSPSISEIADRLEVSEEEVLEAMEmgQSYNAL 163
Cdd:PRK07405 135 STYAYWWIRQAITRAIAEKSRTIRLPIHITEKLNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLE--RARQPL 212
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 164 SVDHSIEADKDGSTVTLLDIMGQQDDHYDL-TEKRMILEKILPILSDREREIIQCTF--IEG--LSQKETGERIGLSQMH 238
Cdd:PRK07405 213 SLDLRVGDNQDTELGELLEDTGASPEDFATqSSLQLDLERLMEDLTPQQKEVIALRFglEDGqpLTLAKIGERLNISRER 292
|
250
....*....|....*
gi 446963851 239 VSRLQRTAIKKLQEA 253
Cdd:PRK07405 293 VRQIEREALSKLRKR 307
|
|
| PRK07406 |
PRK07406 |
RNA polymerase sigma factor RpoD; Validated |
31-156 |
3.80e-11 |
|
RNA polymerase sigma factor RpoD; Validated
Pssm-ID: 236012 [Multi-domain] Cd Length: 373 Bit Score: 62.11 E-value: 3.80e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 31 AQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDMSFERKFEAFLVPTVIGEIKRYLRDKTWSVHVPR 110
Cdd:PRK07406 137 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV 216
|
90 100 110 120
....*....|....*....|....*....|....*....|....*.
gi 446963851 111 RIKEIGPRIKKVSDELTAELERSPSISEIADRlevseeevleaMEM 156
Cdd:PRK07406 217 HLYETISRIKKTTKVLSQEFGRKPTEEEIAES-----------MEM 251
|
|
| RpoE |
COG1595 |
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ... |
28-253 |
1.21e-10 |
|
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: 58.85 E-value: 1.21e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 28 NTDAQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDmsFERKFEAFLVPTVIGEIKRYLRDKTwsvh 107
Cdd:COG1595 15 DEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFR--GRGSFRAWLYRIARNLAIDHLRKRR---- 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 108 vprrikeigpRIKKVSDELTAELERSpsiseiadrlevseeevleamemgqsynALSVDHSIEADkdgstvtlldimgqq 187
Cdd:COG1595 89 ----------RRRELLDELAEELPDE----------------------------AADPEEALEAE--------------- 115
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446963851 188 ddhydltEKRMILEKILPILSDREREIIQCTFIEGLSQKETGERIGLSQMHV-SRLQRtAIKKLQEA 253
Cdd:COG1595 116 -------ELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVkSRLSR-ARKKLREA 174
|
|
| Sigma70_r4 |
cd06171 |
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ... |
200-251 |
2.48e-10 |
|
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: 54.80 E-value: 2.48e-10
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|..
gi 446963851 200 LEKILPILSDREREIIQCTFIEGLSQKETGERIGLSQMHVSRLQRTAIKKLQ 251
Cdd:cd06171 4 LEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
|
|
| Sigma70_r3 |
pfam04539 |
Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the ... |
114-188 |
5.04e-09 |
|
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: 51.84 E-value: 5.04e-09
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446963851 114 EIGPRIKKVSDELTAELERSPSISEIADRLEVSEEEVLEAMEMGQSYNALSVDHSIEADKD-GSTVTLLDIMGQQD 188
Cdd:pfam04539 1 ELLNKIKRAQRELEQELGREPTPEEIAEELGLSPEKVREVLEAAREPVSLDTPVGEEEDGElGDLLEDDDIESPEE 76
|
|
| PRK07598 |
PRK07598 |
RNA polymerase sigma factor SigC; Validated |
10-252 |
7.98e-09 |
|
RNA polymerase sigma factor SigC; Validated
Pssm-ID: 236067 [Multi-domain] Cd Length: 415 Bit Score: 55.65 E-value: 7.98e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 10 EVSPEQINQWIKEHQEnkntdAQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDMSFERKFEAFLVP 89
Cdd:PRK07598 160 KLTVEELEQIQKQGLR-----AKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYW 234
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 90 TVIGEIKRYLRDKTWSVHVPRRIKEIGPRIKKVSDELTAELERSPSISEIADRLEVSEEEVLEAMEmgQSYNALSVDHSI 169
Cdd:PRK07598 235 WIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLL--RVPRSVSLETKV 312
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 170 EADKDGSTVTLLDIMGQQDDHYDLTEK-RMILEKILPILSDREREIIQCTFieGL------SQKETGERIGLSQMHVSRL 242
Cdd:PRK07598 313 GKDKDTELGDLLETDDISPEEMLMRESlQRDLQHLLADLTSRERDVIRMRF--GLadghtySLAEIGRALDLSRERVRQI 390
|
250
....*....|
gi 446963851 243 QRTAIKKLQE 252
Cdd:PRK07598 391 ESKALQKLRQ 400
|
|
| PRK08301 |
PRK08301 |
RNA polymerase sporulation sigma factor SigE; |
58-256 |
9.88e-09 |
|
RNA polymerase sporulation sigma factor SigE;
Pssm-ID: 236228 [Multi-domain] Cd Length: 234 Bit Score: 54.09 E-value: 9.88e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 58 EDLVQVGMVGLIGAINRFDMSFERKFEAFLVPTVIGEIKRYLRdktwsvhvprrikeigpRIKKVSDELtaelerspsis 137
Cdd:PRK08301 80 EDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMYLR-----------------RNNKVKAEV----------- 131
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 138 eiadrlevseeevleamemgqsynalSVDHSIEADKDGSTVTLLDIMGQQDD--HYDLTEK--RMILEKILPILSDRERE 213
Cdd:PRK08301 132 --------------------------SFDEPLNIDWDGNELLLSDVLGTDNDiiYKDIEDEvdRKLLKKALKKLSDREKQ 185
|
170 180 190 200
....*....|....*....|....*....|....*....|....*....
gi 446963851 214 IIQCTFieGLS------QKETGERIGLSQMHVSRLQRTAIKKLQEAAHK 256
Cdd:PRK08301 186 IMELRF--GLNggeektQKEVADMLGISQSYISRLEKRIIKRLKKEINK 232
|
|
| PRK08295 |
PRK08295 |
RNA polymerase sporulation sigma factor SigH; |
28-233 |
6.43e-08 |
|
RNA polymerase sporulation sigma factor SigH;
Pssm-ID: 181361 [Multi-domain] Cd Length: 208 Bit Score: 51.45 E-value: 6.43e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 28 NTDAQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDMSFERKFEAFLVPTVIGEIKRYLRDKTWSVH 107
Cdd:PRK08295 22 DKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCITRQIITAIKTANRQKH 101
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 108 VPrrikeigprikkvsdeLTaelerspsiseiadrlevseeevleamemgqsyNALSVDHSIEADKDGStvTLLDIMGQ- 186
Cdd:PRK08295 102 IP----------------LN---------------------------------SYVSLDKPIYDEESDR--TLLDVISEa 130
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|..
gi 446963851 187 --QDDHYDL---TEKRMILEKILPILSDREREIIQcTFIEGLSQKETGERIG 233
Cdd:PRK08295 131 kvTDPEELIiskEELEDIEEKIEELLSELEKEVLE-LYLDGKSYQEIAEELN 181
|
|
| PRK07921 |
PRK07921 |
RNA polymerase sigma factor SigB; Reviewed |
31-252 |
6.09e-07 |
|
RNA polymerase sigma factor SigB; Reviewed
Pssm-ID: 181169 [Multi-domain] Cd Length: 324 Bit Score: 49.73 E-value: 6.09e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 31 AQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDMSFERKFEAFLVPTVIGEIKRYLRDKTWSVHVPR 110
Cdd:PRK07921 87 ARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPV 166
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 111 RIKEIGPRIKKVSDELTAELERSPSISEIAdrLEVSEEEVLEAMEMGQSYNALSVDHSIEADKD---GSTVTLLDIMgQQ 187
Cdd:PRK07921 167 HLVEQVNKLARIKRELHQQLGREATDEELA--EESGIPEEKIADLLEHSRDPVSLDMPVGSDEEaplGDFIEDSEAT-SA 243
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446963851 188 DDHYDLTEKRMILEKILPILSDREREIIQCTFieGLSQ------KETGERIGLSQMHVSRLQRTAIKKLQE 252
Cdd:PRK07921 244 ENAVIAGLLHTDIRSVLATLDEREQQVIRLRF--GLDDgqprtlDQIGKLFGLSRERVRQIEREVMSKLRN 312
|
|
| PRK12427 |
PRK12427 |
FliA/WhiG family RNA polymerase sigma factor; |
24-252 |
8.50e-06 |
|
FliA/WhiG family RNA polymerase sigma factor;
Pssm-ID: 183523 [Multi-domain] Cd Length: 231 Bit Score: 45.62 E-value: 8.50e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 24 QENKNTDAQDKLVKhyqKLIESLAYKYSkGQSHHEDLVQVGMVGLIGAINRFDMSFErKFEAFLVPTVIGEIKRYLRDKT 103
Cdd:PRK12427 16 EEGKYLNAYLPLVK---KVVRQLAFQAD-SVIDREDMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILDELRELD 90
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 104 WSvhvPRRIKEIGPRIKKVSDELTAELERSPSISEIADRLEVSEEEVLEAMEMGQSYNALSVDHSIEADKDGstvtllDI 183
Cdd:PRK12427 91 WR---PRRLRQKTHKTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLLLENAGTLESLDELLALEAHN------DI 161
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446963851 184 MGQQDDHYDLTEKRMiLEKILPILSDREREIIQCTFIEGLSQKETGERIGLSQMHVSRLQRTAIKKLQE 252
Cdd:PRK12427 162 LQSRDLEENIIIEDN-LKQALSQLDEREQLILHLYYQHEMSLKEIALVLDLTEARICQLNKKIAQKIKS 229
|
|
| rpoH2 |
PRK07500 |
RNA polymerase factor sigma-32; Reviewed |
25-253 |
1.24e-05 |
|
RNA polymerase factor sigma-32; Reviewed
Pssm-ID: 236033 [Multi-domain] Cd Length: 289 Bit Score: 45.41 E-value: 1.24e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 25 ENKNTDAQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDMSFERKFEAFLVPTVIGEIKRY-LRDkt 103
Cdd:PRK07500 35 DHRDEDALHRIISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYiLRN-- 112
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 104 WSVhVP--------------RRIKeigPRIKKVSDELT-AELERspsisEIADRLEVSEEEVLEaMEMGQSYNALSVDHS 168
Cdd:PRK07500 113 WSI-VRggtssaqkalffnlRRLR---ARLAQADEELTkQEIHR-----EIATALGVSLSDVEM-MDARLSGPDASLNAP 182
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 169 IEADKDGSTV---TLLDIMGQQD----DHYDLTEKRMILEKILPILSDREREIIQCTFI--EGLSQKETGERIGLSQMHV 239
Cdd:PRK07500 183 QSEEDEGRSErmdFLVDDSPLPDeqveSSIDGERRRRWLTQALQTLNERELRIIRERRLreDGATLEALGEELGISKERV 262
|
250
....*....|....
gi 446963851 240 SRLQRTAIKKLQEA 253
Cdd:PRK07500 263 RQIEARALEKLRRA 276
|
|
| PRK05657 |
PRK05657 |
RNA polymerase sigma factor RpoS; Validated |
40-252 |
6.74e-05 |
|
RNA polymerase sigma factor RpoS; Validated
Pssm-ID: 235548 [Multi-domain] Cd Length: 325 Bit Score: 43.41 E-value: 6.74e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 40 QKLIES---LAYKYSKGQSHHE----DLVQVGMVGLIGAINRFDMsfERKFeaflvptvigeikRYLRDKTW-------- 104
Cdd:PRK05657 89 QRMIESnlrLVVKIAKRYLNRGlallDLIEEGNLGLIRAVEKFDP--ERGF-------------RFSTYATWwirqtier 153
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 105 -----------SVHVprrIKEIGP--RIKKvsdELTAELERSPSISEIADRLEVSEEEVLEAMEMGQSynALSVDHSIEA 171
Cdd:PRK05657 154 aimnqtrtirlPVHV---VKELNVylRAAR---ELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNER--ITSLDTPLGG 225
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446963851 172 DkdgSTVTLLDIMgqQDDHY----DLTEKR---MILEKILPILSDREREIIQCTF----IEGLSQKETGERIGLSQMHVS 240
Cdd:PRK05657 226 D---PEKSLLDIL--ADEQEngpeDTTQDDdmkQSIVKWLFELNDKQREVLARRFgllgYEAATLEDVAREIGLTRERVR 300
|
250
....*....|..
gi 446963851 241 RLQRTAIKKLQE 252
Cdd:PRK05657 301 QIQVEALRRLRE 312
|
|
| CitB |
COG2197 |
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ... |
178-244 |
4.76e-04 |
|
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal transduction mechanisms, Transcription];
Pssm-ID: 441799 [Multi-domain] Cd Length: 131 Bit Score: 39.11 E-value: 4.76e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446963851 178 VTLLDIMGQQDDHYDLTEKrmilekilpILSDREREIIQCtFIEGLSQKETGERIGLSQ----MHVSRLQR 244
Cdd:COG2197 50 VVLLDIRMPGMDGLEALRR---------LLTPREREVLRL-LAEGLSNKEIAERLGISErtvkTHVSNILR 110
|
|
| Sigma70_r4_2 |
pfam08281 |
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ... |
197-250 |
1.75e-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: 35.51 E-value: 1.75e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*
gi 446963851 197 RMILEKILPILSDREREIIQCTFIEGLSQKETGERIGLSQMHV-SRLQRtAIKKL 250
Cdd:pfam08281 1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVkSRLSR-ARKKL 54
|
|
| HTH_LUXR |
smart00421 |
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon |
204-256 |
2.31e-03 |
|
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
Pssm-ID: 197715 [Multi-domain] Cd Length: 58 Bit Score: 35.58 E-value: 2.31e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*...
gi 446963851 204 LPILSDREREIIQCTfIEGLSQKETGERIGLS----QMHVSRLQR-TAIKKLQEAAHK 256
Cdd:smart00421 1 LASLTPREREVLRLL-AEGLTNKEIAERLGISektvKTHLSNIMRkLGVRSRTQAVRL 57
|
|
| |
