|
Name |
Accession |
Description |
Interval |
E-value |
| PRK06704 |
PRK06704 |
RNA polymerase subunit sigma-70; |
1-228 |
6.22e-163 |
|
RNA polymerase subunit sigma-70;
Pssm-ID: 180663 [Multi-domain] Cd Length: 228 Bit Score: 449.09 E-value: 6.22e-163
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446259664 1 MCTKVTHVLKNHIDMNHSNINFLIEQYGELKRYCTFLTKNKWDGEDLAQETVCKVLQKYRNKEICMTLVYKIARNRWLDQ 80
Cdd:PRK06704 1 MCTKVTHILKNHIDMNHSNINFLIEQYGELKRYCTFLTKNKWDGEDLAQETVCKVLQKYSNKDICMTLVYKIARNRWLDQ 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446259664 81 MKSKSVHEKIREQITFEEPHENIADLHEMVGKVLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRL 160
Cdd:PRK06704 81 IKSKSVHEKIRDQITFEEPHEKIADLHEMVGKVLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRL 160
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446259664 161 KTVSEEGIEIVEFTEDIEVVVTSIREERPELLTKLLPTIDFTKLPSKQPVLLFNVKNPSSYSYMLYAA 228
Cdd:PRK06704 161 KTVSEEGIEIVEFTDDMEVVVTSIREERPELLTKLLPTIDFTKLPSKQPVLLFNVKQPSSYSCMLCVA 228
|
|
| RpoE |
COG1595 |
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ... |
23-161 |
1.76e-28 |
|
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: 105.85 E-value: 1.76e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446259664 23 LIEQY-GELKRYCTFLTKNKWDGEDLAQETVCKVLQK---YRNKEICMTLVYKIARNRWLDQMKSKSVHEKIREQITFEE 98
Cdd:COG1595 22 LYERYrPRLYRYARRLLGDRADAEDLVQETFLRLWRKldsFRGRGSFRAWLYRIARNLAIDHLRKRRRRRELLDELAEEL 101
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446259664 99 PHENI--------ADLHEMVGKVLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRLK 161
Cdd:COG1595 102 PDEAAdpeealeaEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLR 172
|
|
| sigma70-ECF |
TIGR02937 |
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ... |
23-161 |
2.33e-21 |
|
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: 86.63 E-value: 2.33e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446259664 23 LIEQYGE-LKRYCTFLTKNKWDGEDLAQETVCKVLQ---KYRNKEICMTLVYKIARNRWLDQMKSKSVHEKIREQI---- 94
Cdd:TIGR02937 6 LYERYLPlVYRYARRYLGDDADAEDLVQEAFLKLLEaldRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDLLeell 85
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446259664 95 -TFEEPHENI--ADLHEMVGKVLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRLK 161
Cdd:TIGR02937 86 dSDPSPEEELeqEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLR 155
|
|
| Sigma70_r4_2 |
pfam08281 |
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ... |
107-160 |
1.42e-09 |
|
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: 52.46 E-value: 1.42e-09
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....
gi 446259664 107 HEMVGKVLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRL 160
Cdd:pfam08281 1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
|
|
| Sigma70_r4 |
cd06171 |
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ... |
107-161 |
1.83e-03 |
|
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: 35.54 E-value: 1.83e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*
gi 446259664 107 HEMVGKVLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRLK 161
Cdd:cd06171 1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PRK06704 |
PRK06704 |
RNA polymerase subunit sigma-70; |
1-228 |
6.22e-163 |
|
RNA polymerase subunit sigma-70;
Pssm-ID: 180663 [Multi-domain] Cd Length: 228 Bit Score: 449.09 E-value: 6.22e-163
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446259664 1 MCTKVTHVLKNHIDMNHSNINFLIEQYGELKRYCTFLTKNKWDGEDLAQETVCKVLQKYRNKEICMTLVYKIARNRWLDQ 80
Cdd:PRK06704 1 MCTKVTHILKNHIDMNHSNINFLIEQYGELKRYCTFLTKNKWDGEDLAQETVCKVLQKYSNKDICMTLVYKIARNRWLDQ 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446259664 81 MKSKSVHEKIREQITFEEPHENIADLHEMVGKVLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRL 160
Cdd:PRK06704 81 IKSKSVHEKIRDQITFEEPHEKIADLHEMVGKVLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRL 160
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446259664 161 KTVSEEGIEIVEFTEDIEVVVTSIREERPELLTKLLPTIDFTKLPSKQPVLLFNVKNPSSYSYMLYAA 228
Cdd:PRK06704 161 KTVSEEGIEIVEFTDDMEVVVTSIREERPELLTKLLPTIDFTKLPSKQPVLLFNVKQPSSYSCMLCVA 228
|
|
| RpoE |
COG1595 |
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ... |
23-161 |
1.76e-28 |
|
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: 105.85 E-value: 1.76e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446259664 23 LIEQY-GELKRYCTFLTKNKWDGEDLAQETVCKVLQK---YRNKEICMTLVYKIARNRWLDQMKSKSVHEKIREQITFEE 98
Cdd:COG1595 22 LYERYrPRLYRYARRLLGDRADAEDLVQETFLRLWRKldsFRGRGSFRAWLYRIARNLAIDHLRKRRRRRELLDELAEEL 101
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446259664 99 PHENI--------ADLHEMVGKVLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRLK 161
Cdd:COG1595 102 PDEAAdpeealeaEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLR 172
|
|
| sigma70-ECF |
TIGR02937 |
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ... |
23-161 |
2.33e-21 |
|
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: 86.63 E-value: 2.33e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446259664 23 LIEQYGE-LKRYCTFLTKNKWDGEDLAQETVCKVLQ---KYRNKEICMTLVYKIARNRWLDQMKSKSVHEKIREQI---- 94
Cdd:TIGR02937 6 LYERYLPlVYRYARRYLGDDADAEDLVQEAFLKLLEaldRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDLLeell 85
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446259664 95 -TFEEPHENI--ADLHEMVGKVLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRLK 161
Cdd:TIGR02937 86 dSDPSPEEELeqEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLR 155
|
|
| PRK11924 |
PRK11924 |
RNA polymerase sigma factor; Provisional |
27-161 |
7.22e-13 |
|
RNA polymerase sigma factor; Provisional
Pssm-ID: 183384 [Multi-domain] Cd Length: 179 Bit Score: 64.61 E-value: 7.22e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446259664 27 YGELKRYCTFLTKNKWDGEDLAQETVCKVLQ---KYRNKEICMTLVYKIARN--------RWLDQMKSKSVHEKIREQIT 95
Cdd:PRK11924 23 APDLLRYARRQLGDRALAEDAVQEAFLRAWRkadLFNGKGSARTWLLTIARNvcydllrrRRREKAVLSDDALEPEFAET 102
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446259664 96 FEEPHENI--ADLHEMVGKVLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRLK 161
Cdd:PRK11924 103 AETPEAALlaKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQLLR 170
|
|
| SigM_subfam |
TIGR02950 |
RNA polymerase sigma factor, SigM family; This family of RNA polymerase sigma factors is a ... |
24-165 |
5.75e-11 |
|
RNA polymerase sigma factor, SigM family; This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot:
Pssm-ID: 274361 [Multi-domain] Cd Length: 154 Bit Score: 58.62 E-value: 5.75e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446259664 24 IEQYGELKRYCTFLTKNKWDGEDLAQETVCKV---LQKYRNKEIcMTLVYKIARNRWLDQMKSKSVHEKI-------REQ 93
Cdd:TIGR02950 2 REYMHDVFRYLYRLTKDKHLAEDLLQETFLKAyihLHSFKDSSI-KPWLFRIARNAFIDWYRKDKKIQTIdddaigdLEQ 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446259664 94 ITFEEP--HENIADLHEMVGKVLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRLKTVSE 165
Cdd:TIGR02950 81 HPVESPehHLLIKIEQEEITHHLSRLPENYRTVLILREFKEFSYKEIAELLNLSLAKVKSNLFRARKELKKLLE 154
|
|
| PRK12541 |
PRK12541 |
RNA polymerase sigma factor; Provisional |
25-165 |
6.41e-11 |
|
RNA polymerase sigma factor; Provisional
Pssm-ID: 183580 [Multi-domain] Cd Length: 161 Bit Score: 58.79 E-value: 6.41e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446259664 25 EQYGELKRYCTFLTKNKWDGEDLAQETVCKVL---QKYRNKEIcMTLVYKIARNRWLDQMKSksvhEKIREQITFEEPH- 100
Cdd:PRK12541 13 EHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLvhiDYYKGEEI-RPWLFTIAYNAFIDWYRK----EKKYKTTTIEEFHl 87
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446259664 101 -------ENIADLHEMVGKV--LSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRLKTVSE 165
Cdd:PRK12541 88 pnvpsteHEYFIKHEIASWLdsLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKETKSIKE 161
|
|
| PRK09639 |
PRK09639 |
RNA polymerase sigma factor SigX; Provisional |
27-166 |
6.70e-11 |
|
RNA polymerase sigma factor SigX; Provisional
Pssm-ID: 236602 [Multi-domain] Cd Length: 166 Bit Score: 58.81 E-value: 6.70e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446259664 27 YGELKRYCTFLTKNKWDGEDLAQETVCKVL-QKYRNKEICMTLVYKIARNRWLDQMKSKSVHeKIRE-------QITFEE 98
Cdd:PRK09639 13 YPDVVQQIFYIVKDRTQAEDLAQEVFLRLYrSDFKGIENEKGWLIKSARNVAYNYLRSEKRR-RARIlgefqwqEVDNEP 91
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446259664 99 PHENIADLHEMVGKV---LSSLNVQQSAILLLKdvFQ-YSIADIAKVCSVSEGAVKASLFRSRNRLKTVSEE 166
Cdd:PRK09639 92 SPEEIWIRKEEITKVqevLAKMTERDRTVLLLR--FSgYSYKEIAEALGIKESSVGTTLARAKKKFRKIYEQ 161
|
|
| PRK09415 |
PRK09415 |
RNA polymerase factor sigma C; Reviewed |
39-167 |
1.11e-10 |
|
RNA polymerase factor sigma C; Reviewed
Pssm-ID: 181835 [Multi-domain] Cd Length: 179 Bit Score: 58.61 E-value: 1.11e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446259664 39 KNKWDGEDLAQETVCKVLQK---YRNKEICMTLVYKIARNRWLDQMKS---KSVH--EKIREQI--TFEEPHENI---AD 105
Cdd:PRK09415 38 KNKEVAEDLTQEIFVKCYKSlhtYKGKSSLKTWLYRIAINHCKDYLKSwhnKKVIvtEDIFTYMesQKESVEEEViqnAE 117
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446259664 106 LHEMVGKVLSsLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRLKTVSEEG 167
Cdd:PRK09415 118 DERLASAVMS-LPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKELLKKGLEEE 178
|
|
| Sigma70_r4_2 |
pfam08281 |
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ... |
107-160 |
1.42e-09 |
|
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: 52.46 E-value: 1.42e-09
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....
gi 446259664 107 HEMVGKVLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRL 160
Cdd:pfam08281 1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
|
|
| PRK09644 |
PRK09644 |
RNA polymerase sigma factor SigM; Provisional |
32-166 |
2.66e-09 |
|
RNA polymerase sigma factor SigM; Provisional
Pssm-ID: 170033 [Multi-domain] Cd Length: 165 Bit Score: 54.50 E-value: 2.66e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446259664 32 RYCTFLTKNKWDGEDLAQETVCKV---LQKYRNKEIcMTLVYKIARNRWLD----QMKSKSVHEKIREQITFEEPHENIA 104
Cdd:PRK09644 16 RYLFSLTKSHHAAEDLLQETFYRAyiyLEDYDNQKV-KPWLFKVAYHTFIDfvrkEKKVSFVGTDEIEAIQAESTEEYVV 94
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446259664 105 --DLHEMVGKVLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRLKTVSEE 166
Cdd:PRK09644 95 akNSYEKLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLKE 158
|
|
| PRK09638 |
PRK09638 |
RNA polymerase sigma factor SigY; Reviewed |
23-154 |
3.84e-09 |
|
RNA polymerase sigma factor SigY; Reviewed
Pssm-ID: 182010 [Multi-domain] Cd Length: 176 Bit Score: 54.26 E-value: 3.84e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446259664 23 LIEQ-YGELKRYCTFLTKNKWDGEDLAQETVCKV---LQKYRNKEICMTLVYKIARNRWLDQMKSKSVHEKIREQITFEE 98
Cdd:PRK09638 23 LFQQhYSFLYKYLLKLTLDPDLAEDLVQETMLKAienLSSFQGRSKFSTWLISIASRLYKDHLRKQKREKLRLQRAKEET 102
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446259664 99 PHENI-------ADLHEMVgKVLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLF 154
Cdd:PRK09638 103 LRKEKweaaikgAEWSEML-DALSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTVKSRVH 164
|
|
| PRK12522 |
PRK12522 |
RNA polymerase sigma factor; Provisional |
20-165 |
4.52e-08 |
|
RNA polymerase sigma factor; Provisional
Pssm-ID: 183571 [Multi-domain] Cd Length: 173 Bit Score: 51.02 E-value: 4.52e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446259664 20 INFLIEQYGE-LKRYCTFLTKNKWDGEDLAQETVCKVLQ---KYRNKEICMTLVYKIARN----------RWLDQMKSkS 85
Cdd:PRK12522 5 VEELIDIYKQqIYSLCYKLAKTKEDAEDIFQETWIKVFSsrhQLSYVENYKKWITTICVRtfydfyrkkkRWKDRILD-L 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446259664 86 VHEKIREQITFEE----PHENIADLH-EMVGKVLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRL 160
Cdd:PRK12522 84 FHKEDGGEIEFADdvniSEEFIQKVEaEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQM 163
|
....*
gi 446259664 161 KTVSE 165
Cdd:PRK12522 164 REHLE 168
|
|
| PRK12518 |
PRK12518 |
RNA polymerase sigma factor; Provisional |
45-169 |
1.56e-07 |
|
RNA polymerase sigma factor; Provisional
Pssm-ID: 237124 [Multi-domain] Cd Length: 175 Bit Score: 49.72 E-value: 1.56e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446259664 45 EDLAQETVCKV---LQKYRNKEICMTLVYKIARNRWLDQ----MKSKSVHEKIREQITFEEPH--ENIADLH--EMVGKV 113
Cdd:PRK12518 38 DDLVQEVFLRVwkgLPKLRNPAYFSTWLYRITWNVATDArrqfAQRPSRIQDDSLNDQPSRPSdtPDLMQLHyqDLVQQG 117
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*..
gi 446259664 114 LSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRLKT-VSEEGIE 169
Cdd:PRK12518 118 LQTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKfLQQQGVL 174
|
|
| PRK12546 |
PRK12546 |
RNA polymerase sigma factor; Provisional |
23-183 |
2.85e-07 |
|
RNA polymerase sigma factor; Provisional
Pssm-ID: 139055 [Multi-domain] Cd Length: 188 Bit Score: 49.07 E-value: 2.85e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446259664 23 LIEQYGELKRYCTFLTKNKWDGEDLAQETVCKV---LQKYRNKEICMTLVYKIARNRWL-DQMKSKSVHEKIREQIT--- 95
Cdd:PRK12546 13 LVEHLPALRAFAISLTRNVAVADDLVQDTIVKAwtnFDKFQEGTNLRAWLFTILRNTFYsDRRKHKREVPDPEGVHAasl 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446259664 96 FEEP-HENIADLHEMvGKVLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRLKTVSE-EGIEIVEF 173
Cdd:PRK12546 93 AVKPaHDGRLAMSDF-RAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARARLAELLQlEEGEELEM 171
|
170
....*....|
gi 446259664 174 TEDIEVVVTS 183
Cdd:PRK12546 172 TDGATLAVMS 181
|
|
| PRK09640 |
PRK09640 |
RNA polymerase sigma factor SigX; Reviewed |
30-161 |
3.53e-07 |
|
RNA polymerase sigma factor SigX; Reviewed
Pssm-ID: 236603 [Multi-domain] Cd Length: 188 Bit Score: 48.78 E-value: 3.53e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446259664 30 LKRYCTFLTKNKWDGEDLAQETVCKVLQKYRN---KEICMTLVYKIARNRWLDQMKSKSVHEKIREQITF---EEPHENI 103
Cdd:PRK09640 39 LFNVCARYLGNDRDADDVCQEVMLKVLYGLKNfegKSKFKTWLYSITYNECITQYRKERRKRRLMDALSLdplEEASEEK 118
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446259664 104 ADLHEMVG---KVLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRLK 161
Cdd:PRK09640 119 APKPEERGgldRWLVHVNPIDREILVLRFVAELEFQEIADIMHMGLSATKMRYKRALDKLR 179
|
|
| PRK12547 |
PRK12547 |
RNA polymerase sigma factor; Provisional |
30-161 |
1.17e-06 |
|
RNA polymerase sigma factor; Provisional
Pssm-ID: 139056 [Multi-domain] Cd Length: 164 Bit Score: 47.18 E-value: 1.17e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446259664 30 LKRYCTFLTKNKWDGEDLAQETVCKVLQKYRNKEICMTL---VYKIARNRWLDQMKSK--SVHEK---IREQITFEEPHE 101
Cdd:PRK12547 19 LRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGTNLkawLFTILRNEFYSQMRKRgrEVQDSdgvFTARVAVHPAQY 98
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|
gi 446259664 102 NIADLHEMvGKVLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRLK 161
Cdd:PRK12547 99 GSLDLQDF-KKALNLLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARNRLQ 157
|
|
| PRK09643 |
PRK09643 |
RNA polymerase sigma factor SigM; Reviewed |
67-160 |
2.41e-06 |
|
RNA polymerase sigma factor SigM; Reviewed
Pssm-ID: 236604 [Multi-domain] Cd Length: 192 Bit Score: 46.63 E-value: 2.41e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446259664 67 TLVYKIARNRWLDQMKSKSVHEKIREQITFEEPHENIA-----DLHEMVGKVLSSLNVQQSAILLLKDVFQYSIADIAKV 141
Cdd:PRK09643 80 SWLHRIVVNACLDRLRRAKARPTVPLDDVYPVAQLERDptarvETALAVQRALMRLPVEQRAALVAVDMQGYSVADAARM 159
|
90
....*....|....*....
gi 446259664 142 CSVSEGAVKASLFRSRNRL 160
Cdd:PRK09643 160 LGVAEGTVKSRCARGRARL 178
|
|
| PRK12536 |
PRK12536 |
RNA polymerase sigma factor; Provisional |
43-155 |
2.73e-06 |
|
RNA polymerase sigma factor; Provisional
Pssm-ID: 237131 [Multi-domain] Cd Length: 181 Bit Score: 46.20 E-value: 2.73e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446259664 43 DGEDLAQETVCKVLQK---YRNKEICMTLVYKIARNRWLDQMKSKSVHEKIREQI-----TFEEPHENIADLHEMVGKVL 114
Cdd:PRK12536 48 EVEDLVQEILLAVHNArhtYRADQPLTAWVHAIARYKLMDFLRSRARREALHDPLddeseLFATSDDEAAEARRDLGKLL 127
|
90 100 110 120
....*....|....*....|....*....|....*....|.
gi 446259664 115 SSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFR 155
Cdd:PRK12536 128 EQLPDRQRLPIVHVKLEGLSVAETAQLTGLSESAVKVGIHR 168
|
|
| PRK09647 |
PRK09647 |
RNA polymerase sigma factor SigE; Reviewed |
37-161 |
1.62e-05 |
|
RNA polymerase sigma factor SigE; Reviewed
Pssm-ID: 236606 [Multi-domain] Cd Length: 203 Bit Score: 44.39 E-value: 1.62e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446259664 37 LTKNKWDGEDLAQETVCKV---LQKYRNKEICMTLvYKIARNRWLDQMKSKSvheKIR--------EQITFEEPHE---- 101
Cdd:PRK09647 48 LSGNQHDAEDLTQETFIRVfrsLQNYQPGTFEGWL-HRITTNLFLDMVRRRA---RIRmealpedyDRVPGDEPNPeqiy 123
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|
gi 446259664 102 NIADLHEMVGKVLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRLK 161
Cdd:PRK09647 124 HDARLDPDLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQQLR 183
|
|
| PRK09652 |
PRK09652 |
RNA polymerase sigma factor RpoE; Provisional |
30-161 |
1.73e-05 |
|
RNA polymerase sigma factor RpoE; Provisional
Pssm-ID: 236608 [Multi-domain] Cd Length: 182 Bit Score: 44.03 E-value: 1.73e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446259664 30 LKRYCTFLTKNKWDGEDLAQETVCKVLQK---YRNKEICMTLVYKIARNRWLDQMKSKS---------VHEKIREQITFE 97
Cdd:PRK09652 23 VKRLLSRLTRDPADAEDLVQETFIKAYRAlhsFRGGAAFYTWLYRIARNTAINYLRKQGrrppasdvdAEEAEDFDLADA 102
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446259664 98 EPHENIAD-------LHEMVGKVLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRLK 161
Cdd:PRK09652 103 LRDISTPEnellsaeLEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRIFRAREALR 173
|
|
| PRK09648 |
PRK09648 |
RNA polymerase sigma factor ShbA; |
45-165 |
2.00e-05 |
|
RNA polymerase sigma factor ShbA;
Pssm-ID: 236607 [Multi-domain] Cd Length: 189 Bit Score: 43.80 E-value: 2.00e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446259664 45 EDLAQEtVC----KVLQKYRNK-EICMTLVYKIARNRWLD----QMKSKS-----VHEKIREQITFEEpHENIADLHEMV 110
Cdd:PRK09648 56 DDVAQE-VClaviTALPRYRDQgRPFLAFVYGIAAHKVADahraAGRDKAvpteeVPERPSDDAGPEE-RALRSESSNRM 133
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*
gi 446259664 111 GKVLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRLKTVSE 165
Cdd:PRK09648 134 RELLDTLPEKQREILILRVVVGLSAEETAEAVGSTPGAVRVAQHRALARLRAEIE 188
|
|
| Sigma70_r2 |
pfam04542 |
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ... |
23-85 |
4.94e-05 |
|
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: 40.26 E-value: 4.94e-05
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446259664 23 LIEQYG-ELKRYCTFLTKNKWDGEDLAQETVCKVLQ---KYRNKEICM--TLVYKIARNRWLDQMKSKS 85
Cdd:pfam04542 1 LVERYLpLVYSLARRYLGDGADAEDLVQEGFLGLWRaieRFDPERGVSfsTWLYTIIRNAIIDYLRKQR 69
|
|
| PRK08241 |
PRK08241 |
RNA polymerase subunit sigma-70; |
23-167 |
8.61e-05 |
|
RNA polymerase subunit sigma-70;
Pssm-ID: 236196 [Multi-domain] Cd Length: 339 Bit Score: 42.62 E-value: 8.61e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446259664 23 LIEQY-GELKRYCTFLTKNKWDGEDLAQETVCKV---LQKYRNKEICMTLVYKIARNRWLDQMKSKS------------- 85
Cdd:PRK08241 24 LVEPHrRELLAHCYRMLGSVHDAEDAVQETLLRAwrgYDRFEGRSSLRTWLYRIATNVCLDALEGRArrplptdlgapaa 103
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446259664 86 ---VHEKIREQITFEEPH------ENIADLHEMVGK----------VLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSE 146
Cdd:PRK08241 104 dpvDELVERPEVPWLEPYpdalldPAAADPAARVVAresvrlafvaALQHLPPRQRAVLILRDVLGWSAAEVAELLDTSV 183
|
170 180
....*....|....*....|.
gi 446259664 147 GAVKASLFRSRNRLKTVSEEG 167
Cdd:PRK08241 184 AAVNSALQRARATLAERGPSA 204
|
|
| PRK09649 |
PRK09649 |
RNA polymerase sigma factor SigC; Reviewed |
32-160 |
2.32e-04 |
|
RNA polymerase sigma factor SigC; Reviewed
Pssm-ID: 137458 [Multi-domain] Cd Length: 185 Bit Score: 40.79 E-value: 2.32e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446259664 32 RYCTFLTkNKWDGEDLAQETVCKVL---QKYRNKEICMTLVYKIARNRWLD-----QMKSKSVHEKIREQITFEEPH-EN 102
Cdd:PRK09649 39 RFVAYLS-DVGSADDLTQETFLRAIgaiPRFSARSSARTWLLAIARHVVADhirhvRSRPRTTRGARPEHLIDGDRHaRG 117
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*...
gi 446259664 103 IADLHEmVGKVLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRL 160
Cdd:PRK09649 118 FEDLVE-VTTMIADLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARARDAL 174
|
|
| PRK12516 |
PRK12516 |
RNA polymerase sigma factor; Provisional |
45-163 |
7.08e-04 |
|
RNA polymerase sigma factor; Provisional
Pssm-ID: 183568 [Multi-domain] Cd Length: 187 Bit Score: 39.18 E-value: 7.08e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446259664 45 EDLAQETVCKVLQKYRNKEICMTL---VYKIARNRWLDQMKS--KSVHEK---IREQITFEEPHENIADLHEMvGKVLSS 116
Cdd:PRK12516 38 DDLVQDTIMKAWAKQDHFEVGTNMkawLFTILRNEFYSQMRKrgREVQDTdgmFTEQLAVHPSQYGTLDLQDF-RAALDQ 116
|
90 100 110 120
....*....|....*....|....*....|....*....|....*..
gi 446259664 117 LNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRLKTV 163
Cdd:PRK12516 117 LPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQRLQEI 163
|
|
| Sigma70_r4 |
cd06171 |
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ... |
107-161 |
1.83e-03 |
|
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: 35.54 E-value: 1.83e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*
gi 446259664 107 HEMVGKVLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRLK 161
Cdd:cd06171 1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
|
|
| PRK12512 |
PRK12512 |
RNA polymerase sigma factor; Provisional |
43-160 |
1.84e-03 |
|
RNA polymerase sigma factor; Provisional
Pssm-ID: 171551 [Multi-domain] Cd Length: 184 Bit Score: 38.14 E-value: 1.84e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446259664 43 DGEDLAQETVCKVLQK---YRNKEICMTLVYKIARNRWLDQMKSKSVH-----EKIREQITFEEPHENIADLHemVGKVL 114
Cdd:PRK12512 52 QAEDIVQEILLAVHLKrhtWDPGAPFAPWLFAIARNKLIDALRRRGRRvfvdiDDFAETLPAEPATETLPAGD--VGRHL 129
|
90 100 110 120
....*....|....*....|....*....|....*....|....*.
gi 446259664 115 SSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRL 160
Cdd:PRK12512 130 ETLPPRQRDVVQSISVEGASIKETAAKLSMSEGAVRVALHRGLAAL 175
|
|
| PRK12511 |
PRK12511 |
RNA polymerase sigma factor; Provisional |
23-167 |
2.26e-03 |
|
RNA polymerase sigma factor; Provisional
Pssm-ID: 237123 [Multi-domain] Cd Length: 182 Bit Score: 37.84 E-value: 2.26e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446259664 23 LIEQYGELKRYCTFLTKNKWDGEDLAQETVCKVLQK---YRNKEICMTLVYKIARNRWLDQMKSKSVHEKIREQITFEE- 98
Cdd:PRK12511 10 VLDQLVPLRRYARSLTRDSAEAEDLVHDALVRALERrasFRSGGNLRTWLMSILHNAFIDELRRRRVEARRADELAVLAd 89
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446259664 99 -----PHENIADLHEmVGKVLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRLKTVsEEG 167
Cdd:PRK12511 90 aslpaAQEHAVRLAQ-IRDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAALRAF-EEG 161
|
|
| |
