|
Name |
Accession |
Description |
Interval |
E-value |
| fliA |
PRK06986 |
flagellar biosynthesis sigma factor; Validated |
5-228 |
1.56e-94 |
|
flagellar biosynthesis sigma factor; Validated
Pssm-ID: 235901 [Multi-domain] Cd Length: 236 Bit Score: 276.34 E-value: 1.56e-94
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277938134 5 AYVNGMKHKEDELAIQYLPAVKAMAYRLKERLPSSIDFLDLSAIGTEELIKLARRYDETLNDSFWGYAKKRVYGAMLDYL 84
Cdd:PRK06986 1 AYTAEGKMDQDELVEQYAPLVKRIALRLKARLPASVDLDDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDEL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277938134 85 RSLDILSRASRKLVKAIDYAVEEYILLHDEEPTDEELSVLLNESVEKVHEARIASSIYTVMPLHDQLHVGDEGAALI--- 161
Cdd:PRK06986 81 RSLDWVPRSVRRNAREVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDELRGEHGDSILVTedh 160
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1277938134 162 -------QVEKDELIEVIKSILNSYNEREQLIIQFYYFEELTLKEISEILNITESRISQIHKSVLQKIKESVGA 228
Cdd:PRK06986 161 qdedplqQLEDEELREALVEAIESLPEREQLVLSLYYQEELNLKEIGAVLGVSESRVSQIHSQAIKRLRARLGE 234
|
|
| FliA_WhiG |
TIGR02479 |
RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar ... |
17-224 |
1.00e-64 |
|
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: 200.19 E-value: 1.00e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277938134 17 LAIQYLPAVKAMAYRLKERLPSSIDFLDLSAIGTEELIKLARRYDETLNDSFWGYAKKRVYGAMLDYLRSLDILSRASRK 96
Cdd:TIGR02479 1 LIRRYLPLVKRIAGRLSVGLPSSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMLDELRRLDWVPRSLRQ 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277938134 97 LVKAIDYAVEEYILLHDEEPTDEELSVLLNESVEKVHEARIASSIYTVMPLHDQLHVGDEGAALIQ-------------V 163
Cdd:TIGR02479 81 KARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELLESGDDGGSLIDrieddksedpeeeL 160
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1277938134 164 EKDELIEVIKSILNSYNEREQLIIQFYYFEELTLKEISEILNITESRISQIHKSVLQKIKE 224
Cdd:TIGR02479 161 EREELREALAEAIESLSEREQLVLSLYYYEELNLKEIGEVLGLTESRVSQIHSQALKKLRA 221
|
|
| FliA |
COG1191 |
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ... |
5-228 |
1.75e-61 |
|
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: 192.35 E-value: 1.75e-61
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277938134 5 AYVNGMKHKEDELAIQYLPAVKAMAYRLKERLPSSIDflDLSAIGTEELIKLARRYDETLNDSFWGYAKKRVYGAMLDYL 84
Cdd:COG1191 8 RYQEGDEEAREELIEEYLPLVKKIASRLAGRLPAELD--DLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRGAILDYL 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277938134 85 RSLDILSRASRKLVKAIDYAVEEYILLHDEEPTDEELSVLLNESVEKVHEARIASSIYTVMPLHDQLHVGDEGAALI--- 161
Cdd:COG1191 86 RDEDWVPRSVRELARKIEEAIEELEQELGREPTDEEIAEELGISLEEVQEALEAANAYQLLSLDEPLEDGDDLLDLLesg 165
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1277938134 162 ----QVEKDELIEVIKSILNSYNEREQLIIQFYYFEELTLKEISEILNITESRISQIHKSVLQKIKESVGA 228
Cdd:COG1191 166 dpeeELEHEELREALAEAIEQLPERERLVLSLYYFEELTLKEIAEVLGVSESRVSRLHKKALARLREYLKE 236
|
|
| Sigma70_r4 |
pfam04545 |
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ... |
176-224 |
1.46e-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: 60.13 E-value: 1.46e-12
10 20 30 40
....*....|....*....|....*....|....*....|....*....
gi 1277938134 176 LNSYNEREQLIIQFYYFEELTLKEISEILNITESRISQIHKSVLQKIKE 224
Cdd:pfam04545 2 LASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
|
|
| Sigma70_r4 |
cd06171 |
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ... |
169-223 |
9.25e-11 |
|
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: 55.57 E-value: 9.25e-11
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*
gi 1277938134 169 IEVIKSILNSYNEREQLIIQFYYFEELTLKEISEILNITESRISQIHKSVLQKIK 223
Cdd:cd06171 1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| fliA |
PRK06986 |
flagellar biosynthesis sigma factor; Validated |
5-228 |
1.56e-94 |
|
flagellar biosynthesis sigma factor; Validated
Pssm-ID: 235901 [Multi-domain] Cd Length: 236 Bit Score: 276.34 E-value: 1.56e-94
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277938134 5 AYVNGMKHKEDELAIQYLPAVKAMAYRLKERLPSSIDFLDLSAIGTEELIKLARRYDETLNDSFWGYAKKRVYGAMLDYL 84
Cdd:PRK06986 1 AYTAEGKMDQDELVEQYAPLVKRIALRLKARLPASVDLDDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDEL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277938134 85 RSLDILSRASRKLVKAIDYAVEEYILLHDEEPTDEELSVLLNESVEKVHEARIASSIYTVMPLHDQLHVGDEGAALI--- 161
Cdd:PRK06986 81 RSLDWVPRSVRRNAREVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDELRGEHGDSILVTedh 160
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1277938134 162 -------QVEKDELIEVIKSILNSYNEREQLIIQFYYFEELTLKEISEILNITESRISQIHKSVLQKIKESVGA 228
Cdd:PRK06986 161 qdedplqQLEDEELREALVEAIESLPEREQLVLSLYYQEELNLKEIGAVLGVSESRVSQIHSQAIKRLRARLGE 234
|
|
| FliA_WhiG |
TIGR02479 |
RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar ... |
17-224 |
1.00e-64 |
|
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: 200.19 E-value: 1.00e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277938134 17 LAIQYLPAVKAMAYRLKERLPSSIDFLDLSAIGTEELIKLARRYDETLNDSFWGYAKKRVYGAMLDYLRSLDILSRASRK 96
Cdd:TIGR02479 1 LIRRYLPLVKRIAGRLSVGLPSSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMLDELRRLDWVPRSLRQ 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277938134 97 LVKAIDYAVEEYILLHDEEPTDEELSVLLNESVEKVHEARIASSIYTVMPLHDQLHVGDEGAALIQ-------------V 163
Cdd:TIGR02479 81 KARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELLESGDDGGSLIDrieddksedpeeeL 160
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1277938134 164 EKDELIEVIKSILNSYNEREQLIIQFYYFEELTLKEISEILNITESRISQIHKSVLQKIKE 224
Cdd:TIGR02479 161 EREELREALAEAIESLSEREQLVLSLYYYEELNLKEIGEVLGLTESRVSQIHSQALKKLRA 221
|
|
| FliA |
COG1191 |
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ... |
5-228 |
1.75e-61 |
|
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: 192.35 E-value: 1.75e-61
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277938134 5 AYVNGMKHKEDELAIQYLPAVKAMAYRLKERLPSSIDflDLSAIGTEELIKLARRYDETLNDSFWGYAKKRVYGAMLDYL 84
Cdd:COG1191 8 RYQEGDEEAREELIEEYLPLVKKIASRLAGRLPAELD--DLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRGAILDYL 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277938134 85 RSLDILSRASRKLVKAIDYAVEEYILLHDEEPTDEELSVLLNESVEKVHEARIASSIYTVMPLHDQLHVGDEGAALI--- 161
Cdd:COG1191 86 RDEDWVPRSVRELARKIEEAIEELEQELGREPTDEEIAEELGISLEEVQEALEAANAYQLLSLDEPLEDGDDLLDLLesg 165
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1277938134 162 ----QVEKDELIEVIKSILNSYNEREQLIIQFYYFEELTLKEISEILNITESRISQIHKSVLQKIKESVGA 228
Cdd:COG1191 166 dpeeELEHEELREALAEAIEQLPERERLVLSLYYFEELTLKEIAEVLGVSESRVSRLHKKALARLREYLKE 236
|
|
| PRK06288 |
PRK06288 |
RNA polymerase sigma factor WhiG; Reviewed |
15-220 |
4.21e-36 |
|
RNA polymerase sigma factor WhiG; Reviewed
Pssm-ID: 235770 [Multi-domain] Cd Length: 268 Bit Score: 127.88 E-value: 4.21e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277938134 15 DELAIQYLPAVKAMAYRLKERLPSSIDFLDLSAIGTEELIKLARRYDETLNDSFWGYAKKRVYGAMLDYLRSLDILSRAS 94
Cdd:PRK06288 34 EYLILKYSPLVKYVAGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDELRSIDWIPRSV 113
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277938134 95 RKLVKAIDYAVEEYILLHDEEPTDEELSVLLNESVEKVHEARIASSIYTVMPLHDQLHVGDEGAAL-------------- 160
Cdd:PRK06288 114 RQKARQIERAIAMLEARLGRTPSDEEIADELGISLEEYNSLLSKLSGTSVVSLNDLWFGGDEGDEVslmdtlespaalnp 193
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1277938134 161 -IQVEKDELIEVIKSILNSYNEREQLIIQFYYFEELTLKEISEILNITESRISQIH-KSVLQ 220
Cdd:PRK06288 194 dEIAEREEIKRVIVEAIKTLPEREKKVLILYYYEDLTLKEIGKVLGVTESRISQLHtKAVLQ 255
|
|
| PRK07670 |
PRK07670 |
FliA/WhiG family RNA polymerase sigma factor; |
15-223 |
3.29e-34 |
|
FliA/WhiG family RNA polymerase sigma factor;
Pssm-ID: 181075 [Multi-domain] Cd Length: 251 Bit Score: 122.85 E-value: 3.29e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277938134 15 DELAIQYLPAVKAMAYRLKERLPSSIDFLDLSAIGTEELIKLARRYDETLNDSFWGYAKKRVYGAMLDYLRSLDILSRAS 94
Cdd:PRK07670 25 DELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRKEDWLPRSM 104
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277938134 95 RKLVKAIDYAVEEYILLHDEEPTDEELSVLLNESVEKVHEARIASSIYTVMPLHDQLHVGDEGAALI------------- 161
Cdd:PRK07670 105 REKTKKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGFFANLLSIDEKTHDQDDGENVSvtirddktptpee 184
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1277938134 162 QVEKDELIEVIKSILNSYNEREQLIIQFYYFEELTLKEISEILNITESRISQIHKSVLQKIK 223
Cdd:PRK07670 185 KLLKEELIEELAEKIKQLSEKEQLVISLFYKEELTLTEIGQVLNLSTSRISQIHSKALFKLK 246
|
|
| PRK05911 |
PRK05911 |
RNA polymerase sigma factor sigma-28; Reviewed |
12-228 |
5.24e-30 |
|
RNA polymerase sigma factor sigma-28; Reviewed
Pssm-ID: 235644 [Multi-domain] Cd Length: 257 Bit Score: 112.02 E-value: 5.24e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277938134 12 HKEDELAIQYLPAVKAMAYRLKERLPSSIDFLDLSAIGTEELIKLARRYDETLNDSFWGYAKKRVYGAMLDYLRSLDILS 91
Cdd:PRK05911 23 EYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRKQDWVP 102
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277938134 92 RASRKLVKAIDYAVEEYILLHDEEPTDEELSVLLNESVEKVHEARIASSIYTVMPLHDQ---LHVGDEGAALIQ------ 162
Cdd:PRK05911 103 RSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILSLNEEfpcQSDDEAGLALEEriader 182
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1277938134 163 -------VEKDELIEVIKSILNSYNEREQLIIQFYYFEELTLKEISEILNITESRISQIHKSVLQKIKESVGA 228
Cdd:PRK05911 183 aetgydvVDKKEFSSILAEAILALEEKERKVMALYYYEELVLKEIGKILGVSESRVSQIHSKALLKLRATLSA 255
|
|
| PRK12427 |
PRK12427 |
FliA/WhiG family RNA polymerase sigma factor; |
21-224 |
1.83e-25 |
|
FliA/WhiG family RNA polymerase sigma factor;
Pssm-ID: 183523 [Multi-domain] Cd Length: 231 Bit Score: 99.17 E-value: 1.83e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277938134 21 YLPAVKAMAYRLKERLPSSIDFLDLSAIGTEELIKLARRYDETlNDSFWGYAKKRVYGAMLDYLRSLDILSRASRKLVKA 100
Cdd:PRK12427 24 YLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEALRRYGHP-DEQFAAYAVHRIRGAILDELRELDWRPRRLRQKTHK 102
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277938134 101 IDYAVEEYILLHDEEPTDEELSVLLNESVEKVHEARIASSIYTVMPLHDQLHVGDEGAALIQVEKDELI---EVIKSILN 177
Cdd:PRK12427 103 TNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLLLENAGTLESLDELLALEAHNDILQSRDLEENIiieDNLKQALS 182
|
170 180 190 200
....*....|....*....|....*....|....*....|....*..
gi 1277938134 178 SYNEREQLIIQFYYFEELTLKEISEILNITESRISQIHKSVLQKIKE 224
Cdd:PRK12427 183 QLDEREQLILHLYYQHEMSLKEIALVLDLTEARICQLNKKIAQKIKS 229
|
|
| sigma70-ECF |
TIGR02937 |
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ... |
15-224 |
1.93e-15 |
|
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: 70.84 E-value: 1.93e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277938134 15 DELAIQYLPAVKAMAYRlkeRLPSSIDFLDLSAIGTEELIKLARRYDEtlNDSFWGYAKKRVYGAMLDYLRSldilsras 94
Cdd:TIGR02937 4 EELYERYLPLVYRYARR---YLGDDADAEDLVQEAFLKLLEALDRFDP--EGSFKAWLFRIARNLILDYLRR-------- 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277938134 95 rklVKAIDYAVEEYILLHDEEPTDEElsvllnesvekvheariassiytvmplhdqlhvgdegaaliQVEKDELIEVIKS 174
Cdd:TIGR02937 71 ---KRRLRRELDLLEELLDSDPSPEE-----------------------------------------ELEQEEEREALRE 106
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|
gi 1277938134 175 ILNSYNEREQLIIQFYYFEELTLKEISEILNITESRISQIHKSVLQKIKE 224
Cdd:TIGR02937 107 ALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRE 156
|
|
| Sigma70_r4 |
pfam04545 |
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ... |
176-224 |
1.46e-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: 60.13 E-value: 1.46e-12
10 20 30 40
....*....|....*....|....*....|....*....|....*....
gi 1277938134 176 LNSYNEREQLIIQFYYFEELTLKEISEILNITESRISQIHKSVLQKIKE 224
Cdd:pfam04545 2 LASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
|
|
| RpoD |
COG0568 |
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ... |
90-226 |
5.51e-12 |
|
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: 63.53 E-value: 5.51e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277938134 90 LSRASRKLVKAidyaveeyillHDEEPTDEELSVLLNESVEKVHEA-RIASSIYTV-MPLHDqlhvgDEGAALI------ 161
Cdd:COG0568 119 LRRAKRQLLQE-----------LGREPTPEEIAEELGVPEEKVREMlRLAREPVSLdAPVGD-----DEDSELGdllede 182
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1277938134 162 -------QVEKDELIEVIKSILNSYNEREQLIIQFYYF----EELTLKEISEILNITESRISQIHKSVLQKIKESV 226
Cdd:COG0568 183 eapspeeALEEELLREELREALDTLTEREREILRLRFGlddgEPHTLEEIGKEFGVSRERVRQIEAKALRKLRHPL 258
|
|
| PRK05572 |
PRK05572 |
RNA polymerase sporulation sigma factor, SigF/SigG family; |
44-224 |
7.13e-12 |
|
RNA polymerase sporulation sigma factor, SigF/SigG family;
Pssm-ID: 180137 [Multi-domain] Cd Length: 252 Bit Score: 63.07 E-value: 7.13e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277938134 44 DLSAIGTEELIKLARRYDETLNDSFWGYAKKRVYGAMLDYLRSLDIL--SRASRKLVKAIDYAVEEYILLHDEEPTDEEL 121
Cdd:PRK05572 61 DLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDGTVkvSRSLKETANKIRKDKDELSKELGREPTIEEL 140
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277938134 122 SVLLNESVEKVHEARIASSiyTVMPLHDQLHVGDeGAALIQVEK------DELIEVI--KSILNSYNEREQLIIQFYYFE 193
Cdd:PRK05572 141 AEYLGVTPEEVVLAQEASR--SPQSIHETVHEND-GDPITLLDQiadqseEDWFDKIalKEAIRELDERERLIVYLRYFK 217
|
170 180 190
....*....|....*....|....*....|.
gi 1277938134 194 ELTLKEISEILNITESRISQIHKSVLQKIKE 224
Cdd:PRK05572 218 DKTQSEVAKRLGISQVQVSRLEKKILKQMKE 248
|
|
| PRK08583 |
PRK08583 |
RNA polymerase sigma factor SigB; Validated |
8-226 |
9.23e-12 |
|
RNA polymerase sigma factor SigB; Validated
Pssm-ID: 236306 [Multi-domain] Cd Length: 257 Bit Score: 62.79 E-value: 9.23e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277938134 8 NGMKHKEDELAIQYLPAVKAMAYRLKERLPSSIDFLDLSAIGteeLIKLARRYDETLNDSFWGYAKKRVYGAMLDYLR-- 85
Cdd:PRK08583 25 NQDEEAQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVG---LLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRdk 101
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277938134 86 --SLDIlSRASRKLVKAIDYAVEEYILLHDEEPTDEELSVLLNESVEKVHEARIASSIYTVMPLHDQLHVGDEGA--ALI 161
Cdd:PRK08583 102 twSVHV-PRRIKELGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEVLEAMEMGKSYQALSVDHSIEADSDGStvTLL 180
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1277938134 162 QV--------EKDELIEVIKSILNSYNEREQLIIQFYYFEELTLKEISEILNITESRISQIHKSVLQKIKESV 226
Cdd:PRK08583 181 DIvgqqedgyELTEQRMILEKILPVLSDREKSIIQCTFIENLSQKETGERLGISQMHVSRLQRQAIKKLREAA 253
|
|
| Sigma70_r4 |
cd06171 |
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ... |
169-223 |
9.25e-11 |
|
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: 55.57 E-value: 9.25e-11
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*
gi 1277938134 169 IEVIKSILNSYNEREQLIIQFYYFEELTLKEISEILNITESRISQIHKSVLQKIK 223
Cdd:cd06171 1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
|
|
| Sigma70_r2 |
pfam04542 |
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ... |
20-88 |
1.45e-08 |
|
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: 49.89 E-value: 1.45e-08
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1277938134 20 QYLPAVKAMAYRLkerLPSSIDFLDLSAIGTEELIKLARRYDETLNDSFWGYAKKRVYGAMLDYLRSLD 88
Cdd:pfam04542 4 RYLPLVYSLARRY---LGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQR 69
|
|
| PRK07408 |
PRK07408 |
RNA polymerase sigma factor SigF; Reviewed |
25-224 |
5.86e-08 |
|
RNA polymerase sigma factor SigF; Reviewed
Pssm-ID: 180965 [Multi-domain] Cd Length: 256 Bit Score: 51.84 E-value: 5.86e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277938134 25 VKAMAYRLKERLPSSIDflDLSAIGTEELIKLARRYDETLNDSFWGYAKKRVYGAMLDYLR----SLDI------LSRAS 94
Cdd:PRK07408 38 VRKEAHRWSNQCSEPYE--DLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRdkspTVRIprrwqeLQRQA 115
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277938134 95 RKLVKaidyaveEYILLHDEEPTDEELSVLLNESVEKVHEARIASSIYTVMPLHDQLHVGDEGA------------ALIQ 162
Cdd:PRK07408 116 KKVRQ-------ELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRTPLSLDAPVNQDEDGStslgdllpdpryRSFQ 188
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1277938134 163 VEKDELIEVIKSiLNSYNEREQLIIQFYYFEELTLKEISEILNI---TESRisQIHKSvLQKIKE 224
Cdd:PRK07408 189 LAQEDRIRLQQA-LAQLEERTREVLEFVFLHDLTQKEAAERLGIspvTVSR--RVKKG-LDQLKK 249
|
|
| PRK08215 |
PRK08215 |
RNA polymerase sporulation sigma factor SigG; |
44-226 |
1.38e-07 |
|
RNA polymerase sporulation sigma factor SigG;
Pssm-ID: 181296 [Multi-domain] Cd Length: 258 Bit Score: 50.72 E-value: 1.38e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277938134 44 DLSAIGTEELIKLARRYDETLNDSFWGYAKKRVYGAMLDYLRSLDILsRASRKL----VKAIdYAVEEYILLHDEEPTDE 119
Cdd:PRK08215 66 DLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNPI-RVSRSLrdiaYKAL-QVREKLINENSKEPTVE 143
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277938134 120 ELSVLLNESVEKVHEARIASS--------IYT-------VMplhDQlhVGDEGaaliqvEKDEL-IE--VIKSILNSYNE 181
Cdd:PRK08215 144 EIAKELEVPREEVVFALDAIQdpvslfepIYHdggdpiyVM---DQ--ISDEK------NKDENwLEeiALKEAMKKLND 212
|
170 180 190 200
....*....|....*....|....*....|....*....|....*
gi 1277938134 182 REQLIIQFYYFEELTLKEISEILNITESRISQIHKSVLQKIKESV 226
Cdd:PRK08215 213 REKLILNLRFFQGKTQMEVAEEIGISQAQVSRLEKAALKHMRKYI 257
|
|
| PRK05901 |
PRK05901 |
RNA polymerase sigma factor; Provisional |
115-223 |
6.75e-07 |
|
RNA polymerase sigma factor; Provisional
Pssm-ID: 235640 [Multi-domain] Cd Length: 509 Bit Score: 49.22 E-value: 6.75e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277938134 115 EPTDEELSVLLNESVEKVHEARIassiYTVMP--LHDQlhVGDEG--------------AALIQVEKDELIEVIKSILNS 178
Cdd:PRK05901 374 EPTPEELAKEMGFTPEKVREIQK----YNREPisLDKT--IGKEGdsqfgdfiedseavSPVDAVSFTLLQDQLQEVLET 447
|
90 100 110 120
....*....|....*....|....*....|....*....|....*....
gi 1277938134 179 YNEREQLIIQFYY----FEELTLKEISEILNITESRISQIHKSVLQKIK 223
Cdd:PRK05901 448 LSEREAGVIRMRFgltdGQPKTLDEIGQVYGVTRERIRQIESKTLRKLR 496
|
|
| PRK07122 |
PRK07122 |
RNA polymerase sigma factor SigF; Reviewed |
13-224 |
1.83e-06 |
|
RNA polymerase sigma factor SigF; Reviewed
Pssm-ID: 168831 [Multi-domain] Cd Length: 264 Bit Score: 47.46 E-value: 1.83e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277938134 13 KEDELAIQYLPAVKAMAYRLKERLPSSIDFLDLSAIGteeLIKLARRYDETLNDSFWGYAKKRVYGAMLDYLR----SLD 88
Cdd:PRK07122 41 QRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVG---LVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRdnswSVK 117
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277938134 89 IlSRASRKLVKAIDYAVEEYILLHDEEPTDEELSVLLNESVEKVHEARIASSIY--------------TVMPLHDQLhvG 154
Cdd:PRK07122 118 V-PRRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAGSAYntlsidsgggsgddDARAIADTL--G 194
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277938134 155 DEGAALIQVEKDElieVIKSILNSYNEREQLIIQFYYFEELTLKEISEILNITESRISQIHKSVLQKIKE 224
Cdd:PRK07122 195 DVDAGLDQIENRE---ALRPLLAALPERERTVLVLRFFESMTQTQIAERVGISQMHVSRLLAKTLARLRD 261
|
|
| RpoE |
COG1595 |
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ... |
162-228 |
1.94e-05 |
|
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: 43.83 E-value: 1.94e-05
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1277938134 162 QVEKDELIEVIKSILNSYNEREQLIIQFYYFEELTLKEISEILNITESRI-SQIHKSvLQKIKESVGA 228
Cdd:COG1595 111 ALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVkSRLSRA-RKKLREALEE 177
|
|
| phage_rinA |
TIGR01636 |
phage transcriptional activator, RinA family; This model represents a family of phage proteins, ... |
167-227 |
5.55e-05 |
|
phage transcriptional activator, RinA family; This model represents a family of phage proteins, including RinA, a transcriptional activator in staphylococcal phage phi 11. This family shows similarity to ArpU, a phage-related putative autolysin regulator, and to some sporulation-specific sigma factors. [Mobile and extrachromosomal element functions, Prophage functions, Regulatory functions, DNA interactions]
Pssm-ID: 130697 Cd Length: 134 Bit Score: 41.81 E-value: 5.55e-05
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1277938134 167 ELIEVIKSILNSYNEREQLIIQFYYFEE--LTLKEISEILNITESRISQIHKSVLQKIKESVG 227
Cdd:TIGR01636 71 RNRDAIENCLNEADEQTRVIIQELYMKKrpLTLVGLAQQLFISKSTAYRLRNHIIEAVAEELG 133
|
|
| PRK07921 |
PRK07921 |
RNA polymerase sigma factor SigB; Reviewed |
42-224 |
2.29e-04 |
|
RNA polymerase sigma factor SigB; Reviewed
Pssm-ID: 181169 [Multi-domain] Cd Length: 324 Bit Score: 41.26 E-value: 2.29e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277938134 42 FLDLSAIGTEELIKLARRYDETLNDSFWGYA----KKRVYGAMLDYLRSLDI----------LSRASRKLVKAIDyavee 107
Cdd:PRK07921 113 LLDLIQEGNLGLIRAMEKFDYTKGFKFSTYAtwwiRQAITRGMADQSRTIRLpvhlveqvnkLARIKRELHQQLG----- 187
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277938134 108 yillhdEEPTDEELSVLLNESVEKVHE----ARIASSI-YTV-----MPLHDQLHVGDEGAALIQVEKDELIEVIKSILN 177
Cdd:PRK07921 188 ------REATDEELAEESGIPEEKIADllehSRDPVSLdMPVgsdeeAPLGDFIEDSEATSAENAVIAGLLHTDIRSVLA 261
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|.
gi 1277938134 178 SYNEREQLIIQFYY----FEELTLKEISEILNITESRISQIHKSVLQKIKE 224
Cdd:PRK07921 262 TLDEREQQVIRLRFglddGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRN 312
|
|
| PRK09641 |
PRK09641 |
RNA polymerase sigma factor SigW; Provisional |
162-216 |
1.66e-03 |
|
RNA polymerase sigma factor SigW; Provisional
Pssm-ID: 182012 [Multi-domain] Cd Length: 187 Bit Score: 38.14 E-value: 1.66e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*.
gi 1277938134 162 QVEKDELIEVIKSILNSYNEREQLIIQFYYFEELTLKEISEILNITESRI-SQIHK 216
Cdd:PRK09641 120 QVVSLELQETIQEAILQLPEKYRTVIVLKYIEDLSLKEISEILDLPVGTVkTRIHR 175
|
|
| PRK09210 |
PRK09210 |
RNA polymerase sigma factor RpoD; Validated |
42-223 |
2.43e-03 |
|
RNA polymerase sigma factor RpoD; Validated
Pssm-ID: 236413 [Multi-domain] Cd Length: 367 Bit Score: 38.43 E-value: 2.43e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277938134 42 FLDLSAIGTEELIKLARRYDETLNDSFWGYA----KKRVYGAMLDYLRSLDI----------LSRASRKLVKAIDyavee 107
Cdd:PRK09210 156 FLDLIQEGNMGLMKAVEKFDYRKGFKFSTYAtwwiRQAITRAIADQARTIRIpvhmvetinkLIRVQRQLLQELG----- 230
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1277938134 108 yillhdEEPTDEELSVLLNESVEKVHEA-RIAS---SIYTVMPLHDQLHVGD----------EGAALIQVEKDELIEVik 173
Cdd:PRK09210 231 ------REPTPEEIAEEMDMPPEKVREIlKIAQepvSLETPIGEEDDSHLGDfiedqdatspADHAAYELLKEQLEDV-- 302
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....
gi 1277938134 174 siLNSYNEREQLIIQFYY----FEELTLKEISEILNITESRISQIHKSVLQKIK 223
Cdd:PRK09210 303 --LDTLTDREENVLRLRFglddGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 354
|
|
| PRK12522 |
PRK12522 |
RNA polymerase sigma factor; Provisional |
170-211 |
2.58e-03 |
|
RNA polymerase sigma factor; Provisional
Pssm-ID: 183571 [Multi-domain] Cd Length: 173 Bit Score: 37.54 E-value: 2.58e-03
10 20 30 40
....*....|....*....|....*....|....*....|..
gi 1277938134 170 EVIKSILNSYNEREQLIIQFYYFEELTLKEISEILNITESRI 211
Cdd:PRK12522 111 EMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTV 152
|
|
| PRK09415 |
PRK09415 |
RNA polymerase factor sigma C; Reviewed |
156-224 |
3.03e-03 |
|
RNA polymerase factor sigma C; Reviewed
Pssm-ID: 181835 [Multi-domain] Cd Length: 179 Bit Score: 37.42 E-value: 3.03e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1277938134 156 EGAALIQVEKDELIEVIKSILNSYNEreqlIIQFYYFEELTLKEISEILNITESRIsqihKSVLQKIKE 224
Cdd:PRK09415 109 EEEVIQNAEDERLASAVMSLPIKYRE----VIYLFYYEELSIKEIAEVTGVNENTV----KTRLKKAKE 169
|
|
| PRK06596 |
PRK06596 |
RNA polymerase factor sigma-32; Reviewed |
170-228 |
7.68e-03 |
|
RNA polymerase factor sigma-32; Reviewed
Pssm-ID: 235838 [Multi-domain] Cd Length: 284 Bit Score: 36.69 E-value: 7.68e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1277938134 170 EVIKSILNSYNEREQLIIQFYYFEE--LTLKEISEILNITESRISQIHKSVLQKIKESVGA 228
Cdd:PRK06596 222 ALLADALEGLDERSRDIIEARWLDDdkSTLQELAAEYGVSAERVRQIEKNAMKKLKAAIEA 282
|
|
| |
