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Conserved domains on  [gi|49176170|ref|NP_416432|]
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RNA polymerase sigma factor FliA [Escherichia coli str. K-12 substr. MG1655]

Protein Classification

RNA polymerase sigma factor FliA( domain architecture ID 11482517)

RNA polymerase sigma factor FliA controls the expression of flagella-related genes; sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released

Gene Ontology:  GO:0016987|GO:0003677|GO:0006352|GO:0003899|GO:0006355

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
fliA PRK06986
flagellar biosynthesis sigma factor; Validated
 4-237 3.92e-136

flagellar biosynthesis sigma factor; Validated


:

Pssm-ID: 235901 [Multi-domain]  Cd Length: 236  Bit Score: 381.89  E-value: 3.92e-136
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170    4 LYTAEGVMDKHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDEL 83
Cdd:PRK06986   1 AYTAEGKMDQDELVEQYAPLVKRIALRLKARLPASVDLDDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDEL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170   84 RSRDWVPRSVRRNAREVAQAIGQLEQELGRNATETEVAERLGIDIADYRQMLLDTNNSQLFSYDEWREEHGDSIELVTDD 163
Cdd:PRK06986  81 RSLDWVPRSVRRNAREVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDELRGEHGDSILVTEDH 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 49176170  164 HQrENPLQQLLDSNLRQRVMEAIETLPEREKLVLTLYYQEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLG 237
Cdd:PRK06986 161 QD-EDPLQQLEDEELREALVEAIESLPEREQLVLSLYYQEELNLKEIGAVLGVSESRVSQIHSQAIKRLRARLG 233
 
Name Accession Description Interval E-value
fliA PRK06986
flagellar biosynthesis sigma factor; Validated
 4-237 3.92e-136

flagellar biosynthesis sigma factor; Validated


Pssm-ID: 235901 [Multi-domain]  Cd Length: 236  Bit Score: 381.89  E-value: 3.92e-136
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170    4 LYTAEGVMDKHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDEL 83
Cdd:PRK06986   1 AYTAEGKMDQDELVEQYAPLVKRIALRLKARLPASVDLDDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDEL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170   84 RSRDWVPRSVRRNAREVAQAIGQLEQELGRNATETEVAERLGIDIADYRQMLLDTNNSQLFSYDEWREEHGDSIELVTDD 163
Cdd:PRK06986  81 RSLDWVPRSVRRNAREVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDELRGEHGDSILVTEDH 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 49176170  164 HQrENPLQQLLDSNLRQRVMEAIETLPEREKLVLTLYYQEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLG 237
Cdd:PRK06986 161 QD-EDPLQQLEDEELREALVEAIESLPEREQLVLSLYYQEELNLKEIGAVLGVSESRVSQIHSQAIKRLRARLG 233
FliA_WhiG TIGR02479
RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar ...
 16-237 2.83e-98

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: 285.71  E-value: 2.83e-98
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170    16 LWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDWVPRSVRR 95
Cdd:TIGR02479   1 LIRRYLPLVKRIAGRLSVGLPSSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMLDELRRLDWVPRSLRQ 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170    96 NAREVAQAIGQLEQELGRNATETEVAERLGIDIADYRQMLLDTNNSQLFSYDEWREEHGDSIEL--VTDDHQRENPLQQL 173
Cdd:TIGR02479  81 KARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELLESGDDGGSLidRIEDDKSEDPEEEL 160

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 49176170   174 LDSNLRQRVMEAIETLPEREKLVLTLYYQEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLG 237
Cdd:TIGR02479 161 EREELREALAEAIESLSEREQLVLSLYYYEELNLKEIGEVLGLTESRVSQIHSQALKKLRAKLS 224
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 5-238 5.16e-94

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: 275.16  E-value: 5.16e-94
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170   5 YTAEGVMDKHSLWQRYVPLVRHEALRLQVRLPAsvELDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELR 84
Cdd:COG1191   9 YQEGDEEAREELIEEYLPLVKKIASRLAGRLPA--ELDDLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRGAILDYLR 86

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170  85 SRDWVPRSVRRNAREVAQAIGQLEQELGRNATETEVAERLGIDIADYRQMLLDTNNSQLFSYDEWREEHGDSIELVTDDh 164
Cdd:COG1191  87 DEDWVPRSVRELARKIEEAIEELEQELGREPTDEEIAEELGISLEEVQEALEAANAYQLLSLDEPLEDGDDLLDLLESG- 165

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 49176170 165 qreNPLQQLLDSNLRQRVMEAIETLPEREKLVLTLYYQEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 238
Cdd:COG1191 166 ---DPEEELEHEELREALAEAIEQLPERERLVLSLYYFEELTLKEIAEVLGVSESRVSRLHKKALARLREYLKE 236
Sigma70_r3 pfam04539
Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the ...
 98-164 7.27e-15

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: 67.24  E-value: 7.27e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 49176170    98 REVAQAIGQLEQELGRNATETEVAERLGIDIADYRQMLLDTNNSQLFSYDEWREEHGDSIELVTDDH 164
Cdd:pfam04539   4 NKIKRAQRELEQELGREPTPEEIAEELGLSPEKVREVLEAAREPVSLDTPVGEEEDGELGDLLEDDD 70
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 179-233 1.53e-13

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: 63.28  E-value: 1.53e-13
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 49176170 179 RQRVMEAIETLPEREKLVLTLYYQEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233
Cdd:cd06171   1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
fliA PRK06986
flagellar biosynthesis sigma factor; Validated
 4-237 3.92e-136

flagellar biosynthesis sigma factor; Validated


Pssm-ID: 235901 [Multi-domain]  Cd Length: 236  Bit Score: 381.89  E-value: 3.92e-136
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170    4 LYTAEGVMDKHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDEL 83
Cdd:PRK06986   1 AYTAEGKMDQDELVEQYAPLVKRIALRLKARLPASVDLDDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDEL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170   84 RSRDWVPRSVRRNAREVAQAIGQLEQELGRNATETEVAERLGIDIADYRQMLLDTNNSQLFSYDEWREEHGDSIELVTDD 163
Cdd:PRK06986  81 RSLDWVPRSVRRNAREVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDELRGEHGDSILVTEDH 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 49176170  164 HQrENPLQQLLDSNLRQRVMEAIETLPEREKLVLTLYYQEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLG 237
Cdd:PRK06986 161 QD-EDPLQQLEDEELREALVEAIESLPEREQLVLSLYYQEELNLKEIGAVLGVSESRVSQIHSQAIKRLRARLG 233
FliA_WhiG TIGR02479
RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar ...
 16-237 2.83e-98

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: 285.71  E-value: 2.83e-98
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170    16 LWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDWVPRSVRR 95
Cdd:TIGR02479   1 LIRRYLPLVKRIAGRLSVGLPSSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMLDELRRLDWVPRSLRQ 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170    96 NAREVAQAIGQLEQELGRNATETEVAERLGIDIADYRQMLLDTNNSQLFSYDEWREEHGDSIEL--VTDDHQRENPLQQL 173
Cdd:TIGR02479  81 KARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELLESGDDGGSLidRIEDDKSEDPEEEL 160

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 49176170   174 LDSNLRQRVMEAIETLPEREKLVLTLYYQEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLG 237
Cdd:TIGR02479 161 EREELREALAEAIESLSEREQLVLSLYYYEELNLKEIGEVLGLTESRVSQIHSQALKKLRAKLS 224
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 5-238 5.16e-94

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: 275.16  E-value: 5.16e-94
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170   5 YTAEGVMDKHSLWQRYVPLVRHEALRLQVRLPAsvELDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELR 84
Cdd:COG1191   9 YQEGDEEAREELIEEYLPLVKKIASRLAGRLPA--ELDDLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRGAILDYLR 86

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170  85 SRDWVPRSVRRNAREVAQAIGQLEQELGRNATETEVAERLGIDIADYRQMLLDTNNSQLFSYDEWREEHGDSIELVTDDh 164
Cdd:COG1191  87 DEDWVPRSVRELARKIEEAIEELEQELGREPTDEEIAEELGISLEEVQEALEAANAYQLLSLDEPLEDGDDLLDLLESG- 165

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 49176170 165 qreNPLQQLLDSNLRQRVMEAIETLPEREKLVLTLYYQEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 238
Cdd:COG1191 166 ---DPEEELEHEELREALAEAIEQLPERERLVLSLYYFEELTLKEIAEVLGVSESRVSRLHKKALARLREYLKE 236
PRK06288 PRK06288
RNA polymerase sigma factor WhiG; Reviewed
 19-238 3.00e-77

RNA polymerase sigma factor WhiG; Reviewed


Pssm-ID: 235770 [Multi-domain]  Cd Length: 268  Bit Score: 233.81  E-value: 3.00e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170   19 RYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDWVPRSVRRNAR 98
Cdd:PRK06288  39 KYSPLVKYVAGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDELRSIDWIPRSVRQKAR 118

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170   99 EVAQAIGQLEQELGRNATETEVAERLGIDIADYRQMLLDTNNSQLFSYDEWRE--EHGDSIELVT--DDHQRENPLQQLL 174
Cdd:PRK06288 119 QIERAIAMLEARLGRTPSDEEIADELGISLEEYNSLLSKLSGTSVVSLNDLWFggDEGDEVSLMDtlESPAALNPDEIAE 198

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 49176170  175 DSNLRQRVMEAIETLPEREKLVLTLYYQEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 238
Cdd:PRK06288 199 REEIKRVIVEAIKTLPEREKKVLILYYYEDLTLKEIGKVLGVTESRISQLHTKAVLQLRAKLAE 262
PRK07670 PRK07670
FliA/WhiG family RNA polymerase sigma factor;
16-238 5.67e-61

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 181075 [Multi-domain]  Cd Length: 251  Bit Score: 191.80  E-value: 5.67e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170   16 LWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDWVPRSVRR 95
Cdd:PRK07670  27 LIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRKEDWLPRSMRE 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170   96 NAREVAQAIGQLEQELGRNATETEVAERLGIDIADYRQMLLDTNNSQLFSYDE--WREEHGDSIELVTDDHQRENPLQQL 173
Cdd:PRK07670 107 KTKKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGFFANLLSIDEktHDQDDGENVSVTIRDDKTPTPEEKL 186

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 49176170  174 LDSNLRQRVMEAIETLPEREKLVLTLYYQEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 238
Cdd:PRK07670 187 LKEELIEELAEKIKQLSEKEQLVISLFYKEELTLTEIGQVLNLSTSRISQIHSKALFKLKKLLEK 251
PRK05911 PRK05911
RNA polymerase sigma factor sigma-28; Reviewed
 13-239 6.28e-44

RNA polymerase sigma factor sigma-28; Reviewed


Pssm-ID: 235644 [Multi-domain]  Cd Length: 257  Bit Score: 148.61  E-value: 6.28e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170   13 KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDWVPRS 92
Cdd:PRK05911  25 RDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRKQDWVPRS 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170   93 VRRNAREVAQAIGQLEQELGRNATETEVAERLGIDIADYRQMLLDTNNSQLFSYDEWR-----EEHGDSIELVTDDHQRE 167
Cdd:PRK05911 105 VHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILSLNEEFpcqsdDEAGLALEERIADERAE 184

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 49176170  168 NPLQQLLDSNLRQRVMEAIETLPEREKLVLTLYYQEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGKL 239
Cdd:PRK05911 185 TGYDVVDKKEFSSILAEAILALEEKERKVMALYYYEELVLKEIGKILGVSESRVSQIHSKALLKLRATLSAF 256
PRK12427 PRK12427
FliA/WhiG family RNA polymerase sigma factor;
18-233 1.22e-36

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 183523 [Multi-domain]  Cd Length: 231  Bit Score: 128.83  E-value: 1.22e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170   18 QRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYdALQGTAFTTYAVQRIRGAMLDELRSRDWVPRSVRRNA 97
Cdd:PRK12427  22 NAYLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEALRRY-GHPDEQFAAYAVHRIRGAILDELRELDWRPRRLRQKT 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170   98 REVAQAIGQLEQELGRNATETEVAERLGIDIADYRQMLLDTNNSQLFSYDEWREEHGDSIELVTDDHQRENPLQQLLDsn 177
Cdd:PRK12427 101 HKTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLLLENAGTLESLDELLALEAHNDILQSRDLEENIIIEDNLK-- 178

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 49176170  178 lrqrvmEAIETLPEREKLVLTLYYQEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233
Cdd:PRK12427 179 ------QALSQLDEREQLILHLYYQHEMSLKEIALVLDLTEARICQLNKKIAQKIK 228
SigBFG TIGR02980
RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; This group of similar sigma-70 factors ...
 19-236 1.31e-35

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: 125.80  E-value: 1.31e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170    19 RYVPLVRHEALRLQVRlpaSVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDW---VPRSVRR 95
Cdd:TIGR02980  11 LNLPLVRSIARRFRNR---GEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIMGEIKRFFRDDTWavrVPRRLKE 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170    96 NAREVAQAIGQLEQELGRNATETEVAERLGIDIADYRQMLLDTNNSQLFSYDEWREEH-GDSIELV----TDDHQRENPL 170
Cdd:TIGR02980  88 LGVKINKATEELTQRLGRSPTIAEIAERLGVSEEEVVEALEAGNAYQALSLDASIEDDdGDPIALLdtlgDEDDALETVE 167

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 49176170   171 QQLLdsnlrqrVMEAIETLPEREKLVLTLYYQEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKL 236
Cdd:TIGR02980 168 DRLA-------LKPLLAALPERERRILLLRFFEDKTQSEIAERLGISQMHVSRLLRRALKKLREQL 226
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 39-236 3.78e-30

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: 112.84  E-value: 3.78e-30
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170  39 VELDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLdelrsrdwvpRSVRRNAREV-------------AQAIG 105
Cdd:COG0568  55 LPLLDLIQEGNLGLMKAVEKFDPERGFRFSTYATWWIRQAIT----------RAIADQWRTIrlpvhmaetlnklRRAKR 124

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170 106 QLEQELGRNATETEVAERLGIDIADYRQMLldTNNSQLFSYDEWREEHGDS--IELVTDDHQrENPLQQLLDSNLRQRVM 183
Cdd:COG0568 125 QLLQELGREPTPEEIAEELGVPEEKVREML--RLAREPVSLDAPVGDDEDSelGDLLEDEEA-PSPEEALEEELLREELR 201

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 49176170 184 EAIETLPEREKLVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKL 236
Cdd:COG0568 202 EALDTLTEREREILRLRFglddGEPHTLEEIGKEFGVSRERVRQIEAKALRKLRHPL 258
PRK07408 PRK07408
RNA polymerase sigma factor SigF; Reviewed
 23-238 2.01e-23

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 180965 [Multi-domain]  Cd Length: 256  Bit Score: 94.60  E-value: 2.01e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170   23 LVRHEALRLQVRLPASveLDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDWVPRSVRRNA---RE 99
Cdd:PRK07408  37 LVRKEAHRWSNQCSEP--YEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPTVRIPRRWQelqRQ 114

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170  100 VAQAIGQLEQELGRNATETEVAERLGIDIADYRQMLLDTNNSQLFSYD-EWREEHGDSI---ELVTDDHQRENPLQQlld 175
Cdd:PRK07408 115 AKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRTPLSLDaPVNQDEDGSTslgDLLPDPRYRSFQLAQ--- 191

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 49176170  176 sNLRQRVMEAIETLPEREKLVLTLYYQEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 238
Cdd:PRK07408 192 -EDRIRLQQALAQLEERTREVLEFVFLHDLTQKEAAERLGISPVTVSRRVKKGLDQLKKLLQP 253
PRK07122 PRK07122
RNA polymerase sigma factor SigF; Reviewed
 18-237 8.18e-23

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 168831 [Multi-domain]  Cd Length: 264  Bit Score: 93.30  E-value: 8.18e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170   18 QRYVPLVRHEALRLQVRLPAsveLDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDW---VPRSVR 94
Cdd:PRK07122  47 TRCLPLADHIARRFDGRGEP---RDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWsvkVPRRLK 123

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170   95 RNAREVAQAIGQLEQELGRNATETEVAERLGIDIADYRQMLLDTNNSQLFSYDEWREEHGDSIELVTDDHQRENP-LQQL 173
Cdd:PRK07122 124 ELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAGSAYNTLSIDSGGGSGDDDARAIADTLGDVDAgLDQI 203

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 49176170  174 LDsnlRQRVMEAIETLPEREKLVLTLYYQEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLG 237
Cdd:PRK07122 204 EN---REALRPLLAALPERERTVLVLRFFESMTQTQIAERVGISQMHVSRLLAKTLARLRDQLE 264
PRK05572 PRK05572
RNA polymerase sporulation sigma factor, SigF/SigG family;
40-238 1.05e-18

RNA polymerase sporulation sigma factor, SigF/SigG family;


Pssm-ID: 180137 [Multi-domain]  Cd Length: 252  Bit Score: 81.94  E-value: 1.05e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170   40 ELDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGamldELRS--RD----WVPRSVRRNAREVAQAIGQLEQELGR 113
Cdd:PRK05572  58 EPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIG----EIQRflRDdgtvKVSRSLKETANKIRKDKDELSKELGR 133

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170  114 NATETEVAERLGIDIADYrQMLLDTNNSQLFSYDEWREEHGDSIELVtdDHQRENPLQQLLDsnlRQRVMEAIETLPERE 193
Cdd:PRK05572 134 EPTIEELAEYLGVTPEEV-VLAQEASRSPQSIHETVHENDGDPITLL--DQIADQSEEDWFD---KIALKEAIRELDERE 207

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 49176170  194 KLVLTLYYQEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 238
Cdd:PRK05572 208 RLIVYLRYFKDKTQSEVAKRLGISQVQVSRLEKKILKQMKEKLDE 252
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 16-236 2.59e-18

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: 78.93  E-value: 2.59e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170    16 LWQRYVPLVRHEALRlqvRLPASVELDDLLQAGGIGLLNAVERYDalQGTAFTTYAVQRIRGAMLDELRSRDWVPRSVRR 95
Cdd:TIGR02937   6 LYERYLPLVYRYARR---YLGDDADAEDLVQEAFLKLLEALDRFD--PEGSFKAWLFRIARNLILDYLRRKRRLRRELDL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170    96 NAREVAQAigqleqelgrnatetevaerlgidiadyrqmlldtnnsqlfsydewreehgdsielvtddhqrENPLQQLLD 175
Cdd:TIGR02937  81 LEELLDSD---------------------------------------------------------------PSPEEELEQ 97

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 49176170   176 SNLRQRVMEAIETLPEREKLVLTLYYQEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKL 236
Cdd:TIGR02937  98 EEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK08583 PRK08583
RNA polymerase sigma factor SigB; Validated
 42-233 2.71e-18

RNA polymerase sigma factor SigB; Validated


Pssm-ID: 236306 [Multi-domain]  Cd Length: 257  Bit Score: 80.89  E-value: 2.71e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170   42 DDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDW---VPRSVRRNAREVAQAIGQLEQELGRNATET 118
Cdd:PRK08583  57 EDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRDKTWsvhVPRRIKELGPKIKKAVDELTTELQRSPKIS 136

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170  119 EVAERLGIDIADYRQMLLDTNNSQLFSYDEWREEHGDS-----IELV--TDDHQRENPLQQLLDSnlrqrvmeAIETLPE 191
Cdd:PRK08583 137 EIADRLGVSEEEVLEAMEMGKSYQALSVDHSIEADSDGstvtlLDIVgqQEDGYELTEQRMILEK--------ILPVLSD 208

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 49176170  192 REKLVLTLYYQEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233
Cdd:PRK08583 209 REKSIIQCTFIENLSQKETGERLGISQMHVSRLQRQAIKKLR 250
Sigma70_r3 pfam04539
Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the ...
 98-164 7.27e-15

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: 67.24  E-value: 7.27e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 49176170    98 REVAQAIGQLEQELGRNATETEVAERLGIDIADYRQMLLDTNNSQLFSYDEWREEHGDSIELVTDDH 164
Cdd:pfam04539   4 NKIKRAQRELEQELGREPTPEEIAEELGLSPEKVREVLEAAREPVSLDTPVGEEEDGELGDLLEDDD 70
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 16-89 8.40e-15

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: 66.84  E-value: 8.40e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 49176170    16 LWQRYVPLVRHEALRLqvrLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDWV 89
Cdd:pfam04542   1 LVERYLPLVYSLARRY---LGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRRT 71
PRK08215 PRK08215
RNA polymerase sporulation sigma factor SigG;
41-233 9.15e-15

RNA polymerase sporulation sigma factor SigG;


Pssm-ID: 181296 [Multi-domain]  Cd Length: 258  Bit Score: 71.52  E-value: 9.15e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170   41 LDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRD--WVPRSVRRNAREVAQAIGQLEQELGRNATET 118
Cdd:PRK08215  64 VDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNpiRVSRSLRDIAYKALQVREKLINENSKEPTVE 143

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170  119 EVAERLGI---DIAdyrqMLLDTNNSQLFSYDEWREEHGDSI----ELVTDDHQRENPLQQLldsnlrqRVMEAIETLPE 191
Cdd:PRK08215 144 EIAKELEVpreEVV----FALDAIQDPVSLFEPIYHDGGDPIyvmdQISDEKNKDENWLEEI-------ALKEAMKKLND 212

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 49176170  192 REKLVLTLYYQEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233
Cdd:PRK08215 213 REKLILNLRFFQGKTQMEVAEEIGISQAQVSRLEKAALKHMR 254
PRK05949 PRK05949
RNA polymerase sigma factor; Validated
 38-239 1.25e-14

RNA polymerase sigma factor; Validated


Pssm-ID: 180321 [Multi-domain]  Cd Length: 327  Bit Score: 71.80  E-value: 1.25e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170   38 SVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRD---WVPRSVRRNAREVAQAIGQLEQELGRN 114
Cdd:PRK05949 115 NMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQArtiRLPIHITEKLNKIKKTQRELSQKLGRS 194

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170  115 ATETEVAERLGIDIADYRQMLldTNNSQLFSYDEWREEHGDS--IELVTDDHQreNPLQQLLDSNLRQRVMEAIETLPER 192
Cdd:PRK05949 195 ATPAEIAKELELEPSQIREYL--SMARQPISLDVRVGDNQDTelSELLEDEGP--SPDQYITQELLRQDLNNLLAELTPQ 270

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 49176170  193 EKLVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGKL 239
Cdd:PRK05949 271 QREVLTLRFgledGKELSLAKVGERLNLSRERVRQLEHQALAHLRRRRANV 321
PRK07406 PRK07406
RNA polymerase sigma factor RpoD; Validated
 43-233 4.72e-14

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236012 [Multi-domain]  Cd Length: 373  Bit Score: 70.58  E-value: 4.72e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170   43 DLLQAGGIGLLNAVERYDALQGTAFTTYAV----QRIRGAMLDELRS-RdwVPRSVRRNAREVAQAIGQLEQELGRNATE 117
Cdd:PRK07406 165 DLIQEGSLGLIRAAEKFDHEKGYKFSTYATwwirQAITRAIADQSRTiR--LPVHLYETISRIKKTTKVLSQEFGRKPTE 242

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170  118 TEVAERLGIDIADYRQMlldTNNSQLFSYDEW---REEH---GDSIElvtddHQRENPLQQLLDSNLRQRVMEAIETLPE 191
Cdd:PRK07406 243 EEIAESMEMTIEKLRFI---AKSAQLPISLETpigKEEDsrlGDFIE-----ADGETPEDDVAKNLLREDLEGVLATLSP 314

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 49176170  192 REKLVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233
Cdd:PRK07406 315 RERDVLRLRYglddGRMKTLEEIGQIFNVTRERIRQIEAKALRKLR 360
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 179-233 1.53e-13

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: 63.28  E-value: 1.53e-13
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 49176170 179 RQRVMEAIETLPEREKLVLTLYYQEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233
Cdd:cd06171   1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK05901 PRK05901
RNA polymerase sigma factor; Provisional
 43-233 2.19e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 235640 [Multi-domain]  Cd Length: 509  Bit Score: 65.79  E-value: 2.19e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170   43 DLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAmldelrsrdwVPRSVRRNAR---------EVAQAIG----QLEQ 109
Cdd:PRK05901 300 DLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQA----------ITRAMADQARtiripvhmvETINKLGrierELLQ 369

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170  110 ELGRNATETEVAERLGID---IADYRQM-----LLDT-----NNSQLfsydewreehGDSIE----LVTDDHQRENPLQQ 172
Cdd:PRK05901 370 ELGREPTPEELAKEMGFTpekVREIQKYnrepiSLDKtigkeGDSQF----------GDFIEdseaVSPVDAVSFTLLQD 439

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 49176170  173 LLDsnlrqrvmEAIETLPEREKLVLTLYYQeeLN------LKEIGAVLEVGESRVSQLHSQAIKRLR 233
Cdd:PRK05901 440 QLQ--------EVLETLSEREAGVIRMRFG--LTdgqpktLDEIGQVYGVTRERIRQIESKTLRKLR 496
PRK07598 PRK07598
RNA polymerase sigma factor SigC; Validated
 39-233 3.14e-12

RNA polymerase sigma factor SigC; Validated


Pssm-ID: 236067 [Multi-domain]  Cd Length: 415  Bit Score: 65.28  E-value: 3.14e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170   39 VELDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDEL--RSRDW-VPRSVRRNAREVAQAIGQLEQELGRNA 115
Cdd:PRK07598 200 LELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAIatQSRTIrLPVHITEKLNKIKKAQRKISQEKGRTP 279

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170  116 TETEVAERLGIDIADYRQMLLDTNNSQLFSYDEWREEHGDSIELVTDDHQreNPLQQLLDSNLRQRVMEAIETLPEREKL 195
Cdd:PRK07598 280 TIEDIAQELEMTPTQVREVLLRVPRSVSLETKVGKDKDTELGDLLETDDI--SPEEMLMRESLQRDLQHLLADLTSRERD 357

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 49176170  196 VLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233
Cdd:PRK07598 358 VIRMRFgladGHTYSLAEIGRALDLSRERVRQIESKALQKLR 399
rpoH2 PRK07500
RNA polymerase factor sigma-32; Reviewed
 41-236 5.47e-12

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 236033 [Multi-domain]  Cd Length: 289  Bit Score: 63.90  E-value: 5.47e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170   41 LDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRsRDWvprSVRR------------NAREVAQAIGQLE 108
Cdd:PRK07500  67 MNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYIL-RNW---SIVRggtssaqkalffNLRRLRARLAQAD 142

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170  109 QELGRNATETEVAERLGIDIADYRQM--LLDTN----NSQLFSYDEWREEHGDSieLVTDDHQRENPLQQLLDS-NLRQR 181
Cdd:PRK07500 143 EELTKQEIHREIATALGVSLSDVEMMdaRLSGPdaslNAPQSEEDEGRSERMDF--LVDDSPLPDEQVESSIDGeRRRRW 220

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 49176170  182 VMEAIETLPEREKLVLtlyyqEELNLKEIGAVLEV-GES------RVSQLHSQAIKRLRTKL 236
Cdd:PRK07500 221 LTQALQTLNERELRII-----RERRLREDGATLEAlGEElgiskeRVRQIEARALEKLRRAL 277
PRK09210 PRK09210
RNA polymerase sigma factor RpoD; Validated
 43-233 7.98e-12

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 63.85  E-value: 7.98e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170   43 DLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAmldelrsrdwVPRSVRRNAREV------AQAIG-------QLEQ 109
Cdd:PRK09210 158 DLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQA----------ITRAIADQARTIripvhmVETINklirvqrQLLQ 227

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170  110 ELGRNATETEVAERLGIDIADYRQML--------LDT-----NNSQLfsydewreehGDSIElvtdDHQRENPLQQLLDS 176
Cdd:PRK09210 228 ELGREPTPEEIAEEMDMPPEKVREILkiaqepvsLETpigeeDDSHL----------GDFIE----DQDATSPADHAAYE 293

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 49176170  177 NLRQRVMEAIETLPEREKLVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233
Cdd:PRK09210 294 LLKEQLEDVLDTLTDREENVLRLRFglddGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 354
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 185-233 8.81e-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: 58.21  E-value: 8.81e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 49176170   185 AIETLPEREKLVLTLYYQEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLR 49
PRK07921 PRK07921
RNA polymerase sigma factor SigB; Reviewed
 43-233 1.46e-11

RNA polymerase sigma factor SigB; Reviewed


Pssm-ID: 181169 [Multi-domain]  Cd Length: 324  Bit Score: 62.83  E-value: 1.46e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170   43 DLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGA----MLDELRS-RdwVPRSVRRNAREVAQAIGQLEQELGRNATE 117
Cdd:PRK07921 115 DLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAitrgMADQSRTiR--LPVHLVEQVNKLARIKRELHQQLGREATD 192

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170  118 TEVAERLGIDiADYRQMLLDTNNSQLfSYDE---WREEH--GDSIElvtdDHQRENPLQQLLDSNLRQRVMEAIETLPER 192
Cdd:PRK07921 193 EELAEESGIP-EEKIADLLEHSRDPV-SLDMpvgSDEEAplGDFIE----DSEATSAENAVIAGLLHTDIRSVLATLDER 266

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 49176170  193 EKLVLTLYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233
Cdd:PRK07921 267 EQQVIRLRFglddGQPRTLDQIGKLFGLSRERVRQIEREVMSKLR 311
PRK05657 PRK05657
RNA polymerase sigma factor RpoS; Validated
 39-233 2.35e-11

RNA polymerase sigma factor RpoS; Validated


Pssm-ID: 235548 [Multi-domain]  Cd Length: 325  Bit Score: 62.28  E-value: 2.35e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170   39 VELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV----QRIRGAMLDELRS-RdwVPRSVRRNAREVAQAIGQLEQELGR 113
Cdd:PRK05657 111 LALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATwwirQTIERAIMNQTRTiR--LPVHVVKELNVYLRAARELEHKLDH 188

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170  114 NATETEVAERLGIDIADYRQML--------LDTnnsqlfSYDewreehGDS----IELVTDDHQrENPLQQLLDSNLRQR 181
Cdd:PRK05657 189 EPSAEEIAELLDKPVDDVSRMLalneritsLDT------PLG------GDPekslLDILADEQE-NGPEDTTQDDDMKQS 255

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 49176170  182 VMEAIETLPEREKLVLT----LYYQEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233
Cdd:PRK05657 256 IVKWLFELNDKQREVLArrfgLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLR 311
PRK07405 PRK07405
RNA polymerase sigma factor SigD; Validated
 39-233 5.82e-11

RNA polymerase sigma factor SigD; Validated


Pssm-ID: 180963 [Multi-domain]  Cd Length: 317  Bit Score: 61.31  E-value: 5.82e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170   39 VELDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDEL--RSRDW-VPRSVRRNAREVAQAIGQLEQELGRNA 115
Cdd:PRK07405 106 VDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIaeKSRTIrLPIHITEKLNKIKKAQRQLSQQLGRAA 185

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170  116 TETEVAERLGIDIADYRQMLldTNNSQLFSYDEWREEHGDSI--ELVTDDHQreNPLQQLLDSNLRQRVMEAIETLPERE 193
Cdd:PRK07405 186 TIGELAEELELTPKQVREYL--ERARQPLSLDLRVGDNQDTElgELLEDTGA--SPEDFATQSSLQLDLERLMEDLTPQQ 261

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 49176170  194 KLVLTLYYQEE----LNLKEIGAVLEVGESRVSQLHSQAIKRLR 233
Cdd:PRK07405 262 KEVIALRFGLEdgqpLTLAKIGERLNISRERVRQIEREALSKLR 305
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 148-238 2.40e-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: 57.70  E-value: 2.40e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170 148 EWREEHGDSIELVTDDHQRENPLQQLLDSNLRQRVMEAIETLPEREKLVLTLYYQEELNLKEIGAVLEVGESRVSQLHSQ 227
Cdd:COG1595  87 RRRRRELLDELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSR 166

                        90
                ....*....|.
gi 49176170 228 AIKRLRTKLGK 238
Cdd:COG1595 167 ARKKLREALEE 177
PRK05658 PRK05658
RNA polymerase sigma factor RpoD; Validated
 43-233 2.22e-09

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 235549 [Multi-domain]  Cd Length: 619  Bit Score: 57.11  E-value: 2.22e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170   43 DLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAmldelrsrdwVPRSVRRNAR-------------EVAQAIGQLEQ 109
Cdd:PRK05658 409 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA----------ITRSIADQARtiripvhmietinKLNRISRQMLQ 478

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170  110 ELGRNATETEVAERLGIDIADYRQML--------LDT-----NNSQLfsydewreehGDSIElvtdDHQRENPLQQLLDS 176
Cdd:PRK05658 479 EIGREPTPEELAERLGMPEDKVRKVLkiakepisLETpigddEDSHL----------GDFIE----DKNAELPIDAAIQE 544

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 49176170  177 NLRQRVMEAIETLPEREKLVLTLYYQEELN----LKEIGAVLEVGESRVSQLHSQAIKRLR 233
Cdd:PRK05658 545 SLREATTDVLASLTPREAKVLRMRFGIDMNtdhtLEEVGKQFDVTRERIRQIEAKALRKLR 605
PRK06596 PRK06596
RNA polymerase factor sigma-32; Reviewed
 43-233 2.45e-09

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 235838 [Multi-domain]  Cd Length: 284  Bit Score: 56.34  E-value: 2.45e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170   43 DLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMlDELRSRDWvpRSV--------RR---NAREVAQAIGQLEQEl 111
Cdd:PRK06596  77 DLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEI-HEYILRNW--RIVkvattkaqRKlffNLRKAKKRLGWLNPE- 152

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170  112 grnatE-TEVAERLGIDIADYRQMlldtnNSQLFSYD--------EWREEHGDSIELVTDDHqrENPLQQL----LDSNL 178
Cdd:PRK06596 153 -----EvEMVAEELGVSEEEVREM-----ESRLSGQDasldapidDDDEESGAPQDYLEDKS--SDPADVLeednWEDQR 220

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 49176170  179 RQRVMEAIETLPEREKLVLTL-YYQEE-LNLKEIGAVLEVGESRVSQLHSQAIKRLR 233
Cdd:PRK06596 221 RALLADALEGLDERSRDIIEArWLDDDkSTLQELAAEYGVSAERVRQIEKNAMKKLK 277
PRK05803 PRK05803
RNA polymerase sporulation sigma factor SigK;
39-232 4.91e-08

RNA polymerase sporulation sigma factor SigK;


Pssm-ID: 180266 [Multi-domain]  Cd Length: 233  Bit Score: 51.87  E-value: 4.91e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170   39 VELDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELrsrdwvpRSVRRNAREVAqaigqLEQELGRNATET 118
Cdd:PRK05803  74 EDVDDLISIGTIGLIKAIESFDAGKGTKLATYAARCIENEILMHL-------RNLKKTKKEVS-----LQDPIGVDKEGN 141

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170  119 EVAerlgidiadyrqmLLDTNNSqlfsydewreEHGDSIELVtddhqrENPLQQlldsnlrQRVMEAIETLPEREKLVLT 198
Cdd:PRK05803 142 EIS-------------LIDILGS----------EEDDVIEQV------ELKMEV-------EKLYKKIDILDEREKEVIE 185

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 49176170  199 LYY----QEELNLKEIGAVLEVGESRVSQLHSQAIKRL 232
Cdd:PRK05803 186 MRYglgnGKEKTQREIAKALGISRSYVSRIEKRALKKL 223
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 150-236 2.39e-07

RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.


Pssm-ID: 274376 [Multi-domain]  Cd Length: 161  Bit Score: 49.10  E-value: 2.39e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170   150 REEHGDSI-ELVTDDHQRENPLQQLLDSNLRQRVMEAIETLPEREKLVLTLYYQEELNLKEIGAVLEVGESRVSQLHSQA 228
Cdd:TIGR02985  74 EEKYQEELaEIEERELSEADPEEELEAKELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKA 153


                  ....*...
gi 49176170   229 IKRLRTKL 236
Cdd:TIGR02985 154 LKFLRKEL 161
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 147-236 8.70e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 47.76  E-value: 8.70e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170  147 DEWRE---------EHGDSIELVTDDHqrENPLQQLLDSNLRQRVMEAIETLPEREKLVLTLYYQEELNLKEIGAVLEVG 217
Cdd:PRK12513  91 DHWRRhgarqapslDADEQLHALADDG--AAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREHGDLELEEIAELTGVP 168

                         90
                 ....*....|....*....
gi 49176170  218 ESRVSQLHSQAIKRLRTKL 236
Cdd:PRK12513 169 EETVKSRLRYALQKLRELL 187
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 179-232 1.96e-06

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: 43.60  E-value: 1.96e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 49176170   179 RQRVMEAIETLPEREKLVLTLYYQEELNLKEIGAVLEVGESRVSQLHSQAIKRL 232
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 169-239 2.20e-06

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 46.61  E-value: 2.20e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 49176170  169 PLQQLLDSNLRQRVMEAIETLPEREKLVLTLYYQEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGKL 239
Cdd:PRK09641 117 PEEQVVSLELQETIQEAILQLPEKYRTVIVLKYIEDLSLKEISEILDLPVGTVKTRIHRGREALRKQLRHL 187
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 165-238 4.44e-06

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 45.51  E-value: 4.44e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 49176170  165 QRENPLQQLLDSNLRQRVMEAIETLPEREKLVLTLYYQEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 238
Cdd:PRK09415 104 QKESVEEEVIQNAEDERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKELLKKGLEE 177
PRK09047 PRK09047
RNA polymerase factor sigma-70; Validated
 147-239 5.65e-06

RNA polymerase factor sigma-70; Validated


Pssm-ID: 236367 [Multi-domain]  Cd Length: 161  Bit Score: 44.96  E-value: 5.65e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170  147 DEWREEHGDSIE-LVTDDHQRENPLQQLLDSNLRQRVMEAIETLPEREKLVLTLYYQEELNLKEIGAVLEVGESRVSQLH 225
Cdd:PRK09047  64 DDDDDDDFDPLEtLDSADEGAESPADKLERAQVLQLIEEAIQKLPARQREAFLLRYWEDMDVAETAAAMGCSEGSVKTHC 143

                         90
                 ....*....|....
gi 49176170  226 SQAIKRLRTKLGKL 239
Cdd:PRK09047 144 SRATHALAKALEAK 157
PRK12522 PRK12522
RNA polymerase sigma factor; Provisional
 147-236 1.13e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183571 [Multi-domain]  Cd Length: 173  Bit Score: 41.39  E-value: 1.13e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170  147 DEWREEHGDSIELvtddHQRENPLQQLLDSNLRQRVMEAIETLPEREKLVLTLYYQEELNLKEIGAVLEVGESRVSQLHS 226
Cdd:PRK12522  82 DLFHKEDGGEIEF----ADDVNISEEFIQKVEAEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLN 157

                         90
                 ....*....|
gi 49176170  227 QAIKRLRTKL 236
Cdd:PRK12522 158 YAKKQMREHL 167
PRK06759 PRK06759
RNA polymerase factor sigma-70; Validated
 20-84 1.26e-04

RNA polymerase factor sigma-70; Validated


Pssm-ID: 235857 [Multi-domain]  Cd Length: 154  Bit Score: 40.96  E-value: 1.26e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 49176170   20 YVPLVRHEALRLQVRLpasvELDDLLQAGGIGLLNAVERYDALQGTaFTTYAVQRIRGAMLDELR 84
Cdd:PRK06759  13 YEGLIVNQIKKLGIYQ----DYEEYYQCGLIGLWHAYERYDEKKGS-FPAYAVVTVRGYILERLK 72
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 150-239 1.51e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 41.20  E-value: 1.51e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 49176170  150 REEHGDSIELVTDDHQREN----PLQQLLDSNLRQRVMEAIETLPEREKLVLTLYYQEELNLKEIGAVLEVGESRVSQLH 225
Cdd:PRK12519  99 RRSRQRLLERWQQELLGEAsedtPLEQASLAERSQRVQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKARA 178

                         90
                 ....*....|....
gi 49176170  226 SQAIKRLRTKLGKL 239
Cdd:PRK12519 179 RQGLLKLRELLQDL 192
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 167-239 8.22e-04

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 39.02  E-value: 8.22e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 49176170  167 ENPLQQLLDSNLRQRVMEAIETLPEREKLVLTLYYQEELNLKEIGAVLE--VGESRvSQLHsQAIKRLRTKLGKL 239
Cdd:PRK09652 107 STPENELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGcpIGTVR-SRIF-RAREALRAKLQPL 179
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 169-239 1.77e-03

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 38.09  E-value: 1.77e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 49176170  169 PLQQLLDSNLRQRVMEAIETLPEREKLVLTLYYQEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGKL 239
Cdd:PRK05602 109 PDAGLEARQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALESLLARGRRALRAQLADL 179
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 167-237 3.71e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 37.26  E-value: 3.71e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 49176170  167 ENPLQQLLDSNLRQRVMEAIETLPEREKLVLTLYYQEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLG 237
Cdd:PRK11924 104 ETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQLLRECLE 174
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 165-233 7.79e-03

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 36.01  E-value: 7.79e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 49176170  165 QRENPLQQLLDSNLRQRVMEAIETLPEREKLVLTLYYQEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233
Cdd:PRK09644  85 QAESTEEYVVAKNSYEKLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRLK 153
PRK06930 PRK06930
positive control sigma-like factor; Validated
 162-238 8.77e-03

positive control sigma-like factor; Validated


Pssm-ID: 180757 [Multi-domain]  Cd Length: 170  Bit Score: 35.86  E-value: 8.77e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 49176170  162 DDHQREnplqQLLDSNLRQRVMEAIETLPEREKLVLTLYYQEELNLKEIGAVLEVGESRVSQLhsqaIKRLRTKLGK 238
Cdd:PRK06930  92 DIEEPE----SVISEWDKIRIEDALSVLTEREKEVYLMHRGYGLSYSEIADYLNIKKSTVQSM----IERAEKKIAR 160
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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