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Conserved domains on  [gi|446861480|ref|WP_000938736|]
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MULTISPECIES: FliA/WhiG family RNA polymerase sigma factor [Enterobacteriaceae]

Protein Classification

PRK12427 family protein( domain architecture ID 11485907)

PRK12427 family protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK12427 PRK12427
FliA/WhiG family RNA polymerase sigma factor;
7-236 4.42e-149

FliA/WhiG family RNA polymerase sigma factor;


:

Pssm-ID: 183523 [Multi-domain]  Cd Length: 231  Bit Score: 414.64  E-value: 4.42e-149
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446861480   7 FESEEFAAAPVLTPQQESHYLQAYLPLVRKVVRQLAPQCNCIIDRQDMEQTALMGLLNAIRRYGLPDEGFAGYAVHRIRG 86
Cdd:PRK12427   1 MENREFEACLTLTPQEEGKYLNAYLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEALRRYGHPDEQFAAYAVHRIRG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446861480  87 AILDELRALDWRPRQLRQKYHQMKDLIRETRKKLGHEPEWQELAEE-GISHEDYLEYQQLEGAETLASLDELLNGEGPGI 165
Cdd:PRK12427  81 AILDELRELDWRPRRLRQKTHKTNDAIREIAKRLGHEPNFEEISAElNLTAEEYQEYLLLENAGTLESLDELLALEAHND 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446861480 166 PLAGRDLEDQFVTQQMLQHALSQLSEKEQLILSMYYQHEMNLKEIALVLGLTEARICQLNKQIAQKIRDFV 236
Cdd:PRK12427 161 ILQSRDLEENIIIEDNLKQALSQLDEREQLILHLYYQHEMSLKEIALVLDLTEARICQLNKKIAQKIKSFF 231
 
Name Accession Description Interval E-value
PRK12427 PRK12427
FliA/WhiG family RNA polymerase sigma factor;
7-236 4.42e-149

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 183523 [Multi-domain]  Cd Length: 231  Bit Score: 414.64  E-value: 4.42e-149
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446861480   7 FESEEFAAAPVLTPQQESHYLQAYLPLVRKVVRQLAPQCNCIIDRQDMEQTALMGLLNAIRRYGLPDEGFAGYAVHRIRG 86
Cdd:PRK12427   1 MENREFEACLTLTPQEEGKYLNAYLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEALRRYGHPDEQFAAYAVHRIRG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446861480  87 AILDELRALDWRPRQLRQKYHQMKDLIRETRKKLGHEPEWQELAEE-GISHEDYLEYQQLEGAETLASLDELLNGEGPGI 165
Cdd:PRK12427  81 AILDELRELDWRPRRLRQKTHKTNDAIREIAKRLGHEPNFEEISAElNLTAEEYQEYLLLENAGTLESLDELLALEAHND 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446861480 166 PLAGRDLEDQFVTQQMLQHALSQLSEKEQLILSMYYQHEMNLKEIALVLGLTEARICQLNKQIAQKIRDFV 236
Cdd:PRK12427 161 ILQSRDLEENIIIEDNLKQALSQLDEREQLILHLYYQHEMSLKEIALVLDLTEARICQLNKKIAQKIKSFF 231
FliA_WhiG TIGR02479
RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar ...
 27-233 1.20e-65

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: 202.89  E-value: 1.20e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446861480   27 LQAYLPLVRKVVRQLAPQCNCIIDRQDMEQTALMGLLNAIRRYGL-PDEGFAGYAVHRIRGAILDELRALDWRPRQLRQK 105
Cdd:TIGR02479   2 IRRYLPLVKRIAGRLSVGLPSSVELDDLIQAGMFGLLDAIERYDPsRGAKFETYAVQRIRGAMLDELRRLDWVPRSLRQK 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446861480  106 YHQMKDLIRETRKKLGHEPEWQELAEE-GISHEDYLEYQQLEGAETLASLDELLN----GEGPGIPLAGRDLEDQFVT-- 178
Cdd:TIGR02479  82 ARKLERAIRELEARLGREPTEEEIAEElGMDLKEYRQALNEINALSLVSLDELLEsgddGGSLIDRIEDDKSEDPEEEle 161

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 446861480  179 QQMLQ----HALSQLSEKEQLILSMYYQHEMNLKEIALVLGLTEARICQLNKQIAQKIR 233
Cdd:TIGR02479 162 REELRealaEAIESLSEREQLVLSLYYYEELNLKEIGEVLGLTESRVSQIHSQALKKLR 220
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 12-236 1.69e-65

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: 202.75  E-value: 1.69e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446861480  12 FAAAPVLTPQQESHYLQAYLPLVRKVVRQLAPQCncIIDRQDMEQTALMGLLNAIRRYGlPDEG--FAGYAVHRIRGAIL 89
Cdd:COG1191    6 LRRYQEGDEEAREELIEEYLPLVKKIASRLAGRL--PAELDDLIQVGLIGLIEAIDRFD-PSKGvsFETYAVPRIRGAIL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446861480  90 DELRALDWRPRQLRQKYHQMKDLIRETRKKLGHEPEWQELAEE-GISHEDYLEYQQLEGAETLASLDELL-NGEGPGIPL 167
Cdd:COG1191   83 DYLRDEDWVPRSVRELARKIEEAIEELEQELGREPTDEEIAEElGISLEEVQEALEAANAYQLLSLDEPLeDGDDLLDLL 162

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446861480 168 AGRDLEDQFV---TQQMLQHALSQLSEKEQLILSMYYQHEMNLKEIALVLGLTEARICQLNKQIAQKIRDFV 236
Cdd:COG1191  163 ESGDPEEELEheeLREALAEAIEQLPERERLVLSLYYFEELTLKEIAEVLGVSESRVSRLHKKALARLREYL 234
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 28-98 1.54e-09

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: 52.98  E-value: 1.54e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446861480   28 QAYLPLVRKVVRQLapqCNCIIDRQDMEQTALMGLLNAIRRYGlPDEG--FAGYAVHRIRGAILDELRALDWR 98
Cdd:pfam04542   3 ERYLPLVYSLARRY---LGDGADAEDLVQEGFLGLWRAIERFD-PERGvsFSTWLYTIIRNAIIDYLRKQRRT 71
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 179-233 1.35e-07

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: 47.10  E-value: 1.35e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 446861480 179 QQMLQHALSQLSEKEQLILSMYYQHEMNLKEIALVLGLTEARICQLNKQIAQKIR 233
Cdd:cd06171    1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
PRK12427 PRK12427
FliA/WhiG family RNA polymerase sigma factor;
7-236 4.42e-149

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 183523 [Multi-domain]  Cd Length: 231  Bit Score: 414.64  E-value: 4.42e-149
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446861480   7 FESEEFAAAPVLTPQQESHYLQAYLPLVRKVVRQLAPQCNCIIDRQDMEQTALMGLLNAIRRYGLPDEGFAGYAVHRIRG 86
Cdd:PRK12427   1 MENREFEACLTLTPQEEGKYLNAYLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEALRRYGHPDEQFAAYAVHRIRG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446861480  87 AILDELRALDWRPRQLRQKYHQMKDLIRETRKKLGHEPEWQELAEE-GISHEDYLEYQQLEGAETLASLDELLNGEGPGI 165
Cdd:PRK12427  81 AILDELRELDWRPRRLRQKTHKTNDAIREIAKRLGHEPNFEEISAElNLTAEEYQEYLLLENAGTLESLDELLALEAHND 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446861480 166 PLAGRDLEDQFVTQQMLQHALSQLSEKEQLILSMYYQHEMNLKEIALVLGLTEARICQLNKQIAQKIRDFV 236
Cdd:PRK12427 161 ILQSRDLEENIIIEDNLKQALSQLDEREQLILHLYYQHEMSLKEIALVLDLTEARICQLNKKIAQKIKSFF 231
FliA_WhiG TIGR02479
RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar ...
 27-233 1.20e-65

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: 202.89  E-value: 1.20e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446861480   27 LQAYLPLVRKVVRQLAPQCNCIIDRQDMEQTALMGLLNAIRRYGL-PDEGFAGYAVHRIRGAILDELRALDWRPRQLRQK 105
Cdd:TIGR02479   2 IRRYLPLVKRIAGRLSVGLPSSVELDDLIQAGMFGLLDAIERYDPsRGAKFETYAVQRIRGAMLDELRRLDWVPRSLRQK 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446861480  106 YHQMKDLIRETRKKLGHEPEWQELAEE-GISHEDYLEYQQLEGAETLASLDELLN----GEGPGIPLAGRDLEDQFVT-- 178
Cdd:TIGR02479  82 ARKLERAIRELEARLGREPTEEEIAEElGMDLKEYRQALNEINALSLVSLDELLEsgddGGSLIDRIEDDKSEDPEEEle 161

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 446861480  179 QQMLQ----HALSQLSEKEQLILSMYYQHEMNLKEIALVLGLTEARICQLNKQIAQKIR 233
Cdd:TIGR02479 162 REELRealaEAIESLSEREQLVLSLYYYEELNLKEIGEVLGLTESRVSQIHSQALKKLR 220
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 12-236 1.69e-65

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: 202.75  E-value: 1.69e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446861480  12 FAAAPVLTPQQESHYLQAYLPLVRKVVRQLAPQCncIIDRQDMEQTALMGLLNAIRRYGlPDEG--FAGYAVHRIRGAIL 89
Cdd:COG1191    6 LRRYQEGDEEAREELIEEYLPLVKKIASRLAGRL--PAELDDLIQVGLIGLIEAIDRFD-PSKGvsFETYAVPRIRGAIL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446861480  90 DELRALDWRPRQLRQKYHQMKDLIRETRKKLGHEPEWQELAEE-GISHEDYLEYQQLEGAETLASLDELL-NGEGPGIPL 167
Cdd:COG1191   83 DYLRDEDWVPRSVRELARKIEEAIEELEQELGREPTDEEIAEElGISLEEVQEALEAANAYQLLSLDEPLeDGDDLLDLL 162

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446861480 168 AGRDLEDQFV---TQQMLQHALSQLSEKEQLILSMYYQHEMNLKEIALVLGLTEARICQLNKQIAQKIRDFV 236
Cdd:COG1191  163 ESGDPEEELEheeLREALAEAIEQLPERERLVLSLYYFEELTLKEIAEVLGVSESRVSRLHKKALARLREYL 234
fliA PRK06986
flagellar biosynthesis sigma factor; Validated
 27-233 1.21e-62

flagellar biosynthesis sigma factor; Validated


Pssm-ID: 235901 [Multi-domain]  Cd Length: 236  Bit Score: 195.45  E-value: 1.21e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446861480  27 LQAYLPLVRKVVRQLAPQCNCIIDRQDMEQTALMGLLNAIRRY-GLPDEGFAGYAVHRIRGAILDELRALDWRPRQLRQK 105
Cdd:PRK06986  14 VEQYAPLVKRIALRLKARLPASVDLDDLIQAGMIGLLEAARRYdGEQGASFETYAGQRIRGAMLDELRSLDWVPRSVRRN 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446861480 106 YHQMKDLIRETRKKLGHEPEWQELAEE-GISHEDYLEYQQLEGAETLASLDELLNGEGPGIPLAGRDLED-------QFV 177
Cdd:PRK06986  94 AREVAQAIRQLEQELGREPTDTEVAEKlGLSLEEYREMLLDTNISQLFSIDELRGEHGDSILVTEDHQDEdplqqleDEE 173

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 446861480 178 TQQMLQHALSQLSEKEQLILSMYYQHEMNLKEIALVLGLTEARICQLNKQIAQKIR 233
Cdd:PRK06986 174 LREALVEAIESLPEREQLVLSLYYQEELNLKEIGAVLGVSESRVSQIHSQAIKRLR 229
PRK06288 PRK06288
RNA polymerase sigma factor WhiG; Reviewed
 30-233 1.91e-38

RNA polymerase sigma factor WhiG; Reviewed


Pssm-ID: 235770 [Multi-domain]  Cd Length: 268  Bit Score: 134.43  E-value: 1.91e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446861480  30 YLPLVRKVVRQLAPQCNCIIDRQDMEQTALMGLLNAIRRYGLPDE-GFAGYAVHRIRGAILDELRALDWRPRQLRQKYHQ 108
Cdd:PRK06288  40 YSPLVKYVAGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREiKFKTYAVTRIRGAIFDELRSIDWIPRSVRQKARQ 119

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446861480 109 MKDLIRETRKKLGHEPEWQELAEE-GISHEDYLE-YQQLEGAETLaSLDELLN-GEGPGIPLAGRDLEDQFV-------- 177
Cdd:PRK06288 120 IERAIAMLEARLGRTPSDEEIADElGISLEEYNSlLSKLSGTSVV-SLNDLWFgGDEGDEVSLMDTLESPAAlnpdeiae 198

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 446861480 178 ---TQQMLQHALSQLSEKEQLILSMYYQHEMNLKEIALVLGLTEARICQLNKQIAQKIR 233
Cdd:PRK06288 199 reeIKRVIVEAIKTLPEREKKVLILYYYEDLTLKEIGKVLGVTESRISQLHTKAVLQLR 257
PRK05911 PRK05911
RNA polymerase sigma factor sigma-28; Reviewed
 22-233 3.02e-30

RNA polymerase sigma factor sigma-28; Reviewed


Pssm-ID: 235644 [Multi-domain]  Cd Length: 257  Bit Score: 112.79  E-value: 3.02e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446861480  22 QESHY----LQAYLPLVRKVVRQLAPQCNCIIDRQDMEQTALMGLLNAIRRYGlPDEG--FAGYAVHRIRGAILDELRAL 95
Cdd:PRK05911  20 QEIEYrdvlIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFD-PEKSrrFEGYALFLIKAAIIDDLRKQ 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446861480  96 DWRPRQLRQKYHQMKDLIRETRKKLGHEPEWQELAEE-GISHEDYLEYQQLEGAETLASLDE---LLNGEGPGIPL---- 167
Cdd:PRK05911  99 DWVPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYlNISQQELSGWFSSARPALILSLNEefpCQSDDEAGLALeeri 178

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446861480 168 ------AGRDLEDQFVTQQMLQHALSQLSEKEQLILSMYYQHEMNLKEIALVLGLTEARICQLNKQIAQKIR 233
Cdd:PRK05911 179 aderaeTGYDVVDKKEFSSILAEAILALEEKERKVMALYYYEELVLKEIGKILGVSESRVSQIHSKALLKLR 250
PRK07670 PRK07670
FliA/WhiG family RNA polymerase sigma factor;
27-235 3.18e-30

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 181075 [Multi-domain]  Cd Length: 251  Bit Score: 112.45  E-value: 3.18e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446861480  27 LQAYLPLVRKVVRQLAPQCNCIIDRQDMEQTALMGLLNAIRRYGlP--DEGFAGYAVHRIRGAILDELRALDWRPRQLRQ 104
Cdd:PRK07670  28 IRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEKFD-PsrDLKFDTYASFRIRGAIIDGLRKEDWLPRSMRE 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446861480 105 KYHQMKDLIRETRKKLGHEPEWQELAEE-GISHEDYLEYQQLEGAETLASLDELLNG--EGPGIPLAGRD-----LEDQF 176
Cdd:PRK07670 107 KTKKVEAAIEKLEQRYMRNVTPKEVAAElGMTEEEVEATMNEGFFANLLSIDEKTHDqdDGENVSVTIRDdktptPEEKL 186

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446861480 177 VTQQM---LQHALSQLSEKEQLILSMYYQHEMNLKEIALVLGLTEARICQLNKQIAQKIRDF 235
Cdd:PRK07670 187 LKEELieeLAEKIKQLSEKEQLVISLFYKEELTLTEIGQVLNLSTSRISQIHSKALFKLKKL 248
PRK07408 PRK07408
RNA polymerase sigma factor SigF; Reviewed
 33-216 7.86e-17

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 180965 [Multi-domain]  Cd Length: 256  Bit Score: 76.88  E-value: 7.86e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446861480  33 LVRKVVRQLAPQCNCIIDrqDMEQTALMGLLNAIRRYGlPDEG--FAGYAVHRIRGAILDELR--ALDWR-PRQLRQKYH 107
Cdd:PRK07408  37 LVRKEAHRWSNQCSEPYE--DLVQVGSLGLIRAIERFD-PSKGhaFSSFAIPYIRGEIQHYLRdkSPTVRiPRRWQELQR 113

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446861480 108 QMKDLIRETRKKLGHEPEWQELAEE-GISHEdylEYQQLEGA---ETLASLDELLNGEGPGIPLAGRDLEDQ----FVTQ 179
Cdd:PRK07408 114 QAKKVRQELRQELGRQPTDQEIAQAlDISLE---EWQEIKLAlqnRTPLSLDAPVNQDEDGSTSLGDLLPDPryrsFQLA 190

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 446861480 180 Q----MLQHALSQLSEKEQLILSMYYQHEMNLKEIALVLGL 216
Cdd:PRK07408 191 QedriRLQQALAQLEERTREVLEFVFLHDLTQKEAAERLGI 231
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 27-236 2.96e-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: 2.96e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446861480   27 LQAYLPLVRKVVRQLapqCNCIIDRQDMEQTALMGLLNAIRRYGlPDEGFAGYAVHRIRGAILDELRALDWRPRQLrqky 106
Cdd:TIGR02937   7 YERYLPLVYRYARRY---LGDDADAEDLVQEAFLKLLEALDRFD-PEGSFKAWLFRIARNLILDYLRRKRRLRREL---- 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446861480  107 hqmkdliretrkklghepewqELAEEGISHEDYLEyqqlegaetlasldellngegpgiplagrDLEDQFVTQQMLQHAL 186
Cdd:TIGR02937  79 ---------------------DLLEELLDSDPSPE-----------------------------EELEQEEEREALREAL 108

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 446861480  187 SQLSEKEQLILSMYYQHEMNLKEIALVLGLTEARICQLNKQIAQKIRDFV 236
Cdd:TIGR02937 109 EKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 60-236 1.05e-13

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: 68.54  E-value: 1.05e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446861480  60 MGLLNAIRRYGlPDEG--FAGYAVHRIRGAILdelRAL--DWR----PRQLRQKYHQMKDLIRETRKKLGHEPEWQELAE 131
Cdd:COG0568   66 LGLMKAVEKFD-PERGfrFSTYATWWIRQAIT---RAIadQWRtirlPVHMAETLNKLRRAKRQLLQELGREPTPEEIAE 141

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446861480 132 E-GISHEDYLEYQQLegAETLASLDELLNGEG----------PGIPLAGRDLEDQFVTQQmLQHALSQLSEKEQLILSMY 200
Cdd:COG0568  142 ElGVPEEKVREMLRL--AREPVSLDAPVGDDEdselgdlledEEAPSPEEALEEELLREE-LREALDTLTEREREILRLR 218

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 446861480 201 Y----QHEMNLKEIALVLGLTEARICQLNKQIAQKIRDFV 236
Cdd:COG0568  219 FglddGEPHTLEEIGKEFGVSRERVRQIEAKALRKLRHPL 258
PRK05572 PRK05572
RNA polymerase sporulation sigma factor, SigF/SigG family;
31-234 8.87e-13

RNA polymerase sporulation sigma factor, SigF/SigG family;


Pssm-ID: 180137 [Multi-domain]  Cd Length: 252  Bit Score: 65.76  E-value: 8.87e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446861480  31 LPLVRKVVRQLApqcNCIIDRQDMEQTALMGLLNAIRRYGLP-DEGFAGYAVHRIRGAILDELR-----ALDWRPRQLRQ 104
Cdd:PRK05572  42 LRLVWSVVQRFL---NRGYEPDDLFQIGCIGLLKAVDKFDLSyDVKFSTYAVPMIIGEIQRFLRddgtvKVSRSLKETAN 118

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446861480 105 KYHQMKDlirETRKKLGHEPEWQELAEE-GISHEDYLEYQqlEGAETLASLDELLNgEGPGIP------LAGRDLEDQFv 177
Cdd:PRK05572 119 KIRKDKD---ELSKELGREPTIEELAEYlGVTPEEVVLAQ--EASRSPQSIHETVH-ENDGDPitlldqIADQSEEDWF- 191

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 446861480 178 TQQMLQHALSQLSEKEQLILSMYYQHEMNLKEIALVLGLTEARICQLNKQIAQKIRD 234
Cdd:PRK05572 192 DKIALKEAIRELDERERLIVYLRYFKDKTQSEVAKRLGISQVQVSRLEKKILKQMKE 248
PRK07122 PRK07122
RNA polymerase sigma factor SigF; Reviewed
 3-234 2.50e-11

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 168831 [Multi-domain]  Cd Length: 264  Bit Score: 61.71  E-value: 2.50e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446861480   3 QDVLFESEEFAAAPVLTPQ---QESHYLQAYLPLVRKVVRQLAPQCNciiDRQDMEQTALMGLLNAIRRYGlPDEG--FA 77
Cdd:PRK07122  19 ADVPEMFRELAGLPAGSPEfqrQRDRIVTRCLPLADHIARRFDGRGE---PRDDLVQVARVGLVNAVNRFD-VETGsdFV 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446861480  78 GYAVHRIRGAILDELRALDWR---PRQLRQKYHQMKDLIRETRKKLGHEPEWQELAEE-GISHEDYLEYQQLEGAETLAS 153
Cdd:PRK07122  95 SFAVPTIMGEVRRHFRDNSWSvkvPRRLKELHLRLGRATAELSQRLGRAPTASELAAElGMDREEVVEGLVAGSAYNTLS 174

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446861480 154 LDELLNGEGPGIP-----LAGRDLE-DQFVTQQMLQHALSQLSEKEQLILSMYYQHEMNLKEIALVLGLTEARICQLNKQ 227
Cdd:PRK07122 175 IDSGGGSGDDDARaiadtLGDVDAGlDQIENREALRPLLAALPERERTVLVLRFFESMTQTQIAERVGISQMHVSRLLAK 254


                 ....*..
gi 446861480 228 IAQKIRD 234
Cdd:PRK07122 255 TLARLRD 261
PRK08583 PRK08583
RNA polymerase sigma factor SigB; Validated
 52-234 5.20e-11

RNA polymerase sigma factor SigB; Validated


Pssm-ID: 236306 [Multi-domain]  Cd Length: 257  Bit Score: 60.86  E-value: 5.20e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446861480  52 QDMEQTALMGLLNAIRRYGLP-DEGFAGYAVHRIRGAILDELRALDWR---PRQLRQKYHQMKDLIRETRKKLGHEPEWQ 127
Cdd:PRK08583  57 EDLVQVGMVGLLGAIRRYDPSfGRSFEAFAVPTIIGEIKRYLRDKTWSvhvPRRIKELGPKIKKAVDELTTELQRSPKIS 136

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446861480 128 ELAEE-GISHEDYLE-------YQQL----------EGAeTLASLDELLNGEGpgiplaGRDLEDQfvtQQMLQHALSQL 189
Cdd:PRK08583 137 EIADRlGVSEEEVLEamemgksYQALsvdhsieadsDGS-TVTLLDIVGQQED------GYELTEQ---RMILEKILPVL 206

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 446861480 190 SEKEQLILSMYYQHEMNLKEIALVLGLTEARICQLNKQIAQKIRD 234
Cdd:PRK08583 207 SDREKSIIQCTFIENLSQKETGERLGISQMHVSRLQRQAIKKLRE 251
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 28-98 1.54e-09

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: 52.98  E-value: 1.54e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446861480   28 QAYLPLVRKVVRQLapqCNCIIDRQDMEQTALMGLLNAIRRYGlPDEG--FAGYAVHRIRGAILDELRALDWR 98
Cdd:pfam04542   3 ERYLPLVYSLARRY---LGDGADAEDLVQEGFLGLWRAIERFD-PERGvsFSTWLYTIIRNAIIDYLRKQRRT 71
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 185-234 6.25e-09

Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. 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: 50.50  E-value: 6.25e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 446861480  185 ALSQLSEKEQLILSMYYQHEMNLKEIALVLGLTEARICQLNKQIAQKIRD 234
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 179-233 1.35e-07

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: 47.10  E-value: 1.35e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 446861480 179 QQMLQHALSQLSEKEQLILSMYYQHEMNLKEIALVLGLTEARICQLNKQIAQKIR 233
Cdd:cd06171    1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 27-219 1.28e-06

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: 47.30  E-value: 1.28e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446861480  27 LQAYLPLVRKVVRQLapqCNCIIDRQDMEQTALMGLLNAIRRYGlPDEGFAGYAVHRIRGAILDELRaldwrprqlrqky 106
Cdd:COG1595   23 YERYRPRLYRYARRL---LGDRADAEDLVQETFLRLWRKLDSFR-GRGSFRAWLYRIARNLAIDHLR------------- 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446861480 107 hqmkdliRETRKKLGHEPEWQELAEEGISHEDYLEYQQLegaetlasldellngegpgiplagrdledqfvtQQMLQHAL 186
Cdd:COG1595   86 -------KRRRRRELLDELAEELPDEAADPEEALEAEEL---------------------------------LEALLAAL 125

                        170       180       190
                 ....*....|....*....|....*....|...
gi 446861480 187 SQLSEKEQLILSMYYQHEMNLKEIALVLGLTEA 219
Cdd:COG1595  126 ERLPPRQREVLVLRYLEGLSYAEIAEILGISEG 158
PRK05901 PRK05901
RNA polymerase sigma factor; Provisional
 114-235 6.80e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 235640 [Multi-domain]  Cd Length: 509  Bit Score: 43.44  E-value: 6.80e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446861480 114 RETRKKLGHEPEWQELAEE-GISHEDYLEYQQLeGAETLaSLDELLNGEGpgiplagrD------LED-------QFVTQ 179
Cdd:PRK05901 365 RELLQELGREPTPEELAKEmGFTPEKVREIQKY-NREPI-SLDKTIGKEG--------DsqfgdfIEDseavspvDAVSF 434

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446861480 180 QMLQHALSQ----LSEKEQLILSMYY----QHEMNLKEIALVLGLTEARICQL-NKQIA--------QKIRDF 235
Cdd:PRK05901 435 TLLQDQLQEvletLSEREAGVIRMRFgltdGQPKTLDEIGQVYGVTRERIRQIeSKTLRklrhpsrsQVLRDF 507
PRK05949 PRK05949
RNA polymerase sigma factor; Validated
 53-233 4.11e-04

RNA polymerase sigma factor; Validated


Pssm-ID: 180321 [Multi-domain]  Cd Length: 327  Bit Score: 40.60  E-value: 4.11e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446861480  53 DMEQTALMGLLNAIRRYGlPDEG--FAGYAVHRIRGAILdelRALDWRPRQLR------QKYHQMKDLIRETRKKLGHEP 124
Cdd:PRK05949 120 DLIQEGTLGLERGVEKFD-PTRGykFSTYAYWWIRQAIT---RAIAQQARTIRlpihitEKLNKIKKTQRELSQKLGRSA 195

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446861480 125 EWQELAEE-GISHEDYLEYqqLEGAETLASLD------------ELLNGEGPGiplagrdlEDQFVTQQML----QHALS 187
Cdd:PRK05949 196 TPAEIAKElELEPSQIREY--LSMARQPISLDvrvgdnqdtelsELLEDEGPS--------PDQYITQELLrqdlNNLLA 265

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 446861480 188 QLSEKEQLILSMYY----QHEMNLKEIALVLGLTEARICQLNKQIAQKIR 233
Cdd:PRK05949 266 ELTPQQREVLTLRFgledGKELSLAKVGERLNLSRERVRQLEHQALAHLR 315
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 179-221 5.95e-04

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: 37.05  E-value: 5.95e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 446861480  179 QQMLQHALSQLSEKEQLILSMYYQHEMNLKEIALVLGLTEARI 221
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTV 43
 
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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