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Conserved domains on  [gi|488377339|ref|WP_002446724|]
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MULTISPECIES: sigma-70 family RNA polymerase sigma factor [Staphylococcus]

Protein Classification

sigma-70 family RNA polymerase sigma factor( domain architecture ID 11495650)

sigma-70 family RNA polymerase sigma factor is a general transcription factor that reversibly binds RNA polymerase and mediates transcription.

Gene Ontology:  GO:0003677|GO:0016987|GO:0006352
PubMed:  28117604

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 1-153 1.27e-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: 69.68  E-value: 1.27e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488377339    1 MSFEESYKKYNN-IIHYLLKSYQITYNYDEFYQQMLIKMWQLTLDFDEqqSSSFKSYLFIRLKFYLIDLFRQKDTTLNIC 79
Cdd:TIGR02937   1 EAFEELYERYLPlVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDP--EGSFKAWLFRIARNLILDYLRRKRRLRREL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488377339   80 S-IDTLSELSPSIS----INEIDLFIKDISQQLLPRERDWLAL-YLQGYKQYEISQILDFSPTTIKKIKSNTIRKLRRYL 153
Cdd:TIGR02937  79 DlLEELLDSDPSPEeeleQEEEREALREALEKLPEREREVLVLrYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
 
Name Accession Description Interval E-value
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 1-153 1.27e-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: 69.68  E-value: 1.27e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488377339    1 MSFEESYKKYNN-IIHYLLKSYQITYNYDEFYQQMLIKMWQLTLDFDEqqSSSFKSYLFIRLKFYLIDLFRQKDTTLNIC 79
Cdd:TIGR02937   1 EAFEELYERYLPlVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDP--EGSFKAWLFRIARNLILDYLRRKRRLRREL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488377339   80 S-IDTLSELSPSIS----INEIDLFIKDISQQLLPRERDWLAL-YLQGYKQYEISQILDFSPTTIKKIKSNTIRKLRRYL 153
Cdd:TIGR02937  79 DlLEELLDSDPSPEeeleQEEEREALREALEKLPEREREVLVLrYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK06759 PRK06759
RNA polymerase factor sigma-70; Validated
 1-153 6.67e-10

RNA polymerase factor sigma-70; Validated


Pssm-ID: 235857 [Multi-domain]  Cd Length: 154  Bit Score: 54.44  E-value: 6.67e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488377339   1 MSFEESYKKYNNIIHYLLKSYQITYNYDEFYQQMLIKMWQLTLDFDEQQsSSFKSYLFIRLKFYLIDLFRQKDTTLNICs 80
Cdd:PRK06759   4 ATFTEAVVLYEGLIVNQIKKLGIYQDYEEYYQCGLIGLWHAYERYDEKK-GSFPAYAVVTVRGYILERLKKEFAVQEKC- 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488377339  81 iDTLSELSPSISINEIDLFIKDISQQLLPRERDWLA-LYLQGYKQYEISQILDFSPTTIKKIKSNTIRKLRRYL 153
Cdd:PRK06759  82 -VCVGEYEDHFHFEDVEMKVKDFMSVLDEKEKYIIFeRFFVGKTMGEIALETEMTYYQVRWIYRQALEKMRNSV 154
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 1-153 3.78e-09

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: 52.69  E-value: 3.78e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488377339   1 MSFEESYKKYNNIIHYLLksYQITYNY---DEFYQQMLIKMWQLTLDFDEQqsSSFKSYLFIRLKFYLIDLFRQKDTTLN 77
Cdd:COG1595   17 AAFEELYERYRPRLYRYA--RRLLGDRadaEDLVQETFLRLWRKLDSFRGR--GSFRAWLYRIARNLAIDHLRKRRRRRE 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488377339  78 IcsIDTLSELSPSISINEIDLFIKDISQQLL--------PRERDWLAL-YLQGYKQYEISQILDFSPTTIKKIKSNTIRK 148
Cdd:COG1595   93 L--LDELAEELPDEAADPEEALEAEELLEALlaalerlpPRQREVLVLrYLEGLSYAEIAEILGISEGTVKSRLSRARKK 170


                 ....*
gi 488377339 149 LRRYL 153
Cdd:COG1595  171 LREAL 175
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 107-149 1.37e-05

helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 40.59  E-value: 1.37e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 488377339   107 LLPRERDWLALYLQGYKQYEISQILDFSPTTIKKIKSNTIRKL 149
Cdd:smart00421   4 LTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKL 46
GerE pfam00196
Bacterial regulatory proteins, luxR family;
105-150 2.80e-05

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 39.88  E-value: 2.80e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 488377339  105 QQLLPRERDWLALYLQGYKQYEISQILDFSPTTIKKIKSNTIRKLR 150
Cdd:pfam00196   1 DSLSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLN 46
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 107-149 1.98e-04

C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental nitrate or nitrite is present under anerobic conditions. FixJ is involved in the transcriptional activation of nitrogen fixation genes. The group also includes small proteins which lack an N-terminal signaling domain, such as Bacillus subtilis GerE. GerE is dimeric and acts in conjunction with sigmaK as an activator or a repressor modulating the expression of various genes in particular those encoding the spore-coat. These LuxR family regulators may share a similar organization of their target binding sites. For example the LuxR dimer binds the lux box, a 20bp inverted repeat, GerE dimers bind two 12bp consensus sequences in inverted orientation having the central four bases overlap, and the NarL dimer binds two 7bp inverted repeats separated by 2 bp.


Pssm-ID: 99777 [Multi-domain]  Cd Length: 57  Bit Score: 37.51  E-value: 1.98e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 488377339 107 LLPRERDWLALYLQGYKQYEISQILDFSPTTIKKIKSNTIRKL 149
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKL 43
 
Name Accession Description Interval E-value
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 1-153 1.27e-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: 69.68  E-value: 1.27e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488377339    1 MSFEESYKKYNN-IIHYLLKSYQITYNYDEFYQQMLIKMWQLTLDFDEqqSSSFKSYLFIRLKFYLIDLFRQKDTTLNIC 79
Cdd:TIGR02937   1 EAFEELYERYLPlVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDP--EGSFKAWLFRIARNLILDYLRRKRRLRREL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488377339   80 S-IDTLSELSPSIS----INEIDLFIKDISQQLLPRERDWLAL-YLQGYKQYEISQILDFSPTTIKKIKSNTIRKLRRYL 153
Cdd:TIGR02937  79 DlLEELLDSDPSPEeeleQEEEREALREALEKLPEREREVLVLrYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK06759 PRK06759
RNA polymerase factor sigma-70; Validated
 1-153 6.67e-10

RNA polymerase factor sigma-70; Validated


Pssm-ID: 235857 [Multi-domain]  Cd Length: 154  Bit Score: 54.44  E-value: 6.67e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488377339   1 MSFEESYKKYNNIIHYLLKSYQITYNYDEFYQQMLIKMWQLTLDFDEQQsSSFKSYLFIRLKFYLIDLFRQKDTTLNICs 80
Cdd:PRK06759   4 ATFTEAVVLYEGLIVNQIKKLGIYQDYEEYYQCGLIGLWHAYERYDEKK-GSFPAYAVVTVRGYILERLKKEFAVQEKC- 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488377339  81 iDTLSELSPSISINEIDLFIKDISQQLLPRERDWLA-LYLQGYKQYEISQILDFSPTTIKKIKSNTIRKLRRYL 153
Cdd:PRK06759  82 -VCVGEYEDHFHFEDVEMKVKDFMSVLDEKEKYIIFeRFFVGKTMGEIALETEMTYYQVRWIYRQALEKMRNSV 154
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 1-153 3.78e-09

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: 52.69  E-value: 3.78e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488377339   1 MSFEESYKKYNNIIHYLLksYQITYNY---DEFYQQMLIKMWQLTLDFDEQqsSSFKSYLFIRLKFYLIDLFRQKDTTLN 77
Cdd:COG1595   17 AAFEELYERYRPRLYRYA--RRLLGDRadaEDLVQETFLRLWRKLDSFRGR--GSFRAWLYRIARNLAIDHLRKRRRRRE 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488377339  78 IcsIDTLSELSPSISINEIDLFIKDISQQLL--------PRERDWLAL-YLQGYKQYEISQILDFSPTTIKKIKSNTIRK 148
Cdd:COG1595   93 L--LDELAEELPDEAADPEEALEAEELLEALlaalerlpPRQREVLVLrYLEGLSYAEIAEILGISEGTVKSRLSRARKK 170


                 ....*
gi 488377339 149 LRRYL 153
Cdd:COG1595  171 LREAL 175
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 81-149 1.96e-07

DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal transduction mechanisms, Transcription];


Pssm-ID: 441799 [Multi-domain]  Cd Length: 131  Bit Score: 47.19  E-value: 1.96e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488377339  81 IDTLSELSPSISIneIDLFIKDIS-----QQLL-PRERDWLALYLQGYKQYEISQILDFSPTTIKKIKSNTIRKL 149
Cdd:COG2197   40 LELLEELRPDVVL--LDIRMPGMDglealRRLLtPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKL 112
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
8-156 4.10e-07

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 47.60  E-value: 4.10e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488377339   8 KKYNNIIHYLLKSYQITY-NYDEFYQQMLIKMWQLTLDFDEQQSSSFKSYLFIRLKFYLID----LFRQKDTTLN-ICSI 81
Cdd:PRK08295  31 EKYKNFVRAKARSYFLIGaDREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCITRQIITaiktANRQKHIPLNsYVSL 110

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488377339  82 DT-----------LSELSPS---------ISINEIDLFIKDISQQLLPRERDWLALYLQGYKQYEISQILDFSP----TT 137
Cdd:PRK08295 111 DKpiydeesdrtlLDVISEAkvtdpeeliISKEELEDIEEKIEELLSELEKEVLELYLDGKSYQEIAEELNRHVksidNA 190

                        170
                 ....*....|....*....
gi 488377339 138 IKKIKsntiRKLRRYLILS 156
Cdd:PRK08295 191 LQRVK----RKLEKYLENR 205
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 107-149 1.37e-05

helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 40.59  E-value: 1.37e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 488377339   107 LLPRERDWLALYLQGYKQYEISQILDFSPTTIKKIKSNTIRKL 149
Cdd:smart00421   4 LTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKL 46
GerE pfam00196
Bacterial regulatory proteins, luxR family;
105-150 2.80e-05

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 39.88  E-value: 2.80e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 488377339  105 QQLLPRERDWLALYLQGYKQYEISQILDFSPTTIKKIKSNTIRKLR 150
Cdd:pfam00196   1 DSLSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLN 46
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
106-149 5.42e-05

DNA-binding transcriptional regulator, CsgD family [Transcription];


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 41.67  E-value: 5.42e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 488377339 106 QLLPRERDWLALYLQGYKQYEISQILDFSPTTIKKIKSNTIRKL 149
Cdd:COG2771  127 GLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKL 170
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 107-149 1.45e-04

Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell division, chromosome partitioning, Transcription];


Pssm-ID: 444607 [Multi-domain]  Cd Length: 76  Bit Score: 38.40  E-value: 1.45e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 488377339 107 LLPRERDWLALYLQGYKQYEISQILDFSPTTIKKIKSNTIRKL 149
Cdd:COG5905   13 LTKREREVLELLAEGLTNKEIARQLFISEKTVKNHVSNILRKL 55
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 107-149 1.98e-04

C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental nitrate or nitrite is present under anerobic conditions. FixJ is involved in the transcriptional activation of nitrogen fixation genes. The group also includes small proteins which lack an N-terminal signaling domain, such as Bacillus subtilis GerE. GerE is dimeric and acts in conjunction with sigmaK as an activator or a repressor modulating the expression of various genes in particular those encoding the spore-coat. These LuxR family regulators may share a similar organization of their target binding sites. For example the LuxR dimer binds the lux box, a 20bp inverted repeat, GerE dimers bind two 12bp consensus sequences in inverted orientation having the central four bases overlap, and the NarL dimer binds two 7bp inverted repeats separated by 2 bp.


Pssm-ID: 99777 [Multi-domain]  Cd Length: 57  Bit Score: 37.51  E-value: 1.98e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 488377339 107 LLPRERDWLALYLQGYKQYEISQILDFSPTTIKKIKSNTIRKL 149
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKL 43
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 105-151 3.01e-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. 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: 36.64  E-value: 3.01e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 488377339  105 QQLLPRERDWLAL-YLQGYKQYEISQILDFSPTTIKKIKSNTIRKLRR 151
Cdd:pfam04545   3 ASLPPRERQVLVLrYGEGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 7-73 3.10e-04

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: 37.18  E-value: 3.10e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488377339    7 YKKYNNIIHYLLKSYQI-TYNYDEFYQQMLIKMWQLTLDFDEQQSSSFKSYLFIRLKFYLIDLFRQKD 73
Cdd:pfam04542   2 VERYLPLVYSLARRYLGdGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQR 69
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 100-150 4.15e-04

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: 36.70  E-value: 4.15e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 488377339 100 IKDISQQLLPRERDWLAL-YLQGYKQYEISQILDFSPTTIKKIKSNTIRKLR 150
Cdd:cd06171    4 LEEALDKLPEREREVILLrFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
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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