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Conserved domains on  [gi|489768158|ref|WP_003672081|]
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RNA polymerase sigma factor [Limosilactobacillus reuteri]

Protein Classification

RNA polymerase sigma factor( domain architecture ID 11446377)

RNA polymerase sigma factor plays a role in bacterial signal transduction and is regulated by anti-sigma factors. May belong to the ECF-type subfamily. Generally, sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released.

CATH:  1.10.1740.10
Gene Ontology:  GO:0016987|GO:0006352|GO:0003677
PubMed:  28575802
SCOP:  4003741

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 13-189 5.14e-16

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: 71.95  E-value: 5.14e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489768158  13 KLINNTRRGSNKDFEELFRRYWPLVRRLWQRYNISGLELADWEQEARVVMLEVIRLYNNQGPrmFSCFFKECLTNRIRDI 92
Cdd:COG1595    6 ELLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGS--FRAWLYRIARNLAIDH 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489768158  93 QRQTQAHKRIPAGCLYALSDDFAETLTDFLHHSPDDIIycRQSLDRLlchcSTFERKVLV--YLHtGYSITEIAGTLDCS 170
Cdd:COG1595   84 LRKRRRRRELLDELAEELPDEAADPEEALEAEELLEAL--LAALERL----PPRQREVLVlrYLE-GLSYAEIAEILGIS 156

                        170
                 ....*....|....*....
gi 489768158 171 KRSVQSALHRCHGKLLKVL 189
Cdd:COG1595  157 EGTVKSRLSRARKKLREAL 175
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 13-189 5.14e-16

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: 71.95  E-value: 5.14e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489768158  13 KLINNTRRGSNKDFEELFRRYWPLVRRLWQRYNISGLELADWEQEARVVMLEVIRLYNNQGPrmFSCFFKECLTNRIRDI 92
Cdd:COG1595    6 ELLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGS--FRAWLYRIARNLAIDH 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489768158  93 QRQTQAHKRIPAGCLYALSDDFAETLTDFLHHSPDDIIycRQSLDRLlchcSTFERKVLV--YLHtGYSITEIAGTLDCS 170
Cdd:COG1595   84 LRKRRRRRELLDELAEELPDEAADPEEALEAEELLEAL--LAALERL----PPRQREVLVlrYLE-GLSYAEIAEILGIS 156

                        170
                 ....*....|....*....
gi 489768158 171 KRSVQSALHRCHGKLLKVL 189
Cdd:COG1595  157 EGTVKSRLSRARKKLREAL 175
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 24-189 2.10e-13

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: 64.68  E-value: 2.10e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489768158   24 KDFEELFRRYWPLVRRLWQRYNISGLELADWEQEARVVMLEVIRLYNNQGPrmFSCFFKECLTNRIRDIQRQTQAHKRIP 103
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGS--FKAWLFRIARNLILDYLRRKRRLRREL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489768158  104 AGcLYALSDDFAETLTDFLHHspddiiYCRQSLDRLLCHCSTFERKVLV--YLHtGYSITEIAGTLDCSKRSVQSALHRC 181
Cdd:TIGR02937  79 DL-LEELLDSDPSPEEELEQE------EEREALREALEKLPEREREVLVlrYLE-GLSYKEIAEILGISVGTVKRRLKRA 150


                  ....*...
gi 489768158  182 HGKLLKVL 189
Cdd:TIGR02937 151 RKKLRELL 158
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
1-189 5.90e-10

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 56.07  E-value: 5.90e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489768158   1 MRFNEKDEEKYLKLInntRRGSNKDFEELFRRYWPLVRRLWQRYNISGLELADWEQEARVVMLEVIRLYNNQGPRMFSCF 80
Cdd:PRK08295   4 KDYDELEDEELVELA---RSGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489768158  81 FKECLTNRIRD-IQRQTQaHKRIPAGCLYALS-----DDFAETLTDFLHHS----PDDIIYCRQSLD----RLLCHCSTF 146
Cdd:PRK08295  81 AELCITRQIITaIKTANR-QKHIPLNSYVSLDkpiydEESDRTLLDVISEAkvtdPEELIISKEELEdieeKIEELLSEL 159

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 489768158 147 ERKVLVYLHTGYSITEIAGTLDCSKRSVQSALHRCHGKLLKVL 189
Cdd:PRK08295 160 EKEVLELYLDGKSYQEIAEELNRHVKSIDNALQRVKRKLEKYL 202
Sigma70_ECF pfam07638
ECF sigma factor; These proteins are probably RNA polymerase sigma factors belonging to the ...
 8-179 4.74e-04

ECF sigma factor; These proteins are probably RNA polymerase sigma factors belonging to the extra-cytoplasmic function (ECF) subfamily and show sequence similarity to pfam04542 and pfam04545.


Pssm-ID: 254323 [Multi-domain]  Cd Length: 185  Bit Score: 39.32  E-value: 4.74e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489768158    8 EEKYLKLINNTRRGSNKDFEELFRRYW-PLVR----RLWQRYNISGLELADWEQEARVVMLEVIRLYNNQGPRMFSCFFK 82
Cdd:pfam07638   1 MQEVTQLLQQVKDGDAAATEQLLPLVYdELRRlagsKLQNERRGHTLQPTALVHEAFVRLVDTEDFPDWSGRGHFFAAAA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489768158   83 ECLTNRIRDIQRQTQAHKRIPAGCLYALSDDFAetltDFLHHSPDDIIYCRQSLDRLLCHCSTFERKVLVYLHTGYSITE 162
Cdd:pfam07638  81 EAMRRILIDHARRRQRQKRGGDVQRRELDEVVD----NGDSPNPDLLLDLDEALEQLFSLSPRQARLVELRFFAGLSNDE 156

                         170
                  ....*....|....*..
gi 489768158  163 IAGTLDCSKRSVQSALH 179
Cdd:pfam07638 157 IAERLGVSERTVERNWA 173
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 147-185 3.89e-03

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: 34.43  E-value: 3.89e-03
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 489768158 147 ERKVLVYLHTGYSITEIAGTLDCSKRSVQSALHRCHGKL 185
Cdd:cd06170    5 EREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKL 43
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 13-189 5.14e-16

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: 71.95  E-value: 5.14e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489768158  13 KLINNTRRGSNKDFEELFRRYWPLVRRLWQRYNISGLELADWEQEARVVMLEVIRLYNNQGPrmFSCFFKECLTNRIRDI 92
Cdd:COG1595    6 ELLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGS--FRAWLYRIARNLAIDH 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489768158  93 QRQTQAHKRIPAGCLYALSDDFAETLTDFLHHSPDDIIycRQSLDRLlchcSTFERKVLV--YLHtGYSITEIAGTLDCS 170
Cdd:COG1595   84 LRKRRRRRELLDELAEELPDEAADPEEALEAEELLEAL--LAALERL----PPRQREVLVlrYLE-GLSYAEIAEILGIS 156

                        170
                 ....*....|....*....
gi 489768158 171 KRSVQSALHRCHGKLLKVL 189
Cdd:COG1595  157 EGTVKSRLSRARKKLREAL 175
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 24-189 2.10e-13

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: 64.68  E-value: 2.10e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489768158   24 KDFEELFRRYWPLVRRLWQRYNISGLELADWEQEARVVMLEVIRLYNNQGPrmFSCFFKECLTNRIRDIQRQTQAHKRIP 103
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGS--FKAWLFRIARNLILDYLRRKRRLRREL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489768158  104 AGcLYALSDDFAETLTDFLHHspddiiYCRQSLDRLLCHCSTFERKVLV--YLHtGYSITEIAGTLDCSKRSVQSALHRC 181
Cdd:TIGR02937  79 DL-LEELLDSDPSPEEELEQE------EEREALREALEKLPEREREVLVlrYLE-GLSYKEIAEILGISVGTVKRRLKRA 150


                  ....*...
gi 489768158  182 HGKLLKVL 189
Cdd:TIGR02937 151 RKKLRELL 158
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
1-189 5.90e-10

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 56.07  E-value: 5.90e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489768158   1 MRFNEKDEEKYLKLInntRRGSNKDFEELFRRYWPLVRRLWQRYNISGLELADWEQEARVVMLEVIRLYNNQGPRMFSCF 80
Cdd:PRK08295   4 KDYDELEDEELVELA---RSGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489768158  81 FKECLTNRIRD-IQRQTQaHKRIPAGCLYALS-----DDFAETLTDFLHHS----PDDIIYCRQSLD----RLLCHCSTF 146
Cdd:PRK08295  81 AELCITRQIITaIKTANR-QKHIPLNSYVSLDkpiydEESDRTLLDVISEAkvtdPEELIISKEELEdieeKIEELLSEL 159

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 489768158 147 ERKVLVYLHTGYSITEIAGTLDCSKRSVQSALHRCHGKLLKVL 189
Cdd:PRK08295 160 EKEVLELYLDGKSYQEIAEELNRHVKSIDNALQRVKRKLEKYL 202
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 125-191 5.97e-05

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 41.47  E-value: 5.97e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489768158 125 SPDDIIYCRQSLDRL---LCHCSTFERKVLVYLHTGYSITEIAGTLDCSKRSVQSALHRCHGKLLKVLMK 191
Cdd:PRK09639  92 SPEEIWIRKEEITKVqevLAKMTERDRTVLLLRFSGYSYKEIAEALGIKESSVGTTLARAKKKFRKIYEQ 161
Sigma70_ECF pfam07638
ECF sigma factor; These proteins are probably RNA polymerase sigma factors belonging to the ...
 8-179 4.74e-04

ECF sigma factor; These proteins are probably RNA polymerase sigma factors belonging to the extra-cytoplasmic function (ECF) subfamily and show sequence similarity to pfam04542 and pfam04545.


Pssm-ID: 254323 [Multi-domain]  Cd Length: 185  Bit Score: 39.32  E-value: 4.74e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489768158    8 EEKYLKLINNTRRGSNKDFEELFRRYW-PLVR----RLWQRYNISGLELADWEQEARVVMLEVIRLYNNQGPRMFSCFFK 82
Cdd:pfam07638   1 MQEVTQLLQQVKDGDAAATEQLLPLVYdELRRlagsKLQNERRGHTLQPTALVHEAFVRLVDTEDFPDWSGRGHFFAAAA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489768158   83 ECLTNRIRDIQRQTQAHKRIPAGCLYALSDDFAetltDFLHHSPDDIIYCRQSLDRLLCHCSTFERKVLVYLHTGYSITE 162
Cdd:pfam07638  81 EAMRRILIDHARRRQRQKRGGDVQRRELDEVVD----NGDSPNPDLLLDLDEALEQLFSLSPRQARLVELRFFAGLSNDE 156

                         170
                  ....*....|....*..
gi 489768158  163 IAGTLDCSKRSVQSALH 179
Cdd:pfam07638 157 IAERLGVSERTVERNWA 173
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
25-185 3.58e-03

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 36.66  E-value: 3.58e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489768158  25 DFEELFRRYWPLVRRLWQRYNISGLELADWEQEARVVMLEVIRLYNNQGPRMFSCFFKECLTNRIRDIQRQTQAHKRIPA 104
Cdd:COG2771   10 LLALLLLLLALLALLLLLLLAALLLLLALLLLAALLLLAAAAAALAAALAAALLLGLLLLLLIALLLLLLLLLALLLLLA 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489768158 105 GCLYALSDDFAETLTDFLHHSPDDIIYCRQSLDRLLCHCSTFERKVLVYLHTGYSITEIAGTLDCSKRSVQSALHRCHGK 184
Cdd:COG2771   90 LLALLAALLARLAALLLALALAALLLAALARLLARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRK 169


                 .
gi 489768158 185 L 185
Cdd:COG2771  170 L 170
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 147-185 3.89e-03

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: 34.43  E-value: 3.89e-03
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 489768158 147 ERKVLVYLHTGYSITEIAGTLDCSKRSVQSALHRCHGKL 185
Cdd:cd06170    5 EREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKL 43
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 112-185 4.33e-03

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: 35.64  E-value: 4.33e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489768158 112 DDFAETLTDFLHHSPDDIIycrqsLD-------------RLLchcSTFERKVLVYLHTGYSITEIAGTLDCSKRSVQSAL 178
Cdd:COG2197   34 ADGEEALELLEELRPDVVL-----LDirmpgmdglealrRLL---TPREREVLRLLAEGLSNKEIAERLGISERTVKTHV 105


                 ....*..
gi 489768158 179 HRCHGKL 185
Cdd:COG2197  106 SNILRKL 112
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 133-180 4.61e-03

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: 33.97  E-value: 4.61e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 489768158  133 RQSLDRLLCHCSTFERKVLV--YLHtGYSITEIAGTLDCSKRSVQSALHR 180
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLlrYLE-GLSYAEIAELLGISEGTVKSRLSR 49
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 29-97 7.04e-03

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: 34.10  E-value: 7.04e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489768158   29 LFRRYWPLVRRLWQRYNISGLELADWEQEARVVMLEVIRLYNNQGPRMFSCFFKECLTNRIRDIQRQTQ 97
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQR 69
 
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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