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Conserved domains on  [gi|896555092|ref|WP_049455150|]
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MULTISPECIES: RNA polymerase sigma factor [Stenotrophomonas]

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]; ...
 20-170 2.37e-21

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: 85.43  E-value: 2.37e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896555092  20 RHYEELVEYLRCRFRSPGLAREVVHDVCVRLLERPAAYDARQPI-ALLRRIAHDAAVDRCRAEDLRRHWVESRAELPDDa 98
Cdd:COG1595   25 RYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFrAWLYRIARNLAIDHLRKRRRRRELLDELAEELPD- 103

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 896555092  99 cPRPGPEQQAQGQQALQRLSATIERMPCRRRQVFILHKIHALPQADVAQRMGIGLKAVERHLRLAMADCRQQ 170
Cdd:COG1595  104 -EAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREA 174
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 20-170 2.37e-21

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: 85.43  E-value: 2.37e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896555092  20 RHYEELVEYLRCRFRSPGLAREVVHDVCVRLLERPAAYDARQPI-ALLRRIAHDAAVDRCRAEDLRRHWVESRAELPDDa 98
Cdd:COG1595   25 RYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFrAWLYRIARNLAIDHLRKRRRRRELLDELAEELPD- 103

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 896555092  99 cPRPGPEQQAQGQQALQRLSATIERMPCRRRQVFILHKIHALPQADVAQRMGIGLKAVERHLRLAMADCRQQ 170
Cdd:COG1595  104 -EAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREA 174
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 18-170 3.05e-20

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: 82.01  E-value: 3.05e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896555092   18 LVRHYEELVEYLRCRFRSPGLAREVVHDVCVRLLERPAAYD-ARQPIALLRRIAHDAAVDRCRAEDLRRHWVESRAELPD 96
Cdd:TIGR02937   7 YERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDpEGSFKAWLFRIARNLILDYLRRKRRLRRELDLLEELLD 86

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 896555092   97 DAcprPGPEQQAQGQQALQRLSATIERMPCRRRQVFILHKIHALPQADVAQRMGIGLKAVERHLRLAMADCRQQ 170
Cdd:TIGR02937  87 SD---PSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLREL 157
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
 17-168 1.02e-15

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 70.48  E-value: 1.02e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896555092  17 SLVRHYEELVEYLRCRFRSPGLAREVVHDVCVRLLERPAAYDARQPIALLRRIAHDAAVDRCRAEDLRRHWVESRAELPD 96
Cdd:PRK07037   3 VFVDNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQDAVKQPVAYLFRIVRNLAIDHYRRQALENKYHGDEEDGLD 82

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 896555092  97 DACPRPGPEQQAQGQQALQRLSATIERMPCRRRQVFILHKIHALPQADVAQRMGIGLKAVERHLRLAMADCR 168
Cdd:PRK07037  83 VPSPEASPEAALINRDTLRHVADALSELPARTRYAFEMYRLHGETQKDIARELGVSPTLVNFMIRDALVHCR 154
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 116-167 1.51e-07

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: 45.91  E-value: 1.51e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 896555092  116 RLSATIERMPCRRRQVFILHKIHALPQADVAQRMGIGLKAVERHLRLAMADC 167
Cdd:pfam08281   3 ALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 116-168 5.19e-03

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: 33.62  E-value: 5.19e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 896555092 116 RLSATIERMPCRRRQVFILHKIHALPQADVAQRMGIGLKAVERHLRLAMADCR 168
Cdd:cd06171    3 RLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 20-170 2.37e-21

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: 85.43  E-value: 2.37e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896555092  20 RHYEELVEYLRCRFRSPGLAREVVHDVCVRLLERPAAYDARQPI-ALLRRIAHDAAVDRCRAEDLRRHWVESRAELPDDa 98
Cdd:COG1595   25 RYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFrAWLYRIARNLAIDHLRKRRRRRELLDELAEELPD- 103

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 896555092  99 cPRPGPEQQAQGQQALQRLSATIERMPCRRRQVFILHKIHALPQADVAQRMGIGLKAVERHLRLAMADCRQQ 170
Cdd:COG1595  104 -EAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREA 174
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 18-170 3.05e-20

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: 82.01  E-value: 3.05e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896555092   18 LVRHYEELVEYLRCRFRSPGLAREVVHDVCVRLLERPAAYD-ARQPIALLRRIAHDAAVDRCRAEDLRRHWVESRAELPD 96
Cdd:TIGR02937   7 YERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDpEGSFKAWLFRIARNLILDYLRRKRRLRRELDLLEELLD 86

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 896555092   97 DAcprPGPEQQAQGQQALQRLSATIERMPCRRRQVFILHKIHALPQADVAQRMGIGLKAVERHLRLAMADCRQQ 170
Cdd:TIGR02937  87 SD---PSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLREL 157
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 19-170 6.87e-17

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: 73.36  E-value: 6.87e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896555092   19 VRHYEELVEYLRCRFRSPGLAREVVHDVCVRLLERPAAYDARQPI-ALLRRIAHDAAVDRCRAEDLRRHWVESRAELPDD 97
Cdd:TIGR02985   8 RRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETLEISESIkAYLFTIVKNRCLNYLRHKQVEEKYQEELAEIEER 87

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 896555092   98 ACPRPGPEQQAQGQQALQRLSATIERMPCRRRQVFILHKIHALPQADVAQRMGIGLKAVERHLRLAMADCRQQ 170
Cdd:TIGR02985  88 ELSEADPEEELEAKELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLRKE 160
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
 17-168 1.02e-15

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 70.48  E-value: 1.02e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896555092  17 SLVRHYEELVEYLRCRFRSPGLAREVVHDVCVRLLERPAAYDARQPIALLRRIAHDAAVDRCRAEDLRRHWVESRAELPD 96
Cdd:PRK07037   3 VFVDNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQDAVKQPVAYLFRIVRNLAIDHYRRQALENKYHGDEEDGLD 82

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 896555092  97 DACPRPGPEQQAQGQQALQRLSATIERMPCRRRQVFILHKIHALPQADVAQRMGIGLKAVERHLRLAMADCR 168
Cdd:PRK07037  83 VPSPEASPEAALINRDTLRHVADALSELPARTRYAFEMYRLHGETQKDIARELGVSPTLVNFMIRDALVHCR 154
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 20-168 1.84e-14

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 67.11  E-value: 1.84e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896555092  20 RHYEELVEYLRCRFRSPGLAREVVHDVCVRLLERPAAYDARQPIALLRRIAHDAAVDRCRAEDLRRhwVESRAELPDDA- 98
Cdd:PRK12527   3 NYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQIEHPRAFLYRTALNLVVDRHRRHRVRQ--AEPLEVLDEEEr 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896555092  99 CPRPGPEQQAQGQQALQRLSATIERMPCRRRQVFILHKIHALPQADVAQRMGIGLKAVERHLRLAMADCR 168
Cdd:PRK12527  81 LHSPSPQTRLDLGQRLALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKHCR 150
PRK12529 PRK12529
RNA polymerase sigma factor; Provisional
 21-167 1.07e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 183574 [Multi-domain]  Cd Length: 178  Bit Score: 59.95  E-value: 1.07e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896555092  21 HYEELVEYLRCRFRSPG--LAREVVHDVCVRLLerpAAYDA------RQPIALLRRIAHDAAVDRCRAEDLRRHWVESRA 92
Cdd:PRK12529  22 NHAWLRNWLAYRLRSWGrgVADDLAHDIFLRIL---ASRDGgqreaiRQPRAYLARIANCVLVSWRRRQSLELAWLEALA 98

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 896555092  93 ELPDDAcpRPGPEQQAQGQQALQRLSATIERMPCRRRQVFILHKIHALPQADVAQRMGIGLKAVERHLRLAMADC 167
Cdd:PRK12529  99 TLPEPL--HPSPEQQSVILETLHEIDALLDTLRPRVKQAFLMATLDGMKQKDIAQALDIALPTVKKYIHQAYVTC 171
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 20-170 3.33e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 58.83  E-value: 3.33e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896555092  20 RHYEELVEYLRCRFRSPGLAREVVHDVCVRLLERPAAYDARQ-PIALLRRIAHDAAVDRCRAEDLRRHWVESRAELPDDA 98
Cdd:PRK11924  21 PHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGsARTWLLTIARNVCYDLLRRRRREKAVLSDDALEPEFA 100

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 896555092  99 CPRPGPEQQAQGQQALQRLSATIERMPCRRRQVFILHKIHALPQADVAQRMGIGLKAVERHLRLAMADCRQQ 170
Cdd:PRK11924 101 ETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQLLREC 172
PRK12523 PRK12523
RNA polymerase sigma factor; Reviewed
 1-167 6.45e-11

RNA polymerase sigma factor; Reviewed


Pssm-ID: 183572 [Multi-domain]  Cd Length: 172  Bit Score: 57.94  E-value: 6.45e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896555092   1 MSQLPSPHPPalpLVSSLVR-HYEELVEYLRCRFRSPGLAREVVHDVCVRLLERPAAYDARQPIALLRRIAHDAAVDRCR 79
Cdd:PRK12523   1 MSSAQSPHSE---LVGALYRdHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGRPELPTPREPRAFLAAVAKGLMFDHFR 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896555092  80 AEDLRRHWVESRAELPDdaCPRPGPEQQAQGQQALQRLSATIERMPCRRRQVFILHKIHALPQADVAQRMGIGLKAVERH 159
Cdd:PRK12523  78 RAALEQAYLAELALVPE--AEQPSPEEQHLILEDLKAIDRLLGKLSSKARAAFLYNRLDGMGHAEIAERLGVSVSRVRQY 155


                 ....*...
gi 896555092 160 LRLAMADC 167
Cdd:PRK12523 156 LAQGLRQC 163
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 20-168 1.42e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 57.39  E-value: 1.42e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896555092  20 RHYEELVEYLRCRFRSPGLAREVVHDVCVRLLERPAAYdarQPIALLR----RIAHDAAVDRCRAEDLRRH----WVESR 91
Cdd:PRK12513  34 RHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQY---QPRARFRtwlyQIARNLLIDHWRRHGARQApsldADEQL 110

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 896555092  92 AELPDDAcprPGPEQQAQGQQALQRLSATIERMPCRRRQVFILHKIHALPQADVAQRMGIGLKAVERHLRLAMADCR 168
Cdd:PRK12513 111 HALADDG---AAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREHGDLELEEIAELTGVPEETVKSRLRYALQKLR 184
PRK12528 PRK12528
RNA polymerase sigma factor; Provisional
 10-167 3.13e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 171561 [Multi-domain]  Cd Length: 161  Bit Score: 52.92  E-value: 3.13e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896555092  10 PALPLVSSLVRHYEELVEYLRCRFRSPGLAREVVHDVCVRLLERPAAYDARQPIALLRRIAHDAAVDRCRAEDLRRHWVE 89
Cdd:PRK12528   2 HSATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQIIEPRAFLTTIAKRVLCNHYRRQDLERAYLE 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 896555092  90 SRAELPDdaCPRPGPEQQAQGQQALQRLSATIERMPCRRRQVFILHKIHALPQADVAQRMGIGLKAVERHLRLAMADC 167
Cdd:PRK12528  82 ALAQLPE--RVAPSEEERAIILETLVELDQLLDGLPPLVKRAFLLAQVDGLGYGEIATELGISLATVKRYLNKAAMRC 157
PRK12525 PRK12525
RNA polymerase sigma factor; Provisional
 22-169 5.81e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 139037 [Multi-domain]  Cd Length: 168  Bit Score: 52.64  E-value: 5.81e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896555092  22 YEELVEYLRCRFRSPGLAREVVHDVCVRLLERPAAYDARQPIALLRRIAHDAAVDRCRAEDLRRHWVESRAELPDDAcpR 101
Cdd:PRK12525  19 YDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPASIREPRALLTTIARRLMYEGWRRQDLERAYLQSLAEAPEAV--Q 96

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 896555092 102 PGPEQQAQGQQALQRLSATIERMPCRRRQVFILHKIHALPQADVAQRMGIGLKAVERHLRLAMADCRQ 169
Cdd:PRK12525  97 PSPEEQWMVIETLLAIDRLLDGLSGKARAAFLMSQLEGLTYVEIGERLGVSLSRIHQYMVEAFKCCYQ 164
PRK09651 PRK09651
RNA polymerase sigma factor FecI; Provisional
 9-167 6.66e-08

RNA polymerase sigma factor FecI; Provisional


Pssm-ID: 182018 [Multi-domain]  Cd Length: 172  Bit Score: 49.81  E-value: 6.66e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896555092   9 PPALPLVSSLVRHYEELVEYLRCRFRSPGLAREVVHDVCVRLLERPAAYDARQPIALLRRIAHDAAVDRCRAEDLRRHWV 88
Cdd:PRK09651   7 TASLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVSETLSTIRDPRSFLCTIAKRVMVDLFRRNALEKAYL 86

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 896555092  89 ESRAELPDDACPrpGPEQQAQGQQALQRLSATIERMPCRRRQVFILHKIHALPQADVAQRMGIGLKAVERHLRLAMADC 167
Cdd:PRK09651  87 EMLALMPEGGAP--SPEERESQLETLQLLDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKATEHC 163
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 116-167 1.51e-07

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: 45.91  E-value: 1.51e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 896555092  116 RLSATIERMPCRRRQVFILHKIHALPQADVAQRMGIGLKAVERHLRLAMADC 167
Cdd:pfam08281   3 ALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 18-163 3.37e-05

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 42.10  E-value: 3.37e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896555092  18 LVRHYEELVEYLRCRF-RSPGLAREVVHDVCVRLLERPAAYDAR-QPIALLRRIAHDAAVDRCRAEDLRRHWVESRAELP 95
Cdd:PRK09652  15 LVRRYQPRVKRLLSRLtRDPADAEDLVQETFIKAYRALHSFRGGaAFYTWLYRIARNTAINYLRKQGRRPPASDVDAEEA 94

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 896555092  96 DD------ACPRPGPEQQAQGQQALQRLSATIERMPCRRRQVFILHKIHALPQADVAQRMGIGLKAVERHLRLA 163
Cdd:PRK09652  95 EDfdladaLRDISTPENELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRIFRA 168
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 39-157 4.25e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 42.18  E-value: 4.25e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896555092  39 AREVVHDVCVRLLErpAAYDARQ----PIALLRRIAHDAAVDRCRAEDLRRHWVESRAELPDDAcprPGPEQQAQGQQAL 114
Cdd:PRK12524  53 AEDVTQEAMLRLWR--IAPDWRQgearVSTWLYRVVCNLCTDRLRRRRRASVDLDDAPEPADAA---PGAEEALIEGDRM 127

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 896555092 115 QRLSATIERMPCRRRQVFILHKIHALPQADVAQRMGIGLKAVE 157
Cdd:PRK12524 128 RALDAALAALPERQRQAVVLRHIEGLSNPEIAEVMEIGVEAVE 170
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 34-166 8.93e-05

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 41.18  E-value: 8.93e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896555092  34 RSPGLAREVVHDVCVRLLERPAAYdaRQPIALLRRIAHDAAVDRCrAEDLRRHWVESRAELPDDACPRPGPEQQAQGQQA 113
Cdd:PRK05602  42 GDPAEAEDVAQETFLRIWKQAPSW--RPGEARFDTWLHRVVLNLC-YDRLRRRREVPVEDAPDVPDPAPGPDAGLEARQR 118

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 896555092 114 LQRLSATIERMPCRRRQVFILHKIHALPQADVAQRMGIGLKAVE-------RHLRLAMAD 166
Cdd:PRK05602 119 ARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALEsllargrRALRAQLAD 178
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 39-170 9.13e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 40.96  E-value: 9.13e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896555092  39 AREVVHDVCVRLLERPAAY--DARQPIALLRRIAHDAAVDRCRAedlRRHWVESRAELPDDACPRPGPEQQAQGQQALQR 116
Cdd:PRK12514  46 AEEALQDVYVKIWTKADRFavSGLSPMTWLITIARNHAIDRLRA---RKAVAVDIDEAHDLADPSPGPEAEVIAGDEGQR 122

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 896555092 117 LSATIERMPCRRRQVFILHKIHALPQADVAQRMGIGLKAVERHLR---LAMADCRQQ 170
Cdd:PRK12514 123 IDACLEELEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMRTWLRrslLKLRECLSR 179
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 1-174 4.52e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 39.27  E-value: 4.52e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896555092   1 MSQLPSPHPPALplvSSLVRHYEELVEYLRCR-FRSPGLAREVVHDVCVRLlERPAAYDARQ--PIALLRRIAHDAAVDR 77
Cdd:PRK12519  20 FSALKAGQSAAL---GVLYDRHAGLVYGLALKiLGNSQEAEDLTQEIFLSL-WRKSSYDPKRgsLSSYLLTLTRSRAIDR 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896555092  78 CRAEDLRRHWVES-RAELPDDACPRPgPEQQAQGQQALQRLSATIERMPCRRRQVFILHKIHALPQADVAQRMGIGLKAV 156
Cdd:PRK12519  96 LRSRRSRQRLLERwQQELLGEASEDT-PLEQASLAERSQRVQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTV 174

                        170
                 ....*....|....*...
gi 896555092 157 ERHLRLAMadCRQQGTLQ 174
Cdd:PRK12519 175 KARARQGL--LKLRELLQ 190
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 36-165 3.70e-03

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 36.43  E-value: 3.70e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896555092  36 PGLAREVVHDVCVRLLERPAAYDARQPIA--LLRRIAHDAAVDRCRAEDLRRHWVESRAELPDdACPRPGPEQQAQGQQA 113
Cdd:PRK13919  47 GAAAEDVVQEVFIRVWKKAKEFDPRRGSAraWLLALAHHAAVDHVRRRAARPQPLEPDEREPE-AFDLPGPGLDEEGHLD 125

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 896555092 114 LQRLSATIERMPCRRRQVFILHKIHALPQADVAQRMGIGLKAVERHLRLAMA 165
Cdd:PRK13919 126 RTRLGRALKALSPEERRVIEVLYYQGYTHREAAQLLGLPLGTLKTRARRALS 177
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 116-168 5.19e-03

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: 33.62  E-value: 5.19e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 896555092 116 RLSATIERMPCRRRQVFILHKIHALPQADVAQRMGIGLKAVERHLRLAMADCR 168
Cdd:cd06171    3 RLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 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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