NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|514231248|ref|YP_008129926|]
View 

RNA polymerase sigma factor [Paenibacillus phage PG1]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
PRK06930 super family cl27143
positive control sigma-like factor; Validated
 4-150 1.68e-45

positive control sigma-like factor; Validated


The actual alignment was detected with superfamily member PRK06930:

Pssm-ID: 180757 [Multi-domain]  Cd Length: 170  Bit Score: 146.41  E-value: 1.68e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514231248   4 LKELLKQYRETRSLLMGYKINAPEEE------KELISGMISDLQYAIDWMNRGHKPDPRRGINRRSRGQRTIPVDPLKIQ 77
Cdd:PRK06930   1 MQDLLKEYKRTLKQLRKMYKDAQEEIdeqlkdKKIIRSMISDLEYVIEWMEKGRQPGNRRGIDRRAAYQREVICDPLLIQ 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 514231248  78 SYAQPAACGSPTT------LSEYERYQIEDALSTLSERERECYIMKYGKCYSIGDIANILNVKRGTIQDYLKKAEEKVK 150
Cdd:PRK06930  81 RYFRSMEDLEWDIeepesvISEWDKIRIEDALSVLTEREKEVYLMHRGYGLSYSEIADYLNIKKSTVQSMIERAEKKIA 159
 
Name Accession Description Interval E-value
PRK06930 PRK06930
positive control sigma-like factor; Validated
 4-150 1.68e-45

positive control sigma-like factor; Validated


Pssm-ID: 180757 [Multi-domain]  Cd Length: 170  Bit Score: 146.41  E-value: 1.68e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514231248   4 LKELLKQYRETRSLLMGYKINAPEEE------KELISGMISDLQYAIDWMNRGHKPDPRRGINRRSRGQRTIPVDPLKIQ 77
Cdd:PRK06930   1 MQDLLKEYKRTLKQLRKMYKDAQEEIdeqlkdKKIIRSMISDLEYVIEWMEKGRQPGNRRGIDRRAAYQREVICDPLLIQ 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 514231248  78 SYAQPAACGSPTT------LSEYERYQIEDALSTLSERERECYIMKYGKCYSIGDIANILNVKRGTIQDYLKKAEEKVK 150
Cdd:PRK06930  81 RYFRSMEDLEWDIeepesvISEWDKIRIEDALSVLTEREKEVYLMHRGYGLSYSEIADYLNIKKSTVQSMIERAEKKIA 159
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 98-150 1.99e-11

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: 55.57  E-value: 1.99e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 514231248  98 QIEDALSTLSERERECYIMKYGKCYSIGDIANILNVKRGTIQDYLKKAEEKVK 150
Cdd:cd06171    3 RLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 56-150 4.58e-11

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: 57.36  E-value: 4.58e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514231248   56 RRGINRRSRGQRTIPVDPLKIQSYAQPAACGSPTTLSEYERYQIEDALSTLSERERECYIMKYGKCYSIGDIANILNVKR 135
Cdd:TIGR02937  61 RNLILDYLRRKRRLRRELDLLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISV 140

                          90
                  ....*....|....*
gi 514231248  136 GTIQDYLKKAEEKVK 150
Cdd:TIGR02937 141 GTVKRRLKRARKKLR 155
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 98-149 1.37e-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: 45.52  E-value: 1.37e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 514231248   98 QIEDALSTLSERERECYIMKYGKCYSIGDIANILNVKRGTIQDYLKKAEEKV 149
Cdd:pfam08281   3 ALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 56-150 3.15e-07

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: 3.15e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514231248  56 RRGINRRSRGQRTIPVDPLKIQSYAQPAACGSPTTLSEYERYQIEDALSTLSERERECYIMKYGKCYSIGDIANILNVKR 135
Cdd:COG1595   78 NLAIDHLRKRRRRRELLDELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISE 157

                         90
                 ....*....|....*
gi 514231248 136 GTIQDYLKKAEEKVK 150
Cdd:COG1595  158 GTVKSRLSRARKKLR 172
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 103-152 1.56e-03

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 34.81  E-value: 1.56e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 514231248   103 LSTLSEREREcyIMKY-GKCYSIGDIANILNVKRGTIQDYLKKAEEKVKIT 152
Cdd:smart00421   1 LASLTPRERE--VLRLlAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVR 49
 
Name Accession Description Interval E-value
PRK06930 PRK06930
positive control sigma-like factor; Validated
 4-150 1.68e-45

positive control sigma-like factor; Validated


Pssm-ID: 180757 [Multi-domain]  Cd Length: 170  Bit Score: 146.41  E-value: 1.68e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514231248   4 LKELLKQYRETRSLLMGYKINAPEEE------KELISGMISDLQYAIDWMNRGHKPDPRRGINRRSRGQRTIPVDPLKIQ 77
Cdd:PRK06930   1 MQDLLKEYKRTLKQLRKMYKDAQEEIdeqlkdKKIIRSMISDLEYVIEWMEKGRQPGNRRGIDRRAAYQREVICDPLLIQ 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 514231248  78 SYAQPAACGSPTT------LSEYERYQIEDALSTLSERERECYIMKYGKCYSIGDIANILNVKRGTIQDYLKKAEEKVK 150
Cdd:PRK06930  81 RYFRSMEDLEWDIeepesvISEWDKIRIEDALSVLTEREKEVYLMHRGYGLSYSEIADYLNIKKSTVQSMIERAEKKIA 159
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 98-150 1.99e-11

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: 55.57  E-value: 1.99e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 514231248  98 QIEDALSTLSERERECYIMKYGKCYSIGDIANILNVKRGTIQDYLKKAEEKVK 150
Cdd:cd06171    3 RLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 56-150 4.58e-11

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: 57.36  E-value: 4.58e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514231248   56 RRGINRRSRGQRTIPVDPLKIQSYAQPAACGSPTTLSEYERYQIEDALSTLSERERECYIMKYGKCYSIGDIANILNVKR 135
Cdd:TIGR02937  61 RNLILDYLRRKRRLRRELDLLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISV 140

                          90
                  ....*....|....*
gi 514231248  136 GTIQDYLKKAEEKVK 150
Cdd:TIGR02937 141 GTVKRRLKRARKKLR 155
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 98-149 1.37e-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: 45.52  E-value: 1.37e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 514231248   98 QIEDALSTLSERERECYIMKYGKCYSIGDIANILNVKRGTIQDYLKKAEEKV 149
Cdd:pfam08281   3 ALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 56-150 3.15e-07

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: 3.15e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514231248  56 RRGINRRSRGQRTIPVDPLKIQSYAQPAACGSPTTLSEYERYQIEDALSTLSERERECYIMKYGKCYSIGDIANILNVKR 135
Cdd:COG1595   78 NLAIDHLRKRRRRRELLDELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISE 157

                         90
                 ....*....|....*
gi 514231248 136 GTIQDYLKKAEEKVK 150
Cdd:COG1595  158 GTVKSRLSRARKKLR 172
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 102-150 1.72e-05

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: 40.10  E-value: 1.72e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 514231248  102 ALSTLSERERECYIMKYGKCYSIGDIANILNVKRGTIQDYLKKAEEKVK 150
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLR 49
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 54-150 2.25e-04

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 39.51  E-value: 2.25e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514231248  54 DPRRGINR---------------RSRGQRTIPVDPlkiqSYAQPAACGSPTT-LSEY---ERYQIEDALSTLSERERECY 114
Cdd:PRK13919  69 DPRRGSARawllalahhaavdhvRRRAARPQPLEP----DEREPEAFDLPGPgLDEEghlDRTRLGRALKALSPEERRVI 144

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 514231248 115 IMKYGKCYSIGDIANILNVKRGTIQDYLKKAEEKVK 150
Cdd:PRK13919 145 EVLYYQGYTHREAAQLLGLPLGTLKTRARRALSRLK 180
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
61-138 2.99e-04

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 38.91  E-value: 2.99e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 514231248  61 RRSRGQRTIPVDPLKIQSYAQPAACGSPTTLseyERYQIEDALSTLSERERECYIMKYGKCYSIGDIANILNVKRGTI 138
Cdd:PRK09645  77 RRSARARPVEGGDDVLGVPEQSAPDEVDRAL---DRLLVADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTV 151
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
49-152 4.60e-04

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 38.58  E-value: 4.60e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514231248  49 RGHKPDPRRGINRRSRGQRTIPVDPLKIQSYAQPAACGSPTTLSEYERYQIEDALSTLSEREREC--YIMKyGKcySIGD 126
Cdd:COG2771   71 LIALLLLLLLLLALLLLLALLALLAALLARLAALLLALALAALLLAALARLLARAPGLTPREREVlrLLAE-GL--TLKE 147

                         90       100
                 ....*....|....*....|....*.
gi 514231248 127 IANILNVKRGTIQDYLKKAEEKVKIT 152
Cdd:COG2771  148 IARILGISERTVRTHLKRIYRKLGVS 173
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 103-152 1.56e-03

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 34.81  E-value: 1.56e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 514231248   103 LSTLSEREREcyIMKY-GKCYSIGDIANILNVKRGTIQDYLKKAEEKVKIT 152
Cdd:smart00421   1 LASLTPRERE--VLRLlAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVR 49
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 64-150 2.55e-03

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 36.47  E-value: 2.55e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514231248  64 RGQRTIPVDPLKIQSYAQPAACGSPTT--LSEYERYQIEDALSTLSERERECYIMKYgKCYSIGDIANILNVKRGTIQDY 141
Cdd:PRK09639  69 RSEKRRRARILGEFQWQEVDNEPSPEEiwIRKEEITKVQEVLAKMTERDRTVLLLRF-SGYSYKEIAEALGIKESSVGTT 147


                 ....*....
gi 514231248 142 LKKAEEKVK 150
Cdd:PRK09639 148 LARAKKKFR 156
BglG COG3711
Transcriptional antiterminator [Transcription];
98-150 2.60e-03

Transcriptional antiterminator [Transcription];


Pssm-ID: 442925 [Multi-domain]  Cd Length: 618  Bit Score: 37.15  E-value: 2.60e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 514231248  98 QIEDALSTLSERERECYIMKY----GKCYSIGDIANILNVKRGTIQDYLKKAEEKVK 150
Cdd:COG3711   69 LLEKSEDPLSPKERVAYILLRlllaGDPISLDDLAEELFVSRSTILNDLKKIEKILK 125
HTH_10 pfam04967
HTH DNA binding domain;
106-149 3.17e-03

HTH DNA binding domain;


Pssm-ID: 282780 [Multi-domain]  Cd Length: 53  Bit Score: 34.12  E-value: 3.17e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 514231248  106 LSERERECYIMKYGKCY-------SIGDIANILNVKRGTIQDYLKKAEEKV 149
Cdd:pfam04967   1 LTDRQLEVLRLAYEMGYfdyprrvTLKELAKELGISKSTLSEHLRRAESKL 51
PRK06811 PRK06811
RNA polymerase factor sigma-70; Validated
 93-151 8.03e-03

RNA polymerase factor sigma-70; Validated


Pssm-ID: 180707 [Multi-domain]  Cd Length: 189  Bit Score: 34.92  E-value: 8.03e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 514231248  93 EYERYQIED------ALSTLSERERECYIMKYGKCYSIGDIANILNVKRGTIQDYLKKAEEKVKI 151
Cdd:PRK06811 113 ENEIILKENkeeilkLINDLEKLDREIFIRRYLLGEKIEEIAKKLGLTRSAIDNRLSRGRKKLQK 177
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 98-145 9.70e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 34.56  E-value: 9.70e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 514231248  98 QIEDALSTLSERERECYIMKYGKCYSIGDIANILNVKRGTIQDYLKKA 145
Cdd:PRK11924 118 RIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRA 165
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH