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Conserved domains on  [gi|476464575|gb|AGI65328|]
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RNA polymerase beta subunit, partial [Lactiplantibacillus plantarum]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Ricin_B_lectin super family cl47023
Ricin-type beta-trefoil lectin domain;
1-85 7.09e-68

Ricin-type beta-trefoil lectin domain;


The actual alignment was detected with superfamily member PRK00405:

Pssm-ID: 481363 [Multi-domain]  Cd Length: 1112  Bit Score: 218.43  E-value: 7.09e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 476464575    1 RRIRSVGELLQNQFRIGLSRMERVVRERMSIQDAATVTPQQLINIRPVVASIKEFFGSSQLSQFMDQTNPLGELTHKRRL 80
Cdd:PRK00405  372 RRVRSVGELLQNQFRIGLSRMERAVRERMSLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRL 451


                  ....*
gi 476464575   81 SALGP 85
Cdd:PRK00405  452 SALGP 456
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 1-85 7.09e-68

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 218.43  E-value: 7.09e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 476464575    1 RRIRSVGELLQNQFRIGLSRMERVVRERMSIQDAATVTPQQLINIRPVVASIKEFFGSSQLSQFMDQTNPLGELTHKRRL 80
Cdd:PRK00405  372 RRVRSVGELLQNQFRIGLSRMERAVRERMSLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRL 451


                  ....*
gi 476464575   81 SALGP 85
Cdd:PRK00405  452 SALGP 456
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-85 2.95e-61

DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA polymerase, beta subunit/140 kD subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 439855 [Multi-domain]  Cd Length: 1001  Bit Score: 199.57  E-value: 2.95e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 476464575    1 RRIRSVGELLQNQFRIGLSRMERVVRERMSIQDAATVTPQQLINIRPVVASIKEFFGSSQLSQFMDQTNPLGELTHKRRL 80
Cdd:COG0085   311 RRVRLVGELLQNQFRVGLSRMERVVRERMTTQDVEAITPQSLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRL 390


                  ....*
gi 476464575   81 SALGP 85
Cdd:COG0085   391 SALGP 395
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 1-85 1.84e-57

DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit of Bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit. [Transcription, DNA-dependent RNA polymerase]


Pssm-ID: 273928 [Multi-domain]  Cd Length: 1065  Bit Score: 189.10  E-value: 1.84e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 476464575     1 RRIRSVGELLQNQFRIGLSRMERVVRERMSIQDAATVTPQQLINIRPVVASIKEFFGSSQLSQFMDQTNPLGELTHKRRL 80
Cdd:TIGR02013  327 RRIRSVGELLQNQFRVGLARMERIVRERMSTQDTDTLTPQDLINAKPISAAIKEFFGSSQLSQFMDQTNPLAELTHKRRL 406


                   ....*
gi 476464575    81 SALGP 85
Cdd:TIGR02013  407 SALGP 411
RNA_pol_Rpb2_1 pfam04563
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ...
 1-48 4.65e-08

RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the protrusion domain. The other lobe (pfam04561) is nested within this domain.


Pssm-ID: 367994 [Multi-domain]  Cd Length: 396  Bit Score: 48.14  E-value: 4.65e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 476464575    1 RRIRSVGELLQNQFRIGLSRMERVVRERM--SIQDAATVTPQQLINIRPV 48
Cdd:pfam04563 345 KRLRLAGPLLASLFRVLFKKLVRDVRERLqkVLGSPDDLMLQLLVNAKPI 394
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 1-85 7.09e-68

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 218.43  E-value: 7.09e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 476464575    1 RRIRSVGELLQNQFRIGLSRMERVVRERMSIQDAATVTPQQLINIRPVVASIKEFFGSSQLSQFMDQTNPLGELTHKRRL 80
Cdd:PRK00405  372 RRVRSVGELLQNQFRIGLSRMERAVRERMSLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRL 451


                  ....*
gi 476464575   81 SALGP 85
Cdd:PRK00405  452 SALGP 456
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-85 2.95e-61

DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA polymerase, beta subunit/140 kD subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 439855 [Multi-domain]  Cd Length: 1001  Bit Score: 199.57  E-value: 2.95e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 476464575    1 RRIRSVGELLQNQFRIGLSRMERVVRERMSIQDAATVTPQQLINIRPVVASIKEFFGSSQLSQFMDQTNPLGELTHKRRL 80
Cdd:COG0085   311 RRVRLVGELLQNQFRVGLSRMERVVRERMTTQDVEAITPQSLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRL 390


                  ....*
gi 476464575   81 SALGP 85
Cdd:COG0085   391 SALGP 395
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 1-85 1.84e-57

DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit of Bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit. [Transcription, DNA-dependent RNA polymerase]


Pssm-ID: 273928 [Multi-domain]  Cd Length: 1065  Bit Score: 189.10  E-value: 1.84e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 476464575     1 RRIRSVGELLQNQFRIGLSRMERVVRERMSIQDAATVTPQQLINIRPVVASIKEFFGSSQLSQFMDQTNPLGELTHKRRL 80
Cdd:TIGR02013  327 RRIRSVGELLQNQFRVGLARMERIVRERMSTQDTDTLTPQDLINAKPISAAIKEFFGSSQLSQFMDQTNPLAELTHKRRL 406


                   ....*
gi 476464575    81 SALGP 85
Cdd:TIGR02013  407 SALGP 411
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 1-85 2.43e-39

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 137.53  E-value: 2.43e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 476464575    1 RRIRSVGELLQNQFRIGLSRMERVVRERMSIQDAATVTPQQLINIRPVVASIKEFFGSSQLSQFMDQTNPLGELTHKRRL 80
Cdd:CHL00207  306 RRVRSVGELLQNQFRIGLKRLERILRNRMTICDIDSLSKFNLINPKPLIALIREFFGSSQLSQYMDQTNPLSELTHKRRI 385


                  ....*
gi 476464575   81 SALGP 85
Cdd:CHL00207  386 SILGP 390
rpoB CHL00001
RNA polymerase beta subunit
 1-85 6.61e-38

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 133.10  E-value: 6.61e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 476464575    1 RRIRSVGELLQNQFRIGLSRMERVVRERMS--IQDAATVTPQQLINIRPVVASIKEFFGSSQLSQFMDQTNPLGELTHKR 78
Cdd:CHL00001  312 KRIRSVADLLQDQFGLALNRLENAVRGTICgaIRRKLIPTPQNLVTSTPLTTTYESFFGSHPLSQFLDQTNPLTEIVHGR 391


                  ....*..
gi 476464575   79 RLSALGP 85
Cdd:CHL00001  392 KLSSLGP 398
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
1-85 5.01e-31

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 113.56  E-value: 5.01e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 476464575    1 RRIRSVGELLQNQFRIGLSRMERVVRERMSIQDAATVTPQQLINIRPVVASIKEFFGSSQLSQFMDQTNPLGELTHKRRL 80
Cdd:PRK14844  472 RRVRSVGEFIENQFRTGLLKLERAVVDSMSTSSLDKVSPSDFINPKVLTNVLRDFFNSSQLSQFMDQTNPLSEITHKRRL 551


                  ....*
gi 476464575   81 SALGP 85
Cdd:PRK14844  552 SALGP 556
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
1-84 6.34e-29

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 107.70  E-value: 6.34e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 476464575    1 RRIRSVGELLQNQFRIGLSRMERVVRERMSIQDAA--TVTPQQLINIRPVVASIKEFFGSSQLSQFMDQTNPLGELTHKR 78
Cdd:PRK09603  463 RRIRAVGELLANELHSGLVKMQKTIKDKLTTMSGAfdSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSEVTHKR 542


                  ....*.
gi 476464575   79 RLSALG 84
Cdd:PRK09603  543 RLSALG 548
RNA_pol_Rpb2_1 pfam04563
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ...
 1-48 4.65e-08

RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the protrusion domain. The other lobe (pfam04561) is nested within this domain.


Pssm-ID: 367994 [Multi-domain]  Cd Length: 396  Bit Score: 48.14  E-value: 4.65e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 476464575    1 RRIRSVGELLQNQFRIGLSRMERVVRERM--SIQDAATVTPQQLINIRPV 48
Cdd:pfam04563 345 KRLRLAGPLLASLFRVLFKKLVRDVRERLqkVLGSPDDLMLQLLVNAKPI 394
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 63-82 1.26e-05

RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is proximal to catalytic site.


Pssm-ID: 428011 [Multi-domain]  Cd Length: 67  Bit Score: 39.05  E-value: 1.26e-05
                         10        20
                 ....*....|....*....|
gi 476464575  63 QFMDQTNPLGELTHKRRLSA 82
Cdd:pfam04565  1 QVLDRTNYLSTLSHLRRVNS 20
 
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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