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Conserved domains on  [gi|558483800|gb|AHA56719|]
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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;
3-68 1.26e-44

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: 151.79  E-value: 1.26e-44
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 558483800    3 IDHLGNRRIRSVGELLQNQFRIGLSRMERVVRERMSIQDSGTVTPQQLINIRAVVAAIEEFFGRSQ 68
Cdd:PRK00405  366 IDHLGNRRVRSVGELLQNQFRIGLSRMERAVRERMSLQDLDTLTPQDLINAKPVVAAIKEFFGSSQ 431
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 3-68 1.26e-44

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 151.79  E-value: 1.26e-44
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 558483800    3 IDHLGNRRIRSVGELLQNQFRIGLSRMERVVRERMSIQDSGTVTPQQLINIRAVVAAIEEFFGRSQ 68
Cdd:PRK00405  366 IDHLGNRRVRSVGELLQNQFRIGLSRMERAVRERMSLQDLDTLTPQDLINAKPVVAAIKEFFGSSQ 431
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 2-69 9.39e-42

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: 143.33  E-value: 9.39e-42
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 558483800    2 EIDHLGNRRIRSVGELLQNQFRIGLSRMERVVRERMSIQDSGTVTPQQLINIRAVVAAIEEFFGRSQV 69
Cdd:COG0085   304 DIDHLGNRRVRLVGELLQNQFRVGLSRMERVVRERMTTQDVEAITPQSLINIRPVVAAIKEFFGSSQL 371
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 2-68 6.86e-38

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: 132.48  E-value: 6.86e-38
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 558483800     2 EIDHLGNRRIRSVGELLQNQFRIGLSRMERVVRERMSIQDSGTVTPQQLINIRAVVAAIEEFFGRSQ 68
Cdd:TIGR02013  320 DIDHLGNRRIRSVGELLQNQFRVGLARMERIVRERMSTQDTDTLTPQDLINAKPISAAIKEFFGSSQ 386
RNA_pol_Rpb2_1 pfam04563
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ...
 3-52 2.32e-11

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: 57.00  E-value: 2.32e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 558483800    3 IDHLGNRRIRSVGELLQNQFRIGLSRMERVVRERM--SIQDSGTVTPQQLIN 52
Cdd:pfam04563 339 RDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLqkVLGSPDDLMLQLLVN 390
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 3-68 1.26e-44

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 151.79  E-value: 1.26e-44
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 558483800    3 IDHLGNRRIRSVGELLQNQFRIGLSRMERVVRERMSIQDSGTVTPQQLINIRAVVAAIEEFFGRSQ 68
Cdd:PRK00405  366 IDHLGNRRVRSVGELLQNQFRIGLSRMERAVRERMSLQDLDTLTPQDLINAKPVVAAIKEFFGSSQ 431
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 2-69 9.39e-42

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: 143.33  E-value: 9.39e-42
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 558483800    2 EIDHLGNRRIRSVGELLQNQFRIGLSRMERVVRERMSIQDSGTVTPQQLINIRAVVAAIEEFFGRSQV 69
Cdd:COG0085   304 DIDHLGNRRVRLVGELLQNQFRVGLSRMERVVRERMTTQDVEAITPQSLINIRPVVAAIKEFFGSSQL 371
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 2-68 6.86e-38

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: 132.48  E-value: 6.86e-38
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 558483800     2 EIDHLGNRRIRSVGELLQNQFRIGLSRMERVVRERMSIQDSGTVTPQQLINIRAVVAAIEEFFGRSQ 68
Cdd:TIGR02013  320 DIDHLGNRRIRSVGELLQNQFRVGLARMERIVRERMSTQDTDTLTPQDLINAKPISAAIKEFFGSSQ 386
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 1-69 4.69e-24

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 93.23  E-value: 4.69e-24
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 558483800    1 IEIDHLGNRRIRSVGELLQNQFRIGLSRMERVVRERMSIQDSGTVTPQQLINIRAVVAAIEEFFGRSQV 69
Cdd:CHL00207  298 DDIDHLKNRRVRSVGELLQNQFRIGLKRLERILRNRMTICDIDSLSKFNLINPKPLIALIREFFGSSQL 366
rpoB CHL00001
RNA polymerase beta subunit
 3-69 1.09e-20

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 83.41  E-value: 1.09e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 558483800    3 IDHLGNRRIRSVGELLQNQFRIGLSRMERVVRERMS--IQDSGTVTPQQLINIRAVVAAIEEFFGR---SQV 69
Cdd:CHL00001  306 IDHLKNKRIRSVADLLQDQFGLALNRLENAVRGTICgaIRRKLIPTPQNLVTSTPLTTTYESFFGShplSQF 377
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
2-70 2.28e-17

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 74.27  E-value: 2.28e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 558483800    2 EIDHLGNRRIRSVGELLQNQFRIGLSRMERVVRERMSIQDSGTVTPQQLINIRAVVAAIEEFFGRSQVA 70
Cdd:PRK14844  465 DIDHLGNRRVRSVGEFIENQFRTGLLKLERAVVDSMSTSSLDKVSPSDFINPKVLTNVLRDFFNSSQLS 533
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
4-70 1.23e-14

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 66.49  E-value: 1.23e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 558483800    4 DHLGNRRIRSVGELLQNQFRIGLSRMERVVRERMSIQDSG--TVTPQQLINIRAVVAAIEEFFGRSQVA 70
Cdd:PRK09603  458 DHLGNRRIRAVGELLANELHSGLVKMQKTIKDKLTTMSGAfdSLMPHDLVNSKMITSTIMEFFMGGQLS 526
RNA_pol_Rpb2_1 pfam04563
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ...
 3-52 2.32e-11

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: 57.00  E-value: 2.32e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 558483800    3 IDHLGNRRIRSVGELLQNQFRIGLSRMERVVRERM--SIQDSGTVTPQQLIN 52
Cdd:pfam04563 339 RDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLqkVLGSPDDLMLQLLVN 390
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 4-37 9.08e-03

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 32.62  E-value: 9.08e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 558483800    4 DHLGNRRIRSVGELLQNQFRIGLSRMERVVRERM 37
Cdd:PRK08565  328 DHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQL 361
 
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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