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Conserved domains on  [gi|343197499|pdb|3S15|J]
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Chain J, DNA-directed RNA polymerases I, II, and III subunit RPABC5

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNA_pol_N super family cl00712
RNA polymerases N / 8 kDa subunit;
1-70 1.22e-32

RNA polymerases N / 8 kDa subunit;


The actual alignment was detected with superfamily member PLN00032:

Pssm-ID: 469886  Cd Length: 71  Bit Score: 107.15  E-value: 1.22e-32
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3S15_J        1 MIVPVRCFSCGKVVGDKWESYLNLLQEDeLDEGTALSRLGLKRYCCRRMILTHVDLIEKFLRYNPLEKRD 70
Cdd:PLN00032  1 MIIPVRCFTCGKVIGNKWDTYLDLLQAD-YSEGDALDALGLVRYCCRRMLMTHVDLIEKLLNYNTLEKSE 69
 
Name Accession Description Interval E-value
PLN00032 PLN00032
DNA-directed RNA polymerase; Provisional
 1-70 1.22e-32

DNA-directed RNA polymerase; Provisional


Pssm-ID: 215034  Cd Length: 71  Bit Score: 107.15  E-value: 1.22e-32
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3S15_J        1 MIVPVRCFSCGKVVGDKWESYLNLLQEDeLDEGTALSRLGLKRYCCRRMILTHVDLIEKFLRYNPLEKRD 70
Cdd:PLN00032  1 MIIPVRCFTCGKVIGNKWDTYLDLLQAD-YSEGDALDALGLVRYCCRRMLMTHVDLIEKLLNYNTLEKSE 69
RNA_pol_N pfam01194
RNA polymerases N / 8 kDa subunit;
2-59 8.89e-31

RNA polymerases N / 8 kDa subunit;


Pssm-ID: 426114  Cd Length: 58  Bit Score: 101.81  E-value: 8.89e-31
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
3S15_J         2 IVPVRCFSCGKVVGDKWESYLNLLQEDElDEGTALSRLGLKRYCCRRMILTHVDLIEK 59
Cdd:pfam01194  1 IIPVRCFTCGKVIGDKWEEYLERLKAGE-DPGDALDDLGLKRYCCRRMLLSHVDLIDK 57
RPB10 COG1644
DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription];
1-63 9.93e-28

DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription];


Pssm-ID: 441250  Cd Length: 62  Bit Score: 94.12  E-value: 9.93e-28
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|...
3S15_J       1 MIVPVRCFSCGKVVGDKWESYLNLLQEDElDEGTALSRLGLKRYCCRRMILTHVDLIEKFLRY 63
Cdd:COG1644  1 MIIPVRCFTCGKVIGHKWEEFKRRVEAGE-DPGKVLDDLGVKRYCCRRMLLSHVELIDEVIPY 62
 
Name Accession Description Interval E-value
PLN00032 PLN00032
DNA-directed RNA polymerase; Provisional
 1-70 1.22e-32

DNA-directed RNA polymerase; Provisional


Pssm-ID: 215034  Cd Length: 71  Bit Score: 107.15  E-value: 1.22e-32
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3S15_J        1 MIVPVRCFSCGKVVGDKWESYLNLLQEDeLDEGTALSRLGLKRYCCRRMILTHVDLIEKFLRYNPLEKRD 70
Cdd:PLN00032  1 MIIPVRCFTCGKVIGNKWDTYLDLLQAD-YSEGDALDALGLVRYCCRRMLMTHVDLIEKLLNYNTLEKSE 69
RNA_pol_N pfam01194
RNA polymerases N / 8 kDa subunit;
2-59 8.89e-31

RNA polymerases N / 8 kDa subunit;


Pssm-ID: 426114  Cd Length: 58  Bit Score: 101.81  E-value: 8.89e-31
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
3S15_J         2 IVPVRCFSCGKVVGDKWESYLNLLQEDElDEGTALSRLGLKRYCCRRMILTHVDLIEK 59
Cdd:pfam01194  1 IIPVRCFTCGKVIGDKWEEYLERLKAGE-DPGDALDDLGLKRYCCRRMLLSHVDLIDK 57
RPB10 COG1644
DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription];
1-63 9.93e-28

DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription];


Pssm-ID: 441250  Cd Length: 62  Bit Score: 94.12  E-value: 9.93e-28
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|...
3S15_J       1 MIVPVRCFSCGKVVGDKWESYLNLLQEDElDEGTALSRLGLKRYCCRRMILTHVDLIEKFLRY 63
Cdd:COG1644  1 MIIPVRCFTCGKVIGHKWEEFKRRVEAGE-DPGKVLDDLGVKRYCCRRMLLSHVELIDEVIPY 62
PRK04016 PRK04016
DNA-directed RNA polymerase subunit N; Provisional
 1-63 4.89e-26

DNA-directed RNA polymerase subunit N; Provisional


Pssm-ID: 235200  Cd Length: 62  Bit Score: 89.95  E-value: 4.89e-26
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
3S15_J        1 MIVPVRCFSCGKVVGDKWESYLNLLQEDElDEGTALSRLGLKRYCCRRMILTHVDLIEKFLRY 63
Cdd:PRK04016  1 MMIPVRCFTCGKVIAEKWEEFKERVEAGE-DPGKVLDDLGVKRYCCRRMLLSHVELIDEVIPY 62
 
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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