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Conserved domains on  [gi|19879534|gb|AAL58620|]
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core protein, partial [Hepacivirus hominis]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HCV_core super family cl46603
Hepatitis C virus core protein; The viral core protein forms the internal viral coat that ...
 2-100 1.12e-40

Hepatitis C virus core protein; The viral core protein forms the internal viral coat that encapsidates the genomic RNA and is enveloped in a host cell-derived lipid membrane. The core protein has been shown, by yeast two-hybrid assay to interact with cellular DEAD box helicases. The N terminus of the core protein is involved in transcriptional repression.


The actual alignment was detected with superfamily member pfam01543:

Pssm-ID: 480943  Cd Length: 121  Bit Score: 130.20  E-value: 1.12e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19879534     2 STNPKPQRKTKRNTNRRPQDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRRQPIPKARRPEGRSWAQPGY 81
Cdd:pfam01543   1 STNPKPQRKTKRNTNRRPQDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRRQPIPKARPPEGRSWLSPGT 80

                          90       100
                  ....*....|....*....|....*.
gi 19879534    82 PWP------LYGNEGM-GWAGWLLSP 100
Cdd:pfam01543  81 LGPstamraLYGNDGScGWAGWLLPP 106
 
Name Accession Description Interval E-value
HCV_capsid pfam01543
Hepatitis C virus capsid protein;
2-100 1.12e-40

Hepatitis C virus capsid protein;


Pssm-ID: 144947  Cd Length: 121  Bit Score: 130.20  E-value: 1.12e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19879534     2 STNPKPQRKTKRNTNRRPQDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRRQPIPKARRPEGRSWAQPGY 81
Cdd:pfam01543   1 STNPKPQRKTKRNTNRRPQDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRRQPIPKARPPEGRSWLSPGT 80

                          90       100
                  ....*....|....*....|....*.
gi 19879534    82 PWP------LYGNEGM-GWAGWLLSP 100
Cdd:pfam01543  81 LGPstamraLYGNDGScGWAGWLLPP 106
 
Name Accession Description Interval E-value
HCV_capsid pfam01543
Hepatitis C virus capsid protein;
2-100 1.12e-40

Hepatitis C virus capsid protein;


Pssm-ID: 144947  Cd Length: 121  Bit Score: 130.20  E-value: 1.12e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19879534     2 STNPKPQRKTKRNTNRRPQDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRRQPIPKARRPEGRSWAQPGY 81
Cdd:pfam01543   1 STNPKPQRKTKRNTNRRPQDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRRQPIPKARPPEGRSWLSPGT 80

                          90       100
                  ....*....|....*....|....*.
gi 19879534    82 PWP------LYGNEGM-GWAGWLLSP 100
Cdd:pfam01543  81 LGPstamraLYGNDGScGWAGWLLPP 106
HCV_core pfam01542
Hepatitis C virus core protein; The viral core protein forms the internal viral coat that ...
 1-75 2.55e-26

Hepatitis C virus core protein; The viral core protein forms the internal viral coat that encapsidates the genomic RNA and is enveloped in a host cell-derived lipid membrane. The core protein has been shown, by yeast two-hybrid assay to interact with cellular DEAD box helicases. The N terminus of the core protein is involved in transcriptional repression.


Pssm-ID: 460245  Cd Length: 75  Bit Score: 92.43  E-value: 2.55e-26
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19879534     1 MSTNPKPQRKTKRNTNRRPQDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRRQPIPKARRPEGRS 75
Cdd:pfam01542   1 MRNLGKPIDKLKCGFADLMGDIKFPGAGLGGAARALAHGRGPLEDGRATAKGNEPGCPFGIFLLALKACLPEGAS 75
 
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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