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Conserved domains on  [gi|1783581423|gb|QGW53353|]
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polyprotein, partial [Hepacivirus hominis]

Protein Classification

capsid and core domain-containing protein( domain architecture ID 10479863)

hepatitis C virus capsid and core domain-containing protein, which forms the internal viral coat that encapsidates the genomic RNA and is enveloped in a host cell-derived lipid membrane

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HCV_capsid pfam01543
Hepatitis C virus capsid protein;
2-115 2.26e-52

Hepatitis C virus capsid protein;


:

Pssm-ID: 144947  Cd Length: 121  Bit Score: 162.56  E-value: 2.26e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1783581423   2 STFPKPQRQTKRNTPRRPQNVKFPGGGQIVGGVYVLPRRGPRLGVRAARKTSERSQPRGRRQPIPKARPSEGRSWAQPGY 81
Cdd:pfam01543   1 STNPKPQRKTKRNTNRRPQDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRRQPIPKARPPEGRSWLSPGT 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1783581423  82 PWP------LYGNEG-CGWAGWLLSPRGSRPSWGPNDPRRR 115
Cdd:pfam01543  81 LGPstamraLYGNDGsCGWAGWLLPPRGSRPSWGQNDPRRR 121
HCV_core super family cl46603
Hepatitis C virus core protein; The viral core protein forms the internal viral coat that ...
 116-164 2.86e-12

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 pfam01542:

Pssm-ID: 480943  Cd Length: 75  Bit Score: 58.92  E-value: 2.86e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1783581423 116 SRNLGKVIDTLTCGFADLMGYIPLVGAPVGGVARALAHGVRALEDGVNY 164
Cdd:pfam01542   1 MRNLGKPIDKLKCGFADLMGDIKFPGAGLGGAARALAHGRGPLEDGRAT 49
 
Name Accession Description Interval E-value
HCV_capsid pfam01543
Hepatitis C virus capsid protein;
2-115 2.26e-52

Hepatitis C virus capsid protein;


Pssm-ID: 144947  Cd Length: 121  Bit Score: 162.56  E-value: 2.26e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1783581423   2 STFPKPQRQTKRNTPRRPQNVKFPGGGQIVGGVYVLPRRGPRLGVRAARKTSERSQPRGRRQPIPKARPSEGRSWAQPGY 81
Cdd:pfam01543   1 STNPKPQRKTKRNTNRRPQDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRRQPIPKARPPEGRSWLSPGT 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1783581423  82 PWP------LYGNEG-CGWAGWLLSPRGSRPSWGPNDPRRR 115
Cdd:pfam01543  81 LGPstamraLYGNDGsCGWAGWLLPPRGSRPSWGQNDPRRR 121
HCV_core pfam01542
Hepatitis C virus core protein; The viral core protein forms the internal viral coat that ...
 116-164 2.86e-12

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: 58.92  E-value: 2.86e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1783581423 116 SRNLGKVIDTLTCGFADLMGYIPLVGAPVGGVARALAHGVRALEDGVNY 164
Cdd:pfam01542   1 MRNLGKPIDKLKCGFADLMGDIKFPGAGLGGAARALAHGRGPLEDGRAT 49
 
Name Accession Description Interval E-value
HCV_capsid pfam01543
Hepatitis C virus capsid protein;
2-115 2.26e-52

Hepatitis C virus capsid protein;


Pssm-ID: 144947  Cd Length: 121  Bit Score: 162.56  E-value: 2.26e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1783581423   2 STFPKPQRQTKRNTPRRPQNVKFPGGGQIVGGVYVLPRRGPRLGVRAARKTSERSQPRGRRQPIPKARPSEGRSWAQPGY 81
Cdd:pfam01543   1 STNPKPQRKTKRNTNRRPQDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRRQPIPKARPPEGRSWLSPGT 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1783581423  82 PWP------LYGNEG-CGWAGWLLSPRGSRPSWGPNDPRRR 115
Cdd:pfam01543  81 LGPstamraLYGNDGsCGWAGWLLPPRGSRPSWGQNDPRRR 121
HCV_core pfam01542
Hepatitis C virus core protein; The viral core protein forms the internal viral coat that ...
 1-75 9.53e-23

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: 85.89  E-value: 9.53e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1783581423   1 MSTFPKPQRQTKRNTPRRPQNVKFPGGGQIVGGVYVLPRRGPRLGVRAARKTSERSQPRGRRQPIPKARPSEGRS 75
Cdd:pfam01542   1 MRNLGKPIDKLKCGFADLMGDIKFPGAGLGGAARALAHGRGPLEDGRATAKGNEPGCPFGIFLLALKACLPEGAS 75
HCV_core pfam01542
Hepatitis C virus core protein; The viral core protein forms the internal viral coat that ...
 116-164 2.86e-12

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: 58.92  E-value: 2.86e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1783581423 116 SRNLGKVIDTLTCGFADLMGYIPLVGAPVGGVARALAHGVRALEDGVNY 164
Cdd:pfam01542   1 MRNLGKPIDKLKCGFADLMGDIKFPGAGLGGAARALAHGRGPLEDGRAT 49
 
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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