NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1770804723|gb|QCF42099|]
View 

polyprotein, partial [dengue virus type 4]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
Flavi_capsid super family cl03064
Flavivirus capsid protein C; Flaviviruses are small enveloped viruses with virions comprised ...
 1-95 2.06e-27

Flavivirus capsid protein C; Flaviviruses are small enveloped viruses with virions comprised of 3 proteins called C, M and E. Multiple copies of the C protein form the nucleocapsid, which contains the ssRNA molecule.


The actual alignment was detected with superfamily member pfam01003:

Pssm-ID: 366413  Cd Length: 117  Bit Score: 97.01  E-value: 2.06e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1770804723   1 RNRVSTPQGLVKRFSTGLFSGKGPLRMVLAFITFLRVLSIPPTAGILKRWGQLKKNKAIKILTGFRKEIGRMLNILNGRK 80
Cdd:pfam01003  14 RGAKRVPLKKTKRKTGQLLDGRGPLRLVLAFLAFFRFTAIAPTPGLKKRWRTVPKRQAIKHLRKFKKEVGTLLDGLNRRG 93

                          90       100
                  ....*....|....*....|....
gi 1770804723  81 R---------STMTLLCLIPTIMA 95
Cdd:pfam01003  94 KrrskrggwtGLLLMLGLLTLVLA 117
 
Name Accession Description Interval E-value
Flavi_capsid pfam01003
Flavivirus capsid protein C; Flaviviruses are small enveloped viruses with virions comprised ...
 1-95 2.06e-27

Flavivirus capsid protein C; Flaviviruses are small enveloped viruses with virions comprised of 3 proteins called C, M and E. Multiple copies of the C protein form the nucleocapsid, which contains the ssRNA molecule.


Pssm-ID: 366413  Cd Length: 117  Bit Score: 97.01  E-value: 2.06e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1770804723   1 RNRVSTPQGLVKRFSTGLFSGKGPLRMVLAFITFLRVLSIPPTAGILKRWGQLKKNKAIKILTGFRKEIGRMLNILNGRK 80
Cdd:pfam01003  14 RGAKRVPLKKTKRKTGQLLDGRGPLRLVLAFLAFFRFTAIAPTPGLKKRWRTVPKRQAIKHLRKFKKEVGTLLDGLNRRG 93

                          90       100
                  ....*....|....*....|....
gi 1770804723  81 R---------STMTLLCLIPTIMA 95
Cdd:pfam01003  94 KrrskrggwtGLLLMLGLLTLVLA 117
 
Name Accession Description Interval E-value
Flavi_capsid pfam01003
Flavivirus capsid protein C; Flaviviruses are small enveloped viruses with virions comprised ...
 1-95 2.06e-27

Flavivirus capsid protein C; Flaviviruses are small enveloped viruses with virions comprised of 3 proteins called C, M and E. Multiple copies of the C protein form the nucleocapsid, which contains the ssRNA molecule.


Pssm-ID: 366413  Cd Length: 117  Bit Score: 97.01  E-value: 2.06e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1770804723   1 RNRVSTPQGLVKRFSTGLFSGKGPLRMVLAFITFLRVLSIPPTAGILKRWGQLKKNKAIKILTGFRKEIGRMLNILNGRK 80
Cdd:pfam01003  14 RGAKRVPLKKTKRKTGQLLDGRGPLRLVLAFLAFFRFTAIAPTPGLKKRWRTVPKRQAIKHLRKFKKEVGTLLDGLNRRG 93

                          90       100
                  ....*....|....*....|....
gi 1770804723  81 R---------STMTLLCLIPTIMA 95
Cdd:pfam01003  94 KrrskrggwtGLLLMLGLLTLVLA 117
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH