SUPERFAMILY 1.75 HMM library and genome assignments server


Retrovirus capsid dimerization domain-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   Acyl carrier protein-like [ 47335] (3)
Superfamily:   Retrovirus capsid dimerization domain-like [ 47353] (2)
Families:   Retrovirus capsid protein C-terminal domain [ 47354] (4)
  SCAN domain [ 140466] (2)


Superfamily statistics
Genomes (70) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 2,585 0 16
Proteins 2,578 0 16


Functional annotation
General category Other
Detailed category Viral proteins

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) regulation of metabolic process 1.307e-05 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.0003758 Least Informative Direct
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.5996 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.8846 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.7255 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.5695 Least Informative Inherited
Biological Process (BP) regulation of biosynthetic process 3.866e-12 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 5.451e-11 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 7.818e-05 Moderately Informative Direct
Biological Process (BP) homeostatic process 0.1866 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 1 Moderately Informative Inherited
Biological Process (BP) system process 0.1577 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.5025 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.2519 Moderately Informative Inherited
Biological Process (BP) regulation of cytokine production 0.0001 Informative Direct
Biological Process (BP) transmission of nerve impulse 0.003365 Informative Inherited
Biological Process (BP) chromosome organization 0.004697 Informative Inherited
Biological Process (BP) DNA metabolic process 0.003337 Informative Inherited
Biological Process (BP) regulation of cytokine biosynthetic process 1.92e-05 Highly Informative Direct
Biological Process (BP) regulation of membrane potential 0.0001954 Highly Informative Direct
Molecular Function (MF) binding 0.01672 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 5.611e-12 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding transcription factor activity 1.524e-11 Informative Direct
Molecular Function (MF) DNA binding 0 Informative Direct
Molecular Function (MF) sequence-specific DNA binding transcription factor activity 2.587e-12 Highly Informative Direct
Molecular Function (MF) protein binding transcription factor activity 0.001316 Highly Informative Inherited
Cellular Component (CC) intracellular organelle part 0.4359 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.05031 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.1193 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.0004763 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.107 Moderately Informative Inherited
Cellular Component (CC) chromosome 0.01344 Informative Inherited
Cellular Component (CC) nuclear chromosome part 0.0006014 Highly Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)0Least InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases0Least InformativeDirect
Enzyme Commission (EC)Acting on ester bonds0Least InformativeDirect
Enzyme Commission (EC)Endoribonucleases producing 5'-phosphomonoesters0Moderately InformativeDirect
Enzyme Commission (EC)DNA-directed DNA polymerase0Moderately InformativeDirect
Enzyme Commission (EC)Retroviral ribonuclease H0InformativeDirect
Enzyme Commission (EC)Aspartic endopeptidases0InformativeDirect
Enzyme Commission (EC)Exoribonuclease H0InformativeDirect
Enzyme Commission (EC)RNA-directed DNA polymerase0InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details) Document: DO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorous-containing groups0Least InformativeDirect
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)0Moderately InformativeDirect
Enzyme Commission (EC)DNA-directed DNA polymerase0InformativeDirect
Enzyme Commission (EC)Exoribonucleases producing 5'-phosphomonoesters0InformativeDirect
Enzyme Commission (EC)Endoribonucleases producing 5'-phosphomonoesters0InformativeDirect
Enzyme Commission (EC)RNA-directed DNA polymerase0Highly InformativeDirect
Enzyme Commission (EC)Exoribonuclease H0Highly InformativeDirect
Enzyme Commission (EC)Retroviral ribonuclease H0Highly InformativeDirect
Enzyme Commission (EC)HIV-1 retropepsin0Highly InformativeDirect
Enzyme Commission (EC)HIV-2 retropepsin3.226e-05Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation0Moderately InformativeDirect
Biological processHost-virus interaction0Moderately InformativeDirect
Biological processApoptosis0.0009816Moderately InformativeDirect
Biological processDNA recombination0InformativeDirect
Biological processVirus entry into host cell0InformativeDirect
Biological processEukaryotic host gene expression shutoff by virus0InformativeDirect
Biological processDNA integration0Highly InformativeDirect
Biological processModulation of host cell apoptosis by virus0Highly InformativeDirect
Biological processViral penetration into host nucleus0Highly InformativeDirect
Biological processViral genome integration0Highly InformativeDirect
Biological processVirus exit from host cell0Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentMembrane1.78e-12Least InformativeDirect
Cellular componentCapsid protein0InformativeDirect
Cellular componentHost cytoplasm0InformativeDirect
Cellular componentHost membrane0InformativeDirect
Cellular componentHost nucleus0InformativeDirect
Cellular componentChromosome0.011InformativeInherited
Cellular componentTelomere6.322e-10Highly InformativeDirect
Coding sequence diversityRibosomal frameshifting0Moderately InformativeDirect
DiseaseAIDS0Moderately InformativeDirect
DomainRepeat0Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionDNA-binding0Moderately InformativeDirect
Molecular functionRNA-binding0Moderately InformativeDirect
Molecular functionMagnesium1.782e-08Moderately InformativeDirect
Molecular functionViral nucleoprotein0Highly InformativeDirect
Post-translational modificationHydrolase3.635e-10Least InformativeDirect
Post-translational modificationTransferase0.06864Least InformativeInherited
Post-translational modificationNuclease0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationProtease0Moderately InformativeDirect
Post-translational modificationRepressor2.01e-10Moderately InformativeDirect
Post-translational modificationDNA-directed DNA polymerase0InformativeDirect
Post-translational modificationEndonuclease0InformativeDirect
Post-translational modificationAspartyl protease0Highly InformativeDirect
Post-translational modificationRNA-directed DNA polymerase0Highly InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationMethylation1.227e-12Moderately InformativeDirect
Post-translational modificationMyristate0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR008916 SSF47353 Protein matches
Abstract

The Gag polyprotein from retroviruses is processed by viral protease to produce the major structural proteins, including the capsid protein. The newly formed capsid protein rearranges to form the capsid core particle that surrounds the viral genome of the mature virus. The capsid is composed of two domains, the N-terminal domain (NTD), which contributes to viral core formation, and the C-terminal domain (CTD), which is required for capsid dimerisation, Gag oligomerization and viral formation. The CTD contains the major homology region (MHR), a stretch of 20 amino acids that is conserved across retroviruses and is essential for viral assembly, maturation and infectivity. The CTD is composed of a bundle of four helices in an up and down arrangement, where helix 3 is shorter than the others [PubMed9346481, PubMed9931251, PubMed10669613].


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Disease Ontology (DO) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 7 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a Retrovirus capsid dimerization domain-like domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 7 hidden Markov models representing the Retrovirus capsid dimerization domain-like superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Disease Ontology (DO) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]