SUPERFAMILY 1.75 HMM library and genome assignments server


Viral glycoprotein, central and dimerisation domains superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Membrane and cell surface proteins and peptides [ 56835] (58)
Fold:   Viral glycoprotein, central and dimerisation domains [ 56982]
Superfamily:   Viral glycoprotein, central and dimerisation domains [ 56983]
Families:   Viral glycoprotein, central and dimerisation domains [ 56984] (2)


Superfamily statistics
Genomes (0) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 0 16,539 9
Proteins 0 16,537 9


Functional annotation
General category Other
Detailed category Viral proteins

Document:
Function annotation of SCOP domain superfamilies

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)Transferring one-carbon groups0Least InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides4.925e-10Least InformativeDirect
Enzyme Commission (EC)In phosphorous-containing anhydrides0Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides; involved in cellular an0Moderately InformativeDirect
Enzyme Commission (EC)Serine endopeptidases0Moderately InformativeDirect
Enzyme Commission (EC)Methyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Nucleoside-triphosphatase0InformativeDirect
Enzyme Commission (EC)mRNA (nucleoside-2'-O-)-methyltransferase0InformativeDirect
Enzyme Commission (EC)mRNA (guanine-N(7)-)-methyltransferase0InformativeDirect
Enzyme Commission (EC)RNA-directed RNA polymerase0InformativeDirect
Enzyme Commission (EC)Flavivirin0InformativeDirect
Enzyme Commission (EC)Togavirin0Highly InformativeDirect

Document: EC 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)Acting on peptide bonds (peptide hydrolases)0Moderately InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Transferring one-carbon groups0Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides3.625e-10Moderately InformativeDirect
Enzyme Commission (EC)In phosphorous-containing anhydrides0InformativeDirect
Enzyme Commission (EC)RNA helicase0InformativeDirect
Enzyme Commission (EC)RNA-directed RNA polymerase0InformativeDirect
Enzyme Commission (EC)Serine endopeptidases0InformativeDirect
Enzyme Commission (EC)Nucleoside-triphosphate phosphatase0Highly InformativeDirect
Enzyme Commission (EC)Methyltransferase cap10Highly InformativeDirect
Enzyme Commission (EC)mRNA (guanine-N(7)-)-methyltransferase0Highly InformativeDirect
Enzyme Commission (EC)Flavivirin0Highly 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 processViral RNA replication0InformativeDirect
Biological processVirus entry into host cell0InformativeDirect
Biological processViral immunoevasion3.794e-05InformativeDirect
Biological processmRNA capping0Highly InformativeDirect
Biological processClathrin-mediated endocytosis of virus by host0Highly InformativeDirect
Biological processActivation of host autophagy by virus0Highly InformativeDirect
Biological processFusion of virus membrane with host endosomal membrane0Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentHost membrane0InformativeDirect
Cellular componentHost cytoplasm0InformativeDirect
Cellular componentHost nucleus0InformativeDirect
Cellular componentCapsid protein0InformativeDirect
Cellular componentHost endoplasmic reticulum0Highly InformativeDirect
Cellular componentViral envelope protein0Highly InformativeDirect
DomainTransmembrane0Least InformativeDirect
Molecular functionNucleotide-binding1.393e-09Least InformativeDirect
Molecular functionMetal-binding8.297e-07Least InformativeDirect
Molecular functionRNA-binding0Moderately InformativeDirect
Molecular functionATP-binding2.723e-12Moderately InformativeDirect
Molecular functionS-adenosyl-L-methionine0InformativeDirect
Molecular functionViral nucleoprotein4.091e-14Highly InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationTransferase6.55e-09Least InformativeDirect
Post-translational modificationProtease0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationMethyltransferase0InformativeDirect
Post-translational modificationHelicase0InformativeDirect
Post-translational modificationSerine protease0InformativeDirect
Post-translational modificationRNA-directed RNA polymerase0Highly InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect
Post-translational modificationPalmitate0Moderately InformativeDirect
Post-translational modificationCleavage on pair of basic residues0Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR011998 SSF56983 Protein matches
Abstract

Flaviviruses and alphaviruses are arthropod-borne, enveloped RNA viruses that cause infections in vertebrate hosts [PubMed15378043]. These viruses have two envelope glycoproteins (also known as ┐spike┐ glycoproteins), one that undergoes proteolytic cleavage to prime the virus (glycoproteins M and P62 in flaviviruses and alphaviruses, respectively), and the other to mediate receptor binding and fusion (glycoproteins E and E1 in flaviviruses and alphaviruses, respectively). Glycoprotein E/E1 is comprised of three domains: domain I (dimerisation domain) is a beta-barrel, domain II (central domain) is an elongated beta-stranded and alpha-helical domain, and domain III (immunoglobulin-like domain) is an IgC-like beta-sandwich. This entry represents the intertwined central and dimerisation domains found in flaviviral glycoprotein E [PubMed12759475] and alphaviral glycoprotein E1 [PubMed11301009] proteins.


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 · Enzyme Commission (EC) · 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 3 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 Viral glycoprotein, central and dimerisation domains 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 3 hidden Markov models representing the Viral glycoprotein, central and dimerisation domains 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 · Enzyme Commission (EC) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]