SUPERFAMILY 1.75 HMM library and genome assignments server

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Positive stranded ssRNA viruses superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Nucleoplasmin-like/VP (viral coat and capsid proteins) [ 88632] (7)
Superfamily:   Positive stranded ssRNA viruses [ 88633] (9)
Families:   Picornaviridae-like VP (VP1, VP2, VP3 and VP4) [ 88634] (9)
  Comoviridae-like VP [ 88636] (2)
  Caliciviridae-like VP [ 88637]
  Nodaviridae-like VP [ 88638]
  Tetraviridae-like VP [ 101568]
  Bromoviridae-like VP [ 88639]
  Tymoviridae-like VP [ 88641]
  Tombusviridae-like VP [ 88643] (4)
  Birnaviridae-like VP [ 141109]


Superfamily statistics
Genomes (103) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 146 130,788 163
Proteins 141 118,151 157


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)Nucleotidyltransferases0Least InformativeDirect
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)0Least InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0Least InformativeDirect
Enzyme Commission (EC)In phosphorous-containing anhydrides0Moderately InformativeDirect
Enzyme Commission (EC)Cysteine endopeptidases0Moderately InformativeDirect
Enzyme Commission (EC)Nucleoside-triphosphatase0InformativeDirect
Enzyme Commission (EC)RNA-directed RNA polymerase0InformativeDirect
Enzyme Commission (EC)Aspartic endopeptidases0.1627InformativeInherited
Enzyme Commission (EC)Picornain 3C0Highly InformativeDirect
Enzyme Commission (EC)Picornain 2A0Highly InformativeDirect
Enzyme Commission (EC)Calicivirin0.0006718Highly InformativeDirect

Document: EC annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Transferring phosphorus-containing groups0Least InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0Moderately InformativeDirect
Enzyme Commission (EC)Acting on peptide bonds (peptidases)0Moderately InformativeDirect
Enzyme Commission (EC)In phosphorus-containing anhydrides0InformativeDirect
Enzyme Commission (EC)Cysteine endopeptidases0InformativeDirect
Enzyme Commission (EC)RNA-directed RNA polymerase0InformativeDirect
Enzyme Commission (EC)RNA helicase0.000000000000004493InformativeDirect
Enzyme Commission (EC)Nucleoside-triphosphate phosphatase0Highly InformativeDirect
Enzyme Commission (EC)Picornain 3C0Highly InformativeDirect

Document: EC annotation of SCOP domains

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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 126 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 Positive stranded ssRNA viruses 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 126 hidden Markov models representing the Positive stranded ssRNA viruses 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 · Functional annotation · Enzyme Commission (EC) · Enzyme Commission (EC) · Internal database links ]