SUPERFAMILY 1.75 HMM library and genome assignments server

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 (102) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 131 74,413 163
Proteins 131 68,160 157


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 cellular process 0 Least Informative Direct
Biological Process (BP) response to stimulus 0 Least Informative Direct
Biological Process (BP) protein metabolic process 0 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0.00000001204 Least Informative Direct
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) multi-organism process 0 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0 Moderately Informative Direct
Biological Process (BP) positive regulation of metabolic process 0 Moderately Informative Direct
Biological Process (BP) regulation of biological quality 0 Moderately Informative Direct
Biological Process (BP) regulation of localization 0 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0.000000000000003755 Moderately Informative Direct
Biological Process (BP) regulation of signal transduction 0.000000000000007347 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 0.000000000007383 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0.0000000004663 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.000004572 Moderately Informative Direct
Biological Process (BP) response to abiotic stimulus 1 Moderately Informative Inherited
Biological Process (BP) signal transduction 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.009441 Moderately Informative Inherited
Biological Process (BP) organ development 0.9028 Moderately Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0 Informative Direct
Biological Process (BP) negative regulation of signaling 0 Informative Direct
Biological Process (BP) regulation of immune response 0 Informative Direct
Biological Process (BP) negative regulation of immune system process 0 Informative Direct
Biological Process (BP) proteolysis 0 Informative Direct
Biological Process (BP) regulation of cellular catabolic process 0 Informative Direct
Biological Process (BP) regulation of defense response 0 Informative Direct
Biological Process (BP) regulation of immune effector process 0 Informative Direct
Biological Process (BP) negative regulation of cell communication 0 Informative Direct
Biological Process (BP) negative regulation of gene expression 0 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 0 Informative Direct
Biological Process (BP) defense response 0 Informative Direct
Biological Process (BP) regulation of intracellular transport 0 Informative Direct
Biological Process (BP) embryonic organ development 0.0002105 Informative Direct
Biological Process (BP) embryo development ending in birth or egg hatching 0.003382 Informative Inherited
Biological Process (BP) negative regulation of immune effector process 0 Highly Informative Direct
Biological Process (BP) negative regulation of immune response 0 Highly Informative Direct
Biological Process (BP) regulation of multi-organism process 0 Highly Informative Direct
Biological Process (BP) interaction with host 0 Highly Informative Direct
Biological Process (BP) regulation of autophagy 0 Highly Informative Direct
Biological Process (BP) modification of morphology or physiology of other organism involved in symbiotic interaction 0 Highly Informative Direct
Biological Process (BP) positive regulation of catabolic process 0 Highly Informative Direct
Biological Process (BP) multi-organism cellular process 0 Highly Informative Direct
Biological Process (BP) regulation of translation 0 Highly Informative Direct
Biological Process (BP) response to toxic substance 0.00000002037 Highly Informative Direct
Biological Process (BP) placenta development 0.00000008359 Highly Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) protein dimerization activity 0.0001784 Informative Direct
Molecular Function (MF) receptor activity 0.01712 Informative Inherited
Molecular Function (MF) molecular transducer activity 0.02142 Informative Inherited
Molecular Function (MF) protein heterodimerization activity 0.00000004533 Highly Informative Direct
Molecular Function (MF) transcription factor binding transcription factor activity 0.00000374 Highly Informative Direct
Cellular Component (CC) protein complex 0.9641 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.1616 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.3534 Moderately Informative Inherited
Cellular Component (CC) nucleoplasm part 0.004093 Informative Inherited

Document: GO annotation of SCOP domains

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)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)Acting on acid anhydrides0Moderately InformativeDirect
Enzyme Commission (EC)RNA-directed RNA polymerase0InformativeDirect
Enzyme Commission (EC)Cysteine endopeptidases0InformativeDirect
Enzyme Commission (EC)In phosphorous-containing anhydrides0InformativeDirect
Enzyme Commission (EC)Picornain 3C0Highly InformativeDirect
Enzyme Commission (EC)Picornain 2A0Highly InformativeDirect
Enzyme Commission (EC)Nucleoside-triphosphate phosphatase0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processIon transport0Moderately InformativeDirect
Biological processHost-virus interaction0Moderately InformativeDirect
Biological processViral immunoevasion0InformativeDirect
Biological processViral RNA replication0InformativeDirect
Biological processVirus entry into host cell0InformativeDirect
Biological processDNA replication0InformativeDirect
Biological processEukaryotic host gene expression shutoff by virus0InformativeDirect
Biological processActivation of host autophagy by virus0Highly InformativeDirect
Cellular componentMembrane0.003775Least InformativeInherited
Cellular componentHost membrane0InformativeDirect
Cellular componentHost cytoplasm0InformativeDirect
Cellular componentCapsid protein0InformativeDirect
Cellular componentHost nucleus0.000000009793InformativeDirect
Cellular componentHost cytoplasmic vesicle0Highly InformativeDirect
Coding sequence diversityAlternative promoter usage0Moderately InformativeDirect
Coding sequence diversityAlternative initiation0.00000000000305Moderately InformativeDirect
DomainRepeat0.0000002696Least InformativeDirect
Molecular functionNucleotide-binding0.0000002321Least InformativeDirect
Molecular functionRNA-binding0Moderately InformativeDirect
Molecular functionViral nucleoprotein0Highly InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationTransferase0.00000000001916Least InformativeDirect
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationProtease0Moderately InformativeDirect
Post-translational modificationIon channel0InformativeDirect
Post-translational modificationThiol protease0InformativeDirect
Post-translational modificationHelicase0InformativeDirect
Post-translational modificationRNA-directed RNA polymerase0Highly InformativeDirect
Post-translational modificationViral ion channel0Highly InformativeDirect
Post-translational modificationPhosphoprotein0.00000000000004469Least InformativeDirect
Post-translational modificationMyristate0InformativeDirect
Post-translational modificationCovalent protein-RNA linkage0Highly InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-coverage) · 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 90 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 90 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 · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]