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Retrovirus zinc finger-like domains superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Small proteins [ 56992] (90)
Fold:   Retrovirus zinc finger-like domains [ 57755]
Superfamily:   Retrovirus zinc finger-like domains [ 57756]
Families:   Retrovirus zinc finger-like domains [ 57757] (5)


Superfamily statistics
Genomes (508) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 27,162 89,596 13
Proteins 23,131 79,775 12


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) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.00000000000002436 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.00000003879 Least Informative Direct
Biological Process (BP) primary metabolic process 0.001337 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) gene expression 0.0000000000000376 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.00005538 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.0001561 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 0.0002317 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.8361 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.2983 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.4444 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.8907 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.4446 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.001316 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.2534 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.106 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.1998 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.2549 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.4587 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 0.000000001474 Informative Direct
Biological Process (BP) regulation of cellular amide metabolic process 0.00000001799 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.00000004391 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 0.000005121 Informative Direct
Biological Process (BP) negative regulation of cellular protein metabolic process 0.000103 Informative Direct
Biological Process (BP) negative regulation of gene expression 0.0003348 Informative Direct
Biological Process (BP) response to organic cyclic compound 0.000532 Informative Direct
Biological Process (BP) positive regulation of macromolecule biosynthetic process 0.07674 Informative Inherited
Biological Process (BP) response to nitrogen compound 0.001714 Informative Inherited
Biological Process (BP) positive regulation of cellular biosynthetic process 0.04173 Informative Inherited
Biological Process (BP) positive regulation of gene expression 0.05997 Informative Inherited
Biological Process (BP) positive regulation of cellular protein metabolic process 0.2875 Informative Inherited
Biological Process (BP) negative regulation of cellular biosynthetic process 0.107 Informative Inherited
Biological Process (BP) ncRNA processing 0.9519 Informative Inherited
Biological Process (BP) negative regulation of macromolecule biosynthetic process 0.1222 Informative Inherited
Biological Process (BP) response to temperature stimulus 0.00119 Informative Inherited
Biological Process (BP) gene silencing 0.0000000001745 Highly Informative Direct
Biological Process (BP) negative regulation of translation 0.000000003187 Highly Informative Direct
Biological Process (BP) regulation of gene expression, epigenetic 0.00000002042 Highly Informative Direct
Biological Process (BP) RNA catabolic process 0.00000004342 Highly Informative Direct
Biological Process (BP) response to cold 0.000007678 Highly Informative Direct
Molecular Function (MF) binding 0.01101 Least Informative Inherited
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0 Moderately Informative Direct
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.4311 Moderately Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.2362 Moderately Informative Inherited
Molecular Function (MF) RNA binding 0 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0.0000006488 Informative Direct
Molecular Function (MF) nuclease activity 0.00006254 Informative Direct
Molecular Function (MF) macromolecular complex binding 0.1517 Informative Inherited
Molecular Function (MF) DNA binding 1 Informative Inherited
Molecular Function (MF) single-stranded DNA binding 0.0000006272 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 0.0001585 Least Informative Direct
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.05168 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.01314 Least Informative Inherited
Cellular Component (CC) nuclear part 0.00000001623 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.000002259 Moderately Informative Direct
Cellular Component (CC) ribonucleoprotein granule 0.000000008411 Informative Direct
Cellular Component (CC) nucleoplasm part 0.1255 Informative Inherited
Cellular Component (CC) pole plasm 0.00001556 Highly Informative Direct
Cellular Component (CC) spliceosomal complex 0.0001246 Highly Informative Direct
Cellular Component (CC) nuclear body 0.9466 Highly Informative Inherited

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)Acting on acid anhydrides1Least InformativeInherited
Enzyme Commission (EC)Endoribonucleases producing 5'-phosphomonoesters0Moderately InformativeDirect
Enzyme Commission (EC)DNA-directed DNA polymerase0Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides; involved in cellular an0.00002155Moderately InformativeDirect
Enzyme Commission (EC)Retroviral ribonuclease H0InformativeDirect
Enzyme Commission (EC)Exoribonuclease H0InformativeDirect
Enzyme Commission (EC)Aspartic endopeptidases0InformativeDirect
Enzyme Commission (EC)RNA-directed DNA polymerase0InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processHost-virus interaction0Moderately InformativeDirect
Biological processDNA recombination0InformativeDirect
Biological processmRNA processing0InformativeDirect
Biological processVirus entry into host cell0InformativeDirect
Biological processEukaryotic host gene expression shutoff by virus0InformativeDirect
Biological processDNA integration0Highly InformativeDirect
Biological processViral penetration into host nucleus0Highly InformativeDirect
Biological processViral genome integration0Highly InformativeDirect
Biological processVirus exit from host cell0Highly InformativeDirect
Biological processRNA-mediated gene silencing0.00000000000006282Highly InformativeDirect
Biological processModulation of host cell apoptosis by virus0.00000000001262Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentNucleus0.00000000000002165Least InformativeDirect
Cellular componentVirion0Moderately InformativeDirect
Cellular componentCapsid protein0InformativeDirect
Cellular componentSpliceosome0InformativeDirect
Cellular componentHost cytoplasm0InformativeDirect
Cellular componentHost membrane0InformativeDirect
Cellular componentHost nucleus0InformativeDirect
Cellular componentHost endosome0Highly InformativeDirect
Coding sequence diversityRibosomal frameshifting0Moderately InformativeDirect
Coding sequence diversityRNA suppression of termination0.0006389InformativeDirect
DiseaseAIDS0Moderately InformativeDirect
DomainRepeat0Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionLipid-binding0Moderately InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationTransferase0.02658Least InformativeInherited
Post-translational modificationDNA-binding0Moderately InformativeDirect
Post-translational modificationNuclease0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationProtease0Moderately InformativeDirect
Post-translational modificationRNA-binding0Moderately InformativeDirect
Post-translational modificationEndonuclease0.00000000007549InformativeDirect
Post-translational modificationAspartyl protease0Highly InformativeDirect
Post-translational modificationDNA-directed DNA polymerase0Highly InformativeDirect
Post-translational modificationViral nucleoprotein0Highly InformativeDirect
Post-translational modificationRNA-directed DNA polymerase0Highly InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationMethylation0.0000002139Moderately InformativeDirect
Post-translational modificationMyristate0InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-coverage) · 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 8 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 zinc finger-like 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 8 hidden Markov models representing the Retrovirus zinc finger-like 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 · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]