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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 (501) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 26,755 50,061 13
Proteins 22,786 45,592 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) cellular aromatic compound metabolic process 0.00000000000005973 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.0000000000001359 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.000000000001506 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.00000000002431 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.0000007504 Least Informative Direct
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.00449 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) gene expression 0.00000000002592 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.00005666 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.0004838 Moderately Informative Direct
Biological Process (BP) cellular response to chemical stimulus 0.1952 Moderately Informative Inherited
Biological Process (BP) regulation of nitrogen compound metabolic process 0.005744 Moderately Informative Inherited
Biological Process (BP) regulation of cellular metabolic process 0.01119 Moderately Informative Inherited
Biological Process (BP) regulation of biosynthetic process 0.06925 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.1848 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.188 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.001617 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.4588 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.003089 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.4008 Moderately Informative Inherited
Biological Process (BP) response to stress 1 Moderately Informative Inherited
Biological Process (BP) cellular developmental process 0.5193 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 0.00000001989 Informative Direct
Biological Process (BP) regulation of cellular amide metabolic process 0.00000002278 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 0.0000004253 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.0000004494 Informative Direct
Biological Process (BP) negative regulation of cellular protein metabolic process 0.0001476 Informative Direct
Biological Process (BP) response to organic cyclic compound 0.0001587 Informative Direct
Biological Process (BP) response to nitrogen compound 0.0002605 Informative Direct
Biological Process (BP) response to temperature stimulus 0.0004288 Informative Direct
Biological Process (BP) negative regulation of gene expression 0.001735 Informative Inherited
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.002821 Informative Inherited
Biological Process (BP) ncRNA processing 0.9097 Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.08681 Informative Inherited
Biological Process (BP) gene silencing 0.00000000005152 Highly Informative Direct
Biological Process (BP) negative regulation of translation 0.0000000001618 Highly Informative Direct
Biological Process (BP) regulation of gene expression, epigenetic 0.000000001798 Highly Informative Direct
Biological Process (BP) RNA catabolic process 0.00000008871 Highly Informative Direct
Biological Process (BP) response to cold 0.000002071 Highly Informative Direct
Biological Process (BP) mRNA metabolic process 0.000238 Highly Informative Direct
Molecular Function (MF) transferase activity 0.9896 Least Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) binding 0.002924 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0.0000005633 Moderately Informative Direct
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.3506 Moderately Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.6515 Moderately Informative Inherited
Molecular Function (MF) hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides 0.6344 Moderately Informative Inherited
Molecular Function (MF) RNA binding 0.0000000000001417 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0.0000003118 Informative Direct
Molecular Function (MF) nuclease activity 0.005985 Informative Inherited
Molecular Function (MF) DNA binding 1 Informative Inherited
Molecular Function (MF) single-stranded DNA binding 0.0000003065 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 0.0005273 Least Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0.05012 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.01449 Least Informative Inherited
Cellular Component (CC) nuclear part 0.000000002013 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.000005306 Moderately Informative Direct
Cellular Component (CC) ribonucleoprotein granule 0.000000001016 Informative Direct
Cellular Component (CC) nucleoplasm part 0.01343 Informative Inherited
Cellular Component (CC) pole plasm 0.00001347 Highly Informative Direct
Cellular Component (CC) spliceosomal complex 0.00007773 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)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

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)mortality/aging0Least InformativeDirect
Mammalian Phenotype (MP)growth/size/body region phenotype0.01181Least InformativeInherited
Mammalian Phenotype (MP)abnormal prenatal growth/weight/body size0.02404InformativeInherited
Mammalian Phenotype (MP)abnormal embryonic growth/weight/body size0.0007912Highly InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organ system morphology variant0.004328Least InformativeInherited
Worm Phenotype (WP)reproductive system morphology variant0.0001821Moderately InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)cell0Least InformativeDirect

Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)organism subdivision0Least InformativeDirect

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details) Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorus-containing groups0Least InformativeDirect
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Acting on peptide bonds (peptidases)0Moderately InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides1Moderately InformativeInherited
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 helicase0.000215InformativeDirect
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)RNA uridylyltransferase0.0000004333Highly InformativeDirect
Enzyme Commission (EC)HIV-2 retropepsin0.00002967Highly InformativeDirect

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 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
Biological processRNA-mediated gene silencing0.00000000000004182Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentNucleus0.0000000000002176Least 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 termination0.0005593InformativeDirect
DiseaseAIDS0Moderately InformativeDirect
DomainRepeat0Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionLipid-binding0Moderately InformativeDirect
Molecular functionRNA-binding0Moderately InformativeDirect
Molecular functionMagnesium0.000001544Moderately InformativeDirect
Molecular functionViral nucleoprotein0Highly InformativeDirect
Post-translational modificationHydrolase8.974e-16Least InformativeDirect
Post-translational modificationTransferase0.0257Least InformativeInherited
Post-translational modificationNuclease0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationProtease0Moderately InformativeDirect
Post-translational modificationDNA-directed DNA polymerase0InformativeDirect
Post-translational modificationEndonuclease0.00000000007428InformativeDirect
Post-translational modificationAspartyl protease0Highly InformativeDirect
Post-translational modificationRNA-directed DNA polymerase0Highly InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationMethylation0.0000001399Moderately 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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · 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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]