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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 (505) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 26,955 50,061 13
Proteins 22,970 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 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.0000000000003658 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.0000001393 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.00000000000002124 Least Informative Direct
Biological Process (BP) response to stimulus 1 Least Informative Inherited
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 0.002433 Least Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.00002591 Moderately Informative Direct
Biological Process (BP) gene expression 0.000000000001311 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.00001788 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.00005626 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.001239 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.8326 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.5395 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.2916 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.1117 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.2628 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.1145 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.46 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.4598 Moderately Informative Inherited
Biological Process (BP) cellular developmental process 1 Moderately Informative Inherited
Biological Process (BP) response to temperature stimulus 0.0005608 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 0.000007164 Informative Direct
Biological Process (BP) negative regulation of gene expression 0.00002908 Informative Direct
Biological Process (BP) response to organic cyclic compound 0.0002444 Informative Direct
Biological Process (BP) regulation of cellular amide metabolic process 0.00000002495 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0.00000001287 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0.0000000002961 Informative Direct
Biological Process (BP) negative regulation of protein metabolic process 0.0004014 Informative Direct
Biological Process (BP) response to nitrogen compound 0.0008425 Informative Direct
Biological Process (BP) negative regulation of cellular biosynthetic process 0.05924 Informative Inherited
Biological Process (BP) negative regulation of macromolecule biosynthetic process 0.1131 Informative Inherited
Biological Process (BP) ncRNA processing 0.821 Informative Inherited
Biological Process (BP) RNA catabolic process 0.0000000123 Highly Informative Direct
Biological Process (BP) response to cold 0.000002733 Highly Informative Direct
Biological Process (BP) gene silencing 0.0000000000949 Highly Informative Direct
Biological Process (BP) negative regulation of cellular amide metabolic process 0.0000000001282 Highly Informative Direct
Biological Process (BP) regulation of gene expression, epigenetic 0.00000002788 Highly Informative Direct
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) binding 0.001182 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0 Moderately Informative Direct
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.36 Moderately Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.1933 Moderately Informative Inherited
Molecular Function (MF) RNA binding 0.000000000000001646 Informative Direct
Molecular Function (MF) nuclease activity 0.00005035 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0.0000003209 Informative Direct
Molecular Function (MF) DNA binding 1 Informative Inherited
Molecular Function (MF) single-stranded DNA binding 0.0000004349 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 0.0001809 Least Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0.04627 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) macromolecular complex 0.002924 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.01179 Least Informative Inherited
Cellular Component (CC) nuclear part 0.0000000005645 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.0000009407 Moderately Informative Direct
Cellular Component (CC) ribonucleoprotein granule 0.00000000469 Informative Direct
Cellular Component (CC) nucleoplasm part 0.1168 Informative Inherited
Cellular Component (CC) spliceosomal complex 0.0001027 Highly Informative Direct
Cellular Component (CC) pole plasm 0.00001308 Highly Informative Direct
Cellular Component (CC) nuclear body 0.9247 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

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organ system morphology variant0.006246Least InformativeInherited
Worm Phenotype (WP)reproductive system morphology variant0.000181Moderately InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details) Document: FP 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 helicase0.00008684InformativeDirect
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)HIV-2 retropepsin0.00003714Highly 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 processViral penetration into host nucleus0Highly InformativeDirect
Biological processViral genome integration0Highly InformativeDirect
Biological processVirus exit from host cell0Highly InformativeDirect
Biological processRNA-mediated gene silencing0.0000000000000507Highly InformativeDirect
Biological processModulation of host cell apoptosis by virus0.00000000001281Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentNucleus0.00000000000002819Least 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 termination0.0005876InformativeDirect
DiseaseAIDS0Moderately InformativeDirect
DomainRepeat0Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionLipid-binding0Moderately InformativeDirect
Post-translational modificationHydrolase4.405e-16Least InformativeDirect
Post-translational modificationTransferase0.0225Least 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 modificationEndonuclease0.00000000007428InformativeDirect
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 modificationMethylation0.0000001762Moderately 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) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · 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) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]