SUPERFAMILY 1.75 HMM library and genome assignments server


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 (448) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 23,349 40,381 13
Proteins 19,819 37,336 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) heterocycle metabolic process 3.749e-15 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 5.591e-15 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 1.946e-13 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 1.69e-11 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 2.608e-10 Least Informative Direct
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) developmental process 0.2057 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.8643 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.6655 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.01453 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) RNA metabolic process 3.749e-15 Moderately Informative Direct
Biological Process (BP) gene expression 6.999e-10 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 5.262e-05 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.0009481 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.0636 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.2491 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.2661 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.00808 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.09939 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.3952 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.01405 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound catabolic process 0.009102 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.01141 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) RNA processing 1.126e-11 Informative Direct
Biological Process (BP) cellular response to nitrogen compound 1.888e-11 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 2.309e-08 Informative Direct
Biological Process (BP) response to organic cyclic compound 7.689e-08 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 1.572e-06 Informative Direct
Biological Process (BP) negative regulation of gene expression 0.000568 Informative Direct
Biological Process (BP) negative regulation of developmental process 0.001656 Informative Inherited
Biological Process (BP) ncRNA metabolic process 0.1176 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0.04665 Informative Inherited
Biological Process (BP) DNA metabolic process 0.1707 Informative Inherited
Biological Process (BP) gene silencing 0 Highly Informative Direct
Biological Process (BP) regulation of gene expression, epigenetic 2.447e-14 Highly Informative Direct
Biological Process (BP) cellular response to organic cyclic compound 1.63e-12 Highly Informative Direct
Biological Process (BP) RNA catabolic process 2.805e-10 Highly Informative Direct
Biological Process (BP) response to cold 1.109e-06 Highly Informative Direct
Biological Process (BP) stem cell development 3.59e-05 Highly Informative Direct
Biological Process (BP) DNA replication 7.604e-05 Highly Informative Direct
Biological Process (BP) negative regulation of cell differentiation 0.0001242 Highly Informative Direct
Biological Process (BP) RNA splicing 0.3291 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) binding 0.1191 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0.0001861 Moderately Informative Direct
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.2023 Moderately Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.4908 Moderately Informative Inherited
Molecular Function (MF) RNA binding 1.781e-08 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 1.959e-08 Informative Direct
Molecular Function (MF) nuclease activity 0.00146 Informative Inherited
Molecular Function (MF) nucleoside-triphosphatase activity 0.3622 Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.01959 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 organelle part 0.002437 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.2567 Least Informative Inherited
Cellular Component (CC) ribonucleoprotein complex 2.157e-12 Moderately Informative Direct
Cellular Component (CC) nuclear part 1.084e-07 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.005719 Moderately Informative Inherited
Cellular Component (CC) nucleoplasm part 0.6935 Informative Inherited
Cellular Component (CC) cytoplasmic mRNA processing body 3.934e-13 Highly Informative Direct
Cellular Component (CC) spliceosomal complex 0.0004979 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 an2.155e-05Moderately 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) 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)nervous system0Least InformativeDirect
Zebrafish Anatomy (ZA)trunk0Least InformativeDirect

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0Least InformativeDirect
Xenopus ANatomical entity (XAN)gamete0Moderately InformativeDirect

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 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 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 helicase0.0001989InformativeDirect
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 uridylyltransferase9.55e-08Highly InformativeDirect
Enzyme Commission (EC)HIV-2 retropepsin3.225e-05Highly 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 processVirus entry into host cell0InformativeDirect
Biological processHost 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 silencing6.862e-15Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentNucleus2.604e-09Least 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 termination0.0006945InformativeDirect
DiseaseAIDS0Moderately InformativeDirect
DomainRepeat0Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionRNA-binding0Moderately InformativeDirect
Molecular functionMagnesium4.054e-09Moderately InformativeDirect
Molecular functionViral nucleoprotein0Highly InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationTransferase0.02058Least InformativeInherited
Post-translational modificationNuclease0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationProtease0Moderately InformativeDirect
Post-translational modificationDNA-directed DNA polymerase0InformativeDirect
Post-translational modificationEndonuclease7.572e-11InformativeDirect
Post-translational modificationAspartyl protease0Highly InformativeDirect
Post-translational modificationRNA-directed DNA polymerase0Highly InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationMethylation1.42e-08Moderately 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 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) · 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 ]