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Acid proteases superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Acid proteases [ 50629]
Superfamily:   Acid proteases [ 50630] (3)
Families:   Retroviral protease (retropepsin) [ 50631] (8)
  Pepsin-like [ 50646] (10)
  LPG0085-like [ 159190]


Superfamily statistics
Genomes (1,257) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 23,297 303,877 136
Proteins 22,823 301,921 133


Functional annotation
General category Processes_IC
Detailed category Proteases

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)macromolecule metabolic process0.000000012220.0000005125Least InformativeDirect
Biological Process (BP)organonitrogen compound metabolic process0.0000070550.00000005722Least InformativeDirect
Biological Process (BP)biological regulation0.04371Least InformativeInherited
Biological Process (BP)primary metabolic process0.0035840.01127Least InformativeInherited
Biological Process (BP)response to stimulus0.21781Least InformativeInherited
Biological Process (BP)multicellular organismal process0.000000000074390.9292Least InformativeInherited
Biological Process (BP)response to biotic stimulus0.00027260.0001775Moderately InformativeDirect
Biological Process (BP)animal organ development0.00002251Moderately InformativeInherited
Biological Process (BP)tissue development0.000054530.8872Moderately InformativeInherited
Biological Process (BP)immune system process0.00028170.0891Moderately InformativeInherited
Biological Process (BP)regulation of biological quality0.0000069940.6536Moderately InformativeInherited
Biological Process (BP)proteolysis00InformativeDirect
Biological Process (BP)epithelium development0.000000028810.1703InformativeInherited
Biological Process (BP)anatomical structure homeostasis00.00000004437Highly InformativeDirect
Biological Process (BP)multicellular organismal homeostasis0.0000000000097460.000000002121Highly InformativeDirect
Biological Process (BP)camera-type eye development0.000000011070.003332Highly InformativeInherited
Molecular Function (MF)hydrolase activity00Least InformativeDirect
Molecular Function (MF)peptidase activity, acting on L-amino acid peptides0.063880.172InformativeInherited
Cellular Component (CC)cytoplasmic part0.0064990.1802Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle11Least InformativeInherited
Cellular Component (CC)vacuole00Moderately InformativeDirect
Cellular Component (CC)vesicle0.0000000000000077290.0000000008711Moderately InformativeDirect
Cellular Component (CC)endomembrane system0.0000000000008860.000000003348Moderately InformativeDirect
Cellular Component (CC)extracellular region part0.000000000022360.0002147Moderately InformativeDirect
Cellular Component (CC)lytic vacuole00.00003041InformativeDirect
Cellular Component (CC)secretory granule0.00000041430.0000193InformativeDirect
Cellular Component (CC)endosome0.000087650.001814InformativeInherited
Cellular Component (CC)alveolar lamellar body00Highly InformativeDirect
Cellular Component (CC)late endosome0.68780.4751Highly InformativeInherited

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) macromolecule metabolic process 0.0000005125 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0.00000005722 Least Informative Direct
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.01127 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.9292 Least Informative Inherited
Biological Process (BP) response to biotic stimulus 0.0001775 Moderately Informative Direct
Biological Process (BP) response to external stimulus 0.1054 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.003119 Moderately Informative Inherited
Biological Process (BP) animal organ development 1 Moderately Informative Inherited
Biological Process (BP) gene expression 1 Moderately Informative Inherited
Biological Process (BP) peptide metabolic process 0.02677 Moderately Informative Inherited
Biological Process (BP) tissue development 0.8872 Moderately Informative Inherited
Biological Process (BP) immune system process 0.0891 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.6536 Moderately Informative Inherited
Biological Process (BP) proteolysis 0 Informative Direct
Biological Process (BP) interspecies interaction between organisms 0.06353 Informative Inherited
Biological Process (BP) epithelium development 0.1703 Informative Inherited
Biological Process (BP) anatomical structure homeostasis 0.00000004437 Highly Informative Direct
Biological Process (BP) multicellular organismal homeostasis 0.000000002121 Highly Informative Direct
Biological Process (BP) protein maturation 0.000001313 Highly Informative Direct
Biological Process (BP) multi-organism cellular process 0.0001348 Highly Informative Direct
Biological Process (BP) modification of morphology or physiology of other organism involved in symbiotic interaction 0.1656 Highly Informative Inherited
Biological Process (BP) biological adhesion 0.01914 Highly Informative Inherited
Biological Process (BP) camera-type eye development 0.003332 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0 Least Informative Direct
Molecular Function (MF) peptidase activity, acting on L-amino acid peptides 0.172 Informative Inherited
Cellular Component (CC) membrane 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.1802 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) vacuole 0 Moderately Informative Direct
Cellular Component (CC) vesicle 0.0000000008711 Moderately Informative Direct
Cellular Component (CC) endomembrane system 0.000000003348 Moderately Informative Direct
Cellular Component (CC) extracellular region part 0.0002147 Moderately Informative Direct
Cellular Component (CC) intrinsic component of membrane 0.00529 Moderately Informative Inherited
Cellular Component (CC) plasma membrane 1 Moderately Informative Inherited
Cellular Component (CC) lytic vacuole 0.00003041 Informative Direct
Cellular Component (CC) secretory granule 0.0000193 Informative Direct
Cellular Component (CC) external encapsulating structure 0.0000000003931 Informative Direct
Cellular Component (CC) Golgi apparatus 0.005808 Informative Inherited
Cellular Component (CC) endosome 0.001814 Informative Inherited
Cellular Component (CC) alveolar lamellar body 0 Highly Informative Direct
Cellular Component (CC) anchored component of membrane 0 Highly Informative Direct
Cellular Component (CC) plant-type cell wall 0.000004979 Highly Informative Direct
Cellular Component (CC) intrinsic component of plasma membrane 0.535 Highly Informative Inherited
Cellular Component (CC) Golgi subcompartment 0.01379 Highly Informative Inherited
Cellular Component (CC) late endosome 0.4751 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)Nucleotidyltransferases0Least InformativeDirect
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)0Least InformativeDirect
Enzyme Commission (EC)Acting on ester bonds0.000008641Least 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)In phosphorous-containing anhydrides0.006219Moderately InformativeInherited
Enzyme Commission (EC)Retroviral ribonuclease H0InformativeDirect
Enzyme Commission (EC)RNA-directed DNA polymerase0InformativeDirect
Enzyme Commission (EC)Exoribonuclease H0InformativeDirect
Enzyme Commission (EC)Aspartic endopeptidases0InformativeDirect
Enzyme Commission (EC)dUTP diphosphatase0.000000001981Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport1Least InformativeInherited
Biological processVirulence0Moderately InformativeDirect
Biological processHost-virus interaction0Moderately InformativeDirect
Biological processProtein transport0.00003992Moderately InformativeDirect
Biological processDNA recombination0InformativeDirect
Biological processEukaryotic host gene expression shutoff by virus0InformativeDirect
Biological processVirus entry into host cell0InformativeDirect
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 processNucleotide metabolism0.0001154Highly InformativeDirect
Cellular componentMembrane0.000001151Least InformativeDirect
Cellular componentVirion0Moderately InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentEndosome0.000000004827Moderately InformativeDirect
Cellular componentEndoplasmic reticulum0.0002161Moderately InformativeDirect
Cellular componentHost membrane0InformativeDirect
Cellular componentHost nucleus0InformativeDirect
Cellular componentHost cytoplasm0InformativeDirect
Cellular componentVacuole0InformativeDirect
Cellular componentCapsid protein0InformativeDirect
Cellular componentGPI-anchor0InformativeDirect
Cellular componentLysosome0.000000003135InformativeDirect
Cellular componentHost endosome0Highly InformativeDirect
Coding sequence diversityRibosomal frameshifting0Moderately InformativeDirect
Coding sequence diversityRNA suppression of termination0InformativeDirect
DiseaseAIDS0Moderately InformativeDirect
DomainSignal0Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionMagnesium0.00000000000001071Least InformativeDirect
Molecular functionLipid-binding0Moderately InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationTransferase0.0313Least InformativeInherited
Post-translational modificationDNA-binding0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationProtease0Moderately InformativeDirect
Post-translational modificationNuclease0.00000000000004154Moderately InformativeDirect
Post-translational modificationRNA-binding0.0000006394Moderately InformativeDirect
Post-translational modificationEndonuclease0InformativeDirect
Post-translational modificationRNA-directed DNA polymerase0Highly InformativeDirect
Post-translational modificationDNA-directed DNA polymerase0Highly InformativeDirect
Post-translational modificationViral nucleoprotein0Highly InformativeDirect
Post-translational modificationAspartyl protease0Highly InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationCleavage on pair of basic residues0.00000000000009006Moderately InformativeDirect
Post-translational modificationZymogen0InformativeDirect
Post-translational modificationMyristate0InformativeDirect
Post-translational modificationAutocatalytic cleavage0.000005746InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR009007 SSF50630 Protein matches
Abstract

These aspartate proteases all contain a common closed beta barrel structure, which includes pepsin, cathepsin, chymosin, beta-secretase, plasmepsin, plant acid proteases and retroviral proteases [PubMed12475196, PubMed15153096].


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · 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 43 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 Acid proteases 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 43 hidden Markov models representing the Acid proteases 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 · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]