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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 (1,252) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 23,049 193,184 136
Proteins 22,575 192,494 133


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 process0.0000000061590.00000326Least InformativeDirect
Biological Process (BP)biological regulation0.031221Least InformativeInherited
Biological Process (BP)primary metabolic process0.0024260.07196Least InformativeInherited
Biological Process (BP)system development0.0171Moderately InformativeInherited
Biological Process (BP)regulation of biological quality0.0000040460.3137Moderately InformativeInherited
Biological Process (BP)immune system process0.000096130.1058Moderately InformativeInherited
Biological Process (BP)proteolysis00InformativeDirect
Biological Process (BP)epithelium development0.00000012760.1912InformativeInherited
Biological Process (BP)antigen processing and presentation of exogenous peptide antigen0.000000000000025370.000000002809Highly InformativeDirect
Biological Process (BP)multicellular organismal homeostasis0.0000000000081670.0000000006608Highly InformativeDirect
Biological Process (BP)anatomical structure homeostasis00.0000000233Highly InformativeDirect
Biological Process (BP)camera-type eye development0.00000018470.007953Highly InformativeInherited
Molecular Function (MF)hydrolase activity00Least InformativeDirect
Molecular Function (MF)peptidase activity, acting on L-amino acid peptides0.21870.2456InformativeInherited
Cellular Component (CC)cytoplasmic part0.0021650.09579Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle10.997Least InformativeInherited
Cellular Component (CC)vacuole00Moderately InformativeDirect
Cellular Component (CC)vesicle0.00000000000014950.0000000005381Moderately InformativeDirect
Cellular Component (CC)extracellular region part0.000000000010680.0005683Moderately InformativeDirect
Cellular Component (CC)lytic vacuole00.00001459InformativeDirect
Cellular Component (CC)secretory vesicle0.0025370.01786InformativeInherited
Cellular Component (CC)endosome0.00029840.004065InformativeInherited
Cellular Component (CC)alveolar lamellar body00Highly InformativeDirect
Cellular Component (CC)late endosome0.61050.4073Highly 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 0.00000326 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic 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) primary metabolic process 0.07196 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) peptide metabolic process 0.0002359 Moderately Informative Direct
Biological Process (BP) system development 1 Moderately Informative Inherited
Biological Process (BP) gene expression 1 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.3137 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.02019 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 0.2573 Moderately Informative Inherited
Biological Process (BP) immune system process 0.1058 Moderately Informative Inherited
Biological Process (BP) proteolysis 0 Informative Direct
Biological Process (BP) symbiosis, encompassing mutualism through parasitism 0.1441 Informative Inherited
Biological Process (BP) epithelium development 0.1912 Informative Inherited
Biological Process (BP) antigen processing and presentation of exogenous peptide antigen 0.000000002809 Highly Informative Direct
Biological Process (BP) multicellular organismal homeostasis 0.0000000006608 Highly Informative Direct
Biological Process (BP) protein maturation 0.0000003909 Highly Informative Direct
Biological Process (BP) anatomical structure homeostasis 0.0000000233 Highly Informative Direct
Biological Process (BP) camera-type eye development 0.007953 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0 Least Informative Direct
Molecular Function (MF) peptidase activity, acting on L-amino acid peptides 0.2456 Informative Inherited
Cellular Component (CC) membrane 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.09579 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.997 Least Informative Inherited
Cellular Component (CC) vacuole 0 Moderately Informative Direct
Cellular Component (CC) vesicle 0.0000000005381 Moderately Informative Direct
Cellular Component (CC) extracellular region part 0.0005683 Moderately Informative Direct
Cellular Component (CC) plasma membrane 1 Moderately Informative Inherited
Cellular Component (CC) intrinsic component of membrane 0.002349 Moderately Informative Inherited
Cellular Component (CC) lytic vacuole 0.00001459 Informative Direct
Cellular Component (CC) extracellular space 0.0005934 Informative Direct
Cellular Component (CC) external encapsulating structure 0.000000001081 Informative Direct
Cellular Component (CC) secretory vesicle 0.01786 Informative Inherited
Cellular Component (CC) endosome 0.004065 Informative Inherited
Cellular Component (CC) plant-type cell wall 0.000001983 Highly Informative Direct
Cellular Component (CC) anchored component of membrane 0 Highly Informative Direct
Cellular Component (CC) alveolar lamellar body 0 Highly Informative Direct
Cellular Component (CC) intrinsic component of plasma membrane 0.1375 Highly Informative Inherited
Cellular Component (CC) late endosome 0.4073 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

Disease Ontology (DO)

(show details) Document: DO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)growth/size/body region phenotype0.06618Least InformativeInherited
Mammalian Phenotype (MP)abnormal body size0.1655Moderately InformativeInherited
Mammalian Phenotype (MP)decreased total tissue mass0.05857InformativeInherited
Mammalian Phenotype (MP)decreased body size0.1216InformativeInherited
Mammalian Phenotype (MP)weight loss0.02318Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism metabolism processing variant0.0001799Least InformativeDirect
Worm Phenotype (WP)pericellular component development variant0.000000000000003422Moderately InformativeDirect
Worm Phenotype (WP)protein protein interaction variant0.0000000000007773Moderately InformativeDirect
Worm Phenotype (WP)pattern of transgene expression variant0.00000004038Moderately InformativeDirect
Worm Phenotype (WP)basement membrane remodeling variant0InformativeDirect
Worm Phenotype (WP)osmotic integrity variant0.0004007Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details) Document: XA 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)In phosphorus-containing anhydrides0.006377InformativeInherited
Enzyme Commission (EC)RNA-directed DNA polymerase0Highly InformativeDirect
Enzyme Commission (EC)Exoribonuclease H0Highly InformativeDirect
Enzyme Commission (EC)Retroviral ribonuclease H0Highly 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 transport0.00003873Moderately InformativeDirect
Biological processDNA recombination0InformativeDirect
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 processNucleotide metabolism0.0001153Highly InformativeDirect
Cellular componentMembrane0.0000005366Least InformativeDirect
Cellular componentVirion0Moderately InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentEndosome0.000000003074Moderately InformativeDirect
Cellular componentEndoplasmic reticulum0.0001617Moderately InformativeDirect
Cellular componentCapsid protein0InformativeDirect
Cellular componentGPI-anchor0InformativeDirect
Cellular componentVacuole0InformativeDirect
Cellular componentHost cytoplasm0InformativeDirect
Cellular componentHost membrane0InformativeDirect
Cellular componentHost nucleus0InformativeDirect
Cellular componentLysosome0.000000001509InformativeDirect
Cellular componentHost endosome0Highly InformativeDirect
Coding sequence diversityRibosomal frameshifting0Moderately InformativeDirect
Coding sequence diversityRNA suppression of termination0InformativeDirect
DiseaseAIDS0Moderately InformativeDirect
DomainSignal0Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionLipid-binding0Moderately InformativeDirect
Molecular functionMagnesium0.000000000000001857Moderately InformativeDirect
Molecular functionRNA-binding0.000000003737Moderately InformativeDirect
Molecular functionViral nucleoprotein0Highly InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationTransferase0.06825Least InformativeInherited
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationProtease0Moderately InformativeDirect
Post-translational modificationNuclease0.00000000000003421Moderately InformativeDirect
Post-translational modificationDNA-directed DNA polymerase0InformativeDirect
Post-translational modificationEndonuclease0InformativeDirect
Post-translational modificationAspartyl protease0Highly InformativeDirect
Post-translational modificationRNA-directed DNA polymerase0Highly InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect
Post-translational modificationGlycoprotein0.000000000000001883Least InformativeDirect
Post-translational modificationCleavage on pair of basic residues0.00000000000006832Moderately InformativeDirect
Post-translational modificationMyristate0InformativeDirect
Post-translational modificationZymogen0InformativeDirect
Post-translational modificationAutocatalytic cleavage0.000005463InformativeDirect

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) · Disease Ontology (DO) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · 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) · Disease Ontology (DO) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]