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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 (1,256) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 23,267 193,184 136
Proteins 22,793 192,494 133


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 process0.0000000072320.0000003916Least InformativeDirect
Biological Process (BP)organonitrogen compound metabolic process0.00000490.00000004573Least InformativeDirect
Biological Process (BP)biological regulation0.039461Least InformativeInherited
Biological Process (BP)response to stimulus0.26461Least InformativeInherited
Biological Process (BP)primary metabolic process0.0029080.01037Least InformativeInherited
Biological Process (BP)response to biotic stimulus0.00075380.0003354Moderately InformativeDirect
Biological Process (BP)regulation of biological quality0.0000077660.6046Moderately InformativeInherited
Biological Process (BP)system development0.015391Moderately InformativeInherited
Biological Process (BP)immune system process0.00021980.07377Moderately InformativeInherited
Biological Process (BP)proteolysis00InformativeDirect
Biological Process (BP)sensory organ development0.00011280.3224InformativeInherited
Biological Process (BP)tissue development0.00011180.9154InformativeInherited
Biological Process (BP)multicellular organismal homeostasis0.0000000000093240.000000001991Highly InformativeDirect
Biological Process (BP)anatomical structure homeostasis00.00000004015Highly InformativeDirect
Biological Process (BP)camera-type eye development0.00000015830.009109Highly InformativeInherited
Molecular Function (MF)hydrolase activity00Least InformativeDirect
Molecular Function (MF)peptidase activity, acting on L-amino acid peptides0.099350.2058InformativeInherited
Cellular Component (CC)cytoplasmic part0.0052950.28Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle11Least InformativeInherited
Cellular Component (CC)vesicle0.0000000000000077670.0000000008718Moderately InformativeDirect
Cellular Component (CC)extracellular region part0.000000000014590.0001441Moderately InformativeDirect
Cellular Component (CC)lytic vacuole00.00002592InformativeDirect
Cellular Component (CC)secretory granule0.00000027660.00001943InformativeDirect
Cellular Component (CC)endosome0.00010590.001862InformativeInherited
Cellular Component (CC)alveolar lamellar body00Highly InformativeDirect
Cellular Component (CC)late endosome0.67890.4503Highly 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 0.0000003916 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0.00000004573 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.01037 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) response to biotic stimulus 0.0003354 Moderately Informative Direct
Biological Process (BP) regulation of biological quality 0.6046 Moderately Informative Inherited
Biological Process (BP) system development 1 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 0.1189 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.00694 Moderately Informative Inherited
Biological Process (BP) gene expression 1 Moderately Informative Inherited
Biological Process (BP) peptide metabolic process 0.02808 Moderately Informative Inherited
Biological Process (BP) immune system process 0.07377 Moderately Informative Inherited
Biological Process (BP) proteolysis 0 Informative Direct
Biological Process (BP) cell wall organization or biogenesis 0.00006942 Informative Direct
Biological Process (BP) interspecies interaction between organisms 0.04106 Informative Inherited
Biological Process (BP) sensory organ development 0.3224 Informative Inherited
Biological Process (BP) tissue development 0.9154 Informative Inherited
Biological Process (BP) multi-organism cellular process 0.0005704 Highly Informative Direct
Biological Process (BP) multicellular organismal homeostasis 0.000000001991 Highly Informative Direct
Biological Process (BP) protein maturation 0.0000004417 Highly Informative Direct
Biological Process (BP) anatomical structure homeostasis 0.00000004015 Highly Informative Direct
Biological Process (BP) camera-type eye development 0.009109 Highly Informative Inherited
Biological Process (BP) modification of morphology or physiology of other organism involved in symbiotic interaction 0.1789 Highly Informative Inherited
Biological Process (BP) biological adhesion 0.01758 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0 Least Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) peptidase activity, acting on L-amino acid peptides 0.2058 Informative Inherited
Cellular Component (CC) membrane 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.28 Least Informative Inherited
Cellular Component (CC) vesicle 0.0000000008718 Moderately Informative Direct
Cellular Component (CC) extracellular region part 0.0001441 Moderately Informative Direct
Cellular Component (CC) intrinsic component of membrane 0.004395 Moderately Informative Inherited
Cellular Component (CC) plasma membrane 1 Moderately Informative Inherited
Cellular Component (CC) lytic vacuole 0.00002592 Informative Direct
Cellular Component (CC) secretory granule 0.00001943 Informative Direct
Cellular Component (CC) external encapsulating structure 0.0000000004205 Informative Direct
Cellular Component (CC) Golgi apparatus 0.004404 Informative Inherited
Cellular Component (CC) endosome 0.001862 Informative Inherited
Cellular Component (CC) plant-type cell wall 0.000005833 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 0.529 Highly Informative Inherited
Cellular Component (CC) Golgi subcompartment 0.01321 Highly Informative Inherited
Cellular Component (CC) late endosome 0.4503 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 phenotype0.06559Least InformativeInherited
Mammalian Phenotype (MP)abnormal body composition0.3594Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal postnatal growth/weight/body size0.7343Moderately InformativeInherited
Mammalian Phenotype (MP)decreased total tissue mass0.0562InformativeInherited
Mammalian Phenotype (MP)decreased body size0.119InformativeInherited
Mammalian Phenotype (MP)weight loss0.02298Highly 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 variant0.0002662Least InformativeDirect
Worm Phenotype (WP)pericellular component development variant0.000000000000003467Moderately InformativeDirect
Worm Phenotype (WP)protein protein interaction variant0.0000000000008441Moderately InformativeDirect
Worm Phenotype (WP)pattern of transgene expression variant0.00000004333Moderately InformativeDirect
Worm Phenotype (WP)basement membrane remodeling variant0InformativeDirect
Worm Phenotype (WP)osmotic integrity variant0.0005964Highly 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 anhydrides0.005301InformativeInherited
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 transport0.00003784Moderately 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 metabolism0.0001132Highly InformativeDirect
Cellular componentMembrane0.0000006582Least InformativeDirect
Cellular componentVirion0Moderately InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentEndosome0.000000004285Moderately InformativeDirect
Cellular componentEndoplasmic reticulum0.0002036Moderately InformativeDirect
Cellular componentCapsid protein0InformativeDirect
Cellular componentGPI-anchor0InformativeDirect
Cellular componentVacuole0InformativeDirect
Cellular componentHost cytoplasm0InformativeDirect
Cellular componentHost membrane0InformativeDirect
Cellular componentHost nucleus0InformativeDirect
Cellular componentLysosome0.00000000296InformativeDirect
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 functionMagnesium0.00000000000000879Least InformativeDirect
Molecular functionLipid-binding0Moderately InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationTransferase0.02787Least InformativeInherited
Post-translational modificationDNA-binding0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationProtease0Moderately InformativeDirect
Post-translational modificationNuclease0.00000000000003014Moderately InformativeDirect
Post-translational modificationRNA-binding0.0000005491Moderately InformativeDirect
Post-translational modificationEndonuclease0InformativeDirect
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 modificationDisulfide bond0Least InformativeDirect
Post-translational modificationGlycoprotein4.818e-16Least InformativeDirect
Post-translational modificationCleavage on pair of basic residues0.00000000000004978Moderately InformativeDirect
Post-translational modificationMyristate0InformativeDirect
Post-translational modificationZymogen0InformativeDirect
Post-translational modificationAutocatalytic cleavage0.000005547InformativeDirect

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 ]