SUPERFAMILY 1.75 HMM library and genome assignments server

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 (1,251) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 23,015 193,184 136
Proteins 22,539 192,494 133


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)protein metabolic process00Least InformativeDirect
Biological Process (BP)cellular component organization or biogenesis0.00006120.4117Least InformativeInherited
Biological Process (BP)regulation of cellular process11Least InformativeInherited
Biological Process (BP)positive regulation of biological process11Least InformativeInherited
Biological Process (BP)response to stimulus0.0054521Least InformativeInherited
Biological Process (BP)multicellular organismal process0.00010061Least InformativeInherited
Biological Process (BP)single-organism cellular process11Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.95251Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process11Least InformativeInherited
Biological Process (BP)cellular macromolecule metabolic process11Least InformativeInherited
Biological Process (BP)response to external stimulus0.00000000012310.00002606Moderately InformativeDirect
Biological Process (BP)cellular catabolic process0.0000023140.0000003424Moderately InformativeDirect
Biological Process (BP)single-organism catabolic process0.00000087720.0002581Moderately InformativeDirect
Biological Process (BP)regulation of signal transduction0.3951Moderately InformativeInherited
Biological Process (BP)multi-organism process0.2960.06084Moderately InformativeInherited
Biological Process (BP)regulation of biological quality0.00000033890.1083Moderately InformativeInherited
Biological Process (BP)positive regulation of response to stimulus0.53871Moderately InformativeInherited
Biological Process (BP)gene expression11Moderately InformativeInherited
Biological Process (BP)immune system process0.00036460.1859Moderately InformativeInherited
Biological Process (BP)cellular component biogenesis0.0010990.1489Moderately InformativeInherited
Biological Process (BP)cellular response to stress0.0000018510.02178Moderately InformativeInherited
Biological Process (BP)proteolysis00InformativeDirect
Biological Process (BP)peptide metabolic process0.0000027440.00000000000007575InformativeDirect
Biological Process (BP)response to nutrient levels00.00000001515InformativeDirect
Biological Process (BP)multicellular organismal homeostasis0.000000000000079160.0000000004762InformativeDirect
Biological Process (BP)anatomical structure homeostasis0.0000000000000016820.0000002661InformativeDirect
Biological Process (BP)organelle assembly00.0000000001536InformativeDirect
Biological Process (BP)cellular response to external stimulus0.00000000053970.0000005843InformativeDirect
Biological Process (BP)regulation of defense response0.058150.02105InformativeInherited
Biological Process (BP)biological adhesion0.008970.001676InformativeInherited
Biological Process (BP)protein maturation0.002770.000001121InformativeInherited
Biological Process (BP)macroautophagy00Highly InformativeDirect
Biological Process (BP)antigen processing and presentation0.0000000020830.0000009517Highly InformativeDirect
Biological Process (BP)chemical homeostasis within a tissue00Highly InformativeDirect
Biological Process (BP)regulation of calcium-mediated signaling0.000083540.00000001335Highly InformativeDirect
Biological Process (BP)symbiosis, encompassing mutualism through parasitism0.017220.000003367Highly InformativeInherited
Biological Process (BP)modification of morphology or physiology of other organism0.01340.000007273Highly InformativeInherited
Biological Process (BP)positive regulation of defense response0.0030280.000872Highly InformativeInherited
Molecular Function (MF)hydrolase activity00Least InformativeDirect
Molecular Function (MF)peptidase activity00InformativeDirect
Molecular Function (MF)endopeptidase activity00Highly InformativeDirect
Cellular Component (CC)cytoplasmic part0.000023840.004612Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.12670.5999Least InformativeInherited
Cellular Component (CC)vesicle0.00001740.0000002577Moderately InformativeDirect
Cellular Component (CC)lytic vacuole00.00000002393InformativeDirect
Cellular Component (CC)endosome0.0002150.00003556InformativeDirect
Cellular Component (CC)secretory granule0.0000000011120.00000114InformativeDirect

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) protein metabolic process 0 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.4117 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) positive regulation of biological process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) response to external stimulus 0.00002606 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.0000003424 Moderately Informative Direct
Biological Process (BP) single-organism catabolic process 0.0002581 Moderately Informative Direct
Biological Process (BP) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 1 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.06084 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.1083 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) gene expression 1 Moderately Informative Inherited
Biological Process (BP) immune system process 0.1859 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 1 Moderately Informative Inherited
Biological Process (BP) reproductive process 0.3187 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.1489 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.02178 Moderately Informative Inherited
Biological Process (BP) proteolysis 0 Informative Direct
Biological Process (BP) peptide metabolic process 0.00000000000007575 Informative Direct
Biological Process (BP) response to nutrient levels 0.00000001515 Informative Direct
Biological Process (BP) multicellular organismal homeostasis 0.0000000004762 Informative Direct
Biological Process (BP) protein maturation 0.000001121 Informative Direct
Biological Process (BP) anatomical structure homeostasis 0.0000002661 Informative Direct
Biological Process (BP) organelle assembly 0.0000000001536 Informative Direct
Biological Process (BP) cellular response to external stimulus 0.0000005843 Informative Direct
Biological Process (BP) cell wall organization or biogenesis 0.0000002579 Informative Direct
Biological Process (BP) biological adhesion 0.001676 Informative Inherited
Biological Process (BP) regulation of defense response 0.02105 Informative Inherited
Biological Process (BP) sexual reproduction 0.3636 Informative Inherited
Biological Process (BP) pathogenesis 0.000006159 Highly Informative Direct
Biological Process (BP) macroautophagy 0 Highly Informative Direct
Biological Process (BP) antigen processing and presentation 0.0000009517 Highly Informative Direct
Biological Process (BP) positive regulation of defense response 0.000872 Highly Informative Direct
Biological Process (BP) modification of morphology or physiology of other organism 0.000007273 Highly Informative Direct
Biological Process (BP) symbiosis, encompassing mutualism through parasitism 0.000003367 Highly Informative Direct
Biological Process (BP) external encapsulating structure organization 0.000000001662 Highly Informative Direct
Biological Process (BP) chemical homeostasis within a tissue 0 Highly Informative Direct
Biological Process (BP) regulation of calcium-mediated signaling 0.00000001335 Highly Informative Direct
Biological Process (BP) multi-organism cellular process 0.007226 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0 Least Informative Direct
Molecular Function (MF) peptidase activity 0 Informative Direct
Molecular Function (MF) endopeptidase activity 0 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 0.004612 Least Informative Inherited
Cellular Component (CC) membrane 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.5999 Least Informative Inherited
Cellular Component (CC) vesicle 0.0000002577 Moderately Informative Direct
Cellular Component (CC) intrinsic component of membrane 0.006374 Moderately Informative Inherited
Cellular Component (CC) plasma membrane part 1 Moderately Informative Inherited
Cellular Component (CC) extracellular region part 0.003995 Moderately Informative Inherited
Cellular Component (CC) lytic vacuole 0.00000002393 Informative Direct
Cellular Component (CC) extracellular space 0.0001617 Informative Direct
Cellular Component (CC) endosome 0.00003556 Informative Direct
Cellular Component (CC) secretory granule 0.00000114 Informative Direct
Cellular Component (CC) external encapsulating structure 0.0000000001572 Informative Direct
Cellular Component (CC) intrinsic component of plasma membrane 0.2153 Informative Inherited
Cellular Component (CC) anchored component of membrane 0 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)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

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism metabolism processing variant0.0002777Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.06747Least InformativeInherited
Worm Phenotype (WP)pericellular component development variant0.0000000000002532Moderately InformativeDirect
Worm Phenotype (WP)protein aggregation variant0.00000000111Moderately InformativeDirect
Worm Phenotype (WP)pattern of transgene expression variant0.0000003412Moderately InformativeDirect
Worm Phenotype (WP)cell death variant0.00006347Moderately InformativeDirect
Worm Phenotype (WP)basement membrane remodeling variant0.00000000000003282InformativeDirect
Worm Phenotype (WP)osmotic integrity variant0.00009931Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)morphology0.3772Moderately InformativeInherited

Document: YP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect

Document: XA 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)In phosphorous-containing anhydrides0.006161InformativeInherited
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 processHost-virus interaction0Moderately InformativeDirect
Biological processProtein transport0.00001863Moderately InformativeDirect
Biological processDNA recombination0InformativeDirect
Biological processVirulence0InformativeDirect
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 metabolism0.0000918Highly InformativeDirect
Cellular componentMembrane0.0000004251Least InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentEndosome0.0000000003331Moderately InformativeDirect
Cellular componentEndoplasmic reticulum0.00005272Moderately InformativeDirect
Cellular componentCapsid protein0InformativeDirect
Cellular componentVacuole0InformativeDirect
Cellular componentHost cytoplasm0InformativeDirect
Cellular componentHost membrane0InformativeDirect
Cellular componentHost nucleus0InformativeDirect
Cellular componentGPI-anchor0.00000000000001995InformativeDirect
Cellular componentLysosome0.0000000003375InformativeDirect
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 functionMagnesium0Moderately InformativeDirect
Molecular functionRNA-binding0.0000000003885Moderately InformativeDirect
Molecular functionViral nucleoprotein0Highly InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationTransferase0.02157Least InformativeInherited
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationProtease0Moderately InformativeDirect
Post-translational modificationNuclease0.0000000000000109Moderately 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 bond0.000000000000005732Least InformativeDirect
Post-translational modificationGlycoprotein0.0000000000002408Least InformativeDirect
Post-translational modificationCleavage on pair of basic residues0.00000000000004388Moderately InformativeDirect
Post-translational modificationMyristate0InformativeDirect
Post-translational modificationZymogen0InformativeDirect

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