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 (1,198) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 19,833 157,887 136
Proteins 19,532 157,475 133


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)single-organism cellular process0.23681Least InformativeInherited
Biological Process (BP)multicellular organismal process0.00058381Least InformativeInherited
Biological Process (BP)response to stimulus0.076031Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis0.0002190.3225Least InformativeInherited
Biological Process (BP)cellular catabolic process2.369e-065.617e-07Moderately InformativeDirect
Biological Process (BP)organelle organization2.116e-060.3447Moderately InformativeInherited
Biological Process (BP)cellular component biogenesis7.294e-050.04992Moderately InformativeInherited
Biological Process (BP)homeostatic process0.007690.3299Moderately InformativeInherited
Biological Process (BP)immune system process0.0052110.4605Moderately InformativeInherited
Biological Process (BP)gene expression11Moderately InformativeInherited
Biological Process (BP)cellular response to stress6.362e-090.01064Moderately InformativeInherited
Biological Process (BP)proteolysis00InformativeDirect
Biological Process (BP)response to nutrient levels01.876e-09InformativeDirect
Biological Process (BP)organelle assembly01.144e-11InformativeDirect
Biological Process (BP)tissue homeostasis01.725e-11Highly InformativeDirect
Biological Process (BP)autophagy00Highly InformativeDirect
Biological Process (BP)cellular response to starvation07.645e-14Highly InformativeDirect
Biological Process (BP)protein processing1.122e-063.749e-15Highly InformativeDirect
Biological Process (BP)antigen processing and presentation3.292e-127.825e-07Highly InformativeDirect
Molecular Function (MF)hydrolase activity00Least InformativeDirect
Molecular Function (MF)peptidase activity00InformativeDirect
Molecular Function (MF)endopeptidase activity00Highly InformativeDirect
Cellular Component (CC)cytoplasmic part3.919e-050.0001032Least InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.0029660.1703Least InformativeInherited
Cellular Component (CC)vesicle0.00033011.611e-06Moderately InformativeDirect
Cellular Component (CC)extracellular region part1.215e-080.007078Moderately InformativeInherited
Cellular Component (CC)lytic vacuole07.784e-09InformativeDirect
Cellular Component (CC)extracellular space5.794e-146.552e-08InformativeDirect
Cellular Component (CC)endosome0.00025571.674e-05InformativeDirect
Cellular Component (CC)secretory granule6.555e-156.211e-07InformativeDirect
Cellular Component (CC)alveolar lamellar body00Highly InformativeDirect

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) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.3225 Least Informative Inherited
Biological Process (BP) cellular catabolic process 5.617e-07 Moderately Informative Direct
Biological Process (BP) organelle organization 0.3447 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.04992 Moderately Informative Inherited
Biological Process (BP) homeostatic process 0.3299 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 1 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.03098 Moderately Informative Inherited
Biological Process (BP) immune system process 0.4605 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.01064 Moderately Informative Inherited
Biological Process (BP) gene expression 1 Moderately Informative Inherited
Biological Process (BP) proteolysis 0 Informative Direct
Biological Process (BP) response to nutrient levels 1.876e-09 Informative Direct
Biological Process (BP) cellular amide metabolic process 5.34e-08 Informative Direct
Biological Process (BP) organelle assembly 1.144e-11 Informative Direct
Biological Process (BP) regulation of defense response 0.0779 Informative Inherited
Biological Process (BP) biological adhesion 0.05141 Informative Inherited
Biological Process (BP) tissue homeostasis 1.725e-11 Highly Informative Direct
Biological Process (BP) autophagy 0 Highly Informative Direct
Biological Process (BP) cellular response to starvation 7.645e-14 Highly Informative Direct
Biological Process (BP) pathogenesis 0.0009483 Highly Informative Direct
Biological Process (BP) protein processing 3.749e-15 Highly Informative Direct
Biological Process (BP) antigen processing and presentation 7.825e-07 Highly Informative Direct
Biological Process (BP) external encapsulating structure organization 9.458e-10 Highly Informative Direct
Biological Process (BP) regulation of calcium-mediated signaling 1.854e-07 Highly Informative Direct
Biological Process (BP) interaction with host 5.547e-06 Highly Informative Direct
Biological Process (BP) positive regulation of defense response 0.001895 Highly Informative Inherited
Biological Process (BP) modification of morphology or physiology of other organism involved in symbiotic interaction 0.01482 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 0.0001032 Least Informative Direct
Cellular Component (CC) membrane 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.1703 Least Informative Inherited
Cellular Component (CC) vesicle 1.611e-06 Moderately Informative Direct
Cellular Component (CC) plasma membrane part 1 Moderately Informative Inherited
Cellular Component (CC) intrinsic to membrane 0.002798 Moderately Informative Inherited
Cellular Component (CC) extracellular region part 0.007078 Moderately Informative Inherited
Cellular Component (CC) lytic vacuole 7.784e-09 Informative Direct
Cellular Component (CC) extracellular space 6.552e-08 Informative Direct
Cellular Component (CC) endosome 1.674e-05 Informative Direct
Cellular Component (CC) secretory granule 6.211e-07 Informative Direct
Cellular Component (CC) external encapsulating structure 5.788e-13 Informative Direct
Cellular Component (CC) intrinsic to plasma membrane 0.2558 Informative Inherited
Cellular Component (CC) anchored to membrane 0 Highly Informative Direct
Cellular Component (CC) alveolar lamellar body 0 Highly Informative Direct
Cellular Component (CC) cell wall 0.005659 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 bonds8.641e-06Least 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 diphosphatase1.981e-09Highly 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 variant2.532e-13Moderately InformativeDirect
Worm Phenotype (WP)protein aggregation variant1.11e-09Moderately InformativeDirect
Worm Phenotype (WP)pattern of transgene expression variant3.412e-07Moderately InformativeDirect
Worm Phenotype (WP)cell death variant6.347e-05Moderately InformativeDirect
Worm Phenotype (WP)basement membrane remodeling variant3.282e-14InformativeDirect
Worm Phenotype (WP)osmotic integrity variant9.931e-05Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)morphology0.3609Moderately 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 anhydrides0.006676InformativeInherited
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 transport1.633e-05Moderately InformativeDirect
Biological processDNA recombination0InformativeDirect
Biological processVirulence0InformativeDirect
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 processNucleotide metabolism8.849e-05Highly InformativeDirect
Cellular componentMembrane2.14e-07Least InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentEndosome2.835e-10Moderately InformativeDirect
Cellular componentEndoplasmic reticulum1.138e-05Moderately InformativeDirect
Cellular componentCapsid protein0InformativeDirect
Cellular componentVacuole0InformativeDirect
Cellular componentHost cytoplasm0InformativeDirect
Cellular componentHost membrane0InformativeDirect
Cellular componentHost nucleus0InformativeDirect
Cellular componentGPI-anchor1.912e-14InformativeDirect
Cellular componentLysosome3.416e-10InformativeDirect
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-binding3.327e-09Moderately InformativeDirect
Molecular functionViral nucleoprotein0Highly InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationTransferase0.03415Least InformativeInherited
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationProtease0Moderately InformativeDirect
Post-translational modificationNuclease5.583e-14Moderately 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 bond1.742e-14Least InformativeDirect
Post-translational modificationGlycoprotein6.647e-13Least InformativeDirect
Post-translational modificationCleavage on pair of basic residues4.369e-14Moderately 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 ]