SUPERFAMILY 1.75 HMM library and genome assignments server

PA domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   The "swivelling" beta/beta/alpha domain [ 52008] (10)
Superfamily:   PA domain [ 52025]
Families:   PA domain [ 52026] (2)


Superfamily statistics
Genomes (1,113) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 6,235 9,375 5
Proteins 6,200 9,349 5


Functional annotation
General category Processes_IC
Detailed category Proteases

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details) 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 0.000000000000007347 Least Informative Direct
Biological Process (BP) localization 0.9088 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.8505 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.003161 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.5345 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.3452 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.1251 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.1582 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.1082 Moderately Informative Inherited
Biological Process (BP) proteolysis 0.0000000003008 Informative Direct
Biological Process (BP) protein modification by small protein conjugation or removal 0.000002302 Informative Direct
Biological Process (BP) cellular chemical homeostasis 0.0002524 Informative Direct
Biological Process (BP) cation homeostasis 0.0003327 Informative Direct
Biological Process (BP) protein localization to organelle 0.0009327 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0.001833 Informative Inherited
Biological Process (BP) protein transport 0.002858 Informative Inherited
Biological Process (BP) cytoplasmic transport 0.02068 Informative Inherited
Biological Process (BP) protein catabolic process 0.07051 Informative Inherited
Biological Process (BP) protein ubiquitination 0.00000002445 Highly Informative Direct
Biological Process (BP) transition metal ion homeostasis 0.0000001303 Highly Informative Direct
Biological Process (BP) ubiquitin-dependent protein catabolic process 0.0000101 Highly Informative Direct
Biological Process (BP) establishment of protein localization to organelle 0.0001201 Highly Informative Direct
Molecular Function (MF) hydrolase activity 0.000508 Least Informative Direct
Molecular Function (MF) peptidase activity 0.00000000001192 Informative Direct
Molecular Function (MF) ligase activity 0.0000003076 Informative Direct
Molecular Function (MF) receptor activity 0.06713 Informative Inherited
Molecular Function (MF) small conjugating protein ligase activity 0.000000000006194 Highly Informative Direct
Molecular Function (MF) exopeptidase activity 0.000004422 Highly Informative Direct
Cellular Component (CC) membrane 0.00003103 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.00003787 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.05412 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.1253 Least Informative Inherited
Cellular Component (CC) endoplasmic reticulum 0.00000008161 Moderately Informative Direct
Cellular Component (CC) organelle membrane 0.00000009411 Moderately Informative Direct
Cellular Component (CC) endomembrane system 0.0000004024 Moderately Informative Direct
Cellular Component (CC) intrinsic to membrane 0.001228 Moderately Informative Inherited
Cellular Component (CC) vesicle 0.002533 Moderately Informative Inherited
Cellular Component (CC) endosome 0 Informative Direct
Cellular Component (CC) vacuolar part 0.000000000000003095 Informative Direct
Cellular Component (CC) integral to membrane 0.000000001665 Informative Direct
Cellular Component (CC) Golgi apparatus 0.0000008806 Informative Direct
Cellular Component (CC) endoplasmic reticulum membrane 0.001937 Informative Inherited
Cellular Component (CC) lytic vacuole 0.07525 Informative Inherited
Cellular Component (CC) endosomal part 0.0000000000002567 Highly Informative Direct
Cellular Component (CC) intrinsic to organelle membrane 0.0000001993 Highly Informative Direct
Cellular Component (CC) Golgi-associated vesicle 0.0000002874 Highly Informative Direct
Cellular Component (CC) cytoplasmic vesicle membrane 0.0002551 Highly Informative Direct
Cellular Component (CC) late endosome 0.1622 Highly Informative Inherited
Cellular Component (CC) lysosome 1 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)Acting on peptide bonds (peptide hydrolases)0Least InformativeDirect
Enzyme Commission (EC)Serine endopeptidases0.3108Moderately InformativeInherited
Enzyme Commission (EC)Metallocarboxypeptidases0Highly InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details) Document: DO annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)resistance to chemicals0Least InformativeDirect

Document: YP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)multi-tissue structure0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)oviduct0InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details) Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)0Moderately InformativeDirect
Enzyme Commission (EC)Glycosylases0.3051Moderately InformativeInherited
Enzyme Commission (EC)Serine endopeptidases0.2957InformativeInherited
Enzyme Commission (EC)Metallocarboxypeptidases0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0.03711Least InformativeInherited
Biological processProtein transport0.0000000000006707Moderately InformativeDirect
Biological processUbl conjugation pathway0InformativeDirect
Biological processEndocytosis9.345e-16InformativeDirect
Biological processVirulence0.000000000000007559InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentGolgi apparatus0.00000000000000128Moderately InformativeDirect
Cellular componentEndosome0.00000000000004014Moderately InformativeDirect
Cellular componentCytoplasmic vesicle0.00001167Moderately InformativeDirect
Cellular componentSecreted0.00001353Moderately InformativeDirect
Cellular componentEndoplasmic reticulum0.00001665Moderately InformativeDirect
Cellular componentVacuole0.00000000002411InformativeDirect
Cellular componentLysosome0.000000648InformativeDirect
Cellular componentCell wall0.00000001825Highly InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransmembrane0Least InformativeDirect
DomainZinc-finger0.000000000003342Moderately InformativeDirect
DomainSignal-anchor0.00000000000953InformativeDirect
DomainEGF-like domain0.000006589InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionMetal-binding0.000000000000268Least InformativeDirect
Molecular functionCalcium0.0000002605Moderately InformativeDirect
Post-translational modificationHydrolase0.000000000000008298Least InformativeDirect
Post-translational modificationProtease0Moderately InformativeDirect
Post-translational modificationReceptor0.000000005349Moderately InformativeDirect
Post-translational modificationLigase0.000009215Moderately InformativeDirect
Post-translational modificationMetalloprotease0.00006299InformativeDirect
Post-translational modificationCarboxypeptidase0.0000004654Highly InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationPalmitate0.00000001371Moderately InformativeDirect
Post-translational modificationUbl conjugation0.0004141Moderately InformativeDirect
Post-translational modificationPeptidoglycan-anchor0.000000000000101Highly InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)biopolymer metabolism0Least InformativeDirect
UniPathway (UP)protein ubiquitination0Moderately InformativeDirect

Document: UP annotation of SCOP domains

Jump to [ Top of page · SCOP classification · 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) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

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 2 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 PA domain 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 2 hidden Markov models representing the PA domain 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 · 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) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]