SUPERFAMILY 1.75 HMM library and genome assignments server

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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 (1,120) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 6,319 20,712 5
Proteins 6,283 20,643 5


Functional annotation
General category Processes_IC
Detailed category Proteases

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) macromolecule metabolic process 0.00000000000003429 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0.0002104 Least Informative Direct
Biological Process (BP) biological regulation 0.1976 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.6806 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.2157 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.7196 Least Informative Inherited
Biological Process (BP) nitrogen compound transport 0.00000008471 Moderately Informative Direct
Biological Process (BP) macromolecule localization 0.0000002216 Moderately Informative Direct
Biological Process (BP) organic substance transport 0.000005115 Moderately Informative Direct
Biological Process (BP) cellular localization 0.409 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.5373 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.4334 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.1259 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.002802 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.05045 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.02121 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.922 Moderately Informative Inherited
Biological Process (BP) single-organism catabolic process 0.2155 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.3518 Moderately Informative Inherited
Biological Process (BP) single-organism transport 0.1882 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.5864 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.2617 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.2475 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.8193 Moderately Informative Inherited
Biological Process (BP) ion transport 0.02146 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 0.01032 Moderately Informative Inherited
Biological Process (BP) protein transport 0.0000000000193 Informative Direct
Biological Process (BP) regulation of immune response 0.0000000002165 Informative Direct
Biological Process (BP) proteolysis 0.00000003686 Informative Direct
Biological Process (BP) metal ion transport 0.0000002816 Informative Direct
Biological Process (BP) cellular chemical homeostasis 0.000001048 Informative Direct
Biological Process (BP) cation homeostasis 0.000001183 Informative Direct
Biological Process (BP) inorganic ion homeostasis 0.000001397 Informative Direct
Biological Process (BP) positive regulation of immune system process 0.00001153 Informative Direct
Biological Process (BP) vesicle-mediated transport 0.0001715 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0.0005779 Informative Direct
Biological Process (BP) protein localization to organelle 0.01115 Informative Inherited
Biological Process (BP) positive regulation of nucleobase-containing compound metabolic process 0.005576 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.00124 Informative Inherited
Biological Process (BP) positive regulation of multicellular organismal process 0.004592 Informative Inherited
Biological Process (BP) response to nitrogen compound 0.0427 Informative Inherited
Biological Process (BP) regulation of cell proliferation 0.001638 Informative Inherited
Biological Process (BP) intracellular transport 0.2466 Informative Inherited
Biological Process (BP) positive regulation of adaptive immune response based on somatic recombination of immune receptors b 0.000000000000005563 Highly Informative Direct
Biological Process (BP) transition metal ion transport 0.0000000000001649 Highly Informative Direct
Biological Process (BP) positive regulation of leukocyte proliferation 0.000000000000397 Highly Informative Direct
Biological Process (BP) transition metal ion homeostasis 0.000000000002386 Highly Informative Direct
Biological Process (BP) regulation of leukocyte mediated immunity 0.000000000002982 Highly Informative Direct
Biological Process (BP) positive regulation of immune effector process 0.000000000005093 Highly Informative Direct
Biological Process (BP) regulation of production of molecular mediator of immune response 0.000000000005882 Highly Informative Direct
Biological Process (BP) regulation of lymphocyte proliferation 0.00000000001292 Highly Informative Direct
Biological Process (BP) regulation of T cell activation 0.0000000001438 Highly Informative Direct
Biological Process (BP) positive regulation of lymphocyte activation 0.0000000001617 Highly Informative Direct
Biological Process (BP) positive regulation of cell adhesion 0.000000006132 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 0.00000004962 Highly Informative Direct
Biological Process (BP) protein modification by small protein conjugation 0.0000002775 Highly Informative Direct
Biological Process (BP) response to endoplasmic reticulum stress 0.000006694 Highly Informative Direct
Biological Process (BP) cellular protein catabolic process 0.000007527 Highly Informative Direct
Biological Process (BP) modification-dependent macromolecule catabolic process 0.009228 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0.00108 Least Informative Inherited
Molecular Function (MF) transferase activity 0.4439 Least Informative Inherited
Molecular Function (MF) transporter activity 0.02608 Moderately Informative Inherited
Molecular Function (MF) P-P-bond-hydrolysis-driven transmembrane transporter activity 0.00000005372 Informative Direct
Molecular Function (MF) metal ion transmembrane transporter activity 0.000001103 Informative Direct
Molecular Function (MF) peptidase activity, acting on L-amino acid peptides 0.4688 Informative Inherited
Molecular Function (MF) molecular transducer activity 0.2287 Informative Inherited
Molecular Function (MF) macromolecule transmembrane transporter activity 0 Highly Informative Direct
Molecular Function (MF) amide transmembrane transporter activity 0.00000000000002122 Highly Informative Direct
Molecular Function (MF) protein transporter activity 0.0000000000001067 Highly Informative Direct
Molecular Function (MF) ubiquitin-like protein transferase activity 0.00000000001345 Highly Informative Direct
Molecular Function (MF) exopeptidase activity 0.001892 Highly Informative Inherited
Cellular Component (CC) membrane 0.00001391 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.9131 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.009149 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.001392 Least Informative Inherited
Cellular Component (CC) vacuole 0.000000000000003036 Moderately Informative Direct
Cellular Component (CC) endomembrane system 0.00000000000005523 Moderately Informative Direct
Cellular Component (CC) vesicle 0.00000000001465 Moderately Informative Direct
Cellular Component (CC) bounding membrane of organelle 0.000000002692 Moderately Informative Direct
Cellular Component (CC) whole membrane 0.00002302 Moderately Informative Direct
Cellular Component (CC) intrinsic component of membrane 0.009125 Moderately Informative Inherited
Cellular Component (CC) vacuolar part 0.000000000008225 Informative Direct
Cellular Component (CC) endosome 0.0000000007232 Informative Direct
Cellular Component (CC) cytoplasmic vesicle part 0.0000001617 Informative Direct
Cellular Component (CC) Golgi apparatus 0.000001949 Informative Direct
Cellular Component (CC) side of membrane 0.000005408 Informative Direct
Cellular Component (CC) endoplasmic reticulum membrane 0.0004192 Informative Direct
Cellular Component (CC) lytic vacuole 0.2188 Informative Inherited
Cellular Component (CC) endosome membrane 0.000006015 Highly Informative Direct
Cellular Component (CC) integral component of endoplasmic reticulum membrane 0.000007818 Highly Informative Direct
Cellular Component (CC) lysosomal membrane 0.00005927 Highly Informative Direct
Cellular Component (CC) Golgi-associated vesicle 0.01167 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

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0.06341Least InformativeInherited
Biological processUbl conjugation pathway0Moderately InformativeDirect
Biological processVirulence0.00000000000007948Moderately InformativeDirect
Biological processProtein transport0.000000000002519Moderately InformativeDirect
Biological processEndocytosis0.00000000000000239InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentEndosome0Moderately InformativeDirect
Cellular componentGolgi apparatus0.000000000000007083Moderately InformativeDirect
Cellular componentEndoplasmic reticulum0.00000006424Moderately InformativeDirect
Cellular componentSecreted0.00000243Moderately InformativeDirect
Cellular componentCytoplasmic vesicle0.00005822Moderately InformativeDirect
Cellular componentLysosome0.00000000002317InformativeDirect
Cellular componentVacuole0.00000000011InformativeDirect
Cellular componentCell wall0.0000001412Highly InformativeDirect
DomainTransmembrane0Least InformativeDirect
DomainSignal0Least InformativeDirect
DomainZinc-finger0.00000000002108Moderately InformativeDirect
DomainSignal-anchor0.00000000000008738InformativeDirect
DomainEGF-like domain0.00001033InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionMetal-binding9.905e-16Least InformativeDirect
Molecular functionCalcium0.0000008737Moderately InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationProtease0Moderately InformativeDirect
Post-translational modificationReceptor0.00000001466Moderately InformativeDirect
Post-translational modificationMetalloprotease0.00001673InformativeDirect
Post-translational modificationCarboxypeptidase0.0000003118Highly InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationPalmitate0.000000003148Moderately InformativeDirect
Post-translational modificationPeptidoglycan-anchor0.0000000000001192Highly InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-coverage) · 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 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-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]