SUPERFAMILY 1.75 HMM library and genome assignments server


Cyclophilin-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Cyclophilin-like [ 50890]
Superfamily:   Cyclophilin-like [ 50891] (4)
Families:   Cyclophilin (peptidylprolyl isomerase) [ 50892] (12)
  Outer surface protein, C-terminal domain [ 110278]
  TM1367-like [ 141519]
  PH0987 C-terminal domain-like [ 159249]


Superfamily statistics
Genomes (2,828) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 17,707 0 38
Proteins 17,100 0 38


Functional annotation
General category Processes_IC
Detailed category Protein modification

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 process6.624e-120Least InformativeDirect
Biological Process (BP)cellular macromolecule metabolic process00Least InformativeDirect
Biological Process (BP)regulation of cellular process0.10891Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process11Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process11Least InformativeInherited
Biological Process (BP)heterocycle metabolic process11Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process11Least InformativeInherited
Biological Process (BP)cellular protein modification process3.024e-051.711e-06Moderately InformativeDirect
Biological Process (BP)regulation of localization0.5320.8685Moderately InformativeInherited
Biological Process (BP)RNA metabolic process0.9931Moderately InformativeInherited
Biological Process (BP)gene expression11Moderately InformativeInherited
Biological Process (BP)RNA processing2.483e-052.811e-08InformativeDirect
Biological Process (BP)peptidyl-amino acid modification00InformativeDirect
Biological Process (BP)regulation of ion transport0.0049220.02373InformativeInherited
Biological Process (BP)mRNA processing0.00058540.0001103Highly InformativeDirect
Biological Process (BP)protein folding2.058e-060Highly InformativeDirect
Biological Process (BP)regulation of proton transport2.626e-067.773e-08Highly InformativeDirect
Biological Process (BP)peptidyl-proline modification00Highly InformativeDirect
Biological Process (BP)regulation of multi-organism process8.059e-111.723e-07Highly InformativeDirect
Biological Process (BP)RNA splicing0.002444.177e-06Highly InformativeInherited
Molecular Function (MF)binding0.11690.08045Least InformativeInherited
Molecular Function (MF)isomerase activity00Moderately InformativeDirect
Molecular Function (MF)amide binding1.85e-140InformativeDirect
Molecular Function (MF)drug binding2.604e-150Highly InformativeDirect
Molecular Function (MF)peptide binding5.137e-150Highly InformativeDirect
Cellular Component (CC)cytoplasmic part0.026060.1118Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.011290.0009299Least InformativeInherited
Cellular Component (CC)intracellular organelle part0.79340.124Least InformativeInherited
Cellular Component (CC)cytosol0.00023050.0007214Moderately InformativeDirect
Cellular Component (CC)ribonucleoprotein complex0.017033.557e-05Moderately InformativeInherited
Cellular Component (CC)nuclear part0.40510.00176Moderately InformativeInherited
Cellular Component (CC)spliceosomal complex1.75e-090Highly 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) cellular macromolecule metabolic process 0 Least Informative Direct
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular protein modification process 1.711e-06 Moderately Informative Direct
Biological Process (BP) regulation of localization 0.8685 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 1 Moderately Informative Inherited
Biological Process (BP) gene expression 1 Moderately Informative Inherited
Biological Process (BP) RNA processing 2.811e-08 Informative Direct
Biological Process (BP) peptidyl-amino acid modification 0 Informative Direct
Biological Process (BP) regulation of ion transport 0.02373 Informative Inherited
Biological Process (BP) mRNA processing 0.0001103 Highly Informative Direct
Biological Process (BP) protein folding 0 Highly Informative Direct
Biological Process (BP) RNA splicing 4.177e-06 Highly Informative Direct
Biological Process (BP) regulation of proton transport 7.773e-08 Highly Informative Direct
Biological Process (BP) peptidyl-proline modification 0 Highly Informative Direct
Biological Process (BP) regulation of multi-organism process 1.723e-07 Highly Informative Direct
Molecular Function (MF) binding 0.08045 Least Informative Inherited
Molecular Function (MF) isomerase activity 0 Moderately Informative Direct
Molecular Function (MF) amide binding 0 Informative Direct
Molecular Function (MF) drug binding 0 Highly Informative Direct
Molecular Function (MF) protein complex binding 0 Highly Informative Direct
Molecular Function (MF) peptide binding 0 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.0009299 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.1118 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.124 Least Informative Inherited
Cellular Component (CC) cytosol 0.0007214 Moderately Informative Direct
Cellular Component (CC) ribonucleoprotein complex 3.557e-05 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.00176 Moderately Informative Inherited
Cellular Component (CC) plastid 0.01602 Informative Inherited
Cellular Component (CC) spliceosomal complex 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)Isomerases0Least InformativeDirect
Enzyme Commission (EC)Peptidylprolyl isomerase0InformativeDirect

Document: EC annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism metabolism processing variant6.61e-05Least InformativeDirect
Worm Phenotype (WP)protein aggregation variant3.439e-09Moderately InformativeDirect
Worm Phenotype (WP)pattern of transgene expression variant6.69e-08Moderately InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)freeze-thaw resistance3.817e-05Highly 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)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)gamete0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)anatomical entity in vitro0.000532InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six leaves visible stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Isomerases0Moderately InformativeDirect
Enzyme Commission (EC)Ligases1Moderately InformativeInherited
Enzyme Commission (EC)Other carbon--nitrogen ligases0.869InformativeInherited
Enzyme Commission (EC)Peptidylprolyl isomerase0Highly InformativeDirect
Enzyme Commission (EC)Urea carboxylase4.315e-11Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processApoptosis3.487e-05Moderately InformativeDirect
Biological processmRNA splicing0InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentEndoplasmic reticulum3.025e-14Moderately InformativeDirect
Cellular componentSpliceosome0InformativeDirect
DomainTPR repeat0Highly InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationChaperone2.578e-09InformativeDirect
Post-translational modificationRotamase0Highly InformativeDirect
Post-translational modificationAcetylation1.335e-12Least InformativeDirect
Post-translational modificationIsopeptide bond2.399e-08Moderately InformativeDirect
Post-translational modificationUbl conjugation0.0001417Moderately InformativeDirect
Post-translational modificationS-nitrosylation8.649e-06InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)biopolymer metabolism0.0001807Least InformativeDirect
UniPathway (UP)protein sumoylation5.31e-15Highly InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR015891 SSF50891 Protein matches
Abstract

This entry represents the core beta-barrel (8,10) domain found in cyclophilin (peptidylprolyl isomerise). This domain is related to a beta-barrel domain found in several outer membrane proteins, usually at the C-terminus; in these proteins, the beta-barrel (7,10) lacks the N-terminal strand of the cyclophilin domain, but remains closed.

Cyclophilin is the major high-affinity binding protein in vertebrates for the immunosuppressive drug cyclosporin A (CSA), but is also found in other organisms. It exhibits a peptidyl-prolyl cis-trans isomerase activity (PPIase or rotamase). PPIase is an enzyme that accelerates protein folding by catalyzing the cis-trans isomerization of proline imidic peptide bonds in oligopeptides [PubMed2186809]. It is probable that CSA mediates some of its effects via an forming a tight complex with cyclophilin that inhibits the phosphatase activity of calcineurin [PubMed7514602], [PubMed8117697]. Cyclophilin A is a cytosolic and highly abundant protein. The protein belongs to a family of isozymes, including cyclophilins B and C, and natural killer cell cyclophilin-related protein [PubMed1464374, PubMed8404888, PubMed7526121]. Major isoforms have been found throughout the cell, including the ER, and some are even secreted. The sequences of the different forms of cyclophilin-type PPIases are well conserved.

  • Note: FKBP's, a family of proteins that bind the immunosuppressive drug FK506, are also PPIases, but their sequence is not at all related to that of cyclophilin (see ).

  • 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) · 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 29 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 Cyclophilin-like 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 29 hidden Markov models representing the Cyclophilin-like 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) · 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 ]