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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 (2,838) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 18,037 76,611 38
Proteins 17,421 73,875 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)macromolecule metabolic process0.00058340.0000001534Least InformativeDirect
Biological Process (BP)biological regulation0.045671Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.45360.8921Least InformativeInherited
Biological Process (BP)cellular nitrogen compound metabolic process0.64911Least InformativeInherited
Biological Process (BP)primary metabolic process0.21920.004839Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.45770.764Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.5950.8947Least InformativeInherited
Biological Process (BP)cellular protein modification process0.000027190.000000000002918Moderately InformativeDirect
Biological Process (BP)gene expression0.4430.4255Moderately InformativeInherited
Biological Process (BP)RNA metabolic process0.25690.3062Moderately InformativeInherited
Biological Process (BP)peptidyl-amino acid modification0.0000058570InformativeDirect
Biological Process (BP)protein folding00Highly InformativeDirect
Biological Process (BP)RNA splicing0.00000065160.00000009255Highly InformativeDirect
Biological Process (BP)mRNA metabolic process0.0000044910.00001324Highly InformativeDirect
Biological Process (BP)regulation of viral life cycle0.0000000000050090.000000000006998Highly InformativeDirect
Molecular Function (MF)binding0.024450.01055Least InformativeInherited
Molecular Function (MF)isomerase activity00Moderately InformativeDirect
Molecular Function (MF)amide binding0.0000000000000027030InformativeDirect
Molecular Function (MF)drug binding00Highly InformativeDirect
Molecular Function (MF)peptide binding00Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.010490.000003441Least InformativeInherited
Cellular Component (CC)intracellular organelle part10.03284Least InformativeInherited
Cellular Component (CC)nuclear part0.33330.001225Moderately InformativeInherited
Cellular Component (CC)spliceosomal complex0.0000000034430Highly 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) macromolecule metabolic process 0.0000001534 Least Informative Direct
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.8921 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.004839 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.764 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.8947 Least Informative Inherited
Biological Process (BP) cellular protein modification process 0.000000000002918 Moderately Informative Direct
Biological Process (BP) gene expression 0.4255 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.3062 Moderately Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 0 Informative Direct
Biological Process (BP) protein folding 0 Highly Informative Direct
Biological Process (BP) RNA splicing 0.00000009255 Highly Informative Direct
Biological Process (BP) mRNA metabolic process 0.00001324 Highly Informative Direct
Biological Process (BP) regulation of viral life cycle 0.000000000006998 Highly Informative Direct
Molecular Function (MF) binding 0.01055 Least Informative Inherited
Molecular Function (MF) isomerase activity 0 Moderately Informative Direct
Molecular Function (MF) protein binding 0.2459 Moderately Informative Inherited
Molecular Function (MF) amide binding 0 Informative Direct
Molecular Function (MF) macromolecular complex binding 0.0000000000004391 Informative Direct
Molecular Function (MF) receptor binding 0.1442 Informative Inherited
Molecular Function (MF) drug binding 0 Highly Informative Direct
Molecular Function (MF) peptide binding 0 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.000003441 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.03284 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) nuclear part 0.001225 Moderately Informative Inherited
Cellular Component (CC) organelle envelope 0.04677 Moderately Informative Inherited
Cellular Component (CC) organelle subcompartment 0.0002621 Informative Direct
Cellular Component (CC) nuclear envelope 0.04842 Informative Inherited
Cellular Component (CC) nuclear pore 0.00006276 Highly Informative Direct
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 variant0.0007537Least InformativeDirect
Worm Phenotype (WP)protein protein interaction variant0.000000006871Moderately InformativeDirect
Worm Phenotype (WP)pattern of transgene expression variant0.00000115Moderately 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 resistance0.00003962Highly 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)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0.002826Least InformativeInherited
Xenopus ANatomical entity (XAN)egg0.0008703Moderately InformativeDirect
Xenopus ANatomical entity (XAN)anatomical entity in vitro0.00003572InformativeDirect

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 ligases0.8532InformativeInherited
Enzyme Commission (EC)Peptidylprolyl isomerase0Highly InformativeDirect
Enzyme Commission (EC)Urea carboxylase0.0000000000401Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processUbl conjugation pathway0.000000005337Moderately InformativeDirect
Biological processApoptosis0.00004066Moderately InformativeDirect
Biological processmRNA processing0InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentEndoplasmic reticulum0.0000000000001653Moderately InformativeDirect
Cellular componentSpliceosome0InformativeDirect
DomainTPR repeat0Highly InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationChaperone0.000000002721InformativeDirect
Post-translational modificationRotamase0Highly InformativeDirect
Post-translational modificationAcetylation0.000000000007194Least InformativeDirect
Post-translational modificationIsopeptide bond0.000006617Moderately InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)biopolymer metabolism0.000000000000006058Least InformativeDirect
UniPathway (UP)protein sumoylation0.00001483Highly 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 ]