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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 (2,843) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 18,148 79,824 38
Proteins 17,525 75,533 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 process0.00072910.0000006341Least InformativeDirect
Biological Process (BP)biological regulation0.057531Least InformativeInherited
Biological Process (BP)cellular nitrogen compound metabolic process0.64961Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.62130.9663Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.46930.9423Least InformativeInherited
Biological Process (BP)organonitrogen compound metabolic process0.49410.05693Least InformativeInherited
Biological Process (BP)primary metabolic process0.25170.01446Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.47340.8221Least InformativeInherited
Biological Process (BP)cellular protein modification process0.000036410.00000000001605Moderately InformativeDirect
Biological Process (BP)RNA metabolic process0.24970.3914Moderately InformativeInherited
Biological Process (BP)gene expression0.44210.4098Moderately InformativeInherited
Biological Process (BP)peptidyl-amino acid modification0.0000067190InformativeDirect
Biological Process (BP)mRNA processing0.0000005040.00001127Highly InformativeDirect
Biological Process (BP)protein folding00Highly InformativeDirect
Biological Process (BP)RNA splicing0.00000072580.0000001049Highly InformativeDirect
Biological Process (BP)regulation of viral process0.000000000016860.00000000002958Highly InformativeDirect
Molecular Function (MF)binding0.042140.04536Least InformativeInherited
Molecular Function (MF)isomerase activity00Moderately InformativeDirect
Molecular Function (MF)amide binding0.0000000000000027330InformativeDirect
Molecular Function (MF)drug binding00Highly InformativeDirect
Molecular Function (MF)peptide binding00Highly InformativeDirect
Cellular Component (CC)macromolecular complex0.30710.0001643Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.0017240.000002375Least InformativeInherited
Cellular Component (CC)intracellular organelle part10.02303Least InformativeInherited
Cellular Component (CC)nuclear part0.16810.00006681Moderately InformativeInherited
Cellular Component (CC)spliceosomal complex0.000000000097520Highly 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 0.0000006341 Least Informative Direct
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.9663 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.9423 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 0.05693 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.01446 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.8221 Least Informative Inherited
Biological Process (BP) cellular protein modification process 0.00000000001605 Moderately Informative Direct
Biological Process (BP) response to abiotic stimulus 0.7046 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.3914 Moderately Informative Inherited
Biological Process (BP) gene expression 0.4098 Moderately Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 0 Informative Direct
Biological Process (BP) response to radiation 0.06609 Informative Inherited
Biological Process (BP) mRNA processing 0.00001127 Highly Informative Direct
Biological Process (BP) protein folding 0 Highly Informative Direct
Biological Process (BP) RNA splicing 0.0000001049 Highly Informative Direct
Biological Process (BP) regulation of viral process 0.00000000002958 Highly Informative Direct
Biological Process (BP) cellular response to abiotic stimulus 0.02023 Highly Informative Inherited
Molecular Function (MF) binding 0.04536 Least Informative Inherited
Molecular Function (MF) isomerase activity 0 Moderately Informative Direct
Molecular Function (MF) amide binding 0 Informative Direct
Molecular Function (MF) macromolecular complex binding 0 Informative Direct
Molecular Function (MF) receptor binding 0.1375 Informative Inherited
Molecular Function (MF) drug binding 0 Highly Informative Direct
Molecular Function (MF) peptide binding 0 Highly Informative Direct
Cellular Component (CC) macromolecular complex 0.0001643 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.000002375 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.02303 Least Informative Inherited
Cellular Component (CC) nuclear part 0.00006681 Moderately Informative Direct
Cellular Component (CC) organelle envelope 0.02904 Moderately Informative Inherited
Cellular Component (CC) nuclear envelope 0.0219 Informative Inherited
Cellular Component (CC) nuclear pore 0.000005674 Highly Informative Direct
Cellular Component (CC) spliceosomal complex 0 Highly Informative Direct
Cellular Component (CC) thylakoid 0.0007128 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 variant0.001026Least InformativeInherited
Worm Phenotype (WP)protein protein interaction variant0.000000007295Moderately InformativeDirect
Worm Phenotype (WP)pattern of transgene expression variant0.000001215Moderately 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 resistance0.00003928Highly 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)cell0.002874Least InformativeInherited
Xenopus ANatomical entity (XAN)egg0.0008487Moderately InformativeDirect
Xenopus ANatomical entity (XAN)anatomical entity in vitro0.00003504InformativeDirect

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)Acyltransferases0.5048Moderately InformativeInherited
Enzyme Commission (EC)Ligases1Moderately InformativeInherited
Enzyme Commission (EC)RING-type E3 ubiquitin transferase0.000000008304InformativeDirect
Enzyme Commission (EC)Other carbon--nitrogen ligases0.8453InformativeInherited
Enzyme Commission (EC)Peptidylprolyl isomerase0Highly InformativeDirect
Enzyme Commission (EC)Urea carboxylase0.00000000003867Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processUbl conjugation pathway0.000000005928Moderately InformativeDirect
Biological processApoptosis0.00004104Moderately InformativeDirect
Biological processmRNA processing0InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentEndoplasmic reticulum0.0000000000002368Moderately InformativeDirect
Cellular componentSpliceosome0InformativeDirect
DomainTPR repeat0Highly InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationChaperone0.0000000008086InformativeDirect
Post-translational modificationRotamase0Highly InformativeDirect
Post-translational modificationAcetylation0.000000000007956Least InformativeDirect
Post-translational modificationIsopeptide bond0.000006567Moderately InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)biopolymer metabolism0.000000000000006296Least InformativeDirect
UniPathway (UP)protein sumoylation0.00001427Highly 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 ]