SUPERFAMILY 1.75 HMM library and genome assignments server


Trefoil superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Small proteins [ 56992] (90)
Fold:   Trefoil/Plexin domain-like [ 57491] (3)
Superfamily:   Trefoil [ 57492]
Families:   Trefoil [ 57493] (3)


Superfamily statistics
Genomes (115) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 923 910 5
Proteins 733 761 4


Functional annotation
General category Processes_IC
Detailed category Proteases

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)response to stimulus3.366e-050.01014Least InformativeInherited
Biological Process (BP)multicellular organismal process0.0028920.01232Least InformativeInherited
Biological Process (BP)response to organic substance0.00012010.0003439Moderately InformativeDirect
Biological Process (BP)digestion2.249e-104.006e-10Highly 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) regulation of cellular process 0.7751 Least Informative Inherited
Biological Process (BP) response to stimulus 0.01014 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.01232 Least Informative Inherited
Biological Process (BP) carbohydrate metabolic process 3.375e-05 Moderately Informative Direct
Biological Process (BP) response to organic substance 0.0003439 Moderately Informative Direct
Biological Process (BP) digestion 4.006e-10 Highly Informative Direct
Molecular Function (MF) hydrolase activity 0.001408 Least Informative Inherited
Molecular Function (MF) hydrolase activity, acting on glycosyl bonds 5.649e-11 Informative Direct
Molecular Function (MF) hydrolase activity, hydrolyzing O-glycosyl compounds 1.508e-11 Highly Informative Direct
Cellular Component (CC) vesicle 0.0003943 Moderately Informative Direct
Cellular Component (CC) extracellular region part 0.0008831 Moderately Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Glycosidases, i.e. enzymes hydrolyzing O- and S-gl0Moderately InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)nervous system disease0.06121Least InformativeInherited
Disease Ontology (DO)organ system cancer0.2353Least InformativeInherited
Disease Ontology (DO)sensory system disease0.003455Moderately InformativeInherited
Disease Ontology (DO)bile duct adenocarcinoma1.183e-05Highly InformativeDirect

Document: DO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)digestive/alimentary phenotype0.03812Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal intestine morphology0.002238InformativeInherited

Document: MP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)cell0Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect

Document: XA 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)Glycosylases0Moderately InformativeDirect
Enzyme Commission (EC)Alpha-glucosidase1.983e-06Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processFertilization0Highly InformativeDirect
Cellular componentMembrane0.0003018Least InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentExtracellular matrix6.373e-16InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransmembrane0.155Least InformativeInherited
Post-translational modificationHydrolase0.5071Least InformativeInherited
Post-translational modificationReceptor1.151e-05Moderately InformativeDirect
Post-translational modificationGrowth factor0InformativeDirect
Post-translational modificationGlycosidase5.632e-07InformativeDirect
Post-translational modificationDisulfide bond1.354e-15Least InformativeDirect
Post-translational modificationCleavage on pair of basic residues1.216e-08Moderately InformativeDirect
Post-translational modificationPyrrolidone carboxylic acid1.143e-09InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR000519 SSF57492 Protein matches
Abstract A cysteine-rich domain of approximately forty five amino-acid residues has been found in some extracellular eukaryotic proteins [PubMed7820556, PubMed9187350, PubMed8518738, PubMed8267796]. It is known as either the 'P', 'trefoil' or 'TFF' domain, and contains six cysteines linked by three disulphide bonds with connectivity 1-5, 2-4, 3-6. The domain has been found in a variety of extracellular eukaryotic proteins [PubMed7820556, PubMed8518738, PubMed8267796], including protein pS2 (TFF1), a protein secreted by the stomach mucosa; spasmolytic polypeptide (SP) (TFF2), a protein of about 115 residues that inhibits gastrointestinal motility and gastric acid secretion; intestinal trefoil factor (ITF) (TFF3); Xenopus laevis stomach proteins xP1 and xP4; xenopus integumentary mucins A.1 (FIM-A.1 or preprospasmolysin) and C.1 (FIM-C.1), proteins which may be involved in defense against microbial infections by protecting the epithelia from the external environment; xenopus skin protein xp2 (or APEG); Zona pellucida sperm-binding protein B (ZP-B); intestinal sucrase-isomaltase , a vertebrate membrane bound, multifunctional enzyme complex which hydrolyzes sucrose, maltose and isomaltose; and lysosomal alpha-glucosidase .

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) · Disease Ontology (DO) · Mouse Phenotype (MP) · Xenopus Anatomy (XA) · 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 4 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 Trefoil 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 4 hidden Markov models representing the Trefoil 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) · Disease Ontology (DO) · Mouse Phenotype (MP) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]