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TSP-1 type 1 repeat superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Small proteins [ 56992] (90)
Fold:   TSP-1 type 1 repeat [ 82894]
Superfamily:   TSP-1 type 1 repeat [ 82895]
Families:   TSP-1 type 1 repeat [ 82896]

 Superfamily statistics
Genomes (185) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 24,928 24,662 2
Proteins 7,218 7,876 1

 Functional annotation
General category Processes_EC
Detailed category Cell adhesion

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) developmental process 1.813e-07 Least Informative Direct
Biological Process (BP) multicellular organismal process 1.393e-06 Least Informative Direct
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.003052 Least Informative Inherited
Biological Process (BP) response to stimulus 0.2632 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.4501 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.009008 Least Informative Inherited
Biological Process (BP) single-organism developmental process 5.798e-06 Moderately Informative Direct
Biological Process (BP) anatomical structure morphogenesis 0.0003271 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 0.0008479 Moderately Informative Direct
Biological Process (BP) tissue development 1 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.2026 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.05285 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.4882 Moderately Informative Inherited
Biological Process (BP) reproduction 0.6415 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.1011 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.2211 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 0.06172 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 0.07712 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.001335 Moderately Informative Inherited
Biological Process (BP) gene expression 1 Moderately Informative Inherited
Biological Process (BP) organ development 1 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 0.01882 Moderately Informative Inherited
Biological Process (BP) immune system process 0.5323 Moderately Informative Inherited
Biological Process (BP) locomotion 3.07e-13 Informative Direct
Biological Process (BP) proteolysis 4.69e-10 Informative Direct
Biological Process (BP) cell projection organization 4.768e-09 Informative Direct
Biological Process (BP) response to external stimulus 6.589e-08 Informative Direct
Biological Process (BP) regulation of locomotion 4.919e-05 Informative Direct
Biological Process (BP) regulation of cellular component movement 5.807e-05 Informative Direct
Biological Process (BP) regulation of apoptotic process 7.241e-05 Informative Direct
Biological Process (BP) cellular component morphogenesis 7.405e-05 Informative Direct
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.0927 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.003565 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.217 Informative Inherited
Biological Process (BP) single organism reproductive process 0.478 Informative Inherited
Biological Process (BP) generation of neurons 0.02626 Informative Inherited
Biological Process (BP) regulation of anatomical structure morphogenesis 0.1262 Informative Inherited
Biological Process (BP) negative regulation of developmental process 0.005039 Informative Inherited
Biological Process (BP) biological adhesion 0.00107 Informative Inherited
Biological Process (BP) immune response 0.03445 Informative Inherited
Biological Process (BP) immune effector process 0.01466 Informative Inherited
Biological Process (BP) positive regulation of immune system process 0.02933 Informative Inherited
Biological Process (BP) regulation of immune response 0.2505 Informative Inherited
Biological Process (BP) organ morphogenesis 0.1906 Informative Inherited
Biological Process (BP) cardiovascular system development 0.001024 Informative Inherited
Biological Process (BP) sexual reproduction 0.1758 Informative Inherited
Biological Process (BP) reproductive system development 0.7018 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 1 Informative Inherited
Biological Process (BP) extracellular matrix organization 0 Highly Informative Direct
Biological Process (BP) axonogenesis 4.008e-15 Highly Informative Direct
Biological Process (BP) chemotaxis 2.294e-13 Highly Informative Direct
Biological Process (BP) regulation of angiogenesis 9.343e-10 Highly Informative Direct
Biological Process (BP) protein processing 4.64e-07 Highly Informative Direct
Biological Process (BP) protein activation cascade 1.824e-06 Highly Informative Direct
Biological Process (BP) angiogenesis 1.217e-05 Highly Informative Direct
Biological Process (BP) connective tissue development 2.181e-05 Highly Informative Direct
Biological Process (BP) heart morphogenesis 3.051e-05 Highly Informative Direct
Biological Process (BP) ovulation cycle process 3.214e-05 Highly Informative Direct
Biological Process (BP) regulation of epithelial cell differentiation 0.0002093 Highly Informative Direct
Biological Process (BP) humoral immune response 0.0002834 Highly Informative Direct
Biological Process (BP) gonad development 0.0006067 Highly Informative Direct
Biological Process (BP) cell adhesion 0.0006767 Highly Informative Direct
Biological Process (BP) skeletal system development 0.02396 Highly Informative Inherited
Biological Process (BP) positive regulation of cell differentiation 0.001458 Highly Informative Inherited
Biological Process (BP) regulation of cell adhesion 0.01073 Highly Informative Inherited
Biological Process (BP) activation of immune response 0.001194 Highly Informative Inherited
Biological Process (BP) female gamete generation 0.1191 Highly Informative Inherited
Biological Process (BP) development of primary female sexual characteristics 0.08408 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 5.625e-10 Least Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) protein binding 0.94 Moderately Informative Inherited
Molecular Function (MF) anion binding 0.005951 Moderately Informative Inherited
Molecular Function (MF) peptidase activity 0 Informative Direct
Molecular Function (MF) receptor binding 0.00165 Informative Inherited
Molecular Function (MF) receptor activity 0.002364 Informative Inherited
Molecular Function (MF) molecular transducer activity 0.009766 Informative Inherited
Molecular Function (MF) metallopeptidase activity 0 Highly Informative Direct
Molecular Function (MF) glycosaminoglycan binding 7.973e-16 Highly Informative Direct
Molecular Function (MF) sulfur compound binding 1.562e-15 Highly Informative Direct
Molecular Function (MF) protein complex binding 3.113e-05 Highly Informative Direct
Cellular Component (CC) extracellular region 0 Moderately Informative Direct
Cellular Component (CC) extracellular matrix 0 Informative Direct
Cellular Component (CC) cell surface 1.323e-05 Informative Direct
Cellular Component (CC) extracellular matrix part 0 Highly Informative Direct
Cellular Component (CC) proteinaceous extracellular matrix 0.0001235 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)Acting on peptide bonds (peptide hydrolases)0Least InformativeDirect
Enzyme Commission (EC)Metalloendopeptidases0InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)organ system cancer0.392Least InformativeInherited
Disease Ontology (DO)nervous system cancer0.4337Moderately InformativeInherited
Disease Ontology (DO)peripheral nervous system neoplasm0.2013InformativeInherited
Disease Ontology (DO)neurofibroma1.447e-05Highly InformativeDirect

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of the immune system0.04528Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the anterior segment of the eye0.3455Moderately InformativeInherited
Phenotypic Abnormality (PA)Recurrent bacterial infections0.007365InformativeInherited
Phenotypic Abnormality (PA)Abnormality of humoral immunity0.06639InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the lens0.1369InformativeInherited
Phenotypic Abnormality (PA)Abnormality of complement system2.217e-07Highly InformativeDirect

Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)pericellular component development variant4.574e-09Moderately InformativeDirect
Worm Phenotype (WP)organ system development variant0.01464Moderately InformativeInherited
Worm Phenotype (WP)basement membrane remodeling variant7.606e-10InformativeDirect
Worm Phenotype (WP)anchor cell invasion variant0.0003855InformativeDirect
Worm Phenotype (WP)cell migration variant0.005766InformativeInherited
Worm Phenotype (WP)distal tip cell migration variant0.000517Highly InformativeDirect

Document: WP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)organ system0Least InformativeDirect

Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)portion of tissue0.7867Least InformativeInherited
Xenopus ANatomical entity (XAN)embryo0.8873Least InformativeInherited
Xenopus ANatomical entity (XAN)central nervous system0.9381Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.153Moderately InformativeInherited
Xenopus ANatomical entity (XAN)multi-tissue structure0.3869Moderately InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm1Moderately InformativeInherited
Xenopus ANatomical entity (XAN)endoderm7.423e-05InformativeDirect
Xenopus ANatomical entity (XAN)spinal cord0.04831InformativeInherited
Xenopus ANatomical entity (XAN)hypochord1.194e-06Highly InformativeDirect
Xenopus ANatomical entity (XAN)floor plate8.333e-05Highly InformativeDirect
Xenopus ANatomical entity (XAN)neural tube0.0002857Highly InformativeDirect
Xenopus ANatomical entity (XAN)hyoid crest0.0003891Highly InformativeDirect
Xenopus ANatomical entity (XAN)cranial neural crest0.006089Highly InformativeInherited
Xenopus DEvelopment stage (XDE)embryonic stage0.0006381Least 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)Acting on peptide bonds (peptide hydrolases)0Moderately InformativeDirect
Enzyme Commission (EC)Metalloendopeptidases0InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processApoptosis1.259e-12Moderately InformativeDirect
Biological processDifferentiation0.0001932Moderately InformativeDirect
Biological processCell adhesion0InformativeDirect
Biological processCytolysis0InformativeDirect
Biological processInnate immunity0InformativeDirect
Biological processWnt signaling pathway0InformativeDirect
Biological processSensory transduction4.437e-11InformativeDirect
Biological processNeurogenesis3.545e-05InformativeDirect
Biological processComplement alternate pathway0Highly InformativeDirect
Biological processComplement pathway6.929e-13Highly InformativeDirect
Biological processDNA synthesis3.136e-08Highly InformativeDirect
Cellular componentMembrane0.8848Least InformativeInherited
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentExtracellular matrix0InformativeDirect
Cellular componentTransmembrane beta strand1.217e-09Highly InformativeDirect
Coding sequence diversityPolymorphism3.102e-05Moderately InformativeDirect
Developmental stageSporozoite0InformativeDirect
DiseaseMalaria0InformativeDirect
DomainRepeat0Least InformativeDirect
DomainSignal0Least InformativeDirect
DomainEGF-like domain0InformativeDirect
DomainImmunoglobulin domain7.054e-12InformativeDirect
DomainSushi3.444e-11Highly InformativeDirect
Molecular functionZinc3.278e-09Least InformativeDirect
Molecular functionCalcium7.887e-10Moderately InformativeDirect
Molecular functionHeparin-binding0InformativeDirect
Molecular functionGrowth factor binding2.153e-11Highly InformativeDirect
Post-translational modificationHydrolase0.0007313Least InformativeDirect
Post-translational modificationDevelopmental protein0Moderately InformativeDirect
Post-translational modificationProtease0Moderately InformativeDirect
Post-translational modificationReceptor8.101e-11Moderately InformativeDirect
Post-translational modificationMetalloprotease0InformativeDirect
Post-translational modificationGrowth factor1.094e-08InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect
Post-translational modificationCleavage on pair of basic residues0Moderately InformativeDirect
Post-translational modificationZymogen1.756e-15InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR000884 SSF82895 Protein matches
Abstract

This repeat was first described in 1986 by Lawler and Hynes [PubMed2430973]. It was found in the thrombospondin protein where it is repeated 3 times. Now a number of proteins involved in the complement pathway (properdin, C6, C7, C8A, C8B, C9) [PubMed2459396] as well as extracellular matrix protein like mindin, F-spondin [PubMed10409509], SCO-spondin and even the circumsporozoite surface protein 2 and TRAP proteins of Plasmodium [PubMed10508153, PubMed1501644] contain one or more instance of this repeat. It has been involved in cell-cell interraction, inhibition of angiogenesis [PubMed10500044] and apoptosis [PubMed9135017].

The intron-exon organisation of the properdin gene confirms the hypothesis that the repeat might have evolved by a process involving exon shuffling [PubMed1417780]. A study of properdin structure provides some information about the structure of the thrombospondin type I repeat [PubMed1868073].


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-coverage) · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Worm Phenotype (WP) · Fly Anatomy (FA) · 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 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 TSP-1 type 1 repeat 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 TSP-1 type 1 repeat 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-coverage) · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Worm Phenotype (WP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]
Please cite: Gough, J., Karplus, K., Hughey, R. and Chothia, C. (2001). "Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure." J. Mol. Biol., 313(4), 903-919.

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© Copyright 2013 The SUPERFAMILY authors and Julian Gough.