SUPERFAMILY 1.75 HMM library and genome assignments server


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 (219) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 28,026 29,725 2
Proteins 8,039 9,613 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) protein metabolic process 0.0001766 Least Informative Direct
Biological Process (BP) multicellular organismal process 2.599e-09 Least Informative Direct
Biological Process (BP) developmental process 8.063e-10 Least Informative Direct
Biological Process (BP) response to stimulus 0.0008485 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.000141 Least Informative Direct
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) localization 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.003947 Least Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 2.395e-05 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 0.0001062 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 2.469e-08 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.1009 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.8054 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) tissue development 1 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.1561 Moderately Informative Inherited
Biological Process (BP) organ development 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.3344 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.6306 Moderately Informative Inherited
Biological Process (BP) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.1734 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.1846 Moderately Informative Inherited
Biological Process (BP) gene expression 0.994 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.2627 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) reproduction 0.5967 Moderately Informative Inherited
Biological Process (BP) immune system process 0.0534 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 0.01848 Moderately Informative Inherited
Biological Process (BP) immune effector process 4.817e-06 Informative Direct
Biological Process (BP) regulation of immune effector process 2.61e-08 Informative Direct
Biological Process (BP) proteolysis 3.074e-10 Informative Direct
Biological Process (BP) cellular component movement 3.755e-15 Informative Direct
Biological Process (BP) defense response 1.791e-07 Informative Direct
Biological Process (BP) immune response 0.0008219 Informative Direct
Biological Process (BP) response to bacterium 0.0007617 Informative Direct
Biological Process (BP) biological adhesion 0.0002434 Informative Direct
Biological Process (BP) cell projection organization 1.334e-10 Informative Direct
Biological Process (BP) regulation of response to external stimulus 4.474e-08 Informative Direct
Biological Process (BP) cellular component morphogenesis 3.333e-05 Informative Direct
Biological Process (BP) locomotion 0 Informative Direct
Biological Process (BP) regulation of locomotion 5.426e-07 Informative Direct
Biological Process (BP) generation of neurons 4.323e-09 Informative Direct
Biological Process (BP) regulation of cellular component movement 2.489e-08 Informative Direct
Biological Process (BP) localization of cell 5.009e-05 Informative Direct
Biological Process (BP) cardiovascular system development 4.522e-05 Informative Direct
Biological Process (BP) regulation of nervous system development 1 Informative Inherited
Biological Process (BP) regulation of cell development 1 Informative Inherited
Biological Process (BP) regulation of cell activation 0.01359 Informative Inherited
Biological Process (BP) tissue morphogenesis 0.4422 Informative Inherited
Biological Process (BP) epithelium development 1 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.03685 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.02426 Informative Inherited
Biological Process (BP) single organism reproductive process 0.5929 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.08814 Informative Inherited
Biological Process (BP) response to cytokine stimulus 0.04875 Informative Inherited
Biological Process (BP) regulation of cytokine production 0.6236 Informative Inherited
Biological Process (BP) regulation of anatomical structure morphogenesis 0.1269 Informative Inherited
Biological Process (BP) negative regulation of developmental process 0.002406 Informative Inherited
Biological Process (BP) regulation of anatomical structure size 0.01013 Informative Inherited
Biological Process (BP) organ morphogenesis 0.4814 Informative Inherited
Biological Process (BP) regulation of immune response 0.0353 Informative Inherited
Biological Process (BP) regulation of defense response 0.3001 Informative Inherited
Biological Process (BP) positive regulation of immune system process 0.001106 Informative Inherited
Biological Process (BP) regulation of cell proliferation 0.02923 Informative Inherited
Biological Process (BP) sexual reproduction 0.07342 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 1 Informative Inherited
Biological Process (BP) reproductive system development 0.9499 Informative Inherited
Biological Process (BP) cell morphogenesis involved in differentiation 5.12e-12 Highly Informative Direct
Biological Process (BP) angiogenesis 2.786e-06 Highly Informative Direct
Biological Process (BP) regulation of acute inflammatory response 1.261e-07 Highly Informative Direct
Biological Process (BP) regulation of humoral immune response 2.765e-10 Highly Informative Direct
Biological Process (BP) heart morphogenesis 0.000575 Highly Informative Direct
Biological Process (BP) chemotaxis 7.043e-14 Highly Informative Direct
Biological Process (BP) humoral immune response 8.338e-07 Highly Informative Direct
Biological Process (BP) cell adhesion 0.0008252 Highly Informative Direct
Biological Process (BP) regulation of cell size 5.835e-05 Highly Informative Direct
Biological Process (BP) protein processing 4.17e-09 Highly Informative Direct
Biological Process (BP) ovulation cycle process 5.998e-05 Highly Informative Direct
Biological Process (BP) regulation of cell adhesion 2.218e-07 Highly Informative Direct
Biological Process (BP) extracellular matrix organization 0 Highly Informative Direct
Biological Process (BP) neuron projection development 0 Highly Informative Direct
Biological Process (BP) cell part morphogenesis 2.654e-07 Highly Informative Direct
Biological Process (BP) positive regulation of programmed cell death 0.0002806 Highly Informative Direct
Biological Process (BP) regulation of angiogenesis 7.861e-10 Highly Informative Direct
Biological Process (BP) regulation of coagulation 0.0004181 Highly Informative Direct
Biological Process (BP) regulation of wound healing 0.0009797 Highly Informative Direct
Biological Process (BP) connective tissue development 1.936e-05 Highly Informative Direct
Biological Process (BP) regulation of protein processing 1.938e-15 Highly Informative Direct
Biological Process (BP) protein activation cascade 9.794e-08 Highly Informative Direct
Biological Process (BP) regulation of hemostasis 0.0002955 Highly Informative Direct
Biological Process (BP) skeletal system development 0.07528 Highly Informative Inherited
Biological Process (BP) regulation of epithelial cell differentiation 0.002561 Highly Informative Inherited
Biological Process (BP) post-embryonic development 1 Highly Informative Inherited
Biological Process (BP) female gamete generation 0.3074 Highly Informative Inherited
Biological Process (BP) gonad development 0.002307 Highly Informative Inherited
Biological Process (BP) development of primary female sexual characteristics 0.0617 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 1.433e-10 Least Informative Direct
Molecular Function (MF) binding 0.4228 Least Informative Inherited
Molecular Function (MF) anion binding 0.000145 Moderately Informative Direct
Molecular Function (MF) receptor binding 7.819e-06 Informative Direct
Molecular Function (MF) peptidase activity 0 Informative Direct
Molecular Function (MF) carbohydrate derivative binding 0 Informative Direct
Molecular Function (MF) sulfur compound binding 0 Informative Direct
Molecular Function (MF) receptor activity 0.00271 Informative Inherited
Molecular Function (MF) molecular transducer activity 0.009577 Informative Inherited
Molecular Function (MF) enzyme binding 0.8663 Informative Inherited
Molecular Function (MF) heparin binding 0 Highly Informative Direct
Molecular Function (MF) metallopeptidase activity 0 Highly Informative Direct
Molecular Function (MF) protein complex binding 0.0004111 Highly Informative Direct
Molecular Function (MF) endopeptidase activity 0.2302 Highly Informative Inherited
Cellular Component (CC) vesicle 0.0005384 Moderately Informative Direct
Cellular Component (CC) extracellular region part 0 Moderately Informative Direct
Cellular Component (CC) cell surface 4.428e-07 Informative Direct
Cellular Component (CC) extracellular matrix 0 Informative Direct
Cellular Component (CC) extracellular membrane-bounded organelle 4.709e-05 Informative Direct
Cellular Component (CC) proteinaceous extracellular matrix 6.397e-07 Highly Informative Direct
Cellular Component (CC) extracellular matrix part 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)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 cancer0.3066Least InformativeInherited
Disease Ontology (DO)nervous system cancer0.4905Moderately InformativeInherited
Disease Ontology (DO)peripheral nervous system neoplasm0.2113InformativeInherited
Disease Ontology (DO)neurofibroma1.435e-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 skeletal morphology0.4193Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the immune system0.04675Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of digit0.07254Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the lower limb0.1167Moderately InformativeInherited
Phenotypic Abnormality (PA)Aplasia/hypoplasia involving the skeleton0.2451Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the globe0.4355Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of complement system3.094e-07InformativeDirect
Phenotypic Abnormality (PA)Abnormality of toe0.01881InformativeInherited
Phenotypic Abnormality (PA)Aplasia/Hypoplasia involving bones of the feet0.03354InformativeInherited
Phenotypic Abnormality (PA)Short digit0.1251InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the lens0.1374InformativeInherited
Phenotypic Abnormality (PA)Recurrent infections0.4439InformativeInherited
Phenotypic Abnormality (PA)Short toe0.0009994Highly 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

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)portion of tissue0.9303Least InformativeInherited
Xenopus ANatomical entity (XAN)embryo0.9831Least InformativeInherited
Xenopus ANatomical entity (XAN)central nervous system1Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.4377Moderately InformativeInherited
Xenopus ANatomical entity (XAN)multi-tissue structure0.5479Moderately InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm1Moderately InformativeInherited
Xenopus ANatomical entity (XAN)endoderm1.383e-05InformativeDirect
Xenopus ANatomical entity (XAN)spinal cord0.02496InformativeInherited
Xenopus ANatomical entity (XAN)hypochord7.166e-07Highly InformativeDirect
Xenopus ANatomical entity (XAN)floor plate0.0002364Highly InformativeDirect
Xenopus ANatomical entity (XAN)neural tube0.0006097Highly InformativeDirect
Xenopus ANatomical entity (XAN)cranial neural crest0.01691Highly InformativeInherited
Xenopus DEvelopment stage (XDE)embryonic stage0.0002623Least InformativeDirect
Xenopus DEvelopment stage (XDE)NF stage0.0004684Least 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 processApoptosis2.04e-12Moderately InformativeDirect
Biological processDifferentiation0.0002676Moderately InformativeDirect
Biological processCell adhesion0InformativeDirect
Biological processCytolysis0InformativeDirect
Biological processInnate immunity0InformativeDirect
Biological processWnt signaling pathway0InformativeDirect
Biological processSensory transduction5.331e-11InformativeDirect
Biological processNeurogenesis4.169e-06InformativeDirect
Biological processComplement alternate pathway0Highly InformativeDirect
Biological processComplement pathway2.611e-14Highly InformativeDirect
Biological processDNA synthesis3.124e-08Highly InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentExtracellular matrix0InformativeDirect
Coding sequence diversityPolymorphism3.582e-05Moderately InformativeDirect
Developmental stageSporozoite0InformativeDirect
DiseaseMalaria0InformativeDirect
DomainRepeat0Least InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransmembrane1Least InformativeInherited
DomainEGF-like domain0InformativeDirect
DomainImmunoglobulin domain1.573e-12InformativeDirect
DomainTransmembrane beta strand9.907e-08InformativeDirect
DomainSushi1.976e-11Highly InformativeDirect
Molecular functionZinc6.756e-09Least InformativeDirect
Molecular functionCalcium8.168e-12Moderately InformativeDirect
Molecular functionHeparin-binding0InformativeDirect
Molecular functionGrowth factor binding2.076e-11Highly InformativeDirect
Post-translational modificationHydrolase0.001085Least InformativeInherited
Post-translational modificationDevelopmental protein0Moderately InformativeDirect
Post-translational modificationProtease0Moderately InformativeDirect
Post-translational modificationReceptor8.077e-11Moderately InformativeDirect
Post-translational modificationMetalloprotease0InformativeDirect
Post-translational modificationGrowth factor1.166e-08InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect
Post-translational modificationCleavage on pair of basic residues0Moderately InformativeDirect
Post-translational modificationZymogen1.355e-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) · 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) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]