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 (220) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 28,499 29,725 2
Proteins 8,114 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) multicellular organismal process 0.0000000005661 Least Informative Direct
Biological Process (BP) developmental process 0.0000000007755 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.00008726 Least Informative Direct
Biological Process (BP) protein metabolic process 0.0002537 Least Informative Direct
Biological Process (BP) response to stimulus 0.0008455 Least Informative Direct
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) positive regulation of biological process 0.004502 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 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.00000002919 Moderately Informative Direct
Biological Process (BP) defense response 0.0000000671 Moderately Informative Direct
Biological Process (BP) response to external stimulus 0.0000002372 Moderately Informative Direct
Biological Process (BP) anatomical structure morphogenesis 0.00002364 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 0.0001057 Moderately Informative Direct
Biological Process (BP) nervous system development 0.1996 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.8192 Moderately Informative Inherited
Biological Process (BP) tissue development 1 Moderately Informative Inherited
Biological Process (BP) gene expression 1 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.1747 Moderately Informative Inherited
Biological Process (BP) reproductive process 0.4485 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.6289 Moderately Informative Inherited
Biological Process (BP) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.1923 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.5607 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.1525 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 1 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.06739 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.8704 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 0.002244 Moderately Informative Inherited
Biological Process (BP) immune system process 0.05272 Moderately Informative Inherited
Biological Process (BP) organ development 0.9556 Moderately Informative Inherited
Biological Process (BP) cellular component movement 0 Informative Direct
Biological Process (BP) locomotion 0 Informative Direct
Biological Process (BP) cell projection organization 0.000000000002296 Informative Direct
Biological Process (BP) regulation of response to wounding 0.0000000001369 Informative Direct
Biological Process (BP) proteolysis 0.0000000002826 Informative Direct
Biological Process (BP) generation of neurons 0.000000005135 Informative Direct
Biological Process (BP) regulation of cellular component movement 0.00000002391 Informative Direct
Biological Process (BP) regulation of immune effector process 0.0000000308 Informative Direct
Biological Process (BP) regulation of locomotion 0.0000005596 Informative Direct
Biological Process (BP) regulation of response to external stimulus 0.00000181 Informative Direct
Biological Process (BP) immune effector process 0.00000496 Informative Direct
Biological Process (BP) protein maturation 0.000007194 Informative Direct
Biological Process (BP) positive regulation of cell death 0.000009981 Informative Direct
Biological Process (BP) regulation of apoptotic process 0.00002554 Informative Direct
Biological Process (BP) cellular component morphogenesis 0.00002793 Informative Direct
Biological Process (BP) cardiovascular system development 0.0000496 Informative Direct
Biological Process (BP) localization of cell 0.00005521 Informative Direct
Biological Process (BP) negative regulation of multicellular organismal process 0.0001503 Informative Direct
Biological Process (BP) biological adhesion 0.0001891 Informative Direct
Biological Process (BP) immune response 0.0008033 Informative Direct
Biological Process (BP) response to bacterium 0.0008128 Informative Direct
Biological Process (BP) regulation of cell development 1 Informative Inherited
Biological Process (BP) regulation of nervous system development 1 Informative Inherited
Biological Process (BP) regulation of anatomical structure morphogenesis 0.1118 Informative Inherited
Biological Process (BP) positive regulation of cellular component organization 0.3076 Informative Inherited
Biological Process (BP) tissue morphogenesis 0.3343 Informative Inherited
Biological Process (BP) epithelium development 1 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.1308 Informative Inherited
Biological Process (BP) organ morphogenesis 0.3373 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.03834 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.03713 Informative Inherited
Biological Process (BP) regulation of defense response 0.2677 Informative Inherited
Biological Process (BP) defense response to other organism 0.2233 Informative Inherited
Biological Process (BP) response to cytokine 0.04995 Informative Inherited
Biological Process (BP) positive regulation of multicellular organismal process 0.1096 Informative Inherited
Biological Process (BP) regulation of cytokine production 0.6514 Informative Inherited
Biological Process (BP) single organism reproductive process 0.3356 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.1024 Informative Inherited
Biological Process (BP) central nervous system development 0.2729 Informative Inherited
Biological Process (BP) negative regulation of developmental process 0.004266 Informative Inherited
Biological Process (BP) regulation of cell activation 0.01339 Informative Inherited
Biological Process (BP) regulation of anatomical structure size 0.01031 Informative Inherited
Biological Process (BP) regulation of immune response 0.03466 Informative Inherited
Biological Process (BP) positive regulation of immune system process 0.001752 Informative Inherited
Biological Process (BP) regulation of cell proliferation 0.02839 Informative Inherited
Biological Process (BP) sexual reproduction 0.1033 Informative Inherited
Biological Process (BP) reproductive structure development 0.7138 Informative Inherited
Biological Process (BP) neuron projection development 0 Highly Informative Direct
Biological Process (BP) extracellular matrix organization 0 Highly Informative Direct
Biological Process (BP) chemotaxis 0.00000000000006627 Highly Informative Direct
Biological Process (BP) cell morphogenesis involved in differentiation 0.000000000003031 Highly Informative Direct
Biological Process (BP) regulation of humoral immune response 0.0000000002621 Highly Informative Direct
Biological Process (BP) protein activation cascade 0.00000001223 Highly Informative Direct
Biological Process (BP) regulation of acute inflammatory response 0.0000001261 Highly Informative Direct
Biological Process (BP) cell projection morphogenesis 0.0000002199 Highly Informative Direct
Biological Process (BP) regulation of cell adhesion 0.0000002264 Highly Informative Direct
Biological Process (BP) humoral immune response 0.0000008158 Highly Informative Direct
Biological Process (BP) angiogenesis 0.000001274 Highly Informative Direct
Biological Process (BP) defense response to bacterium 0.000002417 Highly Informative Direct
Biological Process (BP) ovulation cycle process 0.00001973 Highly Informative Direct
Biological Process (BP) connective tissue development 0.00001985 Highly Informative Direct
Biological Process (BP) cell adhesion 0.00005427 Highly Informative Direct
Biological Process (BP) regulation of cell size 0.00006043 Highly Informative Direct
Biological Process (BP) negative regulation of hemostasis 0.0001877 Highly Informative Direct
Biological Process (BP) negative regulation of coagulation 0.0003159 Highly Informative Direct
Biological Process (BP) heart morphogenesis 0.0005637 Highly Informative Direct
Biological Process (BP) regulation of wound healing 0.3288 Highly Informative Inherited
Biological Process (BP) negative regulation of response to wounding 0.05612 Highly Informative Inherited
Biological Process (BP) skeletal system development 0.07832 Highly Informative Inherited
Biological Process (BP) regulation of epithelial cell differentiation 0.002791 Highly Informative Inherited
Biological Process (BP) positive regulation of cytokine production 0.05643 Highly Informative Inherited
Biological Process (BP) negative regulation of response to external stimulus 0.009 Highly Informative Inherited
Biological Process (BP) post-embryonic development 1 Highly Informative Inherited
Biological Process (BP) female gamete generation 0.3056 Highly Informative Inherited
Biological Process (BP) gonad development 0.001434 Highly Informative Inherited
Biological Process (BP) development of primary female sexual characteristics 0.04539 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0.0000000001707 Least Informative Direct
Molecular Function (MF) binding 0.448 Least Informative Inherited
Molecular Function (MF) carbohydrate derivative binding 0.00000000008941 Moderately Informative Direct
Molecular Function (MF) anion binding 0.0001447 Moderately Informative Direct
Molecular Function (MF) sulfur compound binding 0 Informative Direct
Molecular Function (MF) peptidase activity 0 Informative Direct
Molecular Function (MF) receptor binding 0.000007607 Informative Direct
Molecular Function (MF) protein complex binding 0.07904 Informative Inherited
Molecular Function (MF) receptor activity 0.002005 Informative Inherited
Molecular Function (MF) molecular transducer activity 0.007409 Informative Inherited
Molecular Function (MF) enzyme binding 0.8715 Informative Inherited
Molecular Function (MF) heparin binding 0 Highly Informative Direct
Molecular Function (MF) metallopeptidase activity 0 Highly Informative Direct
Molecular Function (MF) transmembrane signaling receptor activity 0.0001349 Highly Informative Direct
Molecular Function (MF) cell adhesion molecule binding 0.0001772 Highly Informative Direct
Molecular Function (MF) endopeptidase activity 0.2257 Highly Informative Inherited
Cellular Component (CC) extracellular region part 0 Moderately Informative Direct
Cellular Component (CC) vesicle 0.0002632 Moderately Informative Direct
Cellular Component (CC) extracellular matrix 0 Informative Direct
Cellular Component (CC) cell surface 0.000001324 Informative Direct
Cellular Component (CC) extracellular membrane-bounded organelle 0.00001646 Informative Direct
Cellular Component (CC) extracellular matrix part 0 Highly Informative Direct
Cellular Component (CC) proteinaceous extracellular matrix 0.000000196 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)neurofibroma0.00001435Highly 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 system0.0000003094InformativeDirect
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 variant0.000000004574Moderately InformativeDirect
Worm Phenotype (WP)organ system development variant0.01464Moderately InformativeInherited
Worm Phenotype (WP)basement membrane remodeling variant0.0000000007606InformativeDirect
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)endoderm0.00001383InformativeDirect
Xenopus ANatomical entity (XAN)spinal cord0.02496InformativeInherited
Xenopus ANatomical entity (XAN)hypochord0.0000007166Highly 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 processApoptosis0.00000000000204Moderately InformativeDirect
Biological processDifferentiation0.0002676Moderately InformativeDirect
Biological processCell adhesion0InformativeDirect
Biological processCytolysis0InformativeDirect
Biological processInnate immunity0InformativeDirect
Biological processWnt signaling pathway0InformativeDirect
Biological processSensory transduction0.00000000005331InformativeDirect
Biological processNeurogenesis0.000004169InformativeDirect
Biological processComplement alternate pathway0Highly InformativeDirect
Biological processComplement pathway0.00000000000002611Highly InformativeDirect
Biological processDNA synthesis0.00000003124Highly InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentExtracellular matrix0InformativeDirect
Coding sequence diversityPolymorphism0.00003582Moderately InformativeDirect
Developmental stageSporozoite0InformativeDirect
DiseaseMalaria0InformativeDirect
DomainRepeat0Least InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransmembrane1Least InformativeInherited
DomainEGF-like domain0InformativeDirect
DomainImmunoglobulin domain0.000000000001573InformativeDirect
DomainTransmembrane beta strand0.00000009907InformativeDirect
DomainSushi0.00000000001976Highly InformativeDirect
Molecular functionZinc0.000000006756Least InformativeDirect
Molecular functionCalcium0.000000000008168Moderately InformativeDirect
Molecular functionHeparin-binding0InformativeDirect
Molecular functionGrowth factor binding0.00000000002076Highly InformativeDirect
Post-translational modificationHydrolase0.001085Least InformativeInherited
Post-translational modificationDevelopmental protein0Moderately InformativeDirect
Post-translational modificationProtease0Moderately InformativeDirect
Post-translational modificationReceptor0.00000000008077Moderately InformativeDirect
Post-translational modificationMetalloprotease0InformativeDirect
Post-translational modificationGrowth factor0.00000001166InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect
Post-translational modificationCleavage on pair of basic residues0Moderately InformativeDirect
Post-translational modificationZymogen0.000000000000001355InformativeDirect

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 ]