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 (190) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 25,415 24,662 2
Proteins 7,354 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 2.983e-10 Least Informative Direct
Biological Process (BP) multicellular organismal process 1.564e-09 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 5.213e-05 Least Informative Direct
Biological Process (BP) response to stimulus 0.0001453 Least Informative Direct
Biological Process (BP) protein metabolic process 0.0003879 Least Informative Direct
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.01238 Least Informative Inherited
Biological Process (BP) localization 1 Least Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 2.495e-07 Moderately Informative Direct
Biological Process (BP) single-organism developmental process 3.955e-06 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 1.237e-05 Moderately Informative Direct
Biological Process (BP) anatomical structure morphogenesis 2.574e-05 Moderately Informative Direct
Biological Process (BP) regulation of programmed cell death 6.028e-05 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.1327 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 0.07117 Moderately Informative Inherited
Biological Process (BP) organ development 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.2017 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.4593 Moderately Informative Inherited
Biological Process (BP) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.1369 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.1751 Moderately Informative Inherited
Biological Process (BP) gene expression 1 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.5659 Moderately Informative Inherited
Biological Process (BP) reproduction 0.4884 Moderately Informative Inherited
Biological Process (BP) immune system process 0.04398 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 0.008455 Moderately Informative Inherited
Biological Process (BP) locomotion 0 Informative Direct
Biological Process (BP) cellular component movement 3.746e-15 Informative Direct
Biological Process (BP) cell projection organization 1.043e-11 Informative Direct
Biological Process (BP) proteolysis 5.11e-11 Informative Direct
Biological Process (BP) regulation of cellular component movement 5.063e-09 Informative Direct
Biological Process (BP) generation of neurons 6.652e-09 Informative Direct
Biological Process (BP) regulation of immune effector process 2.428e-08 Informative Direct
Biological Process (BP) defense response 8.757e-08 Informative Direct
Biological Process (BP) regulation of locomotion 1.729e-07 Informative Direct
Biological Process (BP) regulation of response to external stimulus 8.864e-06 Informative Direct
Biological Process (BP) cellular component morphogenesis 1.082e-05 Informative Direct
Biological Process (BP) immune effector process 2.453e-05 Informative Direct
Biological Process (BP) cardiovascular system development 8.55e-05 Informative Direct
Biological Process (BP) localization of cell 0.00011 Informative Direct
Biological Process (BP) biological adhesion 0.0004037 Informative Direct
Biological Process (BP) response to bacterium 0.0005598 Informative Direct
Biological Process (BP) negative regulation of developmental process 0.0006892 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) anatomical structure formation involved in morphogenesis 0.02392 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.02172 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.07483 Informative Inherited
Biological Process (BP) single organism reproductive process 0.4862 Informative Inherited
Biological Process (BP) response to cytokine stimulus 0.04441 Informative Inherited
Biological Process (BP) regulation of cytokine production 0.4865 Informative Inherited
Biological Process (BP) regulation of anatomical structure morphogenesis 0.1451 Informative Inherited
Biological Process (BP) regulation of anatomical structure size 0.006336 Informative Inherited
Biological Process (BP) immune response 0.001771 Informative Inherited
Biological Process (BP) organ morphogenesis 0.3764 Informative Inherited
Biological Process (BP) regulation of immune response 0.01082 Informative Inherited
Biological Process (BP) regulation of defense response 0.009897 Informative Inherited
Biological Process (BP) positive regulation of immune system process 0.001084 Informative Inherited
Biological Process (BP) sexual reproduction 0.06331 Informative Inherited
Biological Process (BP) reproductive structure development 0.735 Informative Inherited
Biological Process (BP) regulation of protein processing 0 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) chemotaxis 3.746e-15 Highly Informative Direct
Biological Process (BP) cell morphogenesis involved in differentiation 8.815e-12 Highly Informative Direct
Biological Process (BP) regulation of humoral immune response 2.878e-10 Highly Informative Direct
Biological Process (BP) regulation of angiogenesis 1.041e-09 Highly Informative Direct
Biological Process (BP) protein activation cascade 8.138e-08 Highly Informative Direct
Biological Process (BP) cell part morphogenesis 2.077e-07 Highly Informative Direct
Biological Process (BP) humoral immune response 3.71e-07 Highly Informative Direct
Biological Process (BP) protein processing 5.272e-07 Highly Informative Direct
Biological Process (BP) angiogenesis 2.231e-06 Highly Informative Direct
Biological Process (BP) connective tissue development 5.788e-06 Highly Informative Direct
Biological Process (BP) regulation of inflammatory response 2.612e-05 Highly Informative Direct
Biological Process (BP) regulation of cell size 2.893e-05 Highly Informative Direct
Biological Process (BP) ovulation cycle process 6.775e-05 Highly Informative Direct
Biological Process (BP) positive regulation of programmed cell death 0.000237 Highly Informative Direct
Biological Process (BP) regulation of cell adhesion 0.0003335 Highly Informative Direct
Biological Process (BP) heart morphogenesis 0.0003345 Highly Informative Direct
Biological Process (BP) activation of immune response 0.0007216 Highly Informative Direct
Biological Process (BP) cell adhesion 0.0009132 Highly Informative Direct
Biological Process (BP) skeletal system development 0.0606 Highly Informative Inherited
Biological Process (BP) positive regulation of cell differentiation 0.002287 Highly Informative Inherited
Biological Process (BP) regulation of epithelial cell differentiation 0.002761 Highly Informative Inherited
Biological Process (BP) post-embryonic development 1 Highly Informative Inherited
Biological Process (BP) female gamete generation 0.2906 Highly Informative Inherited
Biological Process (BP) gonad development 0.001683 Highly Informative Inherited
Biological Process (BP) development of primary female sexual characteristics 0.0726 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 7.143e-11 Least Informative Direct
Molecular Function (MF) binding 0.3451 Least Informative Inherited
Molecular Function (MF) anion binding 0.0004317 Moderately Informative Direct
Molecular Function (MF) peptidase activity 0 Informative Direct
Molecular Function (MF) sulfur compound binding 0 Informative Direct
Molecular Function (MF) carbohydrate derivative binding 0 Informative Direct
Molecular Function (MF) receptor binding 1.083e-05 Informative Direct
Molecular Function (MF) receptor activity 0.001738 Informative Inherited
Molecular Function (MF) molecular transducer activity 0.006693 Informative Inherited
Molecular Function (MF) metallopeptidase activity 0 Highly Informative Direct
Molecular Function (MF) heparin binding 0 Highly Informative Direct
Molecular Function (MF) protein complex binding 0.0002185 Highly Informative Direct
Molecular Function (MF) endopeptidase activity 0.2204 Highly Informative Inherited
Cellular Component (CC) extracellular region part 0 Moderately Informative Direct
Cellular Component (CC) extracellular matrix 0 Informative Direct
Cellular Component (CC) cell surface 1.708e-05 Informative Direct
Cellular Component (CC) extracellular matrix part 0 Highly Informative Direct
Cellular Component (CC) proteinaceous extracellular matrix 3.026e-07 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 cancer0.3628Least InformativeInherited
Disease Ontology (DO)nervous system cancer0.423Moderately InformativeInherited
Disease Ontology (DO)peripheral nervous system neoplasm0.1951InformativeInherited
Disease Ontology (DO)neurofibroma8.99e-06Highly 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 system0.04703Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the globe0.4411Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of humoral immunity0.06657InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the lens0.1439InformativeInherited
Phenotypic Abnormality (PA)Recurrent infections0.4308InformativeInherited
Phenotypic Abnormality (PA)Abnormality of complement system1.034e-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 tissue0.9256Least InformativeInherited
Xenopus ANatomical entity (XAN)embryo0.979Least InformativeInherited
Xenopus ANatomical entity (XAN)central nervous system1Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.4072Moderately InformativeInherited
Xenopus ANatomical entity (XAN)multi-tissue structure0.5233Moderately InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm1Moderately InformativeInherited
Xenopus ANatomical entity (XAN)endoderm1.159e-05InformativeDirect
Xenopus ANatomical entity (XAN)spinal cord0.01811InformativeInherited
Xenopus ANatomical entity (XAN)hypochord7.117e-07Highly InformativeDirect
Xenopus ANatomical entity (XAN)floor plate0.0001495Highly InformativeDirect
Xenopus ANatomical entity (XAN)neural tube0.0004643Highly InformativeDirect
Xenopus ANatomical entity (XAN)cranial neural crest0.01202Highly InformativeInherited
Xenopus DEvelopment stage (XDE)embryonic stage0.0002608Least InformativeDirect
Xenopus DEvelopment stage (XDE)NF stage0.0004629Least 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 processApoptosis2.005e-12Moderately InformativeDirect
Biological processDifferentiation0.0002434Moderately InformativeDirect
Biological processCell adhesion0InformativeDirect
Biological processCytolysis0InformativeDirect
Biological processInnate immunity0InformativeDirect
Biological processWnt signaling pathway0InformativeDirect
Biological processSensory transduction4.726e-11InformativeDirect
Biological processNeurogenesis3.688e-06InformativeDirect
Biological processComplement alternate pathway0Highly InformativeDirect
Biological processComplement pathway4.404e-14Highly InformativeDirect
Biological processDNA synthesis3.025e-08Highly InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentExtracellular matrix0InformativeDirect
Coding sequence diversityPolymorphism6.535e-05Moderately InformativeDirect
Developmental stageSporozoite0InformativeDirect
DiseaseMalaria0InformativeDirect
DomainRepeat0Least InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransmembrane1Least InformativeInherited
DomainEGF-like domain0InformativeDirect
DomainImmunoglobulin domain1.849e-12InformativeDirect
DomainSushi2.049e-11Highly InformativeDirect
DomainTransmembrane beta strand1.008e-07Highly InformativeDirect
Molecular functionZinc5.096e-09Least InformativeDirect
Molecular functionCalcium5.235e-12Moderately InformativeDirect
Molecular functionHeparin-binding0InformativeDirect
Molecular functionGrowth factor binding2.139e-11Highly InformativeDirect
Post-translational modificationHydrolase0.001011Least InformativeInherited
Post-translational modificationDevelopmental protein0Moderately InformativeDirect
Post-translational modificationProtease0Moderately InformativeDirect
Post-translational modificationReceptor8.666e-11Moderately InformativeDirect
Post-translational modificationMetalloprotease0InformativeDirect
Post-translational modificationGrowth factor1.101e-08InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect
Post-translational modificationCleavage on pair of basic residues0Moderately InformativeDirect
Post-translational modificationZymogen1.788e-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 ]