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) developmental process 7.953e-10 Least Informative Direct
Biological Process (BP) multicellular organismal process 2.497e-09 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.0001211 Least Informative Direct
Biological Process (BP) protein metabolic process 0.0001655 Least Informative Direct
Biological Process (BP) response to stimulus 0.0007865 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 0.01527 Least Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 2.065e-08 Moderately Informative Direct
Biological Process (BP) single-organism developmental process 8.139e-06 Moderately Informative Direct
Biological Process (BP) anatomical structure morphogenesis 2.306e-05 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 9.342e-05 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.09618 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 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 0.1519 Moderately Informative Inherited
Biological Process (BP) organ development 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.3125 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.645 Moderately Informative Inherited
Biological Process (BP) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.2336 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.1913 Moderately Informative Inherited
Biological Process (BP) gene expression 0.9934 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.2468 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) reproduction 0.593 Moderately Informative Inherited
Biological Process (BP) immune system process 0.05324 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 0.01897 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 5.932e-11 Informative Direct
Biological Process (BP) proteolysis 2.708e-10 Informative Direct
Biological Process (BP) generation of neurons 1.394e-08 Informative Direct
Biological Process (BP) regulation of cellular component movement 2.711e-08 Informative Direct
Biological Process (BP) regulation of immune effector process 2.744e-08 Informative Direct
Biological Process (BP) regulation of response to external stimulus 4.674e-08 Informative Direct
Biological Process (BP) defense response 1.754e-07 Informative Direct
Biological Process (BP) regulation of locomotion 5.643e-07 Informative Direct
Biological Process (BP) immune effector process 4.81e-06 Informative Direct
Biological Process (BP) regulation of apoptotic process 2.252e-05 Informative Direct
Biological Process (BP) cellular component morphogenesis 3.469e-05 Informative Direct
Biological Process (BP) cardiovascular system development 4.642e-05 Informative Direct
Biological Process (BP) localization of cell 4.94e-05 Informative Direct
Biological Process (BP) biological adhesion 0.000243 Informative Direct
Biological Process (BP) immune response 0.0008466 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) tissue morphogenesis 0.4474 Informative Inherited
Biological Process (BP) epithelium development 0.9995 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.03475 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.0241 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.08609 Informative Inherited
Biological Process (BP) single organism reproductive process 0.5859 Informative Inherited
Biological Process (BP) response to cytokine stimulus 0.04726 Informative Inherited
Biological Process (BP) regulation of cytokine production 0.6291 Informative Inherited
Biological Process (BP) regulation of anatomical structure morphogenesis 0.1295 Informative Inherited
Biological Process (BP) negative regulation of developmental process 0.002277 Informative Inherited
Biological Process (BP) response to other organism 0.1434 Informative Inherited
Biological Process (BP) organ morphogenesis 0.4799 Informative Inherited
Biological Process (BP) regulation of immune response 0.0364 Informative Inherited
Biological Process (BP) regulation of defense response 0.3045 Informative Inherited
Biological Process (BP) positive regulation of immune system process 0.001218 Informative Inherited
Biological Process (BP) sexual reproduction 0.07044 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 1 Informative Inherited
Biological Process (BP) reproductive system development 0.9498 Informative Inherited
Biological Process (BP) extracellular matrix organization 0 Highly Informative Direct
Biological Process (BP) neuron projection development 0 Highly Informative Direct
Biological Process (BP) regulation of protein processing 1.931e-15 Highly Informative Direct
Biological Process (BP) chemotaxis 3.741e-15 Highly Informative Direct
Biological Process (BP) cell morphogenesis involved in differentiation 6.233e-12 Highly Informative Direct
Biological Process (BP) regulation of humoral immune response 2.973e-10 Highly Informative Direct
Biological Process (BP) regulation of angiogenesis 9.087e-10 Highly Informative Direct
Biological Process (BP) protein processing 3.93e-09 Highly Informative Direct
Biological Process (BP) protein activation cascade 1.002e-07 Highly Informative Direct
Biological Process (BP) regulation of acute inflammatory response 1.346e-07 Highly Informative Direct
Biological Process (BP) regulation of cell adhesion 2.127e-07 Highly Informative Direct
Biological Process (BP) cell part morphogenesis 2.691e-07 Highly Informative Direct
Biological Process (BP) humoral immune response 8.462e-07 Highly Informative Direct
Biological Process (BP) angiogenesis 2.874e-06 Highly Informative Direct
Biological Process (BP) connective tissue development 1.871e-05 Highly Informative Direct
Biological Process (BP) regulation of cell size 3.747e-05 Highly Informative Direct
Biological Process (BP) ovulation cycle process 7.994e-05 Highly Informative Direct
Biological Process (BP) positive regulation of programmed cell death 0.0002792 Highly Informative Direct
Biological Process (BP) regulation of hemostasis 0.0003143 Highly Informative Direct
Biological Process (BP) regulation of coagulation 0.0004443 Highly Informative Direct
Biological Process (BP) heart morphogenesis 0.000582 Highly Informative Direct
Biological Process (BP) cell adhesion 0.0006567 Highly Informative Direct
Biological Process (BP) skeletal system development 0.07476 Highly Informative Inherited
Biological Process (BP) regulation of epithelial cell differentiation 0.002235 Highly Informative Inherited
Biological Process (BP) regulation of wound healing 0.00104 Highly Informative Inherited
Biological Process (BP) post-embryonic development 1 Highly Informative Inherited
Biological Process (BP) female gamete generation 0.3029 Highly Informative Inherited
Biological Process (BP) gonad development 0.002323 Highly Informative Inherited
Biological Process (BP) development of primary female sexual characteristics 0.062 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 1.46e-10 Least Informative Direct
Molecular Function (MF) binding 0.4062 Least Informative Inherited
Molecular Function (MF) anion binding 0.0001395 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 7.929e-06 Informative Direct
Molecular Function (MF) receptor activity 0.00273 Informative Inherited
Molecular Function (MF) molecular transducer activity 0.009538 Informative Inherited
Molecular Function (MF) enzyme binding 0.8643 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 0.0004074 Highly Informative Direct
Molecular Function (MF) endopeptidase activity 0.2313 Highly Informative Inherited
Cellular Component (CC) extracellular region part 0 Moderately Informative Direct
Cellular Component (CC) vesicle 0.000535 Moderately Informative Direct
Cellular Component (CC) extracellular matrix 0 Informative Direct
Cellular Component (CC) cell surface 4.278e-07 Informative Direct
Cellular Component (CC) extracellular membrane-bounded organelle 4.771e-05 Informative Direct
Cellular Component (CC) extracellular matrix part 0 Highly Informative Direct
Cellular Component (CC) proteinaceous extracellular matrix 4.421e-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 cancer0.3039Least InformativeInherited
Disease Ontology (DO)nervous system cancer0.4719Moderately InformativeInherited
Disease Ontology (DO)peripheral nervous system neoplasm0.2104InformativeInherited
Disease Ontology (DO)neurofibroma1.437e-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 system0.04689Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the globe0.4371Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of complement system3.154e-07InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the lens0.1386InformativeInherited
Phenotypic Abnormality (PA)Recurrent infections0.4442InformativeInherited

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 tissue0.9291Least InformativeInherited
Xenopus ANatomical entity (XAN)embryo0.9818Least InformativeInherited
Xenopus ANatomical entity (XAN)central nervous system1Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.4334Moderately InformativeInherited
Xenopus ANatomical entity (XAN)multi-tissue structure0.5462Moderately InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm1Moderately InformativeInherited
Xenopus ANatomical entity (XAN)endoderm1.382e-05InformativeDirect
Xenopus ANatomical entity (XAN)spinal cord0.02427InformativeInherited
Xenopus ANatomical entity (XAN)hypochord7.158e-07Highly InformativeDirect
Xenopus ANatomical entity (XAN)floor plate0.0002122Highly InformativeDirect
Xenopus ANatomical entity (XAN)neural tube0.0005831Highly InformativeDirect
Xenopus ANatomical entity (XAN)cranial neural crest0.01573Highly InformativeInherited
Xenopus DEvelopment stage (XDE)embryonic stage0.0002641Least InformativeDirect
Xenopus DEvelopment stage (XDE)NF stage0.0004714Least 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 processApoptosis2.035e-12Moderately InformativeDirect
Biological processDifferentiation0.0002559Moderately InformativeDirect
Biological processCell adhesion0InformativeDirect
Biological processCytolysis0InformativeDirect
Biological processInnate immunity0InformativeDirect
Biological processWnt signaling pathway0InformativeDirect
Biological processSensory transduction5.044e-11InformativeDirect
Biological processNeurogenesis4.086e-06InformativeDirect
Biological processComplement alternate pathway0Highly InformativeDirect
Biological processComplement pathway2.609e-14Highly InformativeDirect
Biological processDNA synthesis3.143e-08Highly InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentExtracellular matrix0InformativeDirect
Coding sequence diversityPolymorphism5.086e-05Moderately InformativeDirect
Developmental stageSporozoite0InformativeDirect
DiseaseMalaria0InformativeDirect
DomainRepeat0Least InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransmembrane1Least InformativeInherited
DomainEGF-like domain0InformativeDirect
DomainImmunoglobulin domain1.616e-12InformativeDirect
DomainTransmembrane beta strand1.001e-07InformativeDirect
DomainSushi1.924e-11Highly InformativeDirect
Molecular functionZinc5.526e-09Least InformativeDirect
Molecular functionCalcium6.523e-12Moderately InformativeDirect
Molecular functionHeparin-binding0InformativeDirect
Molecular functionGrowth factor binding2.089e-11Highly InformativeDirect
Post-translational modificationHydrolase0.00102Least InformativeInherited
Post-translational modificationDevelopmental protein0Moderately InformativeDirect
Post-translational modificationProtease0Moderately InformativeDirect
Post-translational modificationReceptor8.147e-11Moderately InformativeDirect
Post-translational modificationMetalloprotease0InformativeDirect
Post-translational modificationGrowth factor1.173e-08InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect
Post-translational modificationCleavage on pair of basic residues0Moderately InformativeDirect
Post-translational modificationZymogen1.353e-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 ]