SUPERFAMILY 1.75 HMM library and genome assignments server

Superfamily is undergoing a server migration - you are now browsing on the new server. Please contact us if you experience any problems.


TIMP-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   OB-fold [ 50198] (16)
Superfamily:   TIMP-like [ 50242] (3)
Families:   Tissue inhibitor of metalloproteinases, TIMP [ 50243] (2)
  Netrin-like domain (NTR/C345C module) [ 89320] (2)
  The laminin-binding domain of agrin [ 63767]


Superfamily statistics
Genomes (205) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 2,233 6,632 11
Proteins 2,213 6,557 11


Functional annotation
General category Processes_IC
Detailed category Proteases

Document:
Function annotation of SCOP domain superfamilies

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)organ system cancer0.05613Least InformativeInherited
Disease Ontology (DO)nervous system disease0.07834Least InformativeInherited
Disease Ontology (DO)connective tissue disease0.00003827Moderately InformativeDirect
Disease Ontology (DO)gastrointestinal system disease0.05886Moderately InformativeInherited
Disease Ontology (DO)hematologic cancer0.06058Moderately InformativeInherited
Disease Ontology (DO)sensory system disease0.2064Moderately InformativeInherited
Disease Ontology (DO)artery disease0.8985Moderately InformativeInherited
Disease Ontology (DO)myeloid neoplasm0.0001384InformativeDirect
Disease Ontology (DO)periodontal disease0.0001867InformativeDirect
Disease Ontology (DO)arthritis0.0004944InformativeDirect
Disease Ontology (DO)urinary system cancer0.02473InformativeInherited
Disease Ontology (DO)degeneration of macula and posterior pole0.0001938Highly InformativeDirect
Disease Ontology (DO)cerebrovascular disease0.008687Highly InformativeInherited

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.4049Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of immune system physiology0.04519Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of complement system0.00000003076InformativeDirect
Phenotypic Abnormality (PA)Unusual CNS infection0.0002929InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)nervous system phenotype0.1296Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype0.3487Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.3678Least InformativeInherited
Mammalian Phenotype (MP)abnormal myeloid cell morphology0.09738Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic cell number0.2533Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system development0.259Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood cell morphology0.4032Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal muscle morphology0.4751Moderately InformativeInherited
Mammalian Phenotype (MP)embryo phenotype0.5483Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.6821Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal phagocyte morphology0.004449InformativeInherited
Mammalian Phenotype (MP)abnormal thoracic cage morphology0.02437InformativeInherited
Mammalian Phenotype (MP)abnormal vertebrae morphology0.03361InformativeInherited
Mammalian Phenotype (MP)abnormal appendicular skeleton morphology0.03487InformativeInherited
Mammalian Phenotype (MP)abnormal limb morphology0.2633InformativeInherited
Mammalian Phenotype (MP)abnormal neural tube morphology0.3126InformativeInherited
Mammalian Phenotype (MP)abnormal embryo development0.363InformativeInherited
Mammalian Phenotype (MP)fused somites0.000003419Highly InformativeDirect
Mammalian Phenotype (MP)craniorachischisis0.000005524Highly InformativeDirect
Mammalian Phenotype (MP)abnormal rostral-caudal body axis extension0.00001011Highly InformativeDirect
Mammalian Phenotype (MP)decreased somite size0.00006296Highly InformativeDirect
Mammalian Phenotype (MP)amyloid beta deposits0.0002234Highly InformativeDirect
Mammalian Phenotype (MP)incomplete somite formation0.0002396Highly InformativeDirect
Mammalian Phenotype (MP)decreased skeletal muscle size0.0006339Highly InformativeDirect
Mammalian Phenotype (MP)abnormal vertebrae number0.0007666Highly InformativeDirect
Mammalian Phenotype (MP)abnormal limb long bone morphology0.0007716Highly InformativeDirect
Mammalian Phenotype (MP)abnormal granulocyte number0.00725Highly InformativeInherited
Mammalian Phenotype (MP)abnormal neutrophil morphology0.01054Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)viable0Least InformativeDirect
Fly Phenotype (FP)neuroanatomy defective0InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)larva0Least InformativeDirect
Fly Anatomy (FA)nervous system0Least InformativeDirect
Fly Anatomy (FA)organ system subdivision0Least InformativeDirect
Fly Anatomy (FA)somatic cell0Least InformativeDirect
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)neuron0Moderately InformativeDirect
Fly Anatomy (FA)late embryo0Moderately InformativeDirect
Fly Anatomy (FA)sensory system0Moderately InformativeDirect

Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details) Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)tissue0.6916Least InformativeInherited
Xenopus ANatomical entity (XAN)embryo0.7421Least InformativeInherited
Xenopus ANatomical entity (XAN)anatomical system1Least InformativeInherited
Xenopus ANatomical entity (XAN)alimentary system0.1742Moderately InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.2474Moderately InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm0.7114Moderately InformativeInherited
Xenopus ANatomical entity (XAN)endoderm0.00004029InformativeDirect
Xenopus ANatomical entity (XAN)cardiovascular system0.0004514InformativeDirect
Xenopus ANatomical entity (XAN)neural plate0.006688InformativeInherited
Xenopus ANatomical entity (XAN)foregut0.0002083Highly InformativeDirect
Xenopus ANatomical entity (XAN)optic field0.0002647Highly InformativeDirect
Xenopus ANatomical entity (XAN)axial mesoderm0.001287Highly InformativeInherited
Xenopus ANatomical entity (XAN)primordium0.002177Highly InformativeInherited
Xenopus ANatomical entity (XAN)neural tube0.008287Highly InformativeInherited

Document: XA annotation of SCOP domains

InterPro annotation
Cross references IPR008993 SSF50242 Protein matches
Abstract

Tissue inhibitors of metalloproteinases (TIMP) are a family of proteins that can form complexes with extracellular matrix metalloproteinases (such as collagenases) and irreversibly inactivate them [PubMed2793861]. TIMP and related proteins contains a five-stranded antiparallel beta-sheet that is rolled over on itself to form a closed beta-barrel, and two short helices, which pack close to one another on the same barrel face. A comparison of the delta TIMP-2 structure with other known protein folds reveals that the beta-barrel topology is homologous to that seen in proteins of the oligosaccharide/oligonucleotide binding (OB) fold family, a five-stranded beta-sheet coiled to form a closed beta-barrel capped by an alpha-helix located between the third and fourth strands [PubMed7918391].

Other proteins contain domains with a similar OB-like fold:

  • Netrin-like domain (NTR/C345C module), found in procollagen c-proteinase enhancer protein PCOLCE, and in the complement C5 domain.
  • Laminin-binding domain, found in agrin.


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 · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) ]

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 8 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 TIMP-like 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 8 hidden Markov models representing the TIMP-like 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 · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Internal database links ]