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 cancer0.05623Least InformativeInherited
Disease Ontology (DO)nervous system disease0.07833Least InformativeInherited
Disease Ontology (DO)connective tissue disease0.00003821Moderately InformativeDirect
Disease Ontology (DO)gastrointestinal system disease0.05888Moderately InformativeInherited
Disease Ontology (DO)hematologic cancer0.06054Moderately InformativeInherited
Disease Ontology (DO)sensory system disease0.2064Moderately InformativeInherited
Disease Ontology (DO)artery disease0.8985Moderately InformativeInherited
Disease Ontology (DO)myeloid neoplasm0.0001382InformativeDirect
Disease Ontology (DO)periodontal disease0.0001865InformativeDirect
Disease Ontology (DO)arthritis0.0004938InformativeDirect
Disease Ontology (DO)urinary system cancer0.02471InformativeInherited
Disease Ontology (DO)degeneration of macula and posterior pole0.0001937Highly InformativeDirect
Disease Ontology (DO)cerebrovascular disease0.008688Highly 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 morphology0.5662Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of immune system physiology0.08617Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of complement system0.0000001611InformativeDirect
Phenotypic Abnormality (PA)Unusual CNS infection0.0005052InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)nervous system phenotype0.1294Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype0.3491Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.368Least InformativeInherited
Mammalian Phenotype (MP)abnormal myeloid cell morphology0.09747Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic cell number0.2523Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system development0.2594Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood cell morphology0.4035Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal muscle morphology0.4752Moderately InformativeInherited
Mammalian Phenotype (MP)embryo phenotype0.5488Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.6821Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal phagocyte morphology0.004443InformativeInherited
Mammalian Phenotype (MP)abnormal thoracic cage morphology0.02419InformativeInherited
Mammalian Phenotype (MP)abnormal vertebrae morphology0.0336InformativeInherited
Mammalian Phenotype (MP)abnormal appendicular skeleton morphology0.03493InformativeInherited
Mammalian Phenotype (MP)abnormal limb morphology0.2633InformativeInherited
Mammalian Phenotype (MP)abnormal neural tube morphology0.3138InformativeInherited
Mammalian Phenotype (MP)abnormal embryo development0.3637InformativeInherited
Mammalian Phenotype (MP)fused somites0.000003421Highly InformativeDirect
Mammalian Phenotype (MP)craniorachischisis0.000005526Highly InformativeDirect
Mammalian Phenotype (MP)abnormal rostral-caudal body axis extension0.00001009Highly InformativeDirect
Mammalian Phenotype (MP)decreased somite size0.00006297Highly InformativeDirect
Mammalian Phenotype (MP)amyloid beta deposits0.0002237Highly InformativeDirect
Mammalian Phenotype (MP)incomplete somite formation0.0002398Highly InformativeDirect
Mammalian Phenotype (MP)decreased skeletal muscle size0.0006318Highly InformativeDirect
Mammalian Phenotype (MP)abnormal vertebrae number0.0007652Highly InformativeDirect
Mammalian Phenotype (MP)abnormal limb long bone morphology0.0007694Highly InformativeDirect
Mammalian Phenotype (MP)abnormal granulocyte number0.007216Highly InformativeInherited
Mammalian Phenotype (MP)abnormal neutrophil morphology0.01048Highly 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)embryo0.3319Least InformativeInherited
Xenopus ANatomical entity (XAN)tissue0.6974Least InformativeInherited
Xenopus ANatomical entity (XAN)anatomical system1Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.128Moderately InformativeInherited
Xenopus ANatomical entity (XAN)alimentary system0.179Moderately InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm0.6535Moderately InformativeInherited
Xenopus ANatomical entity (XAN)endoderm0.0000002021InformativeDirect
Xenopus ANatomical entity (XAN)cardiovascular system0.0005908InformativeDirect
Xenopus ANatomical entity (XAN)neural plate0.007494InformativeInherited
Xenopus ANatomical entity (XAN)optic field0.0002682Highly InformativeDirect
Xenopus ANatomical entity (XAN)foregut0.0004057Highly InformativeDirect
Xenopus ANatomical entity (XAN)axial mesoderm0.002286Highly InformativeInherited
Xenopus ANatomical entity (XAN)primordium0.006428Highly 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 ]