SUPERFAMILY 1.75 HMM library and genome assignments server

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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

Function annotation of SCOP domain superfamilies

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)organ system cancer0.05593Least InformativeInherited
Disease Ontology (DO)nervous system disease0.07846Least InformativeInherited
Disease Ontology (DO)connective tissue disease0.00003758Moderately InformativeDirect
Disease Ontology (DO)gastrointestinal system disease0.05871Moderately InformativeInherited
Disease Ontology (DO)hematologic cancer0.06029Moderately InformativeInherited
Disease Ontology (DO)sensory system disease0.2058Moderately InformativeInherited
Disease Ontology (DO)artery disease0.8968Moderately InformativeInherited
Disease Ontology (DO)myeloid neoplasm0.0001366InformativeDirect
Disease Ontology (DO)periodontal disease0.000185InformativeDirect
Disease Ontology (DO)arthritis0.0004936InformativeDirect
Disease Ontology (DO)urinary system cancer0.02458InformativeInherited
Disease Ontology (DO)degeneration of macula and posterior pole0.0001921Highly InformativeDirect
Disease Ontology (DO)cerebrovascular disease0.008643Highly 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 morphology0.4699Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of immune system physiology0.06553Moderately InformativeInherited
Phenotypic Abnormality (PA)Complement deficiency0.00000001028InformativeDirect
Phenotypic Abnormality (PA)CNS infection0.0001642InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)nervous system phenotype0.1293Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype0.3496Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.3681Least InformativeInherited
Mammalian Phenotype (MP)limbs/digits/tail phenotype0.0006013Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal myeloid cell morphology0.09738Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic cell number0.2531Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system development0.2594Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood cell morphology0.4031Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal muscle morphology0.4745Moderately InformativeInherited
Mammalian Phenotype (MP)embryo phenotype0.5484Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.6815Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal phagocyte morphology0.00446InformativeInherited
Mammalian Phenotype (MP)abnormal thoracic cage morphology0.02424InformativeInherited
Mammalian Phenotype (MP)abnormal vertebrae morphology0.0332InformativeInherited
Mammalian Phenotype (MP)abnormal appendicular skeleton morphology0.03515InformativeInherited
Mammalian Phenotype (MP)abnormal limb morphology0.2632InformativeInherited
Mammalian Phenotype (MP)abnormal neural tube morphology0.3117InformativeInherited
Mammalian Phenotype (MP)abnormal embryo development0.3628InformativeInherited
Mammalian Phenotype (MP)fused somites0.000003424Highly InformativeDirect
Mammalian Phenotype (MP)craniorachischisis0.000005531Highly InformativeDirect
Mammalian Phenotype (MP)abnormal rostral-caudal body axis extension0.00001011Highly InformativeDirect
Mammalian Phenotype (MP)decreased somite size0.00006302Highly InformativeDirect
Mammalian Phenotype (MP)amyloid beta deposits0.0002236Highly InformativeDirect
Mammalian Phenotype (MP)incomplete somite formation0.0002398Highly InformativeDirect
Mammalian Phenotype (MP)decreased skeletal muscle size0.0006342Highly InformativeDirect
Mammalian Phenotype (MP)abnormal vertebrae number0.0007675Highly InformativeDirect
Mammalian Phenotype (MP)abnormal limb long bone morphology0.0007729Highly InformativeDirect
Mammalian Phenotype (MP)abnormal granulocyte number0.00724Highly InformativeInherited
Mammalian Phenotype (MP)abnormal neutrophil morphology0.01052Highly 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 defective0Moderately InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)embryo0Least InformativeDirect
Fly Anatomy (FA)larva0Least InformativeDirect
Fly Anatomy (FA)nervous system0Least InformativeDirect
Fly Anatomy (FA)anatomical group0Least 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)sensory neuron0Moderately InformativeDirect
Fly Anatomy (FA)late embryo0Moderately 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)tissue0.6557Least InformativeInherited
Xenopus ANatomical entity (XAN)embryo0.6974Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.2028Moderately InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm0.6853Moderately InformativeInherited
Xenopus ANatomical entity (XAN)endoderm0.000168InformativeDirect
Xenopus ANatomical entity (XAN)neural plate0.004105InformativeInherited
Xenopus ANatomical entity (XAN)axial mesoderm0.00005417Highly InformativeDirect
Xenopus ANatomical entity (XAN)optic field0.0002141Highly InformativeDirect
Xenopus ANatomical entity (XAN)chordal neural plate0.000481Highly InformativeDirect
Xenopus ANatomical entity (XAN)primordium0.00225Highly InformativeInherited

Document: XA annotation of SCOP domains

InterPro annotation
Cross references IPR008993 SSF50242 Protein matches

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 6 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 6 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 ]