SUPERFAMILY 1.75 HMM library and genome assignments server

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 (199) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 2,217 2,888 11
Proteins 2,197 2,871 11


Functional annotation
General category Processes_IC
Detailed category Proteases

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)regulation of metabolic process00.01551Least InformativeInherited
Biological Process (BP)multicellular organismal process0.018310.000001951Least InformativeInherited
Biological Process (BP)developmental process0.0079490.000000009628Least InformativeInherited
Biological Process (BP)single-organism cellular process0.31130.6701Least InformativeInherited
Biological Process (BP)response to stimulus0.0059630.000005383Least InformativeInherited
Biological Process (BP)regulation of cellular process0.00000000000027140.7603Least InformativeInherited
Biological Process (BP)regulation of signal transduction00.0003917Moderately InformativeDirect
Biological Process (BP)negative regulation of cellular process0.000000063950.0002318Moderately InformativeDirect
Biological Process (BP)regulation of catalytic activity0.00000036320.000002956Moderately InformativeDirect
Biological Process (BP)regulation of protein metabolic process0.0000017710.00000000000007887Moderately InformativeDirect
Biological Process (BP)regulation of developmental process0.030090.0000002957Moderately InformativeInherited
Biological Process (BP)regulation of multicellular organismal process0.081020.00001974Moderately InformativeInherited
Biological Process (BP)negative regulation of metabolic process0.00000000052890.02271Moderately InformativeInherited
Biological Process (BP)regulation of gene expression00.04325Moderately InformativeInherited
Biological Process (BP)regulation of nucleobase-containing compound metabolic process11Moderately InformativeInherited
Biological Process (BP)regulation of phosphorus metabolic process0.97450.01099Moderately InformativeInherited
Biological Process (BP)nervous system development0.019880.01562Moderately InformativeInherited
Biological Process (BP)cell differentiation0.0029250.0000000007675Moderately InformativeInherited
Biological Process (BP)negative regulation of cellular protein metabolic process00.000000000007647InformativeDirect
Biological Process (BP)regulation of cell proliferation0.00000000011250.00000008636InformativeDirect
Biological Process (BP)negative regulation of catalytic activity0.000000000001980.000000000007239InformativeDirect
Biological Process (BP)generation of neurons0.000017120.000000002717InformativeDirect
Biological Process (BP)regulation of peptidase activity0.00000002280.00000000004851InformativeDirect
Biological Process (BP)regulation of purine nucleotide metabolic process0.00000029720.000006505InformativeDirect
Biological Process (BP)negative regulation of protein processing00.01705InformativeInherited
Biological Process (BP)regulation of nervous system development0.0000000001310.01286InformativeInherited
Biological Process (BP)regulation of cell development0.000000460.2636InformativeInherited
Biological Process (BP)negative regulation of endopeptidase activity00Highly InformativeDirect
Molecular Function (MF)binding0.000034510.00000001858Least InformativeDirect
Molecular Function (MF)enzyme regulator activity00Moderately InformativeDirect
Molecular Function (MF)enzyme inhibitor activity00.0000003045InformativeDirect
Molecular Function (MF)receptor binding00InformativeDirect
Molecular Function (MF)peptidase regulator activity00InformativeDirect
Molecular Function (MF)protein complex binding0.00032390.0125InformativeInherited
Molecular Function (MF)cytokine activity0.00090950.00003112Highly InformativeDirect
Molecular Function (MF)cell adhesion molecule binding0.0000000016040.00002074Highly InformativeDirect
Cellular Component (CC)extracellular region part00Moderately InformativeDirect
Cellular Component (CC)cell surface0.00000000019850.000001431InformativeDirect
Cellular Component (CC)extracellular matrix00InformativeDirect
Cellular Component (CC)proteinaceous extracellular matrix0.00000000002950.00000001869Highly InformativeDirect
Cellular Component (CC)extracellular matrix part00Highly InformativeDirect

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) multicellular organismal process 0.000001951 Least Informative Direct
Biological Process (BP) developmental process 0.000000009628 Least Informative Direct
Biological Process (BP) response to stimulus 0.000005383 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.7603 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.01551 Least Informative Inherited
Biological Process (BP) localization 1 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.05799 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.08321 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) positive regulation of biological process 0.004036 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.6701 Least Informative Inherited
Biological Process (BP) regulation of signal transduction 0.0003917 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.0000000007675 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.0002318 Moderately Informative Direct
Biological Process (BP) regulation of catalytic activity 0.000002956 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 0.0000002957 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 0.00001974 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.00000000000007887 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.04325 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.09816 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.3105 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.01562 Moderately Informative Inherited
Biological Process (BP) tissue development 0.9012 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.0391 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.1211 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.08937 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.7326 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.02271 Moderately Informative Inherited
Biological Process (BP) regulation of phosphorus metabolic process 0.01099 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.1256 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 0.01958 Moderately Informative Inherited
Biological Process (BP) signal transduction 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.08057 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 0.1977 Moderately Informative Inherited
Biological Process (BP) immune system process 0.001593 Moderately Informative Inherited
Biological Process (BP) immune effector process 0.000005135 Informative Direct
Biological Process (BP) cellular component movement 0.0005114 Informative Direct
Biological Process (BP) cell projection organization 0.00001028 Informative Direct
Biological Process (BP) negative regulation of cellular protein metabolic process 0.000000000007647 Informative Direct
Biological Process (BP) regulation of growth 0.00001946 Informative Direct
Biological Process (BP) locomotion 0.0000886 Informative Direct
Biological Process (BP) regulation of cell proliferation 0.00000008636 Informative Direct
Biological Process (BP) regulation of apoptotic process 0.000001102 Informative Direct
Biological Process (BP) negative regulation of catalytic activity 0.000000000007239 Informative Direct
Biological Process (BP) generation of neurons 0.000000002717 Informative Direct
Biological Process (BP) regulation of peptidase activity 0.00000000004851 Informative Direct
Biological Process (BP) regulation of purine nucleotide metabolic process 0.000006505 Informative Direct
Biological Process (BP) negative regulation of cell communication 0.003334 Informative Inherited
Biological Process (BP) cellular component morphogenesis 0.004343 Informative Inherited
Biological Process (BP) regulation of lipid metabolic process 0.02401 Informative Inherited
Biological Process (BP) single-organism membrane organization 0.0138 Informative Inherited
Biological Process (BP) epithelium development 0.2611 Informative Inherited
Biological Process (BP) synaptic transmission 0.0655 Informative Inherited
Biological Process (BP) regulation of defense response 0.4246 Informative Inherited
Biological Process (BP) regulation of response to external stimulus 0.4155 Informative Inherited
Biological Process (BP) regulation of response to wounding 0.003232 Informative Inherited
Biological Process (BP) tube development 0.01921 Informative Inherited
Biological Process (BP) regulation of MAPK cascade 0.03979 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.001715 Informative Inherited
Biological Process (BP) negative regulation of protein processing 0.01705 Informative Inherited
Biological Process (BP) regulation of nervous system development 0.01286 Informative Inherited
Biological Process (BP) regulation of cell development 0.2636 Informative Inherited
Biological Process (BP) response to organic cyclic compound 0.6152 Informative Inherited
Biological Process (BP) response to lipid 0.1192 Informative Inherited
Biological Process (BP) single-organism cellular localization 0.008 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.01312 Informative Inherited
Biological Process (BP) regulation of immune effector process 0.001256 Informative Inherited
Biological Process (BP) positive regulation of transport 0.02149 Informative Inherited
Biological Process (BP) immune response 0.006262 Informative Inherited
Biological Process (BP) regulation of immune response 0.8492 Informative Inherited
Biological Process (BP) positive regulation of immune system process 0.01976 Informative Inherited
Biological Process (BP) tissue morphogenesis 0.02794 Informative Inherited
Biological Process (BP) cell morphogenesis involved in differentiation 0.0007974 Highly Informative Direct
Biological Process (BP) regulation of acute inflammatory response 0.000001981 Highly Informative Direct
Biological Process (BP) regulation of humoral immune response 0.000000001045 Highly Informative Direct
Biological Process (BP) humoral immune response 0.0000000000002685 Highly Informative Direct
Biological Process (BP) regulation of lipid storage 0.0000001064 Highly Informative Direct
Biological Process (BP) negative regulation of endopeptidase activity 0 Highly Informative Direct
Biological Process (BP) extracellular matrix organization 0.00001092 Highly Informative Direct
Biological Process (BP) regulation of developmental growth 0.00001718 Highly Informative Direct
Biological Process (BP) protein activation cascade 0.000000000000003707 Highly Informative Direct
Biological Process (BP) protein localization to membrane 0.00004214 Highly Informative Direct
Biological Process (BP) neuron projection development 0.01747 Highly Informative Inherited
Biological Process (BP) chemotaxis 0.001894 Highly Informative Inherited
Biological Process (BP) cell projection morphogenesis 0.003173 Highly Informative Inherited
Biological Process (BP) negative regulation of intracellular signal transduction 0.1394 Highly Informative Inherited
Biological Process (BP) regulation of G-protein coupled receptor protein signaling pathway 0.01177 Highly Informative Inherited
Biological Process (BP) regulation of cellular response to stress 0.03975 Highly Informative Inherited
Molecular Function (MF) binding 0.00000001858 Least Informative Direct
Molecular Function (MF) enzyme regulator activity 0 Moderately Informative Direct
Molecular Function (MF) anion binding 0.05863 Moderately Informative Inherited
Molecular Function (MF) carbohydrate derivative binding 0.1644 Moderately Informative Inherited
Molecular Function (MF) enzyme inhibitor activity 0.0000003045 Informative Direct
Molecular Function (MF) receptor binding 0 Informative Direct
Molecular Function (MF) peptidase regulator activity 0 Informative Direct
Molecular Function (MF) sulfur compound binding 0.00003667 Informative Direct
Molecular Function (MF) protein complex binding 0.0125 Informative Inherited
Molecular Function (MF) cytokine activity 0.00003112 Highly Informative Direct
Molecular Function (MF) heparin binding 0.0000007276 Highly Informative Direct
Molecular Function (MF) cell adhesion molecule binding 0.00002074 Highly Informative Direct
Cellular Component (CC) extracellular region part 0 Moderately Informative Direct
Cellular Component (CC) vesicle 0.004983 Moderately Informative Inherited
Cellular Component (CC) cell surface 0.000001431 Informative Direct
Cellular Component (CC) extracellular matrix 0 Informative Direct
Cellular Component (CC) extracellular membrane-bounded organelle 0.00000794 Informative Direct
Cellular Component (CC) proteinaceous extracellular matrix 0.00000001869 Highly Informative Direct
Cellular Component (CC) extracellular matrix part 0 Highly Informative Direct

Document: GO annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)organ system cancer0.04732Least InformativeInherited
Disease Ontology (DO)nervous system disease0.08442Least InformativeInherited
Disease Ontology (DO)connective tissue disease0.00003517Moderately InformativeDirect
Disease Ontology (DO)mouth disease0.007011Moderately InformativeInherited
Disease Ontology (DO)hematologic cancer0.06226Moderately InformativeInherited
Disease Ontology (DO)sensory system disease0.2261Moderately InformativeInherited
Disease Ontology (DO)artery disease0.8711Moderately InformativeInherited
Disease Ontology (DO)periodontitis0.0001241InformativeDirect
Disease Ontology (DO)myeloma0.0001478InformativeDirect
Disease Ontology (DO)arthritis0.0004921InformativeDirect
Disease Ontology (DO)eye disease0.02261InformativeInherited
Disease Ontology (DO)urinary system cancer0.02767InformativeInherited
Disease Ontology (DO)degeneration of macula and posterior pole0.0002269Highly InformativeDirect
Disease Ontology (DO)cerebrovascular disease0.009552Highly InformativeInherited

Document: DO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)nervous system phenotype0.2543Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype0.2968Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.3734Least InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system development0.1428Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic cell number0.3381Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.7147Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal embryogenesis/ development1Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal phagocyte morphology0.003556InformativeInherited
Mammalian Phenotype (MP)abnormal vertebrae morphology0.03295InformativeInherited
Mammalian Phenotype (MP)abnormal neural tube morphology/development0.1878InformativeInherited
Mammalian Phenotype (MP)fused somites0.000001287Highly InformativeDirect
Mammalian Phenotype (MP)craniorachischisis0.000003716Highly InformativeDirect
Mammalian Phenotype (MP)abnormal rostral-caudal body axis extension0.000005677Highly InformativeDirect
Mammalian Phenotype (MP)decreased somite size0.00003513Highly InformativeDirect
Mammalian Phenotype (MP)abnormal neutrophil morphology0.00004116Highly InformativeDirect
Mammalian Phenotype (MP)incomplete somite formation0.0001625Highly InformativeDirect
Mammalian Phenotype (MP)abnormal granulocyte number0.0003353Highly InformativeDirect
Mammalian Phenotype (MP)abnormal neural tube closure0.02928Highly 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)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)larva0Least InformativeDirect
Fly Anatomy (FA)organ system0Least InformativeDirect
Fly Anatomy (FA)cell0Least InformativeDirect
Fly Anatomy (FA)late embryo0Moderately InformativeDirect

Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)alimentary system0.2735Least InformativeInherited
Xenopus ANatomical entity (XAN)portion of tissue0.6024Least InformativeInherited
Xenopus ANatomical entity (XAN)embryo0.699Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.07835Moderately InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm0.7481Moderately InformativeInherited
Xenopus ANatomical entity (XAN)neural plate0.0002145InformativeDirect
Xenopus ANatomical entity (XAN)endoderm0.0002913InformativeDirect
Xenopus ANatomical entity (XAN)anatomical direction0.0007508InformativeDirect
Xenopus ANatomical entity (XAN)primordium0.001098InformativeInherited
Xenopus ANatomical entity (XAN)stomodeal-hypophyseal primordium0.00005527Highly InformativeDirect
Xenopus ANatomical entity (XAN)optic field0.00006837Highly InformativeDirect
Xenopus ANatomical entity (XAN)foregut0.0004181Highly InformativeDirect
Xenopus ANatomical entity (XAN)axial mesoderm0.000812Highly InformativeDirect
Xenopus DEvelopment stage (XDE)embryonic stage0.00008806Least InformativeDirect

Document: XA annotation of SCOP domains

DrugBank ATC (DB)

(show details)
DB termFDR (all)SDDB levelAnnotation (direct or inherited)
Drugbank ATC_code (DB)antiinfectives for systemic use0Least InformativeDirect
Drugbank ATC_code (DB)immunoglobulins, normal human0InformativeDirect

Document: DB annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDifferentiation0Moderately InformativeDirect
Biological processInflammatory response0InformativeDirect
Biological processInnate immunity0InformativeDirect
Biological processWnt signaling pathway0InformativeDirect
Biological processComplement pathway0Highly InformativeDirect
Biological processComplement alternate pathway0.00000000001376Highly InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentExtracellular matrix0.00000000001941InformativeDirect
DomainSignal0Least InformativeDirect
DomainLaminin EGF-like domain0Highly InformativeDirect
Molecular functionZinc0.00000000001105Least InformativeDirect
Post-translational modificationDevelopmental protein0Moderately InformativeDirect
Post-translational modificationProtease inhibitor0InformativeDirect
Post-translational modificationGrowth factor8.866e-16InformativeDirect
Post-translational modificationToxin0.001921InformativeInherited
Post-translational modificationMetalloenzyme inhibitor0Highly InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect
Post-translational modificationCleavage on pair of basic residues0.000000000001935Moderately InformativeDirect
Post-translational modificationSulfation0.000005682InformativeDirect
Post-translational modificationThioester bond0Highly InformativeDirect

Document: KW 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 · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Disease Ontology (DO) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · DrugBank ATC (DB) · 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 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 · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Disease Ontology (DO) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · DrugBank ATC (DB) · UniProtKB KeyWords (KW) · Internal database links ]