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)developmental process0.00054840.00000000002082Least InformativeDirect
Biological Process (BP)regulation of metabolic process00.01516Least InformativeInherited
Biological Process (BP)single-organism cellular process0.0020440.02221Least InformativeInherited
Biological Process (BP)multicellular organismal process0.002130.00000000478Least InformativeInherited
Biological Process (BP)regulation of cellular process0.056691Least InformativeInherited
Biological Process (BP)response to stimulus0.0061810.000005401Least InformativeInherited
Biological Process (BP)regulation of signal transduction00.0002863Moderately InformativeDirect
Biological Process (BP)cell differentiation0.000066560.000000000001519Moderately InformativeDirect
Biological Process (BP)regulation of catalytic activity0.00000066570.000002887Moderately InformativeDirect
Biological Process (BP)regulation of nucleobase-containing compound metabolic process0.086581Moderately InformativeInherited
Biological Process (BP)regulation of phosphate metabolic process10.0000000001937Moderately InformativeInherited
Biological Process (BP)regulation of developmental process0.030170.000000298Moderately InformativeInherited
Biological Process (BP)regulation of multicellular organismal process0.1130.00007416Moderately InformativeInherited
Biological Process (BP)nervous system development0.095070.08177Moderately InformativeInherited
Biological Process (BP)regulation of cell proliferation0.000000000039830.0000000225InformativeDirect
Biological Process (BP)negative regulation of catalytic activity00.0000006576InformativeDirect
Biological Process (BP)generation of neurons0.000016530.00000000256InformativeDirect
Biological Process (BP)regulation of peptidase activity00.0000000005497InformativeDirect
Biological Process (BP)regulation of purine nucleotide metabolic process0.00000023920.000005212InformativeDirect
Biological Process (BP)regulation of nervous system development0.00000000012480.01123InformativeInherited
Biological Process (BP)regulation of cell development0.00000000057180.09334InformativeInherited
Biological Process (BP)negative regulation of endopeptidase activity00Highly InformativeDirect
Molecular Function (MF)binding0.00003230.00000001361Least InformativeDirect
Molecular Function (MF)enzyme regulator activity00Moderately InformativeDirect
Molecular Function (MF)enzyme inhibitor activity00.000000005222InformativeDirect
Molecular Function (MF)receptor binding00InformativeDirect
Molecular Function (MF)peptidase regulator activity00InformativeDirect
Molecular Function (MF)cytokine activity0.00090230.00003125Highly InformativeDirect
Molecular Function (MF)protein complex binding0.0000024640.0009506Highly InformativeDirect
Cellular Component (CC)extracellular region part00Moderately InformativeDirect
Cellular Component (CC)cell surface0.000000000076630.000000686InformativeDirect
Cellular Component (CC)extracellular matrix00InformativeDirect
Cellular Component (CC)proteinaceous extracellular matrix0.000000000070980.00000006246Highly 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 0.00000000478 Least Informative Direct
Biological Process (BP) developmental process 0.00000000002082 Least Informative Direct
Biological Process (BP) response to stimulus 0.000005401 Least Informative Direct
Biological Process (BP) localization 0.9853 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.01516 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.02221 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.05263 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.06714 Least Informative Inherited
Biological Process (BP) regulation of signal transduction 0.0002863 Moderately Informative Direct
Biological Process (BP) regulation of phosphate metabolic process 0.0000000001937 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.000000000001519 Moderately Informative Direct
Biological Process (BP) regulation of catalytic activity 0.000002887 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 0.000000298 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 0.00007416 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.00005264 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.1024 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.809 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) organ development 1 Moderately Informative Inherited
Biological Process (BP) tissue development 0.4025 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.02599 Moderately Informative Inherited
Biological Process (BP) system process 1 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.0883 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.7199 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.05755 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.08177 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.1226 Moderately Informative Inherited
Biological Process (BP) signal transduction 1 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.07132 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 0.1135 Moderately Informative Inherited
Biological Process (BP) immune system process 0.001613 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.3327 Moderately Informative Inherited
Biological Process (BP) regulation of protein phosphorylation 0.00000001839 Informative Direct
Biological Process (BP) immune effector process 0.000005011 Informative Direct
Biological Process (BP) negative regulation of signaling 0.0006536 Informative Direct
Biological Process (BP) cell projection organization 0.0001249 Informative Direct
Biological Process (BP) regulation of growth 0.00002569 Informative Direct
Biological Process (BP) locomotion 0.00008917 Informative Direct
Biological Process (BP) regulation of cell proliferation 0.0000000225 Informative Direct
Biological Process (BP) negative regulation of catalytic activity 0.0000006576 Informative Direct
Biological Process (BP) generation of neurons 0.00000000256 Informative Direct
Biological Process (BP) regulation of peptidase activity 0.0000000005497 Informative Direct
Biological Process (BP) regulation of purine nucleotide metabolic process 0.000005212 Informative Direct
Biological Process (BP) cellular component morphogenesis 0.003879 Informative Inherited
Biological Process (BP) cellular component movement 0.003495 Informative Inherited
Biological Process (BP) cellular membrane organization 0.008079 Informative Inherited
Biological Process (BP) tissue morphogenesis 0.02761 Informative Inherited
Biological Process (BP) epithelium development 0.7522 Informative Inherited
Biological Process (BP) synaptic transmission 0.3801 Informative Inherited
Biological Process (BP) positive regulation of immune system process 0.007535 Informative Inherited
Biological Process (BP) muscle structure development 0.03146 Informative Inherited
Biological Process (BP) response to hormone stimulus 0.1061 Informative Inherited
Biological Process (BP) response to organic cyclic compound 0.6124 Informative Inherited
Biological Process (BP) response to lipid 0.1179 Informative Inherited
Biological Process (BP) regulation of intracellular protein kinase cascade 1 Informative Inherited
Biological Process (BP) positive regulation of signal transduction 1 Informative Inherited
Biological Process (BP) regulation of nervous system development 0.01123 Informative Inherited
Biological Process (BP) regulation of cell development 0.09334 Informative Inherited
Biological Process (BP) regulation of immune effector process 0.001143 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.001271 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.005121 Informative Inherited
Biological Process (BP) muscle tissue development 0.06884 Informative Inherited
Biological Process (BP) regulation of lipid metabolic process 0.004646 Informative Inherited
Biological Process (BP) positive regulation of transport 0.01326 Informative Inherited
Biological Process (BP) immune response 0.006341 Informative Inherited
Biological Process (BP) regulation of immune response 0.8521 Informative Inherited
Biological Process (BP) regulation of defense response 0.4621 Informative Inherited
Biological Process (BP) regulation of response to external stimulus 0.1571 Informative Inherited
Biological Process (BP) regulation of acute inflammatory response 0.000001981 Highly Informative Direct
Biological Process (BP) regulation of humoral immune response 0.000000001095 Highly Informative Direct
Biological Process (BP) humoral immune response 0.0000000000002765 Highly Informative Direct
Biological Process (BP) regulation of lipid storage 0.000000121 Highly Informative Direct
Biological Process (BP) negative regulation of endopeptidase activity 0 Highly Informative Direct
Biological Process (BP) regulation of striated muscle tissue development 0.000007549 Highly Informative Direct
Biological Process (BP) extracellular matrix organization 0.0000111 Highly Informative Direct
Biological Process (BP) regulation of developmental growth 0.00001638 Highly Informative Direct
Biological Process (BP) muscle fiber development 0.00000005138 Highly Informative Direct
Biological Process (BP) regulation of protein processing 0.00000000001201 Highly Informative Direct
Biological Process (BP) protein activation cascade 0.00000000000003788 Highly Informative Direct
Biological Process (BP) neuron projection development 0.01804 Highly Informative Inherited
Biological Process (BP) cell part morphogenesis 0.009456 Highly Informative Inherited
Biological Process (BP) chemotaxis 0.001909 Highly Informative Inherited
Biological Process (BP) muscle organ development 0.0813 Highly Informative Inherited
Biological Process (BP) regulation of cellular response to stress 0.0279 Highly Informative Inherited
Biological Process (BP) regulation of G-protein coupled receptor protein signaling pathway 0.01172 Highly Informative Inherited
Biological Process (BP) cell morphogenesis involved in differentiation 0.01187 Highly Informative Inherited
Molecular Function (MF) binding 0.00000001361 Least Informative Direct
Molecular Function (MF) enzyme regulator activity 0 Moderately Informative Direct
Molecular Function (MF) anion binding 0.05855 Moderately Informative Inherited
Molecular Function (MF) enzyme inhibitor activity 0.000000005222 Informative Direct
Molecular Function (MF) receptor binding 0 Informative Direct
Molecular Function (MF) peptidase regulator activity 0 Informative Direct
Molecular Function (MF) carbohydrate derivative binding 0.00008238 Informative Direct
Molecular Function (MF) sulfur compound binding 0.00002499 Informative Direct
Molecular Function (MF) cytokine activity 0.00003125 Highly Informative Direct
Molecular Function (MF) heparin binding 0.0000007236 Highly Informative Direct
Molecular Function (MF) protein complex binding 0.0009506 Highly Informative Direct
Cellular Component (CC) extracellular region part 0 Moderately Informative Direct
Cellular Component (CC) vesicle 0.004668 Moderately Informative Inherited
Cellular Component (CC) cell surface 0.000000686 Informative Direct
Cellular Component (CC) extracellular matrix 0 Informative Direct
Cellular Component (CC) extracellular membrane-bounded organelle 0.000006746 Informative Direct
Cellular Component (CC) proteinaceous extracellular matrix 0.00000006246 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 ]