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 process0.00052241.493e-11Least InformativeDirect
Biological Process (BP)regulation of metabolic process00.01434Least InformativeInherited
Biological Process (BP)single-organism cellular process0.0018080.02292Least InformativeInherited
Biological Process (BP)multicellular organismal process0.0020623.412e-09Least InformativeInherited
Biological Process (BP)regulation of cellular process0.056291Least InformativeInherited
Biological Process (BP)response to stimulus0.0054263.298e-06Least InformativeInherited
Biological Process (BP)regulation of signal transduction00.0003788Moderately InformativeDirect
Biological Process (BP)cell differentiation6.487e-051.168e-12Moderately InformativeDirect
Biological Process (BP)regulation of catalytic activity8.967e-073.049e-06Moderately InformativeDirect
Biological Process (BP)regulation of nucleobase-containing compound metabolic process0.087821Moderately InformativeInherited
Biological Process (BP)regulation of phosphate metabolic process11.289e-10Moderately InformativeInherited
Biological Process (BP)regulation of developmental process0.029062.494e-07Moderately InformativeInherited
Biological Process (BP)regulation of multicellular organismal process0.10796.798e-05Moderately InformativeInherited
Biological Process (BP)nervous system development0.092690.07874Moderately InformativeInherited
Biological Process (BP)negative regulation of catalytic activity06.425e-07InformativeDirect
Biological Process (BP)generation of neurons1.631e-052.194e-09InformativeDirect
Biological Process (BP)regulation of peptidase activity05.687e-10InformativeDirect
Biological Process (BP)regulation of purine nucleotide metabolic process3.039e-075.004e-06InformativeDirect
Biological Process (BP)regulation of nervous system development1.046e-100.01199InformativeInherited
Biological Process (BP)regulation of cell development3.839e-100.08871InformativeInherited
Biological Process (BP)negative regulation of endopeptidase activity00Highly InformativeDirect
Molecular Function (MF)binding2.44e-056.315e-09Least InformativeDirect
Molecular Function (MF)enzyme regulator activity00Moderately InformativeDirect
Molecular Function (MF)enzyme inhibitor activity05.618e-09InformativeDirect
Molecular Function (MF)receptor binding00InformativeDirect
Molecular Function (MF)peptidase regulator activity00InformativeDirect
Molecular Function (MF)cytokine activity0.0009433.428e-05Highly InformativeDirect
Molecular Function (MF)protein complex binding2.643e-060.0009352Highly InformativeDirect
Cellular Component (CC)extracellular region part00Moderately InformativeDirect
Cellular Component (CC)cell surface8.308e-116.922e-07InformativeDirect
Cellular Component (CC)extracellular matrix00InformativeDirect
Cellular Component (CC)proteinaceous extracellular matrix6.416e-114.636e-08Highly 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 3.412e-09 Least Informative Direct
Biological Process (BP) developmental process 1.493e-11 Least Informative Direct
Biological Process (BP) response to stimulus 3.298e-06 Least Informative Direct
Biological Process (BP) localization 0.9673 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.01434 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.02292 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.04779 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.05737 Least Informative Inherited
Biological Process (BP) regulation of signal transduction 0.0003788 Moderately Informative Direct
Biological Process (BP) regulation of phosphate metabolic process 1.289e-10 Moderately Informative Direct
Biological Process (BP) cell differentiation 1.168e-12 Moderately Informative Direct
Biological Process (BP) regulation of programmed cell death 2.712e-06 Moderately Informative Direct
Biological Process (BP) regulation of catalytic activity 3.049e-06 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 2.494e-07 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 6.798e-05 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 4.945e-05 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.09733 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.8049 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 0.4009 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.02472 Moderately Informative Inherited
Biological Process (BP) system process 1 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.08525 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.7048 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.04949 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.07874 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.1079 Moderately Informative Inherited
Biological Process (BP) signal transduction 1 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.06758 Moderately Informative Inherited
Biological Process (BP) regulation of biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 0.1129 Moderately Informative Inherited
Biological Process (BP) immune system process 0.001483 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.3338 Moderately Informative Inherited
Biological Process (BP) regulation of protein phosphorylation 1.251e-08 Informative Direct
Biological Process (BP) immune effector process 5.237e-06 Informative Direct
Biological Process (BP) negative regulation of signaling 0.0006049 Informative Direct
Biological Process (BP) cell projection organization 0.0001316 Informative Direct
Biological Process (BP) regulation of growth 2.447e-05 Informative Direct
Biological Process (BP) locomotion 8.16e-05 Informative Direct
Biological Process (BP) negative regulation of catalytic activity 6.425e-07 Informative Direct
Biological Process (BP) generation of neurons 2.194e-09 Informative Direct
Biological Process (BP) regulation of peptidase activity 5.687e-10 Informative Direct
Biological Process (BP) regulation of purine nucleotide metabolic process 5.004e-06 Informative Direct
Biological Process (BP) cellular component morphogenesis 0.004073 Informative Inherited
Biological Process (BP) cellular component movement 0.003674 Informative Inherited
Biological Process (BP) cellular membrane organization 0.007988 Informative Inherited
Biological Process (BP) tissue morphogenesis 0.02673 Informative Inherited
Biological Process (BP) epithelium development 0.7479 Informative Inherited
Biological Process (BP) synaptic transmission 0.3745 Informative Inherited
Biological Process (BP) positive regulation of immune system process 0.008288 Informative Inherited
Biological Process (BP) muscle structure development 0.0309 Informative Inherited
Biological Process (BP) response to hormone stimulus 0.1092 Informative Inherited
Biological Process (BP) response to organic cyclic compound 0.6205 Informative Inherited
Biological Process (BP) response to lipid 0.1141 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 0.01199 Informative Inherited
Biological Process (BP) regulation of cell development 0.08871 Informative Inherited
Biological Process (BP) regulation of immune effector process 0.001203 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.001199 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.004804 Informative Inherited
Biological Process (BP) muscle tissue development 0.06725 Informative Inherited
Biological Process (BP) regulation of lipid metabolic process 0.004681 Informative Inherited
Biological Process (BP) positive regulation of transport 0.01347 Informative Inherited
Biological Process (BP) immune response 0.006762 Informative Inherited
Biological Process (BP) regulation of immune response 0.859 Informative Inherited
Biological Process (BP) regulation of defense response 0.4721 Informative Inherited
Biological Process (BP) regulation of response to external stimulus 0.1488 Informative Inherited
Biological Process (BP) regulation of acute inflammatory response 2.091e-06 Highly Informative Direct
Biological Process (BP) regulation of humoral immune response 1.312e-09 Highly Informative Direct
Biological Process (BP) humoral immune response 2.557e-13 Highly Informative Direct
Biological Process (BP) regulation of lipid storage 1.273e-07 Highly Informative Direct
Biological Process (BP) negative regulation of endopeptidase activity 0 Highly Informative Direct
Biological Process (BP) regulation of striated muscle tissue development 5.291e-06 Highly Informative Direct
Biological Process (BP) extracellular matrix organization 1.067e-05 Highly Informative Direct
Biological Process (BP) regulation of developmental growth 1.826e-05 Highly Informative Direct
Biological Process (BP) muscle fiber development 4.603e-08 Highly Informative Direct
Biological Process (BP) axon development 5.448e-10 Highly Informative Direct
Biological Process (BP) regulation of protein processing 1.355e-11 Highly Informative Direct
Biological Process (BP) protein activation cascade 4.131e-14 Highly Informative Direct
Biological Process (BP) cell projection morphogenesis 0.00321 Highly Informative Inherited
Biological Process (BP) chemotaxis 0.002176 Highly Informative Inherited
Biological Process (BP) muscle organ development 0.07452 Highly Informative Inherited
Biological Process (BP) regulation of cellular response to stress 0.02563 Highly Informative Inherited
Biological Process (BP) regulation of G-protein coupled receptor protein signaling pathway 0.01115 Highly Informative Inherited
Biological Process (BP) cell morphogenesis involved in neuron differentiation 0.01433 Highly Informative Inherited
Molecular Function (MF) binding 6.315e-09 Least Informative Direct
Molecular Function (MF) enzyme regulator activity 0 Moderately Informative Direct
Molecular Function (MF) anion binding 0.05297 Moderately Informative Inherited
Molecular Function (MF) enzyme inhibitor activity 5.618e-09 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 8.573e-05 Informative Direct
Molecular Function (MF) sulfur compound binding 2.432e-05 Informative Direct
Molecular Function (MF) cytokine activity 3.428e-05 Highly Informative Direct
Molecular Function (MF) heparin binding 7.583e-07 Highly Informative Direct
Molecular Function (MF) protein complex binding 0.0009352 Highly Informative Direct
Cellular Component (CC) extracellular region part 0 Moderately Informative Direct
Cellular Component (CC) vesicle 0.004281 Moderately Informative Inherited
Cellular Component (CC) cell surface 6.922e-07 Informative Direct
Cellular Component (CC) extracellular matrix 0 Informative Direct
Cellular Component (CC) extracellular membrane-bounded organelle 6.269e-06 Informative Direct
Cellular Component (CC) proteinaceous extracellular matrix 4.636e-08 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 cancer0.04675Least InformativeInherited
Disease Ontology (DO)nervous system disease0.1144Least InformativeInherited
Disease Ontology (DO)cell type cancer0.007831Moderately InformativeInherited
Disease Ontology (DO)gastrointestinal system disease0.03999Moderately InformativeInherited
Disease Ontology (DO)hematologic cancer0.06183Moderately InformativeInherited
Disease Ontology (DO)sensory system disease0.2334Moderately InformativeInherited
Disease Ontology (DO)bone disease0.5656Moderately InformativeInherited
Disease Ontology (DO)artery disease0.8673Moderately InformativeInherited
Disease Ontology (DO)periodontitis0.0001162InformativeDirect
Disease Ontology (DO)myeloma0.0001577InformativeDirect
Disease Ontology (DO)arthritis0.0004749InformativeDirect
Disease Ontology (DO)kidney cancer0.001739InformativeInherited
Disease Ontology (DO)retinal disease0.01234InformativeInherited
Disease Ontology (DO)medulloblastoma0.0001758Highly InformativeDirect
Disease Ontology (DO)degeneration of macula and posterior pole0.0002128Highly InformativeDirect
Disease Ontology (DO)cerebrovascular disease0.009369Highly 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 phenotype0.2494Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype0.2937Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.3682Least InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system development0.1407Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic cell number0.3275Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.7131Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal embryogenesis/ development1Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal vertebrae morphology0.03091InformativeInherited
Mammalian Phenotype (MP)abnormal neural tube morphology/development0.184InformativeInherited
Mammalian Phenotype (MP)fused somites1.301e-06Highly InformativeDirect
Mammalian Phenotype (MP)craniorachischisis3.753e-06Highly InformativeDirect
Mammalian Phenotype (MP)abnormal rostral-caudal body axis extension5.746e-06Highly InformativeDirect
Mammalian Phenotype (MP)decreased somite size3.494e-05Highly InformativeDirect
Mammalian Phenotype (MP)abnormal neutrophil morphology4.036e-05Highly InformativeDirect
Mammalian Phenotype (MP)incomplete somite formation0.0001626Highly InformativeDirect
Mammalian Phenotype (MP)abnormal granulocyte number0.0003334Highly InformativeDirect
Mammalian Phenotype (MP)abnormal neural tube closure0.02843Highly 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 system0.2726Least InformativeInherited
Xenopus ANatomical entity (XAN)portion of tissue0.5996Least InformativeInherited
Xenopus ANatomical entity (XAN)embryo0.6936Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.0759Moderately InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm0.7434Moderately InformativeInherited
Xenopus ANatomical entity (XAN)neural plate0.0001872InformativeDirect
Xenopus ANatomical entity (XAN)endoderm0.0002854InformativeDirect
Xenopus ANatomical entity (XAN)anatomical direction0.0006999InformativeDirect
Xenopus ANatomical entity (XAN)primordium0.001026InformativeInherited
Xenopus ANatomical entity (XAN)stomodeal-hypophyseal primordium5.522e-05Highly InformativeDirect
Xenopus ANatomical entity (XAN)optic field6.829e-05Highly InformativeDirect
Xenopus ANatomical entity (XAN)foregut0.0004196Highly InformativeDirect
Xenopus ANatomical entity (XAN)axial mesoderm0.0008318Highly InformativeDirect
Xenopus DEvelopment stage (XDE)embryonic stage8.823e-05Least InformativeDirect

Document: XA 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 pathway1.375e-11Highly InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentExtracellular matrix1.962e-11InformativeDirect
DomainSignal0Least InformativeDirect
DomainLaminin EGF-like domain0Highly InformativeDirect
Molecular functionZinc9.183e-12Least InformativeDirect
Post-translational modificationDevelopmental protein0Moderately InformativeDirect
Post-translational modificationProtease inhibitor0InformativeDirect
Post-translational modificationGrowth factor8.845e-16InformativeDirect
Post-translational modificationToxin0.001925InformativeInherited
Post-translational modificationMetalloenzyme inhibitor0Highly InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect
Post-translational modificationCleavage on pair of basic residues1.982e-12Moderately InformativeDirect
Post-translational modificationSulfation5.606e-06InformativeDirect
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) · 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) · UniProtKB KeyWords (KW) · Internal database links ]