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 (194) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 2,055 0 11
Proteins 2,035 0 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 process0.00045515.9e-12Least InformativeDirect
Biological Process (BP)regulation of metabolic process00.01541Least InformativeInherited
Biological Process (BP)single-organism cellular process0.0015660.02245Least InformativeInherited
Biological Process (BP)multicellular organismal process0.0063294.867e-09Least InformativeInherited
Biological Process (BP)regulation of cellular process0.06381Least InformativeInherited
Biological Process (BP)response to stimulus0.0046321.541e-06Least InformativeInherited
Biological Process (BP)regulation of signal transduction00.0003638Moderately InformativeDirect
Biological Process (BP)cell differentiation5.423e-054.953e-13Moderately InformativeDirect
Biological Process (BP)regulation of catalytic activity1.116e-063.46e-06Moderately InformativeDirect
Biological Process (BP)regulation of nucleobase-containing compound metabolic process0.089671Moderately InformativeInherited
Biological Process (BP)regulation of phosphate metabolic process18.561e-11Moderately InformativeInherited
Biological Process (BP)regulation of developmental process0.031332.562e-07Moderately InformativeInherited
Biological Process (BP)regulation of multicellular organismal process0.11146.741e-05Moderately InformativeInherited
Biological Process (BP)nervous system development0.046760.05853Moderately InformativeInherited
Biological Process (BP)regulation of cell proliferation4.984e-112.422e-08InformativeDirect
Biological Process (BP)negative regulation of catalytic activity06.314e-07InformativeDirect
Biological Process (BP)generation of neurons1.439e-051.398e-09InformativeDirect
Biological Process (BP)regulation of peptidase activity06.418e-10InformativeDirect
Biological Process (BP)regulation of purine nucleotide metabolic process2.882e-073.989e-06InformativeDirect
Biological Process (BP)regulation of nervous system development9.376e-110.0114InformativeInherited
Biological Process (BP)regulation of cell development3.568e-100.08994InformativeInherited
Biological Process (BP)negative regulation of endopeptidase activity00Highly InformativeDirect
Molecular Function (MF)binding1.66e-052.352e-09Least InformativeDirect
Molecular Function (MF)enzyme regulator activity00Moderately InformativeDirect
Molecular Function (MF)enzyme inhibitor activity05.657e-09InformativeDirect
Molecular Function (MF)receptor binding00InformativeDirect
Molecular Function (MF)peptidase regulator activity00InformativeDirect
Molecular Function (MF)cytokine activity0.00094263.514e-05Highly InformativeDirect
Molecular Function (MF)protein complex binding2.351e-060.0008988Highly InformativeDirect
Cellular Component (CC)extracellular region part00Moderately InformativeDirect
Cellular Component (CC)cell surface7.097e-114.495e-07InformativeDirect
Cellular Component (CC)extracellular matrix00InformativeDirect
Cellular Component (CC)proteinaceous extracellular matrix9.323e-118.959e-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 4.867e-09 Least Informative Direct
Biological Process (BP) developmental process 5.9e-12 Least Informative Direct
Biological Process (BP) response to stimulus 1.541e-06 Least Informative Direct
Biological Process (BP) localization 0.9435 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.01541 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.02245 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.04079 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.04366 Least Informative Inherited
Biological Process (BP) regulation of signal transduction 0.0003638 Moderately Informative Direct
Biological Process (BP) regulation of phosphate metabolic process 8.561e-11 Moderately Informative Direct
Biological Process (BP) cell differentiation 4.953e-13 Moderately Informative Direct
Biological Process (BP) single-organism developmental process 0.0006368 Moderately Informative Direct
Biological Process (BP) regulation of catalytic activity 3.46e-06 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 2.562e-07 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 6.741e-05 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 5.105e-05 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.08725 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.8034 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 0.4804 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.02498 Moderately Informative Inherited
Biological Process (BP) system process 1 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.0747 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.6766 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.04844 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.05853 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.109 Moderately Informative Inherited
Biological Process (BP) signal transduction 1 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.06631 Moderately Informative Inherited
Biological Process (BP) regulation of biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 0.1091 Moderately Informative Inherited
Biological Process (BP) immune system process 0.001192 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.3289 Moderately Informative Inherited
Biological Process (BP) regulation of protein phosphorylation 9.555e-09 Informative Direct
Biological Process (BP) immune effector process 5.304e-06 Informative Direct
Biological Process (BP) negative regulation of signaling 0.0005438 Informative Direct
Biological Process (BP) cell projection organization 0.0001258 Informative Direct
Biological Process (BP) regulation of growth 2.458e-05 Informative Direct
Biological Process (BP) locomotion 6.554e-05 Informative Direct
Biological Process (BP) regulation of cell proliferation 2.422e-08 Informative Direct
Biological Process (BP) regulation of apoptotic process 6.243e-07 Informative Direct
Biological Process (BP) negative regulation of catalytic activity 6.314e-07 Informative Direct
Biological Process (BP) generation of neurons 1.398e-09 Informative Direct
Biological Process (BP) regulation of peptidase activity 6.418e-10 Informative Direct
Biological Process (BP) regulation of purine nucleotide metabolic process 3.989e-06 Informative Direct
Biological Process (BP) cellular component morphogenesis 0.003972 Informative Inherited
Biological Process (BP) cellular component movement 0.003728 Informative Inherited
Biological Process (BP) cellular membrane organization 0.00764 Informative Inherited
Biological Process (BP) tissue morphogenesis 0.02711 Informative Inherited
Biological Process (BP) epithelium development 0.6438 Informative Inherited
Biological Process (BP) cell-cell signaling 0.01016 Informative Inherited
Biological Process (BP) transmission of nerve impulse 0.04904 Informative Inherited
Biological Process (BP) positive regulation of immune system process 0.008518 Informative Inherited
Biological Process (BP) regulation of response to stress 0.863 Informative Inherited
Biological Process (BP) muscle structure development 0.0296 Informative Inherited
Biological Process (BP) response to hormone stimulus 0.09925 Informative Inherited
Biological Process (BP) response to organic cyclic compound 0.626 Informative Inherited
Biological Process (BP) response to lipid 0.117 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 0.0114 Informative Inherited
Biological Process (BP) regulation of cell development 0.08994 Informative Inherited
Biological Process (BP) regulation of immune effector process 0.001224 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.001063 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.004454 Informative Inherited
Biological Process (BP) muscle tissue development 0.04967 Informative Inherited
Biological Process (BP) regulation of lipid metabolic process 0.00445 Informative Inherited
Biological Process (BP) positive regulation of transport 0.01309 Informative Inherited
Biological Process (BP) immune response 0.006657 Informative Inherited
Biological Process (BP) regulation of immune response 0.8623 Informative Inherited
Biological Process (BP) regulation of response to external stimulus 0.1523 Informative Inherited
Biological Process (BP) activation of immune response 3.372e-08 Highly Informative Direct
Biological Process (BP) regulation of acute inflammatory response 2.102e-06 Highly Informative Direct
Biological Process (BP) regulation of humoral immune response 1.3e-09 Highly Informative Direct
Biological Process (BP) humoral immune response 2.021e-13 Highly Informative Direct
Biological Process (BP) regulation of lipid storage 1.277e-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 4.647e-06 Highly Informative Direct
Biological Process (BP) extracellular matrix organization 9.53e-06 Highly Informative Direct
Biological Process (BP) regulation of developmental growth 2.758e-05 Highly Informative Direct
Biological Process (BP) muscle fiber development 3.695e-08 Highly Informative Direct
Biological Process (BP) axon development 4.126e-10 Highly Informative Direct
Biological Process (BP) regulation of protein processing 1.277e-11 Highly Informative Direct
Biological Process (BP) protein activation cascade 4.401e-14 Highly Informative Direct
Biological Process (BP) cell projection morphogenesis 0.003186 Highly Informative Inherited
Biological Process (BP) chemotaxis 0.002391 Highly Informative Inherited
Biological Process (BP) muscle organ development 0.06212 Highly Informative Inherited
Biological Process (BP) regulation of cellular response to stress 0.02437 Highly Informative Inherited
Biological Process (BP) regulation of G-protein coupled receptor protein signaling pathway 0.01131 Highly Informative Inherited
Biological Process (BP) cell morphogenesis involved in neuron differentiation 0.01421 Highly Informative Inherited
Molecular Function (MF) binding 2.352e-09 Least Informative Direct
Molecular Function (MF) enzyme regulator activity 0 Moderately Informative Direct
Molecular Function (MF) anion binding 0.0482 Moderately Informative Inherited
Molecular Function (MF) enzyme inhibitor activity 5.657e-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 8.89e-05 Informative Direct
Molecular Function (MF) sulfur compound binding 2.494e-05 Informative Direct
Molecular Function (MF) cytokine activity 3.514e-05 Highly Informative Direct
Molecular Function (MF) heparin binding 7.746e-07 Highly Informative Direct
Molecular Function (MF) protein complex binding 0.0008988 Highly Informative Direct
Cellular Component (CC) extracellular region part 0 Moderately Informative Direct
Cellular Component (CC) vesicle 0.0082 Moderately Informative Inherited
Cellular Component (CC) cell surface 4.495e-07 Informative Direct
Cellular Component (CC) extracellular matrix 0 Informative Direct
Cellular Component (CC) extracellular membrane-bounded organelle 1.411e-05 Informative Direct
Cellular Component (CC) proteinaceous extracellular matrix 8.959e-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 cancer0.04632Least InformativeInherited
Disease Ontology (DO)nervous system disease0.1075Least InformativeInherited
Disease Ontology (DO)musculoskeletal system disease0.0002328Moderately InformativeDirect
Disease Ontology (DO)cell type cancer0.00783Moderately InformativeInherited
Disease Ontology (DO)gastrointestinal system disease0.05941Moderately InformativeInherited
Disease Ontology (DO)hematologic cancer0.0613Moderately InformativeInherited
Disease Ontology (DO)sensory system disease0.2756Moderately InformativeInherited
Disease Ontology (DO)artery disease0.8657Moderately InformativeInherited
Disease Ontology (DO)periodontitis0.0001178InformativeDirect
Disease Ontology (DO)myeloma0.000155InformativeDirect
Disease Ontology (DO)arthritis0.0004825InformativeDirect
Disease Ontology (DO)renal carcinoma0.0009164InformativeDirect
Disease Ontology (DO)retinal disease0.01224InformativeInherited
Disease Ontology (DO)medulloblastoma0.0001781Highly InformativeDirect
Disease Ontology (DO)degeneration of macula and posterior pole0.0002223Highly InformativeDirect
Disease Ontology (DO)cerebrovascular disease0.009386Highly 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 phenotype0.2509Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype0.293Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.3704Least InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system development0.1399Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic cell number0.3281Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.7126Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal embryogenesis/ development1Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal vertebrae morphology0.03065InformativeInherited
Mammalian Phenotype (MP)abnormal neural tube morphology/development0.1848InformativeInherited
Mammalian Phenotype (MP)fused somites1.326e-06Highly InformativeDirect
Mammalian Phenotype (MP)craniorachischisis3.825e-06Highly InformativeDirect
Mammalian Phenotype (MP)abnormal rostral-caudal body axis extension5.851e-06Highly InformativeDirect
Mammalian Phenotype (MP)decreased somite size3.558e-05Highly InformativeDirect
Mammalian Phenotype (MP)abnormal neutrophil morphology4.037e-05Highly InformativeDirect
Mammalian Phenotype (MP)incomplete somite formation0.0001651Highly InformativeDirect
Mammalian Phenotype (MP)abnormal granulocyte number0.0003349Highly InformativeDirect
Mammalian Phenotype (MP)abnormal neural tube closure0.02868Highly 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 system0.2727Least InformativeInherited
Xenopus ANatomical entity (XAN)portion of tissue0.5998Least InformativeInherited
Xenopus ANatomical entity (XAN)embryo0.6935Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.07409Moderately InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm0.7419Moderately InformativeInherited
Xenopus ANatomical entity (XAN)neural plate0.0001685InformativeDirect
Xenopus ANatomical entity (XAN)endoderm0.0002795InformativeDirect
Xenopus ANatomical entity (XAN)anatomical direction0.0006911InformativeDirect
Xenopus ANatomical entity (XAN)primordium0.0009879InformativeDirect
Xenopus ANatomical entity (XAN)optic field5.271e-05Highly InformativeDirect
Xenopus ANatomical entity (XAN)stomodeal-hypophyseal primordium5.515e-05Highly InformativeDirect
Xenopus ANatomical entity (XAN)foregut0.0003926Highly InformativeDirect
Xenopus ANatomical entity (XAN)axial mesoderm0.0008459Highly InformativeDirect
Xenopus DEvelopment stage (XDE)embryonic stage8.835e-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 pathway1.372e-11Highly InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentExtracellular matrix2.05e-11InformativeDirect
DomainSignal0Least InformativeDirect
DomainLaminin EGF-like domain0Highly InformativeDirect
Molecular functionZinc9.365e-12Least InformativeDirect
Post-translational modificationDevelopmental protein0Moderately InformativeDirect
Post-translational modificationProtease inhibitor0InformativeDirect
Post-translational modificationGrowth factor8.838e-16InformativeDirect
Post-translational modificationToxin0.001825InformativeInherited
Post-translational modificationMetalloenzyme inhibitor0Highly InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect
Post-translational modificationCleavage on pair of basic residues2.083e-12Moderately InformativeDirect
Post-translational modificationSulfation5.668e-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 ]