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 (187) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 2,012 2,290 11
Proteins 1,993 2,275 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)multicellular organismal process5.502e-055.874e-10Least InformativeDirect
Biological Process (BP)developmental process1.169e-051.032e-11Least InformativeDirect
Biological Process (BP)response to stimulus1.256e-053.958e-08Least InformativeDirect
Biological Process (BP)regulation of metabolic process1.629e-100.05821Least InformativeInherited
Biological Process (BP)single-organism cellular process7.053e-050.0247Least InformativeInherited
Biological Process (BP)regulation of cellular process0.21231Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis0.033530.00744Least InformativeInherited
Biological Process (BP)cell differentiation4.229e-062.319e-11Moderately InformativeDirect
Biological Process (BP)regulation of developmental process8.444e-055.177e-09Moderately InformativeDirect
Biological Process (BP)regulation of multicellular organismal process0.00056392.631e-06Moderately InformativeDirect
Biological Process (BP)regulation of nucleobase-containing compound metabolic process0.20621Moderately InformativeInherited
Biological Process (BP)regulation of phosphate metabolic process13.32e-11Moderately InformativeInherited
Biological Process (BP)regulation of catalytic activity0.0015970.0005715Moderately InformativeInherited
Biological Process (BP)nervous system development0.046750.01899Moderately InformativeInherited
Biological Process (BP)negative regulation of metabolic process0.42831Moderately InformativeInherited
Biological Process (BP)negative regulation of cellular process0.00024840.001174Moderately InformativeInherited
Biological Process (BP)regulation of protein metabolic process0.67762.022e-05Moderately InformativeInherited
Biological Process (BP)negative regulation of catalytic activity00.0002045InformativeDirect
Biological Process (BP)generation of neurons2.27e-063.976e-10InformativeDirect
Biological Process (BP)regulation of peptidase activity05.611e-06InformativeDirect
Biological Process (BP)regulation of purine nucleotide metabolic process4.876e-082.822e-06InformativeDirect
Biological Process (BP)regulation of nervous system development0.00036190.0101InformativeInherited
Biological Process (BP)regulation of cell development2.096e-110.05124InformativeInherited
Biological Process (BP)negative regulation of protein metabolic process0.00010120.009022InformativeInherited
Biological Process (BP)negative regulation of endopeptidase activity00Highly InformativeDirect
Biological Process (BP)extracellular matrix organization6.328e-075.574e-07Highly InformativeDirect
Molecular Function (MF)binding0.024925.747e-05Least InformativeInherited
Molecular Function (MF)enzyme regulator activity1.976e-132.959e-11Moderately InformativeDirect
Molecular Function (MF)enzyme inhibitor activity00.0001012InformativeDirect
Molecular Function (MF)receptor binding4.956e-051.129e-08InformativeDirect
Molecular Function (MF)peptidase regulator activity04.819e-12InformativeDirect
Molecular Function (MF)protein complex binding1.341e-080.0001683Highly InformativeDirect
Cellular Component (CC)extracellular region part7.086e-120Moderately InformativeDirect
Cellular Component (CC)cell surface1.049e-112.015e-07InformativeDirect
Cellular Component (CC)extracellular matrix00InformativeDirect
Cellular Component (CC)proteinaceous extracellular matrix4.002e-156.401e-10Highly 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 5.874e-10 Least Informative Direct
Biological Process (BP) developmental process 1.032e-11 Least Informative Direct
Biological Process (BP) response to stimulus 3.958e-08 Least Informative Direct
Biological Process (BP) localization 0.7973 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.05821 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.0247 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.02535 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.00744 Least Informative Inherited
Biological Process (BP) immune system process 0.0003456 Moderately Informative Direct
Biological Process (BP) regulation of phosphate metabolic process 3.32e-11 Moderately Informative Direct
Biological Process (BP) cell differentiation 2.319e-11 Moderately Informative Direct
Biological Process (BP) regulation of programmed cell death 1.026e-06 Moderately Informative Direct
Biological Process (BP) regulation of catalytic activity 0.0005715 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 5.177e-09 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 2.631e-06 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 2.022e-05 Moderately Informative Direct
Biological Process (BP) regulation of signal transduction 0.004248 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.003947 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.06885 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.5724 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 0.3356 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.03572 Moderately Informative Inherited
Biological Process (BP) system process 1 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.07667 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.7567 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.01899 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.001174 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.02885 Moderately Informative Inherited
Biological Process (BP) signal transduction 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.4478 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 0.01181 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.2248 Moderately Informative Inherited
Biological Process (BP) regulation of protein phosphorylation 4.743e-09 Informative Direct
Biological Process (BP) immune effector process 7.999e-06 Informative Direct
Biological Process (BP) positive regulation of immune system process 0.000854 Informative Direct
Biological Process (BP) negative regulation of cell communication 4.305e-05 Informative Direct
Biological Process (BP) negative regulation of signaling 1.635e-05 Informative Direct
Biological Process (BP) cell projection organization 8.777e-05 Informative Direct
Biological Process (BP) regulation of growth 2.752e-06 Informative Direct
Biological Process (BP) locomotion 2.007e-05 Informative Direct
Biological Process (BP) negative regulation of catalytic activity 0.0002045 Informative Direct
Biological Process (BP) negative regulation of response to stimulus 0.000792 Informative Direct
Biological Process (BP) generation of neurons 3.976e-10 Informative Direct
Biological Process (BP) regulation of peptidase activity 5.611e-06 Informative Direct
Biological Process (BP) regulation of purine nucleotide metabolic process 2.822e-06 Informative Direct
Biological Process (BP) cellular component morphogenesis 0.001932 Informative Inherited
Biological Process (BP) cellular component movement 0.002779 Informative Inherited
Biological Process (BP) membrane organization 0.01943 Informative Inherited
Biological Process (BP) muscle structure development 0.2141 Informative Inherited
Biological Process (BP) tissue morphogenesis 0.01518 Informative Inherited
Biological Process (BP) epithelium development 0.633 Informative Inherited
Biological Process (BP) cell-cell signaling 0.008819 Informative Inherited
Biological Process (BP) transmission of nerve impulse 0.04487 Informative Inherited
Biological Process (BP) response to hormone stimulus 0.07267 Informative Inherited
Biological Process (BP) response to organic cyclic compound 0.542 Informative Inherited
Biological Process (BP) response to lipid 0.08708 Informative Inherited
Biological Process (BP) regulation of intracellular protein kinase cascade 0.7121 Informative Inherited
Biological Process (BP) positive regulation of signal transduction 0.9667 Informative Inherited
Biological Process (BP) regulation of nervous system development 0.0101 Informative Inherited
Biological Process (BP) regulation of cell development 0.05124 Informative Inherited
Biological Process (BP) negative regulation of protein metabolic process 0.009022 Informative Inherited
Biological Process (BP) regulation of immune effector process 0.001095 Informative Inherited
Biological Process (BP) regulation of locomotion 0.01853 Informative Inherited
Biological Process (BP) regulation of cellular component movement 0.0041 Informative Inherited
Biological Process (BP) muscle tissue development 0.0492 Informative Inherited
Biological Process (BP) regulation of lipid metabolic process 0.005296 Informative Inherited
Biological Process (BP) positive regulation of transport 0.01434 Informative Inherited
Biological Process (BP) immune response 0.006221 Informative Inherited
Biological Process (BP) regulation of immune response 0.482 Informative Inherited
Biological Process (BP) regulation of defense response 0.5945 Informative Inherited
Biological Process (BP) regulation of response to external stimulus 0.06778 Informative Inherited
Biological Process (BP) activation of immune response 5.377e-08 Highly Informative Direct
Biological Process (BP) regulation of humoral immune response 1.129e-09 Highly Informative Direct
Biological Process (BP) humoral immune response 1.142e-13 Highly Informative Direct
Biological Process (BP) negative regulation of cell proliferation 0.0001302 Highly Informative Direct
Biological Process (BP) regulation of lipid storage 8.98e-08 Highly Informative Direct
Biological Process (BP) negative regulation of endopeptidase activity 0 Highly Informative Direct
Biological Process (BP) extracellular matrix organization 5.574e-07 Highly Informative Direct
Biological Process (BP) regulation of developmental growth 1.426e-05 Highly Informative Direct
Biological Process (BP) regulation of inflammatory response 1.988e-05 Highly Informative Direct
Biological Process (BP) regulation of protein processing 1.133e-11 Highly Informative Direct
Biological Process (BP) protein activation cascade 4.427e-14 Highly Informative Direct
Biological Process (BP) neuron projection development 0.01916 Highly Informative Inherited
Biological Process (BP) cell part morphogenesis 0.008567 Highly Informative Inherited
Biological Process (BP) chemotaxis 0.001694 Highly Informative Inherited
Biological Process (BP) muscle organ development 0.03741 Highly Informative Inherited
Biological Process (BP) regulation of cellular response to stress 0.009271 Highly Informative Inherited
Biological Process (BP) regulation of G-protein coupled receptor protein signaling pathway 0.003041 Highly Informative Inherited
Biological Process (BP) cell morphogenesis involved in differentiation 0.002521 Highly Informative Inherited
Molecular Function (MF) binding 5.747e-05 Least Informative Direct
Molecular Function (MF) enzyme regulator activity 2.959e-11 Moderately Informative Direct
Molecular Function (MF) anion binding 0.03671 Moderately Informative Inherited
Molecular Function (MF) enzyme inhibitor activity 0.0001012 Informative Direct
Molecular Function (MF) receptor binding 1.129e-08 Informative Direct
Molecular Function (MF) peptidase regulator activity 4.819e-12 Informative Direct
Molecular Function (MF) carbohydrate derivative binding 1.998e-05 Informative Direct
Molecular Function (MF) sulfur compound binding 5.195e-06 Informative Direct
Molecular Function (MF) heparin binding 7.536e-07 Highly Informative Direct
Molecular Function (MF) protein complex binding 0.0001683 Highly Informative Direct
Cellular Component (CC) extracellular region part 0 Moderately Informative Direct
Cellular Component (CC) cell surface 2.015e-07 Informative Direct
Cellular Component (CC) extracellular matrix 0 Informative Direct
Cellular Component (CC) proteinaceous extracellular matrix 6.401e-10 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 cancer0.04658Least InformativeInherited
Disease Ontology (DO)nervous system disease0.111Least InformativeInherited
Disease Ontology (DO)musculoskeletal system disease0.0002293Moderately InformativeDirect
Disease Ontology (DO)cell type cancer0.007889Moderately InformativeInherited
Disease Ontology (DO)gastrointestinal system disease0.05944Moderately InformativeInherited
Disease Ontology (DO)hematologic cancer0.06178Moderately InformativeInherited
Disease Ontology (DO)sensory system disease0.2735Moderately InformativeInherited
Disease Ontology (DO)artery disease0.8717Moderately InformativeInherited
Disease Ontology (DO)periodontitis0.0001178InformativeDirect
Disease Ontology (DO)myeloma0.0001555InformativeDirect
Disease Ontology (DO)arthritis0.0004839InformativeDirect
Disease Ontology (DO)renal carcinoma0.0009168InformativeDirect
Disease Ontology (DO)retinal disease0.01229InformativeInherited
Disease Ontology (DO)medulloblastoma0.0001783Highly InformativeDirect
Disease Ontology (DO)degeneration of macula and posterior pole0.0002225Highly InformativeDirect
Disease Ontology (DO)cerebrovascular disease0.009447Highly 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 phenotype0.2459Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype0.2936Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.3711Least InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system development0.1409Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.711Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal embryogenesis/ development1Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal vertebrae morphology0.03106InformativeInherited
Mammalian Phenotype (MP)abnormal neural tube morphology/development0.1897InformativeInherited
Mammalian Phenotype (MP)fused somites1.361e-06Highly InformativeDirect
Mammalian Phenotype (MP)craniorachischisis3.927e-06Highly InformativeDirect
Mammalian Phenotype (MP)abnormal rostral-caudal body axis extension4.881e-06Highly InformativeDirect
Mammalian Phenotype (MP)abnormal neutrophil cell number2.822e-05Highly InformativeDirect
Mammalian Phenotype (MP)decreased somite size3.667e-05Highly InformativeDirect
Mammalian Phenotype (MP)incomplete somite formation0.0001702Highly InformativeDirect
Mammalian Phenotype (MP)abnormal neural tube closure0.02882Highly 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 system0.2728Least InformativeInherited
Xenopus ANatomical entity (XAN)portion of tissue0.5969Least InformativeInherited
Xenopus ANatomical entity (XAN)embryo0.6903Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.06929Moderately InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm0.739Moderately InformativeInherited
Xenopus ANatomical entity (XAN)neural plate0.0001354InformativeDirect
Xenopus ANatomical entity (XAN)endoderm0.0002568InformativeDirect
Xenopus ANatomical entity (XAN)anatomical direction0.0005489InformativeDirect
Xenopus ANatomical entity (XAN)optic field4.987e-05Highly InformativeDirect
Xenopus ANatomical entity (XAN)foregut0.000297Highly InformativeDirect
Xenopus ANatomical entity (XAN)axial mesoderm0.0008196Highly InformativeDirect
Xenopus DEvelopment stage (XDE)embryonic stage8.821e-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 pathway1.834e-11Highly InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentExtracellular matrix2.407e-11InformativeDirect
DomainSignal0Least InformativeDirect
DomainLaminin EGF-like domain0Highly InformativeDirect
Molecular functionZinc8.52e-12Least InformativeDirect
Post-translational modificationDevelopmental protein0Moderately InformativeDirect
Post-translational modificationProtease inhibitor0InformativeDirect
Post-translational modificationToxin0.001758InformativeInherited
Post-translational modificationMetalloenzyme inhibitor0Highly InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect
Post-translational modificationCleavage on pair of basic residues2.189e-12Moderately InformativeDirect
Post-translational modificationSulfation5.857e-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 ]