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Notch domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Small proteins [ 56992] (90)
Fold:   Notch domain [ 90192]
Superfamily:   Notch domain [ 90193]
Families:   Notch domain [ 90194]

 Superfamily statistics
Genomes (134) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 1,021 1,072 1
Proteins 465 486 1

 Functional annotation
General category Regulation
Detailed category Receptor activity

Document: Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) developmental process 7.637e-12 Least Informative Direct
Biological Process (BP) multicellular organismal process 1.493e-08 Least Informative Direct
Biological Process (BP) regulation of cellular process 2.981e-06 Least Informative Direct
Biological Process (BP) response to stimulus 6.545e-06 Least Informative Direct
Biological Process (BP) single-organism cellular process 1.984e-05 Least Informative Direct
Biological Process (BP) localization 0.02979 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.9175 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.1297 Least Informative Inherited
Biological Process (BP) cell differentiation 4.642e-13 Moderately Informative Direct
Biological Process (BP) single-organism developmental process 8.429e-07 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 5.681e-06 Moderately Informative Direct
Biological Process (BP) immune system process 1.757e-05 Moderately Informative Direct
Biological Process (BP) tissue development 5.96e-05 Moderately Informative Direct
Biological Process (BP) anatomical structure morphogenesis 7.861e-05 Moderately Informative Direct
Biological Process (BP) signal transduction 0.0001711 Moderately Informative Direct
Biological Process (BP) organic substance transport 0.0001822 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 0.0003529 Moderately Informative Direct
Biological Process (BP) regulation of cellular metabolic process 0.7868 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.08823 Moderately Informative Inherited
Biological Process (BP) regulation of nitrogen compound metabolic process 0.001892 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.003555 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 0.03471 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.0119 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 0.06022 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 0.1325 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.005857 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.4281 Moderately Informative Inherited
Biological Process (BP) regulation of biosynthetic process 0.001473 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.002003 Moderately Informative Inherited
Biological Process (BP) growth 1.381e-08 Informative Direct
Biological Process (BP) negative regulation of developmental process 1.082e-07 Informative Direct
Biological Process (BP) secretion 1.642e-07 Informative Direct
Biological Process (BP) generation of neurons 2.6e-07 Informative Direct
Biological Process (BP) positive regulation of signal transduction 2.769e-07 Informative Direct
Biological Process (BP) response to wounding 7.646e-07 Informative Direct
Biological Process (BP) protein transport 2.688e-06 Informative Direct
Biological Process (BP) regulation of apoptotic process 2.632e-05 Informative Direct
Biological Process (BP) cardiovascular system development 3.242e-05 Informative Direct
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.0003015 Informative Direct
Biological Process (BP) regulation of cell proliferation 0.0003565 Informative Direct
Biological Process (BP) regulation of nervous system development 0.1429 Informative Inherited
Biological Process (BP) regulation of cell development 0.8201 Informative Inherited
Biological Process (BP) tube development 0.001619 Informative Inherited
Biological Process (BP) cell projection organization 0.02713 Informative Inherited
Biological Process (BP) tissue morphogenesis 0.001659 Informative Inherited
Biological Process (BP) epithelium development 0.1361 Informative Inherited
Biological Process (BP) cellular component morphogenesis 0.02862 Informative Inherited
Biological Process (BP) limb morphogenesis 1.322e-08 Highly Informative Direct
Biological Process (BP) pattern specification process 6.678e-06 Highly Informative Direct
Biological Process (BP) axonogenesis 1.125e-05 Highly Informative Direct
Biological Process (BP) cell fate commitment 0.0001076 Highly Informative Direct
Biological Process (BP) developmental growth 0.0001578 Highly Informative Direct
Biological Process (BP) negative regulation of cell proliferation 0.0007081 Highly Informative Direct
Biological Process (BP) negative regulation of cell development 0.002465 Highly Informative Inherited
Molecular Function (MF) binding 0.1189 Least Informative Inherited
Molecular Function (MF) protein binding 0.01219 Moderately Informative Inherited
Molecular Function (MF) receptor activity 2.744e-05 Informative Direct
Molecular Function (MF) enzyme binding 0.0002235 Informative Direct
Cellular Component (CC) membrane 7.891e-05 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.1687 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.04742 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.05626 Least Informative Inherited
Cellular Component (CC) endomembrane system 3.147e-07 Moderately Informative Direct
Cellular Component (CC) plasma membrane 3.744e-06 Moderately Informative Direct
Cellular Component (CC) endoplasmic reticulum 2.039e-05 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.0001664 Moderately Informative Direct
Cellular Component (CC) organelle membrane 0.0002479 Moderately Informative Direct
Cellular Component (CC) extracellular region 0.000289 Moderately Informative Direct
Cellular Component (CC) intrinsic to membrane 0.1097 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.026 Moderately Informative Inherited
Cellular Component (CC) Golgi apparatus 9.918e-09 Informative Direct
Cellular Component (CC) cell surface 2.57e-08 Informative Direct
Cellular Component (CC) integral to membrane 2.917e-06 Informative Direct
Cellular Component (CC) endoplasmic reticulum membrane 0.0005151 Informative Direct
Cellular Component (CC) Golgi membrane 3.974e-06 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)immune system disease0.001674Least InformativeInherited
Disease Ontology (DO)organ system cancer0.05188Least InformativeInherited
Disease Ontology (DO)benign neoplasm5.908e-05Moderately InformativeDirect
Disease Ontology (DO)hypersensitivity reaction type II disease0.0002142Moderately InformativeDirect
Disease Ontology (DO)hematologic cancer0.02367Moderately InformativeInherited
Disease Ontology (DO)hematopoietic system disease0.07292Moderately InformativeInherited
Disease Ontology (DO)organ system benign neoplasm7.405e-07InformativeDirect
Disease Ontology (DO)kidney cancer1.548e-05InformativeDirect
Disease Ontology (DO)hemorrhagic disease3.318e-05InformativeDirect
Disease Ontology (DO)liver carcinoma0.0004188InformativeDirect
Disease Ontology (DO)lymphoblastic leukemia0.0006367InformativeDirect
Disease Ontology (DO)skin hemangioma4.851e-13Highly InformativeDirect
Disease Ontology (DO)hemangioma3.77e-09Highly InformativeDirect
Disease Ontology (DO)primary thrombocytopenia1.702e-08Highly InformativeDirect
Disease Ontology (DO)purpura2.33e-06Highly InformativeDirect

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Malformation of the heart and great vessels0.01519Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal respiratory system morphology0.03111Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the aortic valve1.834e-05InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the upper respiratory tract0.001588InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)abnormal homeostasis0Least InformativeDirect
Mammalian Phenotype (MP)nervous system phenotype0Least InformativeDirect
Mammalian Phenotype (MP)cardiovascular system phenotype0.01455Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.1708Least InformativeInherited
Mammalian Phenotype (MP)abnormal cardiovascular development0.0003778Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal blood vessel morphology0.001466Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal gland morphology0.003491Moderately InformativeInherited
Mammalian Phenotype (MP)embryogenesis phenotype0.005281Moderately InformativeInherited
Mammalian Phenotype (MP)tumorigenesis0.008357Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune system organ morphology0.01888Moderately InformativeInherited
Mammalian Phenotype (MP)digestive/alimentary phenotype0.02132Moderately InformativeInherited
Mammalian Phenotype (MP)integument phenotype0.03728Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal heart morphology0.3653Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal artery morphology3.528e-05InformativeDirect
Mammalian Phenotype (MP)abnormal developmental patterning3.756e-05InformativeDirect
Mammalian Phenotype (MP)increased hemolymphoid system tumor incidence0.0002117InformativeDirect
Mammalian Phenotype (MP)abnormal epidermal layer morphology0.0004094InformativeDirect
Mammalian Phenotype (MP)abnormal skin appearance0.001315InformativeInherited
Mammalian Phenotype (MP)abnormal spleen morphology0.008728InformativeInherited
Mammalian Phenotype (MP)abnormal fluid regulation0.0592InformativeInherited
Mammalian Phenotype (MP)abnormal extraembryonic tissue morphology0.1265InformativeInherited
Mammalian Phenotype (MP)abnormal pancreatic acinus morphology5.419e-07Highly InformativeDirect
Mammalian Phenotype (MP)scaly skin1.224e-06Highly InformativeDirect
Mammalian Phenotype (MP)leukemia3.727e-06Highly InformativeDirect
Mammalian Phenotype (MP)abnormal spleen red pulp morphology2.755e-05Highly InformativeDirect
Mammalian Phenotype (MP)extramedullary hematopoiesis4.342e-05Highly InformativeDirect
Mammalian Phenotype (MP)abnormal sebaceous gland morphology8.247e-05Highly InformativeDirect
Mammalian Phenotype (MP)abnormal hair follicle morphology8.506e-05Highly InformativeDirect
Mammalian Phenotype (MP)abnormal pericardium morphology0.0003979Highly InformativeDirect
Mammalian Phenotype (MP)edema0.001105Highly InformativeInherited

Document: MP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorous-containing groups0Least InformativeDirect
Enzyme Commission (EC)Transferases for other substituted phosphate groups0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDifferentiation0Moderately InformativeDirect
Biological processTranscription regulation6.525e-15Moderately InformativeDirect
Biological processNotch signaling pathway0Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentNucleus3.085e-08Least InformativeDirect
DomainRepeat0Least InformativeDirect
DomainTransmembrane0Least InformativeDirect
DomainSignal8.426e-08Least InformativeDirect
DomainANK repeat0InformativeDirect
DomainEGF-like domain0InformativeDirect
Molecular functionCalcium2.009e-08Moderately InformativeDirect
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationDevelopmental protein0Moderately InformativeDirect
Post-translational modificationReceptor0Moderately InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR000800 SSF90193 Protein matches
Abstract The Notch domain is also called the 'DSL' domain or the Lin-12/Notch repeat (LNR). The LNR region is present only in Notch related proteins C-terminal to EGF repeats. The lin-12/Notch proteins act as transmembrane receptors for intercellular signals that specify cell fates during animal development. In response to a ligand, proteolytic cleavages release the intracellular domain of Notch, which then gains access to the nucleus and acts as a transcriptional co-activator [PubMed3119223]. The LNR region is supposed to negatively regulate the Lin-12/Notch proteins activity. It is a triplication of an around 35-40 amino acids module present on the extracellular part of the protein [PubMed7697721, PubMed8139658]. Each module contains six cysteine residues engaged in three disulphide bonds and three conserved aspartate and asparagine residues [PubMed3119223]. The biochemical characterization of a recombinantly expressed LIN-12.1 module from the human Notch1 receptor indicate that the disulphide bonds are formed between the first and fifth, second and fourth, and third and sixth cysteines. The formation of this particular disulphide isomer is favored by the presence of Ca2+, which is also required to maintain the structural integrity of the rLIN-12.1 module. The conserved aspartate and asparagine residues are likely to be important for Ca2+ binding, and thereby contribute to the native fold.

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-coverage) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Enzyme Commission (EC) · 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 1 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 Notch domain 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 1 hidden Markov models representing the Notch domain 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-coverage) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]
Please cite: Gough, J., Karplus, K., Hughey, R. and Chothia, C. (2001). "Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure." J. Mol. Biol., 313(4), 903-919.

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© Copyright 2013 The SUPERFAMILY authors and Julian Gough.