SUPERFAMILY 1.75 HMM library and genome assignments server


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 (144) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 1,060 1,266 1
Proteins 482 581 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) multicellular organismal process 0.0000000002978 Least Informative Direct
Biological Process (BP) developmental process 0.0000000000001105 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.000001716 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.00000004457 Least Informative Direct
Biological Process (BP) response to stimulus 0.0000002039 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.00005561 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0.6991 Least Informative Inherited
Biological Process (BP) localization 0.0451 Least Informative Inherited
Biological Process (BP) immune system process 0.00004373 Moderately Informative Direct
Biological Process (BP) signal transduction 0.0000009148 Moderately Informative Direct
Biological Process (BP) anatomical structure morphogenesis 0.00007071 Moderately Informative Direct
Biological Process (BP) tissue development 0.000774 Moderately Informative Direct
Biological Process (BP) regulation of biosynthetic process 0.00001217 Moderately Informative Direct
Biological Process (BP) regulation of signal transduction 0.000005082 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.0000178 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.00001712 Moderately Informative Direct
Biological Process (BP) single-organism developmental process 0.000001493 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.0008815 Moderately Informative Direct
Biological Process (BP) positive regulation of response to stimulus 0.0001383 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 0.000114 Moderately Informative Direct
Biological Process (BP) organic substance transport 0.0001987 Moderately Informative Direct
Biological Process (BP) organ development 0.003759 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.211 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.02042 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.01123 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.02359 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.00337 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.07567 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.7013 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) response to wounding 0.000000599 Informative Direct
Biological Process (BP) positive regulation of signal transduction 0.000000004382 Informative Direct
Biological Process (BP) protein transport 0.000002536 Informative Direct
Biological Process (BP) phosphorylation 0.0003776 Informative Direct
Biological Process (BP) cell projection organization 0.00005876 Informative Direct
Biological Process (BP) secretion by cell 0.00006311 Informative Direct
Biological Process (BP) growth 0.000000007695 Informative Direct
Biological Process (BP) regulation of cell proliferation 0.00003657 Informative Direct
Biological Process (BP) regulation of apoptotic process 0.00002546 Informative Direct
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.0008569 Informative Direct
Biological Process (BP) generation of neurons 0.0000004153 Informative Direct
Biological Process (BP) negative regulation of developmental process 0.000004583 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.0009145 Informative Direct
Biological Process (BP) cardiovascular system development 0.0000000003451 Informative Direct
Biological Process (BP) regulation of nervous system development 0.1183 Informative Inherited
Biological Process (BP) regulation of cell development 0.773 Informative Inherited
Biological Process (BP) tube development 0.002109 Informative Inherited
Biological Process (BP) hematopoietic or lymphoid organ development 0.01491 Informative Inherited
Biological Process (BP) tissue morphogenesis 0.003783 Informative Inherited
Biological Process (BP) epithelium development 0.1406 Informative Inherited
Biological Process (BP) cellular component morphogenesis 0.00142 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.02523 Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.002688 Informative Inherited
Biological Process (BP) pattern specification process 0.00001904 Highly Informative Direct
Biological Process (BP) glial cell differentiation 0.0002015 Highly Informative Direct
Biological Process (BP) limb morphogenesis 0.00000001435 Highly Informative Direct
Biological Process (BP) cell fate commitment 0.0007183 Highly Informative Direct
Biological Process (BP) negative regulation of cell differentiation 0.000001654 Highly Informative Direct
Biological Process (BP) developmental growth 0.0005185 Highly Informative Direct
Biological Process (BP) stem cell development 0.00008976 Highly Informative Direct
Biological Process (BP) axon development 0.00001186 Highly Informative Direct
Biological Process (BP) cell projection morphogenesis 0.00421 Highly Informative Inherited
Biological Process (BP) cell morphogenesis involved in neuron differentiation 0.1365 Highly Informative Inherited
Biological Process (BP) negative regulation of transcription, DNA-dependent 0.003291 Highly Informative Inherited
Molecular Function (MF) binding 0.005273 Least Informative Inherited
Molecular Function (MF) receptor activity 0.0000269 Informative Direct
Cellular Component (CC) membrane 0.0000005974 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.0002895 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.08141 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.01074 Least Informative Inherited
Cellular Component (CC) endoplasmic reticulum 0.0003498 Moderately Informative Direct
Cellular Component (CC) plasma membrane 0.00006506 Moderately Informative Direct
Cellular Component (CC) endomembrane system 0.0000000004801 Moderately Informative Direct
Cellular Component (CC) organelle membrane 0.000008256 Moderately Informative Direct
Cellular Component (CC) intrinsic to membrane 0.2329 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.04319 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.01467 Moderately Informative Inherited
Cellular Component (CC) Golgi apparatus 0.00000000004475 Informative Direct
Cellular Component (CC) cell surface 0.0000007139 Informative Direct
Cellular Component (CC) integral to membrane 0.00002609 Informative Direct
Cellular Component (CC) Golgi membrane 0.000000007888 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 disease0.001621Least InformativeInherited
Disease Ontology (DO)organ system cancer0.05264Least InformativeInherited
Disease Ontology (DO)benign neoplasm0.0000545Moderately InformativeDirect
Disease Ontology (DO)hypersensitivity reaction type II disease0.0001932Moderately InformativeDirect
Disease Ontology (DO)hematologic cancer0.02403Moderately InformativeInherited
Disease Ontology (DO)hematopoietic system disease0.07282Moderately InformativeInherited
Disease Ontology (DO)organ system benign neoplasm0.0000006344InformativeDirect
Disease Ontology (DO)renal carcinoma0.000007639InformativeDirect
Disease Ontology (DO)hemorrhagic disease0.00002455InformativeDirect
Disease Ontology (DO)liver carcinoma0.0003962InformativeDirect
Disease Ontology (DO)lymphoblastic leukemia0.0006407InformativeDirect
Disease Ontology (DO)skin hemangioma0.0000000000004153Highly InformativeDirect
Disease Ontology (DO)hemangioma0.000000003258Highly InformativeDirect
Disease Ontology (DO)primary thrombocytopenia0.00000001489Highly InformativeDirect
Disease Ontology (DO)purpura0.000002037Highly InformativeDirect

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of cardiac morphology0.2473Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the aortic valve0.00002253InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the voice0.0001552InformativeDirect

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)growth/size/body phenotype0Least InformativeDirect
Mammalian Phenotype (MP)cardiovascular system phenotype0.0135Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype0.0292Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.03855Least InformativeInherited
Mammalian Phenotype (MP)abnormal postnatal growth/weight/body size0Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal cardiovascular development0.0002419Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal blood vessel morphology0.001133Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic cell number0.004667Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal tumor incidence0.005737Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal gland morphology0.006058Moderately InformativeInherited
Mammalian Phenotype (MP)digestive/alimentary phenotype0.01952Moderately InformativeInherited
Mammalian Phenotype (MP)integument phenotype0.03983Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune system organ morphology0.2368Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal heart morphology0.3981Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal embryogenesis/ development1Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal developmental patterning0.00003622InformativeDirect
Mammalian Phenotype (MP)increased hemolymphoid system tumor incidence0.0002161InformativeDirect
Mammalian Phenotype (MP)abnormal epidermal layer morphology0.0004132InformativeDirect
Mammalian Phenotype (MP)abnormal angiogenesis0.0005977InformativeDirect
Mammalian Phenotype (MP)abnormal placenta morphology0.0006867InformativeDirect
Mammalian Phenotype (MP)increased hematopoietic cell number0.0008495InformativeDirect
Mammalian Phenotype (MP)abnormal skin appearance0.001196InformativeInherited
Mammalian Phenotype (MP)abnormal pancreas morphology0.009182InformativeInherited
Mammalian Phenotype (MP)abnormal fluid regulation0.06093InformativeInherited
Mammalian Phenotype (MP)abnormal spleen morphology0.08386InformativeInherited
Mammalian Phenotype (MP)absent sebaceous gland0.0000000001464Highly InformativeDirect
Mammalian Phenotype (MP)abnormal pancreatic acinus morphology0.0000004877Highly InformativeDirect
Mammalian Phenotype (MP)scaly skin0.000001131Highly InformativeDirect
Mammalian Phenotype (MP)increased leukemia incidence0.000003894Highly InformativeDirect
Mammalian Phenotype (MP)abnormal hair follicle morphology0.0001016Highly InformativeDirect
Mammalian Phenotype (MP)abnormal pericardium morphology0.0003132Highly InformativeDirect
Mammalian Phenotype (MP)extramedullary hematopoiesis0.0007728Highly InformativeDirect
Mammalian Phenotype (MP)edema0.001283Highly 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 regulation0Moderately InformativeDirect
Biological processAngiogenesis0InformativeDirect
Biological processNotch signaling pathway0Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentNucleus0.000000000002142Least InformativeDirect
DomainRepeat0Least InformativeDirect
DomainTransmembrane0Least InformativeDirect
DomainSignal0.00000000325Least InformativeDirect
DomainANK repeat0InformativeDirect
DomainEGF-like domain0InformativeDirect
Molecular functionCalcium0.00000000000001726Moderately 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 ]