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 (149) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 1,121 1,266 1
Proteins 508 581 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 0.0000000002395 Least Informative Direct
Biological Process (BP) developmental process 0.0000000000002255 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.0000001142 Least Informative Direct
Biological Process (BP) response to stimulus 0.0000004276 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.0001174 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0.7572 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.003772 Least Informative Inherited
Biological Process (BP) positive regulation of biological process 0.203 Least Informative Inherited
Biological Process (BP) localization 0.06008 Least Informative Inherited
Biological Process (BP) immune system process 0.00005492 Moderately Informative Direct
Biological Process (BP) signal transduction 0.0000008119 Moderately Informative Direct
Biological Process (BP) anatomical structure morphogenesis 0.00007231 Moderately Informative Direct
Biological Process (BP) tissue development 0.0008223 Moderately Informative Direct
Biological Process (BP) regulation of signal transduction 0.000008254 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.00004907 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0.000009034 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.00002799 Moderately Informative Direct
Biological Process (BP) reproductive process 0.0006685 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0.00001545 Moderately Informative Direct
Biological Process (BP) positive regulation of response to stimulus 0.0002011 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 0.0001215 Moderately Informative Direct
Biological Process (BP) organic substance transport 0.0002421 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0.1268 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.7294 Moderately Informative Inherited
Biological Process (BP) organ development 0.00316 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.007387 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.001324 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.002791 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 0.785 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.01784 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.03383 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.04945 Moderately Informative Inherited
Biological Process (BP) protein transport 0.000003219 Informative Direct
Biological Process (BP) phosphorylation 0.0008032 Informative Direct
Biological Process (BP) cell projection organization 0.00001717 Informative Direct
Biological Process (BP) secretion by cell 0.00001638 Informative Direct
Biological Process (BP) growth 0.0000000377 Informative Direct
Biological Process (BP) regulation of cell proliferation 0.00003451 Informative Direct
Biological Process (BP) regulation of apoptotic process 0.00003418 Informative Direct
Biological Process (BP) generation of neurons 0.0000005796 Informative Direct
Biological Process (BP) negative regulation of developmental process 0.000007924 Informative Direct
Biological Process (BP) cardiovascular system development 0.0000000003465 Informative Direct
Biological Process (BP) negative regulation of multicellular organismal process 0.01441 Informative Inherited
Biological Process (BP) regulation of nervous system development 0.1239 Informative Inherited
Biological Process (BP) regulation of cell development 0.6772 Informative Inherited
Biological Process (BP) tube development 0.001676 Informative Inherited
Biological Process (BP) hematopoietic or lymphoid organ development 0.008878 Informative Inherited
Biological Process (BP) tissue morphogenesis 0.001851 Informative Inherited
Biological Process (BP) epithelium development 0.257 Informative Inherited
Biological Process (BP) cellular component morphogenesis 0.003917 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.02825 Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.001989 Informative Inherited
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.001011 Informative Inherited
Biological Process (BP) pattern specification process 0.00002652 Highly Informative Direct
Biological Process (BP) glial cell differentiation 0.0002343 Highly Informative Direct
Biological Process (BP) wound healing 0.0000006289 Highly Informative Direct
Biological Process (BP) cell fate commitment 0.0005624 Highly Informative Direct
Biological Process (BP) negative regulation of cell differentiation 0.000003179 Highly Informative Direct
Biological Process (BP) developmental growth 0.0002041 Highly Informative Direct
Biological Process (BP) stem cell development 0.00008272 Highly Informative Direct
Biological Process (BP) negative regulation of nervous system development 0.0008321 Highly Informative Direct
Biological Process (BP) regulation of transmembrane receptor protein serine/threonine kinase signaling pathway 0.000002189 Highly Informative Direct
Biological Process (BP) neuron projection development 0.936 Highly Informative Inherited
Biological Process (BP) cell projection morphogenesis 0.004203 Highly Informative Inherited
Biological Process (BP) cell morphogenesis involved in differentiation 0.1562 Highly Informative Inherited
Biological Process (BP) negative regulation of transcription, DNA-templated 0.002491 Highly Informative Inherited
Molecular Function (MF) binding 0.00884 Least Informative Inherited
Molecular Function (MF) receptor activity 0.0000276 Informative Direct
Cellular Component (CC) membrane 0.000001379 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.01878 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.00325 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.00166 Least Informative Inherited
Cellular Component (CC) endoplasmic reticulum 0.000259 Moderately Informative Direct
Cellular Component (CC) plasma membrane part 0.00003719 Moderately Informative Direct
Cellular Component (CC) bounding membrane of organelle 0.000000006898 Moderately Informative Direct
Cellular Component (CC) membrane region 0.006409 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.0247 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.007166 Moderately Informative Inherited
Cellular Component (CC) Golgi apparatus 0.00000000004839 Informative Direct
Cellular Component (CC) cell surface 0.000001197 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 disease0.001628Least InformativeInherited
Disease Ontology (DO)organ system cancer0.05336Least InformativeInherited
Disease Ontology (DO)benign neoplasm0.00005558Moderately InformativeDirect
Disease Ontology (DO)hypersensitivity reaction type II disease0.0001901Moderately InformativeDirect
Disease Ontology (DO)hematologic cancer0.02431Moderately InformativeInherited
Disease Ontology (DO)hematopoietic system disease0.0731Moderately InformativeInherited
Disease Ontology (DO)organ system benign neoplasm0.0000006978InformativeDirect
Disease Ontology (DO)urinary system cancer0.00002016InformativeDirect
Disease Ontology (DO)hemorrhagic disease0.00002559InformativeDirect
Disease Ontology (DO)cell type benign neoplasm0.00003291InformativeDirect
Disease Ontology (DO)lymphoblastic leukemia0.0006751InformativeDirect
Disease Ontology (DO)gastrointestinal system cancer0.003219InformativeInherited
Disease Ontology (DO)skin hemangioma0.0000000000004332Highly InformativeDirect
Disease Ontology (DO)hemangioma0.000000003279Highly InformativeDirect
Disease Ontology (DO)primary thrombocytopenia0.00000001873Highly InformativeDirect
Disease Ontology (DO)purpura0.000002234Highly InformativeDirect
Disease Ontology (DO)liver carcinoma0.0004139Highly 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 morphology0.2411Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the aortic valve0.00001973InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the voice0.0001538InformativeDirect

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 phenotype0.01388Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype0.02992Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.03916Least InformativeInherited
Mammalian Phenotype (MP)abnormal postnatal growth/weight/body size0Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal cardiovascular development0.0002491Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal blood vessel morphology0.001176Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic cell number0.00471Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal gland morphology0.006045Moderately InformativeInherited
Mammalian Phenotype (MP)tumorigenesis0.008011Moderately InformativeInherited
Mammalian Phenotype (MP)digestive/alimentary phenotype0.01995Moderately InformativeInherited
Mammalian Phenotype (MP)integument phenotype0.04015Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune system organ morphology0.2345Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal heart morphology0.3967Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal embryogenesis/ development1Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal developmental patterning0.00003625InformativeDirect
Mammalian Phenotype (MP)increased hemolymphoid system tumor incidence0.0002162InformativeDirect
Mammalian Phenotype (MP)abnormal epidermal layer morphology0.0004015InformativeDirect
Mammalian Phenotype (MP)abnormal angiogenesis0.0006115InformativeDirect
Mammalian Phenotype (MP)increased hematopoietic cell number0.0008694InformativeDirect
Mammalian Phenotype (MP)abnormal skin appearance0.001242InformativeInherited
Mammalian Phenotype (MP)abnormal pancreas morphology0.009945InformativeInherited
Mammalian Phenotype (MP)abnormal fluid regulation0.06322InformativeInherited
Mammalian Phenotype (MP)abnormal spleen morphology0.08271InformativeInherited
Mammalian Phenotype (MP)abnormal extraembryonic tissue morphology0.1155InformativeInherited
Mammalian Phenotype (MP)abnormal pancreatic acinus morphology0.0000004278Highly InformativeDirect
Mammalian Phenotype (MP)scaly skin0.000001094Highly InformativeDirect
Mammalian Phenotype (MP)increased leukemia incidence0.000003776Highly InformativeDirect
Mammalian Phenotype (MP)abnormal sebaceous gland morphology0.00009613Highly InformativeDirect
Mammalian Phenotype (MP)abnormal hair follicle morphology0.0001015Highly InformativeDirect
Mammalian Phenotype (MP)abnormal pericardium morphology0.000316Highly InformativeDirect
Mammalian Phenotype (MP)extramedullary hematopoiesis0.0007563Highly InformativeDirect
Mammalian Phenotype (MP)edema0.001379Highly 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 componentNucleus0.000000000002163Least InformativeDirect
DomainRepeat0Least InformativeDirect
DomainTransmembrane0Least InformativeDirect
DomainSignal0.000000003194Least InformativeDirect
DomainANK repeat0InformativeDirect
DomainEGF-like domain0InformativeDirect
Molecular functionCalcium0.00000000000001946Moderately 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 ]