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 (136) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 1,030 1,072 1
Proteins 470 486 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) multicellular organismal process 4.378e-10 Least Informative Direct
Biological Process (BP) developmental process 1.762e-13 Least Informative Direct
Biological Process (BP) single-organism cellular process 1.536e-06 Least Informative Direct
Biological Process (BP) regulation of cellular process 8.682e-08 Least Informative Direct
Biological Process (BP) response to stimulus 3.39e-07 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 7.011e-05 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0.7064 Least Informative Inherited
Biological Process (BP) localization 0.05055 Least Informative Inherited
Biological Process (BP) immune system process 4.212e-05 Moderately Informative Direct
Biological Process (BP) signal transduction 1.177e-06 Moderately Informative Direct
Biological Process (BP) anatomical structure morphogenesis 6.707e-05 Moderately Informative Direct
Biological Process (BP) tissue development 0.0007223 Moderately Informative Direct
Biological Process (BP) regulation of signal transduction 6.393e-06 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 2.61e-05 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 9.211e-06 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 2.561e-05 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 1.578e-05 Moderately Informative Direct
Biological Process (BP) regulation of programmed cell death 5.631e-05 Moderately Informative Direct
Biological Process (BP) single-organism developmental process 1.39e-06 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.0008322 Moderately Informative Direct
Biological Process (BP) positive regulation of response to stimulus 0.0001444 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 0.0001026 Moderately Informative Direct
Biological Process (BP) organic substance transport 0.0002434 Moderately Informative Direct
Biological Process (BP) organ development 0.003135 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.2073 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.01923 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.01059 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.02797 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.00339 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.07043 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.6955 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cell proliferation 2.979e-05 Informative Direct
Biological Process (BP) response to wounding 6.307e-07 Informative Direct
Biological Process (BP) positive regulation of signal transduction 5.72e-09 Informative Direct
Biological Process (BP) protein transport 3.205e-06 Informative Direct
Biological Process (BP) phosphorylation 0.0004616 Informative Direct
Biological Process (BP) cell projection organization 5.27e-05 Informative Direct
Biological Process (BP) secretion by cell 6.718e-05 Informative Direct
Biological Process (BP) growth 9.06e-09 Informative Direct
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.0009099 Informative Direct
Biological Process (BP) generation of neurons 5.056e-07 Informative Direct
Biological Process (BP) negative regulation of developmental process 4.365e-06 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.0008236 Informative Direct
Biological Process (BP) cardiovascular system development 4.453e-10 Informative Direct
Biological Process (BP) regulation of nervous system development 0.1129 Informative Inherited
Biological Process (BP) regulation of cell development 0.7673 Informative Inherited
Biological Process (BP) tissue morphogenesis 0.003544 Informative Inherited
Biological Process (BP) epithelium development 0.1358 Informative Inherited
Biological Process (BP) cellular component morphogenesis 0.001381 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.02319 Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.002439 Informative Inherited
Biological Process (BP) negative regulation of gene expression 0.001963 Informative Inherited
Biological Process (BP) pattern specification process 2.051e-05 Highly Informative Direct
Biological Process (BP) glial cell differentiation 9.271e-05 Highly Informative Direct
Biological Process (BP) limb morphogenesis 1.7e-08 Highly Informative Direct
Biological Process (BP) cell fate commitment 0.0003186 Highly Informative Direct
Biological Process (BP) negative regulation of cell differentiation 1.811e-06 Highly Informative Direct
Biological Process (BP) developmental growth 0.0004717 Highly Informative Direct
Biological Process (BP) stem cell development 8.786e-05 Highly Informative Direct
Biological Process (BP) neuron projection development 0.9439 Highly Informative Inherited
Biological Process (BP) cell part morphogenesis 0.009256 Highly Informative Inherited
Biological Process (BP) cell morphogenesis involved in differentiation 0.1818 Highly Informative Inherited
Biological Process (BP) negative regulation of transcription, DNA-dependent 0.002881 Highly Informative Inherited
Molecular Function (MF) binding 0.007497 Least Informative Inherited
Molecular Function (MF) receptor activity 3.445e-05 Informative Direct
Cellular Component (CC) membrane 5.306e-07 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.0002516 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.09971 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.007722 Least Informative Inherited
Cellular Component (CC) endoplasmic reticulum 0.0003854 Moderately Informative Direct
Cellular Component (CC) endomembrane system 4.123e-10 Moderately Informative Direct
Cellular Component (CC) organelle membrane 9.663e-06 Moderately Informative Direct
Cellular Component (CC) plasma membrane part 2.975e-05 Moderately Informative Direct
Cellular Component (CC) intrinsic to membrane 0.2292 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.01906 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.00584 Moderately Informative Inherited
Cellular Component (CC) Golgi apparatus 3.202e-11 Informative Direct
Cellular Component (CC) cell surface 7.256e-07 Informative Direct
Cellular Component (CC) integral to membrane 3.13e-05 Informative Direct
Cellular Component (CC) Golgi membrane 1.08e-08 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 disease0.001622Least InformativeInherited
Disease Ontology (DO)organ system cancer0.05297Least InformativeInherited
Disease Ontology (DO)benign neoplasm5.449e-05Moderately InformativeDirect
Disease Ontology (DO)hypersensitivity reaction type II disease0.0001934Moderately InformativeDirect
Disease Ontology (DO)hematologic cancer0.02419Moderately InformativeInherited
Disease Ontology (DO)hematopoietic system disease0.07325Moderately InformativeInherited
Disease Ontology (DO)organ system benign neoplasm6.351e-07InformativeDirect
Disease Ontology (DO)renal carcinoma7.636e-06InformativeDirect
Disease Ontology (DO)hemorrhagic disease2.457e-05InformativeDirect
Disease Ontology (DO)liver carcinoma0.0003963InformativeDirect
Disease Ontology (DO)lymphoblastic leukemia0.0006408InformativeDirect
Disease Ontology (DO)skin hemangioma4.154e-13Highly InformativeDirect
Disease Ontology (DO)hemangioma3.262e-09Highly InformativeDirect
Disease Ontology (DO)primary thrombocytopenia1.49e-08Highly InformativeDirect
Disease Ontology (DO)purpura2.039e-06Highly 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 the respiratory system0.04484Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of cardiac morphology0.2469Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the aortic valve2.255e-05InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the upper respiratory tract0.001579InformativeInherited

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 phenotype0.0131Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype0.02918Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.03851Least InformativeInherited
Mammalian Phenotype (MP)abnormal postnatal growth/weight/body size0Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal cardiovascular development0.0003317Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal blood vessel morphology0.001223Moderately InformativeInherited
Mammalian Phenotype (MP)endocrine/exocrine gland phenotype0.004204Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic cell number0.004593Moderately InformativeInherited
Mammalian Phenotype (MP)tumorigenesis0.007658Moderately InformativeInherited
Mammalian Phenotype (MP)digestive/alimentary phenotype0.01915Moderately InformativeInherited
Mammalian Phenotype (MP)integument phenotype0.03988Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune system organ morphology0.2355Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal heart morphology0.3799Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal embryogenesis/ development1Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal developmental patterning3.644e-05InformativeDirect
Mammalian Phenotype (MP)increased hemolymphoid system tumor incidence0.0002127InformativeDirect
Mammalian Phenotype (MP)abnormal epidermal layer morphology0.0004161InformativeDirect
Mammalian Phenotype (MP)abnormal placenta morphology0.0007153InformativeDirect
Mammalian Phenotype (MP)abnormal skin appearance0.001184InformativeInherited
Mammalian Phenotype (MP)abnormal fluid regulation0.05799InformativeInherited
Mammalian Phenotype (MP)abnormal spleen morphology0.08238InformativeInherited
Mammalian Phenotype (MP)absent sebaceous gland1.489e-10Highly InformativeDirect
Mammalian Phenotype (MP)abnormal pancreatic acinus morphology4.96e-07Highly InformativeDirect
Mammalian Phenotype (MP)scaly skin1.071e-06Highly InformativeDirect
Mammalian Phenotype (MP)increased leukemia incidence3.8e-06Highly InformativeDirect
Mammalian Phenotype (MP)abnormal hair follicle morphology0.0001026Highly InformativeDirect
Mammalian Phenotype (MP)abnormal pericardium morphology0.0003219Highly InformativeDirect
Mammalian Phenotype (MP)extramedullary hematopoiesis0.000798Highly InformativeDirect
Mammalian Phenotype (MP)edema0.001272Highly 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 componentNucleus1.994e-12Least InformativeDirect
DomainRepeat0Least InformativeDirect
DomainTransmembrane0Least InformativeDirect
DomainSignal3.081e-09Least InformativeDirect
DomainANK repeat0InformativeDirect
DomainEGF-like domain0InformativeDirect
Molecular functionCalcium1.543e-14Moderately 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 ]