SUPERFAMILY 1.75 HMM library and genome assignments server

Superfamily is undergoing a server migration - you are now browsing on the new server. Please contact us if you experience any problems.


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 (156) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 1,149 2,770 1
Proteins 520 1,240 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 0.00000000000002273 Least Informative Direct
Biological Process (BP) response to stimulus 0.00000000002099 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.00000005056 Least Informative Direct
Biological Process (BP) biological regulation 0.00002227 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.002622 Least Informative Inherited
Biological Process (BP) cell differentiation 0 Moderately Informative Direct
Biological Process (BP) immune system process 0.000000000001326 Moderately Informative Direct
Biological Process (BP) cell communication 0.0000001143 Moderately Informative Direct
Biological Process (BP) single organism signaling 0.0000005828 Moderately Informative Direct
Biological Process (BP) tissue development 0.000006234 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 0.00001389 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.00001398 Moderately Informative Direct
Biological Process (BP) animal organ development 0.00002635 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0.00003258 Moderately Informative Direct
Biological Process (BP) anatomical structure morphogenesis 0.0002861 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 0.0003284 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.0003729 Moderately Informative Direct
Biological Process (BP) nitrogen compound transport 0.0004497 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0.01061 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.0137 Moderately Informative Inherited
Biological Process (BP) cellular component assembly 0.3899 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.01436 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.5816 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.001535 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 0.06434 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 0.1126 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 0.2215 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.1266 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.01011 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.2138 Moderately Informative Inherited
Biological Process (BP) growth 0 Informative Direct
Biological Process (BP) hemopoiesis 0 Informative Direct
Biological Process (BP) cell surface receptor signaling pathway 0 Informative Direct
Biological Process (BP) generation of neurons 0.0000000000002873 Informative Direct
Biological Process (BP) circulatory system development 0.0000000000004583 Informative Direct
Biological Process (BP) response to wounding 0.000000002375 Informative Direct
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.000000002846 Informative Direct
Biological Process (BP) regulation of cell differentiation 0.00000007158 Informative Direct
Biological Process (BP) protein transport 0.0000462 Informative Direct
Biological Process (BP) organelle assembly 0.0001068 Informative Direct
Biological Process (BP) regulation of cell proliferation 0.0002282 Informative Direct
Biological Process (BP) negative regulation of multicellular organismal process 0.000327 Informative Direct
Biological Process (BP) central nervous system development 0.0003931 Informative Direct
Biological Process (BP) cell development 0.03267 Informative Inherited
Biological Process (BP) epithelium development 1 Informative Inherited
Biological Process (BP) regulation of nervous system development 0.02637 Informative Inherited
Biological Process (BP) cellular component morphogenesis 0.001114 Informative Inherited
Biological Process (BP) negative regulation of macromolecule biosynthetic process 0.01371 Informative Inherited
Biological Process (BP) negative regulation of cellular biosynthetic process 0.01797 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.01874 Informative Inherited
Biological Process (BP) negative regulation of gene expression 0.06066 Informative Inherited
Biological Process (BP) wound healing 0 Highly Informative Direct
Biological Process (BP) plasma membrane bounded cell projection organization 0 Highly Informative Direct
Biological Process (BP) regeneration 0.0000000001078 Highly Informative Direct
Biological Process (BP) negative regulation of nervous system development 0.000005022 Highly Informative Direct
Biological Process (BP) negative regulation of cell development 0.00007133 Highly Informative Direct
Biological Process (BP) cell morphogenesis involved in differentiation 0.0001296 Highly Informative Direct
Biological Process (BP) regulation of vesicle-mediated transport 0.0001498 Highly Informative Direct
Biological Process (BP) gliogenesis 0.0001715 Highly Informative Direct
Biological Process (BP) cell proliferation 0.0001955 Highly Informative Direct
Biological Process (BP) cell projection assembly 0.0002597 Highly Informative Direct
Biological Process (BP) forebrain development 0.0003187 Highly Informative Direct
Biological Process (BP) kidney development 0.0004653 Highly Informative Direct
Biological Process (BP) heart development 0.0004857 Highly Informative Direct
Biological Process (BP) neuron development 0.04487 Highly Informative Inherited
Biological Process (BP) epithelial cell differentiation 0.004332 Highly Informative Inherited
Biological Process (BP) negative regulation of RNA metabolic process 0.006525 Highly Informative Inherited
Molecular Function (MF) molecular transducer activity 0.0000009361 Informative Direct
Molecular Function (MF) signal transducer activity 0.0009635 Informative Direct
Cellular Component (CC) membrane 0.000008887 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.0002011 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.0008056 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.07014 Least Informative Inherited
Cellular Component (CC) bounding membrane of organelle 0.00000001002 Moderately Informative Direct
Cellular Component (CC) endomembrane system 0.00000002126 Moderately Informative Direct
Cellular Component (CC) plasma membrane 0.00000553 Moderately Informative Direct
Cellular Component (CC) intrinsic component of membrane 0.2766 Moderately Informative Inherited
Cellular Component (CC) Golgi apparatus 0.0000000004 Informative Direct
Cellular Component (CC) cell surface 0.0000001949 Informative Direct
Cellular Component (CC) apical part of cell 0.000001554 Informative Direct
Cellular Component (CC) endoplasmic reticulum membrane 0.0004974 Informative Direct
Cellular Component (CC) plasma membrane region 0.005935 Informative Inherited
Cellular Component (CC) apical plasma membrane 0.00000006194 Highly Informative Direct
Cellular Component (CC) Golgi subcompartment 0.0002906 Highly Informative Direct

Document: GO 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 componentNucleus0.000000000003997Least InformativeDirect
DomainRepeat0Least InformativeDirect
DomainTransmembrane0Least InformativeDirect
DomainSignal0.000000004039Least InformativeDirect
DomainANK repeat0InformativeDirect
DomainEGF-like domain0InformativeDirect
Molecular functionCalcium0.00000000000002714Moderately 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) · 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) · UniProtKB KeyWords (KW) · Internal database links ]