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SAM/Pointed domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   SAM domain-like [ 47768] (16)
Superfamily:   SAM/Pointed domain [ 47769] (3)
Families:   Pointed domain [ 47770] (6)
  SAM (sterile alpha motif) domain [ 47773] (15)
  Variant SAM domain [ 158526] (2)

Superfamily statistics
Genomes (522) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 17,915 0 33
Proteins 15,513 0 33

Functional annotation
General category Regulation
Detailed category DNA-binding

Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Acting on ester bonds0.558Least InformativeInherited
Enzyme Commission (EC)Phosphoric monoester hydrolases0.007561Moderately InformativeInherited
Enzyme Commission (EC)Protein-serine/threonine kinases0.00471Moderately InformativeInherited
Enzyme Commission (EC)Phosphotransferases with an alcohol group as accep1Moderately InformativeInherited
Enzyme Commission (EC)Receptor protein-tyrosine kinase0.00000000001004InformativeDirect
Enzyme Commission (EC)Phosphatidylinositol-3,4,5-trisphosphate 5-phospha0Highly InformativeDirect
Enzyme Commission (EC)Diacylglycerol kinase0Highly InformativeDirect
Enzyme Commission (EC)Mitogen-activated protein kinase kinase kinase0.0000000000009763Highly InformativeDirect
Enzyme Commission (EC)Transferases for other substituted phosphate group0.01424Highly InformativeInherited

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)organ system cancer0.4771Least InformativeInherited
Disease Ontology (DO)breast cancer0.004642InformativeInherited
Disease Ontology (DO)invasive ductal carcinoma0.0004296Highly InformativeDirect

Document: DO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)cellular phenotype0.29Least InformativeInherited
Mammalian Phenotype (MP)nervous system phenotype0.4812Least InformativeInherited
Mammalian Phenotype (MP)abnormal neuron morphology0.238Moderately InformativeInherited
Mammalian Phenotype (MP)embryo phenotype0.2736Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system development0.4094Moderately InformativeInherited
Mammalian Phenotype (MP)limbs/digits/tail phenotype0.8415Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell differentiation0.2446InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism environmental stimulus response variant0.1385Least InformativeInherited
Worm Phenotype (WP)chemical response variant0.06255Moderately InformativeInherited
Worm Phenotype (WP)aldicarb response variant0.0001362InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)metabolism and growth0Least InformativeDirect

Document: YP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)embryo0.2157Least InformativeInherited
Fly Anatomy (FA)anatomical group0.2908Least InformativeInherited
Fly Anatomy (FA)somatic cell0.8791Least InformativeInherited
Fly Anatomy (FA)developing embryonic structure0.1676Moderately InformativeInherited
Fly Anatomy (FA)non-connected developing system0.2258Moderately InformativeInherited
Fly Anatomy (FA)somatic precursor cell0.5308Moderately InformativeInherited
Fly Anatomy (FA)dorsal closure embryo0.04396InformativeInherited
Fly Anatomy (FA)extended germ band embryo0.06527InformativeInherited
Fly Anatomy (FA)primordium0.2328InformativeInherited
Fly Anatomy (FA)trunk mesoderm derivative0.001093Highly InformativeInherited

Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details) Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)multi-tissue structure0.255Moderately InformativeInherited
Xenopus ANatomical entity (XAN)cardiovascular system0.05316InformativeInherited
Xenopus ANatomical entity (XAN)circulatory system0.03365Highly InformativeInherited
Xenopus DEvelopment stage (XDE)embryonic stage0.0007191Moderately InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorus-containing groups0Least InformativeDirect
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Protein-serine/threonine kinases0.00406Moderately InformativeInherited
Enzyme Commission (EC)Phosphoric monoester hydrolases0.008374Moderately InformativeInherited
Enzyme Commission (EC)Glycosyltransferases1Moderately InformativeInherited
Enzyme Commission (EC)Phosphotransferases with an alcohol group as acceptor1Moderately InformativeInherited
Enzyme Commission (EC)Protein-tyrosine kinases0InformativeDirect
Enzyme Commission (EC)Pentosyltransferases0.02208InformativeInherited
Enzyme Commission (EC)Diacylglycerol kinase (ATP)0Highly InformativeDirect
Enzyme Commission (EC)NAD(+) ADP-ribosyltransferase0.000000000001616Highly InformativeDirect
Enzyme Commission (EC)Receptor protein-tyrosine kinase0.000000000006713Highly InformativeDirect
Enzyme Commission (EC)Transferases for other substituted phosphate groups0.01115Highly InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport1Least InformativeInherited
Biological processApoptosis0Moderately InformativeDirect
Biological processDifferentiation0Moderately InformativeDirect
Biological processTranscription regulation0Moderately InformativeDirect
Biological processImmunity0.000000000005238Moderately InformativeDirect
Biological processProtein transport0.000002248Moderately InformativeDirect
Biological processLipid metabolism0.535Moderately InformativeInherited
Biological processIon transport0.8418Moderately InformativeInherited
Biological processCell adhesion0InformativeDirect
Biological processMeiosis0InformativeDirect
Biological processNeurogenesis0InformativeDirect
Biological processAngiogenesis0.0000000003972InformativeDirect
Biological processTranslation regulation0.00001175InformativeDirect
Biological processRNA-mediated gene silencing0Highly InformativeDirect
Biological processSphingolipid metabolism0.00000000000003404Highly InformativeDirect
Biological processSpermatogenesis0.0000000001006Highly InformativeDirect
Biological processCalcium transport0.0000000008507Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentMembrane0.00004842Least InformativeDirect
Cellular componentCytoplasm1Least InformativeInherited
Cellular componentCell junction0Moderately InformativeDirect
Cellular componentCell projection0Moderately InformativeDirect
Cellular componentEndosome0.000000001495Moderately InformativeDirect
Cellular componentCytoskeleton0.00000006043Moderately InformativeDirect
Coding sequence diversityAlternative splicing0.000000002374Least InformativeDirect
Coding sequence diversityAlternative promoter usage0.000002674Moderately InformativeDirect
DiseaseProto-oncogene0.00007338Moderately InformativeDirect
DiseaseTumor suppressor0.0001638Moderately InformativeDirect
DomainRepeat0Least InformativeDirect
DomainTransmembrane1Least InformativeInherited
DomainCoiled coil0.0000000007233Moderately InformativeDirect
DomainANK repeat0InformativeDirect
DomainSH3 domain0InformativeDirect
DomainSH2 domain0.00003473InformativeDirect
Molecular functionZinc0.0004259Least InformativeDirect
Post-translational modificationTransferase0.1699Least InformativeInherited
Post-translational modificationDevelopmental protein0Moderately InformativeDirect
Post-translational modificationKinase0Moderately InformativeDirect
Post-translational modificationReceptor0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationDNA-binding0.00000000000001309Moderately InformativeDirect
Post-translational modificationActivator0.000007539Moderately InformativeDirect
Post-translational modificationGTPase activation0.0000000000007272InformativeDirect
Post-translational modificationChromatin regulator0.00000000826InformativeDirect
Post-translational modificationActin-binding0.0000005525InformativeDirect
Post-translational modificationTyrosine-protein kinase0Highly InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationUbl conjugation0.000001618Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR010993 SSF47769 Protein matches

Sterile alpha motif (SAM) domains are known to be involved in diverse protein-protein interactions, associating with both SAM-containing and non-SAM-containing proteins pathway [PubMed14659692]. SAM domains exhibit a conserved structure, consisting of a 4-5-helical bundle of two orthogonally packed alpha-hairpins. However SAM domains display a diversity of function, being involved in interactions with proteins, DNA and RNA [PubMed12858164]. The name sterile alpha motif arose from its presence in proteins that are essential for yeast sexual differentiation. The SAM domain has had various names, including SPM, PTN (pointed), SEP (yeast sterility, Ets-related, PcG proteins), NCR (N-terminal conserved region) and HLH (helix-loop-helix) domain, all of which are related and can be classified as SAM domains.

SAM domains occur in eukaryotic and in some bacterial proteins. Structures have been determined for several proteins that contain SAM domains, including Ets-1 transcription factor, which plays a role in the development and invasion of tumour cells by regulating the expression of matrix-degrading proteases [PubMed14704859]; Etv6 transcription factor, gene rearrangements of which have been demonstrated in several malignancies [PubMed9031109]; EphA4 receptor tyrosine kinase, which is believed to be important for the correct localization of a motoneuron pool to a specific position in the spinal cord [PubMed12577325]; EphB2 receptor, which is involved in spine morphogenesis via intersectin, Cdc42 and N-Wasp [PubMed12389031]; p73, a p53 homologue involved in neuronal development [PubMed14659698]; and polyhomeotic, which is a member of the Polycomb group of genes (Pc-G) required for the maintenance of the spatial expression pattern of homeotic genes [PubMed14499651].

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 · Enzyme Commission (EC) · Disease Ontology (DO) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · 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 24 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 SAM/Pointed 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 24 hidden Markov models representing the SAM/Pointed 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 · Enzyme Commission (EC) · Disease Ontology (DO) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]