SUPERFAMILY 1.75 HMM library and genome assignments server

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LEM domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   LEM/SAP HeH motif [ 63450] (6)
Superfamily:   LEM domain [ 63451]
Families:   LEM domain [ 63452] (2)


Superfamily statistics
Genomes (145) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 817 817 6
Proteins 703 693 5


Functional annotation
General category General
Detailed category Lipid/membrane binding

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) single-organism cellular process 0.00006211 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.000009623 Least Informative Direct
Biological Process (BP) organelle organization 0.00000000006262 Moderately Informative Direct
Biological Process (BP) system development 0.356 Moderately Informative Inherited
Biological Process (BP) mitotic cell cycle 0 Informative Direct
Biological Process (BP) cell cycle process 0.000000000001494 Informative Direct
Biological Process (BP) membrane organization 0 Informative Direct
Biological Process (BP) nucleus organization 0 Highly Informative Direct
Biological Process (BP) endomembrane system organization 0 Highly Informative Direct
Biological Process (BP) muscle structure development 0.0002583 Highly Informative Direct
Molecular Function (MF) binding 0.000009325 Least Informative Direct
Molecular Function (MF) chromatin binding 0.000000006202 Highly Informative Direct
Cellular Component (CC) membrane 0.00000002625 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.1783 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.003034 Least Informative Inherited
Cellular Component (CC) intrinsic component of membrane 0.0004322 Moderately Informative Direct
Cellular Component (CC) organelle envelope 0 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.000001971 Moderately Informative Direct
Cellular Component (CC) nuclear envelope 0 Informative Direct
Cellular Component (CC) chromosome 0.000004975 Informative Direct
Cellular Component (CC) nuclear membrane 0.000000000001542 Highly Informative Direct

Document: GO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of the musculature0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of muscle physiology0Moderately InformativeDirect

Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)general pace of development variant0Least InformativeDirect
Worm Phenotype (WP)larval lethal0Least InformativeDirect
Worm Phenotype (WP)retarded heterochronic variations0Least InformativeDirect
Worm Phenotype (WP)cell development variant0Least InformativeDirect
Worm Phenotype (WP)cell morphology variant0Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0Least InformativeDirect
Worm Phenotype (WP)organism environmental stimulus response variant0Least InformativeDirect
Worm Phenotype (WP)larval development variant0Least InformativeDirect
Worm Phenotype (WP)larval growth variant0Least InformativeDirect
Worm Phenotype (WP)cell homeostasis metabolism variant0Moderately InformativeDirect
Worm Phenotype (WP)cell division variant0Moderately InformativeDirect
Worm Phenotype (WP)gametogenesis variant0Moderately InformativeDirect
Worm Phenotype (WP)sterile progeny0Moderately InformativeDirect
Worm Phenotype (WP)chromosome segregation variant0InformativeDirect
Worm Phenotype (WP)meiotic chromosome organization variant0InformativeDirect

Document: WP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)egg0Moderately InformativeDirect

Document: XA annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processCell cycle0.0000002431Moderately InformativeDirect
Biological processMitosis0.000000001377InformativeDirect
Cellular componentNucleus0.00000000000001406Least InformativeDirect
Cellular componentMembrane0.00000001246Least InformativeDirect
Cellular componentChromosome0.000000003802InformativeDirect
DomainTransmembrane0.000005956Least InformativeDirect
DomainANK repeat0.00000001669InformativeDirect
DomainSignal-anchor0.00002555InformativeDirect
Post-translational modificationDNA-binding0.0003716Moderately InformativeDirect
Post-translational modificationPhosphoprotein0.00000000003609Least InformativeDirect
Post-translational modificationAcetylation0.000001061Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR011015 SSF63451 Protein matches
Abstract

The LEM domain is a ~40-residue motif found in nuclear membrane-associated proteins, including lamino-associated polypeptide 2 (LAP2), emerin, MAN1, otefin and Lem-3 [PubMed11792821]. Defects in the emerin gene are a cause of Emery-Dreifuss muscular dystrophy, an X-linked disorder characterised by early contractures, muscle wasting, weakness and cardiomyopathy. The N-terminal LEM domain in emerin mediates binding to BAF (barrier-to-autointegration factor).


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) · Human Phenotype (HP) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · 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 3 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 LEM 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 3 hidden Markov models representing the LEM 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) · Human Phenotype (HP) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · UniProtKB KeyWords (KW) · Internal database links ]