SUPERFAMILY 1.75 HMM library and genome assignments server


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 (130) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 735 688 6
Proteins 632 575 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) developmental process 0.06421 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.1266 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.2445 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.005268 Least Informative Inherited
Biological Process (BP) tissue development 0.0011 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.001395 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.04499 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.02266 Moderately Informative Inherited
Biological Process (BP) organ development 0.02852 Moderately Informative Inherited
Biological Process (BP) cell cycle process 0.0005318 Informative Direct
Biological Process (BP) muscle tissue development 2.494e-11 Informative Direct
Biological Process (BP) membrane organization 6.396e-09 Informative Direct
Biological Process (BP) muscle structure development 2.774e-10 Informative Direct
Biological Process (BP) nucleus organization 7.333e-15 Highly Informative Direct
Biological Process (BP) muscle organ development 7.808e-13 Highly Informative Direct
Molecular Function (MF) binding 0.002097 Least Informative Inherited
Cellular Component (CC) membrane 8.387e-05 Least Informative Direct
Cellular Component (CC) intracellular organelle part 1.338e-11 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.02882 Least Informative Inherited
Cellular Component (CC) endomembrane system 0 Moderately Informative Direct
Cellular Component (CC) organelle membrane 1.536e-07 Moderately Informative Direct
Cellular Component (CC) organelle envelope 0 Moderately Informative Direct
Cellular Component (CC) nuclear part 5.252e-13 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 1 Moderately Informative Inherited
Cellular Component (CC) intrinsic to membrane 0.002006 Moderately Informative Inherited
Cellular Component (CC) nuclear envelope 0 Informative Direct
Cellular Component (CC) integral to membrane 4.898e-07 Informative Direct
Cellular Component (CC) intrinsic to organelle membrane 1.261e-05 Highly Informative Direct
Cellular Component (CC) nuclear membrane 1.539e-12 Highly Informative Direct
Cellular Component (CC) nuclear periphery 0.000375 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 connective tissue0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of muscle physiology0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of muscle morphology0Moderately InformativeDirect

Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell physiology variant0Least InformativeDirect
Worm Phenotype (WP)growth variant0Least InformativeDirect
Worm Phenotype (WP)larval development variant0Least InformativeDirect
Worm Phenotype (WP)developmental timing variant0Least InformativeDirect
Worm Phenotype (WP)gametogenesis variant0Moderately InformativeDirect
Worm Phenotype (WP)larval lethal0Moderately InformativeDirect
Worm Phenotype (WP)cell homeostasis metabolism variant0Moderately InformativeDirect
Worm Phenotype (WP)sterile progeny0Moderately InformativeDirect
Worm Phenotype (WP)meiotic chromosome organization variant0InformativeDirect
Worm Phenotype (WP)chromosome segregation 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)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)multi-tissue structure0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)gamete0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)immune system0Moderately InformativeDirect

Document: XA annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processCell cycle2.033e-05Moderately InformativeDirect
Cellular componentNucleus3.03e-12Least InformativeDirect
Cellular componentMembrane6.628e-10Least InformativeDirect
DomainTransmembrane9.148e-07Least InformativeDirect
DomainSignal-anchor1.514e-05InformativeDirect
Molecular functionDNA-binding9.433e-05Least InformativeDirect
Post-translational modificationPhosphoprotein1.656e-14Least InformativeDirect
Post-translational modificationAcetylation1.321e-06Least 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 ]