SUPERFAMILY 1.75 HMM library and genome assignments server


LDL receptor-like module superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Small proteins [ 56992] (90)
Fold:   LDL receptor-like module [ 57423]
Superfamily:   LDL receptor-like module [ 57424]
Families:   LDL receptor-like module [ 57425] (6)


Superfamily statistics
Genomes (200) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 29,522 0 26
Proteins 7,048 0 18


Functional annotation
General category Processes_IC
Detailed category Transport

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details) Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) developmental process 0 Least Informative Direct
Biological Process (BP) multicellular organismal process 0 Least Informative Direct
Biological Process (BP) localization 3.722e-15 Least Informative Direct
Biological Process (BP) response to stimulus 9.101e-10 Least Informative Direct
Biological Process (BP) protein metabolic process 1.617e-05 Least Informative Direct
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.1095 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.01547 Least Informative Inherited
Biological Process (BP) cell differentiation 3.94e-13 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 3.013e-09 Moderately Informative Direct
Biological Process (BP) single-organism developmental process 3.704e-08 Moderately Informative Direct
Biological Process (BP) regulation of phosphate metabolic process 2.08e-05 Moderately Informative Direct
Biological Process (BP) organic hydroxy compound metabolic process 9.548e-05 Moderately Informative Direct
Biological Process (BP) regulation of catalytic activity 0.0002071 Moderately Informative Direct
Biological Process (BP) regulation of signal transduction 0.2908 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.05967 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 0.08383 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) tissue development 1 Moderately Informative Inherited
Biological Process (BP) gene expression 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of molecular function 0.1573 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 1 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 1 Moderately Informative Inherited
Biological Process (BP) homeostatic process 0.2361 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 1 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.001147 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.009332 Moderately Informative Inherited
Biological Process (BP) organ development 0.5782 Moderately Informative Inherited
Biological Process (BP) cellular lipid metabolic process 0.9141 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.1515 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.914 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 1 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.5795 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.5873 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 1 Moderately Informative Inherited
Biological Process (BP) system process 1 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.001589 Moderately Informative Inherited
Biological Process (BP) reproduction 0.03085 Moderately Informative Inherited
Biological Process (BP) cellular localization 1 Moderately Informative Inherited
Biological Process (BP) immune system process 0.5594 Moderately Informative Inherited
Biological Process (BP) vesicle-mediated transport 0 Informative Direct
Biological Process (BP) generation of neurons 0 Informative Direct
Biological Process (BP) locomotion 0 Informative Direct
Biological Process (BP) cellular component movement 7.603e-14 Informative Direct
Biological Process (BP) cell projection organization 3.395e-08 Informative Direct
Biological Process (BP) single-organism behavior 4.358e-08 Informative Direct
Biological Process (BP) regulation of protein phosphorylation 5.017e-08 Informative Direct
Biological Process (BP) proteolysis 1.205e-07 Informative Direct
Biological Process (BP) alcohol metabolic process 8.026e-07 Informative Direct
Biological Process (BP) cellular component morphogenesis 5.519e-06 Informative Direct
Biological Process (BP) regulation of immune effector process 1.122e-05 Informative Direct
Biological Process (BP) vitamin metabolic process 3.437e-05 Informative Direct
Biological Process (BP) regulation of locomotion 0.0002231 Informative Direct
Biological Process (BP) lipid localization 0.0003442 Informative Direct
Biological Process (BP) regulation of nervous system development 0.0004155 Informative Direct
Biological Process (BP) negative regulation of developmental process 0.0006058 Informative Direct
Biological Process (BP) embryo development ending in birth or egg hatching 0.0006872 Informative Direct
Biological Process (BP) regulation of kinase activity 0.0009511 Informative Direct
Biological Process (BP) positive regulation of signal transduction 0.1289 Informative Inherited
Biological Process (BP) positive regulation of cellular component organization 0.6838 Informative Inherited
Biological Process (BP) protein localization to organelle 0.7609 Informative Inherited
Biological Process (BP) cellular membrane organization 0.2719 Informative Inherited
Biological Process (BP) muscle tissue development 0.00378 Informative Inherited
Biological Process (BP) sensory organ development 0.7676 Informative Inherited
Biological Process (BP) cardiovascular system development 0.3097 Informative Inherited
Biological Process (BP) epithelium development 1 Informative Inherited
Biological Process (BP) tissue morphogenesis 1 Informative Inherited
Biological Process (BP) tube development 0.8105 Informative Inherited
Biological Process (BP) organ morphogenesis 0.139 Informative Inherited
Biological Process (BP) protein complex assembly 0.2861 Informative Inherited
Biological Process (BP) growth 0.005603 Informative Inherited
Biological Process (BP) regulation of response to stress 1 Informative Inherited
Biological Process (BP) muscle structure development 0.0555 Informative Inherited
Biological Process (BP) cell-cell signaling 0.7011 Informative Inherited
Biological Process (BP) defense response 0.08014 Informative Inherited
Biological Process (BP) single organism reproductive process 0.7537 Informative Inherited
Biological Process (BP) protein catabolic process 0.5662 Informative Inherited
Biological Process (BP) embryonic morphogenesis 0.436 Informative Inherited
Biological Process (BP) enzyme linked receptor protein signaling pathway 1 Informative Inherited
Biological Process (BP) regulation of anatomical structure size 0.1548 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0.006272 Informative Inherited
Biological Process (BP) gland development 0.1473 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.006859 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.01208 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.1478 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.9966 Informative Inherited
Biological Process (BP) localization of cell 0.001639 Informative Inherited
Biological Process (BP) central nervous system development 0.12 Informative Inherited
Biological Process (BP) isoprenoid metabolic process 0.009367 Informative Inherited
Biological Process (BP) regulation of cell development 0.01129 Informative Inherited
Biological Process (BP) regulation of cell proliferation 1 Informative Inherited
Biological Process (BP) response to light stimulus 0.1393 Informative Inherited
Biological Process (BP) reproductive system development 1 Informative Inherited
Biological Process (BP) response to nutrient levels 0.1528 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 1 Informative Inherited
Biological Process (BP) immune response 0.4229 Informative Inherited
Biological Process (BP) immune effector process 0.01317 Informative Inherited
Biological Process (BP) positive regulation of immune system process 0.7929 Informative Inherited
Biological Process (BP) protein transport 0.6673 Informative Inherited
Biological Process (BP) cytoplasmic transport 0.7296 Informative Inherited
Biological Process (BP) regulation of immune response 0.8355 Informative Inherited
Biological Process (BP) regulation of response to external stimulus 0.08152 Informative Inherited
Biological Process (BP) response to drug 0 Highly Informative Direct
Biological Process (BP) regulation of protein processing 1.922e-15 Highly Informative Direct
Biological Process (BP) regulation of acute inflammatory response 2.499e-13 Highly Informative Direct
Biological Process (BP) organic hydroxy compound transport 1.785e-12 Highly Informative Direct
Biological Process (BP) regulation of humoral immune response 3.918e-12 Highly Informative Direct
Biological Process (BP) establishment or maintenance of cell polarity 7.159e-11 Highly Informative Direct
Biological Process (BP) sterol metabolic process 3.539e-09 Highly Informative Direct
Biological Process (BP) chemotaxis 1.302e-07 Highly Informative Direct
Biological Process (BP) extracellular matrix organization 2.299e-07 Highly Informative Direct
Biological Process (BP) mammary gland epithelium development 6.263e-07 Highly Informative Direct
Biological Process (BP) lipoprotein metabolic process 6.616e-07 Highly Informative Direct
Biological Process (BP) retinoid metabolic process 3.179e-06 Highly Informative Direct
Biological Process (BP) telencephalon development 3.406e-06 Highly Informative Direct
Biological Process (BP) regulation of neuron projection development 4.015e-06 Highly Informative Direct
Biological Process (BP) negative regulation of cell differentiation 7.41e-06 Highly Informative Direct
Biological Process (BP) connective tissue development 1.756e-05 Highly Informative Direct
Biological Process (BP) cell junction organization 2.61e-05 Highly Informative Direct
Biological Process (BP) protein activation cascade 2.648e-05 Highly Informative Direct
Biological Process (BP) cell projection morphogenesis 4.873e-05 Highly Informative Direct
Biological Process (BP) transmembrane receptor protein tyrosine kinase signaling pathway 0.0002512 Highly Informative Direct
Biological Process (BP) protein tetramerization 0.0002976 Highly Informative Direct
Biological Process (BP) innate immune response 0.0003291 Highly Informative Direct
Biological Process (BP) muscle organ development 0.0005594 Highly Informative Direct
Biological Process (BP) humoral immune response 0.0008251 Highly Informative Direct
Biological Process (BP) establishment of protein localization to organelle 0.02836 Highly Informative Inherited
Biological Process (BP) retina development in camera-type eye 0.002811 Highly Informative Inherited
Biological Process (BP) branching morphogenesis of an epithelial tube 0.03531 Highly Informative Inherited
Biological Process (BP) respiratory system development 0.00377 Highly Informative Inherited
Biological Process (BP) developmental growth 0.02136 Highly Informative Inherited
Biological Process (BP) cell fate commitment 0.818 Highly Informative Inherited
Biological Process (BP) mesenchyme development 0.1441 Highly Informative Inherited
Biological Process (BP) phagocytosis 0.1623 Highly Informative Inherited
Biological Process (BP) limb morphogenesis 0.001666 Highly Informative Inherited
Biological Process (BP) pattern specification process 0.929 Highly Informative Inherited
Biological Process (BP) detection of light stimulus 0.001778 Highly Informative Inherited
Biological Process (BP) gonad development 0.2913 Highly Informative Inherited
Biological Process (BP) cell morphogenesis involved in neuron differentiation 0.05947 Highly Informative Inherited
Biological Process (BP) learning or memory 0.002022 Highly Informative Inherited
Biological Process (BP) muscle fiber development 0.02452 Highly Informative Inherited
Biological Process (BP) axon development 1 Highly Informative Inherited
Biological Process (BP) G-protein coupled receptor signaling pathway 0.1023 Highly Informative Inherited
Biological Process (BP) activation of immune response 0.001264 Highly Informative Inherited
Molecular Function (MF) binding 0.00319 Least Informative Inherited
Molecular Function (MF) hydrolase activity 0.001048 Least Informative Inherited
Molecular Function (MF) receptor activity 0 Informative Direct
Molecular Function (MF) peptidase activity 7.982e-16 Informative Direct
Molecular Function (MF) molecular transducer activity 1.046e-08 Informative Direct
Molecular Function (MF) receptor binding 0.05141 Informative Inherited
Molecular Function (MF) carbohydrate derivative binding 0.001579 Informative Inherited
Molecular Function (MF) hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds 0.02197 Informative Inherited
Molecular Function (MF) deacetylase activity 1.634e-05 Highly Informative Direct
Molecular Function (MF) G-protein coupled receptor activity 0.4962 Highly Informative Inherited
Molecular Function (MF) endopeptidase activity 0.06453 Highly Informative Inherited
Cellular Component (CC) membrane 0 Least Informative Direct
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.002496 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) extracellular region part 0 Moderately Informative Direct
Cellular Component (CC) plasma membrane 1.344e-10 Moderately Informative Direct
Cellular Component (CC) vesicle 6.392e-05 Moderately Informative Direct
Cellular Component (CC) intrinsic to membrane 0.1644 Moderately Informative Inherited
Cellular Component (CC) cytoskeleton 0.1951 Moderately Informative Inherited
Cellular Component (CC) cell projection 0.001118 Moderately Informative Inherited
Cellular Component (CC) organelle membrane 0.6918 Moderately Informative Inherited
Cellular Component (CC) endosome 0 Informative Direct
Cellular Component (CC) extracellular matrix 0 Informative Direct
Cellular Component (CC) lytic vacuole 2.146e-08 Informative Direct
Cellular Component (CC) integral to membrane 1.545e-07 Informative Direct
Cellular Component (CC) synapse part 5.064e-07 Informative Direct
Cellular Component (CC) cell surface 2.753e-06 Informative Direct
Cellular Component (CC) Golgi apparatus 1.451e-05 Informative Direct
Cellular Component (CC) vacuolar part 0.0003777 Informative Direct
Cellular Component (CC) lipid particle 0 Highly Informative Direct
Cellular Component (CC) extracellular matrix part 0 Highly Informative Direct
Cellular Component (CC) proteinaceous extracellular matrix 1.206e-14 Highly Informative Direct
Cellular Component (CC) lysosome 2.008e-09 Highly Informative Direct
Cellular Component (CC) cell body 1.454e-06 Highly Informative Direct
Cellular Component (CC) brush border 3.471e-05 Highly Informative Direct
Cellular Component (CC) receptor complex 4.25e-05 Highly Informative Direct
Cellular Component (CC) membrane raft 0.001287 Highly Informative Inherited

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)0Least InformativeDirect
Enzyme Commission (EC)Serine endopeptidases0Moderately InformativeDirect

Document: EC annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of the immune system0.6645Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of humoral immunity0.034InformativeInherited
Phenotypic Abnormality (PA)Recurrent infections0.3528InformativeInherited
Phenotypic Abnormality (PA)Abnormality of complement system1.67e-05Highly InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)cardiovascular system phenotype0.05369Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.4674Least InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.0273Moderately InformativeInherited
Mammalian Phenotype (MP)integument phenotype0.1081Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal lipid homeostasis0.1574Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood vessel morphology0.1918Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal coat appearance0.000975InformativeDirect
Mammalian Phenotype (MP)abnormal circulating cholesterol level0.02261InformativeInherited
Mammalian Phenotype (MP)abnormal circulating lipoprotein level0.03872InformativeInherited
Mammalian Phenotype (MP)abnormal systemic artery morphology0.07187InformativeInherited
Mammalian Phenotype (MP)abnormal limb morphology0.8928InformativeInherited
Mammalian Phenotype (MP)abnormal circulating VLDL cholesterol level0.0003822Highly InformativeDirect
Mammalian Phenotype (MP)abnormal eye pigmentation0.01071Highly InformativeInherited
Mammalian Phenotype (MP)abnormal digit morphology0.03561Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)locomotion variant0.5864Moderately InformativeInherited
Worm Phenotype (WP)activity level variant0.01144InformativeInherited
Worm Phenotype (WP)paralyzed0.000304Highly InformativeDirect

Document: WP annotation of SCOP domains

Fly Anatomy (FA)

(show details) Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)alimentary system0.02296Least InformativeInherited
Xenopus ANatomical entity (XAN)embryo0.7776Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.3044Moderately InformativeInherited
Xenopus ANatomical entity (XAN)hindgut7.131e-06Highly InformativeDirect

Document: XA annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases1.643e-07Least InformativeDirect
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)0Moderately InformativeDirect
Enzyme Commission (EC)Serine endopeptidases0InformativeDirect
Enzyme Commission (EC)Enteropeptidase4.088e-11Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0.01113Least InformativeInherited
Biological processLipid metabolism2.345e-07Moderately InformativeDirect
Biological processCytolysis0InformativeDirect
Biological processEndocytosis0InformativeDirect
Biological processInnate immunity0InformativeDirect
Biological processLipid transport0InformativeDirect
Biological processSteroid metabolism0InformativeDirect
Biological processWnt signaling pathway2.629e-10InformativeDirect
Biological processCell adhesion9.1e-08InformativeDirect
Biological processCholesterol metabolism0Highly InformativeDirect
Biological processComplement pathway0Highly InformativeDirect
Biological processComplement alternate pathway9.334e-16Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentEndosome3.43e-07Moderately InformativeDirect
Cellular componentGolgi apparatus9.177e-05Moderately InformativeDirect
Cellular componentLysosome2.937e-06InformativeDirect
Cellular componentCoated pit0Highly InformativeDirect
DiseaseDisease mutation8.226e-07Least InformativeDirect
DomainRepeat0Least InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransmembrane0Least InformativeDirect
DomainEGF-like domain0InformativeDirect
DomainSignal-anchor6.914e-08InformativeDirect
DomainTransmembrane beta strand4.262e-05InformativeDirect
DomainSushi3.995e-10Highly InformativeDirect
Molecular functionCalcium0Moderately InformativeDirect
Post-translational modificationHydrolase0.04229Least InformativeInherited
Post-translational modificationProtease0Moderately InformativeDirect
Post-translational modificationReceptor0Moderately InformativeDirect
Post-translational modificationDevelopmental protein3.241e-06Moderately InformativeDirect
Post-translational modificationSerine protease0InformativeDirect
Post-translational modificationTransducer2.876e-05InformativeDirect
Post-translational modificationG-protein coupled receptor9.503e-06Highly InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect
Post-translational modificationZymogen0.000101InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)glycan metabolism0Moderately InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR002172 SSF57424 Protein matches
Abstract

Low density lipoprotein (LDL) is the major cholesterol-carrying lipoprotein of plasma. The receptor protein binds LDL and transports it into cells by endocytosis. In order to be internalised, the receptor-ligand complex must first cluster into clathrin-coated pits. Seven successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein [PubMed6091915].

The LDL-receptor class A domain contains 6 disulphide-bound cysteines [PubMed7548065] and a highly conserved cluster of negatively charged amino acids, of which many are clustered on one face of the module [PubMed7603991]. A schematic representation of this domain is shown here:

   +---------------------+        +--------------------------------+
   |                     |        |                                |
  -CxxxxxxxxxxxxCxxxxxxxxCxxxxxxxxCxxxxxxxxxxCxxxxxxxxxxxxxxxxxxxxxC-
                |                            |
                +----------------------------+

'C': conserved cysteine involved in a disulphide bond.
'x': any residue.

In LDL-receptors the class A domains form the binding site for LDL [PubMed6091915] and calcium [PubMed3320043]. The acidic residues between the fourth and sixth cysteines are important for high-affinity binding of positively charged sequences in LDLR's ligands [PubMed3283935]. The repeat has been shown [PubMed7603991] to consist of a beta-hairpin structure followed by a series of beta turns. In the absence of calcium, LDL-A domains are unstructured; the bound calcium ion imparts structural integrity.

Following these repeats is a 350 residue domain that resembles part of the epidermal growth factor (EGF) precursor [PubMed6327078, PubMed6091915].

Similar domains have been found (see references in [PubMed7603991]) in several extracellular and membrane proteins (see examples).

Numerous familial hypercholestorolemia mutations of the LDL receptor alter the calcium coordinating residue of LDL-A domains or other crucial scaffolding residues.


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-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

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 15 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 LDL receptor-like module 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 15 hidden Markov models representing the LDL receptor-like module 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-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]