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 (205) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 31,135 31,536 26
Proteins 7,372 7,746 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 2.462e-14 Least Informative Direct
Biological Process (BP) response to stimulus 6.688e-09 Least Informative Direct
Biological Process (BP) protein metabolic process 1.601e-05 Least Informative Direct
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.132 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) cellular component organization or biogenesis 0.02898 Least Informative Inherited
Biological Process (BP) cell differentiation 1.906e-12 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 4.596e-10 Moderately Informative Direct
Biological Process (BP) regulation of phosphate metabolic process 4.032e-06 Moderately Informative Direct
Biological Process (BP) organic hydroxy compound metabolic process 0.0001298 Moderately Informative Direct
Biological Process (BP) regulation of catalytic activity 0.0004263 Moderately Informative Direct
Biological Process (BP) regulation of signal transduction 0.2302 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.08341 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 0.1107 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 0.1652 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 0.2365 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.001223 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.6803 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.009167 Moderately Informative Inherited
Biological Process (BP) organ development 0.578 Moderately Informative Inherited
Biological Process (BP) cellular lipid metabolic process 0.9394 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.16 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.8755 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.8777 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.4543 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.4266 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 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 0.002533 Moderately Informative Inherited
Biological Process (BP) reproduction 0.04239 Moderately Informative Inherited
Biological Process (BP) cellular localization 1 Moderately Informative Inherited
Biological Process (BP) immune system process 0.614 Moderately Informative Inherited
Biological Process (BP) vesicle-mediated transport 0 Informative Direct
Biological Process (BP) locomotion 0 Informative Direct
Biological Process (BP) generation of neurons 3.77e-15 Informative Direct
Biological Process (BP) cellular component movement 7.373e-14 Informative Direct
Biological Process (BP) regulation of protein phosphorylation 3.855e-09 Informative Direct
Biological Process (BP) cell projection organization 3.74e-08 Informative Direct
Biological Process (BP) single-organism behavior 8.015e-08 Informative Direct
Biological Process (BP) proteolysis 2.264e-07 Informative Direct
Biological Process (BP) alcohol metabolic process 1.14e-06 Informative Direct
Biological Process (BP) cellular component morphogenesis 5.843e-06 Informative Direct
Biological Process (BP) regulation of immune effector process 1.461e-05 Informative Direct
Biological Process (BP) regulation of locomotion 3.3e-05 Informative Direct
Biological Process (BP) vitamin metabolic process 4.154e-05 Informative Direct
Biological Process (BP) negative regulation of developmental process 9.553e-05 Informative Direct
Biological Process (BP) lipid localization 0.0003253 Informative Direct
Biological Process (BP) embryo development ending in birth or egg hatching 0.0005496 Informative Direct
Biological Process (BP) negative regulation of cellular component organization 0.0007342 Informative Direct
Biological Process (BP) positive regulation of signal transduction 0.1972 Informative Inherited
Biological Process (BP) positive regulation of cell proliferation 0.822 Informative Inherited
Biological Process (BP) positive regulation of cellular component organization 0.7203 Informative Inherited
Biological Process (BP) protein localization to organelle 0.7436 Informative Inherited
Biological Process (BP) cellular membrane organization 0.2793 Informative Inherited
Biological Process (BP) muscle tissue development 0.003883 Informative Inherited
Biological Process (BP) sensory organ development 0.7634 Informative Inherited
Biological Process (BP) cardiovascular system development 0.3012 Informative Inherited
Biological Process (BP) epithelium development 1 Informative Inherited
Biological Process (BP) tissue morphogenesis 1 Informative Inherited
Biological Process (BP) tube development 0.8039 Informative Inherited
Biological Process (BP) organ morphogenesis 0.1346 Informative Inherited
Biological Process (BP) protein complex assembly 0.3301 Informative Inherited
Biological Process (BP) growth 0.02045 Informative Inherited
Biological Process (BP) muscle structure development 0.05869 Informative Inherited
Biological Process (BP) defense response 0.09835 Informative Inherited
Biological Process (BP) single organism reproductive process 0.7597 Informative Inherited
Biological Process (BP) protein catabolic process 0.599 Informative Inherited
Biological Process (BP) embryonic morphogenesis 0.4476 Informative Inherited
Biological Process (BP) enzyme linked receptor protein signaling pathway 1 Informative Inherited
Biological Process (BP) regulation of anatomical structure size 0.1545 Informative Inherited
Biological Process (BP) gland development 0.1421 Informative Inherited
Biological Process (BP) regulation of cellular component movement 0.106 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.001901 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.003774 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.06898 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 1 Informative Inherited
Biological Process (BP) localization of cell 0.001669 Informative Inherited
Biological Process (BP) central nervous system development 0.1225 Informative Inherited
Biological Process (BP) isoprenoid metabolic process 0.01043 Informative Inherited
Biological Process (BP) regulation of cell development 0.005028 Informative Inherited
Biological Process (BP) regulation of nervous system development 0.002539 Informative Inherited
Biological Process (BP) response to light stimulus 0.1394 Informative Inherited
Biological Process (BP) reproductive system development 1 Informative Inherited
Biological Process (BP) response to nutrient levels 0.1704 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 1 Informative Inherited
Biological Process (BP) immune response 0.4263 Informative Inherited
Biological Process (BP) immune effector process 0.01539 Informative Inherited
Biological Process (BP) positive regulation of immune system process 0.7877 Informative Inherited
Biological Process (BP) protein transport 0.6662 Informative Inherited
Biological Process (BP) cytoplasmic transport 0.7304 Informative Inherited
Biological Process (BP) regulation of immune response 0.8842 Informative Inherited
Biological Process (BP) regulation of defense response 0.02174 Informative Inherited
Biological Process (BP) regulation of response to external stimulus 0.09952 Informative Inherited
Biological Process (BP) response to drug 0 Highly Informative Direct
Biological Process (BP) regulation of protein processing 3.77e-15 Highly Informative Direct
Biological Process (BP) regulation of acute inflammatory response 3.489e-13 Highly Informative Direct
Biological Process (BP) organic hydroxy compound transport 2.417e-12 Highly Informative Direct
Biological Process (BP) regulation of humoral immune response 5.609e-12 Highly Informative Direct
Biological Process (BP) establishment or maintenance of cell polarity 8.834e-11 Highly Informative Direct
Biological Process (BP) sterol metabolic process 3.517e-09 Highly Informative Direct
Biological Process (BP) chemotaxis 1.088e-07 Highly Informative Direct
Biological Process (BP) extracellular matrix organization 2.951e-07 Highly Informative Direct
Biological Process (BP) negative regulation of cell differentiation 6.126e-07 Highly Informative Direct
Biological Process (BP) mammary gland epithelium development 6.154e-07 Highly Informative Direct
Biological Process (BP) lipoprotein metabolic process 8.507e-07 Highly Informative Direct
Biological Process (BP) retinoid metabolic process 3.635e-06 Highly Informative Direct
Biological Process (BP) telencephalon development 3.807e-06 Highly Informative Direct
Biological Process (BP) regulation of neuron projection development 6.257e-06 Highly Informative Direct
Biological Process (BP) connective tissue development 1.904e-05 Highly Informative Direct
Biological Process (BP) cell junction organization 2.636e-05 Highly Informative Direct
Biological Process (BP) protein activation cascade 2.666e-05 Highly Informative Direct
Biological Process (BP) cell projection morphogenesis 4.936e-05 Highly Informative Direct
Biological Process (BP) transmembrane receptor protein tyrosine kinase signaling pathway 0.0003152 Highly Informative Direct
Biological Process (BP) protein tetramerization 0.0003502 Highly Informative Direct
Biological Process (BP) innate immune response 0.0004552 Highly Informative Direct
Biological Process (BP) muscle organ development 0.0005999 Highly Informative Direct
Biological Process (BP) humoral immune response 0.0007817 Highly Informative Direct
Biological Process (BP) establishment of protein localization to organelle 0.02816 Highly Informative Inherited
Biological Process (BP) retina development in camera-type eye 0.002717 Highly Informative Inherited
Biological Process (BP) branching morphogenesis of an epithelial tube 0.0352 Highly Informative Inherited
Biological Process (BP) respiratory system development 0.003569 Highly Informative Inherited
Biological Process (BP) developmental growth 0.0192 Highly Informative Inherited
Biological Process (BP) cell fate commitment 0.8065 Highly Informative Inherited
Biological Process (BP) mesenchyme development 0.1461 Highly Informative Inherited
Biological Process (BP) phagocytosis 0.1606 Highly Informative Inherited
Biological Process (BP) limb morphogenesis 0.001635 Highly Informative Inherited
Biological Process (BP) pattern specification process 0.9255 Highly Informative Inherited
Biological Process (BP) detection of light stimulus 0.001718 Highly Informative Inherited
Biological Process (BP) gonad development 0.2955 Highly Informative Inherited
Biological Process (BP) cell morphogenesis involved in neuron differentiation 0.06001 Highly Informative Inherited
Biological Process (BP) learning or memory 0.002231 Highly Informative Inherited
Biological Process (BP) muscle fiber development 0.02224 Highly Informative Inherited
Biological Process (BP) axon development 1 Highly Informative Inherited
Biological Process (BP) G-protein coupled receptor signaling pathway 0.09939 Highly Informative Inherited
Molecular Function (MF) binding 0.006996 Least Informative Inherited
Molecular Function (MF) hydrolase activity 0.00172 Least Informative Inherited
Molecular Function (MF) receptor activity 0 Informative Direct
Molecular Function (MF) peptidase activity 8.007e-16 Informative Direct
Molecular Function (MF) molecular transducer activity 2.004e-08 Informative Direct
Molecular Function (MF) receptor binding 0.05427 Informative Inherited
Molecular Function (MF) carbohydrate derivative binding 0.001618 Informative Inherited
Molecular Function (MF) hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds 0.02214 Informative Inherited
Molecular Function (MF) serine hydrolase activity 0 Highly Informative Direct
Molecular Function (MF) deacetylase activity 1.641e-05 Highly Informative Direct
Molecular Function (MF) G-protein coupled receptor activity 0.4973 Highly Informative Inherited
Molecular Function (MF) endopeptidase activity 0.06697 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 0.002791 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 9.172e-10 Moderately Informative Direct
Cellular Component (CC) vesicle 2.561e-05 Moderately Informative Direct
Cellular Component (CC) intrinsic to membrane 0.1668 Moderately Informative Inherited
Cellular Component (CC) cytoskeleton 0.2262 Moderately Informative Inherited
Cellular Component (CC) organelle membrane 0.4302 Moderately Informative Inherited
Cellular Component (CC) cell projection 0.001246 Moderately Informative Inherited
Cellular Component (CC) endosome 0 Informative Direct
Cellular Component (CC) extracellular matrix 0 Informative Direct
Cellular Component (CC) lytic vacuole 2.906e-08 Informative Direct
Cellular Component (CC) integral to membrane 3.098e-07 Informative Direct
Cellular Component (CC) synapse part 8.196e-07 Informative Direct
Cellular Component (CC) cell surface 3.891e-06 Informative Direct
Cellular Component (CC) Golgi apparatus 1.942e-05 Informative Direct
Cellular Component (CC) vacuolar part 0.000432 Informative Direct
Cellular Component (CC) extracellular matrix part 0 Highly Informative Direct
Cellular Component (CC) proteinaceous extracellular matrix 2.069e-14 Highly Informative Direct
Cellular Component (CC) lysosome 2.663e-09 Highly Informative Direct
Cellular Component (CC) cell body 1.501e-06 Highly Informative Direct
Cellular Component (CC) brush border 3.318e-05 Highly Informative Direct
Cellular Component (CC) receptor complex 5.16e-05 Highly Informative Direct
Cellular Component (CC) endosomal part 0.000959 Highly Informative Direct
Cellular Component (CC) membrane raft 0.001256 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 system0.665Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of humoral immunity0.03296InformativeInherited
Phenotypic Abnormality (PA)Recurrent infections0.3616InformativeInherited
Phenotypic Abnormality (PA)Abnormality of complement system1.59e-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 phenotype0.05336Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.4678Least InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.027Moderately InformativeInherited
Mammalian Phenotype (MP)integument phenotype0.1069Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal lipid homeostasis0.1578Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood vessel morphology0.1931Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal coat appearance0.0009689InformativeDirect
Mammalian Phenotype (MP)abnormal circulating cholesterol level0.02235InformativeInherited
Mammalian Phenotype (MP)abnormal circulating lipoprotein level0.0386InformativeInherited
Mammalian Phenotype (MP)abnormal systemic artery morphology0.07353InformativeInherited
Mammalian Phenotype (MP)abnormal limb morphology0.8937InformativeInherited
Mammalian Phenotype (MP)abnormal circulating VLDL cholesterol level0.0003769Highly InformativeDirect
Mammalian Phenotype (MP)abnormal eye pigmentation0.01068Highly InformativeInherited
Mammalian Phenotype (MP)abnormal digit morphology0.03577Highly 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 system0.02299Least InformativeInherited
Xenopus ANatomical entity (XAN)embryo0.7778Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.308Moderately InformativeInherited
Xenopus ANatomical entity (XAN)hindgut7.121e-06Highly InformativeDirect

Document: XA annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases1.641e-07Least InformativeDirect
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)0Moderately InformativeDirect
Enzyme Commission (EC)Serine endopeptidases0InformativeDirect
Enzyme Commission (EC)Enteropeptidase4.08e-11Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0.01112Least InformativeInherited
Biological processLipid metabolism2.469e-07Moderately InformativeDirect
Biological processCytolysis0InformativeDirect
Biological processEndocytosis0InformativeDirect
Biological processInnate immunity0InformativeDirect
Biological processLipid transport0InformativeDirect
Biological processSteroid metabolism0InformativeDirect
Biological processWnt signaling pathway2.603e-10InformativeDirect
Biological processCell adhesion8.99e-08InformativeDirect
Biological processCholesterol metabolism0Highly InformativeDirect
Biological processComplement pathway0Highly InformativeDirect
Biological processComplement alternate pathway9.352e-16Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentEndosome3.397e-07Moderately InformativeDirect
Cellular componentGolgi apparatus9.097e-05Moderately InformativeDirect
Cellular componentLysosome2.918e-06InformativeDirect
Cellular componentCoated pit0Highly InformativeDirect
DiseaseDisease mutation8.226e-07Least InformativeDirect
DomainRepeat0Least InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransmembrane0Least InformativeDirect
DomainEGF-like domain0InformativeDirect
DomainSignal-anchor6.542e-08InformativeDirect
DomainTransmembrane beta strand4.15e-05InformativeDirect
DomainSushi3.946e-10Highly InformativeDirect
Molecular functionCalcium0Moderately InformativeDirect
Post-translational modificationHydrolase0.04257Least InformativeInherited
Post-translational modificationProtease0Moderately InformativeDirect
Post-translational modificationReceptor0Moderately InformativeDirect
Post-translational modificationDevelopmental protein3.19e-06Moderately InformativeDirect
Post-translational modificationSerine protease0InformativeDirect
Post-translational modificationTransducer2.843e-05InformativeDirect
Post-translational modificationG-protein coupled receptor9.383e-06Highly InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect
Post-translational modificationZymogen9.805e-05InformativeDirect

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 ]