SUPERFAMILY 1.75 HMM library and genome assignments server


Lipovitellin-phosvitin complex; beta-sheet shell regions superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Membrane and cell surface proteins and peptides [ 56835] (58)
Fold:   Lipovitellin-phosvitin complex; beta-sheet shell regions [ 56967]
Superfamily:   Lipovitellin-phosvitin complex; beta-sheet shell regions [ 56968]
Families:   Lipovitellin-phosvitin complex; beta-sheet shell regions [ 56969]


Superfamily statistics
Genomes (141) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 1,427 2,276 3
Proteins 837 1,349 2


Functional annotation
General category Metabolism
Detailed category Lipid metabolism and transport

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) localization 3.67e-05 Least Informative Direct
Biological Process (BP) protein metabolic process 0.001327 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.2866 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.8595 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.008856 Least Informative Inherited
Biological Process (BP) lipid metabolic process 2.438e-07 Moderately Informative Direct
Biological Process (BP) macromolecule localization 2.167e-11 Moderately Informative Direct
Biological Process (BP) regulation of biological quality 1.633e-05 Moderately Informative Direct
Biological Process (BP) organic substance transport 1.417e-11 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0.001769 Moderately Informative Inherited
Biological Process (BP) lipid localization 1.045e-08 Informative Direct
Biological Process (BP) glycerolipid metabolic process 0.0001979 Informative Direct
Biological Process (BP) protein transport 0.7382 Informative Inherited
Biological Process (BP) acylglycerol metabolic process 1.674e-13 Highly Informative Direct
Biological Process (BP) organic hydroxy compound transport 1.307e-06 Highly Informative Direct
Biological Process (BP) lipoprotein metabolic process 0 Highly Informative Direct
Molecular Function (MF) transporter activity 4.663e-11 Moderately Informative Direct
Molecular Function (MF) lipid transporter activity 0 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 0.003099 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.9394 Least Informative Inherited
Cellular Component (CC) endoplasmic reticulum 9.579e-07 Moderately Informative Direct
Cellular Component (CC) vesicle 0.001137 Moderately Informative Inherited
Cellular Component (CC) extracellular region part 0.002358 Moderately Informative Inherited
Cellular Component (CC) extracellular space 3.263e-05 Informative Direct
Cellular Component (CC) Golgi apparatus 0.0003351 Informative Direct

Document: GO annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)life span variant0.0002396InformativeDirect

Document: WP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport8.124e-05Least InformativeDirect
Biological processLipid transport5.43e-12InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentEndoplasmic reticulum3.155e-05Moderately InformativeDirect
DomainSignal0Least InformativeDirect
Molecular functionLipid-binding5.01e-15InformativeDirect
Post-translational modificationStorage protein0Highly InformativeDirect
Post-translational modificationGlycoprotein2.453e-11Least InformativeDirect
Post-translational modificationCleavage on pair of basic residues0.000104Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR015819 SSF56968 Protein matches
Abstract

This entry represents beta-sheet shell domains found in lipid transport proteins such as vitellinogen. Vitellinogen precursors provide the major egg yolk proteins that are a source of nutrients during early development of oviparous vertebrates and invertebrates. Vitellinogen precursors are multi-domain apolipoproteins that are cleaved into distinct yolk proteins. Different vitellinogen precursors exist, which are composed of variable combinations of yolk protein components; however, the cleavage sites are conserved. In vertebrates, a complete vitellinogen is composed of an N-terminal signal peptide for export, followed by four regions that can be cleaved into yolk proteins: lipovitellin-1, phosvitin, lipovitellin-2, and a von Willebrand factor type D domain (YGP40) [PubMed17314313, PubMed12135361]. Domains with a beta-sheet shell topology can be found within both lipovitellin-1 and lipoviteliin-2 peptide products.


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) · Worm Phenotype (WP) · 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 Lipovitellin-phosvitin complex; beta-sheet shell regions 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 Lipovitellin-phosvitin complex; beta-sheet shell regions 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) · Worm Phenotype (WP) · UniProtKB KeyWords (KW) · Internal database links ]