SUPERFAMILY 1.75 HMM library and genome assignments server

Superfamily is undergoing a server migration - you are now browsing on the new server. Please contact us if you experience any problems.


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 (146) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 1,494 6,908 3
Proteins 890 4,241 2


Functional annotation
General category Metabolism
Detailed category Lipid metabolism and transport

Document:
Function annotation of SCOP domain superfamilies

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism environmental stimulus response variant0.0002077Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.009755Least InformativeInherited
Worm Phenotype (WP)organism behavior variant0.06771Least InformativeInherited
Worm Phenotype (WP)life span variant0.000007896Moderately InformativeDirect
Worm Phenotype (WP)feeding behavior variant0.0004065Moderately InformativeDirect
Worm Phenotype (WP)organism pathogen response variant0.0000001046InformativeDirect
Worm Phenotype (WP)avoids bacterial lawn0.00006183InformativeDirect
Worm Phenotype (WP)endocytic transport defect0.001437InformativeInherited
Worm Phenotype (WP)pathogen susceptibility increased0.0000000001022Highly InformativeDirect
Worm Phenotype (WP)peptide uptake by intestinal cell variant0.000002063Highly InformativeDirect

Document: WP annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)compound organ0Least InformativeDirect
Zebrafish Anatomy (ZA)organism subdivision0Least InformativeDirect
Zebrafish Anatomy (ZA)multi-tissue structure0Least InformativeDirect

Document: ZA 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)trunk0Least InformativeDirect
Xenopus ANatomical entity (XAN)cavitated compound organ0Least InformativeDirect
Xenopus ANatomical entity (XAN)alimentary system0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)testis0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)viscus0Moderately InformativeDirect

Document: XA 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 · Worm Phenotype (WP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) ]

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 · Worm Phenotype (WP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Internal database links ]