SUPERFAMILY 1.75 HMM library and genome assignments server


Agglutinin superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   beta-Trefoil [ 50352] (8)
Superfamily:   Agglutinin [ 50382]
Families:   Agglutinin [ 50383]


Superfamily statistics
Genomes (23) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 274 109 2
Proteins 175 77 1


Functional annotation
General category Other
Detailed category Viral proteins

Document:
Function annotation of SCOP domain superfamilies

InterPro annotation
Cross references IPR008998 SSF50382 Protein matches
Abstract

Agglutinins are sugar-specific lectins that can agglutinate erythrocytes and other cell types. Lectins occur widely in plants, as well as some microorganisms and animal [PubMed15229195]. Agglutinin from Amaranthus caudatus (amaranthin) is a lectin from the ancient South American crop, amaranth grain. Although its biological function is unknown, it can agglutinate A, B and O red blood cells, and has a carbohydrate-binding site that is specific for the methyl-glycoside of the T-antigen found linked to serine or threonine residues of cell surface glycoproteins [PubMed2271665]. The protein is comprised of a homodimer, with each homodimer consisting of two beta-trefoil domains [PubMed2777780]. Lectin B chains from ricin and related toxins also contain beta-trefoil domain, however they are not related to agglutinin, showing little sequence similarity [PubMed9334739].


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

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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 2 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 Agglutinin 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 2 hidden Markov models representing the Agglutinin 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 · Internal database links ]