SUPERFAMILY 1.75 HMM library and genome assignments server


AFP III-like domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   beta-clip [ 51268] (7)
Superfamily:   AFP III-like domain [ 51269]
Families:   AFP III-like domain [ 51270] (3)


Superfamily statistics
Genomes (739) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 915 3,837 36
Proteins 915 3,834 35


Functional annotation
General category General
Detailed category Structural protein

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Molecular Function (MF) transferase activity 1.86e-06 Least Informative Direct
Molecular Function (MF) transferase activity, transferring alkyl or aryl (other than methyl) groups 6.115e-08 Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring alkyl or aryl groups, other than methyl groups1InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Cellular componentSecreted0Moderately InformativeDirect
DomainSignal0.0005233Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR006190 SSF51269 Protein matches
Abstract

Antifreeze proteins (AFPs) are defined by their ability to bind ice and prevent it from growing. In this way they function in both freeze-resistance and freeze-tolerance strategies of organisms that live at sub-zero temperatures and require protection from ice growth. In fish, five AFP types have been described that are remarkably diverse in their 3D structures. They have completely dissimilar folds and no sequence homology. Type III AFPs found in eel pounts are 65-residue proteins with a compact globular fold formed from short beta strands, which presents a flat ice binding surface. These proteins are homologous to the C-terminal region of mammalian and prokaryotic sialic acid synthase (SAS; gene neuB), which has been called AFP-like domain [PubMed12171656]. The similarity is greatest in the protein core and the flat ice-binding region. SAS is involved in the condensation of phosphoenolpyruvate with N-acetylmannosamine derivatives to generate N-acetylneuraminic acid, an intermediate used for the sialylation of glycoconjugates. The function of the AFP-like domain, which is a beta-clip fold [PubMed15146494], in SAS is not known, but it has been proposed that it could be involved in sugar binding.


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) · Enzyme Commission (EC) · 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 6 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 AFP III-like domain 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 6 hidden Markov models representing the AFP III-like domain 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) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]