SUPERFAMILY 1.75 HMM library and genome assignments server


PHL pollen allergen superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   C2 domain-like [ 49561] (5)
Superfamily:   PHL pollen allergen [ 49590]
Families:   PHL pollen allergen [ 49591] (2)


Superfamily statistics
Genomes (227) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,566 2,979 2
Proteins 3,498 2,964 2


Functional annotation
General category Other
Detailed category Unknown function

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) developmental process 0.0001022 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.02232 Least Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1.236e-08 Moderately Informative Direct
Biological Process (BP) anatomical structure formation involved in morphogenesis 9.426e-07 Informative Direct
Cellular Component (CC) external encapsulating structure 3.443e-11 Informative Direct

Document: GO annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)root system0.1567Least InformativeInherited
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0.6395Least InformativeInherited
Plant ANatomical entity (PAN)root tip9.44e-05InformativeDirect
Plant ANatomical entity (PAN)lateral root1.828e-06Highly InformativeDirect

Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processCell wall biogenesis/degradation0InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentCell wall0Highly InformativeDirect
DiseaseAllergen0Moderately InformativeDirect
DomainSignal0Least InformativeDirect
Post-translational modificationGlycoprotein7.203e-11Least InformativeDirect
Post-translational modificationDisulfide bond5.805e-10Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR007117 SSF49590 Protein matches
Abstract

Expansins are unusual proteins that mediate cell wall extension in plants [PubMed7568110]. They are believed to act as a sort of chemical grease, allowing polymers to slide past one another by disrupting non-covalent hydrogen bonds that hold many wall polymers to one another. This process is not degradative and hence does not weaken the wall, which could otherwise rupture under internal pressure during growth.

Sequence comparisons indicate at least four distinct expansin cDNAs in rice and at least six in Arabidopsis. The proteins are highly conserved in size and sequence (75-95% amino acid sequence similarity between any pairwise comparison), and phylogenetic trees indicate that this multigene family formed before the evolutionary divergence of monocotyledons and dicotyledons [PubMed7568110]. Sequence and motif analyses show no similarities to known functional domains that might account for expansin action on wall extension. It is thought that several highly-conserved tryptophans may function in expansin binding to cellulose, or other glycans. The high conservation of the family indicates that the mechanism by which expansins promote wall extensin tolerates little variation in protein structure.

Grass pollens, such as pollen from timothy grass, represent a major cause of type I allergy [PubMed7930302]. Interestingly, expansins share a high degree of sequence similarity with the Lol p I family of allergens. This entry represents the C-terminal domain.


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) · Arabidopsis Plant Ontology (AP) · 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 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 PHL pollen allergen 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 PHL pollen allergen 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) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]