AllFam - Database of allergen families Department of Pathophysiology and Allergy Research Medical University of Vienna

About AllFam

The AllFam database is a resource for classifying allergens into protein families. The database merges data from the Allergome allergen database and the Pfam protein family database.

Background

In the last two decades, hundreds of allergens have been identified, cloned and sequenced. This wealth of data now enables us to classify allergens into protein families that are defined by sequence and structural similarity

Employing different methods, several groups have shown that most allergens belong to a limited set of protein families thus disproving the assumption that every protein can become an allergen. Hence, the classification of allergenic proteins based on biochemical and structural similarities including the comparison of allergenic and non-allergenic members of a protein family will lead to new insights into factors that contribute to allergenicity. In addition, these data will provide the foundation for elucidating the structural basis of allergenic cross-reactivity.

Stadler MB, Stadler BM:
Allergenicity prediction by protein sequence.
FASEB J 2003, 17, 1141-3. [PubMed]

Jenkins JA, Griffiths-Jones S, Shewry PR, Breiteneder H, Mills EN:
Structural relatedness of plant food allergens with specific reference to cross-reactive allergens: an in silico analysis.
J Allergy Clin Immunol 2005, 115, 163-70. [PubMed]

Radauer C, Breiteneder H:
Pollen allergens are restricted to few protein families and show distinct patterns of species distribution.
J Allergy Clin Immunol 2006, 117, 141-7. [PubMed]

Jenkins JA, Breiteneder H, Mills EN:
Evolutionary distance from human homologs reflects allergenicity of animal food proteins.
J Allergy Clin Immunol 2007, 120, 1399-405. [PubMed]

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How AllFam was created

Allergen data and a list of allergen sources in AllFam are derived from the Allergome database in a collaboration with Adriano Mari, Allergy Data Laboratories, Latina, Italy.

Allergen sequences are classified into protein families using the Pfam database, a comprehensive collection of sequence alignments and hidden Markov models that define more than 9,000 protein families covering most known protein sequences, and its associated database, SwissPfam, a compilation of precalculated Pfam domain compositions of all Uniprot sequences.

AllFam contains all allergens with known sequences that can be assigned to at least one Pfam family. Many allergens are multi-domain proteins. The domains of these proteins are merged into a single AllFam family, if the Pfam domains of this allergen occur only in combination with a single other Pfam domain (e. g. propeptides of proteases that occur only together with certain catalytic domains). Domains that are part of proteins from different families (e. g. the hevein-like domain) represent separate AllFam families.

AllFam construction flow chart

Fig. 1. Flow chart for constructing AllFam

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How to cite AllFam

If you use data from AllFam in your work, please cite the following paper:

Radauer C, Bublin M, Wagner S, Mari A, Breiteneder H:
Allergens are distributed into few protein families and possess a restricted number of biochemical functions.
J Allergy Clin Immunol 2008, 121, 847-52. [PubMed]

In addition, please include also the AllFam URL: http://www.meduniwien.ac.at/allergens/allfam/.

A list of publication that have already cited the AllFam paper can be found in Papers citing AllFam.

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The AllFam team

Project leader, database design, site administration:
Christian Radauer (christian.radauer@meduniwien.ac.at)
Scientific advisory board:
Heimo Breiteneder (heimo.breiteneder@meduniwien.ac.at)
Merima Bublin (merima.bublin@meduniwien.ac.at)

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