Domains BLAST

This chapter begins with an introduction to protein domains, followed by the steps usually attempted to define domains in a protein. The process begins by looking for well-known domains in the sequence using domain family databases. Then other less well-known domains are sought in the sequence using two popular methods, HMMER and PSI-BLAST. 

The SBASE database is a collection of annotated protein sequence segments (Murvai et al., 1999). SBASE avoids using consensus methods such as profile-HMMs and uses pairwise methods to detect domains. The database includes more than 130,000 annotated sequence segments that have been clustered into groups on the basis of BLAST similarities. SBASE currently contains 1038 domain families. 

Fibrinogen-like COLFI domains C. elegans neurexin IV FBG- PSI-BLAST (2) 2 X 10 4 COLFI domain of chick... 

LamG (Jelly Usher syndrome type type S, coelicolor LamG domain PSI-BLAST (3) 2 X lO 4 Human Usher syndrome... 

PH domain IPL Pleckstrin PHI (1-105) PSI-BLAST (4) 2 X 10 Human Imprinted in Placenta and Liver... 

SH3 domain Kakapo, plectin, and Bullous pemphigoid antigen 1 Drosophila Kakapo (917-971) PSI-BLAST (3) 7 X 10 Human ITK Tyrosine kinase SH3... 

ZP C. elegans cuticlins O.latipes choriogenin H ZP domain (273-555) PSI-BLAST (2) 6 X 10 C. elegans cuticlin 1... 

However, the PSI-BLAST search method, using a very conservative inclusion threshold of E < 10 4, can detect, with significance, the similarities in sequence between previously known VWA domains and integrin /3 subunits (Table II). The hypothesis that all integrin [3 subunits contain a VWA domain appears to be correct. 

The first reference is for the identification of the respective domain by using PSI-BLAST-constructed PSSMs, and the other references are for similar findings made by alternative computational methods. 

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