Xs mean gaps, which can be considered as 'insertion' or 'deletion' in biology.
Btw, you may try BLAST service in RCSB PDB, you will find more hits. http://www.rcsb.org/pdb/search/searchSequence.do 2008/5/29 Xue Li <[EMAIL PROTECTED]>: > Hello all, > > I installed blast-2.2.18 on my Ubuntu, and did blastp on > 1RREQ_B.fasta.txt on pdb database. > > I got the following results: > > Score = 1147 bits (2967), Expect = 0.0, Method: Composition-based stats. > Identities = 596/637 (93%), Positives = 596/637 (93%) > > Query: 1 SSTDQGTNPAXXXXXXXXXXXXAGDFPKATEEQWEREVEKVLNRGRPPEKQLTFAECLKR 60 > SSTDQGTNPA AGDFPKATEEQWEREVEKVLNRGRPPEKQLTFAECLKR > Sbjct: 1 SSTDQGTNPADTDDLTPTTLSLAGDFPKATEEQWEREVEKVLNRGRPPEKQLTFAECLKR 60 > > Would someone please tell me what do the Xs mean in the query sequence? > > Also, the results is different from the NCBI blast result. I > downloaded pdb database today. Local Blast results show that there are > 36, 353 sequences in pdbaa, while NCBI blast shows 36,476 sequences in > pdb database. > > Even I installed blast-2.2.18, local Blast results show that I am > using BLASTP2.2.17. NCBI shows that they are using blast-2.2.18+. > > Did I do something wrong? > > > -- > Xue, Li > Bioinformatics and Computational Biology program @ ISU > Ames, IA 50010 > 515-450-7183 > > _______________________________________________ > BBB mailing list > [email protected] > http://www.bioinformatics.org/mailman/listinfo/bbb > -- 黄韬， Tao Huang _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
