The phylogenetic distribution of hisIE genes was obtained by retrieving homologous sequences using the E. coli HisIE amino acid sequence as a query to probe genome database.
In order to check the distribution of the CeoB-like proteins in the entire genus Burkholderia, the B. cenocepacia J2315 CeoB amino acid sequence (gi 206564391) was used as a query to probe the 21 completely sequenced genomes of strains belonging to Burkholderia genus available at NCBI database http://www.ncbi.nlm.nih.gov (1/05/2009), using default parameters.
The amino acid sequence of each of the E. coli lysine (DAP), leucine, and T. thermophilus lysine (AAA) biosynthetic enzymes, was used as a query to probe the completely sequenced genomes database of KEGG (Kyoto Encyclopaedia of Genes and Genomes) consisting of 29 Archaea, 423 Bacteria and 35 Eucaryotes.
Using CD38, CD157, and Aplysia ARC as query sequences to probe the Strongylocentrotus purpuratus genome [7] and expressed-sequence tag (EST) cDNA databases [8], we identified three ARC isoforms, ARCα, ARCβ, and ARCγ.
Due to the limit of sequences that PSI-BLAST database searching can report, the 6 query sequences used to probe the databases (see Methods) each retrieved 1000 similar sequences with the statistical significance threshold of 0.005.
The Gnutella protocol supports five types of messages: ping and pong used to probe the network, query and queryhit used to exchange data, and push used to deal with peers behind the firewall.
Open-ended initial questions on each domain and each item were followed-up with more specific queries to clarify responses and probe any confusing issues.
The UCSC database (http://genome.ucsc.edu, February 2009 release) was queried to localize the probe.
Medication queries to answer.
