Computational protocol: Identification of trkH, Encoding a Potassium Uptake Protein Required for Francisella tularensis Systemic Dissemination in Mice

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Protocol publication

[…] LVS genome sequence analyses were performed essentially from the KEGG database (http://www.genome.jp/kegg-bin/show_organism?org=ftl) and associated sofware.F. tularensis complete genomes were available at the NCBI entrez Genome project site (http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&list_uids=20197,16421,17265,19571,17375,9,18459).The program BLASTN 2.2.22 was used on the nucleotide collection (nr/nt) available at http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?PROGRAM=blastn&BLAST_PROGRAMS=megaBlast&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&LINK_LOC=blasthome.Protein sequence similarity searches were performed using BLASTP against non-redundant protein data bases. Multiple sequence alignment of homologous sequences was carried out using ClustalW .TMHMM server version 2.0 (http://www.cbs.dtu.dk/services/TMHMM-2.0/) was used to perform TMS predictions.” […]

Pipeline specifications

Software tools BLASTN, BLASTP, Clustal W, TMHMM
Databases KEGG
Application Membrane protein analysis
Organisms Francisella tularensis, Mus musculus
Diseases Tularemia, Zoonoses, Mastocytosis, Systemic
Chemicals Potassium