PMC:3475487 / 4818-6573 JSONTXT

{"project":"2_test","denotations":[{"id":"23105923-15044751-44845613","span":{"begin":237,"end":239},"obj":"15044751"},{"id":"23105923-2231712-44845614","span":{"begin":427,"end":429},"obj":"2231712"},{"id":"23105923-9254694-44845615","span":{"begin":526,"end":528},"obj":"9254694"},{"id":"23105923-15215404-44845616","span":{"begin":990,"end":992},"obj":"15215404"},{"id":"23105923-21109532-44845617","span":{"begin":994,"end":996},"obj":"21109532"},{"id":"23105923-21075798-44845618","span":{"begin":1374,"end":1376},"obj":"21075798"},{"id":"23105923-14681412-44845619","span":{"begin":1751,"end":1753},"obj":"14681412"}],"text":"Methods\n\nSequence source\nCryptosporidium parvum strain Iowa type II (NCBI taxonomy accession 353152) was chosen for this study. One of its genes, cgd2_1810, encodes CysQ, a sulfite synthesis pathway protein (accession no. XP_001388206) [12]. The protein sequence was retrieved from the NCBI Protein Database (http://www.ncbi.nlm.nih.gov/protein).\n\nBLAST search\nSequence similarity searches were performed using BLASTP 2.2.26+ [20] with C. parvum CysQ protein against a nonredundant protein sequence database. TBLASTN 2.2.26+ [21] was performed in order to search for the orthologs of the sulfur metabolism pathway in the C. parvum genome sequence using E. coli and Mycobacterium tuberculosis protein sequences as queries.\n\nConserved domain analysis\nWe obtained information of conserved domains using the NCBI online Conserved Domain-search tool (http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi) and Conserved Domain Database (CDD) (http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml) [22, 23]. After the matching CDD model and the corresponding Conserved Domain Tree (CDTree) were identified, the CysQ sequence was added to the matched model, and the corresponding CDTree was then recalculated.\n\nPhylogenetic tree analysis\nPhylomeDB is a collection of phylogenetic trees that have been precalculated automatically with a variety of options for a wide range of species [24]. We queried PhylomeDB and downloaded the phylogenetic trees that included CysQ protein.\n\nPathway and ortholog analysis\nCysQ enzyme was found in sulfate assimilation on sulfur metabolism of the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. The list of organisms that harbored this pathway was compiled from KEGG orthology (KO) (http://www.genome.jp/kegg/ko.html) [25]."}