PMC:1794230 / 51802-52658 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/1794230","sourcedb":"PMC","sourceid":"1794230","source_url":"https://www.ncbi.nlm.nih.gov/pmc/1794230","text":"Genome sequence data and annotations were downloaded from the NCBI RefSeq database [42]: Escherichia coli K12 (NC_000913.1), Salmonella enterica serovar Typhi (S. typhi)(NC_003198), Yersinia pestis CO92 (NC_003143), Haemophilus influenzae Rd (NC_000907), Vibrio cholerae El Tor (NC_002505 and NC_002506), Shewanella oneidensis MR-1 (NC_004347 and NC_004349), and Pseudomonas aeruginosa PA01 (NC_002516). Orthologs for each of the annotated E. coli genes were identified in each of the remaining six species, using INPARANOID v.1.35 [43]. This program uses BLAST [44] to compare the complete set of predicted protein sequences from one genome with that of another, and identifies the reciprocal best hits. We set the parameters to use the BLOSUM62 matrix and a minimum bit score of 30, and we required that the alignment cover at least 50% of both proteins.","tracks":[{"project":"2_test","denotations":[{"id":"17244358-11125071-1689330","span":{"begin":84,"end":86},"obj":"11125071"},{"id":"17244358-11743721-1689331","span":{"begin":533,"end":535},"obj":"11743721"},{"id":"17244358-9254694-1689332","span":{"begin":563,"end":565},"obj":"9254694"}],"attributes":[{"subj":"17244358-11125071-1689330","pred":"source","obj":"2_test"},{"subj":"17244358-11743721-1689331","pred":"source","obj":"2_test"},{"subj":"17244358-9254694-1689332","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#ec93de","default":true}]}]}}