Computational protocol: Sialic acid utilization by Cronobacter sakazakii

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Protocol publication

[…] The amino acid sequences of the genes nanK, nanT, nanE, nanA, nanC, nagA and nagB from the fourteen Cronobacter spp. genomes (CALG01000001-C201, CALF01000001-569, CALE01000001-768, AFMO00000000, NC_009778-80, CALD01000001-249, CALC01000001-171, CALB01000001-114, NC_013282-85, CALA01000001-427, CAKZ01000001-221, CAKY01000001-365, CAKX01000001-231, CAKW01000001-155) were obtained from RAST prokaryotic genome annotation server. The gene sequences from the genome of C. sakazakii BAA-894 was used to perform tblastx searches to obtain the corresponding sequences of closely related organisms showing >50% amino acid identity. The corresponding protein sequences were downloaded from the genomes of E. coli O7:K1 strain CE10 (Accession No. NC_017646); E. cloacae subsp. cloacae ATCC 13047 (Accession No. NC_014121); E. hormaechei ATCC 49162 (Accession No. AFHR00000000); Enterobacter spp. strain 683 (Accession No. CP000653); Cit. freundii strain 4_7_47CFAA (Accession No. ADLG00000000); Cit. koseri ATCC BAA-895 (Accession No. NC_009792); Ed. tarda strain EIB202 (Accession No. NC_013508); Salmonella enterica subsp. enterica serovar Typhimurium strain LT2 (Accession No. NC_003197); Pantoea agglomerans strain IG1 (Accession No. BAEF00000000). The sequences of each gene were aligned using ClustalW [] and phylogenetic analysis was performed using the Maximum-Likelihood algorithm in PhyML [,]. Stability of the relationships was assessed by the bootstrap method (1000 replicates) and the trees were viewed and annotated using TreeDyn at http://www.phylogeny.fr[,]. […]

Pipeline specifications

Software tools TBLASTX, Clustal W, PhyML, TreeDyn, Phylogeny.fr
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Cronobacter sakazakii, Homo sapiens, Escherichia coli, Citrobacter koseri
Diseases Meningitis, Osteochondrodysplasias, Enterocolitis, Necrotizing
Chemicals Carbon, G(M1) Ganglioside, Gangliosides, N-Acetylneuraminic Acid