Computational protocol: Production of poly(3-hydroxybutyrate) by Halomonas boliviensis in an air-lift reactor

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Protocol publication

[…] Four genome sequences corresponding to strains of the family Halomonadaceae were selected for this study. The strains were Halomonas boliviensis LC1T (=DSM 15516T) [], Halomonas elongata DSM 2581T [], Halomonas sp. TD01 [], and Chromohalobacter salexigens DSM 3043 [].A total of 6901 alignments of clusters of orthologous proteins (COGs) of 88 microorganisms, as classified in COGs [] and EggNOG [] databases, were obtained from that described by Puigbò et al. []. The protein sequences of these 88 microorganisms were used as reference for the evolutionary analysis. Protein sequences of strains of the family Halomonadaceae were included in the alignments with the references for each corresponding COG using the Muscle program [] included in the MEGA 5 software package [] with default parameters. Unrooted maximum likelihood phylogenetic trees for each COG were constructed using MEGA 5 under a WAG with frequencies (+F) model, with uniform mutation rates among amino acid sites and complete deletion of gaps and missing data. […]

Pipeline specifications

Software tools MUSCLE, MEGA
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Halomonas boliviensis, Escherichia coli, Triticum aestivum
Chemicals Carbohydrates, Carbon, Coenzyme A, Glucose, Maltose, NADP, Pentosephosphates, Xylose