Extended Data Fig. 7: AlkB diversity underlying the North Atlantic subtropical gyre.
From: Microbial production and consumption of hydrocarbons in the global ocean
Phylogenetic analysis of genes closely related to alkB from Tara Ocean dataset reveal bacterial and archaeal clades distinct from xylene monooxygenase and fatty acid desaturases. a, Protein domain architecture across select representatives of xylene monooxygenase, alkane-1 monooxygenase, fatty acid desaturase, and related proteins from the Tara Oceans dataset which share a core fatty acid desaturase-like region (blue) expanded on in panel b. b, Abbreviated protein alignment for phylogenetic analyses (for details see Methods). Each column of alignment figure represents a sliding window of 5 bp with the following identity to consensus sequence coloration: green (100%), mustard (80-99% similar), yellow (60-79% similar), gray (<60% similar). The black box represents the region containing the eight histidine residues considered catalytically essential which were used for phylogenetic analyses in panels c-d. c, Maximum-likelihood phylogenetic tree with scale bar of substitutions per site. For clarity, bootstrap values are not shown for the full tree. Δ-X indicates activity X carbons from the carboxylic end of the fatty acid and ω-X indicates activity X carbons from the methyl end of the fatty acid. d, Expanded subtree of membrane monooxygenases and delta-9 fatty acid desaturases (outgroup). Clade coloration in panel d is according to position in panel c. NCBI accession codes are given for functional representatives in the subtree (accession_ORF#).
