GapMind: Automated Annotation of Amino Acid Biosynthesis

GapMind handles fusion proteins and split proteins. (A) HSERO_RS20920 from Herbaspirillum seropedicae SmR1 is a fusion of AroL and AroB (shown with Swiss-Prot identifiers). (B) Split candidates for vitamin B₁₂-dependent methionine synthase (MetH) in Burkholderia phytofirmans PsJN and Bacteroides thetaiotaomicron VPI-5482. a.a., amino acids.

Arginine biosynthesis with succinylated intermediates. (A) The standard pathway. Protein names are from Escherichia coli or Bacillus subtilis. The formation of carbamoyl phosphate (catalyzed by CarAB) is not shown. (B) The pathway in Bacteroides and in other Bacteroidetes. (C) Fitness data from Bacteroides thetaiotaomicron VPI-5482, Echinicola vietnamensis KMM 6221 (DSSM 17526), and Pedobacter sp. strain GW460-11-11-14-LB5 (from references 8 and 20). Each fitness value is the log₂ change in the abundance of the mutants in a gene during an experiment. Each experiment went from an optical density at 600 nm of 0.02 to saturation (usually 4 to 8 doublings). Fitness values for CA265_RS18510 were not estimated, because mutants of this gene were at low abundance in the starting samples.

Tyrosine synthesis via phenylalanine hydroxylase in Dyella japonica and Echinicola vietnamensis. (A) Gene fitness in Dyella japonica UNC79MFTsu3.2. The x axis shows the median fitness across 59 genes that are predicted to be involved in amino acid biosynthesis (by TIGRFam role [14]), and the y axis shows the fitness of the predicted phenylalanine hydroxylase (PAH). (B) Gene fitness in Echinicola vietnamensis KMM 6221 (DSM 17526) for prephenate dehydrogenase (x axis) and for PAH (y axis). In both panels, we color code experiments by whether or not tyrosine was present in the media. The experiments with tyrosine usually included it via yeast extract or Casamino Acids, while the experiments without tyrosine are in defined media with just one or no amino acids added. Lines show x = 0 and y = 0, corresponding to no effect of mutating the genes. In panel A, lines show x = y.

Number of gaps in amino acid biosynthesis in 148 diverse bacteria and archaea that can grow without amino acids. (These are distinct from the 35 bacteria with fitness data.)