On 2017 Sep 30, Yuichi Hongoh commented:

Dear Dr.Price, your comment is very helpful to us. I agree with your suggestions. Thank you very much.

On 2017 Sep 25, Morgan Price commented:

The authors suggest that D. trichonymphae cannot synthesize threonine or methionine, but I think pathways for synthesizing both amino acids are present. First, the only gap in threonine synthesis appears to be a missing homoserine kinase. In Desulfivibrio vulgaris Miyazaki F, a misannotated shikimate kinase (DvMF_0971) provides the missing homoserine kinase activity (https://www.biorxiv.org/content/early/2017/09/23/192971). RSDT_0983 from D. trichonymphae is over 50% identical to DvMF_0971 and is also probably a homoserine kinase. Second, I found plausible candidates for all steps in methionine synthesis. D. trichonymphae has putative genes converting aspartate to homoserine (RSDT_0709, RSDT_1035, RSDT_0549), for activating homoserine (RSDT_0485), for sulfhydrylation of the activated homoserine (RSDT_0816), and for B12-dependent methionine synthase (RSDT_0316). Thus, D. trichonymphae contains the genes to synthesize threonine and methionine.

On 2017 Sep 25, Morgan Price commented:

The authors suggest that D. trichonymphae cannot synthesize threonine or methionine, but I think pathways for synthesizing both amino acids are present. First, the only gap in threonine synthesis appears to be a missing homoserine kinase. In Desulfivibrio vulgaris Miyazaki F, a misannotated shikimate kinase (DvMF_0971) provides the missing homoserine kinase activity (https://www.biorxiv.org/content/early/2017/09/23/192971). RSDT_0983 from D. trichonymphae is over 50% identical to DvMF_0971 and is also probably a homoserine kinase. Second, I found plausible candidates for all steps in methionine synthesis. D. trichonymphae has putative genes converting aspartate to homoserine (RSDT_0709, RSDT_1035, RSDT_0549), for activating homoserine (RSDT_0485), for sulfhydrylation of the activated homoserine (RSDT_0816), and for B12-dependent methionine synthase (RSDT_0316). Thus, D. trichonymphae contains the genes to synthesize threonine and methionine.

On 2017 Sep 30, Yuichi Hongoh commented:

Dear Dr.Price, your comment is very helpful to us. I agree with your suggestions. Thank you very much.