Major changes to amino acid biosynthesis since the original 2019
publication:

arg: Better described the lysW-based pathway and argX. Added putative
Steroidobacter dgcN-like argA. Proposed that "argA3" substitutes for
argE.

chorismate: Added putative aroA and aroD from Pyrolobus.

gln: Added putative glnA from Clostridium kluyveri.

gly: Added glyXL/glyXS from Bifidobacterium and Methanococcus

his: Added Bifidobacterium hisN

ile: Improved definition of cimA.

lys: Improved the lysW-based pathway to include genes from
Thermococcus kodakarensis. Added predicted dapL and dapF2 from
Staphylococcus.q

met: Added the core methionine synthase mesB, the mesD-mesX system,
and renamed metE' to mesA. Added the predicted synthases mesC and
split metE. Added a homoserine dehydrogenase from Brevundimonas. Added
a putative B12 reactivation protein from Heliobacterium. Added a
putative NIL/ferredoxin component (for reductive sulfuration of
L-aspartate semialdehyde) from Methanococcus. Added a putative
persulfide-forming protein (for reductive sulfuration of L-aspartate
semialdehyde) from Hippea.

phe: Improved definition of prephenate dehydratase, including a
diverged enzyme from Brevundimonas and a putative enzyme from
Carboxydothermus.

pro: Added synthesis via ornithine 5-aminotransferase (EC 2.6.1.13),
and allowed more options for ornithine biosynthesis (such as the lysW
pathway). Added archaeal ornithine cyclodeaminase.

ser: Added serA from Thermococcus and a predicted serA from
Roseburia. Added serC from Methanocaldococcus and from
Staphylococcus. Added predicted serC from Clostridia ("serC3") and some
related enzymes. Added serB from Entamoeba histolytica, as this is
similar to some putative bacterial serB. Added a subfamily of DUF1015 as
a predicted replacement for serB.

thr: Added the putative alternative to homoserine kinase,
homK/thrB2/TIGR02535.

tyr: Improved the definition of prephenate dehydrogenase, including a
predicted enzyme from Desulfarculus.

val: Fixed names of ilvI/ilvH (which had been swapped). Added various
short ilvH proteins (with an ACT domain only).