Missing parent: GO:0042450 arginine biosynthetic process via ornithine

[ValWood]

• GO term ID and label for which you request a new superclass

GO:0042450 arginine biosynthetic process via ornithine

This is the classical pathway of arginine biosynthesis used in plants fungi and bacteria

• New superclass (parent) suggested

GO:0006526 L-arginine biosynthetic process

• Reference(s), if appropriate
  PMID:nnnnnnn

add exact synonyms:
arginine biosynthesis, N-acetylated pathway
arginine biosynthesis, acetylated Pathway
classical arginine biosynthesis pathway
arginine biosynthesis via N-acetyl intermediates

This pathway involves the production of ornithine as an intermediate through a series of acetylated intermediates (e.g., N-acetylglutamate, N-acetylornithine).

[ValWood]

1. L-arginine biosynthesis I (via L-ornithine) https://metacyc.org/pathway?orgid=META&id=ARGSYN-PWY
   Expected Taxonomic Range: [Archaea] [Bacteria [Viridiplantae]

2. L-arginine biosynthesis II (acetyl cycle)https://metacyc.org/pathway?orgid=META&id=ARGSYNBSUB-PWYis also via ornithine
   Expected Taxonomic Range: [Archaea] [Bacteria ][Fungi], [Viridiplantae]

3. L-arginine biosynthesis III (via N-acetyl-L-citrulline)
   Expected Taxonomic Range: [Bacteria]

4. L-arginine biosynthesis IV (archaea)is via ornithine

So need better differentia than 'ornithine' if we want to represent the pathways separately
but. we could split as
arginine biosynthetic process via ornithine and via
arginine biosynthetic process via N-acetyl-L-citrulline
to fix the current problem and deepen when people need specific pathways for bacteria.

[ValWood]

Action,

• rename arginine biosynthetic process via ornithine to
  L-arginine biosynthetic process via ornithine

• and add GO:0006526 L-arginine biosynthetic process as a parent

• add GONEW L-arginine biosynthetic process via N-acetyl-L-citrulline
  as a sibling of
  L-arginine biosynthetic process via ornithine
  so that " L-arginine biosynthetic process via ornithine " isn't single inheritance

• add synonyms from initial comment as appropriate

[pgaudet]

What is the reference for the proposed new GO term?

[pgaudet]

The reason why the parent is missing is that arginine biosynthetic process via ornithine and GO:0006526 L-arginine biosynthetic process are not using the same for of arginine (arginine biosynthetic process via ornithine is not using L as the output).

[pgaudet]

I am not sure that 'GO:0006591 ornithine metabolic process' is a useful grouping class here.
Do we need this term? 12 EXP

[ValWood]

Ref should come from L-arginine biosynthesis III (via N-acetyl-L-citrulline)
but I have used up my daily accesses

[ValWood]

I have "ornithine metabolic process" on the list I have been compiling of pathway intermediates that don't need specific metabolism terms, so based on what I have curated so far, I would agree.

[ValWood]

This is the refernece for the proposed new term:
Acetylornithine transcarbamylase: a novel enzyme in arginine biosynthesis
PMID: 16585758
"In Xanthomonas campestris, the protein annotated as ornithine transcarbamylase, and encoded by the argF gene, is unable to synthesize citrulline directly from ornithine. We cloned and overexpressed this X. campestris gene in Escherichia coli and show that it catalyzes the formation of N-acetyl-L-citrulline from N-acetyl-L-ornithine and carbamyl phosphate. "