Review of amino acid catabolic process terms

[sjm41]

Spreadsheet is here.

• 1st tab is L-amino acid degradation (proteinogenic amino acids are listed first)
• 3nd tab id D-amino acid degradation

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Here's one view of the current tree (focussing on L- and D-amino acid classification):

alpha-amino acid catabolic process
|__D-amino acid catabolic process
	|__D-alanine catabolic process
	|__D-cysteine catabolic process
	|__D-leucine catabolic process
	|__D-lysine catabolic process
	|__D-serine catabolic process
	|__D-tyrosine catabolic process
	|__D-valine catabolic process
|__L-amino acid catabolic process
    |__3-cyano-L-alanine catabolic process
    |__aspartate family amino acid catabolic process
	|__asparagine catabolic process(+)
	|__aspartate catabolic process
	|__hydroxylysine catabolic process
        |__L-isoleucine catabolic process
	|__L-lysine catabolic process(+)
	|__methionine catabolic process(+)
	|__threonine catabolic process(+)
    |__discadenine catabolic process
    |__erythrose 4-phosphate/phosphoenolpyruvate family amino acid catabolic process
	|__L-phenylalanine catabolic process(+)
	|__L-tryptophan catabolic process(+)
	|__tyrosine catabolic process(+)
   |__glutamine family amino acid catabolic process(+)
	|__arginine catabolic process(+)
	|__asparagine catabolic process(+)
	|__glutamate catabolic process(+)
	|__glutamine catabolic process
	|__proline catabolic process(+)
    |__L-cysteine catabolic process(+)
    |__L-histidine catabolic process(+)
    |__L-kynurenine catabolic process
    |__L-proline betaine catabolic process
    |__L-serine catabolic process
    |__N(omega),N(omega)-dimethyl-L-arginine catabolic process
    |__N(omega)-methyl-L-arginine catabolic process
    |__N-alpha,N-alpha,N-alpha-trimethyl-L-histidine catabolic process
    |__phosphoarginine catabolic process
    |__pyruvate family amino acid catabolic process(+)
	|__L-alanine catabolic process(+)
	|__L-leucine catabolic process
	|__valine catabolic process
    |__S-adenosylhomocysteine catabolic process
|__L-tryptophan catabolic process to catechol
|__valine catabolic process to isobutanol

Note that glycine doesn't have L/D enantiomers, and so the 'serine family amino acid catabolic process' tree does not classify under 'L-amino acid catabolic process':

|__serine family amino acid catabolic process
	|__glycine catabolic process(+)
	|__homoserine catabolic process
	|__L-cysteine catabolic process(+)
	|__L-serine catabolic process
	|__selenocysteine catabolic process

[sjm41]

First batch of straightforward edits:

• arginine catabolic process (GO:0006527): change name and LD to specify L-arginine

• asparagine catabolic process (GO:0006530): change name and LD to specify L-asparagine

• aspartate catabolic process (GO:0006533): change name and LD to specify L-aspartate

• glutamate catabolic process (GO:0006538): change name and LD to specify L-glutamate

• glutamine catabolic process (GO:0006543): change name and LD to specify L-glutamine

• methionine catabolic process (GO:0009087): change name and LD to specify L-methionine

• proline catabolic process (GO:0006562): change name and LD to specify L-proline

• threonine catabolic process (GO:0006567): change name and LD to specify L-threonine & remove MetaCyc:THREOCAT-PWY superpathway xref

• tyrosine catabolic process (GO:0006572): change name and LD to specify L-tyrosine

• L-histidine catabolic process to glutamate and formate (GO:0019557): Add MetaCyc:PWY-5028 xref

• methionine catabolic process to 3-methylthiopropanol (GO:0000951): Add PWY-5082 xref

• L-tryptophan catabolic process to catechol (GO:0019444): Change LD to specify 'L-tryptophan zwitterion'

• valine catabolic process to isobutanol (GO:1902697): Add MetaCyc:PWY-5057 xref & change LD to specify 'L-valine zwitterion'

• homoserine catabolic process (GO:0009091): Remove HOMOCYSDEGR-PWY (that's for homocysteine degradation)

• methionine catabolic process to succinyl-CoA (GO:0019457): change name and LD to specify L-methionine

• methionine catabolic process to 3-methylthiopropanol (GO:0000951): change name and LD to specify L-methionine

• methionine catabolic process to 3-methylthiopropanoate (GO:0000954): change name and LD to specify L-methionine

• glutamate catabolic process to aspartate (GO:0019550): change name and LD to specify L-glutamate

• glutamate catabolic process to butyrate (GO:0033508): change name and LD to specify L-glutamate

• glutamate catabolic process to ornithine (GO:0019555): change name and LD to specify L-glutamate

• glutamate catabolic process to propionate (GO:0033509): change name and LD to specify L-glutamate

• gamma-aminobutyrate shunt (GO:0006540): change LD to specify L-glutamate

• citrulline catabolic process (GO:0019241): change LD to specify L-citrulline

• arginine catabolic process to succinate (GO:0019545): change LD to specify L-arginine

• arginine catabolic process to proline (GO:0019493): change LD to specify L-arginine

• arginine catabolic process to glutamate (GO:0019544): change LD to specify L-arginine

• glutamate catabolic process via 2-hydroxyglutarate (GO:0019552): add LD

• anaerobic glutamate catabolic process (GO:0019670): change name and LD to specify L-glutamate

• 4-hydroxyproline catabolic process (GO:0019470): change LD to specify 4-hydroxy-L-proline

• histidine catabolic process to imidazol-5-yl-lactate (GO:0019559): change name to specify L-histidine

• histidine catabolic process to hydantoin-5-propionate (GO:0019560): change name to specify L-histidine

• glutamate catabolic process to 4-hydroxybutyrate (GO:0036241): remove PWY-4321 from def and synonym because its obsolete

• glutamate catabolic process via L-citramalate (GO:0019553): change name to specify L-glutamate

• arginine deiminase pathway (GO:0019546): change name and add LD to specify L-arginine

• tyrosine catabolic process to fumarate (GO:0019445): change name to specify L-tyrosine

• anaerobic phenylalanine oxidation (GO:0019561): change name to specify L-phenylalanine

• methionine catabolic process via 2-oxobutanoate (GO:0019458): change name and LD to specify L-methionine

• asparagine catabolic process via 2-oxosuccinamate (GO:0033346): change name and LD to specify L-asparagine

• asparagine catabolic process via L-aspartate (GO:0033345): change name and LD to specify L-asparagine

• proline catabolic process to glutamate (GO:0010133): change name and LD to specify L-proline

• glycine decarboxylation via glycine cleavage system (GO:0019464): give LD

(changes from unspecified enantiomer to L-specific form are based on the given MetaCyc xref)