GO term name and textual definition update: GO:0051164 (L-xylitol metabolic process and children)

[rozaru]

xylitol is a meso compound, thus there is no L or D-versions. Although there are incorectly used in some publications. "Meso compounds are achiral compounds that have multiple chiral centers. It is superimposed on its mirror image and is optically inactive despite its stereocenters"

• GO term ID and label for which you request a definition update

• GO:0051164: L-xylitol metabolic process

• New proposed definition (genus-differentia pattern, plus additional information if needed)

• Name: xylitol metabolic process

• Def: The chemical reactions and pathways involving xylitol, a five-carbon sugar alcohol derived from xylose by reduction of the carbonyl group. It is as sweet as sucrose and is used as a non-cariogenic sweetener and as a sugar substitute in diabetic diets.

• see L-xylitol in synonyms as well

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• GO term ID and label for which you request a definition update

• GO:0051160: L-xylitol catabolic process

• New proposed definition (genus-differentia pattern, plus additional information if needed)

• Name: xylitol catabolic process

• Def: The chemical reactions and pathways resulting in the breakdown of xylitol, a five-carbon sugar alcohol derived from xylose by reduction of the carbonyl group.

• see L-xylitol in synonyms as well

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• GO term ID and label for which you request a definition update

• GO:0019697: L-xylitol catabolic process to xylulose 5-phosphate

• New proposed definition (genus-differentia pattern, plus additional information if needed)

• Name: xylitol catabolic process to xylulose 5-phosphate

• Def: The chemical reactions and pathways resulting in the breakdown of xylitol to form xylulose 5-phosphate.

• Add: xref: MetaCyc:PWY-8393

• see L-xylitol in synonyms as well

• Additional information

• The last sentence of the definition has been removed as it does not describe the pathway in MetaCyc that has been used as a reference for the definition.

[rozaru]

@pgaudet, thanks for updating the terms. I am sorry to reopen the tickets but it looks like the changes for GO:0019697 didn't go through (only the comment has been added)

New proposed definition (genus-differentia pattern, plus additional information if needed) Name: xylitol catabolic process to D-xylulose 5-phosphate Def: The chemical reactions and pathways resulting in the breakdown of xylitol to form D-xylulose 5-phosphate.

Add: xref: MetaCyc:PWY-8393 Change xref to intersection_of: has_primary_output CHEBI:57737 ! D-xylulose 5-phosphate(2-)

see L-xylitol in synonyms as well

Additional information The last sentence of the definition has been removed as it does not describe the pathway in MetaCyc that has been used as a reference for the definition.

[rozaru]

Looking at the other xylulose 5-phosphate metabolic process terms, I was wondering if it would be worth to replace all the xylulose 5-phosphate instances with the D-xylulose 5-phosphate form.

It looks like the L form is found in Bacteria where it is an intermediate in the production of D-xylulose 5-phosphate (PMID: 18849419).

Suggested changes:

GO:0051167
D-xylulose 5-phosphate metabolic process The chemical reactions and pathways involving D-xylulose 5-phosphate, a derivative of the ketopentose xylulose phosphorylated at the 5 carbon; it is an intermediate in the pentose phosphate pathway. has_primary_output CHEBI:57737 ! D-xylulose 5-phosphate(2-)

GO:1901159
D-xylulose 5-phosphate biosynthetic process The chemical reactions and pathways resulting in the formation of D-xylulose 5-phosphate. [GOC:bf, GOC:TermGenie]
has_primary_output CHEBI:57737 ! D-xylulose 5-phosphate(2-)

GO:0019569
L-arabinose catabolic process to D-xylulose 5-phosphate The chemical reactions and pathways resulting in the breakdown of L-arabinose into D-xylulose 5-phosphate. [GOC:go_curators] has_primary_output CHEBI:57737 ! D-xylulose 5-phosphate(2-)

GO:0019590 L-arabitol catabolic process to D-xylulose 5-phosphate The chemical reactions and pathways resulting in the breakdown of L-arabitol to form D-xylulose 5-phosphate. L-arabitol is converted into L-xylulose, which is then phosphorylated to L-xylulose-5-phosphate. This is converted to D-xylulose-5-phosphate via the intermediate L-ribulose-5-phosphate. [GOC:curators] has_primary_output CHEBI:57737 ! D-xylulose 5-phosphate(2-)

GO:0019528 D-arabitol catabolic process to D-xylulose 5-phosphate The chemical reactions and pathways resulting in the breakdown of D-arabitol to form D-xylulose 5-phosphate. D-arabitol is converted into D-xylulose, which is then phosphorylated to form D-xylulose-5-phosphate. [MetaCyc:DARABITOLUTIL-PWY] has_primary_output CHEBI:57737 ! D-xylulose 5-phosphate(2-)

GO:0019488 ribitol catabolic process to D-xylulose 5-phosphate The chemical reactions and pathways resulting in the breakdown of ribitol to form D-xylulose 5-phosphate. Ribitol is initially converted to D-ribulose, which is phosphorylated to form D-ribulose 5-phosphate, which is then converted into D-xylulose 5-phosphate. [MetaCyc:RIBITOLUTIL-PWY]
has_primary_output CHEBI:57737 ! D-xylulose 5-phosphate(2-)

GO:0019573 D-arabinose catabolic process to D-xylulose 5-phosphate The chemical reactions and pathways resulting in the breakdown of D-arabinose to form D-xylulose 5-phosphate. D-arabinose is converted into D-ribulose, which is phosphorylated to D-ribulose-5-phosphate, which is isomerized to give D-xylulose-5-phosphate. has_primary_output CHEBI:57737 ! D-xylulose 5-phosphate(2-)