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Terms sharing the same KEGG_REACTION xref #28133

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sjm41 opened this issue Jun 14, 2024 · 8 comments
Closed

Terms sharing the same KEGG_REACTION xref #28133

sjm41 opened this issue Jun 14, 2024 · 8 comments
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sjm41 commented Jun 14, 2024

xref: KEGG_REACTION:R02368
id: GO:0047376name: all-trans-retinyl-palmitate hydrolase, all-trans-retinol forming activity
id: GO:0050253name: retinyl-palmitate esterase activity

xref: KEGG_REACTION:R04556
id: GO:0036132name: 13-prostaglandin reductase activity
id: GO:0047522name: 15-oxoprostaglandin 13-oxidase activity
 
 
xref: KEGG_REACTION:R04557
id: GO:0036132name: 13-prostaglandin reductase activity
id: GO:0047522name: 15-oxoprostaglandin 13-oxidase activity
 
 
xref: KEGG_REACTION:R05779
id: GO:0052842name: inositol diphosphate pentakisphosphate diphosphatase activity
id: GO:0052845name: inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity
 
 
xref: KEGG_REACTION:R06722
id: GO:0004571name: mannosyl-oligosaccharide 1,2-alpha-mannosidase activity
id: GO:0036509name: trimming of terminal mannose on B branch
 
 
xref: KEGG_REACTION:R06847
id: GO:0052734name: shikimate 3-dehydrogenase (NAD+) activity
id: GO:0004764name: shikimate 3-dehydrogenase (NADP+) activity
 
 
xref: KEGG_REACTION:R07233
id: GO:0052911name: 23S rRNA (guanine(745)-N(1))-methyltransferase activity
id: GO:0052912name: 23S rRNA (guanine(748)-N(1))-methyltransferase activity
 
 
xref: KEGG_REACTION:R07234
id: GO:0052913name: 16S rRNA (guanine(966)-N(2))-methyltransferase activity
id: GO:0052914name: 16S rRNA (guanine(1207)-N(2))-methyltransferase activity
id: GO:0052915name: 23S rRNA (guanine(2445)-N(2))-methyltransferase activity
id: GO:0052916name: 23S rRNA (guanine(1835)-N(2))-methyltransferase activity

xref: KEGG_REACTION:R07288
id: GO:0036443name: dermatan 6-sulfotransferase activity
id: GO:0050659name: N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase activity
@sjm41 sjm41 self-assigned this Jun 14, 2024
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sjm41 commented Jun 14, 2024 •
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xref: KEGG_REACTION:R02368
id: GO:0047376name: all-trans-retinyl-palmitate hydrolase, all-trans-retinol forming activity
id: GO:0050253name: retinyl-palmitate esterase activity

R02368
Retinyl palmitate + H2O <=> Retinol + Hexadecanoic acid

id: GO:0050253
name: retinyl-palmitate esterase activity
namespace: molecular_function
def: "Catalysis of the reaction: retinyl palmitate + H2O = retinol + palmitate + H+." [RHEA:21508]
synonym: "retinyl ester hydrolase activity" RELATED []
synonym: "retinyl palmitate hydrolase activity" RELATED []
synonym: "retinyl palmitate hydrolyase activity" RELATED []
synonym: "retinyl-palmitate palmitohydrolase activity" RELATED []
xref: KEGG_REACTION:R02368
xref: MetaCyc:RETINYL-PALMITATE-ESTERASE-RXN
xref: RHEA:21508
is_a: GO:0052689 ! carboxylic ester hydrolase activity

RHEA:21508
all-trans-retinyl hexadecanoate + H2O = H(+) + hexadecanoate + retinol
=> RHEA does not map to R02368

id: GO:0047376
name: all-trans-retinyl-palmitate hydrolase, all-trans-retinol forming activity
namespace: molecular_function
def: "Catalysis of the reaction: all-trans-retinyl palmitate + H2O = all-trans-retinol + H+ + palmitate." [RHEA:13933]
synonym: "all-trans-retinyl-palmitate acylhydrolase activity" BROAD []
synonym: "all-trans-retinyl-palmitate hydrolase activity" BROAD []
synonym: "retinyl-palmitate palmitohydrolase activity" BROAD [KEGG_REACTION:R02368]
xref: KEGG_REACTION:R02368
xref: MetaCyc:3.1.1.64-RXN
xref: RHEA:13933
is_a: GO:0050253 ! retinyl-palmitate esterase activity
is_a: GO:0052689 ! carboxylic ester hydrolase activity

RHEA:13933
all-trans-retinyl hexadecanoate + H2O = all-trans-retinol + H(+) + hexadecanoate
=> RHEA maps to R02368

  • remove R02368 from GO:0050253
  • also remove redundant GO:0052689 parent on GO:0047376

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sjm41 commented Jun 14, 2024 •
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xref: KEGG_REACTION:R04556
id: GO:0036132name: 13-prostaglandin reductase activity
id: GO:0047522name: 15-oxoprostaglandin 13-oxidase activity

xref: KEGG_REACTION:R04557
id: GO:0036132name: 13-prostaglandin reductase activity
id: GO:0047522name: 15-oxoprostaglandin 13-oxidase activity

R04556 is:
(5Z)-11alpha-Hydroxy-9,15-dioxoprostanoate + NAD+ <=> (5Z,13E)-11alpha-Hydroxy-9,15-dioxoprost-5,13-dienoate + NADH + H+

R04557 is:
(5Z)-11alpha-Hydroxy-9,15-dioxoprostanoate + NADP+ <=> (5Z,13E)-11alpha-Hydroxy-9,15-dioxoprost-5,13-dienoate + NADPH + H+

id: GO:0036132 (5 EXP annotations: human PTGR1 and orthologs)
name: 13-prostaglandin reductase activity
namespace: molecular_function
def: "Catalysis of the reaction: 15-keto-prostaglandin + NAD(P)H + H+ -> 13,14-dihydro-15-keto-prostaglandin + NAD(P)+. This reaction is the reduction of 15-keto-prostaglandin." [EC:1.3.1.48, GOC:mw, KEGG_REACTION:R04556, KEGG_REACTION:R04557, PMID:17449869]
comment: Note that this is the reverse of the reaction described in '15-oxoprostaglandin 13-oxidase activity ; GO:0047522'.
synonym: "15-ketoprostaglandin delta13-reductase activity" RELATED [EC:1.3.1.48]
synonym: "15-oxo-delta13-prostaglandin reductase activity" RELATED [EC:1.3.1.48]
synonym: "15-oxoprostaglandin 13-reductase activity" EXACT []
synonym: "delta13-15-ketoprostaglandin reductase activity" RELATED [EC:1.3.1.48]
synonym: "prostaglandin 13-reductase activity" RELATED [EC:1.3.1.48]
synonym: "prostaglandin delta13-reductase activity" RELATED [EC:1.3.1.48]
xref: EC:1.3.1.48
xref: KEGG_REACTION:R04556
xref: KEGG_REACTION:R04557
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor

id: GO:0047522 (1 EXP annotation: human PTGR2)
name: 15-oxoprostaglandin 13-oxidase activity
namespace: molecular_function
def: "Catalysis of the reaction: (5Z)-(15S)-11-alpha-hydroxy-9,15-dioxoprostanoate + NAD(P)+ -> (5Z)-(15S)-11-alpha-hydroxy-9,15-dioxoprosta-13-enoate + NAD(P)H + H+." [EC:1.3.1.48, KEGG_REACTION:R04556, KEGG_REACTION:R04557, MetaCyc:15-OXOPROSTAGLANDIN-13-REDUCTASE-RXN]
comment: Note that this is the reverse of the reaction described in '13-prostaglandin reductase activity ; GO:0036132'.
synonym: "(5Z)-(15S)-11alpha-hydroxy-9,15-dioxoprostanoate:NAD(P)+ delta13-oxidoreductase activity" RELATED [EC:1.3.1.48]
xref: EC:1.3.1.48
xref: KEGG_REACTION:R04556
xref: KEGG_REACTION:R04557
xref: MetaCyc:15-OXOPROSTAGLANDIN-13-REDUCTASE-RXN
is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor

EC:1.3.1.48 is:

Name: 15-oxoprostaglandin 13-reductase
AKA: 15-oxo-Delta(13)-prostaglandin reductase, prostaglandin 13-reductase
Reactions:
13,14-dihydro-15-oxo-prostaglandin E2 + NADP(+) <=> 15-oxoprostaglandin E2 + H(+) + NADPH
13,14-dihydro-15-oxo-prostaglandin E2 + NAD(+) <=> 15-oxoprostaglandin E2 + H(+) + NADH

mapped to RHEA:11912 and RHEA:11916

This looks like a GO merge - will make separate ticket. #28134

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sjm41 commented Jun 14, 2024 •
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xref: KEGG_REACTION:R05779
id: GO:0052842name: inositol diphosphate pentakisphosphate diphosphatase activity
id: GO:0052845name: inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity

R05779:
5-PP-InsP5 + H2O <=> Phytic acid + Orthophosphate

id: GO:0052842
name: inositol diphosphate pentakisphosphate diphosphatase activity
namespace: molecular_function
def: "Catalysis of the reaction: diphospho-1D-myo-inositol pentakisphosphate + H2O = 1D-myo-inositol hexakisphosphate + phosphate." [PMID:10827188, PMID:11502751]
xref: KEGG_REACTION:R05779
is_a: GO:0008486 ! diphosphoinositol-polyphosphate diphosphatase activity

id: GO:0052845
name: inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity
namespace: molecular_function
def: "Catalysis of the reaction: 5-diphospho-1D-myo-inositol 1,2,3,4,6-pentakisphosphate + H2O = 1D-myo-inositol 1,2,3,4,5,6-hexakisphosphate + phosphate + H+." [PMID:10827188, PMID:11502751, RHEA:22384]
xref: KEGG_REACTION:R05779
xref: MetaCyc:RXN-10964
xref: RHEA:22384
is_a: GO:0052842 ! inositol diphosphate pentakisphosphate diphosphatase activity

These should be merged - make new ticket. #28135

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sjm41 commented Jun 14, 2024 •
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xref: KEGG_REACTION:R06722
id: GO:0004571name: mannosyl-oligosaccharide 1,2-alpha-mannosidase activity
id: GO:0036509name: trimming of terminal mannose on B branch

id: GO:0004571
name: mannosyl-oligosaccharide 1,2-alpha-mannosidase activity
namespace: molecular_function
def: "Catalysis of the hydrolysis of the terminal (1->2)-linked alpha-D-mannose residues in an oligo-mannose oligosaccharide." [GOC:bf, PMID:25092655]
synonym: "1,2-alpha-mannosidase" RELATED [EC:3.2.1.113]
synonym: "1,2-alpha-mannosyl-oligosaccharide alpha-D-mannohydrolase activity" RELATED [EC:3.2.1.113]
synonym: "exo-alpha-1,2-mannanase activity" RELATED [EC:3.2.1.113]
synonym: "glycoprotein processing mannosidase I" RELATED [EC:3.2.1.113]
synonym: "Man9-mannosidase activity" NARROW [EC:3.2.1.113]
synonym: "ManI activity" NARROW [EC:3.2.1.113]
synonym: "mannose-9 processing alpha-mannosidase activity" NARROW [EC:3.2.1.113]
synonym: "mannosidase 1A activity" NARROW [EC:3.2.1.113]
synonym: "mannosidase 1B activity" NARROW [EC:3.2.1.113]
synonym: "mannosidase I" RELATED [EC:3.2.1.113]
xref: EC:3.2.1.113
xref: KEGG_REACTION:R05982
xref: KEGG_REACTION:R06722
xref: MetaCyc:RXN-18910
xref: MetaCyc:RXN-18911

id: GO:0036509
name: trimming of terminal mannose on B branch
namespace: biological_process
def: "The removal of an alpha-1,2-linked mannose from the B-chain of a glycoprotein oligosaccharide in the endoplasmic reticulum." [GOC:bf, GOC:PARL, KEGG_REACTION:R06722, PMID:22160784]
comment: Consider also annotating to 'mannosyl-oligosaccharide 1,2-alpha-mannosidase activity ; GO:0004571'.
subset: gocheck_do_not_annotate
synonym: "conversion of (Man)9(GlcNAc)2 to (Man)8B(GlcNAc)2" RELATED [PMID:22160784]
synonym: "conversion of M9 to M8B" RELATED [PMID:25092655]
synonym: "glycoprotein mannose trimming on B branch" EXACT [GOC:bf]
xref: KEGG_REACTION:R06722
is_a: GO:1904380 ! endoplasmic reticulum mannose trimming

  • remove KEGG_REACTION term and def xref from the GO:0036509 BP term
  • add RHEA:56008 and RHEA:56028 as narrowMatch xrefs on GO:0004571
  • remove KEGG_REACTION:R05982 xref from GO:0004571 (obsolete at KEGG - let RHEA know)
  • remove KEGG_REACTION: R06722 xref from GO:0004571 - mapped to EC:3.2.1.209 by KEGG. Replace with R12479 (mapped to EC:3.2.1.113)

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sjm41 commented Jun 14, 2024 •
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xref: KEGG_REACTION:R06847
id: GO:0052734name: shikimate 3-dehydrogenase (NAD+) activity
id: GO:0004764name: shikimate 3-dehydrogenase (NADP+) activity

R06847 is:
Shikimate + NAD+ <=> 3-Dehydroshikimate + NADH + H+

id: GO:0052734
name: shikimate 3-dehydrogenase (NAD+) activity
namespace: molecular_function
def: "Catalysis of the reaction: shikimate + NAD+ = 3-dehydroshikimate + NADH + H+." [RHEA:17741]
synonym: "3-dehydroshikimate reductase activity" RELATED [EC:1.1.1.25]
synonym: "3-dehydroshikimic reductase activity" RELATED [EC:1.1.1.25]
synonym: "dehydroshikimic reductase activity" BROAD [EC:1.1.1.25]
synonym: "DHS reductase activity" BROAD [EC:1.1.1.25]
synonym: "shikimate oxidoreductase activity" BROAD [EC:1.1.1.25]
synonym: "shikimate:NAD(P)(+) 3-oxidoreductase activity" RELATED [EC:1.1.1.25]
synonym: "shikimate:NAD(P)(+) oxidoreductase activity" BROAD [EC:1.1.1.25]
xref: EC:1.1.1.282
xref: KEGG_REACTION:R06847
xref: RHEA:17741
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor

id: GO:0004764
name: shikimate 3-dehydrogenase (NADP+) activity
namespace: molecular_function
def: "Catalysis of the reaction: shikimate + NADP+ = 3-dehydroshikimate + NADPH + H+." [EC:1.1.1.25]
synonym: "5-dehydroshikimate reductase activity" RELATED [EC:1.1.1.25]
synonym: "5-dehydroshikimic reductase activity" RELATED [EC:1.1.1.25]
synonym: "dehydroshikimic reductase activity" BROAD [EC:1.1.1.25]
synonym: "DHS reductase activity" BROAD [EC:1.1.1.25]
synonym: "shikimate oxidoreductase activity" BROAD [EC:1.1.1.25]
synonym: "shikimate:NADP(+) 5-oxidoreductase activity" RELATED [EC:1.1.1.25]
synonym: "shikimate:NADP(+) oxidoreductase activity" BROAD [EC:1.1.1.25]
xref: EC:1.1.1.25
xref: EC:1.1.1.282
xref: KEGG_REACTION:R06847
xref: MetaCyc:SHIKIMATE-5-DEHYDROGENASE-RXN
xref: RHEA:17737
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor

  • change KEGG xref on GO:0004764 to R02413
  • EC:1.1.1.282 is an xref on 4 terms - these should all be broadMatch
  • EC:1.1.1.25 should be exactMatch on GO:0004764

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sjm41 commented Jun 14, 2024 •
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xref: KEGG_REACTION:R07233
id: GO:0052911name: 23S rRNA (guanine(745)-N(1))-methyltransferase activity
id: GO:0052912name: 23S rRNA (guanine(748)-N(1))-methyltransferase activity

R07233:
S-Adenosyl-L-methionine + rRNA <=> S-Adenosyl-L-homocysteine + rRNA containing N1-methylguanine
Comment | general reaction: The enzyme ec 2.1.1.187 specifically methylates guanine745 at N1 in 23S rRNA.The enzyme ec 2.1.1.188 specifically methylates guanine748 at N1 in 23S rRNA.

name: 23S rRNA (guanine(745)-N(1))-methyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: S-adenosyl-L-methionine + guanine(745) in 23S rRNA = N(1)-methylguanine(745) in 23S rRNA + S-adenosyl-L-homocysteine." [EC:2.1.1.187]
synonym: "23S rRNA m(1)G(745) methyltransferase activity" RELATED [EC:2.1.1.187]
synonym: "ribosomal ribonucleate guanine 1-methyltransferase activity" BROAD [EC:2.1.1.187]
synonym: "ribosomal RNA(m(1)G)-methylase activity" BROAD [EC:2.1.1.187]
synonym: "rlmA(I) methyltransferase activity" BROAD [EC:2.1.1.187]
synonym: "rRNA(m(1)G)methylase activity" BROAD [EC:2.1.1.187]
synonym: "S-adenosyl-L-methionine:rRNA (guanine-1-N-)-methyltransferase activity" BROAD [EC:2.1.1.187]
xref: EC:2.1.1.187
xref: KEGG_REACTION:R07233
xref: MetaCyc:RXN-11573
xref: RHEA:42900
is_a: GO:0008989 ! rRNA (guanine-N1-)-methyltransferase activity

id: GO:0052912
name: 23S rRNA (guanine(748)-N(1))-methyltransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: S-adenosyl-L-methionine + guanine(748) in 23S rRNA = N(1)-methylguanine(748) in 23S rRNA + S-adenosyl-L-homocysteine." [EC:2.1.1.188]
synonym: "23S rRNA m(1)G(748) methyltransferase activity" BROAD [EC:2.1.1.188]
xref: EC:2.1.1.188
xref: KEGG_REACTION:R07233
xref: MetaCyc:RXN-11599
xref: RHEA:42904
is_a: GO:0008989 ! rRNA (guanine-N1-)-methyltransferase activity

  • Delete KEGG xref from these two GO terms and add to parent instead:
    id: GO:0008989
    name: rRNA (guanine-N1-)-methyltransferase activity
    namespace: molecular_function
    def: "Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing N1-methylguanine." [GOC:curators]
    synonym: "ribosomal ribonucleate guanine 1-methyltransferase activity" EXACT []
    synonym: "S-adenosyl-L-methionine:rRNA (guanine-1-N-)-methyltransferase activity" EXACT []
    synonym: "S-adenosyl-L-methionine:rRNA (guanine-N1-)-methyltransferase activity" RELATED []
    is_a: GO:0008170 ! N-methyltransferase activity
    is_a: GO:0016435 ! rRNA (guanine) methyltransferase activity

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sjm41 commented Jun 14, 2024 •
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xref: KEGG_REACTION:R07234
id: GO:0052913name: 16S rRNA (guanine(966)-N(2))-methyltransferase activity
id: GO:0052914name: 16S rRNA (guanine(1207)-N(2))-methyltransferase activity
id: GO:0052915name: 23S rRNA (guanine(2445)-N(2))-methyltransferase activity
id: GO:0052916name: 23S rRNA (guanine(1835)-N(2))-methyltransferase activity

R07234:
S-Adenosyl-L-methionine + rRNA <=> S-Adenosyl-L-homocysteine + rRNA containing N2-methylguanine
Comment | general reaction:
The enzyme ec 2.1.1.171 specifically methylates guanine966 at N2 in 16S rRNA.
The enzyme ec 2.1.1.172 specifically methylates guanine1207 at N2 in 16S rRNA.
The enzyme ec 2.1.1.173 specifically methylates guanine2445 at N2 in 23S rRNA.
The enzyme ec 2.1.1.174 specifically methylates guanine1835 at N2 in 23S rRNA.

  • Remove KEGG xref from these 4 terms and add to parent instead:
    id: GO:0008990
    name: rRNA (guanine-N2-)-methyltransferase activity
    namespace: molecular_function
    def: "Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing N2-methylguanine." [PMID:17389639]
    synonym: "ribosomal ribonucleate guanine-2-methyltransferase activity" RELATED []
    synonym: "S-adenosyl-L-methionine:rRNA (guanine-2-N-)-methyltransferase activity" RELATED []
    synonym: "S-adenosyl-L-methionine:rRNA (guanine-N2-)-methyltransferase activity" RELATED []
    is_a: GO:0008170 ! N-methyltransferase activity
    is_a: GO:0016435 ! rRNA (guanine) methyltransferase activity
    property_value: term_tracker_item "Obsolete & transferred ECs 2021-05-11 #21412" xsd:anyURI

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sjm41 commented Jun 14, 2024 •
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xref: KEGG_REACTION:R07288
id: GO:0036443name: dermatan 6-sulfotransferase activity
id: GO:0050659name: N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase activity

R07288 is
3'-Phosphoadenylyl sulfate + Dermatan <=> Adenosine 3',5'-bisphosphate + Dermatan 6'-sulfate

id: GO:0036443
name: dermatan 6-sulfotransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: 3'-phosphoadenylyl sulfate + dermatan = adenosine 3',5'-bisphosphate + dermatan 6'-sulfate." [EC:2.8.2.33, GOC:bf, KEGG_REACTION:R07288]
xref: KEGG_REACTION:R07288
is_a: GO:0008146 ! sulfotransferase activity

id: GO:0050659
name: N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase activity
namespace: molecular_function
def: "Catalysis of the reactions: 3'-phosphoadenylyl sulfate + dermatan = adenosine 3',5'-bisphosphate + dermatan 6'-sulfate and 3'-phosphoadenylyl sulfate + chondroitin = adenosine 3',5'-bisphosphate + chondroitin 6'-sulfate." [EC:2.8.2.33]
comment: Consider instead annotating to the individual reactions: 'chondroitin 6-sulfotransferase activity ; GO:0008459' and 'dermatan 6-sulfotransferase activity ; GO:0036443'.
synonym: "3'-phosphoadenylyl-sulfate:dermatan 6'-sulfotransferase activity" RELATED [EC:2.8.2.33]
synonym: "GalNAc4S-6ST" RELATED [EC:2.8.2.33]
synonym: "N-acetylgalactosamine 4-sulfate 6-O-sulphotransferase activity" RELATED [EC:2.8.2.33]
xref: EC:2.8.2.33
xref: KEGG_REACTION:R02181
xref: KEGG_REACTION:R07288
xref: MetaCyc:RXN-7953
xref: MetaCyc:RXN-7954
is_a: GO:0008146 ! sulfotransferase activity

This is a bit complicated - make new ticket. #28136

@sjm41 sjm41 closed this as completed in b9cc8d2 Jun 14, 2024
sjm41 added a commit that referenced this issue Jun 14, 2024
@sjm41
Merge pull request #28140 from geneontology/issue-28133
c23f9e0 
Fixing KEGG reaction duplicates. Fixes #28133
@sjm41 sjm41 mentioned this issue Jun 14, 2024
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