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| This guide is for editors adding molecular function terms to represent enzyme reactions.
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| There are five websites that are particularly useful when adding reaction terms. These are:
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| *[http://www.chem.qmul.ac.uk/iubmb/enzyme/index.html EC enzyme nomenclature]
| | [[Category:GO Editors]] |
| *[http://www.ebi.ac.uk/intenz IntEnz]
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| *[http://www.genome.jp/kegg KEGG]
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| *[http://www.metacyc.org MetaCyc]
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| *[http://www.ebi.ac.uk/rhea Rhea]
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| For chemical names, one should consult [http://www.ebi.ac.uk/chebi ChEBI].
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| ==Example 1: S-(hydroxymethyl)mycothiol dehydrogenase==
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| Add a term for EC:1.1.1.306, S-(hydroxymethyl)mycothiol dehydrogenase
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| *Check the reaction does not exist in GO by search on the name (in this case, I searched for terms with 'mycothiol' in the name) and the EC number.
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| *Look up the reaction in EC (using IntEnz), MetaCyc and KEGG.
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| *IntEnz: [http://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=1.1.1.306 1.1.1.306]
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| *MetaCyc: [http://biocyc.org/META/NEW-IMAGE?type=REACTION&object=1.2.1.66-RXN 1.2.1.66-RXN]
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| *There is only one KEGG reaction for EC:1.1.1.306, [http://www.genome.jp/dbget-bin/www_bget?rn:R09129 R09129]
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| S-(Hydroxymethyl)mycothiol + NAD+ <=> S-Formylmycothiol + NADH + H+
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| ==Example 2: farnesol kinase==
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| From SourceForge:
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| definition: farnesol + an NTP = farnesol phosphate + an NDP
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| EC: 2.7.1.-
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| One example of a more specific case of this is: MetaCyc RXN-11625
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| PMID 21395888
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| PMID 10557276
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| NARROW synonym: trans,trans-farnesol kinase
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| NARROW synonym: 2-trans, 6-trans-farnesol kinase
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| *Look up the MetaCyc reaction. It's
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| 2-trans,-6-trans-farnesol + CTP = 2-trans,-6-trans-farnesyl monophosphate + CDP + H+
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| *Search GO, EC, KEGG and RHEA for farnesol. No results for reactions of a similar form.
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| *Checking the literature references, it is not clear whether the farnesol reactions are limited to the 2-trans,6-trans isomer, so we'll refer to 'farnesol' in the reaction.
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| *ChEBI searches for farnesol phosphates turn up a blank; however, "farnesyl phosphate" is a parent term for "farnesyl diphosphate" so we should use the name "farnesyl monophosphate" instead of "farnesol phosphate" to refer to the reaction product.
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| *Parentage: MetaCyc gives an EC ref of 2.7.1.- for RXN-11625; this corresponds to GO:0016773. We can have a look at the ChEBI hierarchy for "farnesyl phosphate" to get some hints as to whether there may be any generic terms under GO:0016773, but there don't seem to be any.
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| *Reaction equation: NTP and NDP are referred to in ChEBI as nucleoside triphosphate and nucleoside diphosphate.
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| name: farnesol kinase activity
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| definition: Catalysis of the reaction: farnesol + nucleoside triphosphate = farnesyl monophosphate + nucleoside diphosphate. [MetaCyc:RXN-11625]
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| synonym: "trans,trans-farnesol kinase activity" NARROW
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| xrefs: EC:2.7.1.-
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| *Add the MetaCyc reaction cited as a child of this new term. I gave it the name "2-trans,-6-trans-farnesol kinase activity" to reflect the specific substrate.
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| ==Example 3: phosphomethylethanolamine N-methyltransferase activity==
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| From SourceForge:
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| Def: Catalysis of the reaction: phosphomethylethanolamine (PMEA) + AdoMet -> phosphodimethylethanolamine
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| Ref: GOC:tb
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| PMID 20650897
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| Searching for the enzyme name brings up no results in GO, EC, MetaCyc and KEGG, so let's look up the reaction instead.
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| Look up all three compounds mentioned in MetaCyc and KEGG.
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| *KEGG contains [http://www.genome.jp/dbget-bin/www_bget?cpd:C13482 Phosphodimethylethanolamine]
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| *MetaCyc contains [http://biocyc.org/META/NEW-IMAGE?type=COMPOUND&object=S-ADENOSYLMETHIONINE AdoMet]
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| Check the reactions for these compounds.
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| *KEGG: [http://www.genome.jp/dbget-bin/www_bget?rn:R06868 R06868] looks like a match:
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| S-Adenosyl-L-methionine + N-Methylethanolamine phosphate <=>
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| S-Adenosyl-L-homocysteine + Phosphodimethylethanolamine
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| *MetaCyc: [http://biocyc.org/META/NEW-IMAGE?type=REACTION&object=RXN-5642 RXN-5642] looks like a match:
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| N-methylethanolamine phosphate + S-adenosyl-L-methionine <=>
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| N-dimethylethanolamine phosphate + S-adenosyl-L-homocysteine + H+
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| *Check that N-dimethylethanolamine phosphate (from the MetaCyc reaction) is also known as phosphodimethylethanolamine
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| **phosphodimethylethanolamine is a synonym on the MetaCyc compound page; the KEGG compound ID [http://www.genome.jp/dbget-bin/www_bget?cpd:C13482 C13482] matches that in the KEGG reaction
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| **If in doubt, search for the compound in ChEBI and check the synonyms.
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| *MetaCyc states that the reaction is one of three catalysed by EC:2.1.1.103, so go to IntEnz and look up [http://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=2.1.1.103 2.1.1.103]. Although the comments mention subsequent reactions, the reaction list doesn't, so we will use the more generic EC:2.1.1.- as a reference.
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| *Get the ChEBI names for the substances and generate a balanced equation. Check to see if the reaction is in Rhea. I looked at the [http://www.ebi.ac.uk/chebi/displayAutoXrefs.do?chebiId=CHEBI:57781 automatic xrefs for N-methylethanolamine phosphate in ChEBI] and clicked on the Rhea xrefs. [http://www.ebi.ac.uk/rhea/reaction.xhtml?id=RHEA:25322 RHEA:25322] is a match! Checking the xrefs for the Rhea reaction, they match the reactions in KEGG and MetaCyc that we found earlier.
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| *Term name: a quick Google search reveals that 'phosphomethylethanolamine N-methyltransferase' appears to be the most common name for this term.
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| *Synonyms: added the KEGG name for the reaction as an exact synonym with the scope set as 'systematic synonym'; also added a synonym using the ChEBI name for the chemical instead of phosphomethylethanolamine.
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| *Term parentage: this term can go under N-methyltransferase activity.
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| name: phosphomethylethanolamine N-methyltransferase activity
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| definition: Catalysis of the reaction: N-methylethanolamine phosphate + S-adenosyl-L-methionine = N,N-dimethylethanolamine phosphate + S-adenosyl-L-homocysteine + H(+). [RHEA:25322, KEGG:R06868, MetaCyc:RXN-5642]
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| synonym: "N-methylethanolamine phosphate N-methyltransferase activity" EXACT
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| synonym: "S-adenosyl-L-methionine:methylethanolamine phosphate N-methyltransferase activity" EXACT systematic_synonym [KEGG:R06868]
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| xref: EC:2.1.1.-
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| xref: KEGG:R06868
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| xref: MetaCyc:RXN-5642
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| xref: RHEA:25322
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