#7472 EC2GO, in badly need of an update

enzymes (180)
Kristian Axelsen


I have a list of ~200 EC numbers that has not been linked to GO. Do you want them all listed here or is there a place I can send them?




  • Jane Lomax
    Jane Lomax

    • labels: 795638 -->
    • assigned_to: nobody --> jl242
  • Jane Lomax
    Jane Lomax

    Hi Kristian - if you could submit your list that would be great, and I'll get to doing the updates as soon as I can. You can just attach the file to this item.



  • Dear Jane,

    You find the list below.
    If you want to see more details about all these new enzymes, you can look at:

    Should I submit a report each time new EC numbers are approved? There is currently a substantial increase in number of new EC numbers approved.



    EC momilactone-A synthase
    EC dihydrocarveol dehydrogenase
    EC limonene-1,2-diol dehydrogenase
    EC 3-hydroxypropionate dehydrogenase (NADP+)
    EC malate dehydrogenase [NAD(P)+]
    EC NADP-retinol dehydrogenase
    EC D-arabitol-phosphate dehydrogenase
    EC 2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate reductase
    EC diacetyl reductase [(R)-acetoin forming]
    EC diacetyl reductase [(S)-acetoin forming]
    EC -> and EC
    EC glycerol-3-phosphate dehydrogenase
    EC malate dehydrogenase (quinone)
    EC alcohol dehydrogenase (quinone)
    EC formate dehydrogenase-N
    EC cyclic alcohol dehydrogenase (quinone)
    EC -> EC
    EC L-sorbose 1-dehydrogenase
    EC formate dehydrogenase (acceptor)
    EC -> EC
    EC glutathione amide-dependent peroxidase
    EC -> EC
    EC 1,2-dihydroxynaphthalene dioxygenase
    EC 3,4-dihydroxyphenylalanine oxidative deaminase
    EC nitronate monooxygenase
    EC dichloroarcyriaflavin A synthase
    EC benzoyl-CoA 2,3-dioxygenase
    EC (+)-menthofuran synthase
    EC monocyclic monoterpene ketone monooxygenase
    EC epi-isozizaene 5-monooxygenase
    EC limonene 1,2-monooxygenase
    EC methanesulfonate monooxygenase
    EC 3-epi-6-deoxocathasterone 23-monooxygenase
    EC FAD-dependent urate hydroxylase
    EC methanesulfonate monooxygenase
    EC -> EC
    EC tryptophan 7-halogenase
    EC steroid 15?-monooxygenase
    EC Delta8-fatty-acid desaturase
    EC Delta11-fatty-acid desaturase
    EC Delta12-fatty-acid desaturase
    EC biflaviolin synthase
    EC ammonia monooxygenase
    EC 5,6-dimethylbenzimidazole synthase
    EC -> EC
    EC (E)-4-hydroxy-3-methylbut-2-enyl-diphosphate synthase
    EC sulfoacetaldehyde dehydrogenase
    EC malonyl CoA reductase (malonate semialdehyde-forming)
    EC succinate-semialdehyde dehydrogenase (acetylating)
    EC 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase (NADP+)
    EC 2-formylbenzoate dehydrogenase
    EC mycoredoxin
    EC 1.22 Acting on halogen in donors
    EC 1.22.1 With NAD+ or NADP+ as acceptor
    EC iodotyrosine deiodinase
    EC (+)-pulegone reductase
    EC (-)-isopiperitenone reductase
    EC acrylyl-CoA reductase (NADPH)
    EC dihydroorotate dehydrogenase
    EC phycoerythrobilin synthase
    EC -> EC
    EC 2-amino-4-deoxychorismate dehydrogenase
    EC carvone reductase
    EC primary-amine oxidase
    EC diamine oxidase
    EC 7-chloro-L-tryptophan oxidase
    EC -> EC and EC
    EC 1.4.5 with a quinone or similar compound as acceptor
    EC D-amino acid dehydrogenase (quinone)
    EC -> EC, EC, EC, EC and EC
    EC N1-acetylpolyamine oxidase
    EC polyamine oxidase (propane-1,3-diamine-forming)
    EC N8-acetylspermidine oxidase (propane-1,3-diamine-forming)
    EC spermine oxidase
    EC non-specific polyamine oxidase
    EC D-proline dehydrogenase
    EC 1.7.5 With a quinone or similar compound as acceptor
    EC nitrate reductase (quinone)
    EC glutathione amide reductase
    EC demethylmenaquinone methyltransferase
    EC demethylrebeccamycin-D-glucose O-methyltransferase
    EC methyl halide transferase
    EC deleted
    EC malonyl-S-ACP:biotin-protein carboxyltransferase
    EC N-succinylornithine carbamoyltransferase
    EC 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase
    EC tropine acyltransferase
    EC pseudotropine acyltransferase
    EC acetyl-S-ACP:malonate ACP transferase
    EC omega-hydroxypalmitate O-feruloyl transferase
    EC mycothiol synthase
    EC acetoin dehydrogenase
    EC deleted
    EC alpha,alpha-trehalose synthase
    EC mannosylfructose-phosphate synthase
    EC beta-D-galactosyl-(1->4)-L-rhamnose phosphorylase
    EC cycloisomaltooligosaccharide glucanotransferase
    EC delphinidin 3',5'-O-glucosyltransferase
    EC D-inositol-3-phosphate glycosyltransferase
    EC xylogalacturonan ?-1,3-xylosyltransferase
    EC UDP-D-xylose:?-D-glucoside beta-1,3-D-xylosyltransferase
    EC -> EC and EC
    EC quinolinate synthase
    EC O-phospho-L-seryl-tRNA:Cys-tRNA synthase
    EC 1,4-dihydroxy-2-naphthoate polyprenyltransferase
    EC tRNA dimethylallyltransferase
    EC cysteate synthase
    EC 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase
    EC 6,7-dimethyl-8-ribityllumazine synthase
    EC thermospermine synthase
    EC -> EC
    EC 7-dimethylallyltryptophan synthase
    EC 2-amino-4-deoxychorismate synthase
    EC CTP-dependent riboflavin kinase
    EC N-acetylhexosamine 1-kinase
    EC hygromycin B 4-O-kinase
    EC O-phosphoseryl-tRNASec kinase
    EC glycerate 2-kinase
    EC diguanylate cyclase
    EC malonate decarboxylase holo-[acyl-carrier protein] synthase
    EC CDP-archaeol synthase
    EC 2-phospho-L-lactate guanylyltransferase
    EC 2-phospho-L-lactate transferase
    EC arsenate-mycothiol transferase
    EC O-phospho-L-seryl-tRNASec:L-selenocysteinyl-tRNA synthase
    EC monoterpene epsilon-lactone hydrolase
    EC cocaine esterase
    EC ribonuclease E
    EC retroviral ribonuclease H
    EC phosphatidylinositol-4,5-bisphosphate 4-phosphatase
    EC mannosylfructose-phosphate phosphatase
    EC 2,3-bisphosphoglycerate 3-phosphatase
    EC cyclic-guanylate-specific phosphodiesterase
    EC 3',5'-cyclic-AMP phosphodiesterase
    EC sclareol cyclase
    EC deleted
    EC exo-1,4-beta-D-glucosaminidase
    EC futalosine hydrolase
    EC uracil-DNA glycosylase
    EC double-stranded uracil-DNA glycosylase
    EC thymine-DNA glycosylase
    EC aminopeptidase S
    EC angiotensin-converting enzyme 2
    EC Ulp1 peptidase
    EC SARS coronavirus main proteinase
    EC sortase A
    EC sortase B
    EC human endogenous retrovirus K endopeptidase
    EC HycI peptidase
    EC ADAMTS13 endopeptidase
    EC HslU--HslV peptidase
    EC (R)-amidase
    EC L-proline amide hydrolase
    EC 2-amino-5-formylamino-6-ribosylaminopyrimidin-4(3H)-one 5'-monophosphate deformylase
    EC N-acetyl-1D-myo-inositol-2-amino-2-deoxy-alpha-D-glucopyranoside deacetylase
    EC histone deacetylase
    EC fatty acid amide hydrolase
    EC Mn2+-dependent ADP-ribose/CDP-alcohol diphosphatase
    EC DNA helicase
    EC RNA helicase
    EC cyclohexane-1,2-dione hydrolase
    EC malonyl-S-ACP decarboxylase
    EC biotin-independent malonate decarboxylase
    EC biotin-dependent malonate decarboxylase
    EC peptidyl-glutamate 4-carboxylase
    EC 3-hexulose-6-phosphate synthase
    EC benzoyl-CoA-dihydrodiol lyase
    EC trans-o-hydroxybenzylidenepyruvate hydratase-aldolase
    EC (6-4)DNA photolyase
    EC spore photoproduct lyase
    EC methanogen homoaconitase
    EC UDP-N-acetylglucosamine 4,6-dehydratase (inverting)
    EC 3-hydroxypropionyl-CoA dehydratase
    EC 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
    EC 3-dehydroshikimate dehydratase
    EC enoyl-CoA hydratase 2
    EC 4-hydroxybutanoyl-CoA dehydratase
    EC ent-cassa-12,15-diene synthase
    EC ent-sandaracopimaradiene synthase
    EC ent-pimara-8(14),15-diene synthase
    EC ent-pimara-9(11),15-diene synthase
    EC levopimaradiene synthase
    EC stemar-13-ene synthase
    EC stemod-13(17)-ene synthase
    EC syn-pimara-7,15-diene synthase
    EC terpentetriene synthase
    EC epi-isozizaene synthase
    EC alpha-bisabolene synthase
    EC epi-cedrol synthase
    EC (Z)-gamma-bisabolene synthase
    EC 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase
    EC tyrosine ammonia-lyase
    EC phenylalanine ammonia-lyase
    EC phenylalanine/tyrosine ammonia-lyase
    EC chromopyrrolate synthase
    EC -> EC, EC and EC
    EC 4'-demethylrebeccamycin synthase
    EC carboxybiotin decarboxylase
    EC heme ligase
    EC hydantoin racemase
    EC 6-phospho-3-hexuloisomerase
    EC syn-copalyl diphosphate synthase
    EC terpentedienyl-diphosphate synthase
    EC halimadienyl-diphosphate synthase
    EC 2-hydroxychromene-2-carboxylate isomerase
    EC O-phosphoserine--tRNA ligase
    EC ACP-SH:acetate ligase
    EC 3-hydroxypropionyl-CoA synthase
    EC L-cysteine:1D-myo-inositol 2-amino-2-deoxy-alpha-D-glucopyranoside ligase
    EC coenzyme F420-0:L-glutamate ligase
    EC coenzyme gamma-F420-2:alpha-L-glutamate ligase
    EC tetrahydrosarcinapterin synthase
    EC coenzyme F420-1:gamma-L-glutamate ligase

  • RFoulger

    A request from Michel Schneider to make the following three a high priority if poss, as he needs GO terms for his manual paper annotation:



  • RFoulger

    • priority: 5 --> 7
  • Jane Lomax
    Jane Lomax

    Amelia's going to look into this.

  • Jane Lomax
    Jane Lomax

    • assigned_to: jl242 --> girlwithglasses
  • Hi,

    I just realised that I had missed some of the new EC numbers, so here is an additional list:
    EC abietadienal dehydrogenase
    EC geranylgeranyl diphosphate reductase
    EC abietadiene hydroxylase
    EC abietadienol hydroxylase
    EC geranylgeraniol 18-hydroxylase
    EC geranylgeranyl diphosphate diphosphatase
    EC elisabethatriene synthase
    EC aphidicolan-16?-ol synthase
    EC fusicocca-2,10(14)-diene synthase
    EC isopimara-7,15-diene synthase

    These entries are also missing from the "sup" files at the IUBMB site.


  • Here are those urgently need terms:

    EC: (two reactions)
    GO:0052579 (+)-pulegone reductase, (+)-isomenthone as substrate, activity
    GO:0052580 (+)-pulegone reductase, (-)-menthone as substrate, activity

    GO:0052581 (-)-isopiperitenone reductase activity

    GO:0052582 (+)-menthofuran synthase activity

  • EC deleted --> not in GO
    EC deleted --> already obsolete
    EC deleted --> removed EC ref, kept term as MetaCyc have an entry for that reaction

    Added new terms for the following EC categories:
    EC:1.22 - GO:0052583 oxidoreductase activity, acting on halogen in donors
    EC:1.22.1 - GO:0052584 oxidoreductase activity, acting on halogen in donors, with NAD or NADP as acceptor
    EC:1.4.5 - GO:0052585 oxidoreductase activity, acting on the CH-NH2 group of donors, with a quinone or similar compound as acceptor
    EC:1.7.5 - GO:0052586 oxidoreductase activity, acting on other nitrogenous compounds as donors, with a quinone or similar compound as acceptor

  • Hi Amelia,

    We were wondering if these are all in now? If so, would you please close this?

    Jane, Becky, Paola

  • RFoulger

    • labels: --> enzymes
  • Hi Kristian,
    Do you basically want all the EC enzymes to be in GO, or are there certain specific enzymes or reactions that you want GO to cover?

  • Hi Amelia,

    It is not my decision how the coverage should be of the EC numbers. I have just noticed that the EC2GO existed and that it had full coverage until ~June last year when it suddenly was no longer updated.

    When I - as a user - see a list called EC2GO I would by default expect it to provide full coverage, but as I said above it is not my decision if this should continue to be so. I only opened the ticket since I work with EC numbers in the Swiss-Prot group and noted that the list was not up-to-date (with the assumption it was meant to provide full coverage).



  • Jane Lomax
    Jane Lomax

    I think we should aim to add terms to GO for all EC numbers, although this is likely to be fairly onerous for us.

    Amelia - are you going to attempt to add some of these before you leave? I notice that a whole new set were added at the end of 2011 too - I'll make a new ticket for those.

  • Jane Lomax
    Jane Lomax

    • milestone: --> Uniprot
  • At the moment I am working through all the entries that have been deleted or transferred; some of the new terms I'm adding as a result are probably in the list of new EC entries. When that's done, I'll add new entries; I will get as much done as I can before I leave.

  • Enzyme activities in need of obsoletion

  • I've attached a list of the terms that need to be obsoleted for the EC update. The replacements are already in place, so it should be straightforward to do.

    All (bar possibly one?) of the EC numbers are up to date now.

    • status: open --> closed