#7472 EC2GO, in badly need of an update

Uniprot
closed
enzymes (180)
7
2012-04-19
2010-06-18
Kristian Axelsen
No

Hi,

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?

Regards,

Kristian
kristian.axelsen@isb-sib.ch

Discussion

  • Jane Lomax
    Jane Lomax
    2010-07-07

    • labels: 795638 -->
    • assigned_to: nobody --> jl242
     
  • Jane Lomax
    Jane Lomax
    2010-07-07

    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.

    thanks,

    Jane

     
  • Dear Jane,

    You find the list below.
    If you want to see more details about all these new enzymes, you can look at:
    http://www.chem.qmul.ac.uk/iubmb/enzyme/supplements/sup2008/
    http://www.chem.qmul.ac.uk/iubmb/enzyme/supplements/sup2009/
    http://www.chem.qmul.ac.uk/iubmb/enzyme/supplements/sup2010/

    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.

    Regards,

    Kristian

    EC 1.1.1.295 momilactone-A synthase
    EC 1.1.1.296 dihydrocarveol dehydrogenase
    EC 1.1.1.297 limonene-1,2-diol dehydrogenase
    EC 1.1.1.298 3-hydroxypropionate dehydrogenase (NADP+)
    EC 1.1.1.299 malate dehydrogenase [NAD(P)+]
    EC 1.1.1.300 NADP-retinol dehydrogenase
    EC 1.1.1.301 D-arabitol-phosphate dehydrogenase
    EC 1.1.1.302 2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate reductase
    EC 1.1.1.303 diacetyl reductase [(R)-acetoin forming]
    EC 1.1.1.304 diacetyl reductase [(S)-acetoin forming]
    EC 1.1.1.5 -> 1.1.1.303 and EC 1.1.1.304
    EC 1.1.5.3 glycerol-3-phosphate dehydrogenase
    EC 1.1.5.4 malate dehydrogenase (quinone)
    EC 1.1.5.5 alcohol dehydrogenase (quinone)
    EC 1.1.5.6 formate dehydrogenase-N
    EC 1.1.5.7 cyclic alcohol dehydrogenase (quinone)
    EC 1.1.99.16 -> EC 1.1.5.4
    EC 1.1.99.32 L-sorbose 1-dehydrogenase
    EC 1.1.99.33 formate dehydrogenase (acceptor)
    EC 1.1.99.5 -> EC 1.1.5.3
    EC 1.11.1.17 glutathione amide-dependent peroxidase
    EC 1.13.11.32 -> EC 1.13.12.16
    EC 1.13.11.56 1,2-dihydroxynaphthalene dioxygenase
    EC 1.13.12.15 3,4-dihydroxyphenylalanine oxidative deaminase
    EC 1.13.12.16 nitronate monooxygenase
    EC 1.13.12.17 dichloroarcyriaflavin A synthase
    EC 1.14.12.21 benzoyl-CoA 2,3-dioxygenase
    EC 1.14.13.104 (+)-menthofuran synthase
    EC 1.14.13.105 monocyclic monoterpene ketone monooxygenase
    EC 1.14.13.106 epi-isozizaene 5-monooxygenase
    EC 1.14.13.107 limonene 1,2-monooxygenase
    EC 1.14.13.111 methanesulfonate monooxygenase
    EC 1.14.13.112 3-epi-6-deoxocathasterone 23-monooxygenase
    EC 1.14.13.113 FAD-dependent urate hydroxylase
    EC 1.14.14.6 methanesulfonate monooxygenase
    EC 1.14.14.6 -> EC 1.14.13.111
    EC 1.14.14.7 tryptophan 7-halogenase
    EC 1.14.15.8 steroid 15?-monooxygenase
    EC 1.14.19.4 Delta8-fatty-acid desaturase
    EC 1.14.19.5 Delta11-fatty-acid desaturase
    EC 1.14.19.6 Delta12-fatty-acid desaturase
    EC 1.14.21.7 biflaviolin synthase
    EC 1.14.99.39 ammonia monooxygenase
    EC 1.14.99.40 5,6-dimethylbenzimidazole synthase
    EC 1.17.4.3 -> EC 1.17.7.1
    EC 1.17.7.1 (E)-4-hydroxy-3-methylbut-2-enyl-diphosphate synthase
    EC 1.2.1.73 sulfoacetaldehyde dehydrogenase
    EC 1.2.1.75 malonyl CoA reductase (malonate semialdehyde-forming)
    EC 1.2.1.76 succinate-semialdehyde dehydrogenase (acetylating)
    EC 1.2.1.77 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase (NADP+)
    EC 1.2.1.78 2-formylbenzoate dehydrogenase
    EC 1.20.4.3 mycoredoxin
    EC 1.22 Acting on halogen in donors
    EC 1.22.1 With NAD+ or NADP+ as acceptor
    EC 1.22.1.1 iodotyrosine deiodinase
    EC 1.3.1.81 (+)-pulegone reductase
    EC 1.3.1.82 (-)-isopiperitenone reductase
    EC 1.3.1.84 acrylyl-CoA reductase (NADPH)
    EC 1.3.5.2 dihydroorotate dehydrogenase
    EC 1.3.7.6 phycoerythrobilin synthase
    EC 1.3.99.11 -> EC 1.3.5.2
    EC 1.3.99.24 2-amino-4-deoxychorismate dehydrogenase
    EC 1.3.99.25 carvone reductase
    EC 1.4.3.21 primary-amine oxidase
    EC 1.4.3.22 diamine oxidase
    EC 1.4.3.23 7-chloro-L-tryptophan oxidase
    EC 1.4.3.6 -> EC 1.4.3.21 and EC 1.4.3.22
    EC 1.4.5 with a quinone or similar compound as acceptor
    EC 1.4.5.1 D-amino acid dehydrogenase (quinone)
    EC 1.5.3.11 -> EC 1.5.3.13, EC 1.5.3.14, EC 1.5.3.15, EC 1.5.3.16 and EC 1.5.3.17
    EC 1.5.3.13 N1-acetylpolyamine oxidase
    EC 1.5.3.14 polyamine oxidase (propane-1,3-diamine-forming)
    EC 1.5.3.15 N8-acetylspermidine oxidase (propane-1,3-diamine-forming)
    EC 1.5.3.16 spermine oxidase
    EC 1.5.3.17 non-specific polyamine oxidase
    EC 1.5.99.13 D-proline dehydrogenase
    EC 1.7.5 With a quinone or similar compound as acceptor
    EC 1.7.5.1 nitrate reductase (quinone)
    EC 1.8.1.16 glutathione amide reductase
    EC 2.1.1.163 demethylmenaquinone methyltransferase
    EC 2.1.1.164 demethylrebeccamycin-D-glucose O-methyltransferase
    EC 2.1.1.165 methyl halide transferase
    EC 2.1.1.93 deleted
    EC 2.1.3.10 malonyl-S-ACP:biotin-protein carboxyltransferase
    EC 2.1.3.11 N-succinylornithine carbamoyltransferase
    EC 2.2.1.9 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase
    EC 2.3.1.185 tropine acyltransferase
    EC 2.3.1.186 pseudotropine acyltransferase
    EC 2.3.1.187 acetyl-S-ACP:malonate ACP transferase
    EC 2.3.1.188 omega-hydroxypalmitate O-feruloyl transferase
    EC 2.3.1.189 mycothiol synthase
    EC 2.3.1.190 acetoin dehydrogenase
    EC 2.3.1.70 deleted
    EC 2.4.1.245 alpha,alpha-trehalose synthase
    EC 2.4.1.246 mannosylfructose-phosphate synthase
    EC 2.4.1.247 beta-D-galactosyl-(1->4)-L-rhamnose phosphorylase
    EC 2.4.1.248 cycloisomaltooligosaccharide glucanotransferase
    EC 2.4.1.249 delphinidin 3',5'-O-glucosyltransferase
    EC 2.4.1.250 D-inositol-3-phosphate glycosyltransferase
    EC 2.4.2.41 xylogalacturonan ?-1,3-xylosyltransferase
    EC 2.4.2.42 UDP-D-xylose:?-D-glucoside beta-1,3-D-xylosyltransferase
    EC 2.5.1.64 -> EC 2.2.1.9 and EC 4.2.99.20
    EC 2.5.1.72 quinolinate synthase
    EC 2.5.1.73 O-phospho-L-seryl-tRNA:Cys-tRNA synthase
    EC 2.5.1.74 1,4-dihydroxy-2-naphthoate polyprenyltransferase
    EC 2.5.1.75 tRNA dimethylallyltransferase
    EC 2.5.1.76 cysteate synthase
    EC 2.5.1.77 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase
    EC 2.5.1.78 6,7-dimethyl-8-ribityllumazine synthase
    EC 2.5.1.79 thermospermine synthase
    EC 2.5.1.8 -> EC 2.5.1.75
    EC 2.5.1.80 7-dimethylallyltryptophan synthase
    EC 2.6.1.86 2-amino-4-deoxychorismate synthase
    EC 2.7.1.161 CTP-dependent riboflavin kinase
    EC 2.7.1.162 N-acetylhexosamine 1-kinase
    EC 2.7.1.163 hygromycin B 4-O-kinase
    EC 2.7.1.164 O-phosphoseryl-tRNASec kinase
    EC 2.7.1.165 glycerate 2-kinase
    EC 2.7.7.65 diguanylate cyclase
    EC 2.7.7.66 malonate decarboxylase holo-[acyl-carrier protein] synthase
    EC 2.7.7.67 CDP-archaeol synthase
    EC 2.7.7.68 2-phospho-L-lactate guanylyltransferase
    EC 2.7.8.28 2-phospho-L-lactate transferase
    EC 2.8.4.2 arsenate-mycothiol transferase
    EC 2.9.1.2 O-phospho-L-seryl-tRNASec:L-selenocysteinyl-tRNA synthase
    EC 3.1.1.83 monoterpene epsilon-lactone hydrolase
    EC 3.1.1.84 cocaine esterase
    EC 3.1.26.12 ribonuclease E
    EC 3.1.26.13 retroviral ribonuclease H
    EC 3.1.3.78 phosphatidylinositol-4,5-bisphosphate 4-phosphatase
    EC 3.1.3.79 mannosylfructose-phosphate phosphatase
    EC 3.1.3.80 2,3-bisphosphoglycerate 3-phosphatase
    EC 3.1.4.52 cyclic-guanylate-specific phosphodiesterase
    EC 3.1.4.53 3',5'-cyclic-AMP phosphodiesterase
    EC 3.1.7.4 sclareol cyclase
    EC 3.2.1.110 deleted
    EC 3.2.1.165 exo-1,4-beta-D-glucosaminidase
    EC 3.2.2.26 futalosine hydrolase
    EC 3.2.2.27 uracil-DNA glycosylase
    EC 3.2.2.28 double-stranded uracil-DNA glycosylase
    EC 3.2.2.29 thymine-DNA glycosylase
    EC 3.4.11.24 aminopeptidase S
    EC 3.4.17.23 angiotensin-converting enzyme 2
    EC 3.4.22.68 Ulp1 peptidase
    EC 3.4.22.69 SARS coronavirus main proteinase
    EC 3.4.22.70 sortase A
    EC 3.4.22.71 sortase B
    EC 3.4.23.50 human endogenous retrovirus K endopeptidase
    EC 3.4.23.51 HycI peptidase
    EC 3.4.24.87 ADAMTS13 endopeptidase
    EC 3.4.25.2 HslU--HslV peptidase
    EC 3.5.1.100 (R)-amidase
    EC 3.5.1.101 L-proline amide hydrolase
    EC 3.5.1.102 2-amino-5-formylamino-6-ribosylaminopyrimidin-4(3H)-one 5'-monophosphate deformylase
    EC 3.5.1.103 N-acetyl-1D-myo-inositol-2-amino-2-deoxy-alpha-D-glucopyranoside deacetylase
    EC 3.5.1.98 histone deacetylase
    EC 3.5.1.99 fatty acid amide hydrolase
    EC 3.6.1.53 Mn2+-dependent ADP-ribose/CDP-alcohol diphosphatase
    EC 3.6.4.12 DNA helicase
    EC 3.6.4.13 RNA helicase
    EC 3.7.1.11 cyclohexane-1,2-dione hydrolase
    EC 4.1.1.87 malonyl-S-ACP decarboxylase
    EC 4.1.1.88 biotin-independent malonate decarboxylase
    EC 4.1.1.89 biotin-dependent malonate decarboxylase
    EC 4.1.1.90 peptidyl-glutamate 4-carboxylase
    EC 4.1.2.43 3-hexulose-6-phosphate synthase
    EC 4.1.2.44 benzoyl-CoA-dihydrodiol lyase
    EC 4.1.2.45 trans-o-hydroxybenzylidenepyruvate hydratase-aldolase
    EC 4.1.99.13 (6-4)DNA photolyase
    EC 4.1.99.14 spore photoproduct lyase
    EC 4.2.1.114 methanogen homoaconitase
    EC 4.2.1.115 UDP-N-acetylglucosamine 4,6-dehydratase (inverting)
    EC 4.2.1.116 3-hydroxypropionyl-CoA dehydratase
    EC 4.2.1.117 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
    EC 4.2.1.118 3-dehydroshikimate dehydratase
    EC 4.2.1.119 enoyl-CoA hydratase 2
    EC 4.2.1.120 4-hydroxybutanoyl-CoA dehydratase
    EC 4.2.3.28 ent-cassa-12,15-diene synthase
    EC 4.2.3.29 ent-sandaracopimaradiene synthase
    EC 4.2.3.30 ent-pimara-8(14),15-diene synthase
    EC 4.2.3.31 ent-pimara-9(11),15-diene synthase
    EC 4.2.3.32 levopimaradiene synthase
    EC 4.2.3.33 stemar-13-ene synthase
    EC 4.2.3.34 stemod-13(17)-ene synthase
    EC 4.2.3.35 syn-pimara-7,15-diene synthase
    EC 4.2.3.36 terpentetriene synthase
    EC 4.2.3.37 epi-isozizaene synthase
    EC 4.2.3.38 alpha-bisabolene synthase
    EC 4.2.3.39 epi-cedrol synthase
    EC 4.2.3.40 (Z)-gamma-bisabolene synthase
    EC 4.2.99.20 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase
    EC 4.3.1.23 tyrosine ammonia-lyase
    EC 4.3.1.24 phenylalanine ammonia-lyase
    EC 4.3.1.25 phenylalanine/tyrosine ammonia-lyase
    EC 4.3.1.26 chromopyrrolate synthase
    EC 4.3.1.5 -> EC 4.3.1.23, EC 4.3.1.24 and EC 4.3.1.25
    EC 4.3.3.5 4'-demethylrebeccamycin synthase
    EC 4.3.99.2 carboxybiotin decarboxylase
    EC 4.99.1.8 heme ligase
    EC 5.1.99.5 hydantoin racemase
    EC 5.3.1.27 6-phospho-3-hexuloisomerase
    EC 5.5.1.14 syn-copalyl diphosphate synthase
    EC 5.5.1.15 terpentedienyl-diphosphate synthase
    EC 5.5.1.16 halimadienyl-diphosphate synthase
    EC 5.99.1.4 2-hydroxychromene-2-carboxylate isomerase
    EC 6.1.1.27 O-phosphoserine--tRNA ligase
    EC 6.2.1.35 ACP-SH:acetate ligase
    EC 6.2.1.36 3-hydroxypropionyl-CoA synthase
    EC 6.3.1.13 L-cysteine:1D-myo-inositol 2-amino-2-deoxy-alpha-D-glucopyranoside ligase
    EC 6.3.2.31 coenzyme F420-0:L-glutamate ligase
    EC 6.3.2.32 coenzyme gamma-F420-2:alpha-L-glutamate ligase
    EC 6.3.2.33 tetrahydrosarcinapterin synthase
    EC 6.3.2.34 coenzyme F420-1:gamma-L-glutamate ligase

     
  • RFoulger
    RFoulger
    2010-07-27

    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:

    EC=1.14.13.104
    EC=1.3.1.82
    EC=1.3.1.81

    thanks,
    Becky

     
  • RFoulger
    RFoulger
    2010-07-27

    • priority: 5 --> 7
     
  • Jane Lomax
    Jane Lomax
    2010-07-27

    Amelia's going to look into this.

     
  • Jane Lomax
    Jane Lomax
    2010-07-27

    • 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 1.2.1.74 abietadienal dehydrogenase
    EC 1.3.1.83 geranylgeranyl diphosphate reductase
    EC 1.14.13.108 abietadiene hydroxylase
    EC 1.14.13.109 abietadienol hydroxylase
    EC 1.14.13.110 geranylgeraniol 18-hydroxylase
    EC 3.1.7.5 geranylgeranyl diphosphate diphosphatase
    EC 4.2.3.41 elisabethatriene synthase
    EC 4.2.3.42 aphidicolan-16?-ol synthase
    EC 4.2.3.43 fusicocca-2,10(14)-diene synthase
    EC 4.2.3.44 isopimara-7,15-diene synthase

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

    /Kristian

     
  • Here are those urgently need terms:

    EC:1.3.1.81 (two reactions)
    GO:0052579 (+)-pulegone reductase, (+)-isomenthone as substrate, activity
    GO:0052580 (+)-pulegone reductase, (-)-menthone as substrate, activity

    EC:1.3.1.82
    GO:0052581 (-)-isopiperitenone reductase activity

    EC:1.14.13.104
    GO:0052582 (+)-menthofuran synthase activity

     
  • EC 2.1.1.93 deleted --> not in GO
    EC 2.3.1.70 deleted --> already obsolete
    EC 3.2.1.110 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?

    Thanks,
    Jane, Becky, Paola

     
  • RFoulger
    RFoulger
    2011-08-17

    • 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).

    Regards,

    Kristian

     
  • Jane Lomax
    Jane Lomax
    2012-02-22

    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
    2012-02-22

    • 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

     
    Attachments
  • 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