EC2GO, in badly need of an update

[gocentral]

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

Reported by: axelsen

Original Ticket: geneontology/ontology-requests/7472

[gocentral]

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

Original comment by: jl242

[gocentral]

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

Original comment by: jl242

[gocentral]

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

Original comment by: axelsen

[gocentral]

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

Original comment by: rebeccafoulger

[gocentral]

• priority: 5 --> 7

Original comment by: rebeccafoulger

[gocentral]

Amelia's going to look into this.

Original comment by: jl242

[gocentral]

• assigned_to: jl242 --> girlwithglasses

Original comment by: jl242

[gocentral]

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

Original comment by: axelsen

[gocentral]

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

Original comment by: girlwithglasses

[gocentral]

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

Original comment by: girlwithglasses

[gocentral]

Hi Amelia,

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

Thanks, Jane, Becky, Paola

Original comment by: paolaroncaglia

[gocentral]

• labels: --> enzymes

Original comment by: rebeccafoulger

[gocentral]

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?

Original comment by: girlwithglasses

[gocentral]

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

Original comment by: axelsen

[gocentral]

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.

Original comment by: jl242

[gocentral]

• milestone: --> Uniprot

Original comment by: jl242

[gocentral]

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.

Original comment by: girlwithglasses

[gocentral]

Enzyme activities in need of obsoletion

Original comment by: girlwithglasses

[gocentral]

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.

Original comment by: girlwithglasses

[gocentral]

Moved to https://sourceforge.net/tracker/?func=detail&aid=3490893&group\_id=36855&atid=440764

Original comment by: paolaroncaglia

[gocentral]

• status: open --> closed

Original comment by: paolaroncaglia