A talk I gave at the Automated Function Prediction meeting, 2005. Highlights different challenges in running a competition between protein function prediction servers. Talks of the use of semantic similarity in Gene Ontology as a metric for assessment, the problems in determining a "Gold Standard" and more

5. Describing Function: From English to Keywords “ HAL—which is the first enzyme in the degradation pathway of L-histidine—catalyzes the non-oxidative deamination of its substrate to trans-urocanic acid”. László Poppe, (2001) COCB “ HAL— which is the first enzyme in the degradation pathway of L-histidine — catalyzes the non-oxidative deamination of its substrate to trans -urocanic acid ”.

6. Describing Function: From English to Keywords “ HAL—which is the first enzyme in the degradation pathway of L-histidine—catalyzes the non-oxidative deamination of its substrate to trans-urocanic acid”. László Poppe, (2001) COCB “ HAL— which is the first enzyme in the degradation pathway of L-histidine — catalyzes the non-oxidative deamination of its substrate to trans -urocanic acid ”. “ HAL — which is the first enzyme in the degradation pathway of L-histidine — catalyzes the non-oxidative deamination of its substrate to trans -urocanic acid ”. “ HAL — which is the first enzyme in the degradation pathway of L-histidine — catalyzes the non-oxidative deamination of its substrate to trans -urocanic acid ”. “ HAL — which is the first enzyme in the degradation pathway of L-histidine — catalyzes the non-oxidative deamination of its substrate to trans -urocanic acid ”.

11. EC1 oxidoreductases EC2 transferases EC3 hydrolases EC4 lyases EC5 isomaerase EC6 ligases EC4.1 carbon-carbon EC4.2 carbon-oxygen EC4.3 carbon-nitrogen EC4.5 phosphorus-oxygen EC4.99 others EC4.4 carbon-sulfur EC 4.3.1 ammonia lyases EC 4.3.1.1 aspartate ammonia lyase EC 4.3.1.2 met-aspartate ammonia lyase EC 4.3.1.3 histidine ammonia lyase EC 4.3.3 amine lyases Enzyme Commission Classification Enzyme

14. GO: molecular function of HAL Histidine ammonia-lyase activity (GO:003456)‏ ammonia-lyase activity C-N lyase activity lyase activity Molecular Function

15. GO: biological process of HAL Histidine biosynthesis Histidine family biosynthesis Histidine metabolism Physiological process Cellular process Biological process

24. Assessed Servers

25. Server Scorecard (empty)‏ Spearmint ___ RuleBase ___ AnnoLite ___ PFP ___ PhydBac ___ ProKnow ___ Proteome Analyst __ GOPET ___

27. in cluster FIG ID Function TM ID #1 ASPDH: Aspartate dehydrogenase [same functional role as] (EC 1.4.3.16 ) TM1643* #2 QSYN: Quinolinate synthetase (EC 4.1.99.-) TM1644 #3 QAPRT: Quinolinate phosphoribosyltransferase [decarboxylating] (EC 2.4.2.19 ) TM1645* *Structures solved Biological Process: NAD/NADP Biosynthesis Summary: Genomic cluster conserved between T,maritima and several methanogenic archaea contains a novel gene* for the first step of NAD biosynthesis I II ASPOX ASPDH NAD + NADH QSYN PRPP IV FAD + FADH III QAPRT PP i Experimentally confirmed by: Z.Yang et al. (Toronto)‏ “ Aspartate Dehydrogenase, a Novel Enzyme Identified from Structural and Functional Studies of TM1643”, J. Biol. Chem., Vol. 278,, 2003 Connecting intermediates I L-Aspartate II Iminoaspartate III Dihydroxyacetone-P IV Quinolinic acid TM1643

28. T7: GO Tree and Probabilities Oxidoreductase CH-NH 2 bonds Molecular Function Catalytic Oxidoreductase Oxidoreductase CH-NH 2 bonds NAD/NADP acceptor Oxidoreductase CH-NH 2 bonds Oxygen acceptor Aspartate Dehydrogenase Aspartate Oxidoreductase Spearmint : homoserine dehydrogenase A nnoLite : L-lactate dehydrogenase ProKnow: oxidoreductase activity p=1; gosim=0 p=0.26; gosim=192. p=0.03; gosim=484. p=8.65x10 -4 ; gosim=1017 p=4.74x10 -4 ; gosim=1104 PhydBac : nicotinate nuc. dephosphorylase PFP :3-5 nucleotide phosphodiesterase

30. T1: the little Thiamine synthesis enzyme who couldn't (and neither could we)‏

31. T1: the Thiamine synthesis hypothesis Beck & Downs, JB 1998

33. T1 Beck & Downs, JB 1998 ApbE

34. T1: a non oligomerizing T-fold T-fold: normally forms homo-oligomeric barrels Uricase T1 Active site Oligomerization region Catalytic site Cat. site Oligomerization region

38. T2 aligned to Ran-GTPASE MOVIE

41. T4: Pantothenate Kinase, CoA synthesis Boxes: enzymes Circles: substrates/products Arrows: “preferred” reaction directionality Color: organism in which enzyme exists UNIVERSAL PATHWAY Fatty Acid metabolism Central Carbon metabolism CoA B5 PANK VI ATP ADP PPCS VIII CTP CMP, PP i VII Cysteine metabolism PPCDC IX CO 2 PPAT X PP i ATP DPCK ADP ATP PANK2 PANK3 PPAT2 present in H.sapiens present in both present in E.coli absent in both

42. Brand, L. A. et al. J. Biol. Chem. 2005;280:20185-20188 Cluster analysis of the predicted coaX gene in selected organisms

46. Server Scorecard (empty)‏ Spearmint ___ RuleBase ___ AnnoLite ___ PFP ___ PhydBac ___ ProKnow ___ Proteome Analyst __ GOPET ___

47. Server Scorecard (Full)‏ Spearmint ___ RuleBase ___ AnnoLite ___ PFP ___ PhydBac ___ ProKnow ___ Proteome Analyst __ GOPET ___

52. The End