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Table 3 Status of the families invalidated by us (cases 20-23) or in progress (cases 24-31).

From: Synergistic use of plant-prokaryote comparative genomics for functional annotations

Case no. TAIR ID COG number/ gene name Subsystem in SEED Working functional prediction Experimental verification status Homologs annotated  
20 At5g43600 0624 Experimental - Histidine Degradation Alternative form of N-formylglutamate deformylase (EC 3.5.1.68) No deformylase actiivity detected in Streptomyces avermitilis protein 24 a  
21 At2g23390 3146 COG3146 Pterin-dependent enzyme Xanthomonas campestris protein lacks benzoate hydroxylase activity in complementation assay 236  
22 At2g04900 2363 ywdK COG2363 Thiamine-related transporter E. coli protein does not mediate uptake of thiazole or hydroxymethylpyrminidine 221  
23 At1g09150 2016 rRNA modification Archaea; DOE-COG2016 Ribosome assembly/translation termination In progress in yeast and H. volcanii. Hypothesis that it is involved in acp3psi synthesis invalidated by Fournier labb 30  
24 At4g26860 At1g11930 0325 yggS PROSC Pyridoxal phosphate enzyme related to glutamate metabolism In progress in E. coli 589  
25 At1g78620 At5g19930 1836 alr1612 COG1836 Phytol-phosphate metabolism Shown to be an essential gene in Synechocystis 6803. Further work in progress in Arabidopsis 77  
26 At5g12950 At5g12960 3533 SAV1144 DOE COG3533 Hydroxyproline-galactosyl hydrolase In progress in X. campestris 82  
27 At3g09250 4319 gll0142 COG4319 Folate or pterin metabolism enzyme, possibly an alternative DHFR (EC 1.5.1.3), a pterin reductase, or a dihydroneopterin triphosphate hydrolase Streptomyces coelicolor, Arabidopsis At3g09250, and Nostoc punctiforme proteins failed to complement E. coli folA (DHFR) strains 59  
28 At3g12930 At1g67620 0799 alr4169 Iojap NAD-dependent ribosomal modification, possibly involving phosphoester hydrolysis No pyrophosphatase or NAD cleavage activity detected in E. coli YbeB or NadD-YbeB fusion protein from Wolinella succinogenes 672  
29 At3g01920 0009 yciO YrdC-YciO-Sua5 protein family RNA/protein modification In progress in E. coli 195  
30 At1g03030 1072 yggC Experimental-yggC Sugar/polyol kinase In progress in E. coli 48  
31 At4g28830 2263 rRNA modification Archaea Predicted RNA methylase COG2263 In progress in H. volcanii 49  
  1. a Numbers in italics are for members of families for which the prediction has been invalidated or is in progress, they have not been included in the final count.
  2. b S. Fournier and W. Decatur, University of Massachusetts (unpublished)