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 | Â |
|---|---|---|---|---|---|---|---|
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 | Â |
21 | At2g23390 | 3146 | COG3146 | Pterin-dependent enzyme | Xanthomonas campestris protein lacks benzoate hydroxylase activity in complementation assay | 236 | Â |
22 | At2g04900 | 2363 ywdK | COG2363 | Thiamine-related transporter | E. coli protein does not mediate uptake of thiazole or hydroxymethylpyrminidine | 221 | Â |
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 | Â |
24 | At4g26860 At1g11930 | 0325 yggS | PROSC | Pyridoxal phosphate enzyme related to glutamate metabolism | In progress in E. coli | 589 | Â |
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 | Â |
26 | At5g12950 At5g12960 | 3533 SAV1144 | DOE COG3533 | Hydroxyproline-galactosyl hydrolase | In progress in X. campestris | 82 | Â |
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 | Â |
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 | Â |
29 | At3g01920 | 0009 yciO | YrdC-YciO-Sua5 protein family | RNA/protein modification | In progress in E. coli | 195 | Â |
30 | At1g03030 | 1072 yggC | Experimental-yggC | Sugar/polyol kinase | In progress in E. coli | 48 | Â |
31 | At4g28830 | 2263 | rRNA modification Archaea | Predicted RNA methylase COG2263 | In progress in H. volcanii | 49 | Â |