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Table 2 Status of the experimentally validated families: cases 1-9 verified by us; cases 10-19 verified by others.

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 Reference
1 At4g12130 At1g60990 0354 ygfZ YgfZ Folate-dependent protein for Fe/S cluster synthesis/repair in oxidative stress Validated in E. coli, Bartonella henselae, Haloferax volcanii, Arabidopsis, Leishmania, yeast, mouse 327 [44] (2010)
2 At2g20830 3643 Experimental-histidine degradation Alternative to 5-FCL (EC 6.3.3.2) as a way to metabolize 5-formyltetrahydrofolate Verified in 5 prokaryotes 65 [45] (2010)
3 At1g29810 At5g51110 2154 phhB Pterin carbinolamine dehydratase Pterin-4-alpha-carbinolamine dehydratase (EC 4.2.1.96) with a role in Moco metabolism Validated in 7 eukaryotes and 8 prokaryotes 217 [81] (2008)
4 none 0720 Experimental-PTPS Replacement for FolB (EC 4.1.2.25) Validated in 1 eukaryote and 8 prokaryotes 65 [40] (2009); [39] (2008)
5 At5g60590 0009 yrdC YrdC-YciO-Sua5 protein family Required for threonylcarbamoyl-adenosine (t(6)A) formation in tRNA Validated in yeast, archaea and 2 bacteria.
Arabidopsis in progress.
745 [60] (2009)
6 At2g45270 At4g22720 0533 ygjD YrdC-YciO-Sua5 protein family Required for threonylcarbamoyl-adenosine (t(6)A) formation in tRNA Validated in yeast 691 [82] (2011)
7 At1g15730 At1g26520 At1g80480 0523 COG0523 Diverse metal chaperones Validated in several bacteria 718 [42] (2009)
8 At3g13050 MFS superfamily NiaP homolog Niacin-choline transport and metabolism Niacin and/or choline transporter Niacin but not choline transport shown for 3 bacterial proteins and the mouse protein
Arabidopsis protein in progress.
133 Manuscript in prep
9 At1g76730 0212 5-FCL-like protein Not a 5-FCL enzyme; involved in thiamine salvage Cannot replace 5-FCL and lacks detectable 5-FCL activity 41 Manuscript submitted
10 At4g36400 0277 bll2569 COG0277 D-2-hydroxyglutarate dehydrogenase D-2-hydroxyglutarate dehydrogenase 158 [83] (2009)
11 At5g10910 0275 mraW 16S rRNA modification within P site of ribosome SAM-dependent methyltransferase involved in a process common to eubacteria and chloroplasts 16S rRNA m(4) C1402 methyltransferase (modification within P site of ribosome) 877 [84] (2010)
12 At1g45110 0313 16S rRNA modification within P site of ribosome Tetrapyrrole family methyltransferase involved in a process common to eubacteria, chloroplasts, and possibly mitochondria 16S rRNA 2'-O-ribose C1402 methyltransferase (modification within P site of ribosome) 836 [84] (2010)
13 At5g18570 At1g07620 0536 Iojap At5g18570 predicted to be plastidial, At1g07615 mitochondrial. Association evidence connects At5g18570 with plastidial iojap (At3g12930) Essential for embryo development but specific function unclear 721 [85] (2009)
14 At1g49350 2313 yeiN Pseudouridine catabolism Sugar catabolism Involved in pseudouridine metabolism in uropathogenic E. coli 108 In EC: [86] (2008)
15 At1g50510 0524 yeiC Pseudouridine catabolism Sugar catabolism Involved in pseudouridine metabolism in uropathogenic E. coli 108 In EC: [86] (2008)
16 At4g10620 At3g57180 At3g47450 1161 yqeH At4g10620 At3g57180 At3g47450 GTP-binding protein YqeH, involved in replication initiation At3g57180 (BPG2) functions in brassinosteroid-mediated post-transcriptional accumulation of chloroplast rRNA. At3g47450 (AtNOA1) is a GTPase that regulates nucleic acid recognition 180 [87] (2010) [88] (2008)
17 At3g24430 At4g19540 At5g50960 2151 apbC Scaffold proteins for [4Fe-4S] cluster assembly (MRP family) Fe-S cluster assembly proteins. The DUF59 (PaaD-like) domain of At3g24430 and its prokaryotic counterparts are also predicted to function in Fe-S cluster assembly. At5g50960 (Nbp35) functions in Fe-S cluster assembly as a bifunctional molecular scaffold At3g24430 acts as a scaffold protein for [4Fe-4S] cluster assembly in chloroplasts 276 [89] (2009) [90] (2005)
18 At3g57000 1756 rRNA modification Archaea; rRNA methylation in clusters rRNA modification enzyme The Methanocaldococcus jannaschii ortholog is a pseudouridine-N1-specific methyltransferase. 31 [91] (2010)
19 At5g12040 0388 Omega-amidase Omega amidase in methionine salvage pathway Biochemical characterization of the rat and mouse orthologs 113 [92] (2009)
[93] (2009)