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

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)

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)

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)

none

0720

Experimental-PTPS

Replacement for FolB (EC 4.1.2.25)

Validated in 1 eukaryote and 8 prokaryotes

65

[40] (2009); [39] (2008)

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)

0533 ygjD

YrdC-YciO-Sua5 protein family

Required for threonylcarbamoyl-adenosine (t(6)A) formation in tRNA

Validated in yeast

691

[82] (2011)

0523

COG0523

Diverse metal chaperones

Validated in several bacteria

718

[42] (2009)

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

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

0277 bll2569

COG0277

D-2-hydroxyglutarate dehydrogenase

D-2-hydroxyglutarate dehydrogenase

158

[83] (2009)

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)

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)

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)

2313 yeiN

Pseudouridine catabolism

Sugar catabolism

Involved in pseudouridine metabolism in uropathogenic E. coli

108

In EC: [86] (2008)

0524 yeiC

Pseudouridine catabolism

Sugar catabolism

Involved in pseudouridine metabolism in uropathogenic E. coli

108

In EC: [86] (2008)

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)

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)

1756

rRNA modification Archaea; rRNA methylation in clusters

rRNA modification enzyme

The Methanocaldococcus jannaschii ortholog is a pseudouridine-N1-specific methyltransferase.

31

[91] (2010)

0388

Omega-amidase

Omega amidase in methionine salvage pathway

Biochemical characterization of the rat and mouse orthologs

113

[92] (2009)

[93] (2009)