RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs

BMC Bioinformatics

Table 2 RIO analysis of A. thaliana lactate/malate dehydrogenase family members

Sequence ID	Annotation	RIO top 1 hit (highest orthology value)
		Domain used for analysis:
		ldh (PF00056)	Ldh_C (PF02866)
dl4665w	LDH (LDH1)	L-LDH (o = 91%, n = 3%)	L-LDH (o = 94%, n = 12%)
F19P19_13	putative MDH	MDH (o = 2%, n = 98%)	cytoplasmic MDH (o = 40%, n = 78%)
F12M16_14	mitochondrial NAD-dependent MDH	mitochondrial MDH (o = 89%, n = 100%)	mitochondrial MDH (o = 94%, n = 66%)
T30L20.4	putative glyoxysomal MDH precursor	MDH (o = 55%, n = 0%)	glyoxysomal MDH (o = 95%, n = 37%)
K15M2_16	mitochondrial NAD-dependent MDH, putative	MDH (o = 89%, n = 100%)	mitochondrial MDH (o = 84%, n = 80%)
F1P2_70	Chloroplast NAD-dependent MDH	MDH (o = 87%, n = 21%)	MDH (o = 85%, n = 6%)
F17I14_150	microbody NAD-dependent MDH	glyoxysomal MDH (o = 100%, n = 100%)	glyoxysomal MDH (o = 80%, n = 97%)
MWF20_2	cytoplasmic MDH	MDH (o = 2%, n = 100%)	MDH (o = 38%, n = 75%)
MIK19_17	cytoplasmic MDH	cytoplasmic MDH (o = 5%, n = 99%)	MDH (o = 31%, n = 84%)
MCK7_20	NADP-dependent MDH	MDH (o = 60%, n = 30%)	chloroplast NADP-MDH (EC 1.1.1.82) (o = 68%, n = 82%)

Annotations are from ATH1.pep.03202001 (Arabidopsis Genome Initiative http://www.arabidopsis.org/info/agi.html). "o=" and "n=" are orthology and subtree-neighboring values for the sequence in the Pfam alignment (ldh or ldh_C) with the highest orthology value towards the respective query sequence. LDH stands for L-lactate dehydrogenase. MDH stands for malate dehydrogenase.

ISSN: 1471-2105