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Table 4 Comparison of functional predictions in eNet and AraNet for 10 of the protein families.

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

TAIR ID E.coli ortholog Working functional prediction eNet predictions AraNet predictionsa
At4g12130, At1g60990 YgfZ Folate-dependent protein for Fe/S cluster synthesis/repair in oxidative stress Annotation based on[94]: Predicted folate-dependent regulatory protein. Prediction: Energy production and conversion, ion transport For At4g12130: NAD biosynthesis (2.96), electron transport, cellular respiration, N-terminal protein amino acid modification, miRNA-mediated gene silencing, production of miRNAs, methylglyoxal catabolic process to D-lactate, embryonic development, etc
At2g20830 none Alternative to 5-FCL (EC as a way to metabolize 5-formyltetrahydrofolate n/a Response to wounding (1.86), defense response, response to oxidative stress, phenylpropanoid biosynthesis, response to other organism, boron transport, glucosinolate biosynthesis (0.89)
At1g29810, At5g51110 none Pterin-4-alpha-carbinolamine dehydratase (EC with a role in Moco metabolism n/a For At1g29810: electron transport (3.13); carotenoid biosynthesis (2.29); brassinosteroid biosynthesis (2.16); fatty acid metabolic process (2.06); photosynthesis, light reaction (1.99); sulfate assimilation (1.98); lignin biosynthesis (1.87)
AT5g12040 YafV Omega amidase in methionine salvage pathway Predicted C-N hydrolase family amidase, NAD(P)-binding indoleacetic acid biosynthesis (4.27), cellular response to sulfate starvation, cyanide metabolic process, glucosinolate catabolic process, detoxification of nitrogen compound, methylglyoxal catabolic process to D-lactate (1.59)
At5g60590 YrdC Required for threonylcarbamoyladenosine (t(6)A) formation in tRNA Annotation based on[57]: Predicted ribosome maturation factor. NO prediction rRNA processing (3.88), dATP biosynthesis from ADP, histidine biosynthesis, mitochondrial ATP synthesis coupled proton transport, cellular respiration, ATP synthesis coupled proton transport, regulation of transcription (2.07)
At2g45270, At4g22720 YgjD Required for threonylcarbamoyladenosine (t(6)A) formation in tRNA Prediction: Predicted peptidase (Amino acid transport and metabolism) For At2g45270: transcription initiation (6.19), positive regulation of transcription, chlorophyll biosynthesis, porphyrin biosynthesis, phospholipid biosynthesis, electron transport, ATP-dependent proteolysis, N-terminal protein amino acid modification (1.81)
At1g15730, At1g26520, At1g80480 YjiA YeiR Metal chaperone-Zinc homeostasis Prediction for b4352: Inorganic ion transport and metabolism, response to stress; Prediction for b2173: Lipid transport and metabolism, RNA related, Regulation of transcription DNA dependent For At1g15730: nitrogen compound metabolic process (4.04); positive regulation of metalloenzyme activity (4.04)
At1g76730 none Not a 5-FCL enzyme; involved in thiamine salvage n/a Tetrahydrofolate metabolic process (4.56), negative regulation of transcription, response to abscisic acid stimulus (0.89)
At4g36400 none D-2-hydroxyglutarate dehydrogenase n/a Cytoskeleton organization and biogenesis (2.39), actin cytoskeleton organization and biogenesis, ubiquitin-dependent protein catabolic process, response to light stimulus, response to wounding, seed germination (1.24)
At1g45110 yraL Tetrapyrrole family methyltransferase involved in a process common to eubacteria, chloroplasts, and possibly mitochondria Prediction: Replication, recombination and repair; RNA related, Translation Toxin catabolic process (5.49), response to oxidative stress, cellular response to water deprivation, response to jasmonic acid stimulus, response to ozone, isoprenoid biosynthesis, electron transport (1.45)
  1. a Only a few top predictions (out of 30 routinely returned) for AraNet are shown. They are sorted by the AraNet score estimating the gene’s association with each particular process (given in brackets for the first and last predictions shown here).