TABLE 2.
Ralstonia sp. strain U2 genes and gene products
| Gene designation | Putative function of gene product | Position in sequence | Product size (residues, kDa) | Most similar gene product(s) (species, % amino acid identity, accession no.) or reference |
|---|---|---|---|---|
| nagY (partial) | Chemotaxis protein | 1–1272 | 422, 44.1 (partial 3′ end) | Chemoreceptor protein, Tar (S. typhimurium, 59, J01809) |
| nagR | Transcription activator | 2144–1239 | 301, 33.8 | Transcription activator, NahR (P. putida plasmid NAH7, 61, J04233) |
| nagAa | Ferredoxin reductase | 2261–3247 | 328, 35.1 | 14 |
| nagG | Salicylate-5-hydroxylase, large oxygenase component | 3293–4564 | 423, 48.8 | 14 |
| nagH | Salicylate-5-hydroxylase, small oxygenase component | 4567–5052 | 161, 18.8 | 14 |
| nagAb | Ferredoxin | 5063–5377 | 104, 11.6 | 14 |
| nagAc | Naphthalene dioxygenase, large oxygenase component | 5464–6807 | 447, 49.6 | 14 |
| nagAd | Naphthalene dioxygenase, small oxygenase component | 6822–7406 | 194, 23.0 | 14 |
| nagB | cis-Naphthalene dihydrodiol dehydrogenase | 7470–8249 | 259, 27.1 | cis-Naphthalene dihydrodiol dehydrogenase-like protein, PahB (C. testosteroni strain H, 98, AF252550) |
| nagF | Salicylaldehyde dehydrogenase | 8298–9749 | 483, 51.9 | Salicylaldehyde dehydrogenase, NahF (P. putida plasmid NPL1, 89, AF010471) |
| nagC | 1,2-Dihydroxynaphthalene dioxygenase | 9775–10683 | 302, 33.8 | 1,2-Dihydroxynaphthalene dioxygenase, NahC (P. putida plasmid NPL1, 88, AF010471) |
| nagQ | Putative aldolase | 10753–11391 | 212, 22.8 | Dibenzothiophene metabolism operon protein, DoxH (Pseudomonas sp. strain C18, 77, M60405) |
| nagE | trans-o-Hydroxybenzylidenepyruvate hydratase–aldolase | 11449–12486 | 345, 38.2 | trans-o-Hydroxybenzylidenepyruvate hydratase–aldolase, DoxI (Pseudomonas sp. strain C18, 88, M60405) |
| nagD | 2-Hydroxychromene carboxylate isomerase | 12669–13268 | 199, 23.1 | 2-Hydroxychromene-2-carboxylate dehydrogenase, NahD (P. stutzeri, 69, AF039533) |
| nagJ | GST homolog | 13327–13932 | 201, 22.1 | GST, BphK (Pseudomonas sp., 58, X76500) |
| nagI | GDO | 14136–15203 | 355, 39.9 | GDO, GdtA (Sphingomonas sp. strain RW5, 35, AJ224977); GDO, XlnE (P. alcaligenes, 34, AF173167) |
| nagK | Fumarylpyruvate hydrolase | 15360–15938 | 192, 20.9 | Unknown Orf2 (Sphingomonas sp. strain RW1, 56, Y13118); unknown Orf2 (Sphiingomonas sp. strain RW5, 51, AJ224977) |
| nagL | Maleylpyruvate isomerase | 15950–16588 | 212, 23.5 | Unknown Orf3 (Sphingomonas sp. strain RW1, 45, Y13118); maleylacetoacetate isomerase, MaiA (S. meliloti, 45, AF 109131) |
| nagM | Unknown | 16651–17676 | 341, 35.5 | NagN (39%) (this study); unknown Orf4 (C. testosteroni TA441, 31, AB024335); unknown Orf5 (C. testosteroni TA441, 31, AB024335) |
| nagN | Unknown | 17693–18688 | 331, 34.9 | NagM (39%) (this study); unknown Orf4 (C. testosteroni TA441, 31, AB024335); unknown Orf5 (C. testosteroni TA441, 30, AB024335) |
| orf1 | Unknown | 19375–19923 | 182, 18.9 | No obvious homolog |
| tnpA (partial) | Transposase | 20038–21159 | 374, 42.2 (partial 5′ end) | Transposase for IS1071 in transposon Tn5271 (Alcaligenes sp. strain BR60, 99, M65135) (970 amino acids) |