Updated annotations for Desulfovibrio vulgaris Hildenborough JW710

17 genes with updated (or confirmed) annotations:

DVU0823 argJ : Glutamate N-acetyltransferase (EC 2.3.1.35)
Original description: arginine biosynthesis bifunctional protein ArgJ (TIGR)
SEED: Glutamate N-acetyltransferase (EC 2.3.1.35) / N-acetylglutamate synthase (EC 2.3.1.1)
KEGG: glutamate N-acetyltransferase / amino-acid N-acetyltransferase
Rationale: # Important for fitness in minimal media unless arginine is provided. Some homologs also catalyze the formation of N-acetylglutamate synthase, but the dedicated synthase (DVU1587) is also required, so DVU0823 probably catalyzes the acetyltransferase reaction (which is necessary to convert N(2)-acetylornithine to ornithine) only.

DVU0908 : ATP-dependent reduction of co(II)balamin
Original description: iron-sulfur cluster-binding protein, putative (TIGR)
SEED: iron-sulfur cluster-binding protein, putative
KEGG: no annotation
Rationale: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM PF14574.

DVU1029 hisC : histidinol-phosphate aminotransferase (EC 2.6.1.9)
Original description: histidinol-phosphate aminotransferase (TIGR)
SEED: Biosynthetic Aromatic amino acid aminotransferase beta (EC 2.6.1.57) @ Histidinol-phosphate aminotransferase (EC 2.6.1.9)
KEGG: histidinol-phosphate aminotransferase
Rationale: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR01141.

DVU1186 mazG : phosphoribosyl-ATP diphosphatase (EC 3.6.1.31)
Original description: MazG family protein (TIGR)
SEED: Nucleoside triphosphate pyrophosphohydrolase MazG (EC 3.6.1.8)
KEGG: nucleoside-triphosphate pyrophosphatase
Rationale: # Important for growth in minimal media, except when histidine is provided. Belongs to the MazG family of pyrophosphatases. Replaces the typical HisI. See PMID:29324779.

DVU1585 : Methionine synthase (cobalamin-dependent) (EC 2.1.1.13)
Original description: vitamin B12-dependent methionine synthase family protein (TIGR)
SEED: 5-methyltetrahydrofolate--homocysteine methyltransferase (EC 2.1.1.13)
KEGG: 5-methyltetrahydrofolate--homocysteine methyltransferase
Rationale: # Important for fitness in most defined media experiments and cofit with metF (DVU0997)

DVU1587 : N-acetylglutamate synthase (EC 2.3.1.1)
Original description: acetyltransferase, GNAT family (TIGR)
SEED: GCN5-related N-acetyltransferase
KEGG: amino-acid N-acetyltransferase
Rationale: # Important for fitness in minimal media, unless arginine is provided.

DVU1914 : (R)-citramalate synthase (EC 2.3.3.21)
Original description: 2-isopropylmalate synthase/homocitrate synthase family protein (TIGR)
SEED: (R)-citramalate synthase (EC 2.3.1.182)
KEGG: 2-isopropylmalate synthase
Rationale: # Important for fitness in defined media, except when isoleucine is added. (Citramalate is a precursor to 2-oxobutanoate and isoleucine in some prokaryotes.)

DVU2242 : asparaginase (EC 3.5.1.1)
Original description: asparaginase family protein (TIGR)
SEED: Isoaspartyl aminopeptidase (EC 3.4.19.5) @ Asp-X dipeptidase
KEGG: beta-aspartyl-peptidase (threonine type)
Rationale: Specific phenotype: utilization of L-Asparagine

DVU2332 proC : pyrroline-5-carboxylate reductase (EC 1.5.1.2)
Original description: pyrroline-5-carboxylate reductase (TIGR)
SEED: Pyrroline-5-carboxylate reductase (EC 1.5.1.2)
KEGG: pyrroline-5-carboxylate reductase
Rationale: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR00112.

DVU2672 : glycine transporter
Original description: membrane protein, putative (TIGR)
SEED: membrane protein, putative
KEGG: no annotation
Rationale: Specific phenotype: utilization of Glycine. Belongs to the UPF0126 family of transporters (see PMID:29769716)

DVU2982 leuC : 3-isopropylmalate dehydratase / (R)-citramalate isomerase, large subunit LeuC (EC 4.2.1.33; EC 4.2.1.35)
Original description: 3-isopropylmalate dehydratase, large subunit, putative (TIGR)
SEED: 3-isopropylmalate dehydratase large subunit (EC 4.2.1.33)
KEGG: 3-isopropylmalate/(R)-2-methylmalate dehydratase large subunit
Rationale: # Important for fitness in defined media, except when both leucine and isoleucine are provided.

DVU2983 leuD : 3-isopropylmalate dehydratase / (R)-citramalate isomerase, small subunit LeuD (EC 4.2.1.33; EC 4.2.1.35)
Original description: 3-isopropylmalate dehydratase, small subunit (TIGR)
SEED: 3-isopropylmalate dehydratase small subunit (EC 4.2.1.33)
KEGG: 3-isopropylmalate/(R)-2-methylmalate dehydratase small subunit
Rationale: # Important for fitness in defined media, except when both leucine and isoleucine are provided.

DVU3251 : nitrite transporter, HPP family
Original description: membrane protein, HPP family (TIGR)
SEED: membrane protein, HPP family
KEGG: no annotation
Rationale: # Specifically important in stress Sodium nitrite; nitrogen source Sodium nitrite; stress Sodium nitrate. Related to Synpcc7942_1745, which is a nitrite transporter (PMID:24904028), but it is not clear why this is important both during nitrite stress and when nitrite is the N source

DVU0114 hisG : ATP phosphoribosyltransferase (EC 2.4.2.17)
Original description: ATP phosphoribosyltransferase (TIGR)
SEED: ATP phosphoribosyltransferase (EC 2.4.2.17)
KEGG: ATP phosphoribosyltransferase
Rationale: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR00070.

DVU0285 hisH : IGP synthase, amidotransferase subunit (EC 4.3.2.10)
Original description: imidazole glycerol phosphate synthase, glutamine amidotransferase subunit (TIGR)
SEED: Imidazole glycerol phosphate synthase amidotransferase subunit (EC 2.4.2.-)
KEGG: glutamine amidotransferase
Rationale: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR01855.

DVU0464 : prephenate and/or arogenate dehydrogenase
Original description: prephenate dehydrogenase (TIGR)
SEED: Prephenate and/or arogenate dehydrogenase (unknown specificity) (EC 1.3.1.12)(EC 1.3.1.43)
KEGG: prephenate dehydrogenase
Rationale: # important for fitness in defined media, and rescued by added tyrosine. This is the second or third step in tyrosine synthesis from chorismate via prephenate; it is not clear if dehydrogenation or transamination occurs first.

DVU0549 : proline/arginine ABC transporter, permease component
Original description: high-affinity branched-chain amino acid ABC transporter, permease protein (TIGR)
SEED: Branched-chain amino acid transport system permease protein LivM (TC 3.A.1.4.1)
KEGG: branched-chain amino acid transport system permease protein
Rationale: Specific phenotype: utilization of L-Arginine, L-Proline

Or download reannotations for Desulfovibrio vulgaris Hildenborough JW710 or for all organisms as tab-delimited tables