Updated annotations for Desulfovibrio vulgaris Miyazaki F

15 genes with updated (or confirmed) annotations:

DvMF_0011 : L-serine ammonia-lyase (EC 4.3.1.17)
Original description: serine dehydratase alpha chain (RefSeq)
SEED: L-serine dehydratase, beta subunit (EC 4.3.1.17) / L-serine dehydratase, alpha subunit (EC 4.3.1.17)
KEGG: L-serine dehydratase
Rationale: Specifically important for utilizing L-Serine. Automated validation from mutant phenotype: the predicted function (4.3.1.17) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

DvMF_0044 : Homocysteine formation from aspartate semialdehyde (COG2122 or apbE like component)
Original description: hypothetical protein (RefSeq)
SEED: Sensory box histidine kinase/response regulator
KEGG: hypothetical protein
Rationale: Mutants in all three genes of this putative system are rescued by casamino acids or methionine but not by threonine. We propose that these three genes act together to enable the formation of homocysteine from asparate semialdehyde (the pathway proposed by Allen et al 2015 (PMID:25938369)). (auxotroph)

DvMF_0262 : Homocysteine formation from aspartate semialdehyde (NIL/ferredoxin component)
Original description: 4Fe-4S ferredoxin iron-sulfur binding domain protein (RefSeq)
SEED: Ferredoxin
KEGG: no annotation
Rationale: Mutants in all three genes of this putative system are rescued by casamino acids or methionine but not by threonine. We propose that these three genes act together to enable the formation of homocysteine from asparate semialdehyde (the pathway proposed by Allen et al 2015 (PMID:25938369)). (auxotroph)

DvMF_0450 : 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8)
Original description: dihydrodipicolinate reductase (RefSeq)
SEED: 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8)
KEGG: dihydrodipicolinate reductase
Rationale: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR00036.

DvMF_0476 : vitamin B12-dependent methionine synthase without a reactivation domain (EC 2.1.1.13)
Original description: homocysteine S-methyltransferase (RefSeq)
SEED: 5-methyltetrahydrofolate--homocysteine methyltransferase (EC 2.1.1.13)
KEGG: 5-methyltetrahydrofolate--homocysteine methyltransferase
Rationale: Important for fitness in most defined media and strongly cofit with the ATP-dependent co(II)balamin reductase (DvMF_1398). This lacks the usual reactivation domain for converting co(II)balamin to co(I)balamin; that activity is instead provided by DvMF_1398.

DvMF_0908 : histidinol-phosphate aminotransferase (EC 2.6.1.9)
Original description: histidinol-phosphate aminotransferase (RefSeq)
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.

DvMF_0971 aroK : Homoserine kinase (EC:2.7.1.39)
Original description: shikimate kinase (RefSeq)
SEED: Shikimate kinase I (EC 2.7.1.71)
KEGG: shikimate kinase
Rationale: Annotated as shikimate kinase, which is a similar reaction, but there is another shikimate kinase; rescued by threonine or CASamino acids (but not by methionine) (auxotroph)

DvMF_1398 : ATP-dependent reduction of co(II)balamin (RamA-like)
Original description: iron-sulfur cluster-binding protein, putative (RefSeq)
SEED: iron-sulfur cluster-binding protein, putative
KEGG: no annotation
Rationale: Cofit with the B12-dependent methionine synthase (DvMF_0476), which lacks a standard domain for the reactivation of vitamin B12.

DvMF_1412 : homoserine dehydrogenase (EC 1.1.1.3)
Original description: homoserine dehydrogenase (RefSeq)
SEED: Homoserine dehydrogenase (EC 1.1.1.3)
KEGG: homoserine dehydrogenase
Rationale: Important for fitness in most defined media and strongly cofit with homoserine kinase (DvMF_0971). 37% identical to homoserine dehydrogenase from Lactococcus lactis (P52985).

DvMF_1464 : Homocysteine formation from aspartate semialdehyde (DUF39 component)
Original description: protein of unknown function DUF39 (RefSeq)
SEED: no annotation
KEGG: no annotation
Rationale: Mutants in all three genes of this putative system are rescued by casamino acids or methionine but not by threonine. We propose that these three genes act together to enable the formation of homocysteine from asparate semialdehyde (the pathway proposed by Allen et al 2015 (PMID:25938369)). (auxotroph)

DvMF_1945 : threonine synthase (EC 4.2.3.1)
Original description: threonine synthase (RefSeq)
SEED: Threonine synthase (EC 4.2.3.1)
KEGG: threonine synthase
Rationale: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR00260.

DvMF_1963 hisG : ATP phosphoribosyltransferase (EC 2.4.2.17)
Original description: ATP phosphoribosyltransferase (RefSeq)
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.

DvMF_2038 aspS : aspartyl-tRNA(Asp/Asn) synthetase (EC 6.1.1.23)
Original description: aspartyl-tRNA synthetase (RefSeq)
SEED: Aspartyl-tRNA synthetase (EC 6.1.1.12)
KEGG: aspartyl-tRNA synthetase
Rationale: A conserved essential gene. This activity is necessary to explain asparagine biosynthesis.

DvMF_2305 hisH : IGP synthase, amidotransferase subunit (EC 4.3.2.10)
Original description: imidazole glycerol phosphate synthase subunit HisH (RefSeq)
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.

DvMF_3161 : pyrroline-5-carboxylate reductase (EC 1.5.1.2)
Original description: pyrroline-5-carboxylate reductase (RefSeq)
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.

Or download reannotations for Desulfovibrio vulgaris Miyazaki F or for all organisms as tab-delimited tables