Updated annotations for Dyella japonica UNC79MFTsu3.2

21 genes with updated (or confirmed) annotations:

ABZR86_RS01205 : D-galactanolactonase
Original description: SMP-30/gluconolactonase/LRE family protein
SEED: L-arabinolactonase (EC 3.1.1.15)
KEGG: L-arabinonolactonase
Rationale: Specifically important for galactose utilization. It is not certain whether the galactose dehydrogenase (N515DRAFT_1230) forms the 1,5-lactone or the 1,4-lactone.

ABZR86_RS01225 : 2-dehydro-3-deoxygalactonokinase dgoK (EC 2.7.1.58)
Original description: 2-dehydro-3-deoxygalactonokinase
SEED: 2-dehydro-3-deoxygalactonokinase (EC 2.7.1.58)
KEGG: no annotation
Rationale: Specifically important for galactose utilization.

ABZR86_RS01395 : Alanine dehydrogenase (EC 1.4.1.1)
Original description: alanine dehydrogenase
SEED: Alanine dehydrogenase (EC 1.4.1.1)
KEGG: alanine dehydrogenase
Rationale: Specifically important for utilizing L-Alanine. Automated validation from mutant phenotype: the predicted function (ALANINE-DEHYDROGENASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

ABZR86_RS03855 : Nitrite reductase (NAD(P)H) (EC 1.7.1.4)
Original description: nitrite reductase large subunit NirB
SEED: Nitrite reductase [NAD(P)H] large subunit (EC 1.7.1.4)
KEGG: nitrite reductase (NAD(P)H) large subunit
Rationale: Specifically important for utilizing Sodium nitrate. Automated validation from mutant phenotype: the predicted function (1.7.1.4) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

ABZR86_RS03860 : Nitrite reductase (NAD(P)H) (EC 1.7.1.4)
Original description: nitrite reductase small subunit NirD
SEED: Nitrite reductase [NAD(P)H] small subunit (EC 1.7.1.4)
KEGG: nitrite reductase (NAD(P)H) small subunit
Rationale: Specifically important for utilizing Sodium nitrate. Automated validation from mutant phenotype: the predicted function (1.7.1.4) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

ABZR86_RS03865 : Nitrate reductase (EC 1.7.99.4)
Original description: nitrate reductase
SEED: Assimilatory nitrate reductase large subunit (EC:1.7.99.4)
KEGG: nitrate reductase catalytic subunit
Rationale: Specifically important for utilizing Sodium nitrate. Automated validation from mutant phenotype: the predicted function (1.7.99.4) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

ABZR86_RS06665 : L-proline transporter
Original description: amino acid permease
SEED: Amino acid transporters
KEGG: basic amino acid/polyamine antiporter, APA family
Rationale: Mildly important for growth with proline as the carbon source, but not in other conditions

ABZR86_RS08695 : arginosuccinate lyase (EC 4.3.2.1)
Original description: argininosuccinate lyase
SEED: Argininosuccinate lyase (EC 4.3.2.1)
KEGG: argininosuccinate lyase
Rationale: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR00838.

ABZR86_RS08700 : N-acetylglutamylphosphate reductase (EC 1.2.1.38)
Original description: N-acetyl-gamma-glutamyl-phosphate reductase
SEED: N-acetyl-gamma-glutamyl-phosphate reductase (EC 1.2.1.38)
KEGG: N-acetyl-gamma-glutamyl-phosphate/N-acetyl-gamma-aminoadipyl-phosphate reductase
Rationale: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR01850.

ABZR86_RS08705 : N-acetylglutamate synthase; N-acetylglutamate kinase (EC 2.3.1.1; EC 2.7.2.8)
Original description: acetylglutamate kinase
SEED: Acetylglutamate kinase (EC 2.7.2.8)
KEGG: acetylglutamate/acetylaminoadipate kinase
Rationale: Important for fitness in most defined media, except when arginine is provided. Contains both acetylglutamate kinase (TIGR00761) and N-acetylglutamate synthase (PF04768) domains.

ABZR86_RS08710 : N-acetylcitrulline deacetylase (EC 3.5.1.-)
Original description: acetylornithine deacetylase
SEED: Acetylornithine deacetylase (EC 3.5.1.16)
KEGG: acetylornithine deacetylase
Rationale: Important for fitness in most defined media, except when arginine is provided. 70% identical to argE¡¯ from Xanthomona campestris (Q8P8J5), which is active on both N-acetylornithine and N-acetylcitrulline. But only the N-acetylcitrulline activity is expected to be relevant (see N-acetylornithine carbamoyltransferase N515DRAFT_3763)

ABZR86_RS08715 : arginosuccinate synthetase (EC 6.3.4.5)
Original description: argininosuccinate synthase
SEED: Argininosuccinate synthase (EC 6.3.4.5)
KEGG: argininosuccinate synthase
Rationale: Important for fitness in most defined media, except when arginine is provided. 35% identical to argininosuccinate synthase from Thermus thermophilus (P59846).

ABZR86_RS11100 : fructose porter FruP
Original description: L-fucose:H+ symporter permease
SEED: Predicted mannose transporter, GGP family
KEGG: MFS transporter, FHS family, L-fucose permease
Rationale: Specifically important for growth on fructose.

ABZR86_RS11105 : Fructokinase (EC 2.7.1.4)
Original description: carbohydrate kinase
SEED: Fructokinase (EC 2.7.1.4)
KEGG: fructokinase
Rationale: Specifically important for utilizing D-Fructose. Automated validation from mutant phenotype: the predicted function (2.7.1.4) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

ABZR86_RS11580 : Branched-chain amino acid aminotransferase (EC 2.6.1.42)
Original description: branched-chain amino acid transaminase
SEED: Branched-chain amino acid aminotransferase (EC 2.6.1.42)
KEGG: branched-chain amino acid aminotransferase
Rationale: Specifically important for utilizing L-Isoleucine. Automated validation from mutant phenotype: the predicted function (BRANCHED-CHAINAMINOTRANSFERILEU-RXN, BRANCHED-CHAINAMINOTRANSFERLEU-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

ABZR86_RS14645 : DNA repair helicase Lhr
Original description: DEAD/DEAH box helicase
SEED: Lhr-like helicases
KEGG: no annotation
Rationale: # Specifically important in stress Cisplatin. Similar to the full length of Lhr from Mycobacterium smegmatis, which is a helicase that is suspected to be involved in DNA repair (see PMC3656269) (SEED_correct)

ABZR86_RS15975 : threonine synthase (EC 4.2.3.1)
Original description: threonine synthase
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.

ABZR86_RS15980 : homoserine kinase (EC 2.7.1.39)
Original description: homoserine kinase
SEED: Homoserine kinase (EC 2.7.1.39)
KEGG: homoserine kinase
Rationale: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR00191.

ABZR86_RS16985 : Alpha-amylase (EC 3.2.1.1)
Original description: alpha-amylase family glycosyl hydrolase
SEED: Alpha-amylase (EC 3.2.1.1)
KEGG: no annotation
Rationale: Specifically important for utilizing a-Cyclodextrin. Automated validation from mutant phenotype: the predicted function (3.2.1.1) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

ABZR86_RS18410 : Arginase (EC 3.5.3.1)
Original description: arginase
SEED: Arginase (EC 3.5.3.1)
KEGG: arginase
Rationale: Specifically important for utilizing L-Arginine. Automated validation from mutant phenotype: the predicted function (ARGINASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

ABZR86_RS19560 : aspartate kinase / diaminopimelate decarboxylase (EC 4.1.1.20; EC 2.7.2.4)
Original description: bifunctional aspartate kinase/diaminopimelate decarboxylase
SEED: Aspartokinase (EC 2.7.2.4) / Diaminopimelate decarboxylase (EC 4.1.1.20)
KEGG: bifunctional diaminopimelate decarboxylase / aspartate kinase
Rationale: Important for fitness in most defined media. Contains TIGR00657 and TIGR01048.

Or download reannotations for Dyella japonica UNC79MFTsu3.2 or for all organisms as tab-delimited tables