Updated annotations for Azospirillum brasilense Sp245

28 genes with updated (or confirmed) annotations:

AZOBR_RS00190 : L-glutamate dehydrogenase (NAD+) (EC 1.4.1.2)
Original description: NAD-glutamate dehydrogenase
SEED: NAD-specific glutamate dehydrogenase (EC 1.4.1.2), large form
KEGG: no annotation
Rationale: Very important for utilization of L-proline and L-glutamine, which are catabolized via glutamate. Also important for utilization of aspartate or leucine as nitrogen sources, which might indicate transamination to form glutamate.

AZOBR_RS01680 : 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16)
Original description: 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
SEED: Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (EC 5.3.1.16)
KEGG: phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase
Rationale: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR00007.

AZOBR_RS01690 : phosphoribosyl-ATP pyrophosphatase (EC 3.6.1.31)
Original description: phosphoribosyl-ATP pyrophosphatase
SEED: Phosphoribosyl-ATP pyrophosphatase (EC 3.6.1.31)
KEGG: phosphoribosyl-ATP pyrophosphohydrolase
Rationale: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR03188.

AZOBR_RS02935 : small component of pyruvate transporter (yjcH-like)
Original description: membrane protein
SEED: Putative membrane protein, clustering with ActP
KEGG: no annotation
Rationale: Specifically important for pyruvate utilization. 54% identical to E. coli yjcH.

AZOBR_RS02940 : large component of pyruvate transporter (actP-like)
Original description: actetate permease
SEED: Acetate permease ActP (cation/acetate symporter)
KEGG: cation/acetate symporter
Rationale: Specifically important for pyruvate utilization.

AZOBR_RS03845 : Histidinol-phosphatase [alternative form] (EC 3.1.3.15)
Original description: histidinol-phosphate phosphatase
SEED: Histidinol-phosphatase [alternative form] (EC 3.1.3.15)
KEGG: no annotation
Rationale: Annotated as this by multiple resources. (auxotroph) (SEED_correct)

AZOBR_RS05755 : Butyryl-CoA dehydrogenase (EC 1.3.8.1)
Original description: acyl-CoA dehydrogenase
SEED: Acyl-CoA dehydrogenase (EC 1.3.8.7)
KEGG: no annotation
Rationale: Specifically important for: Sodium butyrate. KEGG's annotation of azl:AZL_005040 has been updated to 3-(methylthio)propanoyl-CoA dehydrogenase [EC:1.3.8.-], which is questionable; phenotype indicates that butyryl-CoA is a substrate (SEED_correct)

AZOBR_RS06555 : Branched-chain-amino-acid transaminase (EC 2.6.1.42)
Original description: GntR family transcriptional regulator
SEED: Transcriptional regulator, GntR family domain / Aspartate aminotransferase (EC 2.6.1.1)
KEGG: no annotation
Rationale: Specifically important for utilizing L-Leucine. Automated validation from mutant phenotype: the predicted function (2.6.1.42) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

AZOBR_RS08020 : D-alanine dehydrogenase (EC 1.4.99.-)
Original description: D-amino acid dehydrogenase small subunit
SEED: D-amino acid dehydrogenase small subunit (EC 1.4.99.1)
KEGG: D-amino-acid dehydrogenase
Rationale: Specifically important for utilizing D-Alanine. Automated validation from mutant phenotype: the predicted function (DALADEHYDROG-RXN) was linked to the condition via a SEED subsystem. A more specific reaction was selected manually.

AZOBR_RS08235 : L-proline and D-alanine ABC transporter, permease component 1
Original description: branched-chain amino acid transporter permease subunit LivH
SEED: High-affinity branched-chain amino acid transport system permease protein LivH (TC 3.A.1.4.1)
KEGG: no annotation
Rationale: specific phenotype on L-proline and D-alanine and cofit with other subunits nearby

AZOBR_RS08240 : L-proline and D-alanine ABC transporter, permease component 2
Original description: ABC transporter permease
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: Specifically important for utilization of L-proline and D-alanine.

AZOBR_RS08245 : L-proline and D-alanine ABC transporter, ATPase component 1
Original description: branched-chain amino acid ABC transporter ATP-binding protein
SEED: Branched-chain amino acid transport ATP-binding protein LivG (TC 3.A.1.4.1)
KEGG: branched-chain amino acid transport system ATP-binding protein
Rationale: Specifically important for utilization of L-proline and D-alanine.

AZOBR_RS08250 : L-proline and D-alanine ABC transporter, ATPase component 2
Original description: amino acid ABC transporter ATPase
SEED: Branched-chain amino acid transport ATP-binding protein LivF (TC 3.A.1.4.1)
KEGG: branched-chain amino acid transport system ATP-binding protein
Rationale: Specifically important for utilization of L-proline and D-alanine.

AZOBR_RS08260 : L-proline and D-alanine ABC transporter, substrate-binding component
Original description: ABC transporter
SEED: Branched-chain amino acid ABC transporter, amino acid-binding protein (TC 3.A.1.4.1)
KEGG: branched-chain amino acid transport system substrate-binding protein
Rationale: Specifically important for utilization of L-proline and D-alanine.

AZOBR_RS10130 : required for sulfate utilization, putative electron source for sulfite reductase CysI
Original description: hypothetical protein
SEED: Conserved hypothetical protein probably involved in sulfate reduction
KEGG: no annotation
Rationale: PFam PF11011.4 (DUF2849). conserved cofit with sulfite reductase and has a complementary pattern of gene presence as cysJ

AZOBR_RS15915 : gluconate TRAP transporter, periplasmic solute-binding component
Original description: ABC transporter substrate-binding protein
SEED: TRAP-type transport system, periplasmic component, predicted N-acetylneuraminate-binding protein
KEGG: no annotation
Rationale: Specifically important for gluconate utilization. The small component is AZOBR_RS15925 (misannotated as a pseudogene).

AZOBR_RS15920 : Large component of TRAP-type D-gluconate transporter
Original description: dehydroascorbate transporter
SEED: TRAP-type C4-dicarboxylate transport system, large permease component
KEGG: no annotation
Rationale: specific phenotype on D-gluconic acid and cofit with other components nearby; 56% identical to SMa0250 of S. meliloti, which is required for gluconate utilization (PMCid:PMC2631997). Also is 56% identical to Atu2743 of A. tumefaciens, which takes up galacturonate (PMCid:PMC4751846), so this might also be a galacturonate transporter (we did not study galacturonate utilizaton in this organism)

AZOBR_RS15925 : gluconate TRAP transporter, small permease component
Original description: C4-dicarboxylate ABC transporter permease
SEED: no annotation
KEGG: no annotation
Rationale: Specifically important for gluconate utiliation. This region was originally annotated as a pseudogene, but there is a reading frame of 179 a.a.; for its sequence, see AZOBR_p130075 or G8AR26. The large compoennt is AZOBR_RS15915.

AZOBR_RS18550 : ABC transporter for nitrate, ATPase component
Original description: ABC transporter ATPase
SEED: Nitrate ABC transporter, ATP-binding protein
KEGG: no annotation
Rationale: Specific phenotype on Sodium nitrate. (SEED_correct)

AZOBR_RS18555 : ABC transporter for nitrate, permease component
Original description: nitrate ABC transporter permease
SEED: no annotation
KEGG: sulfonate/nitrate/taurine transport system permease protein
Rationale: Specific phenotypes on Sodium nitrate; Sodium nitrate. Other substrates proposed by KEGG )sulfonate and taurine) were not tested. (KEGG_correct)

AZOBR_RS18560 : ABC transporter for nitrate, periplasmic substrate-binding component
Original description: nitrate ABC transporter substrate-binding protein
SEED: Nitrate ABC transporter, nitrate-binding protein
KEGG: sulfonate/nitrate/taurine transport system ATP-binding protein
Rationale: Specific phenotype on Sodium nitrate. (SEED_correct)

AZOBR_RS18565 : Nitrite reductase (NAD(P)H) (EC 1.7.1.4)
Original description: nitrite reductase
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.

AZOBR_RS19025 : acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17]
Original description: acetylornithine aminotransferase
SEED: Acetylornithine aminotransferase (EC 2.6.1.11)
KEGG: acetylornithine/N-succinyldiaminopimelate aminotransferase
Rationale: Annotated as this by KEGG. Bifunctional argD. SEED has only the acetylornithine activity. (essential) (KEGG_correct)

AZOBR_RS19500 : ATP phosphoribosyltransferase (EC 2.4.2.17)
Original description: ATP phosphoribosyltransferase catalytic subunit
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.

AZOBR_RS20485 : histidinol-phosphate aminotransferase [EC:2.6.1.9]
Original description: histidinol-phosphate aminotransferase
SEED: no annotation
KEGG: histidinol-phosphate aminotransferase
Rationale: Annotated as this by multiple resources. AZOBR_RS08675 is also sometimes annotated with this function but has little phenotype. (auxotroph) (KEGG_correct)

AZOBR_RS23695 : L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2)
Original description: transcriptional regulator
SEED: Proline dehydrogenase (EC 1.5.99.8) (Proline oxidase) / Delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.5.1.12)
KEGG: proline dehydrogenase / delta 1-pyrroline-5-carboxylate dehydrogenase
Rationale: Specifically important for utilizing L-Proline. Automated validation from mutant phenotype: the predicted function (1.2.1.88, 1.5.5.2) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

AZOBR_RS32325 : Fructose PTS system (E-I, HPr, and E-IIA components)
Original description: PTS fructose transporter subunit IIA
SEED: Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9)
KEGG: PTS system, fructose-specific IIA component ; phosphotransferase system, enzyme I, PtsI ; phosphocarrier protein FPr
Rationale: Specifically important for utilizing D-Fructose. This gene includes components E-I (PEP-protein phoshpotransferase), HPr, and E-IIA. Components E-IIB and E-IIC are in the adjacent gene AZOBR_RS32335.

AZOBR_RS32335 : fructose-specific PTS system (fructose 1-phosphate forming), EII-B'BC components (FruA)
Original description: PTS fructose transporter subunit IIBC
SEED: PTS system, fructose-specific IIB component (EC 2.7.1.69) / PTS system, fructose-specific IIC component (EC 2.7.1.69)
KEGG: PTS system, fructose-specific IIB component ; PTS system, fructose-specific IIC component
Rationale: Specific phenotype on fructose.

Or download reannotations for Azospirillum brasilense Sp245 or for all organisms as tab-delimited tables