Updated annotations for Shewanella loihica PV-4

16 genes with updated (or confirmed) annotations:

Shew_0548 : yqiA-like hydrolase, affects the cell envelope
Original description: hypothetical protein (RefSeq)
SEED: Putative esterase, FIGfam005057
KEGG: no annotation
Rationale: PFam PF05728.8 (UPF0227). conserved phenotypes: important in most defined media conditions

Shew_0815 : Glucosamine-6-phosphate deaminase (EC 3.5.99.6)
Original description: glucosamine-6-phosphate isomerase (RefSeq)
SEED: Glucosamine-6-phosphate deaminase (EC 3.5.99.6)
KEGG: glucosamine-6-phosphate deaminase
Rationale: Specifically important for utilizing N-Acetyl-D-Glucosamine. Automated validation from mutant phenotype: the predicted function (GLUCOSAMINE-6-P-DEAMIN-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Shew_1116 : N-acetylglucosamine kinase (EC 2.7.1.59)
Original description: ATPase, BadF/BadG/BcrA/BcrD type (RefSeq)
SEED: N-acetylglucosamine kinase of eukaryotic type (EC 2.7.1.59)
KEGG: no annotation
Rationale: Specifically important for: N-Acetyl-D-Glucosamine. The first step in NAG utilization (SEED_correct)

Shew_1117 : N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25)
Original description: N-acetylglucosamine-6-phosphate deacetylase (RefSeq)
SEED: N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25)
KEGG: N-acetylglucosamine-6-phosphate deacetylase
Rationale: Specifically important for utilizing N-Acetyl-D-Glucosamine. Automated validation from mutant phenotype: the predicted function (NAG6PDEACET-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Shew_1136 : 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.

Shew_1276 : Isocitrate lyase (EC 4.1.3.1)
Original description: isocitrate lyase (RefSeq)
SEED: Isocitrate lyase (EC 4.1.3.1)
KEGG: isocitrate lyase
Rationale: Specifically important for utilizing Potassium acetate. Automated validation from mutant phenotype: the predicted function (4.1.3.1) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Shew_1444 : dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), large permease component
Original description: TRAP dicarboxylate transporter, DctM subunit (RefSeq)
SEED: TRAP-type C4-dicarboxylate transport system, large permease component
KEGG: C4-dicarboxylate transporter, DctM subunit
Rationale: Important for utilizing succinate, fumarate, and L-malate, as expected, and also for utilizing a-ketoglutarate

Shew_1445 : dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), small permease component
Original description: tripartite ATP-independent periplasmic transporter DctQ (RefSeq)
SEED: no annotation
KEGG: C4-dicarboxylate transporter, DctQ subunit
Rationale: Important for utilizing succinate, fumarate, and L-malate, as expected, and also for utilizing a-ketoglutarate

Shew_1446 : dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), solute receptor component
Original description: TRAP dicarboxylate transporter, DctP subunit (RefSeq)
SEED: TRAP-type C4-dicarboxylate transport system, periplasmic component
KEGG: C4-dicarboxylate-binding protein DctP
Rationale: Important for utilizing succinate, fumarate, and L-malate, as expected, and also for utilizing a-ketoglutarate

Shew_2360 : D-hydroxyproline dehydrogenase
Original description: D-amino-acid dehydrogenase (RefSeq)
SEED: D-amino acid dehydrogenase (EC 1.4.99.1) family protein in hydroxy-L-proline catabolic cluster
KEGG: D-amino-acid dehydrogenase
Rationale: Specific phenotype: utilization of Gelatin. L-hydroxyproline is a major component of gelatin and converted to D-hydroxyproline by Shew_2363 (PMC4113996). Shew_2360 is 44% identical to the D-hydroxyproline dehydrogenase from Pseudomonas putida (PMC3463351). The P.putida enzyme was studied with an artificial electron acceptor and the in vivo acceptor does not seem to be known. Some related enzymes are D-amino acid oxidases (using O2 as the acceptor) but we suspect that Shew_2360 is not an oxidase.

Shew_2371 : actP-like component of L-lactate and L-malate uptake system
Original description: Na+/solute symporter (RefSeq)
SEED: Acetate permease ActP (cation/acetate symporter)
KEGG: cation/acetate symporter
Rationale: annotated as an acetate transporter, but important for L-lactate and L-malate utilization; see Sama_2372 (DUF4212)

Shew_2372 : small component of L-lactate and L-malate uptake system
Original description: hypothetical protein (RefSeq)
SEED: FIG152265: Sodium:solute symporter associated protein
KEGG: no annotation
Rationale: PFam PF13937.2 (DUF4212). conserved cofit with Shew_2371

Shew_3116 : predicted chromosome partitioning protein (with smc-like Shew_3118)
Original description: hypothetical protein (RefSeq)
SEED: FIG020568: hypothetical protein
KEGG: no annotation
Rationale: conserved cofit with smc-like (Shew_3118)

Shew_3117 : predicted chromosome partitioning protein (with smc-like Shew_3118)
Original description: hypothetical protein (RefSeq)
SEED: FIG020042: hypothetical protein
KEGG: no annotation
Rationale: conserved cofit with smc-like (Shew_3118)

Shew_3118 : smc-like chromosome partitioning protein (DUF3584)
Original description: hypothetical protein (RefSeq)
SEED: FIG020374: hypothetical protein
KEGG: no annotation
Rationale: Conserved phenotypes: important for motility and cisplatin resistance. DUF3584 is distantly related to smc proteins.

Shew_3272 : Aldose 1-epimerase (EC 5.1.3.3)
Original description: aldose 1-epimerase (RefSeq)
SEED: Aldose 1-epimerase (EC 5.1.3.3)
KEGG: aldose 1-epimerase
Rationale: Specifically important for utilizing D-Maltose monohydrate. Automated validation from mutant phenotype: the predicted function (5.1.3.3) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Or download reannotations for Shewanella loihica PV-4 or for all organisms as tab-delimited tables