Updated Annotations for Shewanella amazonensis SB2B

Updated annotations for Shewanella amazonensis SB2B

59 genes with updated (or confirmed) annotations:

Sama_0031 fadA : Acetyl-CoA C-acyltransferase (EC 2.3.1.16)
Original description: 3-ketoacyl-CoA thiolase (RefSeq)
SEED: 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)
KEGG: acetyl-CoA acyltransferase
Rationale: Specifically important for utilizing Tween 20. Automated validation from mutant phenotype: the predicted function (KETOACYLCOATHIOL-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Sama_0032 fadB : Enoyl-CoA hydratase (EC 4.2.1.17); 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35)
Original description: multifunctional fatty acid oxidation complex subunit alpha (RefSeq)
SEED: Enoyl-CoA hydratase (EC 4.2.1.17) / Delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase (EC 5.3.3.8) / 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) / 3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3)
KEGG: 3-hydroxyacyl-CoA dehydrogenase / enoyl-CoA hydratase / 3-hydroxybutyryl-CoA epimerase / enoyl-CoA isomerase
Rationale: Specifically important for utilizing Tween 20. Automated validation from mutant phenotype: the predicted function (ENOYL-COA-HYDRAT-RXN, OHACYL-COA-DEHYDROG-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Sama_0165 : Phosphoenolpyruvate carboxykinase [ATP] (EC 4.1.1.49)
Original description: phosphoenolpyruvate carboxykinase (RefSeq)
SEED: Phosphoenolpyruvate carboxykinase [ATP] (EC 4.1.1.49)
KEGG: phosphoenolpyruvate carboxykinase (ATP)
Rationale: Specifically important for utilizing Tween 20. Automated validation from mutant phenotype: the predicted function (PEPCARBOXYKIN-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Sama_0412 : Uridine phosphorylase (EC 2.4.2.3)
Original description: uridine phosphorylase (RefSeq)
SEED: Uridine phosphorylase (EC 2.4.2.3)
KEGG: uridine phosphorylase
Rationale: Specifically important for utilizing Cytidine and Uridine. Automated validation from mutant phenotype: the predicted function (URPHOS-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Sama_0429 : predicted FeS cluster maintenance protein
Original description: hypothetical protein (RefSeq)
SEED: no annotation
KEGG: no annotation
Rationale: PFam PF06155.8 (DUF971). conserved cofitness with mrp/apbC (Sama_2048)

Sama_0535 : 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.

Sama_0560 : D-mannose isomerase (EC 5.3.1.7)
Original description: hypothetical protein (RefSeq)
SEED: D-mannose isomerase (EC 5.3.1.7)
KEGG: no annotation
Rationale: Specifically important for: D-Mannose. This is the first step in D-mannose catabolism. Also see PMID:20836887, PMCID: PMC4436071

Sama_0561 : Fructokinase (EC 2.7.1.4)
Original description: carbohydrate kinase (RefSeq)
SEED: Fructokinase (EC 2.7.1.4)
KEGG: fructokinase
Rationale: Specifically important for utilizing D-Mannose. 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.

Sama_0562 : D-mannose transporter (MFS superfamily)
Original description: glucose/galactose transporter (RefSeq)
SEED: Predicted mannose transporter, GGP family
KEGG: no annotation
Rationale: Specific phenotype on mannose and no other transporter is apparent in the fitness data.

Sama_0592 : 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.

Sama_0593 : predicted chromosome partitioning protein (with smc-like Sama_0592)
Original description: hypothetical protein (RefSeq)
SEED: FIG020042: hypothetical protein
KEGG: no annotation
Rationale: conserved cofit with smc-like (Sama_0592)

Sama_0594 : predicted chromosome partitioning protein (with smc-like Sama_0592)
Original description: hypothetical protein (RefSeq)
SEED: FIG020568: hypothetical protein
KEGG: no annotation
Rationale: conserved cofit with smc-like (Sama_0592)

Sama_0794 : gamma-glutamyl-gamma-aminobutyrate hydrolase (EC: 3.5.1.94)
Original description: hypothetical protein (RefSeq)
SEED: Para-aminobenzoate synthase, amidotransferase component (EC 2.6.1.85)
KEGG: putative glutamine amidotransferase
Rationale: Specifically important for: Putrescine Dihydrochloride. Similar to puuD (PUUD_ECO57), a step in putrescine catabolism. Also, is cofit with other genes from the gamma-glutamyl-putrescine pathway. However another homolog of puuD (Sama_2645) is also important in putrescine utilization and it is not clear why. Both of the homologs in S. amazonensis have conserved active site residues (see aliignments against puuD in PaperBLAST).

Sama_0944 : N-acetylglucosamine kinase (EC 2.7.1.59)
Original description: hypothetical protein (RefSeq)
SEED: N-acetylglucosamine kinase of eukaryotic type (EC 2.7.1.59)
KEGG: no annotation
Rationale: Specifically important for: N-Acetyl-D-Glucosamine. This is the first step in NAG utilization (SEED_correct)

Sama_0945 : Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6)
Original description: glutamine--fructose-6-phosphate transaminase (isomerizing) (RefSeq)
SEED: Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6)
KEGG: glucosamine--fructose-6-phosphate aminotransferase (isomerizing)
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.

Sama_0946 : 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.

Sama_0947 : transmembrane glucosamine N-acetyltransferase NagX
Original description: hypothetical protein (RefSeq)
SEED: N-acetylglucosamine related transporter, NagX
KEGG: no annotation
Rationale: Specifically important for glucosamine utilization. NagX proteins are distantly related to human HGSNAT (uniprot:Q68CP4), which is a transmembrane acetyl-CoA:alpha-glucosaminide N-acetyltransferase.

Sama_1304 : component of chlorite stress sensing system with DUF692
Original description: hypothetical protein (RefSeq)
SEED: FIG024746: hypothetical protein
KEGG: no annotation
Rationale: specific phenotype; this gene seems to replace DUF2063

Sama_1305 : component of chlorite stress sensing system with Sama_1304
Original description: hypothetical protein (RefSeq)
SEED: FIG023677: hypothetical protein
KEGG: hypothetical protein
Rationale: PFam PF05114.9 (DUF692). conserved specific phenotype, and Sama_1304 seems to replace DUF2063

Sama_1319 : symporter for L-glutamate, L-glutamine, and L-aspartate
Original description: sodium:dicarboxylate symporter (RefSeq)
SEED: no annotation
KEGG: dicarboxylate/amino acid:cation (Na+ or H+) symporter, DAACS family
Rationale: Specifically important for utilization of L-glutamate or L-glutamine as carbon sources or L-aspartate as a nitrogen source. Glutamine is probably cleaved by a cytoplasmic glutaminase (Sama_2487), so glutamine is probably a substrate.

Sama_1321 : Succinylarginine dihydrolase (EC 3.5.3.23)
Original description: succinylarginine dihydrolase (RefSeq)
SEED: Succinylarginine dihydrolase (EC 3.5.3.23)
KEGG: succinylarginine dihydrolase
Rationale: Specifically important for utilizing L-Arginine. Automated validation from mutant phenotype: the predicted function (SUCCARGDIHYDRO-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Sama_1356 : 3-oxoacid CoA-transferase (EC 2.8.3.5), subunit B
Original description: 3-oxoacid CoA-transferase (RefSeq)
SEED: Succinyl-CoA:3-ketoacid-coenzyme A transferase subunit B (EC 2.8.3.5)
KEGG: 3-oxoacid CoA-transferase subunit B
Rationale: Specifically important for utilizing L-Leucine. The A subunit is Sama_1357.

Sama_1357 : 3-oxoacid CoA-transferase (EC 2.8.3.5), subunit A
Original description: 3-oxoacid CoA-transferase (RefSeq)
SEED: Succinyl-CoA:3-ketoacid-coenzyme A transferase subunit A (EC 2.8.3.5)
KEGG: 3-oxoacid CoA-transferase subunit A
Rationale: Specifically important for utilizing L-Leucine. The B subunit is Sama_1356.

Sama_1359 : 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit (EC 6.4.1.4)
Original description: 3-methylcrotonyl-CoA carboxylase alpha subunit (RefSeq)
SEED: Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4)
KEGG: 3-methylcrotonyl-CoA carboxylase alpha subunit
Rationale: Specifically important for utilizing L-Leucine.

Sama_1361 : 3-methylcrotonyl-CoA carboxylase, beta subunit (EC 6.4.1.4)
Original description: propionyl-CoA carboxylase (RefSeq)
SEED: Methylcrotonyl-CoA carboxylase carboxyl transferase subunit (EC 6.4.1.4)
KEGG: 3-methylcrotonyl-CoA carboxylase beta subunit
Rationale: Specifically important for utilizing L-Leucine. Automated validation from mutant phenotype: the predicted function (6.4.1.4) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Sama_1362 : Isovaleryl-CoA dehydrogenase (EC 1.3.8.4)
Original description: isovaleryl-CoA dehydrogenase (RefSeq)
SEED: Isovaleryl-CoA dehydrogenase (EC 1.3.8.4)
KEGG: isovaleryl-CoA dehydrogenase
Rationale: Specifically important for utilizing L-Leucine. Automated validation from mutant phenotype: the predicted function (RXN0-2301) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Sama_1401 : D-cellobiose transporter (MFS superfamily)
Original description: sugar (glycoside-Pentoside-hexuronide) transporter (RefSeq)
SEED: Predicted beta-glucoside transporter, GPH family
KEGG: glycoside/pentoside/hexuronide:cation symporter, GPH family
Rationale: Specific phenotype on cellobiose and no other transporter for this compound was apparent in the fitness data. Also, this protein is 70% identical to bglT from S. fridgimarina, which is a cellobiose transporter (PMC2996990).

Sama_1404 : Beta-glucosidase (EC 3.2.1.21)
Original description: beta-glucosidase (RefSeq)
SEED: Periplasmic beta-glucosidase (EC 3.2.1.21)
KEGG: beta-glucosidase
Rationale: Specifically important for utilizing D-Cellobiose. Automated validation from mutant phenotype: the predicted function (3.2.1.21) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Sama_1405 : glucokinase (EC 2.7.1.2)
Original description: fructokinase (RefSeq)
SEED: Glucokinase, ROK family (EC 2.7.1.2)
KEGG: fructokinase
Rationale: Specifically important for: D-Cellobiose. After cellobiose is cleaved to 2 glucose (by Sama_1404), it would be phosphorylated to enter glycolysis (SEED_correct)

Sama_1522 : small component of lactate 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 Sama_1523

Sama_1523 : actP-like component of lactate uptake system
Original description: sodium/solute symporter family protein (RefSeq)
SEED: Acetate permease ActP (cation/acetate symporter)
KEGG: cation/acetate symporter
Rationale: annotated as an acetate transporter, but important for lactate utilization; see Sama_1522 (DUF4212)

Sama_1588 : putative adhesin (DUF1302)
Original description: hypothetical protein (RefSeq)
SEED: FIG067310: hypothetical protein
KEGG: no annotation
Rationale: Similar to PA3923, which binds laminin (PMC6890786) and is involved in biofilm formation (PMC8547006), so this is probably an adhesin.

Sama_1589 : adhesin-associated sorting protein (DUF1329)
Original description: hypothetical protein (RefSeq)
SEED: FIG002188: hypothetical protein
KEGG: no annotation
Rationale: Conserved cofit with a putative adhesin (Sama_1588). DUF1329 is distantly related to lolB, which inserts lipoproteins into the outer membrane. So we predict that DUF1329 is involved in sorting the adhesin to the outer membrane.

Sama_1590 : adhesin-associated BNR repeat protein
Original description: BNR repeat-containing protein (RefSeq)
SEED: FIG002465: BNR repeat protein
KEGG: no annotation
Rationale: Conserved cofit with a putative adhesin (Sama_1588). This is also predicted to be an outer membrane protein.

Sama_1591 : adhesin-associated MmpL efflux pump
Original description: hypothetical protein (RefSeq)
SEED: FIG005548: transport protein
KEGG: no annotation
Rationale: Conserved cofit with a putative adhesin (Sama_1588). The MmpL family is involved in efflux of lipids or siderophores (see IPR004869); we speculate that this exports a lipid or saccharide that is attached to the adhesin.

Sama_1631 : Histidine ammonia-lyase (EC 4.3.1.3)
Original description: histidine ammonia-lyase (RefSeq)
SEED: Histidine ammonia-lyase (EC 4.3.1.3)
KEGG: histidine ammonia-lyase
Rationale: Specifically important for utilizing L-Histidine. Automated validation from mutant phenotype: the predicted function (HISTIDINE-AMMONIA-LYASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Sama_1632 : Urocanate hydratase (EC 4.2.1.49)
Original description: urocanate hydratase (RefSeq)
SEED: Urocanate hydratase (EC 4.2.1.49)
KEGG: urocanate hydratase
Rationale: Specifically important for utilizing L-Histidine. Automated validation from mutant phenotype: the predicted function (UROCANATE-HYDRATASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Sama_1743 : Acyl-CoA dehydrogenase (EC 1.3.8.-)
Original description: acyl-CoA dehydrogenase family protein (RefSeq)
SEED: Acyl-CoA dehydrogenase (EC 1.3.8.7)
KEGG:
Rationale: Specifically important in carbon source Tween 20. This confirms that it is an acyl-CoA dehydrogenase and not a biosynthetic acyl-ACP dehydrogenase (as suggested by KEGG). Since Tween 20 is hydrolyzed to a C12 fatty acid, this may act on long chain acyl-CoAs, or it might act on medium-chain acyl-CoA intermediates.

Sama_1921 : yeaG component of nitrogen-related signalling system (of yeaGH-ycgB)
Original description: putative serine protein kinase, PrkA (RefSeq)
SEED: Serine protein kinase (prkA protein), P-loop containing
KEGG: serine protein kinase
Rationale: conserved cofitness; yeaG is a protein kinase

Sama_1922 : yeaH component of nitrogen-related signalling system yeaH (of yeaGH-ycgB)
Original description: hypothetical protein (RefSeq)
SEED: no annotation
KEGG: hypothetical protein
Rationale: PFam PF04285.8 (DUF444). conserved cofitness; yeaG is a protein kinase

Sama_1923 : ycgB component of nitrogen-related signalling system (of yeaGH-ycgB)
Original description: SpoVR family protein (RefSeq)
SEED: FIG004684: SpoVR-like protein
KEGG: no annotation
Rationale: conserved cofitness; yeaG is a protein kinase

Sama_1974 : Cytidine deaminase (EC 3.5.4.5)
Original description: cytidine deaminase (RefSeq)
SEED: Cytidine deaminase (EC 3.5.4.5)
KEGG: cytidine deaminase
Rationale: Specifically important for utilizing Cytidine. Automated validation from mutant phenotype: the predicted function (CYTIDEAM2-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Sama_2080 : DNA damage response helicase (yejH or radD)
Original description: helicase (RefSeq)
SEED: ATP-dependent RNA helicase YejH
KEGG: no annotation
Rationale: Conserved and specific phenotype: important for resisting cisplatin. Also important for resisting ionizing radiationa and UV radiation in E. coli (PMID:25425430)

Sama_2099 : UMP phosphatase (EC 3.1.3.5)
Original description: UMP phosphatase (RefSeq)
SEED: Phosphatase NagD predicted to act in N-acetylglucosamine utilization subsystem
KEGG: NagD protein
Rationale: Specifically important for: Thymidine. Probably required for thymidine utilization because it allows overflow metabolism of pyrimidine intermediates, as with umpH from E. coli (which is 72% identical), see PMID 23903661

Sama_2209 : alpha-ketoglutarate TRAP transporter, solute receptor component
Original description: C4-dicarboxylate-binding periplasmic protein (RefSeq)
SEED: TRAP-type C4-dicarboxylate transport system, periplasmic component
KEGG: C4-dicarboxylate-binding protein DctP
Rationale: specific phenotype on a-ketoglutarate. A putrescine ABC transporter (Sama_2642:Sama_2638) is also important in this condition, which is not explained. This organism can also utilize succinate or fumarate (but not L-malate), which we do not have fitness data for these under aerobic conditions. This could also transport some C4 compounds.

Sama_2210 : alpha-ketoglutarate TRAP transporter, small permease component
Original description: C4-dicarboxylate transporter, putative (RefSeq)
SEED: no annotation
KEGG: C4-dicarboxylate transporter, DctQ subunit
Rationale: specific phenotype on a-ketoglutarate. A putrescine ABC transporter (Sama_2642:Sama_2638) is also important in this condition, which is not explained. This organism can also utilize succinate or fumarate (but not L-malate), which we do not have fitness data for these under aerobic conditions. This could also transport some C4 compounds.

Sama_2211 : alpha-ketoglutarate TRAP transporter, large permease component
Original description: C4-dicarboxylate transport protein (RefSeq)
SEED: TRAP-type C4-dicarboxylate transport system, large permease component
KEGG: C4-dicarboxylate transporter, DctM subunit
Rationale: specific phenotype on a-ketoglutarate. A putrescine ABC transporter (Sama_2642:Sama_2638) is also important in this condition, which is not explained. This organism can also utilize succinate or fumarate (but not L-malate), which we do not have fitness data for these under aerobic conditions. This could also transport some C4 compounds.

Sama_2231 : glucokinase (EC 2.7.1.2)
Original description: fructokinase (RefSeq)
SEED: Glucokinase, ROK family (EC 2.7.1.2)
KEGG: fructokinase
Rationale: Specifically important for: D-Maltose monohydrate. Maltose is presumably cleaved to glucose, so the annotation as glucokinase (but not as fructokinase) fits. The other glucokinase (Sama_1405) is not important on maltose. (SEED_correct)

Sama_2380 : 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 Tween 20. Automated validation from mutant phenotype: the predicted function (ISOCIT-CLEAV-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Sama_2487 : Glutaminase (EC 3.5.1.2)
Original description: glutaminase (RefSeq)
SEED: Glutaminase (EC 3.5.1.2)
KEGG: glutaminase
Rationale: Specifically important for utilizing L-Glutamine. Automated validation from mutant phenotype: the predicted function (GLUTAMIN-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Sama_2636 : gamma-aminobutyrate transaminase (EC 2.6.1.19)
Original description: 4-aminobutyrate aminotransferase (RefSeq)
SEED: Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)
KEGG: 4-aminobutyrate aminotransferase / (S)-3-amino-2-methylpropionate transaminase
Rationale: Specifically improtant for putrescine utilization

Sama_2643 : Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)
Original description: putative aminotransferase (RefSeq)
SEED: Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)
KEGG: putrescine aminotransferase
Rationale: Specifically important for: Putrescine Dihydrochloride. Putrescine is catabolized via gamma-aminobutyrate (SEED_correct)

Sama_2645 : Gamma-glutamyl-GABA hydrolase (EC 3.5.1.94)
Original description: glutamine amidotransferase (RefSeq)
SEED: Gamma-glutamyl-GABA hydrolase (EC 3.5.1.94)
KEGG: putative glutamine amidotransferase
Rationale: Specifically important for: Putrescine Dihydrochloride. Part of the gamma-glutamyl-putrescine pathway for putrescine catabolism (SEED_correct)

Sama_2676 : L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2)
Original description: bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase (RefSeq)
SEED: Proline dehydrogenase (EC 1.5.99.8) (Proline oxidase) / Delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88)
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.

Sama_3009 astD : Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71)
Original description: succinylglutamic semialdehyde dehydrogenase (RefSeq)
SEED: Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71)
KEGG: succinylglutamic semialdehyde dehydrogenase
Rationale: Specifically important for utilizing L-Arginine. Automated validation from mutant phenotype: the predicted function (SUCCGLUALDDEHYD-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Sama_3010 : Arginine N-succinyltransferase (EC 2.3.1.109)
Original description: arginine N-succinyltransferase (RefSeq)
SEED: Arginine N-succinyltransferase (EC 2.3.1.109)
KEGG: arginine N-succinyltransferase
Rationale: Specifically important for utilizing L-Arginine. Automated validation from mutant phenotype: the predicted function (ARGININE-N-SUCCINYLTRANSFERASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Sama_3039 : Phosphoglycerate dehydrogenase (EC 1.1.1.95)
Original description: D-isomer specific 2-hydroxyacid dehydrogenase family protein (RefSeq)
SEED: D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95)
KEGG: no annotation
Rationale: Specifically important for utilizing Glycine. Automated validation from mutant phenotype: the predicted function (1.1.1.95) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Sama_3044 : 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

Sama_3201 : Formiminoglutamase (EC 3.5.3.8)
Original description: arginase/agmatinase/formiminoglutamase (RefSeq)
SEED: Formiminoglutamase (EC 3.5.3.8)
KEGG: no annotation
Rationale: Specifically important for utilizing L-Histidine. Automated validation from mutant phenotype: the predicted function (FORMIMINOGLUTAMASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Or download reannotations for Shewanella amazonensis SB2B or for all organisms as tab-delimited tables