Updated Annotations for Sinorhizobium meliloti 1021

Updated annotations for Sinorhizobium meliloti 1021

121 genes with updated (or confirmed) annotations:

SM_b20002 : ABC transporter for Lactose, ATPase component
Original description: sugar ABC transporter ATP-binding protein
SEED: Various polyols ABC transporter, ATP-binding component
KEGG: lactose/L-arabinose transport system ATP-binding protein
Rationale: Specific phenotype on Beta-Lactose. (KEGG_correct)

SM_b20197 : ribulose-1,5-bisphosphate carboxylase small subunit (EC 4.1.1.39)
Original description: ribulose-1,5-bisphosphate carboxylase small subunit protein
SEED: Ribulose bisphosphate carboxylase small chain (EC 4.1.1.39)
KEGG: ribulose-bisphosphate carboxylase small chain
Rationale: Specific phenotype: utilization of L-Proline. It appears that proline is oxidized to release CO2 and the CO2 is fixed by Rubisco.

SM_b20325 : ABC transporter for D-trehalose/D-maltose/sucrose, substrate-binding component (ThuE)
Original description: trehalosemaltose-binding protein
SEED: Maltose/maltodextrin ABC transporter, substrate binding periplasmic protein MalE
KEGG: no annotation
Rationale: Specific phenotype on trehalose, but also reported to transport maltose and sucrose (PMID:12003938; also PMC1635973)

SM_b20326 : ABC transporter for D-trehalose/D-maltose/sucrose, permease component 1 (ThuF)
Original description: trehalosemaltose transporter permease
SEED: Maltose/maltodextrin ABC transporter, permease protein MalF
KEGG: trehalose/maltose transport system permease protein
Rationale: Specific phenotype on trehalose, but also reported to transport maltose and sucrose (PMID:12003938; also PMC1635973)

SM_b20327 : ABC transporter for D-trehalose/D-maltose/sucrose, permease component 2 (ThuG)
Original description: trehalosemaltose transporter permease
SEED: Maltose/maltodextrin ABC transporter, permease protein MalG
KEGG: trehalose/maltose transport system permease protein
Rationale: Specific phenotype on trehalose, but also reported to transport maltose and sucrose (PMID:12003938; also PMC1635973)

SM_b20328 : ABC transporter for D-trehalose/D-maltose/sucrose, ATPase component (ThuK)
Original description: trehalosemaltose transporter ATP-binding protein
SEED: Maltose/maltodextrin transport ATP-binding protein MalK (EC 3.6.3.19)
KEGG: trehalose/maltose transport system ATP-binding protein
Rationale: Specific phenotype on trehalose, but also reported to transport maltose and sucrose (PMID:12003938; also PMC1635973)

SM_b20329 : required for glucoside 3-dehydrogenase activity on raffinose or trehalose (thuA) (EC 1.1.99.13)
Original description: ThuA protein, function
SEED: Trehalose utilization protein ThuA
KEGG: no annotation
Rationale: Specifically important for: D-Raffinose pentahydrate; D-Trehalose dihydrate. a close homolog is described by PMID 23772075; (SEED_correct)

SM_b20330 : glucoside 3-dehydrogenase; active on raffinose or trehalose (thuB) (EC 1.1.99.13)
Original description: trehalosemaltose utilization protein, function
SEED: Nucleoside-diphosphate-sugar epimerases
KEGG: no annotation
Rationale: Specifically important for: D-Raffinose pentahydrate; D-Trehalose dihydrate. a close homolog is described by PMID 23772075

SM_b20850 : L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3)
Original description: L-lactate dehydrogenase
SEED: L-lactate dehydrogenase (EC 1.1.2.3)
KEGG: L-lactate dehydrogenase (cytochrome)
Rationale: Specifically important for utilizing L-Rhamnose monohydrate. Automated validation from mutant phenotype: the predicted function (1.1.2.3) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

SM_b20890 : L-arabonate dehydratase (EC 4.2.1.25)
Original description: dihydroxy-acid dehydratase
SEED: L-arabonate dehydratase (EC 4.2.1.25)
KEGG: dihydroxy-acid dehydratase
Rationale: Specifically important for: L-Arabinose. L-arabonate is an intermediate in the oxidation of L-arabinose (SEED_correct)

SM_b20891 : Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26)
Original description: dehydrogenase
SEED: Aldehyde dehydrogenase B (EC 1.2.1.22)
KEGG: no annotation
Rationale: Specifically important for: L-Arabinose. The only dehydrogenase steps in the arabinose catabolism pathway are L-arabinose 1-dehydrogenase (which is SMc00588) and a-ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26). So, this is the semialdehyde dehydrogenase.

SM_b20892 : 2-dehydro-3-deoxy-L-arabinonate dehydratase (EC 4.2.1.43)
Original description: hypothetical protein
SEED: SUGAR TRANSPORTER
KEGG: no annotation
Rationale: # Specifically important in carbon source L-Arabinose. Similar to PA2216 from Pseudomonas aeruginosa (see PMC:PMC4038344) and to gguC or araD1 (Atu2345) from Agrobacterium tumefaciens (see PMC: PMC3232879), which also have this activity. In Agrobacterium, this reaction is proposed to be a step in L-arabinose oxidation. (Note that 2-keto-3-deoxy-L-lyxonate and 2-keto-3-deoxy-L-arabinonate are the same compound.)

SM_b20894 : L-arabinose ABC transporter, ATPase component
Original description: sugar uptake ABC transporter ATP-binding protein
SEED: ABC transporter ATP-binding protein
KEGG: putative multiple sugar transport system ATP-binding protein
Rationale: Specific phenotype: utilization of L-Arabinose. 79% identical to Atu2347 (GguA) from Agrobacterium, which also transports fucose, galactose, xylose, and glucose, so this may have a broader substrate range.

SM_b20899 : Inositol 2-dehydrogenase (EC 1.1.1.18)
Original description: myo-inositol dehydrogenase
SEED: Myo-inositol 2-dehydrogenase 1 (EC 1.1.1.18)
KEGG: myo-inositol 2-dehydrogenase
Rationale: Specifically important for utilizing m-Inositol. Automated validation from mutant phenotype: the predicted function (MYO-INOSITOL-2-DEHYDROGENASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

SM_b20984 : Nitrite reductase (NAD(P)H) (EC 1.7.1.4)
Original description: nitrite reductase [NAD(P)H], large subunit protein
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.

SM_b20986 : Nitrate reductase (EC 1.7.99.4)
Original description: nitrate reductase, large subunit protein
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.

SM_b21009 : Glycerol kinase (EC 2.7.1.30)
Original description: glycerol kinase
SEED: Glycerol kinase (EC 2.7.1.30)
KEGG: glycerol kinase
Rationale: Specifically important for utilizing Glycerol. Automated validation from mutant phenotype: the predicted function (GLYCEROL-KIN-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

SM_b21101 : L-fucono-1,5-lactonase; D-arabinolactonase
Original description: hypothetical protein
SEED: L-fuconolactone hydrolase
KEGG: no annotation
Rationale: # Specifically important in carbon source D-Arabinose; carbon source L-Fucose. A related protein (29% identical) was shown by Hobbs et al (2013) to be a L-fucono-1,5-lactonase. Note that D-arabinolactone is chemically similar to L-fuconolactone, with one methyl group replaced with a hydrogen.

SM_b21103 : ABC transporter for L-Fucose, periplasmic substrate-binding protein
Original description: sugar ABC transporter substrate-binding protein
SEED: Maltose/maltodextrin ABC transporter, substrate binding periplasmic protein MalE
KEGG: multiple sugar transport system substrate-binding protein
Rationale: Specific phenotype on L-Fucose.

SM_b21104 : ABC transporter for L-Fucose, permease component 1
Original description: sugar ABC transporter permease
SEED: Maltose/maltodextrin ABC transporter, permease protein MalF
KEGG: no annotation
Rationale: Specific phenotypes on L-Fucose.

SM_b21105 : ABC transporter for L-Fucose, permease component 2
Original description: sugar ABC transporter permease
SEED: Maltose/maltodextrin ABC transporter, permease protein MalG
KEGG: multiple sugar transport system permease protein
Rationale: Specific phenotypes on L-Fucose.

SM_b21106 : ABC transporter for L-Fucose, ATPase component
Original description: sugar ABC transporter ATP-binding protein
SEED: Maltose/maltodextrin transport ATP-binding protein MalK (EC 3.6.3.19)
KEGG: multiple sugar transport system ATP-binding protein
Rationale: Specific phenotype on L-Fucose.

SM_b21107 : dehydratase involved in L-fucose catabolism
Original description: mandelate racemase or evolutionary related enzyme of the mandelate racemase muconate lactonizing enzyme family protein
SEED: mandelate racemase/muconate lactonizing enzyme family protein
KEGG: no annotation
Rationale: # Specifically important in carbon source L-Fucose. T. Lukk's 2009 thesis reported that this protein had weak activity as a L-fuconate dehydratase, which was the expected substrate. The fitness data shows that two other dehydratases are involved in fucose catabolism as well (see SMc02776 and SM_b21110), so the pathway is probably more complicated.

SM_b21108 : L-fucose mutarotase (EC 5.1.3.29)
Original description: hypothetical protein
SEED: no annotation
KEGG: no annotation
Rationale: Specifically important for: L-Fucose. The first step in fucose catabolism. This protein is related to XCC4070 (FUCM_XANCP)

SM_b21109 : L-fucose dehydrogenase (EC 1.1.1.122)
Original description: oxidoreductase
SEED: oxidoreductase, Gfo/Idh/MocA family
KEGG: no annotation
Rationale: Specifically important for: L-Fucose. The second step in fucose catabolism.

SM_b21110 : dehydratase involved in L-fucose catabolism
Original description: MaoC-like (monoamine oxidase-like) protein, NodN
SEED: Aldehyde dehydrogenase (EC 1.2.1.3)
KEGG: no annotation
Rationale: # Specifically important in carbon source L-Fucose. This protein is similar to the (R)-enoyl-CoA hydratase portion of E. coli maoC (36% identical). It is one of three dehydratases involved in L-fucose catabolism (see SMc02776 and SM_b21107)

SM_b21112 : L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase
Original description: bifunctional 2-hydroxyhepta-2,4-diene-1, 7-dioatesomerase/5-carboxymethyl-2-oxo-hex-3-ene-1, 7-dioatedecarboxylase
SEED: 2,4-diketo-3-deoxy-L-fuconate hydrolase
KEGG: no annotation
Rationale: # Specifically important in carbon source L-Fucose; carbon source D-Arabinose. SM_b21112 is 58% identical to LRA6, which is L-2,4-diketo-3-deoxyrhamnonate hydrolase (PMID:19187228). This reaction is also proposed to be involved in L-fucose catabolism (PMID:17144652), which explains the phenotype on L-fucose. Its role in D-arabinose catabolism suggests that it also acts on a five-carbon substrate such as 2,4-dioxopentanoate. This protein belongs to the fumarylacetoacetate hydrolase family, which hydrolyses substrates of the form R-CO-CH2-CO-R'. Both keto groups are involved in the catalytic mechanism (Bateman et al 2001) so we propose that 2,4-dioxopentanoate is the intermediate in D-arabinose catabolism. This would be formed from D-arabinoate by two successive dehydratase reactions (see SMa0247 and SM_b21112).

SM_b21121 : Isovaleryl-CoA dehydrogenase (EC 1.3.8.4)
Original description: isovaleryl-CoA dehydrogenase
SEED: Isovaleryl-CoA dehydrogenase (EC 1.3.8.4)
KEGG: no annotation
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.

SM_b21122 : 3-methylcrotonyl-CoA carboxylase, beta subunit (EC 6.4.1.4)
Original description: methylcrotonoyl-CoA carboxylase non-biotinylated subunit protein
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.

SM_b21124 : 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit (EC 6.4.1.4)
Original description: methylcrotonoyl-CoA carboxylase biotinylated subunit
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.

SM_b21125 : Hydroxymethylglutaryl-CoA lyase (EC 4.1.3.4)
Original description: hydroxymethylglutaryl-CoA lyase
SEED: Hydroxymethylglutaryl-CoA lyase (EC 4.1.3.4)
KEGG: hydroxymethylglutaryl-CoA lyase
Rationale: Specifically important for utilizing L-Leucine. Automated validation from mutant phenotype: the predicted function (HYDROXYMETHYLGLUTARYL-COA-LYASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

SM_b21126 : 3-methylglutaconyl-CoA hydratase (EC 4.2.1.18)
Original description: enoyl-CoA hydratase
SEED: Methylglutaconyl-CoA hydratase (EC 4.2.1.18)
KEGG: methylglutaconyl-CoA hydratase
Rationale: Specifically important for utilizing L-Leucine as a carbon or nitrogen source.

SM_b21163 : Urocanate hydratase (EC 4.2.1.49)
Original description: urocanate hydratase
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.

SM_b21164 : N-formylglutamate deformylase (EC 3.5.1.68)
Original description: formiminoglutamase
SEED: N-formylglutamate deformylase (EC 3.5.1.68)
KEGG: formiminoglutamase
Rationale: Specifically important for: L-Histidine. KEGG suggests formimidoyl-L-glutamate as the substrate, while SEED suggests N-formylglutamate. This gene is cofit with a deiminase or iminohydrolase (which produces N-formylglutamate) which suggests that the SEED annotation is correct. (SEED_correct)

SM_b21165 : Histidine ammonia-lyase (EC 4.3.1.3)
Original description: histidine ammonia-lyase
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.

SM_b21166 : Imidazolonepropionase (EC 3.5.2.7)
Original description: imidazolonepropionase
SEED: Imidazolonepropionase (EC 3.5.2.7)
KEGG: no annotation
Rationale: Specifically important for utilizing L-Histidine. Automated validation from mutant phenotype: the predicted function (IMIDAZOLONEPROPIONASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

SM_b21216 : ABC transporter for D-Glucosamine, ATPase component
Original description: sugar ABC transporter ATP-binding protein
SEED: Maltose/maltodextrin transport ATP-binding protein MalK (EC 3.6.3.19)
KEGG: no annotation
Rationale: Specific phenotype on D-Glucosamine Hydrochloride.

SM_b21217 : glucosamine kinase (EC 2.7.1.8)
Original description: sugar kinase
SEED: predicted glucosamine kinase (EC 2.7.1.8)
KEGG: no annotation
Rationale: Specifically important for utilizing glucosamine

SM_b21218 : glucosamine-6-phosphate deaminase, isomerizing (EC 3.5.99.6)
Original description: sugar-processing protein
SEED: Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6)
KEGG: no annotation
Rationale: Specifically important for utilizing D-glucosamine

SM_b21219 : ABC transporter for D-Glucosamine, permease component 1
Original description: sugar ABC transporter permease
SEED: Glycerol-3-phosphate ABC transporter, permease protein UgpE (TC 3.A.1.1.3)
KEGG: multiple sugar transport system permease protein
Rationale: Specific phenotypes on D-Glucosamine Hydrochloride.

SM_b21220 : ABC transporter for D-Glucosamine, permease component 2
Original description: sugar ABC transporter permease
SEED: Glycerol-3-phosphate ABC transporter, permease protein UgpA (TC 3.A.1.1.3)
KEGG: multiple sugar transport system permease protein
Rationale: Specific phenotypes on D-Glucosamine Hydrochloride.

SM_b21221 : ABC transporter for D-Glucosamine, periplasmic substrate-binding protein
Original description: sugar uptake ABC transporter substrate-binding protein precursor
SEED: Glucosamine ABC transport system, periplasmic sugar-binding protein
KEGG: multiple sugar transport system substrate-binding protein
Rationale: Specific phenotype on D-Glucosamine Hydrochloride. (SEED_correct)

SM_b21373 : D-tagatose 6-phosphate 4-epimerase [EC:5.1.3.40]
Original description: sugar kinase
SEED: 6-phosphofructokinase (EC 2.7.1.11), PF08013 family
KEGG: tagatose 6-phosphate kinase
Rationale: Specifically important for: D-Tagatose. This protein is >50% identical to Atu3167, which converts D-tagatose 6-phosphate to D-fructose 6-phosphate (see PMC4661409). This information is in the recent releases of KEGG and MetaCyc.

SM_b21374 : tagatose kinase (EC 2.7.1.101)
Original description: sugar kinase
SEED: Fructokinase (EC 2.7.1.4)
KEGG: no annotation
Rationale: Important on tagatose. This is the first step in tagatose catabolism.

SM_b21644 : ABC transporter for D-Raffinose, ATPase component
Original description: ABC transporter ATP-binding protein
SEED: Oligopeptide transport system permease protein OppB (TC 3.A.1.5.1)
KEGG: peptide/nickel transport system ATP-binding protein
Rationale: Specific phenotype on D-Raffinose pentahydrate.

SM_b21645 : ABC transporter for D-Raffinose, permease component 1
Original description: ABC transporter permease
SEED: ABC transporter, permease protein
KEGG: peptide/nickel transport system permease protein
Rationale: Specific phenotypes on D-Raffinose pentahydrate.

SM_b21646 : ABC transporter for D-Raffinose, permease component 2
Original description: ABC transporter permease
SEED: ABC transporter, permease protein
KEGG: peptide/nickel transport system permease protein
Rationale: Specific phenotypes on D-Raffinose pentahydrate.

SM_b21647 : ABC transporter for D-Raffinose, periplasmic substrate-binding protein
Original description: alpha-galactoside ABC transporter substrate-binding protein precursor
SEED: Periplasmic alpha-galactoside-binding protein precursor
KEGG: peptide/nickel transport system substrate-binding protein
Rationale: Specific phenotype on D-Raffinose pentahydrate.

SM_b21648 : Alpha-galactosidase (EC 3.2.1.22)
Original description: alpha-galactosidase (melibiase) protein
SEED: Alpha-galactosidase (EC 3.2.1.22)
KEGG: alpha-galactosidase
Rationale: Specific phenotype: utilization of D-Raffinose pentahydrate (which is an alpha-galactoside)

SM_b21652 : ABC transporter for Lactose, periplasmic substrate-binding component
Original description: lactose ABC transporter substrate-binding protein
SEED: ABC transporter sugar binding protein
KEGG: lactose/L-arabinose transport system substrate-binding protein
Rationale: Specific phenotype on Beta-Lactose. (KEGG_correct)

SM_b21653 : ABC transporter for Lactose, permease component 1
Original description: lactose ABC transporter permease
SEED: Inositol transport system permease protein
KEGG: lactose/L-arabinose transport system permease protein
Rationale: Specific phenotypes on Beta-Lactose. Not important for arabinose utilization but there is no other clear arabinose tranpsorter so who knows (KEGG_correct)

SM_b21654 : ABC transporter for Lactose, permease component 2
Original description: lactose ABC transporter permease
SEED: Glycerol-3-phosphate ABC transporter, permease protein UgpE (TC 3.A.1.1.3)
KEGG: lactose/L-arabinose transport system permease protein
Rationale: Specific phenotypes on Beta-Lactose. Not important for arabinose utilization but there is no other clear arabinose tranpsorter so who knows (KEGG_correct)

SM_b21655 : Beta-galactosidase (EC 3.2.1.23)
Original description: beta-galactosidase
SEED: Beta-galactosidase (EC 3.2.1.23)
KEGG: beta-galactosidase
Rationale: Specifically important for utilizing Beta-Lactose. Automated validation from mutant phenotype: the predicted function (BETAGALACTOSID-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

SMa0247 : 2-dehydro-3-deoxy-D-arabinonate dehydratase, 2,4-dioxopentanoate forming
Original description: hypothetical protein
SEED: Fumarylacetoacetate hydrolase family protein
KEGG: no annotation
Rationale: # Specifically important in carbon source D-Arabinose. SMa0247 is related to 2-keto-3-deoxyxylonate dehydratase (xylX), which acts on the same substrate. Furthermore, a close homolog (HSERO_RS19360, 59% identical) is important for D-xylose utilization. However, the product of XylX is 2,5-dioxopentanoate, but in S. meliloti the pathway probably proceeds via 2,4-dioxopentanoate (see SM_b21112).

SMc00138 : L-lysine ABC transporter, permease component 2
Original description: amino acid ABC transporter permease
SEED: Amino acid ABC transporter, permease protein
KEGG: polar amino acid transport system permease protein
Rationale: Specifically important for L-lysine utilization. The ATPase component is not encoded nearby and was not evident in the fitness data.

SMc00139 : L-lysine ABC transporter, permease component 1
Original description: amino acid ABC transporter permease
SEED: Arginine transport system permease protein ArtQ
KEGG: polar amino acid transport system permease protein
Rationale: Specifically important for L-lysine utilization. The ATPase component is not encoded nearby and was not evident in the fitness data.

SMc00140 : L-lysine ABC transporter, substrate-binding component
Original description: amino-acid binding periplasmic protein
SEED: no annotation
KEGG: no annotation
Rationale: Specifically important for L-lysine utilization. The ATPase component is not encoded nearby and was not evident in the fitness data.

SMc00432 : 5-deoxy-D-glucuronate isomerase (EC 5.3.1.30)
Original description: myo-inositol catabolism protein
SEED: 5-deoxy-glucuronate isomerase (EC 5.3.1.-)
KEGG: 5-deoxy-glucuronate isomerase
Rationale: Specifically important for utilizing m-Inositol.

SMc00433 : Myo-inosose-2 dehydratase (EC 4.2.1.44)
Original description: myo-inositol catabolism protein
SEED: Inosose dehydratase (EC 4.2.1.44)
KEGG: inosose dehydratase
Rationale: Specifically important for utilizing m-Inositol. Automated validation from mutant phenotype: the predicted function (MYO-INOSOSE-2-DEHYDRATASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

SMc00486 : Glutaminase (EC 3.5.1.2)
Original description: glutaminase
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.

SMc00588 : L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48)
Original description: D-galactose 1-dehydrogenase
SEED: Uncharacterized oxidoreductase ydgJ (EC 1.-.-.-)
KEGG: D-galactose 1-dehydrogenase
Rationale: Important on L-arabinose and D-galactose; may also act on D-glucose, given phenotype with some N sources with glucose as C source; 55% identical to ARAA_AZOBR, which has L-arabinose and D-galactose 1-dehydrogenase activity in vitro

SMc00673 : Formiminoglutamic iminohydrolase (EC 3.5.3.13)
Original description: N-formimino-L-glutamate deiminase
SEED: Formiminoglutamic iminohydrolase (EC 3.5.3.13)
KEGG: no annotation
Rationale: Specifically important for utilizing L-Histidine. Automated validation from mutant phenotype: the predicted function (FORMIMINOGLUTAMATE-DEIMINASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

SMc00774 : Acetoacetate--CoA ligase (EC 6.2.1.16)
Original description: acetoacetyl-CoA synthetase
SEED: Acetoacetyl-CoA synthetase (EC 6.2.1.16)
KEGG: acetoacetyl-CoA synthetase
Rationale: Specifically important for utilizing L-Leucine. Automated validation from mutant phenotype: the predicted function (6.2.1.16) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

SMc00781 : malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18)
Original description: malonic semialdehyde oxidative decarboxylase
SEED: Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27)
KEGG: methylmalonate-semialdehyde dehydrogenase
Rationale: Specifically important for: m-Inositol; Uridine. 3-oxopropionate or malonate semialdehyde is an intermediate in myo-inositol catabolism and also in pyrimidine catabolism

SMc00832 : D-lactate dehydrogenase, FAD-linked subunit GlcD (EC 1.1.99.6)
Original description: glycolate oxidase subunit protein
SEED: Glycolate dehydrogenase (EC 1.1.99.14), subunit GlcD
KEGG: no annotation
Rationale: Specifically important for: Sodium D,L-Lactate. This is the first step in D-lactate oxidation.

SMc00833 : D-lactate dehydrogenase, FAD binding subunit GlcE (EC 1.1.99.6)
Original description: glycolate oxidase subunit protein
SEED: Glycolate dehydrogenase (EC 1.1.99.14), FAD-binding subunit GlcE
KEGG: glycolate oxidase FAD binding subunit
Rationale: Specifically important for: Sodium D,L-Lactate. This is the first step in D-lactate oxidation.

SMc00883 : L-arabinolactonase/D-galactonolactonase (EC 3.1.1.15; EC 3.1.1.25)
Original description: hypothetical protein
SEED: 1,4-lactonase (EC 3.1.1.25)
KEGG: no annotation
Rationale: Specifically important for L-arabinose utilization. Also has a mild phenotype on galactose. PMC3430339 reports that a mutant can grow on galactose, but might not have detected a subtle defect.

SMc00917 : 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.

SMc00926 : D-lactate dehydrogenase, iron-sulfur subunit GlcF (EC 1.1.99.6)
Original description: glycolate oxidase iron-sulfur subunit protein
SEED: Glycolate dehydrogenase (EC 1.1.99.14), iron-sulfur subunit GlcF
KEGG: glycolate oxidase iron-sulfur subunit
Rationale: Specifically important for: Sodium D,L-Lactate. This is the first step in D-lactate oxidation.

SMc01054 : 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

SMc01103 : Ribokinase (EC 2.7.1.15)
Original description: ribokinase
SEED: Ribokinase (EC 2.7.1.15)
KEGG: ribokinase
Rationale: Specifically important for utilizing D-Ribose. Automated validation from mutant phenotype: the predicted function (RIBOKIN-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

SMc01105 : uridine nucleosidase (EC 3.2.2.3)
Original description: nucleoside hydrolase
SEED: Inosine-uridine preferring nucleoside hydrolase (EC 3.2.2.1)
KEGG: purine nucleosidase
Rationale: Specifically important for: Uridine. annotated by SEED as acting on uridine and inosine

SMc01165 : 5-dehydro-2-deoxygluconokinase (EC 2.7.1.92); possible 5-dehydro-2-deoxyphosphogluconate aldolase DUF2090 (EC 4.1.2.29)
Original description: sugar kinase
SEED: 5-keto-2-deoxygluconokinase (EC 2.7.1.92) / uncharacterized domain
KEGG: 5-dehydro-2-deoxygluconokinase
Rationale: # Specifically important in carbon source m-Inositol. This protein is a fusion of 5-keto-deoxygluconate kinase and DUF2090. As DUF2090 has distant similarity to aldolases, it may provide the missing 5-dehydro-2-deoxyphosphogluconate aldolase activity.

SMc01166 : 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase IolD (EC 3.7.1.22)
Original description: malonic semialdehyde oxidative decarboxylase
SEED: Epi-inositol hydrolase (EC 3.7.1.-)
KEGG: 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase
Rationale: Specifically important for utilizing m-Inositol.

SMc01801 : 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.

SMc01815 : Dihydropyrimidine dehydrogenase (NADP(+)) (EC 1.3.1.2)
Original description: dihydropyrimidine dehydrogenase
SEED: Dihydropyrimidine dehydrogenase [NADP+] (EC 1.3.1.2)
KEGG: no annotation
Rationale: Specifically important for utilizing Uridine. Automated validation from mutant phenotype: the predicted function (1.3.1.2) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

SMc01820 : Beta-ureidopropionase (EC 3.5.1.6)
Original description: allantoate amidohydrolase
SEED: Beta-ureidopropionase (EC 3.5.1.6)
KEGG: no annotation
Rationale: Specifically important for utilizing Uridine. Automated validation from mutant phenotype: the predicted function (3.5.1.6) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

SMc01821 : Dihydropyrimidinase (EC 3.5.2.2)
Original description: phenylhydantoinase
SEED: Dihydropyrimidinase (EC 3.5.2.2)
KEGG: dihydropyrimidinase
Rationale: Specifically important for utilizing Uridine. Automated validation from mutant phenotype: the predicted function (3.5.2.2) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

SMc02118 : ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, periplasmic substrate-binding component
Original description: general L-amino acid-binding periplasmic ABC transporter protein
SEED: Glutamate Aspartate periplasmic binding protein precursor GltI (TC 3.A.1.3.4)
KEGG: general L-amino acid transport system substrate-binding protein
Rationale: Specific phenotype on L-Histidine; L-Glutamine.

SMc02119 : ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 1
Original description: general L-amino acid transport permease ABC transporter protein
SEED: Glutamate Aspartate transport system permease protein GltJ (TC 3.A.1.3.4)
KEGG: general L-amino acid transport system permease protein
Rationale: Specific phenotypes on L-Glutamine; L-Histidine. Mild phenotypes on proline or lysine (KEGG_correct)

SMc02120 : ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2
Original description: general L-amino acid transport permease ABC transporter protein
SEED: Glutamate Aspartate transport system permease protein GltK (TC 3.A.1.3.4)
KEGG: general L-amino acid transport system permease protein
Rationale: Specific phenotypes on L-Glutamine; L-Histidine. Mild phenotypes on proline or lysine (KEGG_correct)

SMc02121 : ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component
Original description: general L-amino acid transport ATP-binding ABC transporter protein
SEED: ABC-type polar amino acid transport system, ATPase component
KEGG: general L-amino acid transport system ATP-binding protein
Rationale: Very important for histidine and glutamine utilization and also for lysine utilization. It could be the ATPase component for lysine transport by Smc00140:Smc00138 as well (as there is no ATPase component in that gene cluster or other ATPase component identified in the fitness data)

SMc02123 : required for sulfate utilization, putative electron transport protein for sulfite reductase
Original description: hypothetical protein
SEED: Oxidoreductase probably involved in sulfite reduction
KEGG: no annotation
Rationale: PFam PF06073.8 (DUF934). conserved cofitness with sulfite reductase (SMc02124, sometimes misannotated as nitrite reductase); auxotrophic

SMc02236 : DNA repair nuclease, ligase-associated (TIGR04123)
Original description: hypothetical protein
SEED: FIG006285: ICC-like protein phosphoesterase
KEGG: no annotation
Rationale: # Specifically important in stress Cisplatin. This family was previously annotated as a DNA ligase-associated metallophosphoesterase (TIGR04123). A member of this family (PdeM) has been studied biochemically and found to have nuclease activity, but it was not known if DNA was the physiological substrate (see PMC4320098).

SMc02237 : DNA damage response helicase, ligase-associated
Original description: ATP-dependent helicase
SEED: FIG003033: Helicase domain protein
KEGG: ATP-dependent helicase Lhr and Lhr-like helicase
Rationale: Conserved and specific phenotype: important for resisting cisplatin. Related to Lhr, which is either a DNA:DNA or DNA:RNA helicase, but lacks the long C-terminal extension that might have a regulatory role (see putative winged helix domain in E. coli lhr). This is also related to the archael protein saci_1500, which has also been linked to DNA damage response, as a mutant is sensitive to UV (PMID: 26148716)

SMc02321 : L-rhamnose isomerase (EC 5.3.1.14)
Original description: sugar isomerase
SEED: no annotation
KEGG:
Rationale: Specifically important for: L-Rhamnose monohydrate. KEGG now annotates it as L-rhamnose isomerase, which is correct. The gene is cofit with SMc03003 (rhaK), which is probably rhamnulose kinase. It had been suggested that rhaK might be rhamnose kinase and that the isomerase might act on L-rhamnose 1-phosphate, but the S. meliloti rhaK is not a rhamnose kinase. See the PhD thesis of Damien M. R. Rivers (2015). (KEGG_correct)

SMc02322 : rhamnulose-1-phosphate aldolase (EC 4.1.2.19) / lactaldehyde dehydrogenase (EC 1.2.1.22)
Original description: short chain dehydrogenase
SEED: Predicted rhamnulose-1-phosphate aldolase (EC 4.1.2.19) / Predicted lactaldehyde dehydrogenase (EC 1.2.1.22)
KEGG: no annotation
Rationale: Specifically important for: L-Rhamnose monohydrate. These are the steps after the L-rhamnose 1-phosphate isomerase (SEED_correct)

SMc02520 : glycerol-3-phosphate dehydrogenase (EC 1.1.5.3)
Original description: glycerol-3-phosphate dehydrogenase
SEED: Aerobic glycerol-3-phosphate dehydrogenase (EC 1.1.5.3)
KEGG: glycerol-3-phosphate dehydrogenase
Rationale: Specifically important for glycerol utilization. Expression is induced by glycerol or glycerol-3-phosphate (PMC1635973).

SMc02570 : 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.

SMc02775 : D-arabinose 1-dehydrogenase
Original description: L-fucose dehydrogenase (D-threo aldose 1-dehydrogenase) protein
SEED: L-fuco-beta-pyranose dehydrogenase (EC 1.1.1.122)
KEGG: D-threo-aldose 1-dehydrogenase
Rationale: # Specifically important in carbon source D-Arabinose. This is the first step in the oxidation of D-arabinose. (The fucose dehydrogenase is SM_b21109.) The product is probably the 1,5-lactone, not the 1,4-lactone, see SM_b21101.

SMc02776 : D-arabinoate dehydratase (EC 4.2.1.5); also involved in L-fucose catabolism
Original description: altronate hydrolase
SEED: no annotation
KEGG: altronate hydrolase
Rationale: # Specifically important in carbon source D-Arabinose; carbon source L-Fucose. SMc02776 is 36% identical to D-galactarate dehydratase (garD) from E. coli, which is a similar reaction. The product (2-dehydro-3-deoxy-D-arabinonate) is consumed by SMa0247. The role of SMc02776 role in L-fucose catabolism is unclear because two other dehydratases (SM_b21107 and SM_b21110) are also required but the pathway requires only one dehydratase reaction (PMID:17144652). Probably two of these dehydratases act together (with one of them in reverse) to switch the stereochemistry of a chiral center.

SMc02869 : N-Acetyl-D-glucosamine ABC transport system, ATPase component
Original description: ABC transporter ATP-binding protein
SEED: N-Acetyl-D-glucosamine ABC transport system ATP-binding protein
KEGG: multiple sugar transport system ATP-binding protein
Rationale: Specific phenotype on N-Acetyl-D-Glucosamine. (SEED_correct)

SMc02871 : ABC transporter for N-Acetyl-D-glucosamine, permease protein 2
Original description: ABC transporter permease
SEED: N-Acetyl-D-glucosamine ABC transport system, permease protein 2
KEGG: multiple sugar transport system permease protein
Rationale: Specific phenotypes on N-Acetyl-D-Glucosamine; N-Acetyl-D-Glucosamine. (SEED_correct)

SMc02872 : ABC transporter for N-Acetyl-D-glucosamine, permease protein 1
Original description: ABC transporter permease
SEED: N-Acetyl-D-glucosamine ABC transport system, permease protein 1
KEGG: multiple sugar transport system permease protein
Rationale: Specific phenotypes on N-Acetyl-D-Glucosamine; N-Acetyl-D-Glucosamine. (SEED_correct)

SMc02873 : N-Acetyl-D-glucosamine ABC transport system, periplasmic substrate-binding component
Original description: periplasmic binding (signal peptide) ABC transporter protein
SEED: N-Acetyl-D-glucosamine ABC transport system, sugar-binding protein
KEGG: multiple sugar transport system substrate-binding protein
Rationale: Specific phenotype on N-Acetyl-D-Glucosamine. (SEED_correct)

SMc02875 : N-acetylglucosamine kinase (EC 2.7.1.59)
Original description: hypothetical protein
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 catabolism (SEED_correct)

SMc03003 : Rhamnulokinase RhaK in alpha-proteobacteria (EC 2.7.1.5)
Original description: hypothetical protein
SEED: Rhamnulokinase RhaK in alpha-proteobacteria (EC 2.7.1.5)
KEGG: no annotation
Rationale: Specifically important for: L-Rhamnose monohydrate. Also see comment on SMc02321; this is the first step in L-rhamnose degradation. (SEED_correct)

SMc03061 : ABC transporter for D-maltose/D-trehalose/sucrose, substrate-binding component (AglE)
Original description: alpha-glucoside ABC transporter periplasmic-binding protein
SEED: Alpha-glucosides-binding periplasmic protein AglE precursor
KEGG: alpha-glucoside transport system substrate-binding protein
Rationale: Specific phenotype on D-Maltose monohydrate; D-Trehalose dihydrate. Also mildly important for D-cellobiose utilization, which has its own ABC transporter, so the cause is unclear. Also reported to transport sucrose (PMID:10400573, PMID:12003938)

SMc03062 : ABC transporter for D-maltose/D-trehalose/sucrose, permease component 1 (AglF)
Original description: alpha-glucoside ABC transporter permease
SEED: ABC alpha-glucoside transporter, inner membrane subunit AglF
KEGG: alpha-glucoside transport system permease protein
Rationale: Specific phenotype on D-Maltose monohydrate; D-Trehalose dihydrate. Also mildly important for D-cellobiose utilization, which has its own ABC transporter, so the cause is unclear. Also reported to transport sucrose (PMID:10400573, PMID:12003938)

SMc03063 : ABC transporter for D-maltose/D-trehalose/sucrose, permease component 2 (AglG)
Original description: alpha-glucoside ABC transporter permease
SEED: Alpha-glucoside transport system permease protein AglG
KEGG: alpha-glucoside transport system permease protein
Rationale: Specific phenotype on D-Maltose monohydrate; D-Trehalose dihydrate. Also mildly important for D-cellobiose utilization, which has its own ABC transporter, so the cause is unclear. Also reported to transport sucrose (PMID:10400573, PMID:12003938)

SMc03065 : ABC transporter for D-maltose/D-trehalose/sucrose, ATPase component (AglK)
Original description: alpha-glucoside ABC transporter ATP-binding protein
SEED: Alpha-glucoside transport ATP-binding protein AglK
KEGG: alpha-glucoside transport system ATP-binding protein
Rationale: Specific phenotype on D-Maltose monohydrate; D-Trehalose dihydrate. Also mildly important for D-cellobiose utilization, which has its own ABC transporter, so the cause is unclear. Also reported to transport sucrose (PMID:10400573, PMID:12003938)

SMc03109 : Mannokinase (EC 2.7.1.7)
Original description: hypothetical protein
SEED: ROK family Glucokinase with ambiguous substrate specificity
KEGG: no annotation
Rationale: Specifically important for utilizing D-Mannose. Mannose is catabolized via mannose-6-phosphate isomerase (SMc03111) so this is mannokinase.

SMc03111 : mannose 6-phosphate isomerase (EC 5.3.1.8)
Original description: mannose-6-phosphate isomerase
SEED: Mannose-6-phosphate isomerase (EC 5.3.1.8)
KEGG: mannose-6-phosphate isomerase
Rationale: Specifically important for utilization of mannose (mannose 6-phosphate is formed by SMc03109)

SMc03162 : 3-ketoglucose dehydratase
Original description: hypothetical protein
SEED: Inosose isomerase (EC 5.3.99.-)
KEGG: no annotation
Rationale: Specifically important for: D-Salicin; D-Cellobiose. Cofit with a beta-mannosidase (SMc04255), which is not explained. This protein is 72% identical to AtHyd, which is a 3-ketoglucose dehydratase (PMC10628242). This reaction (in reverse) is part of the 3-ketoglycoside pathway (SMc04253 appears to be the glycoside 3-dehydrogenase; the lyase is not apparent; and SMc03161 appears to be 3-ketoglucose reductase.) The 3-ketoglycoside pathway might occur in parallel with direct hydrolysis by the beta-mannosidase.

SMc03163 : Xylose isomerase (EC 5.3.1.5)
Original description: xylose isomerase
SEED: Xylose isomerase (EC 5.3.1.5)
KEGG: xylose isomerase
Rationale: Specifically important for utilizing D-Xylose. Automated validation from mutant phenotype: the predicted function (XYLISOM-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

SMc03164 : Xylulose kinase (EC 2.7.1.17)
Original description: xylulose kinase
SEED: Xylulose kinase (EC 2.7.1.17)
KEGG: xylulokinase
Rationale: Specifically important for utilizing D-Arabinose and D-Xylose. Automated validation from mutant phenotype: the predicted function (XYLULOKIN-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

SMc03165 : Novel Xylose regulator from LacI family
Original description: transcriptional regulator
SEED: Novel Xylose regulator from LacI family
KEGG: LacI family transcriptional regulator
Rationale: # Specifically important in carbon source D-Xylose. Also see expression evidence for the putative ortholog from Phaeobacter, PGA1_c13990, which is 41% identical (PMC4148808). (SEED_correct)

SMc03201 : branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit (EC 1.2.4.4)
Original description: 2-oxoisovalerate dehydrogenase subunit alpha
SEED: Branched-chain alpha-keto acid dehydrogenase, E1 component, alpha subunit (EC 1.2.4.4)
KEGG: 2-oxoisovalerate dehydrogenase E1 component, alpha subunit
Rationale: Specifically important for utilizing L-Leucine.

SMc03202 : branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit (EC 1.2.4.4)
Original description: 2-oxoisovalerate dehydrogenase subunit beta
SEED: Branched-chain alpha-keto acid dehydrogenase, E1 component, beta subunit (EC 1.2.4.4)
KEGG: 2-oxoisovalerate dehydrogenase E1 component, beta subunit
Rationale: Specifically important for utilizing L-Leucine.

SMc03203 : Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168)
Original description: branched-chain alpha-keto acid dehydrogenase E2 subunit
SEED: Dihydrolipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex (EC 2.3.1.168)
KEGG: 2-oxoisovalerate dehydrogenase E2 component (dihydrolipoyl transacylase)
Rationale: Specifically important for utilizing L-Leucine. Automated validation from mutant phenotype: the predicted function (2.3.1.168) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

SMc03204 : Dihydrolipoyl dehydrogenase (EC 1.8.1.4)
Original description: dihydrolipoamide dehydrogenase
SEED: Dihydrolipoamide dehydrogenase of branched-chain alpha-keto acid dehydrogenase (EC 1.8.1.4)
KEGG: dihydrolipoamide dehydrogenase
Rationale: Specifically important for utilizing L-Leucine. Automated validation from mutant phenotype: the predicted function (1.8.1.4) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

SMc03879 : Acetyl-CoA acetyltransferase (EC 2.3.1.9)
Original description: acetyl-CoA acetyltransferase
SEED: Acetyl-CoA acetyltransferase (EC 2.3.1.9)
KEGG: acetyl-CoA C-acetyltransferase
Rationale: Specifically important for utilizing L-Lysine. Automated validation from mutant phenotype: the predicted function (ACETYL-COA-ACETYLTRANSFER-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

SMc04251 : dctP-like component of a pyruvate transporter
Original description: mannitol-binding periplasmic signal peptide protein
SEED: TRAP transporter solute receptor, unknown substrate 6
KEGG: no annotation
Rationale: Important for pyruvate utilization and detrimental on D,L-lactate. The other components of the transporter are SMc04248 and SMc04249 (conserved cofitness)

SMc04256 : ABC transporter for D-Cellobiose and D-Salicin, ATPase component
Original description: ABC transporter ATP-binding protein
SEED: Nucleoside ABC transporter, permease protein 1
KEGG: multiple sugar transport system ATP-binding protein
Rationale: Specific phenotype on D-Salicin; D-Cellobiose.

SMc04257 : ABC transporter for D-Cellobiose and D-Salicin, permease component 1
Original description: ABC transporter permease
SEED: ABC-type sugar transport system, permease component
KEGG: multiple sugar transport system permease protein
Rationale: Specific phenotypes on D-Cellobiose; D-Salicin.

SMc04258 : ABC transporter for D-Cellobiose and D-Salicin, permease component 2
Original description: ABC transporter permease
SEED: ABC transporter, permease protein
KEGG: multiple sugar transport system permease protein
Rationale: Specific phenotypes on D-Cellobiose; D-Salicin.

SMc04259 : ABC transporter for D-Cellobiose and D-Salicin, periplasmic substrate-binding protein
Original description: periplasmic binding ABC transporter signal peptide protein
SEED: ABC-type sugar transport system, periplasmic component
KEGG: multiple sugar transport system substrate-binding protein
Rationale: Specific phenotype on D-Salicin; D-Cellobiose.

SMc04383 : putative hydrolase, required for lysine catabolism
Original description: hypothetical protein
SEED: FIG00960493: hypothetical protein
KEGG: no annotation
Rationale: PFam PF07063.9 (DUF1338). This gene is specifically important for utilizing lysine, and this phenotype is conserved. It might be the decarboxylating 2-oxoadipate hydrolase of the D-lysine oxidase pathway, which has not been linked to a gene, or the crotonyl-CoA hydratase in the glutaryl-CoA degradation pathway.

SMc04384 : (R)-2-hydroxyglutarate dehydrogenase (EC 1.1.99.39)
Original description: oxidoreductase
SEED: PUTATIVE OXIDOREDUCTASE PROTEIN
KEGG: no annotation
Rationale: Specifically important for L-lysine utilization. This is part of lysine catabolism via 2-aminoadipate and D-2-hydroxyglutarate synthase (also known as 2-oxoadipate dioxygenase/decarboxylase; SMc04383).

SMc04385 : L-2-aminoadipate semialdehyde dehydrogenase (EC 1.2.1.31)
Original description: aldehyde dehydrogenase transmembrane protein
SEED: Aldehyde dehydrogenase B (EC 1.2.1.22)
KEGG: no annotation
Rationale: Specifically important for L-lysine utilization. This reaction is part of lysine catabolism via lysine 6-dehydrogenase (SMc02503), which forms (S)-2,3,4,5-tetrahydropyridine-2-carboxylate, which spontaenously interconverts with L-2-aminoadipate semialdehyde (also known as (S)-2-amino-6-oxohexanoate) in water.

SMc04386 : 2-aminoadipate:2-oxoglutarate aminotransferase (EC 2.6.1.39)
Original description: aspartate aminotransferase B protein
SEED: Aspartate aminotransferase (EC 2.6.1.1)
KEGG: aspartate aminotransferase
Rationale: Specifically important for: L-Lysine. This is required for catabolism of lysine on the way to glutarate. The amino group donor is uncertain

Or download reannotations for Sinorhizobium meliloti 1021 or for all organisms as tab-delimited tables