Updated annotations for Cupriavidus basilensis FW507-4G11

50 genes with updated (or confirmed) annotations:

RR42_RS03025 : Inner membrane protein (FUSC-like) required for 4-hydroxybenzoate transport, together with NodT, MFP, and DUF1656 proteins (RR42_RS03040, RR42_RS03035, and RR42_RS03030)
Original description: transporter
SEED: Inner membrane component of tripartite multidrug resistance system
KEGG: no annotation
Rationale: specific phenotype on 4-hydroxybenzoate and cofit with other nearby components. Not clear if this is primarily an efflux pump (because of the high and potentially toxic concentration of hydroxybenzoate) or for uptake

RR42_RS03030 : required for 4-hydroxybenzoate transport, together with NodT, MFP, and FUSC proteins (RR42_RS03040, RR42_RS03035, and RR42_RS03025)
Original description: membrane protein
SEED: membrane protein, putative
KEGG: no annotation
Rationale: PFam PF07869.8 (DUF1656). Specifically important for utilization of 4-hydroxybenzoate (at 20 mM). Not clear if this system is for uptake or for efflux (as this compound is likely to be toxic at 20 mM)

RR42_RS03040 : Outer membrane protein (NodT-like) required for 4-hydroxybenzoate transport, together with FUSC, MFP, and DUF1656 proteins (RR42_RS03025, RR42_RS03035, and RR42_RS03030)
Original description: RND transporter
SEED: Outer membrane component of tripartite multidrug resistance system
KEGG: no annotation
Rationale: specific phenotype on 4-hydroxybenzoate and cofit with other nearby components. Not clear if this is primarily an efflux pump (because of the high and potentially toxic concentration of hydroxybenzoate) or for uptake

RR42_RS03360 : fructose ABC transporter, ATPase component (FrcA)
Original description: sugar ABC transporter ATP-binding protein
SEED: no annotation
KEGG: no annotation
Rationale: Specific phenotype on fructose

RR42_RS03365 : fructose ABC transporter, permease component (FrcC)
Original description: ribose ABC transporter permease
SEED: Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)
KEGG: ribose transport system permease protein
Rationale: Specific phenotype on fructose

RR42_RS03370 : fructose ABC transporter, substrate-binding component (FrcB)
Original description: ABC transporter
SEED: Xylose ABC transporter, periplasmic xylose-binding protein XylF
KEGG: ribose transport system substrate-binding protein
Rationale: Specific phenotype on fructose

RR42_RS03990 : aspartate:proton symporter Glt
Original description: C4-dicarboxylate ABC transporter
SEED: FIG00975494: hypothetical protein
KEGG: no annotation
Rationale: Specifically important for asparagine utilization. Asparagine is probably cleaved in the periplasm (by RR42_RS12610 or RR42_RS26140) and RR42_RS03990 is 60% identical to aspartate transporter AO356_01905 from Pseudomonas fluorescens FW300-N2C3

RR42_RS04420 : required for efflux of an amino acid polymer
Original description: hypothetical protein
SEED: DUF1854 domain-containing protein
KEGG: no annotation
Rationale: PFam PF08909.7 (DUF1854). In a conserved cofit operon with a mdlB-like transporter (RR42_RS04415) and with two (apparently cytoplasmic) cyanophycin synthetase-like genes that produce a different polymer (RR42_RS04410 and RR42_RS04405, see PMID:23224585)

RR42_RS04580 : Butyryl-CoA dehydrogenase (EC 1.3.8.1)
Original description: acyl-CoA dehydrogenase
SEED: 3-methylmercaptopropionyl-CoA dehydrogenase (DmdC)
KEGG: no annotation
Rationale: # Specifically important in carbon source Sodium butyrate. This indicates that butyryl-CoA is a substrate.

RR42_RS06130 : Gluconokinase (EC 2.7.1.12)
Original description: gluconate kinase
SEED: Gluconokinase (EC 2.7.1.12)
KEGG: gluconokinase
Rationale: Specifically important for utilizing D-Gluconic Acid sodium salt. Automated validation from mutant phenotype: the predicted function (GLUCONOKIN-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

RR42_RS06555 : 3-oxoacid CoA-transferase (EC 2.8.3.5), subunit A
Original description: succinyl-CoA:3-ketoacid-CoA transferase
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 probably RR42_RS06560, but that gene lacks fitness data.

RR42_RS11260 : Methylisocitrate lyase (EC 4.1.3.30)
Original description: 2-methylisocitrate lyase
SEED: Methylisocitrate lyase (EC 4.1.3.30)
KEGG: methylisocitrate lyase
Rationale: Specifically important for utilizing Sodium propionate. Automated validation from mutant phenotype: the predicted function (4.1.3.30) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

RR42_RS13535 : 2-aminobenzoate-CoA ligase (EC 6.2.1.32)
Original description: 2-aminobenzoate-CoA ligase
SEED: Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases
KEGG: 2-aminobenzoate-CoA ligase
Rationale: Specifically important for: L-Tryptophan. This bacterium catabolizes tryptophan via 2-aminobenzoyl-CoA; (KEGG_correct); SEED has a very broad annotation (Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases)

RR42_RS13555 : anthraniloyl-CoA monooxygenase (EC 1.14.13.40)
Original description: salicylyl-CoA 5-hydroxylase
SEED: probable bifunctional hydroxylase/oxidoreductase
KEGG: anthraniloyl-CoA monooxygenase
Rationale: Specifically important for: L-Tryptophan. Antrhanioyl-CoA is a synonym for 2-aminobenzoyl-CoA, an intermediate in the degradation of Trp via 2-aminobenzoate (KEGG_correct)

RR42_RS15385 : Kynureninase (EC 3.7.1.3)
Original description: kynureninase
SEED: Kynureninase (EC 3.7.1.3)
KEGG: kynureninase
Rationale: Specifically important for utilizing L-Tryptophan. Automated validation from mutant phenotype: the predicted function (KYNURENINASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

RR42_RS15390 : Tryptophan 2,3-dioxygenase (EC 1.13.11.11)
Original description: tryptophan 2,3-dioxygenase
SEED: Tryptophan 2,3-dioxygenase (EC 1.13.11.11)
KEGG: tryptophan 2,3-dioxygenase
Rationale: Specifically important for utilizing L-Tryptophan. Automated validation from mutant phenotype: the predicted function (RXN-8665) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

RR42_RS16265 : required for sulfate utilization, putative electron transport protein for sulfite reductase
Original description: oxidoreductase
SEED: Oxidoreductase probably involved in sulfite reduction
KEGG: no annotation
Rationale: PFam PF06073.8 (DUF934). conserved cofitness with sulfite reductase; auxotrophic

RR42_RS16895 : N-formylglutamate deformylase (EC 3.5.1.68)
Original description: N-formylglutamate amidohydrolase
SEED: N-formylglutamate deformylase (EC 3.5.1.68)
KEGG: N-formylglutamate deformylase
Rationale: Specifically important for utilizing L-Histidine. Automated validation from mutant phenotype: the predicted function (N-FORMYLGLUTAMATE-DEFORMYLASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

RR42_RS16905 : Imidazolonepropionase (EC 3.5.2.7)
Original description: imidazolonepropionase
SEED: Imidazolonepropionase (EC 3.5.2.7)
KEGG: imidazolonepropionase
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.

RR42_RS17300 : D-lactate dehydrogenase, FAD-linked subunit GlcD (EC 1.1.99.6)
Original description: glycolate oxidase
SEED: Glycolate dehydrogenase (EC 1.1.99.14), subunit GlcD
KEGG: glycolate oxidase
Rationale: Specifically important for: Sodium D-Lactate.

RR42_RS17310 : D-lactate dehydrogenase, FAD binding subunit GlcE (EC 1.1.99.6)
Original description: glycolate oxidase
SEED: Glycolate dehydrogenase (EC 1.1.99.14), FAD-binding subunit GlcE
KEGG: glycolate oxidase FAD binding subunit
Rationale: Important on D-lactate

RR42_RS17315 : D-lactate dehydrogenase, iron-sulfur subunit GlcF (EC 1.1.99.6)
Original description: glycolate oxidase
SEED: Glycolate dehydrogenase (EC 1.1.99.14), iron-sulfur subunit GlcF
KEGG: glycolate oxidase iron-sulfur subunit
Rationale: Important on D-lactate

RR42_RS19540 : branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused (EC 1.2.7.7)
Original description: indolepyruvate ferredoxin oxidoreductase
SEED: Indolepyruvate ferredoxin oxidoreductase, alpha and beta subunits
KEGG: no annotation
Rationale: Specifically important in nitrogen source L-Valine. This belongs to the indolepyruvate ferredoxin oxidoreductase family, and the mutant phenotype on valine suggests that 3-methyl-2-oxobutanoate (the product of valine transaminase) is a substrate

RR42_RS20080 : L-serine ammonia-lyase (EC 4.3.1.17)
Original description: serine dehydratase
SEED: L-serine dehydratase (EC 4.3.1.17)
KEGG: L-serine dehydratase
Rationale: Specifically important for utilizing L-Serine. Automated validation from mutant phenotype: the predicted function (4.3.1.17) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

RR42_RS20125 : L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2)
Original description: transcriptional regulator
SEED: Transcriptional repressor of PutA and PutP / Proline dehydrogenase (EC 1.5.99.8) (Proline oxidase) / Delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.5.1.12)
KEGG: no annotation
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.

RR42_RS20510 : small component of pyruvate transporter (ybdD-like)
Original description: hypothetical protein
SEED: COG2879, Hypothetical small protein yjiX
KEGG: no annotation
Rationale: Specifically important for pyruvate utilization. 58% identical to E. coli ybdD, which is involved in pyruvate transport (PMID:29358499)

RR42_RS20515 : large component of pyruvate transporter (cstA-like)
Original description: carbon starvation protein A
SEED: Carbon starvation protein A
KEGG: carbon starvation protein
Rationale: Specifically important for pyruvate utilization. 70% identical to E. coli cstA, which is involved in pyruvate transport (PMID:29358499)

RR42_RS21285 : L-lactate dehydrogenase, LutB subunit
Original description: (Fe-S)-binding protein
SEED: Predicted L-lactate dehydrogenase, Iron-sulfur cluster-binding subunit YkgF
KEGG: no annotation
Rationale: Specifically important for utilization of L-lactate or D,L-lactate. (Also important on various nitrogen sources with lactate as the carbon source.) This is related to the LutABC system from Bacillus subtilis (PMC3347220, PMC2668416).

RR42_RS21290 : L-lactate dehydrogenase, LutC subunit
Original description: lactate utilization protein C
SEED: Predicted L-lactate dehydrogenase, hypothetical protein subunit YkgG
KEGG: hypothetical protein
Rationale: Specifically important for utilization of L-lactate or D,L-lactate. (Also important on various nitrogen sources with lactate as the carbon source.) This is related to the LutABC system from Bacillus subtilis (PMC3347220, PMC2668416).

RR42_RS21295 : L-lactate dehydrogenase, LutA subunit
Original description: oxidoreductase
SEED: Predicted L-lactate dehydrogenase, Fe-S oxidoreductase subunit YkgE
KEGG: no annotation
Rationale: Specifically important for utilization of L-lactate or D,L-lactate. (Also important on various nitrogen sources with lactate as the carbon source.) This is related to the LutABC system from Bacillus subtilis (PMC3347220, PMC2668416).

RR42_RS21940 : 4-hydroxybenzoate 3-monooxygenase (EC 1.14.13.2)
Original description: 4-hydroxybenzoate 3-monooxygenase
SEED: P-hydroxybenzoate hydroxylase (EC 1.14.13.2)
KEGG: p-hydroxybenzoate 3-monooxygenase
Rationale: Specifically important for utilizing 4-Hydroxybenzoic Acid. Automated validation from mutant phenotype: the predicted function (1.14.13.2) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

RR42_RS23735 : phenylacetyl-CoA 1,2-epoxidase, structural subunit (EC 1.14.13.149)
Original description: phenylacetic acid degradation protein
SEED: Phenylacetate-CoA oxygenase, PaaI subunit
KEGG: phenylacetic acid degradation protein
Rationale: Specific phenotype: utilization of L-Leucine, Phenylacetic acid. The mild phenotype on leucine is not explained.

RR42_RS25890 : Branched-chain amino acid aminotransferase (EC 2.6.1.42)
Original description: branched-chain amino acid aminotransferase
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) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

RR42_RS25930 : glycine dehydrogenase (deaminating) (EC 1.4.1.10)
Original description: amino acid dehydrogenase
SEED: D-amino acid dehydrogenase small subunit (EC 1.4.99.1)
KEGG: D-amino-acid dehydrogenase
Rationale: Specifically important for: L-Threonine. Annotated as D-amino acid dehydrogenase; SEED has it as the small subunit but do not see why another subunit is expected (i.e. E. coli dadA). Important on Thr as well as Gly because Thr is cleaved (via the threonine dehydrogenase and kbl) to glycine. The electron acceptor is uncertain -- the given EC number implies that NAD is the electron acceptor, which is consistent with an N-terminal NAD binding domain (PF13450).

RR42_RS28295 : 2-amino-3-ketobutyrate coenzyme A ligase (EC 2.3.1.29)
Original description: 2-amino-3-ketobutyrate CoA ligase
SEED: 2-amino-3-ketobutyrate coenzyme A ligase (EC 2.3.1.29)
KEGG: glycine C-acetyltransferase
Rationale: Specifically important for utilizing L-Threonine. Automated validation from mutant phenotype: the predicted function (AKBLIG-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

RR42_RS28300 : L-threonine 3-dehydrogenase (EC 1.1.1.103)
Original description: NAD-dependent epimerase
SEED: L-threonine 3-dehydrogenase (EC 1.1.1.103)
KEGG: no annotation
Rationale: Specifically important for: L-Threonine. The first step in Thr catabolism (SEED_correct)

RR42_RS28305 : L-threonine:H+ symporter
Original description: proline-specific permease
SEED: D-serine/D-alanine/glycine transporter
KEGG: amino acid transporter, AAT family
Rationale: Specifically important for utilizing threonine as a carbon source

RR42_RS28545 : 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4)
Original description: enoyl-CoA hydratase
SEED: 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4)
KEGG: enoyl-CoA hydratase
Rationale: Specifically important for utilizing L-Valine. Automated validation from mutant phenotype: the predicted function (3.1.2.4) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

RR42_RS28835 : gluconate:H+ symporter (gntT)
Original description: permease DsdX
SEED: Gluconate transporter family protein
KEGG: gluconate:H+ symporter, GntP family
Rationale: 67% identical to the gluconate permease (gntT, ACIAD0544) of A. baylayi ADP1 (PMCid:PMC4254613). KEGG_correct

RR42_RS28860 : 2-dehydro-3-deoxygluconokinase (EC 2.7.1.45)
Original description: 2-dehydro-3-deoxygluconokinase
SEED: 2-dehydro-3-deoxygluconate kinase (EC 2.7.1.45)
KEGG: 2-dehydro-3-deoxygluconokinase
Rationale: Specifically important for utilizing D-Gluconic Acid sodium salt. Automated validation from mutant phenotype: the predicted function (2.7.1.45) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

RR42_RS31275 : Homogentisate 1,2-dioxygenase (EC 1.13.11.5)
Original description: homogentisate 1,2-dioxygenase
SEED: Homogentisate 1,2-dioxygenase (EC 1.13.11.5)
KEGG: homogentisate 1,2-dioxygenase
Rationale: Specifically important for utilizing L-Phenylalanine. Automated validation from mutant phenotype: the predicted function (1.13.11.5) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

RR42_RS31785 : 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; Sodium nitrite. 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.

RR42_RS31800 : 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.

RR42_RS32055 : 3-carboxymuconate cycloisomerase PcaB (EC 5.5.1.2)
Original description: 3-carboxy-cis,cis-muconate cycloisomerase
SEED: 3-carboxy-cis,cis-muconate cycloisomerase (EC 5.5.1.2)
KEGG: 3-carboxy-cis,cis-muconate cycloisomerase
Rationale: Specifically important for 4-hydroxybenzoate utilization.

RR42_RS32065 : protocatechuate 3,4-dioxygenase, beta subunit (EC 1.13.11.3)
Original description: protocatechuate 3,4-dioxygenase
SEED: Protocatechuate 3,4-dioxygenase beta chain (EC 1.13.11.3)
KEGG: protocatechuate 3,4-dioxygenase, beta subunit
Rationale: Specific phenotype: utilization of 4-Hydroxybenzoic Acid

RR42_RS33490 : Aromatic-amino-acid aminotransferase (EC 2.6.1.57)
Original description: aromatic amino acid aminotransferase
SEED: Aromatic-amino-acid aminotransferase (EC 2.6.1.57)
KEGG: aromatic-amino-acid transaminase
Rationale: Specifically important for utilizing L-Phenylalanine. Automated validation from mutant phenotype: the predicted function (PHEAMINOTRANS-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

RR42_RS33495 : L-phenylalanine:H+ symporter AroP
Original description: aromatic amino acid transporter
SEED: Aromatic amino acid transport protein AroP
KEGG: amino acid transporter, AAT family
Rationale: Specifically important for utliization of phenylalanine as the nitrogen source.

RR42_RS34240 : putative efflux pump, required for thallium (I) resistance
Original description: membrane protein
SEED: Protein of unknown function UPF0060
KEGG: hypothetical protein
Rationale: PFam PF02694.11 (UPF0060). conserved specific phenotype of UPF0060

RR42_RS34245 : branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
Original description: indolepyruvate ferredoxin oxidoreductase
SEED: Indolepyruvate ferredoxin oxidoreductase, alpha and beta subunits
KEGG: no annotation
Rationale: Specifically important for utilizing L-Leucine as a carbon or nitrogen source.

RR42_RS34260 : Alcohol dehydrogenase (EC 1.1.1.1)
Original description: alcohol dehydrogenase
SEED: Alcohol dehydrogenase (EC 1.1.1.1)
KEGG: alcohol dehydrogenase, propanol-preferring
Rationale: Specifically important for utilizing Ethanol. Automated validation from mutant phenotype: the predicted function (ALCOHOL-DEHYDROG-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Or download reannotations for Cupriavidus basilensis FW507-4G11 or for all organisms as tab-delimited tables