Updated Annotations for Acidovorax sp. GW101-3H11

Updated annotations for Acidovorax sp. GW101-3H11

62 genes with updated (or confirmed) annotations:

Ac3H11_1015 : Aromatic-amino-acid aminotransferase (EC 2.6.1.57)
Original description: Aromatic-amino-acid aminotransferase (EC 2.6.1.57)
SEED: Aromatic-amino-acid aminotransferase (EC 2.6.1.57)
KEGG: no annotation
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.

Ac3H11_1140 : 2-methylisocitrate dehydratase (EC 4.2.1.99)
Original description: Aconitate hydratase (EC 4.2.1.3) @ 2-methylisocitrate dehydratase (EC 4.2.1.99)
SEED: Aconitate hydratase (EC 4.2.1.3) @ 2-methylisocitrate dehydratase (EC 4.2.1.99)
KEGG: aconitate hydratase 1
Rationale: Specifically important for utilizing Sodium propionate. Automated validation from mutant phenotype: the predicted function (4.2.1.99) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Ac3H11_1358 : L-leucine transaminase; L-isoleucine transaminase (EC 2.6.1.42)
Original description: Valine--pyruvate aminotransferase (EC 2.6.1.66)
SEED: Valine--pyruvate aminotransferase (EC 2.6.1.66)
KEGG: no annotation
Rationale: # Specifically important in nitrogen source L-Isoleucine; nitrogen source L-Leucine. Similarity to A0A060PQX5 suggests that glutamate is probably the physiological amino group donor (not alanine), see PMID:24687296

Ac3H11_1623 : L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3)
Original description: L-lactate dehydrogenase (EC 1.1.2.3)
SEED: L-lactate dehydrogenase (EC 1.1.2.3)
KEGG: L-lactate dehydrogenase (cytochrome)
Rationale: Specifically important for utilizing Sodium D,L-Lactate; Sodium L-Lactate. 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.

Ac3H11_1692 : ABC transporter for glutamine/isoleucine/leucine/phenylalanine/proline/serine/tyrosine, ATPase component 2
Original description: Branched-chain amino acid transport ATP-binding protein LivF (TC 3.A.1.4.1)
SEED: Branched-chain amino acid transport ATP-binding protein LivF (TC 3.A.1.4.1)
KEGG: branched-chain amino acid transport system ATP-binding protein
Rationale: Important for utilization of glutamine/isoleucine/leucine/phenylalanine/proline/serine/tyrosine

Ac3H11_1693 : ABC transporter for glutamine/isoleucine/leucine/phenylalanine/proline/serine/tyrosine, ATPase component 1
Original description: Branched-chain amino acid transport ATP-binding protein LivG (TC 3.A.1.4.1)
SEED: Branched-chain amino acid transport ATP-binding protein LivG (TC 3.A.1.4.1)
KEGG: branched-chain amino acid transport system ATP-binding protein
Rationale: Important for utilization of glutamine/isoleucine/leucine/phenylalanine/proline/serine/tyrosine

Ac3H11_1694 : ABC transporter for glutamine/isoleucine/leucine/phenylalanine/proline/serine/tyrosine, permease component 2
Original description: Branched-chain amino acid transport system permease protein LivM (TC 3.A.1.4.1)
SEED: Branched-chain amino acid transport system permease protein LivM (TC 3.A.1.4.1)
KEGG: branched-chain amino acid transport system permease protein
Rationale: Important for utilization of glutamine/isoleucine/leucine/phenylalanine/proline/serine/tyrosine

Ac3H11_1695 : ABC transporter for glutamine/isoleucine/leucine/phenylalanine/proline/serine/tyrosine, permease component 1
Original description: High-affinity branched-chain amino acid transport system permease protein LivH (TC 3.A.1.4.1)
SEED: High-affinity branched-chain amino acid transport system permease protein LivH (TC 3.A.1.4.1)
KEGG: branched-chain amino acid transport system permease protein
Rationale: Important for utilization of glutamine/isoleucine/leucine/phenylalanine/proline/serine/tyrosine

Ac3H11_1847 : Phenylalanine 4-monooxygenase (EC 1.14.16.1)
Original description: Phenylalanine-4-hydroxylase (EC 1.14.16.1)
SEED: Phenylalanine-4-hydroxylase (EC 1.14.16.1)
KEGG: phenylalanine-4-hydroxylase
Rationale: Specifically important for utilizing L-Phenylalanine. Automated validation from mutant phenotype: the predicted function (1.14.16.1) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Ac3H11_1849 : 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27)
Original description: 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27)
SEED: 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27)
KEGG: 4-hydroxyphenylpyruvate dioxygenase
Rationale: Specifically important for utilizing L-Phenylalanine. Automated validation from mutant phenotype: the predicted function (1.13.11.27) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Ac3H11_2062 : glucose ABC transporter, substrate-binding component
Original description: ABC-type sugar transport system, periplasmic component
SEED: ABC-type sugar transport system, periplasmic component
KEGG: multiple sugar transport system substrate-binding protein
Rationale: Specifically important for utilizing glucose. Also mildly important for mannose utilization and likely transports it as well.

Ac3H11_2064 : glucose ABC transporter, permease component 1
Original description: ABC-type sugar transport system, permease component
SEED: ABC-type sugar transport system, permease component
KEGG: multiple sugar transport system permease protein
Rationale: Specifically important for utilizing glucose. Also mildly important for mannose utilization and likely transports it as well.

Ac3H11_2065 : glucose ABC transporter, permease component 2
Original description: Maltose/maltodextrin ABC transporter, permease protein MalG
SEED: Maltose/maltodextrin ABC transporter, permease protein MalG
KEGG: multiple sugar transport system permease protein
Rationale: Specifically important for utilizing glucose. Also mildly important for mannose utilization and likely transports it as well.

Ac3H11_2066 : glucose ABC transporter, ATPase component
Original description: SN-glycerol-3-phosphate transport ATP-binding protein UgpC (TC 3.A.1.1.3)
SEED: SN-glycerol-3-phosphate transport ATP-binding protein UgpC (TC 3.A.1.1.3)
KEGG: multiple sugar transport system ATP-binding protein
Rationale: Specifically important for utilizing glucose. Also mildly important for mannose utilization and likely transports it as well.

Ac3H11_2078 : D-mannose isomerase (EC 5.3.1.7)
Original description: D-mannose isomerase (EC 5.3.1.7)
SEED: D-mannose isomerase (EC 5.3.1.7)
KEGG: no annotation
Rationale: Specifically important for: D-Mannose. Often annotated as N-acylglucosamine 2-epimerase instead

Ac3H11_2306 : Maleylacetoacetate isomerase (EC 5.2.1.2)
Original description: Maleylacetoacetate isomerase (EC 5.2.1.2) @ Glutathione S-transferase, zeta (EC 2.5.1.18)
SEED: Maleylacetoacetate isomerase (EC 5.2.1.2) @ Glutathione S-transferase, zeta (EC 2.5.1.18)
KEGG: maleylacetoacetate isomerase
Rationale: Specifically important for utilizing L-tyrosine disodium salt. Automated validation from mutant phenotype: the predicted function (MALEYLACETOACETATE-ISOMERASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Ac3H11_2396 : ABC transporter for glutamine/isoleucine/leucine/phenylalanine/proline/serine/tyrosine, substrate-binding component
Original description: Extracellular ligand-binding receptor precursor
SEED: Extracellular ligand-binding receptor precursor
KEGG: branched-chain amino acid transport system substrate-binding protein
Rationale: Important for utilization of glutamine/isoleucine/leucine/phenylalanine/proline/serine/tyrosine

Ac3H11_2452 : O-succinylhomoserine sulfhydrylase (EC 2.5.1.48)
Original description: O-acetylhomoserine sulfhydrylase (EC 2.5.1.49) / O-succinylhomoserine sulfhydrylase (EC 2.5.1.48)
SEED: O-acetylhomoserine sulfhydrylase (EC 2.5.1.49) / O-succinylhomoserine sulfhydrylase (EC 2.5.1.48)
KEGG: cystathionine gamma-synthase
Rationale: Important for fitness in defined media and highly cofit with homoserine O-succinyltransferase Ac3H11_4277. The closest characterized homolog is a methionine gamma-lyase (Q84AR1, 36% identical) but this family also includes sulfhydrylases. 92% identical to AAFF19_12795, which can complement both metB- and metC- strains of E. coli (PMID:39375541), which is consistent with direct sulfhydrylation

Ac3H11_2541 : nitrite efflux transporter, HPP family
Original description: CBS-domain-containing membrane protein
SEED: CBS-domain-containing membrane protein
KEGG: CBS domain-containing membrane protein
Rationale: # Specifically important in stress Sodium nitrite. Related to Synpcc7942_1745, which can be a nitrite uptake transporter (PMID:24904028), but this appears to be exporting nitrite. Besides the HPP domain, it encodes two cytoplasmic (?) CBS domains, which might have a regulatory role.

Ac3H11_2548 : N-formylglutamate deformylase (EC 3.5.1.68)
Original description: N-formylglutamate deformylase (EC 3.5.1.68)
SEED: N-formylglutamate deformylase (EC 3.5.1.68)
KEGG: no annotation
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.

Ac3H11_2549 : Formiminoglutamic iminohydrolase (EC 3.5.3.13)
Original description: Formiminoglutamic iminohydrolase (EC 3.5.3.13)
SEED: Formiminoglutamic iminohydrolase (EC 3.5.3.13)
KEGG: formimidoylglutamate deiminase
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.

Ac3H11_2550 : Imidazolonepropionase (EC 3.5.2.7)
Original description: Imidazolonepropionase (EC 3.5.2.7)
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.

Ac3H11_2554 : ABC transporter for L-Histidine, permease component 1
Original description: Amino acid ABC transporter, permease protein
SEED: Amino acid ABC transporter, permease protein
KEGG: polar amino acid transport system permease protein
Rationale: Specific phenotypes on L-Histidine. In a gene cluster that also includes hutD and imidazolonepropionase. Some subunits are annotated as transporting glutamine.

Ac3H11_2555 : ABC transporter for L-Histidine, periplasmic substrate-binding component 1
Original description: Glutamine ABC transporter, periplasmic glutamine-binding protein (TC 3.A.1.3.2)
SEED: Glutamine ABC transporter, periplasmic glutamine-binding protein (TC 3.A.1.3.2)
KEGG: polar amino acid transport system substrate-binding protein
Rationale: Specific phenotype on L-Histidine. Do not understand why there seem to be two substrate binding proteins for this ABC transporter. Both SBPs have signal peptides, so they seem unlikely to be involved in efflux of a waste product instead.

Ac3H11_2557 : Urocanate hydratase (EC 4.2.1.49)
Original description: Urocanate hydratase (EC 4.2.1.49)
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.

Ac3H11_2558 : Histidine ammonia-lyase (EC 4.3.1.3)
Original description: Histidine ammonia-lyase (EC 4.3.1.3)
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.

Ac3H11_2560 : ABC transporter for L-Histidine, ATPase component
Original description: Urea carboxylase-related ABC transporter, ATPase protein
SEED: Urea carboxylase-related ABC transporter, ATPase protein
KEGG: sulfonate/nitrate/taurine transport system ATP-binding protein
Rationale: Specific phenotype on L-Histidine. There may also be a second ATPase component, Ac3H11_2553, but it has no fitness data

Ac3H11_2561 : ABC transporter for L-Histidine, permease component 2
Original description: ABC transporter, permease protein
SEED: ABC transporter, permease protein
KEGG: sulfonate/nitrate/taurine transport system permease protein
Rationale: Specific phenotypes on L-Histidine. In a gene cluster that also includes hutD and imidazolonepropionase. Some subunits are annotated as transporting glutamine.

Ac3H11_2562 : ABC transporter for L-Histidine, periplasmic substrate-binding component 2
Original description: ABC transporter substrate-binding protein
SEED: ABC transporter substrate-binding protein
KEGG: sulfonate/nitrate/taurine transport system substrate-binding protein
Rationale: Specific phenotype on L-Histidine. Do not understand why there seem to be two substrate binding proteins for this ABC transporter. Both SBPs have signal peptides, so they seem unlikely to be involved in efflux of a waste product instead.

Ac3H11_2831 : Isocitrate lyase (EC 4.1.3.1)
Original description: Isocitrate lyase (EC 4.1.3.1)
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.

Ac3H11_2850 : L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2)
Original description: 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)
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.

Ac3H11_2940 : D-sorbitol 2-dehydrogenase (EC 1.1.1.14)
Original description: Ribitol 2-dehydrogenase (EC 1.1.1.56)
SEED: Ribitol 2-dehydrogenase (EC 1.1.1.56)
KEGG: ribitol 2-dehydrogenase
Rationale: Specifically important for: D-Sorbitol. Annotated as ribitol dehydrogenase; it could well have both activities, as with AT5G51970

Ac3H11_2941 : ABC transporter for D-Sorbitol, ATPase component
Original description: Various polyols ABC transporter, ATP-binding component
SEED: Various polyols ABC transporter, ATP-binding component
KEGG: no annotation
Rationale: Specific phenotypes on D-Sorbitol.

Ac3H11_2942 : ABC transporter for D-Sorbitol, permease component 1
Original description: Various polyols ABC transporter, permease component 2
SEED: Various polyols ABC transporter, permease component 2
KEGG: sorbitol/mannitol transport system permease protein
Rationale: Specific phenotypes on D-Sorbitol. The homolog in P. simiae WCS417 is probably a mannitol transporter as well.

Ac3H11_2943 : ABC transporter for D-Sorbitol, permease component 2
Original description: Various polyols ABC transporter, permease component 1
SEED: Various polyols ABC transporter, permease component 1
KEGG: sorbitol/mannitol transport system permease protein
Rationale: Specific phenotypes on D-Sorbitol. The homolog in P. simiae WCS417 is probably a mannitol transporter as well.

Ac3H11_2944 : ABC transporter for D-Sorbitol, periplasmic substrate-binding component
Original description: Various polyols ABC transporter, periplasmic substrate-binding protein
SEED: Various polyols ABC transporter, periplasmic substrate-binding protein
KEGG: sorbitol/mannitol transport system substrate-binding protein
Rationale: Specific phenotype on D-Sorbitol.

Ac3H11_2954 : Dihydropyrimidine dehydrogenase (NADP(+)) (EC 1.3.1.2)
Original description: Dihydropyrimidine dehydrogenase [NADP+] (EC 1.3.1.2)
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.

Ac3H11_2956 : Dihydropyrimidinase (EC 3.5.2.2)
Original description: Dihydropyrimidinase (EC 3.5.2.2)
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.

Ac3H11_2991 : Isovaleryl-CoA dehydrogenase (EC 1.3.8.4)
Original description: Isovaleryl-CoA dehydrogenase (EC 1.3.8.4)
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.

Ac3H11_2994 : 3-ketoacyl-CoA thiolase (EC 2.3.1.16)
Original description: 3-ketoacyl-CoA thiolase (EC 2.3.1.16)
SEED: 3-ketoacyl-CoA thiolase (EC 2.3.1.16)
KEGG: acetyl-CoA C-acetyltransferase
Rationale: Specifically important for utilizing L-Isoleucine. Automated validation from mutant phenotype: the predicted function (METHYLACETOACETYLCOATHIOL-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Ac3H11_2996 : 2-methyl-branched-chain-enoyl-CoA reductase (EC 1.3.8.5)
Original description: Butyryl-CoA dehydrogenase (EC 1.3.99.2)
SEED: Butyryl-CoA dehydrogenase (EC 1.3.99.2)
KEGG: no annotation
Rationale: Specifically important for utilizing L-Isoleucine. Automated validation from mutant phenotype: the predicted function (2-METHYLACYL-COA-DEHYDROGENASE-RXN) was linked to the condition via a SEED subsystem. A more specific reaction was selected manually.

Ac3H11_3009 : Acetoacetate--CoA ligase (EC 6.2.1.16)
Original description: Acetoacetyl-CoA synthetase (EC 6.2.1.16) / Long-chain-fatty-acid--CoA ligase (EC 6.2.1.3)
SEED: Acetoacetyl-CoA synthetase (EC 6.2.1.16) / Long-chain-fatty-acid--CoA ligase (EC 6.2.1.3)
KEGG: fatty-acyl-CoA synthase
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.

Ac3H11_3034 : Fructokinase (EC 2.7.1.4)
Original description: Fructokinase (EC 2.7.1.4)
SEED: Fructokinase (EC 2.7.1.4)
KEGG: fructokinase
Rationale: Specifically important for utilizing D-Fructose. 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.

Ac3H11_3035 : Fructose ABC transporter, substrate-binding component FrcB
Original description: Fructose ABC transporter, substrate-binding component FrcB
SEED: Fructose ABC transporter, substrate-binding component FrcB
KEGG: fructose transport system substrate-binding protein
Rationale: Specific phenotype: utilization of D-Fructose, D-Mannose, D-Sorbitol

Ac3H11_3226 : gluconate TRAP transporter, periplasmic solute-binding component
Original description: TRAP-type transport system, periplasmic component, predicted N-acetylneuraminate-binding protein
SEED: TRAP-type transport system, periplasmic component, predicted N-acetylneuraminate-binding protein
KEGG: no annotation
Rationale: Specifically important for gluconate utilization

Ac3H11_3227 : gluconate TRAP transporter, large permease component
Original description: TRAP-type C4-dicarboxylate transport system, large permease component
SEED: TRAP-type C4-dicarboxylate transport system, large permease component
KEGG: no annotation
Rationale: Specifically important for gluconate utilization

Ac3H11_3228 : gluconate TRAP transporter, small permease component
Original description: Tripartite ATP-independent periplasmic transporter, DctQ component
SEED: Tripartite ATP-independent periplasmic transporter, DctQ component
KEGG: no annotation
Rationale: Specifically important for gluconate utilization

Ac3H11_4058 : required for efflux of an amino acid polymer
Original description: DUF1854 domain-containing protein
SEED: DUF1854 domain-containing protein
KEGG: no annotation
Rationale: PFam PF08909.7 (DUF1854). In a conserved cofit operon with a mdlB-like transporter (Ac3H11_4059) and with two cyanophycin synthetase-like genes that produce a different polymer (Ac3H11_4060 and Ac3H11_4061, see PMID:23224585)

Ac3H11_4729 : histidinol-phosphate transaminase (EC 2.6.1.9)
Original description: Histidinol-phosphate aminotransferase (EC 2.6.1.9)
SEED: Histidinol-phosphate aminotransferase (EC 2.6.1.9)
KEGG: histidinol-phosphate aminotransferase
Rationale: # Essential, as is the ortholog in Cupriavidus basilensis, which is consistent with a role in histidine synthesis. 93% identical to AAFF19_05770, which complements a hisC- strain of E. coli (data of PMID:39375541). Is encoded in a histidine synthesis operon.

Ac3H11_4848 : D-alanine dehydrogenase (EC 1.4.99.-)
Original description: D-amino acid dehydrogenase small subunit (EC 1.4.99.1)
SEED: D-amino acid dehydrogenase small subunit (EC 1.4.99.1)
KEGG: D-amino-acid dehydrogenase
Rationale: Specifically important for utilizing D-Alanine. Automated validation from mutant phenotype: the predicted function (DALADEHYDROG-RXN) was linked to the condition via a SEED subsystem. A more specific reaction was selected manually.

Ac3H11_576 : required for sulfate utilization, putative electron transport protein for sulfite reductase
Original description: Oxidoreductase probably involved in sulfite reduction
SEED: Oxidoreductase probably involved in sulfite reduction
KEGG: no annotation
Rationale: PFam PF06073.8 (DUF934). conserved cofitness with sulfite reductase; auxotrophic

Ac3H11_603 : L-2-keto-3-deoxyarabonate dehydratase (EC 4.2.1.43)
Original description: L-2-keto-3-deoxyarabonate dehydratase (EC 4.2.1.43)
SEED: L-2-keto-3-deoxyarabonate dehydratase (EC 4.2.1.43)
KEGG: dihydrodipicolinate synthase
Rationale: Specifically important for L-arabinose utilization and 80% similar to araD from A. brasilense (KDADA_AZOBR, PMID:16950779). This gene is also important for D-galactose utilization, which might be due to polar effects. SEED_correct

Ac3H11_612 : 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26)
Original description: 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26)
SEED: 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26)
KEGG: no annotation
Rationale: Specifically important for utilizing L-Arabinose. Automated validation from mutant phenotype: the predicted function (25-DIOXOVALERATE-DEHYDROGENASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Ac3H11_614 : L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48)
Original description: Putative oxidoreductase in arabinose utilization cluster
SEED: Putative oxidoreductase in arabinose utilization cluster
KEGG: no annotation
Rationale: Specifically important for: D-Galactose; L-Arabinose. Some other dehydrogenases are known to act on both of these substrates

Ac3H11_615 : L-arabinolactonase/D-galactonolactonase (EC 3.1.1.15; EC 3.1.1.25)
Original description: L-arabinolactonase (EC 3.1.1.15)
SEED: L-arabinolactonase (EC 3.1.1.15)
KEGG: no annotation
Rationale: Specifically important for utilizing L-arabinose or D-galactose; the EC numbers given are for the 1,4-lactonase reactions, but this is not certain. The dehydrogenase (Ac3H11_614) could form 1,5-lactones instead.

Ac3H11_701 : Arginase (EC 3.5.3.1)
Original description: Arginase (EC 3.5.3.1)
SEED: Arginase (EC 3.5.3.1)
KEGG: arginase
Rationale: Specifically important for utilizing L-Arginine. Automated validation from mutant phenotype: the predicted function (ARGINASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Ac3H11_791 : ABC transporter for Glycerol, ATPase component 1
Original description: Glycerol-3-phosphate ABC transporter, ATP-binding protein UgpC (TC 3.A.1.1.3)
SEED: Glycerol-3-phosphate ABC transporter, ATP-binding protein UgpC (TC 3.A.1.1.3)
KEGG: multiple sugar transport system ATP-binding protein
Rationale: Specific phenotype on Glycerol; D-Galactose. Has a TOBE domain after the ATPase domain. The phenotype on galactose is not explained.

Ac3H11_792 : ABC transporter for Glycerol, ATPase component 2
Original description: Glycerol-3-phosphate ABC transporter, ATP-binding protein UgpC (TC 3.A.1.1.3)
SEED: Glycerol-3-phosphate ABC transporter, ATP-binding protein UgpC (TC 3.A.1.1.3)
KEGG: multiple sugar transport system ATP-binding protein
Rationale: Specific phenotype on Glycerol. Has a TOBE domain after the ATPase domain. Also mildly important on phenotype on galactose, which is not explained.

Ac3H11_793 : ABC transporter for Glycerol, permease component 1
Original description: Glycerol-3-phosphate ABC transporter, permease protein UgpA (TC 3.A.1.1.3)
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 Glycerol. in a gene cluster for glycerol utilization; see phenotype on both strands

Ac3H11_794 : ABC transporter for Glycerol, permease component 2
Original description: Glycerol-3-phosphate ABC transporter, permease protein UgpE (TC 3.A.1.1.3)
SEED: Glycerol-3-phosphate ABC transporter, permease protein UgpE (TC 3.A.1.1.3)
KEGG: multiple sugar transport system permease protein
Rationale: Specific phenotype on Glycerol.

Ac3H11_796 : ABC transporter for Glycerol, periplasmic substrate-binding component
Original description: Glycerol-3-phosphate ABC transporter, permease protein UgpA (TC 3.A.1.1.3)
SEED: Glycerol-3-phosphate ABC transporter, permease protein UgpA (TC 3.A.1.1.3)
KEGG: multiple sugar transport system substrate-binding protein
Rationale: Specific phenotype on Glycerol. Has signal peptide but not transmembrane helices, and CDD confirms it in the SBP family, not a permease as sometimes annotated

Ac3H11_929 : L-serine ammonia-lyase (EC 4.3.1.17)
Original description: L-serine dehydratase (EC 4.3.1.17)
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.

Or download reannotations for Acidovorax sp. GW101-3H11 or for all organisms as tab-delimited tables