Updated Annotations for Phaeobacter inhibens DSM 17395

Updated annotations for Phaeobacter inhibens DSM 17395

78 genes with updated (or confirmed) annotations:

PGA1_c10280 : Isovaleryl-CoA dehydrogenase (EC 1.3.8.4)
Original description: isovaleryl-CoA dehydrogenase
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.

PGA1_c11750 : L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2)
Original description: bifunctional protein PutA
SEED: Proline dehydrogenase (EC 1.5.99.8) (Proline oxidase) / Delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.5.1.12)
KEGG: proline dehydrogenase / delta 1-pyrroline-5-carboxylate dehydrogenase
Rationale: Specifically important for utilizing L-Proline. Automated validation from mutant phenotype: the predicted function (1.2.1.88, 1.5.5.2) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

PGA1_c11900 : Propionate--CoA ligase (EC 6.2.1.17)
Original description: propionate-CoA ligase PrpE
SEED: Acetyl-coenzyme A synthetase (EC 6.2.1.1)
KEGG: propionyl-CoA synthetase
Rationale: Specifically important for utilizing Sodium propionate. Automated validation from mutant phenotype: the predicted function (6.2.1.17) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

PGA1_c11910 : Malate dehydrogenase (decarboxylating) (EC 1.1.1.39)
Original description: NAD-dependent malic enzyme
SEED: NADP-dependent malic enzyme (EC 1.1.1.40)
KEGG: malate dehydrogenase (oxaloacetate-decarboxylating)(NADP+)
Rationale: Specifically important for utilizing L-Malic acid disodium salt monohydrate. Automated validation from mutant phenotype: the predicted function (1.1.1.39-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

PGA1_c11930 : Cytidine deaminase (EC 3.5.4.5)
Original description: cytidine deaminase Cdd
SEED: Cytidine deaminase (EC 3.5.4.5)
KEGG: cytidine deaminase
Rationale: Specifically important for utilizing Cytidine. Automated validation from mutant phenotype: the predicted function (CYTIDEAM2-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

PGA1_c12640 : D-lactate transporter, ATP-binding component
Original description: putative high-affinity branched-chain amino acid transport ATP-binding protein
SEED: InterPro IPR001687:IPR003439:IPR003593 COGs COG0411
KEGG: no annotation
Rationale: Specific phenotype on D-lactate and D,L-lactate and cofit with other components

PGA1_c12650 : D-lactate transporter, permease component 1
Original description: putative high-affinity branched-chain amino acid transport system permease protein
SEED: Branched-chain amino acid transport system permease protein LivM (TC 3.A.1.4.1)
KEGG: no annotation
Rationale: Specific phenotype on D-lactate and D,L-lactate and cofit with other components

PGA1_c12660 : D-lactate transporter, permease component 2
Original description: putative high-affinity branched-chain amino acid transport system permease protein
SEED: Possible ABC transporter subunit
KEGG: no annotation
Rationale: Specific phenotype on D-lactate and D,L-lactate and cofit with other components

PGA1_c12670 : D-lactate transporter, substrate binding component
Original description: ABC-type branched-chain amino acid transport systems, periplasmic component
SEED: Branched-chain amino acid ABC transporter, periplasmic substrate- binding protein
KEGG: no annotation
Rationale: Cofit with the other components and important for growth in various D-lactate and D,L-lactate media

PGA1_c12820 : Dihydropyrimidine dehydrogenase (NADP(+)) (EC 1.3.1.2)
Original description: dihydroorotate dehydrogenase-like protein
SEED: Dihydropyrimidine dehydrogenase [NADP+] (EC 1.3.1.2)
KEGG: dihydropyrimidine dehydrogenase (NADP+) ; dihydroorotate dehydrogenase (fumarate)
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.

PGA1_c12840 : Beta-ureidopropionase (EC 3.5.1.6)
Original description: N-carbamoyl-L-amino acid hydrolase AmaB
SEED: Beta-ureidopropionase (EC 3.5.1.6)
KEGG: N-carbamoyl-L-amino-acid hydrolase
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.

PGA1_c12850 : Dihydropyrimidinase (EC 3.5.2.2)
Original description: D-hydantoinase/dihydropyrimidinase Dht
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.

PGA1_c13170 : Sorbitol dehydrogenase (EC 1.1.1.14)
Original description: sorbitol dehydrogenase PolS
SEED: Sorbitol dehydrogenase (EC 1.1.1.14)
KEGG: no annotation
Rationale: Specifically important for: D-Sorbitol. First step is sorbitol catabolism; (SEED_correct)

PGA1_c13180 : ABC transporter for D-Sorbitol, ATPase component
Original description: ABC transporter, ATP binding protein
SEED: Various polyols ABC transporter, ATP-binding component
KEGG: sorbitol/mannitol transport system ATP-binding protein
Rationale: Specific phenotype on D-Sorbitol.

PGA1_c13190 : ABC transporter for D-Sorbitol, permease component 1
Original description: ABC transporter permease protein
SEED: Various polyols ABC transporter, permease component 2
KEGG: sorbitol/mannitol transport system permease protein
Rationale: Specific phenotypes on D-Sorbitol; D-Sorbitol.

PGA1_c13200 : ABC transporter for D-Sorbitol, permease component 2
Original description: ABC transporter permease protein
SEED: Various polyols ABC transporter, permease component 1
KEGG: sorbitol/mannitol transport system permease protein
Rationale: Specific phenotypes on D-Sorbitol; D-Sorbitol.

PGA1_c13210 : ABC transporter for D-Sorbitol, periplasmic substrate-binding component
Original description: extracellular solute-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.

PGA1_c13340 : Accessory protein for co(II)balamin reduction (DUF1638) (EC:2.1.1.13)
Original description: Protein of unknown function (DUF1638).
SEED: no annotation
KEGG: no annotation
Rationale: Apparently required for the reactivation of vitamin B12 (auxotroph)

PGA1_c13350 : Methionine synthase component, B12 binding and B12-binding cap domains (EC:2.1.1.13)
Original description: putative dimethylamine corrinoid protein
SEED: corrinoid methyltransferase protein
KEGG: 5-methyltetrahydrofolate--homocysteine methyltransferase
Rationale: PGA1_c13350 is annotated as putative dimethylamine corrinoid protein. Its auxotrophic phenotype is rescued by added methionine. Compared to MetH from E. cli, it has the B12-binding cap (PF02607) and B12 binding (PF02310) domains but lacks methyltransferase (PF02574) or pterin-binding (PF00809) domains or the B12 activation domain (PF02965). (auxotroph)

PGA1_c13370 : Methionine synthase component, methyltransferase domain (EC:2.1.1.13)
Original description: putative homocysteine S-methyltransferase
SEED: Betaine--homocysteine S-methyltransferase (EC 2.1.1.5)
KEGG: 5-methyltetrahydrofolate--homocysteine methyltransferase
Rationale: PGA1_c13370 has a methyltransferase domain and its auxotrophic phenotype is rescued by added methionine. Also, S. Thole et al. (ISME J. 2012) proposed that PGA1_c13360, which contains a radical SAM domain (PF04055), might be involved in B12 activation, but it lacks phenotypes in our data. (auxotroph)

PGA1_c13990 : Novel Xylose regulator from LacI family
Original description: putative transcriptional regulator, iacl family
SEED: Novel Xylose regulator from LacI family
KEGG: LacI family transcriptional regulator
Rationale: # Specifically important in carbon source D-Xylose. Also see expression evidence (PMC4148808). (SEED_correct)

PGA1_c14000 : Xylose isomerase (EC 5.3.1.5)
Original description: xylose isomerase XylA
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.

PGA1_c14010 : Xylulose kinase (EC 2.7.1.17)
Original description: xylulose kinase XylB
SEED: Xylulose kinase (EC 2.7.1.17)
KEGG: xylulokinase
Rationale: Specifically important for utilizing 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.

PGA1_c15200 : ATP-dependent reduction of co(II)balamin (RamA-like) (EC:2.1.1.13)
Original description: Uncharacterized metal-binding protein
SEED: Iron-sulfur cluster-binding protein
KEGG: no annotation
Rationale: Apparently required for the reactivation of vitamin B12. Distantly related to RamA (see PMID: 19043046) (auxotroph)

PGA1_c16040 : Methionine synthase component, pterin-binding domain (EC:2.1.1.13)
Original description: pterin binding domain-containing protein
SEED: Pterin-binding enzyme domain protein
KEGG: 5-methyltetrahydrofolate--homocysteine methyltransferase
Rationale: Its auxotrophic phenotype is rescued by methionine. PGA1_c16040 has the pterin-binding domain (auxotroph)

PGA1_c16380 : citrulline utilization hydrolase
Original description: Uncharacterized protein conserved in bacteria containing a pentein-type domain
SEED: Amidinotransferase family protein
KEGG: no annotation
Rationale: Specifically important for: L-Citrulline. This enzyme is distantly related to characterized arginine deiminases (see PF02274) and has conserved catalytic residues. It might be a citrullinase.

PGA1_c16670 : D-mannose isomerase (EC 5.3.1.7)
Original description: putative N-acylglucosamine 2-epimerase
SEED: N-acylglucosamine 2-epimerase (EC 5.1.3.8)
KEGG: no annotation
Rationale: Specifically important for: D-Mannose. often annotated as N-acylglucosamine 2-epimerase, but the phenotype confirms that it is mannose isomerase.

PGA1_c17350 : 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4)
Original description: putative 3-hydroxyisobutyryl-CoA hydrolase
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.

PGA1_c20660 : TRAP transporter for fumarate, succinate, L-malate, and 2-oxogulatarate, large permease component
Original description: TRAP transporter, subunit DctM
SEED: TRAP-type C4-dicarboxylate transport system, large permease component
KEGG: no annotation
Rationale: Specifically important for utilization of fumarate, succinate, L-malate, and alpha-ketoglutarate. Phenotypes on alpha-ketoglutarate are more mild, which might indicate some genetic redundancy.

PGA1_c20670 : TRAP transporter for fumarate, succinate, L-malate, and 2-oxogulatarate, small permease component
Original description: TRAP transporter, subunit DctQ
SEED: TRAP-type transport system, small permease component, predicted N-acetylneuraminate transporter
KEGG: C4-dicarboxylate transporter, DctQ subunit
Rationale: Specifically important for utilization of fumarate, succinate, L-malate, and alpha-ketoglutarate. Phenotypes on alpha-ketoglutarate are more mild, which might indicate some genetic redundancy.

PGA1_c20680 : TRAP transporter for fumarate, succinate, L-malate, and 2-oxogulatarate, substrate-binding component
Original description: C4-dicarboxylate-binding periplasmic protein DctP
SEED: TRAP-type C4-dicarboxylate transport system, periplasmic component
KEGG: C4-dicarboxylate-binding protein DctP
Rationale: Specifically important for utilization of fumarate, succinate, L-malate, and alpha-ketoglutarate. Phenotypes on alpha-ketoglutarate are more mild, which might indicate some genetic redundancy.

PGA1_c21010 : component of stress sensing system, with PGA1_c21020 (DUF2063)
Original description: Uncharacterized protein conserved in bacteria
SEED: Uncharacterized protein conserved in bacteria, NMA0228-like
KEGG: hypothetical protein
Rationale: PFam PF05114.9 (DUF692). Conserved cofitness and pleiotropic phenotypes

PGA1_c21020 : component of stress sensing system with PGA1_c21010 (DUF692)
Original description: Uncharacterized protein conserved in bacteria (DUF2063).
SEED: Glutamate synthase [NADPH] large chain (EC 1.4.1.13)
KEGG: no annotation
Rationale: PFam PF09836.5 (DUF2063). Conserved cofitness and pleiotropic phenotypes

PGA1_c21860 : Histidinol-phosphatase [alternative form] (EC 3.1.3.15)
Original description: putative histidinol-phosphate phosphatase HisN
SEED: Histidinol-phosphatase [alternative form] (EC 3.1.3.15)
KEGG: no annotation
Rationale: Annotated as this by multiple resources. (essential) (SEED_correct)

PGA1_c24530 : aspartyl-tRNA(Asp/Asn) synthetase (EC 6.1.1.23)
Original description: aspartyl-tRNA synthetase AspS
SEED: Aspartyl-tRNA synthetase (EC 6.1.1.12) @ Aspartyl-tRNA(Asn) synthetase (EC 6.1.1.23)
KEGG: aspartyl-tRNA synthetase
Rationale: A conserved essential gene. This activity is necessary to explain asparagine biosynthesis. 41% identical to an aspartyl-tRNA(Asn) ligase from Bacillus halodurans (Q9KDG1)

PGA1_c25240 : histidinol-phosphate aminotransferase [EC:2.6.1.9]
Original description: histidinol-phosphate aminotransferase HisC
SEED: Biosynthetic Aromatic amino acid aminotransferase beta (EC 2.6.1.57)
KEGG: histidinol-phosphate aminotransferase
Rationale: Annotated as this by multiple resources. (essential) (KEGG_correct)

PGA1_c27890 : Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6)
Original description: putative hexosephosphate binding protein
SEED: Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6)
KEGG: glucosamine-6-phosphate isomerase
Rationale: Specifically important for utilizing N-Acetyl-D-Glucosamine. Automated validation from mutant phenotype: the predicted function (GLUCOSAMINE-6-P-DEAMIN-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

PGA1_c27910 : N-acetylglucosamine kinase (EC 2.7.1.59)
Original description: putative ATPase, BadF/BadG/BcrA/BcrD type
SEED: N-acetylglucosamine kinase of eukaryotic type (EC 2.7.1.59)
KEGG: no annotation
Rationale: Specifically important for: D-Glucose; N-Acetyl-D-Glucosamine. This is the first step in NAG catabolism. The next step is expected to be N-acetylglucosamine-6-phosphate deacetylase (PGA1_c27880, no data). The phenotype on D-glucose is consistent across replicates and is not explained. It does not seem to be due to polar effects. There is a glucokinase that is important for glucose utilization (PGA1_c05420 ) so we don't expect that this is glucokinase. (SEED_correct)

PGA1_c27930 : N-Acetyl-D-glucosamine ABC transport system, periplasmic substrate-binding component
Original description: putative sugar ABC transporter, periplasmic binding 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)

PGA1_c27940 : N-Acetyl-D-glucosamine ABC transport system, permease component 1
Original description: ABC transporter permease protein
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. (SEED_correct)

PGA1_c27950 : N-Acetyl-D-glucosamine ABC transport system, permease component 2
Original description: ABC transporter permease protein
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. (SEED_correct)

PGA1_c27970 : N-Acetyl-D-glucosamine ABC transport system, ATPase component
Original description: ATP-binding transport protein SmoK
SEED: N-Acetyl-D-glucosamine ABC transport system ATP-binding protein
KEGG: sorbitol/mannitol transport system ATP-binding protein
Rationale: Specific phenotype on N-Acetyl-D-Glucosamine. (SEED_correct)

PGA1_c29420 : aromatic-amino-acid transaminase [EC:2.6.1.57]
Original description: aromatic-amino-acid aminotransferase TyrB
SEED: Aspartate aminotransferase (EC 2.6.1.1)
KEGG: aromatic-amino-acid transaminase
Rationale: Annotated as this by multiple resources. (essential) (KEGG_correct)

PGA1_c29700 : D-lactate dehydrogenase, iron-sulfur subunit GlcF (EC 1.1.99.6)
Original description: glycolate oxidase iron-sulfur subunit
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; Sodium D-Lactate.

PGA1_c29710 : D-lactate dehydrogenase, FAD binding subunit GlcE (EC 1.1.99.6)
Original description: glycolate oxidase subunit GlcE
SEED: Glycolate dehydrogenase (EC 1.1.99.14), FAD-binding subunit GlcE
KEGG: glycolate oxidase FAD binding subunit
Rationale: Specifically important for: Sodium D-Lactate; Sodium D,L-Lactate.

PGA1_c29720 : D-lactate dehydrogenase, FAD-linked subunit GlcD (EC 1.1.99.6)
Original description: glycolate oxidase subunit GlcD
SEED: Glycolate dehydrogenase (EC 1.1.99.14), subunit GlcD
KEGG: glycolate oxidase
Rationale: Specifically important for: Sodium D,L-Lactate; Sodium D-Lactate.

PGA1_c29870 : ATP phosphoribosyltransferase (EC 2.4.2.17)
Original description: ATP phosphoribosyltransferase HisG
SEED: ATP phosphoribosyltransferase (EC 2.4.2.17)
KEGG: ATP phosphoribosyltransferase
Rationale: A conserved essential gene. This activity is necessary to explain histidine biosynthesis. Hits TIGR00070, and no other candidates for this step were identified in the genome.

PGA1_c30490 : Malyl-CoA lyase (EC 4.1.3.24)
Original description: putative citrate lyase subunit beta
SEED: Malyl-CoA lyase (EC 4.1.3.24)
KEGG: L-malyl-CoA/beta-methylmalyl-CoA lyase
Rationale: Specifically important for utilizing Potassium acetate. Automated validation from mutant phenotype: the predicted function (4.1.3.24) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

PGA1_c03400 : acetyl-CoA:acetyl-CoA C-acetyltransferase / acetyl-CoA:propanoyl-CoA 2-C-acetyltransferase (EC 2.3.1.9; EC 2.3.1.16)
Original description: acetyl-CoA acetyltransferase PhaA
SEED: Acetyl-CoA acetyltransferase (EC 2.3.1.9) of ethylmalonyl-CoA pathway
KEGG: acetyl-CoA C-acetyltransferase
Rationale: Specifically important for utilizing Potassium acetate amd threonine. EC 2.3.1.9 (acetoacetyl-CoA) was linked to acetate via a SEED subsystem. The phenotype on threonine suggests that propanyl-CoA is also a substrate, hence the broader EC # 2.3.1.16.

PGA1_c00330 : Error-prone polymerase for DNA repair (imuB or polY like)
Original description: protein imuB-like protein
SEED: DNA polymerase-like protein PA0670
KEGG: protein ImuB
Rationale: Conserved and specific phenotype: important for resisting cisplatin. Related to imuB from Caulobacter. Also similar to PA0670, which is induced by the SOS response, even though it does not seem to have mutant phenotypes related to DNA repair.

PGA1_c34320 : L-threonine 3-dehydrogenase (EC 1.1.1.103)
Original description: L-threonine 3-dehydrogenase Tdh
SEED: L-threonine 3-dehydrogenase (EC 1.1.1.103)
KEGG: threonine 3-dehydrogenase
Rationale: Specifically important for utilizing L-Threonine. Automated validation from mutant phenotype: the predicted function (1.1.1.103) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

PGA1_c34330 : 2-amino-3-ketobutyrate coenzyme A ligase (EC 2.3.1.29)
Original description: 2-amino-3-ketobutyrate coenzyme A ligase Kbl
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.

PGA1_c36210 : L-asparaginase (EC 3.5.1.1)
Original description: L-asparaginase II
SEED: Hypothetical protein of L-Asparaginase type 2-like superfamily
KEGG: no annotation
Rationale: # Specifically important in carbon source L-Asparagine. This protein is homologous to characterized asparaginases (i.e. Q9RFN5, see PMID:22450783)

PGA1_c03680 : (3S)-malyl-CoA thioesterase [EC:3.1.2.30]
Original description: putative citrate lyase subunit beta
SEED: L-malyl-CoA/beta-methylmalyl-CoA lyase (EC 4.1.3.-)
KEGG: (3S)-malyl-CoA thioesterase
Rationale: Specifically important for: L-Threonine; Potassium acetate. This is part of the ethylmalonyl-CoA cycle for acetate assimilation, and hence is important on threonine (cleaved to glycine and acetate via the PGA1_c34330 or kbl) and acetate (where it has a milder phenotype). The annotation of sit:TM1040_3520 has been updated to (3S)-malyl-CoA thioesterase [EC:3.1.2.30]. 69% similar to MCTE_RHOS4 (consistent with the KEGG annotation). SEED suggests that this is the malyl-CoA/methylmalyl-CoA lyase but that activity is probably provided by PGA1_c30490. (KEGG_correct)

PGA1_c36320 : Urocanate hydratase (EC 4.2.1.49)
Original description: urocanate hydratase HutU
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.

PGA1_c36330 : N-formylglutamate deformylase (EC 3.5.1.68)
Original description: N-formylglutamate deformylase HutG
SEED: N-formylglutamate deformylase (EC 3.5.1.68)
KEGG: formiminoglutamase
Rationale: Specifically important for utilizing L-Histidine. Automated validation from mutant phenotype: the predicted function (3.5.1.68) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

PGA1_c36340 : Histidine ammonia-lyase (EC 4.3.1.3)
Original description: histidine ammonia-lyase HutH
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.

PGA1_c36350 : Imidazolonepropionase (EC 3.5.2.7)
Original description: imidazolonepropionase HutI
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.

PGA1_c36360 : Formiminoglutamic iminohydrolase (EC 3.5.3.13)
Original description: putative formiminoglutamate 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.

PGA1_262p00430 : glucose transporter, periplasmic substrate-binding component
Original description: D-xylose-binding periplasmic protein XylF
SEED: Xylose ABC transporter, periplasmic xylose-binding protein XylF
KEGG: D-xylose transport system substrate-binding protein
Rationale: specific phenotype on glucose and cofit with other nearby components. This is similar (65% identity) to gxyS (Atu3576) of Agrobacterium tumefaciens, which is involved in the transport of glucose, glucosamine, and xylose (PMCID: PMC4135649). It is not clear if the Phaeobacter system transports xylose, as it is not required for utilizing xylose, but no other xylose transport system was identified either.

PGA1_262p00440 : glucose transporter, permease component
Original description: xylose transport system permease protein XylH
SEED: Xylose ABC transporter, permease protein XylH
KEGG: D-xylose transport system permease protein
Rationale: specific phenotype on glucose and cofit with nearby xylF (PGA1_262p00430) and xylG (PGA1_262p00450). This is similar to the gxyB (Atu3575) of Agrobacterium tumefaciens, which is involved in the transport of glucose, glucosamine, and xylose (PMCID: PMC4135649). It is not clear if the Phaeobacter system transports xylose, as it is not required for utilizing xylose, but no other xylose transport system was identified either.

PGA1_262p00450 : glucose transporter, ATPase component
Original description: sugar ABC transporter, ATP-binding protein
SEED: D-xylose transport ATP-binding protein XylG
KEGG: D-xylose transport system ATP-binding protein
Rationale: Important for utilizing glucose and cofit with the other components. This is similar (68% identity) to gxyA (Atu3574) of Agrobacterium tumefaciens, which is involved in the transport of glucose, glucosamine, and xylose (PMCID: PMC4135649). It is not clear if the Phaeobacter system transports xylose, as it is not required for utilizing xylose, but no other xylose transport system was identified either.

PGA1_c05420 : glucokinase (EC 2.7.1.2)
Original description: glucokinase Glk
SEED: Glucokinase (EC 2.7.1.2)
KEGG: glucokinase
Rationale: Important for the utilization of glucose, trehalose, and cellobiose; trehalose and cellobiose are cleaved to glucose

PGA1_c06030 : DNA repair nuclease, ligase-associated (TIGR04123)
Original description: Predicted ICC-like phosphoesterases
SEED: FIG006285: ICC-like protein phosphoesterase
KEGG: no annotation
Rationale: # Very important for resisting 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).

PGA1_c06040 : DNA damage response helicase, ligase-associated
Original description: putative DEAD/DEAH box helicase
SEED: ATP-dependent helicase, DEAD/DEAH box family, associated with Flp pilus assembly
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)

PGA1_c07220 : 5-keto-2-deoxy-D-gluconate-6 phosphate aldolase (EC 4.1.2.29)
Original description: putative 6-phospho-5-dehydro-2-deoxy-D-gluconate aldolase
SEED: 5-keto-2-deoxy-D-gluconate-6 phosphate aldolase (EC 4.1.2.29)
KEGG: fructose-bisphosphate aldolase, class II
Rationale: Specifically important for: m-Inositol. Part of inositol catabolism via 5-deoxyglucuronate (SEED_correct)

PGA1_c07230 : 5-deoxy-D-glucuronate isomerase (EC 5.3.1.30)
Original description: putative 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.

PGA1_c07240 : 5-dehydro-2-deoxygluconokinase (EC 2.7.1.92)
Original description: putative 5-dehydro-2-deoxygluconokinase
SEED: 5-keto-2-deoxygluconokinase (EC 2.7.1.92)
KEGG: 5-dehydro-2-deoxygluconokinase
Rationale: Specifically important for utilizing m-Inositol. Automated validation from mutant phenotype: the predicted function (2.7.1.92) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

PGA1_c07250 : 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase IolD (EC 3.7.1.22)
Original description: 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase IolD
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.

PGA1_c07270 : Myo-inosose-2 dehydratase (EC 4.2.1.44)
Original description: putative iolE/mocC family 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.

PGA1_c07300 : Inositol transport system sugar-binding protein
Original description: ABC-type sugar transport system, periplasmic component
SEED: Inositol transport system sugar-binding protein
KEGG: simple sugar transport system substrate-binding protein
Rationale: Specific phenotype on inositol and cofit with other nearby components (SEED_correct)

PGA1_c07310 : Inositol transport system permease protein
Original description: binding protein dependent transport system permease
SEED: Inositol transport system permease protein
KEGG: simple sugar transport system permease protein
Rationale: Specific phenotype on inositol and cofit with other nearby components (SEED_correct)

PGA1_c07320 : Inositol transport system ATP-binding protein
Original description: sugar ABC transporter, ATP-binding protein
SEED: Inositol transport system ATP-binding protein
KEGG: simple sugar transport system ATP-binding protein
Rationale: Specific phenotype on inositol and cofit with other nearby components (SEED_correct)

PGA1_c07840 : Beta-glucosidase (EC 3.2.1.21)
Original description: beta-glucosidase A
SEED: Beta-glucosidase (EC 3.2.1.21)
KEGG: beta-glucosidase
Rationale: Specifically important for utilizing D-Cellobiose. Automated validation from mutant phenotype: the predicted function (3.2.1.21) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

PGA1_c07890 : cytoplasmic trehalase (AlgA)
Original description: putative alpha-glucosidase AglA
SEED: Alpha-glucosidase AglA
KEGG: alpha-glucosidase
Rationale: Specifically important for trehalose utilization and part of an operon with an algEFGK-type transporter for trehalose and cellobiose. Also important for cellobiose utilization, but this may be a polar effect (the cellobiase is PGA1_c07840)

PGA1_c08960 : DNA repair endonuclease mmcB (DUF1052)
Original description: Uncharacterized protein conserved in bacteria
SEED: Transcription elongation factor
KEGG: no annotation
Rationale: Conserved and specific phenotype: important for resisting cisplatin. Also see PMID:26162909 which suggests a role for a homologous protein from Caulobacter in creating substrates for translesion synthesis

PGA1_c00920 : putative transporter, required for glycine utilization
Original description: Predicted membrane protein
SEED: Arginine/ornithine antiporter ArcD
KEGG: no annotation
Rationale: PFam PF03458.9 (UPF0126). conserved specific phenotype of UPF0126

PGA1_c09550 : Glutaminase (EC 3.5.1.2)
Original description: glutaminase A
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.

Or download reannotations for Phaeobacter inhibens DSM 17395 or for all organisms as tab-delimited tables