Updated Annotations for Marinobacter adhaerens HP15

Updated annotations for Marinobacter adhaerens HP15

36 genes with updated (or confirmed) annotations:

HP15_1251 : large component of pyruvate transporter (actP-like)
Original description: sodium: solute symporter family protein
SEED: Acetate permease ActP (cation/acetate symporter)
KEGG: cation/acetate symporter
Rationale: Important for pyruvate utilization. Distantly related to E. coli actP.

HP15_1252 : small component of pyruvate transporter (TIGR03647)
Original description: membrane protein containing probable solute: sodium symporter, small subunit domain
SEED: FIG152265: Sodium:solute symporter associated protein
KEGG: no annotation
Rationale: The data for HP15_1252 is noisy, but it is important for pyruvate utilization, and is 74% identical to Psest_0346, which is also important for pyruvate utilization. HP15_1252 belongs to TIGR03647, which was predicted to be the small subunit of a transporter.

HP15_1334 : Error-prone polymerase for DNA repair (imuB or polY like)
Original description: conserved hypothetical 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.

HP15_1512 : Enoyl-CoA hydratase (EC 4.2.1.17)
Original description: multifunctional fatty acid oxidation complex subunit alpha
SEED: Enoyl-CoA hydratase (EC 4.2.1.17) / Delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase (EC 5.3.3.8) / 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) / 3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3)
KEGG: 3-hydroxyacyl-CoA dehydrogenase / enoyl-CoA hydratase / 3-hydroxybutyryl-CoA epimerase / enoyl-CoA isomerase
Rationale: Specifically important for utilizing Tween 20. Automated validation from mutant phenotype: the predicted function (ENOYL-COA-HYDRAT-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

HP15_1513 : Acetyl-CoA C-acyltransferase (EC 2.3.1.16)
Original description: acetyl-CoA acetyltransferase
SEED: 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)
KEGG: acetyl-CoA acyltransferase
Rationale: Specifically important for utilizing Tween 20. Automated validation from mutant phenotype: the predicted function (KETOACYLCOATHIOL-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

HP15_1631 : Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168)
Original description: dihydrolipoamide acetyltransferase
SEED: Dihydrolipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex (EC 2.3.1.168)
KEGG: no annotation
Rationale: Specifically important for utilizing L-Isoleucine. 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.

HP15_1796 : required for sulfate utilization, putative electron transport protein for sulfite reductase
Original description: uncharacterized conserved protein UCP030820
SEED: Oxidoreductase probably involved in sulfite reduction
KEGG: no annotation
Rationale: PFam PF06073.8 (DUF934). Conserved cofitness with sulfite reductase; auxotrophic.

HP15_216 : DNA damage response protein (yhgF like)
Original description: transcriptional accessory protein
SEED: Transcription accessory protein (S1 RNA-binding domain)
KEGG: uncharacterized protein
Rationale: Conserved and specific phenotype: important for resisting cisplatin. Also important for resisting ionizing radiation in E. coli (PMID:25049088)

HP15_2427 : histidinol-phosphate aminotransferase (EC 2.6.1.9)
Original description: histidinol-phosphate aminotransferase
SEED: Histidinol-phosphate aminotransferase (EC 2.6.1.9)
KEGG: histidinol-phosphate aminotransferase
Rationale: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR01141.

HP15_2429 : ATP phosphoribosyltransferase (EC 2.4.2.17)
Original description: ATP phosphoribosyltransferase
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.

HP15_2478 : Acyl-CoA dehydrogenase (EC 1.3.8.7)
Original description: acyl-CoA dehydrogenase family protein
SEED: Acyl-CoA dehydrogenase (EC 1.3.8.7)
KEGG:
Rationale: Specifically important for: Tween 20. tween 20 hydrolyzes to a mix of C12, C14, and C16 fatty acids; this is probably part of beta oxidation (SEED_correct)

HP15_2659 : Citrate uptake transporter, large transmembrane component TctA
Original description: tricarboxylic transport TctA
SEED: Tricarboxylate transport membrane protein TctA
KEGG: putative tricarboxylic transport membrane protein
Rationale: Specifically important for citrate utilization.

HP15_2660 : Citrate uptake transporter, small transmembrane component TctB
Original description: tricarboxylic transport membrane protein
SEED: Tricarboxylate transport protein TctB
KEGG: putative tricarboxylic transport membrane protein
Rationale: Specifically important for citrate utilization.

HP15_2661 : Citrate uptake transporter, substrate-binding component TctC
Original description: tricarboxylic transport TctC
SEED: Tricarboxylate transport protein TctC
KEGG: putative tricarboxylic transport membrane protein
Rationale: Specifically important for citrate utilization.

HP15_2688 : L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2)
Original description: trifunctional transcriptional regulator/proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase
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.

HP15_2693 : 3-hydroxyacyl-CoA dehydrogenase PaaC (EC 1.1.1.-)
Original description: 3-hydroxybutyryl-CoA dehydrogenase
SEED: 3-hydroxyacyl-CoA dehydrogenase PaaC (EC 1.1.1.-)
KEGG: 3-hydroxybutyryl-CoA dehydrogenase
Rationale: Specifically important for: L-Phenylalanine. Part of phenylalanine catabolism via phenylacetate (SEED_correct)

HP15_2695 : Beta-ketoadipyl CoA thiolase (EC 2.3.1.-)
Original description: acetyl-CoA acetyltransferase
SEED: Acetyl-CoA acetyltransferase (EC 2.3.1.9) @ Beta-ketoadipyl CoA thiolase (EC 2.3.1.-)
KEGG: no annotation
Rationale: Specifically important for: L-Phenylalanine. The second SEED annotation (beta-ketoadipyl-CoA thiolase) is part of phenylalanine catabolism via phenylacetate. Not clear if the acetyl-CoA acetyltransferase annotation is correct, so it was removed, but it remains plausible (SEED_correct)

HP15_2832 : DNA damage response helicase (yejH or radD)
Original description: type III restriction protein res subunit
SEED: ATP-dependent RNA helicase YejH
KEGG: no annotation
Rationale: Conserved and specific phenotype: important for resisting cisplatin. Also important for resisting ionizing radiationa and UV radiation in E. coli (PMID:25425430)

HP15_3028 : TRAP-type D-lactate transporter, periplasmic component
Original description: TRAP dicarboxylate family transporter, DctP subunit
SEED: TRAP-type C4-dicarboxylate transport system, periplasmic component
KEGG: no annotation
Rationale: Specific phenotype: utilization of D-Lactate. (The mutant is possibly polar on D-lactate oxidase HP15_3024, but role is confirmed by similarity to Q5SK82)

HP15_3031 : L-arginine ABC transporter, periplasmic substrate-binding component ArtJ/HisJ/ArtI/AotJ/ArgT
Original description: extracellular solute-binding protein, family 3
SEED: Lysine-arginine-ornithine-binding periplasmic protein precursor (TC 3.A.1.3.1)
KEGG: no annotation
Rationale: Specifically important for utilization of arginine as a nitrogen source.

HP15_3040 : Arginine N-succinyltransferase (EC 2.3.1.109)
Original description: arginine N-succinyltransferase subunit beta
SEED: Arginine N-succinyltransferase (EC 2.3.1.109)
KEGG: arginine N-succinyltransferase
Rationale: Specifically important for utilizing L-Arginine. Automated validation from mutant phenotype: the predicted function (2.3.1.109) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

HP15_3041 : Arginine N-succinyltransferase (EC 2.3.1.109)
Original description: arginine N-succinyltransferase, alpha chain
SEED: Arginine N-succinyltransferase (EC 2.3.1.109)
KEGG: arginine N-succinyltransferase
Rationale: Specifically important for utilizing L-Arginine. Automated validation from mutant phenotype: the predicted function (2.3.1.109) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

HP15_3042 : acetylornithine aminotransferase (EC 2.6.1.11); succinylornithine aminotransferase (EC 2.6.1.81)
Original description: bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein
SEED: Succinylornithine transaminase (EC 2.6.1.81)
KEGG: acetylornithine/N-succinyldiaminopimelate aminotransferase
Rationale: Important for fitness in many minimal media experiments, and mostly rescued by addition of arginine, which suggests a role as acetylornithine aminotransferase. Important for utilization of arginine as a nitrogen source, which suggests a role as succinylornithine aminotransferase in the AST pathway. 65% identical to O30508 (AruC) from P. aeruginosa, which is reported to have these two activities.

HP15_3135 : ethanol oxidation regulatory protein ercA
Original description: iron-containing alcohol dehydrogenase
SEED: Alcohol dehydrogenase (EC 1.1.1.1); Acetaldehyde dehydrogenase (EC 1.2.1.10)
KEGG: no annotation
Rationale: Specifically important for: Ethanol; D-Trehalose dihydrate. Similar to ercA (PA1991) which apparently has a regulatory role (PMCID: PMC3754586) rather than being directly involved in catabolism. Also this gene is adjacent to an apparent ercS (HP15_3134). Do not see why SEED annotates it as aldehyde dehydrogenase. HP15_3164 is probably the ethanol dehydrogenase and HP15_3144 the acetaldehyde dehydrogenase.

HP15_3144 : Aldehyde dehydrogenase (EC 1.2.1.3)
Original description: NAD-dependent aldehyde dehydrogenase
SEED: Aldehyde dehydrogenase (EC 1.2.1.3)
KEGG: aldehyde dehydrogenase (NAD+)
Rationale: Specifically important for utilizing Ethanol. Automated validation from mutant phenotype: the predicted function (RXN66-3) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

HP15_3195 : phosphoribosyl-ATP pyrophosphatase (EC 3.6.1.31)
Original description: phosphoribosyl-ATP pyrophosphatase
SEED: Phosphoribosyl-ATP pyrophosphatase (EC 3.6.1.31)
KEGG: phosphoribosyl-ATP pyrophosphohydrolase
Rationale: Important for fitness in many defined media, and highly cofit with ATP phosphoribosyltransferase HP15_2429. Hits TIGR00070.

HP15_3433 : Aconitate hydratase (EC 4.2.1.3)
Original description: aconitate hydratase 1
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 Potassium acetate. Automated validation from mutant phenotype: the predicted function (4.2.1.3) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

HP15_3720 : DNA damage response nuclease
Original description: protein containing VRR-NUC domain
SEED: Hypothetical protein, restriction endonuclease-like VRR-NUC domain
KEGG: no annotation
Rationale: Conserved and specific phenotype: important for resisting cisplatin. Contains a VRR-NUC domain that is predicted to have nuclease activity.

HP15_4088 : L-lactate dehydrogenase, LutA subunit
Original description: protein of unknown function, cysteine-rich region domain protein
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. This is related to the LutABC system from Bacillus subtilis (PMC3347220, PMC2668416).

HP15_4089 : L-lactate dehydrogenase, LutB subunit
Original description: iron-sulfur cluster 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. This is related to the LutABC system from Bacillus subtilis (PMC3347220, PMC2668416).

HP15_4090 : L-lactate dehydrogenase, LutC subunit
Original description: protein containing DUF162
SEED: Predicted L-lactate dehydrogenase, hypothetical protein subunit YkgG
KEGG: hypothetical protein
Rationale: Specifically important for utilization of L-lactate or D,L-lactate. This is related to the LutABC system from Bacillus subtilis (PMC3347220, PMC2668416).

HP15_461 : Histidinol-phosphatase (EC:3.1.3.15)
Original description: HAD-superfamily hydrolase
SEED: Phosphoserine phosphatase (EC 3.1.3.3)
KEGG: no annotation
Rationale: Similar to the proposed hisB in pseudomonads, and is most cofit with histidinol dehydrogenase and histidinol-phosphate aminotransferase. Another candidate for this activity is HP15_3738 (annotated as bifunctional by SEED), but it has weak phenotypes and is more likely involved in cell wall synthesis (auxotroph)

HP15_722 : TRAP transporter for fumarate, succinate, L-malate, and 2-oxoglutarate, solute receptor component
Original description: immunogenic protein
SEED: TRAP transporter solute receptor, TAXI family precursor
KEGG: no annotation
Rationale: Important for utilization of fumarate, succinate, L-malate, and 2-oxoglutarate. Also important in many nitrogen source experiments with 2-oxoglutarate as the carbon source.

HP15_723 : TRAP transporter for fumarate, succinate, L-malate, and 2-oxoglutarate, fused 4TM/12TM components
Original description: TRAP transporter, 4TM/12TM fusion protein
SEED: TRAP-type uncharacterized transport system, fused permease component
KEGG: no annotation
Rationale: Important for utilization of fumarate, succinate, L-malate, and 2-oxoglutarate. Also important in many nitrogen source experiments with 2-oxoglutarate as the carbon source.

HP15_858 : phenylalanine aminotransferase (EC 2.6.1.57)
Original description: aspartate aminotransferase
SEED: Aspartate aminotransferase (EC 2.6.1.1)
KEGG: aspartate aminotransferase
Rationale: Specifically important for: L-Phenylalanine. The donor for the amine group is uncertain, but this gene is specifically involved in catabolism of phenylalanine via phenylpyruvate (the product of this enzyme)

HP15_859 : phenylpyruvate ferredoxin oxidoreductase (EC 1.2.7.8)
Original description: pyruvate ferredoxin/flavodoxin oxidoreductase
SEED: Indolepyruvate ferredoxin oxidoreductase, alpha and beta subunits
KEGG: no annotation
Rationale: Specifically important for: L-Phenylalanine. This is the second step in phenylalanine catabolism (to phenylacetyl-CoA). Alternatively, could be a decarboxylase (forming phenylacetaldehyde), but we did not identify a separate aldehyde dehydrogenase. Annotated as indolepyruvate ferredoxin oxidoreductase, which has the same EC number but is part of tryptophan catabolism..

Or download reannotations for Marinobacter adhaerens HP15 or for all organisms as tab-delimited tables