Updated annotations for Dinoroseobacter shibae DFL-12

38 genes with updated (or confirmed) annotations:

Dshi_0546 : ABC transporter for Xylitol, ATPase component
Original description: ABC transporter related (RefSeq)
SEED: Various polyols ABC transporter, ATP-binding component
KEGG: multiple sugar transport system ATP-binding protein
Rationale: Specific phenotype on Xylitol.

Dshi_0547 : ABC transporter for Xylitol, periplasmic substrate-binding component
Original description: extracellular solute-binding protein family 1 (RefSeq)
SEED: Various polyols ABC transporter, periplasmic substrate-binding protein
KEGG: multiple sugar transport system substrate-binding protein
Rationale: Specific phenotype on Xylitol.

Dshi_0548 : ABC transporter for Xylitol, permease component 1
Original description: binding-protein-dependent transport systems inner membrane component (RefSeq)
SEED: Various polyols ABC transporter, permease component 1
KEGG: multiple sugar transport system permease protein
Rationale: Specific phenotypes on Xylitol; Xylitol. Phenotype is very specific

Dshi_0549 : ABC transporter for Xylitol, permease component 2
Original description: binding-protein-dependent transport systems inner membrane component (RefSeq)
SEED: Various polyols ABC transporter, permease component 2
KEGG: multiple sugar transport system permease protein
Rationale: Specific phenotypes on Xylitol; Xylitol. Phenotype is very specific

Dshi_0551 : D-xylulose reductase (EC 1.1.1.9)
Original description: Alcohol dehydrogenase GroES domain protein (RefSeq)
SEED: Xylitol dehydrogenase (EC 1.1.1.9)
KEGG: D-xylulose reductase
Rationale: Specifically important for utilizing Xylitol. Automated validation from mutant phenotype: the predicted function (1.1.1.9) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Dshi_0718 : Propionyl-CoA carboxylase carboxyl transferase subunit (EC 6.4.1.3)
Original description: carboxyl transferase (RefSeq)
SEED: Propionyl-CoA carboxylase carboxyl transferase subunit (EC 6.4.1.3)
KEGG: propionyl-CoA carboxylase beta chain
Rationale: Specifically important for utilizing Sodium propionate. Automated validation from mutant phenotype: the predicted function (PROPIONYL-COA-CARBOXY-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Dshi_0723 : Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3)
Original description: Carbamoyl-phosphate synthase L chain ATP-binding (RefSeq)
SEED: Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3)
KEGG: propionyl-CoA carboxylase alpha chain
Rationale: Specifically important for utilizing Sodium propionate. Automated validation from mutant phenotype: the predicted function (PROPIONYL-COA-CARBOXY-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Dshi_0829 : Phosphopentomutase (EC 5.4.2.7)
Original description: phosphopentomutase (RefSeq)
SEED: Phosphopentomutase (EC 5.4.2.7)
KEGG: phosphopentomutase
Rationale: Specifically important for utilizing Adenosine. Automated validation from mutant phenotype: the predicted function (PPENTOMUT-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Dshi_0830 : Adenosine deaminase (EC 3.5.4.4)
Original description: adenosine deaminase (RefSeq)
SEED: Adenosine deaminase (EC 3.5.4.4)
KEGG: adenosine deaminase
Rationale: Specifically important for utilizing Adenosine. Automated validation from mutant phenotype: the predicted function (ADENODEAMIN-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Dshi_1119 : DNA damage response helicase, ligase-associated
Original description: DEAD/H associated domain protein (RefSeq)
SEED: FIG003033: Helicase domain protein
KEGG: ATP-dependent helicase Lhr and Lhr-like helicase
Rationale: Conserved and specific phenotype: important for resisting cisplatin. Related to Lhr, which is either a DNA:DNA or DNA:RNA helicase, but lacks the long C-terminal extension that might have a regulatory role (see putative winged helix domain in E. coli lhr). This is also related to the archael protein saci_1500, which has also been linked to DNA damage response, as a mutant is sensitive to UV (PMID: 26148716)

Dshi_1194 : TRAP transporter for fumarate, succinate, L-malate, and 2-oxoglutarate, fused 4TM/12TM components
Original description: TRAP transporter, 4TM/12TM fusion protein (RefSeq)
SEED: TRAP-type uncharacterized transport system, fused permease component
KEGG: no annotation
Rationale: Specifically important for utilization of fumarate, succinate, L-malate, and alpha-ketoglutarate.

Dshi_1195 : TRAP transporter for fumarate, succinate, L-malate, and 2-oxoglutarate, solute receptor component
Original description: TRAP transporter solute receptor, TAXI family (RefSeq)
SEED: TRAP transporter solute receptor, TAXI family precursor
KEGG: no annotation
Rationale: Specifically important for utilization of fumarate, succinate, L-malate, and alpha-ketoglutarate.

Dshi_1363 : Dihydropyrimidine dehydrogenase (NADP(+)) (EC 1.3.1.2)
Original description: dihydroorotate dehydrogenase family protein (RefSeq)
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.

Dshi_1648 : glucose/maltose/trehalose/sucrose ABC transporter, ATPase component
Original description: ABC transporter related (RefSeq)
SEED: Alpha-glucoside transport ATP-binding protein AglK
KEGG: alpha-glucoside transport system ATP-binding protein
Rationale: Related to alpha-glucoside transporter component aglK. Specifically important for utilization of D-glucose, D-maltose, D-trehalose, and sucrose.

Dshi_1649 : alpha-glucosidase / maltase / trehalase / sucrase (EC 3.2.1.48; EC 3.2.1.20; EC 3.2.1.28)
Original description: alpha amylase catalytic region (RefSeq)
SEED: Alpha-glucosidase AglA
KEGG: alpha-glucosidase
Rationale: # Very important for fitness during growth on maltose, trehalose, or sucrose. 60% identical to Halomonas HaG, which is most active on maltose and sucrose and has some activity on trehalose (PMC3298133). Dshi_1649 is also important for utilization of glucose, which is not explained. The glucose phenotype is variable and might reflect polar effects on Dshi_1648, a component of the glucose/maltose/trehalose/sucrose transporter.

Dshi_1650 : glucose/maltose/trehalose/sucrose ABC transporter, permease component 2
Original description: binding-protein-dependent transport systems inner membrane component (RefSeq)
SEED: Alpha-glucoside transport system permease protein AglG
KEGG: alpha-glucoside transport system permease protein
Rationale: Related to alpha-glucoside transporter component aglG. Specifically important for utilization of D-glucose, D-maltose, D-trehalose, and sucrose.

Dshi_1651 : glucose/maltose/trehalose/sucrose ABC transporter, permease component 1
Original description: binding-protein-dependent transport systems inner membrane component (RefSeq)
SEED: ABC alpha-glucoside transporter, inner membrane subunit AglF
KEGG: alpha-glucoside transport system permease protein
Rationale: Related to alpha-glucoside transporter component aglF. Specifically important for utilization of D-glucose, D-maltose, D-trehalose, and sucrose.

Dshi_1652 : glucose/maltose/trehalose/sucrose ABC transporter, substrate-binding component
Original description: extracellular solute-binding protein family 1 (RefSeq)
SEED: Alpha-glucosides-binding periplasmic protein AglE precursor
KEGG: alpha-glucoside transport system substrate-binding protein
Rationale: Related to alpha-glucoside transporter component aglE. Specifically important for utilization of D-glucose, D-maltose, D-trehalose, and sucrose.

Dshi_1655 : glucokinase (EC 2.7.1.2)
Original description: Glucokinase (RefSeq)
SEED: Glucokinase (EC 2.7.1.2)
KEGG: glucokinase
Rationale: Specifically important for utilization of D-glucose and glucose-containing disaccharides (D-maltose, D-trehalose, and perhaps sucrose)

Dshi_1667 : Nitrite reductase (NAD(P)H) (EC 1.7.1.4)
Original description: nitrite reductase (NAD(P)H), large subunit (RefSeq)
SEED: Nitrite reductase [NAD(P)H] large subunit (EC 1.7.1.4)
KEGG: nitrite reductase (NAD(P)H) large subunit
Rationale: Specifically important for utilizing Sodium nitrate. Automated validation from mutant phenotype: the predicted function (1.7.1.4) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Dshi_1669 : Nitrate reductase (EC 1.7.99.4)
Original description: molybdopterin oxidoreductase (RefSeq)
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.

Dshi_1997 : Xylulose kinase (EC 2.7.1.17)
Original description: xylulokinase (RefSeq)
SEED: Xylulose kinase (EC 2.7.1.17)
KEGG: xylulokinase
Rationale: Specifically important for utilizing Xylitol. 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.

Dshi_2000 : xylitol ABC transporter, periplasmic substrate-binding protein
Original description: D-xylose ABC transporter, periplasmic substrate-binding protein (RefSeq)
SEED: Xylose ABC transporter, periplasmic xylose-binding protein XylF
KEGG: D-xylose transport system substrate-binding protein
Rationale: Specific phenotype: utilization of Xylitol. May also be a glucose transporter (weak phenotypes, and a close homolog is a glucose transporter) and a xylose transporter (Dino grows poorly on xylose, so there’s no fitness data, but this is 66% identical to a glucose/xylose transporter from Agrobacterium)

Dshi_2060 : Aconitate hydratase (EC 4.2.1.3)
Original description: aconitate hydratase 2 (RefSeq)
SEED: Aconitate hydratase 2 (EC 4.2.1.3)
KEGG: aconitate hydratase 2
Rationale: Specifically important for utilizing Trisodium citrate dihydrate. 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.

Dshi_2244 : DNA repair endonuclease mmcB (DUF1052)
Original description: protein of unknown function DUF1052 (RefSeq)
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

Dshi_2429 : Rhamnulokinase RhaK in alpha-proteobacteria (EC 2.7.1.5)
Original description: carbohydrate kinase FGGY (RefSeq)
SEED: Rhamnulokinase RhaK in alpha-proteobacteria (EC 2.7.1.5)
KEGG: no annotation
Rationale: Specifically important for: L-Rhamnose monohydrate. The second step in rhamnose catabolism (SEED_correct)

Dshi_2436 : rhamnulose-1-phosphate aldolase (EC 4.1.2.19) / lactaldehyde dehydrogenase (EC 1.2.1.22)
Original description: rhamnulose-1-phosphate aldolase/alcohol dehydrogenase (RefSeq)
SEED: Predicted rhamnulose-1-phosphate aldolase (EC 4.1.2.19) / Predicted lactaldehyde dehydrogenase (EC 1.2.1.22)
KEGG: no annotation
Rationale: Specifically important for: L-Rhamnose monohydrate. Part of rhamnose catabolism via rhamnulose. TIGR annotates the C terminal part as alcohol dehydrogenase rather than as lactaldehyde dehydrogenase but do not see why (SEED_correct)

Dshi_2437 : L-rhamnose isomerase (EC 5.3.1.14)
Original description: L-rhamnose isomerase (RefSeq)
SEED: L-rhamnose isomerase (EC 5.3.1.14)
KEGG: L-rhamnose isomerase
Rationale: Specifically important for utilizing L-Rhamnose monohydrate. Automated validation from mutant phenotype: the predicted function (5.3.1.14) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Dshi_2587 : DNA damage response exonuclease, associated with a ligase
Original description: exonuclease of the beta-lactamase fold involved in RNA processing-like protein (RefSeq)
SEED: no annotation
KEGG: putative mRNA 3-end processing factor
Rationale: Conserved and specific phenotype: important for resisting cisplatin. In a conserved operon with a DNA ligase

Dshi_2633 : aspartyl-tRNA(Asp/Asn) synthetase (EC 6.1.1.23)
Original description: aspartyl-tRNA synthetase (RefSeq)
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. Related to both tRNA(asp)-specific enzymes (as from E. coli) and tRNA(asp/asn) enzymes (as from Pseudomonas aeruginosa)

Dshi_2797 : Fructokinase (EC 2.7.1.4)
Original description: PfkB domain protein (RefSeq)
SEED: Fructokinase (EC 2.7.1.4)
KEGG: fructokinase
Rationale: Important for utilizing Sucrose, which is catabolized via fructose.

Dshi_2958 : Xanthine dehydrogenase (EC 1.17.1.4)
Original description: Xanthine dehydrogenase small subunit (RefSeq)
SEED: Xanthine dehydrogenase iron-sulfur subunit (EC 1.17.1.4) / Xanthine dehydrogenase, FAD binding subunit (EC 1.17.1.4)
KEGG: xanthine dehydrogenase small subunit
Rationale: Specifically important for utilizing Adenine hydrochloride hydrate. Automated validation from mutant phenotype: the predicted function (1.17.1.4) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Dshi_2959 : Xanthine dehydrogenase (EC 1.17.1.4)
Original description: Xanthine dehydrogenase molybdopterin binding subunit (RefSeq)
SEED: Xanthine dehydrogenase, molybdenum binding subunit (EC 1.17.1.4)
KEGG: xanthine dehydrogenase large subunit
Rationale: Specifically important for utilizing Adenine hydrochloride hydrate. Automated validation from mutant phenotype: the predicted function (1.17.1.4) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Dshi_3121 : Tricarboxylate transport membrane protein TctA
Original description: protein of unknown function DUF112 transmembrane (RefSeq)
SEED: Tricarboxylate transport membrane protein TctA
KEGG: putative tricarboxylic transport membrane protein
Rationale: specific phenotype on citrate and cofit with other nearby components; SEED_correct

Dshi_3122 : Tricarboxylate transport protein TctB
Original description: hypothetical protein (RefSeq)
SEED: Tricarboxylate transport protein TctB
KEGG: putative tricarboxylic transport membrane protein
Rationale: specific phenotype on citrate and cofit with other nearby components; SEED_correct

Dshi_3123 : Tricarboxylate transport protein TctC
Original description: hypothetical protein (RefSeq)
SEED: Tricarboxylate transport protein TctC
KEGG: putative tricarboxylic transport membrane protein
Rationale: specific phenotype on citrate and cofit with other nearby components; SEED_correct

Dshi_3204 : allantoinase (EC 3.5.2.5); 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU) decarboxylase (EC 4.1.1.97)
Original description: Chitin deacetylase (RefSeq)
SEED: no annotation
KEGG: no annotation
Rationale: Specific phenotype: utilization of Adenine hydrochloride, Inosine. The N-terminal part is >50% identical to allantoinases. The C-terminal portion is only 36-37% identical to characterized OHCU decarboxylases (i.e., O32141 or Q283N4), but it is the only OHCU decarboxylase domain encoded in the genome.

Dshi_3420 : Glycerol kinase (EC 2.7.1.30)
Original description: glycerol kinase (RefSeq)
SEED: Glycerol kinase (EC 2.7.1.30)
KEGG: glycerol kinase
Rationale: Specifically important for utilizing Glycerol. Automated validation from mutant phenotype: the predicted function (GLYCEROL-KIN-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Or download reannotations for Dinoroseobacter shibae DFL-12 or for all organisms as tab-delimited tables