Updated Annotations for Herbaspirillum seropedicae SmR1

Updated annotations for Herbaspirillum seropedicae SmR1

57 genes with updated (or confirmed) annotations:

HSERO_RS00735 : Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26)
Original description: 2,5-dioxovalerate dehydrogenase
SEED: Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26)
KEGG: NADP-dependent aldehyde dehydrogenase
Rationale: # Important for utilization of D-Galacturonate, L-Arabinose, and D-Xylose. These are all catabolized by oxidative pathways leading to alpha-ketoglutarate semialdehyde (also known as 2,5-dioxopentanoate)

HSERO_RS00870 : L-proline ABC transporter, substrate-binding component
Original description: ABC transporter substrate-binding protein
SEED: Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein
KEGG: no annotation
Rationale: Specifically important for utilizing proline as a carbon or nitrogen source

HSERO_RS00885 : L-proline ABC transporter, permease component 1
Original description: ABC transporter permease
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: No data for this gene, but fitness data for surrounding genes implies this is part of a proline transporter

HSERO_RS00890 : L-proline ABC transporter, permease component 2
Original description: ABC transporter ATP-binding protein
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: Specifically important for utilizing proline as a carbon or nitrogen source

HSERO_RS00895 : L-proline ABC transporter, ATPase component 1
Original description: ABC transporter
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: Specifically important for utilizing proline as a carbon or nitrogen source

HSERO_RS00900 : L-proline ABC transporter, ATPase component 2
Original description: amino acid ABC transporter ATPase
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: Specifically important for utilizing proline as a carbon or nitrogen source

HSERO_RS00905 : L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2)
Original description: bifunctional 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: 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.

HSERO_RS03635 : D-mannose ABC transporter, substrate-binding component
Original description: sugar ABC transporter periplasmic protein
SEED: no annotation
KEGG: ribose transport system substrate-binding protein
Rationale: Specific phenotype on D-mannose

HSERO_RS03640 : D-mannose ABC transporter, ATPase component
Original description: D-ribose transporter ATP-binding protein
SEED: Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)
KEGG: ribose transport system ATP-binding protein
Rationale: Specific phenotype on D-mannose

HSERO_RS03645 : D-mannose ABC transporter, permease component
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 D-mannose

HSERO_RS03650 : Mannose isomerase (EC 5.3.1.7)
Original description: N-acyl-D-glucosamine 2-epimerase
SEED: D-mannose isomerase (EC 5.3.1.7)
KEGG: no annotation
Rationale: Specifically important for utilizing D-Mannose. Automated validation from mutant phenotype: the predicted function (5.3.1.7) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

HSERO_RS04870 : glycerol ABC transporter, substrate-binding component
Original description: ABC transporter substrate-binding protein
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: utilization of Glycerol

HSERO_RS05160 : 2-dehydro-3-deoxygalactonokinase dgoK (EC 2.7.1.58)
Original description: 2-dehydro-3-deoxygalactonokinase
SEED: 2-dehydro-3-deoxygalactonokinase (EC 2.7.1.58)
KEGG: 2-dehydro-3-deoxygalactonokinase
Rationale: Specifically important for galactose utilization.

HSERO_RS05205 : L-arabonate dehydratase (EC 4.2.1.25)
Original description: dihydroxy-acid dehydratase
SEED: L-arabonate dehydratase (EC 4.2.1.25)
KEGG: dihydroxy-acid dehydratase
Rationale: Specifically important for utilizing L-Arabinose. Automated validation from mutant phenotype: the predicted function (L-ARABINONATE-DEHYDRATASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

HSERO_RS05210 : L-arabinose 1-dehydrogenase (EC 1.1.1.46)
Original description: 3-oxoacyl-ACP reductase
SEED: Putative oxidoreductase in arabinose utilization cluster
KEGG: no annotation
Rationale: Specifically important in carbon source L-Arabinose. Similar to characterized L-arabinose 1-dehydrogenases such as B8H1Z0.

HSERO_RS05225 : L-arabinolactonase (EC 3.1.1.15)
Original description: gluconolaconase
SEED: L-arabinolactonase (EC 3.1.1.15)
KEGG: L-arabinonolactonase
Rationale: Important for L-arabinose utilization, and no other good candidates for this activity were found in the genome. This gene also has other phenotypes and may act on other substrates.

HSERO_RS05235 : L-fuconate dehydratase (EC 4.2.1.68)
Original description: fuconate dehydratase
SEED: L-fuconate dehydratase (EC 4.2.1.68)
KEGG: no annotation
Rationale: Specifically important for fucose utilization.

HSERO_RS05250 : ABC transporter for L-fucose, ATPase component
Original description: D-ribose transporter ATP binding protein
SEED: Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)
KEGG: ribose transport system ATP-binding protein
Rationale: Specifically important for L-fucose utilization.

HSERO_RS05255 : ABC transporter for L-fucose, permease component
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: Specifically important for L-fucose utilization.

HSERO_RS05260 : ABC transporter for L-fucose, substrate-binding component
Original description: LacI family transcriptional regulator
SEED: Possible fucose ABC transporter, substrate-binding component
KEGG: ribose transport system substrate-binding protein
Rationale: Specifically important for L-fucose utilization.

HSERO_RS05265 : L-fucono-1,5-lactonase
Original description: amidohydrolase
SEED: L-fuconolactone hydrolase
KEGG: no annotation
Rationale: Important for utilizing L-fucose.

HSERO_RS06355 : 2,4-diketo-3-deoxy-L-fuconate hydrolase (EC 3.7.1.26)
Original description: ureidoglycolate lyase
SEED: 2,4-diketo-3-deoxy-L-fuconate hydrolase
KEGG: no annotation
Rationale: Specifically important for utilization of L-fucose, L-rhamnose, D-ribose, and D-xylose. The substrate is also known as 2,4-didehydro-3-deoxy-L-rhamnonate. This reaction is part of fucose or rhamonase oxidation. The phenotypes on ribose or xylose are not explained.

HSERO_RS06870 : L-2-keto-3-deoxyarabonate dehydratase (EC 4.2.1.43)
Original description: cytochrome C biogenesis protein CcdA
SEED: L-2-keto-3-deoxyarabonate dehydratase (EC 4.2.1.43)
KEGG: dihydrodipicolinate synthase
Rationale: Specifically important for utilizing L-Arabinose. Automated validation from mutant phenotype: the predicted function (4.2.1.43-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

HSERO_RS07185 : Ornithine carbamoyltransferase (EC 2.1.3.3)
Original description: ornithine carbamoyltransferase
SEED: Ornithine carbamoyltransferase (EC 2.1.3.3)
KEGG: no annotation
Rationale: Annotated as this by multiple resources. (essential) (SEED_correct)

HSERO_RS09565 : nitrite efflux transporter, HPP family
Original description: membrane protein
SEED: Probable transmembrane 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.

HSERO_RS11480 : D-ribose ABC transporter, substrate-binding component RbsB
Original description: LacI family transcriptional regulator
SEED: Ribose ABC transport system, periplasmic ribose-binding protein RbsB (TC 3.A.1.2.1)
KEGG: ribose transport system substrate-binding protein
Rationale: Specifically important for utilizing D-Ribose.

HSERO_RS11485 : D-ribose ABC transporter, ATPase component RbsA
Original description: ribose ABC transporter ATPase
SEED: Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)
KEGG: ribose transport system ATP-binding protein
Rationale: Specifically important for utilizing D-Ribose.

HSERO_RS11490 : D-ribose ABC transporter, permease component RbsC
Original description: ABC transporter permease
SEED: Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)
KEGG: ribose transport system permease protein
Rationale: Specifically important for utilizing D-Ribose.

HSERO_RS11500 : Ribokinase (EC 2.7.1.15)
Original description: ribokinase
SEED: Ribokinase (EC 2.7.1.15)
KEGG: ribokinase
Rationale: Specifically important for utilizing D-Ribose. Automated validation from mutant phenotype: the predicted function (RIBOKIN-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

HSERO_RS12095 : Myo-inositol 2-dehydrogenase (EC 1.1.1.18)
Original description: myo-inositol 2-dehydrogenase
SEED: Myo-inositol 2-dehydrogenase (EC 1.1.1.18)
KEGG: myo-inositol 2-dehydrogenase
Rationale: Specifically important for utilizing m-Inositol. Automated validation from mutant phenotype: the predicted function (MYO-INOSITOL-2-DEHYDROGENASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

HSERO_RS12125 : 5-dehydro-2-deoxygluconokinase (EC 2.7.1.92); possible 5-dehydro-2-deoxyphosphogluconate aldolase DUF2090 (EC 4.1.2.29)
Original description: 5-dehydro-2-deoxygluconokinase
SEED: 5-keto-2-deoxygluconokinase (EC 2.7.1.92) / uncharacterized domain
KEGG: 5-dehydro-2-deoxygluconokinase
Rationale: Specifically important for utilizing m-Inositol. This protein is a fusion of 5-keto-deoxygluconate kinase and DUF2090. As DUF2090 has distant similarity to aldolases, it may provide the missing 5-dehydro-2-deoxyphosphogluconate activity.

HSERO_RS12130 : 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
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.

HSERO_RS12135 : Myo-inosose-2 dehydratase (EC 4.2.1.44)
Original description: xylose isomerase
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.

HSERO_RS15785 : 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41)
Original description: 5-dehydro-4-deoxyglucarate dehydratase
SEED: 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41)
KEGG: 5-dehydro-4-deoxyglucarate dehydratase
Rationale: Specifically important for utilizing D-Galacturonic Acid monohydrate. Automated validation from mutant phenotype: the predicted function (4.2.1.41) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

HSERO_RS15795 : galactaro-1,5-lactonase
Original description: 6-phosphogluconolactonase
SEED: 6-phosphogluconolactonase (EC 3.1.1.31)
KEGG: 6-phosphogluconolactonase
Rationale: # Specifically important in carbon source D-Galacturonic Acid monohydrate. The lactone is probably formed by HSERO_RS23040 and the product (meso-galactarate) is probably consumed by HSERO_RS15800

HSERO_RS15800 : Galactarate dehydratase (EC 4.2.1.42)
Original description: D-galactarate dehydratase
SEED: D-galactarate dehydratase (EC 4.2.1.42)
KEGG: galactarate dehydratase
Rationale: Specifically important for utilizing D-Galacturonic Acid monohydrate. Automated validation from mutant phenotype: the predicted function (4.2.1.42) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

HSERO_RS16440 : O-succinylhomoserine sulfhydrylase (EC 2.5.1.48)
Original description: hypothetical protein
SEED: O-acetylhomoserine sulfhydrylase (EC 2.5.1.49) / O-succinylhomoserine sulfhydrylase (EC 2.5.1.48)
KEGG: O-acetylhomoserine (thiol)-lyase
Rationale: Important for fitness in defined media and strongly cofit with homoserine O-succinyltransferase HSERO_RS00455. The closest characterized homolog is a methionine gamma-lyase (Q8L0X4, 37% identical) but this family also includes sulfhydrylases.

HSERO_RS16820 : 2-oxoglutarate:H+ symporter
Original description: alpha-ketoglutarate permease
SEED: dicarboxylic acid transporter PcaT
KEGG: MFS transporter, MHS family, alpha-ketoglutarate permease
Rationale: Specifically important for the utilization of alpha-ketoglutarate

HSERO_RS17000 : ABC transporter for D-sorbitol/xylitol, substrate-binding component
Original description: sugar ABC transporter substrate-binding protein
SEED: Various polyols ABC transporter, periplasmic substrate-binding protein
KEGG: multiple sugar transport system substrate-binding protein
Rationale: Specifically important for utilization of D-sorbitol and xylitol.

HSERO_RS17005 : ABC transporter for D-sorbitol/xylitol, permease component 1
Original description: sugar ABC transporter permease
SEED: Various polyols ABC transporter, permease component 1
KEGG: multiple sugar transport system permease protein
Rationale: Specifically important for utilization of D-sorbitol and xylitol.

HSERO_RS17010 : ABC transporter for D-sorbitol/xylitol, permease component 2
Original description: sugar ABC transporter permease
SEED: Various polyols ABC transporter, permease component 2
KEGG: multiple sugar transport system permease protein
Rationale: Specifically important for utilization of D-sorbitol and xylitol.

HSERO_RS17015 : sorbitol dehydrogenase (EC 1.1.1.14); xylitol dehydrogenase (EC 1.1.1.9)
Original description: sulfurtransferase
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 (1.1.1.14, 1.1.1.9) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

HSERO_RS17020 : ABC transporter for D-sorbitol/xylitol, ATPase component
Original description: sugar ABC transporter ATP-binding protein
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: Specifically important for utilization of D-sorbitol and xylitol.

HSERO_RS19360 : 2-keto-3-deoxyxylonate dehydratase (EC 4.2.1.141)
Original description: fumarylacetoacetate hydrolase
SEED: Fumarylacetoacetate hydrolase family protein
KEGG: no annotation
Rationale: Nearly identical to C785_RS13680 = WP_039786859.1, which was reported to be D-2-keto-3-deoxypentoate dehydratase by PMC6336799 (this is the same reaction). HSERO_RS19360 is also 55% identical to xylX from Caulobacter crescentus, which is also required for xylose utilization (PMC1855722) and is believed to have this activity as well.

HSERO_RS19365 : 2-keto-3-deoxy-L-fuconate 4-dehydrogenase FucDH
Original description: oxidoreductase
SEED: 2-keto-3-deoxy-L-fuconate dehydrogenase
KEGG: no annotation
Rationale: Specifically important for L-fucose utilization; this is part of the oxidative pathway.

HSERO_RS19500 : Putative phosphoglycerate dehydrogenase (EC:1.1.1.95)
Original description: FAD-linked oxidase
SEED: FAD/FMN-containing dehydrogenases
KEGG: no annotation
Rationale: The annotation of this essential protein is based on its homology to BPHYT_RS03150. Orthologs in Acidovorax sp. GW300-3H11 (Ac3H11_4791) and Dechlorosoma suillum PS (Dsui_0736) are also essential. HSERO_RS21555 is another plausible candidate for this reaction, but it has little phenotype and its ortholog in Cupriavidus basilensis 4G11 (RR42_RS20535) seems to be involved in cell wall synthesis. (essential)

HSERO_RS20310 : phosphoribosyl-AMP cyclohydrolase (EC 3.5.4.19)
Original description: phosphoribosyl-AMP cyclohydrolase
SEED: Phosphoribosyl-AMP cyclohydrolase (EC 3.5.4.19)
KEGG: phosphoribosyl-AMP cyclohydrolase
Rationale: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM PF01502.

HSERO_RS20320 : 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16)
Original description: 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
SEED: Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (EC 5.3.1.16)
KEGG: phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase
Rationale: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR00007.

HSERO_RS20325 : IGP synthase, amidotransferase subunit (EC 4.3.2.10)
Original description: imidazole glycerol phosphate synthase
SEED: Imidazole glycerol phosphate synthase amidotransferase subunit (EC 2.4.2.-)
KEGG: glutamine amidotransferase
Rationale: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR01855.

HSERO_RS20350 : 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.

HSERO_RS20590 : fused 3-oxo-5,6-dehydrosuberyl-CoA semialdehyde dehydrogenase and oxepin-CoA hydrolase (EC 3.3.2.12; EC 1.2.1.91)
Original description: enoyl-CoA hydratase
SEED: Aldehyde dehydrogenase (EC 1.2.1.3), PaaZ
KEGG: phenylacetic acid degradation protein
Rationale: Specific phenotype: utilization of Phenylacetic acid

HSERO_RS20660 : bifunctional thiolase PaaJ: 3-oxo-5,6-dehydrosuberyl-CoA thiolase (EC 2.3.1.223); 3-oxoadipyl-CoA thiolase (EC 2.3.1.174)
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 phenylacetate utilization. This is part of the aerobic phenylacetyl-CoA pathway.

HSERO_RS22200 : Rhamnulokinase (EC 2.7.1.5)
Original description: L-fuculose kinase
SEED: Rhamnulokinase RhaK in alpha-proteobacteria (EC 2.7.1.5)
KEGG: no annotation
Rationale: Specifically important for utilizing L-Rhamnose monohydrate. Automated validation from mutant phenotype: the predicted function (2.7.1.5) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

HSERO_RS22235 : rhamnulose-1-phosphate aldolase (EC 4.1.2.19) / lactaldehyde dehydrogenase (EC 1.2.1.22)
Original description: short-chain dehydrogenase
SEED: Predicted rhamnulose-1-phosphate aldolase (EC 4.1.2.19) / Predicted lactaldehyde dehydrogenase (EC 1.2.1.22)
KEGG: no annotation
Rationale: Specific phenotype: utilization of L-Rhamnose

HSERO_RS22240 : L-rhamnose isomerase (EC 5.3.1.14)
Original description: sugar isomerase
SEED: L-rhamnose isomerase (EC 5.3.1.14)
KEGG: no annotation
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.

HSERO_RS23010 : D-galacturonate transporter ExuT
Original description: hexuronate transporter
SEED: Hexuronate transporter
KEGG: MFS transporter, ACS family, hexuronate transporter
Rationale: Specifically important for D-galacturonate utilization.

HSERO_RS23040 : D-galacturonate dehydrogenase (EC 1.1.1.203)
Original description: NAD-dependent dehydratase
SEED: UDP-glucose 4-epimerase (EC 5.1.3.2)
KEGG: no annotation
Rationale: # Specifically important in carbon source D-Galacturonic Acid monohydrate. Also see related proteins URODH_PSESM and URODH_PSEPK in Swiss-Prot.

Or download reannotations for Herbaspirillum seropedicae SmR1 or for all organisms as tab-delimited tables