GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Lactobacillus oryzae SG293

Found 147 low-confidence and 26 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
2-oxoglutarate kgtP: 2-oxoglutarate:H+ symporter KgtP
4-hydroxybenzoate mhpD: 2-hydroxypentadienoate hydratase
4-hydroxybenzoate mhpE: 4-hydroxy-2-oxovalerate aldolase
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK
4-hydroxybenzoate pobA: 4-hydroxybenzoate 3-monooxygenase
4-hydroxybenzoate praA: protocatechuate 2,3-dioxygenase
4-hydroxybenzoate xylF: 2-hydroxymuconate semialdehyde hydrolase
acetate ybhL: acetate uptake transporter YbhL LOSG293_RS00505
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter
arginine artP: L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA LOSG293_RS08120 LOSG293_RS08560
arginine bgtB: L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) LOSG293_RS08555 LOSG293_RS08125
arginine rocA: 1-pyrroline-5-carboxylate dehydrogenase
arginine rocD: ornithine aminotransferase LOSG293_RS04575
cellobiose bgl: cellobiase
citrate cit1: citrate:H+ symporter Cit1 LOSG293_RS03325
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component LOSG293_RS08120 LOSG293_RS08560
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 LOSG293_RS08555
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 LOSG293_RS07410
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline rocA: 1-pyrroline-5-carboxylate dehydrogenase
citrulline rocD: ornithine aminotransferase LOSG293_RS04575
D-alanine dadA: D-alanine dehydrogenase
D-lactate lctP: D-lactate:H+ symporter LctP or LidP
D-serine dsdA: D-serine ammonia-lyase
deoxyribonate aacS: acetoacetyl-CoA synthetase
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase LOSG293_RS00915 LOSG293_RS03195
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
fructose Slc2a5: fructose:H+ symporter
fucose fucA: L-fuculose-phosphate aldolase FucA
fucose fucI: L-fucose isomerase FucI
fucose fucK: L-fuculose kinase FucK
fucose fucO: L-lactaldehyde reductase LOSG293_RS01215 LOSG293_RS08930
fucose fucP: L-fucose:H+ symporter FucP LOSG293_RS03505
fucose fucU: L-fucose mutarotase FucU
fumarate dctA: fumarate:H+ symporter DctA LOSG293_RS07805
galactose galK: galactokinase (-1-phosphate forming)
galactose galP: galactose:H+ symporter GalP
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate uxaA: D-altronate dehydratase
galacturonate uxaB: tagaturonate reductase
galacturonate uxaC: D-galacturonate isomerase
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate uxaC: D-glucuronate isomerase
glucuronate uxuA: D-mannonate dehydratase
glucuronate uxuB: D-mannonate dehydrogenase
glutamate gdhA: glutamate dehydrogenase, NAD-dependent
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric)
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase LOSG293_RS01110
isoleucine acn: (2R,3S)-2-methylcitrate dehydratase
isoleucine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit LOSG293_RS01670
isoleucine bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit LOSG293_RS01675
isoleucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component LOSG293_RS01680
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase LOSG293_RS00915 LOSG293_RS06955
isoleucine prpB: 2-methylisocitrate lyase
isoleucine prpC: 2-methylcitrate synthase
isoleucine prpD: 2-methylcitrate dehydratase
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
L-malate dctA: L-malate:H+ symporter DctA LOSG293_RS07805
lactose galK: galactokinase (-1-phosphate forming)
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
leucine aacS: acetoacetyl-CoA synthetase
leucine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit LOSG293_RS01670
leucine bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit LOSG293_RS01675
leucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component LOSG293_RS01680
leucine liuA: isovaleryl-CoA dehydrogenase LOSG293_RS01110
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit
leucine liuC: 3-methylglutaconyl-CoA hydratase
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit
leucine liuE: hydroxymethylglutaryl-CoA lyase
lysine amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd)
lysine hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase LOSG293_RS04575
lysine lysN: 2-aminoadipate transaminase LOSG293_RS04845 LOSG293_RS04575
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase
maltose malI: maltose transporter LOSG293_RS01180
mannitol mt2d: mannitol 2-dehydrogenase LOSG293_RS03150 LOSG293_RS06955
mannitol PLT5: polyol transporter PLT5
mannose man-isomerase: D-mannose isomerase
mannose STP6: mannose:H+ symporter
myoinositol iolG: myo-inositol 2-dehydrogenase
myoinositol iolM: 2-inosose 4-dehydrogenase
myoinositol iolN: 2,4-diketo-inositol hydratase
myoinositol iolO: 5-dehydro-L-gluconate epimerase
myoinositol iolT: myo-inositol:H+ symporter
myoinositol uxaE: D-tagaturonate epimerase
myoinositol uxuA: D-mannonate dehydratase
myoinositol uxuB: D-mannonate dehydrogenase
phenylacetate H281DRAFT_04042: phenylacetate:H+ symporter LOSG293_RS01045 LOSG293_RS06885
phenylacetate paaA: phenylacetyl-CoA 1,2-epoxidase, subunit A
phenylacetate paaB: phenylacetyl-CoA 1,2-epoxidase, subunit B
phenylacetate paaC: phenylacetyl-CoA 1,2-epoxidase, subunit C
phenylacetate paaE: phenylacetyl-CoA 1,2-epoxidase, subunit E
phenylacetate paaF: 2,3-dehydroadipyl-CoA hydratase
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase
phenylacetate paaH: 3-hydroxyadipyl-CoA dehydrogenase LOSG293_RS00915 LOSG293_RS06955
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase LOSG293_RS02825
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase LOSG293_RS02825
phenylacetate paaK: phenylacetate-CoA ligase
phenylacetate paaZ1: oxepin-CoA hydrolase
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine aacS: acetoacetyl-CoA synthetase
phenylalanine aroP: L-phenylalanine:H+ symporter AroP LOSG293_RS06885 LOSG293_RS05505
phenylalanine fahA: fumarylacetoacetate hydrolase
phenylalanine hmgA: homogentisate dioxygenase
phenylalanine HPD: 4-hydroxyphenylpyruvate dioxygenase
phenylalanine maiA: maleylacetoacetate isomerase
phenylalanine PAH: phenylalanine 4-monooxygenase
phenylalanine PCBD: pterin-4-alpha-carbinoalamine dehydratase
phenylalanine QDPR: 6,7-dihydropteridine reductase
proline put1: proline dehydrogenase
proline putA: L-glutamate 5-semialdeyde dehydrogenase
propionate acn: (2R,3S)-2-methylcitrate dehydratase
propionate prpB: 2-methylisocitrate lyase
propionate prpC: 2-methylcitrate synthase
propionate prpD: 2-methylcitrate dehydratase
propionate prpE: propionyl-CoA synthetase
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabT: gamma-aminobutyrate transaminase LOSG293_RS04575
putrescine patA: putrescine aminotransferase (PatA/SpuC) LOSG293_RS04575
putrescine patD: gamma-aminobutyraldehyde dehydrogenase LOSG293_RS04965
pyruvate SLC5A8: sodium-coupled pyruvate transporter
rhamnose fucO: L-lactaldehyde reductase LOSG293_RS01215 LOSG293_RS08930
rhamnose rhaA: L-rhamnose isomerase
rhamnose rhaB: L-rhamnulokinase
rhamnose rhaD: rhamnulose 1-phosphate aldolase
rhamnose rhaM: L-rhamnose mutarotase
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsU: probable D-ribose transporter RbsU LOSG293_RS09020
serine sdaB: L-serine ammonia-lyase
sorbitol sdh: sorbitol dehydrogenase LOSG293_RS03195 LOSG293_RS00915
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2
succinate dctA: succinate:H+ symporter DctA LOSG293_RS07805
sucrose ams: sucrose hydrolase (invertase) LOSG293_RS01235
threonine gloB: hydroxyacylglutathione hydrolase (glyoxalase II)
threonine tdh: L-threonine 3-dehydrogenase LOSG293_RS01215 LOSG293_RS08030
threonine tynA: aminoacetone oxidase
trehalose treF: trehalase LOSG293_RS01235
tryptophan aroP: tryptophan:H+ symporter AroP LOSG293_RS05505 LOSG293_RS06885
tryptophan tnaA: tryptophanase
tyrosine aacS: acetoacetyl-CoA synthetase
tyrosine aroP: L-tyrosine transporter (AroP/FywP) LOSG293_RS06885 LOSG293_RS05505
tyrosine fahA: fumarylacetoacetate hydrolase
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase LOSG293_RS01110
valine acn: (2R,3S)-2-methylcitrate dehydratase
valine bch: 3-hydroxyisobutyryl-CoA hydrolase
valine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit LOSG293_RS01670
valine bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit LOSG293_RS01675
valine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component LOSG293_RS01680
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase
valine mmsA: methylmalonate-semialdehyde dehydrogenase
valine mmsB: 3-hydroxyisobutyrate dehydrogenase LOSG293_RS03720
valine prpB: 2-methylisocitrate lyase
valine prpC: 2-methylcitrate synthase
valine prpD: 2-methylcitrate dehydratase
xylitol PLT5: xylitol:H+ symporter PLT5
xylitol xdhA: xylitol dehydrogenase LOSG293_RS03195 LOSG293_RS00915
xylose xylT: D-xylose transporter

Confidence: high confidence medium confidence low confidence

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory