GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Lactobacillus hokkaidonensis LOOC260

Found 124 low-confidence and 32 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
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 LOOC260_RS04310
arginine artP: L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA LOOC260_RS06390 LOOC260_RS00910
arginine bgtB: L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) LOOC260_RS10575 LOOC260_RS09265
arginine rocA: 1-pyrroline-5-carboxylate dehydrogenase LOOC260_RS03035
arginine rocD: ornithine aminotransferase LOOC260_RS04150 LOOC260_RS10925
arginine rocF: arginase
cellobiose bgl: cellobiase LOOC260_RS09295
citrate acn: aconitase
citrate icd: isocitrate dehydrogenase
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component LOOC260_RS00910 LOOC260_RS06390
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 LOOC260_RS02525 LOOC260_RS06290
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 LOOC260_RS02525 LOOC260_RS10575
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline arcC: carbamate kinase
citrulline rocA: 1-pyrroline-5-carboxylate dehydrogenase LOOC260_RS03035
citrulline rocD: ornithine aminotransferase LOOC260_RS04150 LOOC260_RS10925
D-alanine dadA: D-alanine dehydrogenase
D-serine dsdA: D-serine ammonia-lyase LOOC260_RS09495
deoxyribonate aacS: acetoacetyl-CoA synthetase
deoxyribonate atoB: acetyl-CoA C-acetyltransferase
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase LOOC260_RS03945 LOOC260_RS11305
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter LOOC260_RS09890
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoP: deoxyribose transporter
fructose scrK: fructokinase LOOC260_RS04230
fructose Slc2a5: fructose:H+ symporter LOOC260_RS01380 LOOC260_RS09320
fucose fucA: L-fuculose-phosphate aldolase FucA
fucose fucI: L-fucose isomerase FucI
fucose fucK: L-fuculose kinase FucK
fucose fucP: L-fucose:H+ symporter FucP
fucose fucU: L-fucose mutarotase FucU
fumarate dctA: fumarate:H+ symporter DctA LOOC260_RS10270
galactose galP: galactose:H+ symporter GalP LOOC260_RS09320 LOOC260_RS01380
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate uxaA: D-altronate dehydratase
galacturonate uxaB: tagaturonate reductase
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glutamate gdhA: glutamate dehydrogenase, NAD-dependent LOOC260_RS00380
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 LOOC260_RS10630
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase LOOC260_RS09865
isoleucine epi: methylmalonyl-CoA epimerase
isoleucine fadA: 2-methylacetoacetyl-CoA thiolase LOOC260_RS01750
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase LOOC260_RS11305 LOOC260_RS03750
isoleucine mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
isoleucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit LOOC260_RS06485 LOOC260_RS11325
isoleucine pccB: propionyl-CoA carboxylase, beta subunit
lactose lacS: lactose permease LacS LOOC260_RS03720 LOOC260_RS10515
leucine aacS: acetoacetyl-CoA synthetase
leucine atoB: acetyl-CoA C-acetyltransferase
leucine ilvE: L-leucine transaminase LOOC260_RS03615
leucine liuA: isovaleryl-CoA dehydrogenase LOOC260_RS10630
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit LOOC260_RS11325 LOOC260_RS06485
leucine liuC: 3-methylglutaconyl-CoA hydratase LOOC260_RS09865
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit
leucine liuE: hydroxymethylglutaryl-CoA lyase
leucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
lysine amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) LOOC260_RS03035
lysine hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase LOOC260_RS04150 LOOC260_RS10925
lysine lysN: 2-aminoadipate transaminase LOOC260_RS03615 LOOC260_RS00435
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase
mannitol mtlA: mannitol phosphotransferase system, EII-CBA components
mannitol mtlD: mannitol-1-phosphate 5-dehydrogenase
mannose manA: mannose-6-phosphate isomerase
mannose manP: mannose PTS system, EII-CBA components
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 LOOC260_RS09320 LOOC260_RS09930
myoinositol uxaE: D-tagaturonate epimerase LOOC260_RS00855
phenylacetate H281DRAFT_04042: phenylacetate:H+ symporter LOOC260_RS03790 LOOC260_RS00960
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 LOOC260_RS09865
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase LOOC260_RS09865
phenylacetate paaH: 3-hydroxyadipyl-CoA dehydrogenase LOOC260_RS09335 LOOC260_RS11305
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase
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 LOOC260_RS03790 LOOC260_RS09490
phenylalanine atoB: acetyl-CoA C-acetyltransferase
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 LOOC260_RS03035
propionate epi: methylmalonyl-CoA epimerase
propionate lctP: propionate permease LOOC260_RS02070
propionate mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
propionate pccA: propionyl-CoA carboxylase, alpha subunit LOOC260_RS06485 LOOC260_RS11325
propionate pccB: propionyl-CoA carboxylase, beta subunit
propionate prpE: propionyl-CoA synthetase
putrescine gabT: gamma-aminobutyrate transaminase LOOC260_RS00165 LOOC260_RS10925
putrescine patA: putrescine aminotransferase (PatA/SpuC) LOOC260_RS00165 LOOC260_RS04150
putrescine patD: gamma-aminobutyraldehyde dehydrogenase LOOC260_RS03035 LOOC260_RS05895
pyruvate SLC5A8: sodium-coupled pyruvate transporter
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 rbsA: D-ribose ABC transporter, ATPase component RbsA LOOC260_RS02230
ribose rbsB: D-ribose ABC transporter, substrate-binding component RbsB LOOC260_RS02240
ribose rbsC: D-ribose ABC transporter, permease component RbsC LOOC260_RS02235
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase LOOC260_RS03945 LOOC260_RS09870
succinate dctA: succinate:H+ symporter DctA LOOC260_RS10270
sucrose ams: sucrose hydrolase (invertase) LOOC260_RS09330
threonine serP1: L-threonine uptake transporter SerP1 LOOC260_RS08675 LOOC260_RS03790
threonine tynA: aminoacetone oxidase
thymidine nupG: thymidine permease NupG/XapB
trehalose treF: trehalase LOOC260_RS09330
tryptophan aroP: tryptophan:H+ symporter AroP LOOC260_RS03790 LOOC260_RS00960
tryptophan tnaA: tryptophanase
tyrosine aacS: acetoacetyl-CoA synthetase
tyrosine aroP: L-tyrosine transporter (AroP/FywP) LOOC260_RS03790 LOOC260_RS00960
tyrosine atoB: acetyl-CoA C-acetyltransferase
tyrosine fahA: fumarylacetoacetate hydrolase
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase LOOC260_RS10630
valine bch: 3-hydroxyisobutyryl-CoA hydrolase LOOC260_RS09865
valine epi: methylmalonyl-CoA epimerase
valine mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
valine mmsA: methylmalonate-semialdehyde dehydrogenase LOOC260_RS03035
valine mmsB: 3-hydroxyisobutyrate dehydrogenase LOOC260_RS09545
valine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
valine pccA: propionyl-CoA carboxylase, alpha subunit LOOC260_RS06485 LOOC260_RS11325
valine pccB: propionyl-CoA carboxylase, beta subunit
xylitol PLT5: xylitol:H+ symporter PLT5 LOOC260_RS09320 LOOC260_RS09930
xylitol xdhA: xylitol dehydrogenase LOOC260_RS10505 LOOC260_RS09870

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