GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Lactobacillus shenzhenensis LY-73

Found 135 low-confidence and 37 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 actP: cation/acetate symporter ActP
alanine cycA: L-alanine symporter CycA L248_RS04950
arabinose araUsh: L-arabinose ABC transporter, substrate-binding component AraU(Sh) L248_RS11560 L248_RS11565
arabinose araVsh: L-arabinose ABC transporter, ATPase component AraV(Sh) L248_RS11555 L248_RS00360
arabinose araWsh: L-arabinose ABC transporter, permease component 1 AraW(Sh) L248_RS11550
arabinose araZsh: L-arabinose ABC transporter, permease component 2 AraZ(Sh) L248_RS11545 L248_RS11550
arginine artP: L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA L248_RS10630 L248_RS00975
arginine bgtB: L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) L248_RS00970 L248_RS10635
arginine gabT: gamma-aminobutyrate transaminase
arginine patA: putrescine aminotransferase (PatA/SpuC)
arginine patD: gamma-aminobutyraldehyde dehydrogenase L248_RS04605
arginine rocF: arginase
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component L248_RS10630 L248_RS00975
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 L248_RS06285
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 L248_RS00665
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component L248_RS09480
citrulline citrullinase: putative citrullinase
citrulline gabT: gamma-aminobutyrate transaminase
citrulline patA: putrescine aminotransferase (PatA/SpuC)
citrulline patD: gamma-aminobutyraldehyde dehydrogenase L248_RS04605
D-alanine cycA: D-alanine:H+ symporter CycA L248_RS04950
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase L248_RS05220 L248_RS02565
D-lactate larD: D,L-lactic acid transporter L248_RS03605
D-serine cycA: D-serine:H+ symporter CycA L248_RS04950
deoxyribonate aacS: acetoacetyl-CoA synthetase
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase L248_RS00395 L248_RS12645
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoP: deoxyribose transporter
fructose fba: fructose 1,6-bisphosphate aldolase
fucose aldA: lactaldehyde dehydrogenase L248_RS04605
fucose fucA: L-fuculose-phosphate aldolase FucA
fucose fucK: L-fuculose kinase FucK L248_RS04740 L248_RS09605
fucose fucP: L-fucose:H+ symporter FucP
fucose fucU: L-fucose mutarotase FucU
fumarate dctA: fumarate:H+ symporter DctA
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate uxaA: D-altronate dehydratase
galacturonate uxaB: tagaturonate reductase
gluconate gntT: gluconate:H+ symporter GntT
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE)
glucose MFS-glucose: glucose transporter, MFS superfamily L248_RS09215 L248_RS09595
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glutamate gdhA: glutamate dehydrogenase, NAD-dependent
histidine bgtA: L-histidine ABC transporter, ATPase component BgtA L248_RS10630 L248_RS09475
histidine bgtB: L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) L248_RS00970 L248_RS10635
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
isoleucine Bap2: L-isoleucine permease Bap2
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase
isoleucine epi: methylmalonyl-CoA epimerase
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase L248_RS13240 L248_RS12645
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 L248_RS13260
isoleucine pccB: propionyl-CoA carboxylase, beta subunit
L-lactate larD: D,L-lactic acid transporter LarD L248_RS03605
lactose lacK: lactose ABC transporter, ATPase component L248_RS10935 L248_RS05360
leucine aacS: acetoacetyl-CoA synthetase
leucine leuT: L-leucine:Na+ symporter LeuT
leucine liuA: isovaleryl-CoA dehydrogenase
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit L248_RS13260
leucine liuC: 3-methylglutaconyl-CoA hydratase
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)
lysine bgtB: L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) L248_RS00970 L248_RS10635
lysine hglS: D-2-hydroxyglutarate synthase
lysine hisP: L-lysine ABC transporter, ATPase component HisP L248_RS10630 L248_RS00975
lysine lat: L-lysine 6-aminotransferase
lysine lysN: 2-aminoadipate transaminase L248_RS11710 L248_RS01750
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase
maltose malK_Sm: maltose ABC transporter, ATPase component L248_RS10935 L248_RS03710
maltose malX_Sm: maltose ABC transporter, substrate-binding component L248_RS13025 L248_RS14690
mannitol mt2d: mannitol 2-dehydrogenase L248_RS07685 L248_RS03880
mannitol PLT5: polyol transporter PLT5
mannose manP: mannose PTS system, EII-CBA components L248_RS09200 L248_RS08240
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
NAG nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components
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 L248_RS13310 L248_RS11740
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase L248_RS02550
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase L248_RS02550
phenylacetate paaK: phenylacetate-CoA ligase
phenylacetate paaT: phenylacetate transporter Paa
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 L248_RS04950
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 opuBA: proline ABC transporter, ATPase component OpuBA/BusAA L248_RS04775 L248_RS09415
proline put1: proline dehydrogenase
proline putA: L-glutamate 5-semialdeyde dehydrogenase
propionate epi: methylmalonyl-CoA epimerase
propionate mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
propionate pccA: propionyl-CoA carboxylase, alpha subunit L248_RS13260
propionate pccB: propionyl-CoA carboxylase, beta subunit
propionate prpE: propionyl-CoA synthetase
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabT: gamma-aminobutyrate transaminase
putrescine patA: putrescine aminotransferase (PatA/SpuC)
putrescine patD: gamma-aminobutyraldehyde dehydrogenase L248_RS04605
pyruvate SLC5A8: sodium-coupled pyruvate transporter
rhamnose aldA: lactaldehyde dehydrogenase L248_RS04605
rhamnose rhaM: L-rhamnose mutarotase
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsU: probable D-ribose transporter RbsU L248_RS06975
sorbitol sdh: sorbitol dehydrogenase L248_RS12645 L248_RS00395
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2
succinate sdc: succinate:Na+ symporter Sdc
sucrose sacP: sucrose phosphotransferase enzyme EII-BC L248_RS07540 L248_RS02405
threonine aldA: lactaldehyde dehydrogenase L248_RS04605
threonine tdh: L-threonine 3-dehydrogenase L248_RS05640
threonine tynA: aminoacetone oxidase
threonine yvgN: methylglyoxal reductase (NADPH-dependent) L248_RS02320 L248_RS10305
thymidine nupG: thymidine permease NupG/XapB
trehalose malK: trehalose ABC transporter, ATPase component MalK L248_RS10935 L248_RS03710
trehalose malX: trehalose ABC transporter, substrate-binding component MalX L248_RS13025 L248_RS14690
trehalose treF: trehalase L248_RS09350 L248_RS08805
tryptophan tnaA: tryptophanase
tryptophan trpP: energy-coupling factor transporter, tryptophan-specific (S) component TrpP
tyrosine aacS: acetoacetyl-CoA synthetase
tyrosine aroP: L-tyrosine transporter (AroP/FywP) L248_RS04950
tyrosine fahA: fumarylacetoacetate hydrolase
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase
valine Bap2: L-valine permease Bap2
valine bch: 3-hydroxyisobutyryl-CoA hydrolase
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase
valine epi: methylmalonyl-CoA epimerase
valine mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
valine mmsA: methylmalonate-semialdehyde dehydrogenase
valine mmsB: 3-hydroxyisobutyrate dehydrogenase L248_RS09815
valine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
valine pccA: propionyl-CoA carboxylase, alpha subunit L248_RS13260
valine pccB: propionyl-CoA carboxylase, beta subunit
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase
xylose xylA: xylose isomerase
xylose xylB: xylulokinase L248_RS06505
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