GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Lactobacillus curieae CCTCC M 2011381

Found 131 low-confidence and 22 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
2-oxoglutarate kgtP: 2-oxoglutarate:H+ symporter KgtP PL11_RS00140
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 PL11_RS08475
arginine rocA: 1-pyrroline-5-carboxylate dehydrogenase
arginine rocD: ornithine aminotransferase PL11_RS04270 PL11_RS02630
arginine rocE: L-arginine permease PL11_RS06175 PL11_RS06395
citrate acn: aconitase
citrate cit1: citrate:H+ symporter Cit1 PL11_RS02935
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component PL11_RS00475 PL11_RS00320
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 PL11_RS04390 PL11_RS00480
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 PL11_RS09945 PL11_RS06080
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component PL11_RS04400
citrulline rocA: 1-pyrroline-5-carboxylate dehydrogenase
citrulline rocD: ornithine aminotransferase PL11_RS04270 PL11_RS02630
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 PL11_RS04455 PL11_RS01425
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
fructose Slc2a5: fructose:H+ symporter PL11_RS03255 PL11_RS03915
fucose aldA: lactaldehyde dehydrogenase PL11_RS03525
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 PL11_RS03115
fucose fucU: L-fucose mutarotase FucU
fumarate dctA: fumarate:H+ symporter DctA PL11_RS04665
galactose galP: galactose:H+ symporter GalP PL11_RS02700 PL11_RS03255
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate uxaA: D-altronate dehydratase
galacturonate uxaB: tagaturonate reductase
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE)
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) PL11_RS08115
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter PL11_RS03080
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glutamate gdhA: glutamate dehydrogenase, NAD-dependent PL11_RS01680
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
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase
isoleucine epi: methylmalonyl-CoA epimerase
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase PL11_RS06805 PL11_RS01175
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 PL11_RS06825 PL11_RS02865
isoleucine pccB: propionyl-CoA carboxylase, beta subunit
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
L-malate dctA: L-malate:H+ symporter DctA PL11_RS04665
leucine aacS: acetoacetyl-CoA synthetase
leucine liuA: isovaleryl-CoA dehydrogenase
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit PL11_RS06825 PL11_RS02865
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 hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase PL11_RS04270 PL11_RS02630
lysine lysN: 2-aminoadipate transaminase PL11_RS09145 PL11_RS03650
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase
mannitol PLT5: polyol transporter PLT5 PL11_RS03255 PL11_RS03915
mannose manP: mannose PTS system, EII-CBA components
myoinositol iolG: myo-inositol 2-dehydrogenase
myoinositol iolM: 2-inosose 4-dehydrogenase PL11_RS03365 PL11_RS08580
myoinositol iolN: 2,4-diketo-inositol hydratase
myoinositol iolO: 5-dehydro-L-gluconate epimerase
myoinositol iolT: myo-inositol:H+ symporter PL11_RS03255 PL11_RS04935
myoinositol uxaE: D-tagaturonate epimerase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) PL11_RS08115
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 PL11_RS06805 PL11_RS01175
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase PL11_RS04645
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase PL11_RS04645
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 PL11_RS09710 PL11_RS08170
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 PL11_RS06735 PL11_RS04985
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 PL11_RS06825 PL11_RS02865
propionate pccB: propionyl-CoA carboxylase, beta subunit
propionate prpE: propionyl-CoA synthetase
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabT: gamma-aminobutyrate transaminase PL11_RS02630 PL11_RS04270
putrescine patA: putrescine aminotransferase (PatA/SpuC) PL11_RS04270 PL11_RS02630
putrescine patD: gamma-aminobutyraldehyde dehydrogenase PL11_RS03525
pyruvate SLC5A8: sodium-coupled pyruvate transporter
rhamnose LRA1: L-rhamnofuranose dehydrogenase PL11_RS01175 PL11_RS02905
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase
rhamnose LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase PL11_RS06805 PL11_RS01310
rhamnose LRA6: 2,4-diketo-3-deoxyrhamnonate hydrolase PL11_RS05255
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsU: probable D-ribose transporter RbsU
serine sdaB: L-serine ammonia-lyase
sorbitol sdh: sorbitol dehydrogenase PL11_RS01425 PL11_RS04455
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2 PL11_RS03255 PL11_RS03915
succinate dctA: succinate:H+ symporter DctA PL11_RS04665
sucrose sut: sucrose:proton symporter SUT/SUC
threonine aldA: lactaldehyde dehydrogenase PL11_RS03525
threonine tdh: L-threonine 3-dehydrogenase PL11_RS01105 PL11_RS04760
threonine tynA: aminoacetone oxidase
thymidine nupG: thymidine permease NupG/XapB
trehalose treB: trehalose PTS system, EII-BC components TreB PL11_RS02200
trehalose treEIIA: N-acetylglucosamine phosphotransferase system, EII-A component (Crr/PtsG/YpqE/GamP) PL11_RS03935 PL11_RS07015
tryptophan aroP: tryptophan:H+ symporter AroP PL11_RS09710 PL11_RS08170
tryptophan tnaA: tryptophanase
tyrosine aacS: acetoacetyl-CoA synthetase
tyrosine aroP: L-tyrosine transporter (AroP/FywP) PL11_RS09710 PL11_RS08170
tyrosine fahA: fumarylacetoacetate hydrolase
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase
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 PL11_RS01095
valine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
valine pccA: propionyl-CoA carboxylase, alpha subunit PL11_RS06825 PL11_RS02865
valine pccB: propionyl-CoA carboxylase, beta subunit
xylitol PLT5: xylitol:H+ symporter PLT5 PL11_RS03255 PL11_RS03915
xylitol xdhA: xylitol dehydrogenase PL11_RS03365 PL11_RS01295

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