GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Lactobacillus pobuzihii E100301

Found 132 low-confidence and 29 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 LACPOB_RS0110055
arginine gabT: gamma-aminobutyrate transaminase
arginine patA: putrescine aminotransferase (PatA/SpuC)
arginine patD: gamma-aminobutyraldehyde dehydrogenase LACPOB_RS0105235 LACPOB_RS0101940
arginine rocE: L-arginine permease LACPOB_RS0102155 LACPOB_RS0100170
arginine rocF: arginase
citrate acn: aconitase
citrate cit1: citrate:H+ symporter Cit1 LACPOB_RS0104470
citrate icd: isocitrate dehydrogenase
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component LACPOB_RS0106415 LACPOB_RS0108260
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 LACPOB_RS0104385
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 LACPOB_RS0103665
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component LACPOB_RS0104375
citrulline citrullinase: putative citrullinase
citrulline gabT: gamma-aminobutyrate transaminase
citrulline patA: putrescine aminotransferase (PatA/SpuC)
citrulline patD: gamma-aminobutyraldehyde dehydrogenase LACPOB_RS0105235 LACPOB_RS0101940
D-alanine dadA: D-alanine dehydrogenase
D-lactate larD: D,L-lactic acid transporter LACPOB_RS0104170
D-serine dsdA: D-serine ammonia-lyase
deoxyinosine deoD: deoxyinosine phosphorylase
deoxyribonate aacS: acetoacetyl-CoA synthetase LACPOB_RS0104325 LACPOB_RS0105740
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase LACPOB_RS0105155 LACPOB_RS0103545
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoP: deoxyribose transporter
fucose aldA: lactaldehyde dehydrogenase LACPOB_RS0105235 LACPOB_RS0105100
fucose fucA: L-fuculose-phosphate aldolase FucA
fucose fucI: L-fucose isomerase FucI
fucose fucK: L-fuculose kinase FucK LACPOB_RS0101025
fucose fucP: L-fucose:H+ symporter FucP
fucose fucU: L-fucose mutarotase FucU
fumarate dctA: fumarate:H+ symporter DctA
galactose ptcA: galactose PTS system, EIIA component LACPOB_RS0108440 LACPOB_RS0104575
galactose ptcEIIC: galactose PTS system, EIIC component LACPOB_RS0103800 LACPOB_RS0101695
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate uxaA: D-altronate dehydratase
galacturonate uxaB: tagaturonate reductase
galacturonate uxaC: D-galacturonate isomerase
glucosamine manX: glucosamine PTS system, EII-AB component ManX LACPOB_RS0105790
glucosamine manY: glucosamine PTS system, EII-C component ManY LACPOB_RS0105795 LACPOB_RS0101090
glucosamine manZ: glucosamine PTS system, EII-D component ManZ LACPOB_RS0105800 LACPOB_RS0101860
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate garL: 5-dehydro-4-deoxy-D-glucarate aldolase
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate udh: D-glucuronate dehydrogenase
glutamate gdhA: glutamate dehydrogenase, NAD-dependent LACPOB_RS0105200
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
histidine permease: L-histidine permease LACPOB_RS0100170 LACPOB_RS0105030
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase LACPOB_RS0104330 LACPOB_RS0105745
isoleucine epi: methylmalonyl-CoA epimerase
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase LACPOB_RS0102810 LACPOB_RS0104510
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 LACPOB_RS0102790 LACPOB_RS11935
isoleucine pccB: propionyl-CoA carboxylase, beta subunit
L-lactate larD: D,L-lactic acid transporter LarD LACPOB_RS0104170
leucine aacS: acetoacetyl-CoA synthetase LACPOB_RS0104325 LACPOB_RS0105740
leucine liuA: isovaleryl-CoA dehydrogenase
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit LACPOB_RS0102790 LACPOB_RS11935
leucine liuC: 3-methylglutaconyl-CoA hydratase LACPOB_RS0105745 LACPOB_RS0104330
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) LACPOB_RS0105235
lysine hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase
lysine lysN: 2-aminoadipate transaminase LACPOB_RS0107445 LACPOB_RS0109090
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase
maltose susB: alpha-glucosidase (maltase) LACPOB_RS0105990 LACPOB_RS0101565
mannitol mt2d: mannitol 2-dehydrogenase LACPOB_RS0104490 LACPOB_RS0104510
mannitol PLT5: polyol transporter PLT5 LACPOB_RS0104840
myoinositol iolB: 5-deoxy-D-glucuronate isomerase
myoinositol iolC: 5-dehydro-2-deoxy-D-gluconate kinase
myoinositol iolD: 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase
myoinositol iolE: scyllo-inosose 2-dehydratase
myoinositol iolG: myo-inositol 2-dehydrogenase
myoinositol iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase LACPOB_RS0109270
myoinositol mmsA: malonate-semialdehyde dehydrogenase
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 LACPOB_RS0104330
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase LACPOB_RS0105745
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase LACPOB_RS0104335
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase LACPOB_RS0104335
phenylacetate paaK: phenylacetate-CoA ligase
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase LACPOB_RS0105745
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine aacS: acetoacetyl-CoA synthetase LACPOB_RS0104325 LACPOB_RS0105740
phenylalanine aroP: L-phenylalanine:H+ symporter AroP LACPOB_RS0105030 LACPOB_RS0101190
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 LACPOB_RS0105235
propionate epi: methylmalonyl-CoA epimerase
propionate mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
propionate pccA: propionyl-CoA carboxylase, alpha subunit LACPOB_RS0102790 LACPOB_RS11935
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 LACPOB_RS0105235 LACPOB_RS0101940
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate SLC5A8: sodium-coupled pyruvate transporter
rhamnose aldA: lactaldehyde dehydrogenase LACPOB_RS0105235 LACPOB_RS0105100
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
serine sdaB: L-serine ammonia-lyase LACPOB_RS0109445
serine serP: L-serine permease SerP LACPOB_RS0105030 LACPOB_RS0101190
sorbitol sdh: sorbitol dehydrogenase LACPOB_RS0105155 LACPOB_RS0103855
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2 LACPOB_RS0104840
succinate sdc: succinate:Na+ symporter Sdc
sucrose ams: sucrose hydrolase (invertase) LACPOB_RS0101565 LACPOB_RS0105990
threonine aldA: lactaldehyde dehydrogenase LACPOB_RS0105235 LACPOB_RS0105100
threonine RR42_RS28305: L-threonine:H+ symporter LACPOB_RS0105030 LACPOB_RS0101190
threonine tdh: L-threonine 3-dehydrogenase LACPOB_RS0101630 LACPOB_RS0104490
threonine tynA: aminoacetone oxidase
thymidine nupG: thymidine permease NupG/XapB
trehalose treF: trehalase LACPOB_RS0105990 LACPOB_RS0105515
tryptophan aroP: tryptophan:H+ symporter AroP LACPOB_RS0105030 LACPOB_RS0101190
tryptophan tnaA: tryptophanase
tyrosine aacS: acetoacetyl-CoA synthetase LACPOB_RS0104325 LACPOB_RS0105740
tyrosine aroP: L-tyrosine transporter (AroP/FywP) LACPOB_RS0105030 LACPOB_RS0101190
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 LACPOB_RS0104330 LACPOB_RS0105745
valine epi: methylmalonyl-CoA epimerase
valine mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
valine mmsA: methylmalonate-semialdehyde dehydrogenase LACPOB_RS0105235
valine mmsB: 3-hydroxyisobutyrate dehydrogenase LACPOB_RS0104540 LACPOB_RS0105710
valine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
valine pccA: propionyl-CoA carboxylase, alpha subunit LACPOB_RS0102790 LACPOB_RS11935
valine pccB: propionyl-CoA carboxylase, beta subunit
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase LACPOB_RS0104495 LACPOB_RS0108785
xylose xylA: xylose isomerase
xylose xylB: xylulokinase

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