GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Bacteroides thetaiotaomicron VPI-5482

Found 120 low-confidence and 39 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 adh: acetaldehyde dehydrogenase (not acylating) BT4512
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 alsT: L-alanine symporter AlsT/DagA BT4476
arginine rocA: 1-pyrroline-5-carboxylate dehydrogenase BT3115
arginine rocD: ornithine aminotransferase BT1442 BT3758
arginine rocE: L-arginine permease
arginine rocF: arginase
aspartate dauA: dicarboxylic acid transporter DauA BT3181
cellobiose SSS-glucose: Sodium/glucose cotransporter BT0355 BT0341
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component BT2494 BT1751
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline citrullinase: putative citrullinase BT0875
citrulline rocA: 1-pyrroline-5-carboxylate dehydrogenase BT3115
citrulline rocD: ornithine aminotransferase BT1442 BT3758
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-lactate lctP: D-lactate:H+ symporter LctP or LidP BT1453
D-serine cycA: D-serine:H+ symporter CycA
D-serine dsdA: D-serine ammonia-lyase
deoxyinosine adh: acetaldehyde dehydrogenase (not acylating) BT4512
deoxyinosine deoB: phosphopentomutase BT1548
deoxyribonate atoB: acetyl-CoA C-acetyltransferase
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase BT3771
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose adh: acetaldehyde dehydrogenase (not acylating) BT4512
deoxyribose deoP: deoxyribose transporter BT1277
ethanol adh: acetaldehyde dehydrogenase (not acylating) BT4512
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) BT0535 BT3767
fumarate sdcL: fumarate:Na+ symporter SdcL BT3739
galactose galP: galactose:H+ symporter GalP BT0436 BT4397
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
gluconate gntK: D-gluconate kinase
gluconate gntT: gluconate:H+ symporter GntT
glucosamine nagP: N-acetylglucosamine transporter NagP BT3589 BT4311
glucosamine nagX: transmembrane glucosamine N-acetyltransferase NagX BT3619
glucose SSS-glucose: Sodium/glucose cotransporter BT0355 BT0341
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter BT0196 BT4728
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate uxuB: D-mannonate dehydrogenase
glutamate gltS: L-glutamate:Na+ symporter GltS
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric)
glycerol glpF: glycerol facilitator glpF BT4718
glycerol glpK: glycerol kinase
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine permease: L-histidine permease
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase BT1806
isoleucine Bap2: L-isoleucine permease Bap2
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase BT4702
isoleucine fadA: 2-methylacetoacetyl-CoA thiolase
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase BT3771 BT3232
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit BT1915 BT1449
isoleucine vorA: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA BT0330 with BT0329
isoleucine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC BT0333
L-lactate lctP: L-lactate:H+ symporter LctP or LidP BT1453
L-lactate lldG: L-lactate dehydrogenase, LldG subunit BT4457
L-malate sdlC: L-malate:Na+ symporter SdlC BT3739
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
lactose lacP: lactose permease LacP
leucine atoB: acetyl-CoA C-acetyltransferase
leucine leuT: L-leucine:Na+ symporter LeuT BT3642
leucine liuA: isovaleryl-CoA dehydrogenase BT1806
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit BT1915 BT1449
leucine liuC: 3-methylglutaconyl-CoA hydratase BT4702
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit BT1686 BT1917
leucine liuE: hydroxymethylglutaryl-CoA lyase
leucine vorA: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA BT0330 with BT0329
leucine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC BT0333
lysine amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd)
lysine hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase BT3758
lysine lysN: 2-aminoadipate transaminase BT2415 BT3375
lysine lysP: L-lysine:H+ symporter LysP
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase
maltose SSS-glucose: Sodium/glucose cotransporter BT0355 BT0341
mannitol mt2d: mannitol 2-dehydrogenase BT3771 BT3232
mannitol PLT5: polyol transporter PLT5
mannose manA: mannose-6-phosphate isomerase BT0373 BT3950
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 BT0794 BT0436
myoinositol uxaE: D-tagaturonate epimerase
myoinositol uxuB: D-mannonate dehydrogenase
NAG nagP: N-acetylglucosamine transporter NagP BT3589 BT4311
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 BT4702
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase BT4702
phenylacetate paaH: 3-hydroxyadipyl-CoA dehydrogenase BT3771 BT1911
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase BT4702
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
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 proY: proline:H+ symporter
proline put1: proline dehydrogenase
proline putA: L-glutamate 5-semialdeyde dehydrogenase BT3115
propionate pccA: propionyl-CoA carboxylase, alpha subunit BT1915 BT1449
propionate prpE: propionyl-CoA synthetase BT3755
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabD: succinate semialdehyde dehydrogenase
putrescine gabT: gamma-aminobutyrate transaminase BT3758 BT1442
putrescine patA: putrescine aminotransferase (PatA/SpuC) BT3758 BT1442
putrescine patD: gamma-aminobutyraldehyde dehydrogenase
putrescine potB: putrescine ABC transporter, permease component 1 (PotB/PotH) BT1290
putrescine potC: putrescine ABC transporter, permease component 2 (PotC/PotI) BT1289
putrescine potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) BT1288
pyruvate SLC5A8: sodium-coupled pyruvate transporter
serine snatA: L-serine transporter BT2270 BT1108
sorbitol sdh: sorbitol dehydrogenase BT3771 BT3232
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2 BT4397 BT0794
succinate sdc: succinate:Na+ symporter Sdc BT3739
threonine snatA: L-threonine transporter snatA BT2270 BT1108
thymidine adh: acetaldehyde dehydrogenase (not acylating) BT4512
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase BT1548
trehalose SSS-glucose: Sodium/glucose cotransporter BT0355 BT0341
tryptophan aroP: tryptophan:H+ symporter AroP
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
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 BT1806
valine Bap2: L-valine permease Bap2
valine bch: 3-hydroxyisobutyryl-CoA hydrolase
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase BT4702
valine mmsA: methylmalonate-semialdehyde dehydrogenase
valine mmsB: 3-hydroxyisobutyrate dehydrogenase
valine pccA: propionyl-CoA carboxylase, alpha subunit BT1915 BT1449
valine vorA: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA BT0330 with BT0329
valine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC BT0333
xylitol PLT5: xylitol:H+ symporter PLT5 BT4397 BT0794
xylitol xdhA: xylitol dehydrogenase BT3771 BT1911

Confidence: high confidence medium confidence low confidence

This GapMind analysis is from Sep 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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