GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Bacteroides oleiciplenus YIT 12058

Found 128 low-confidence and 26 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)
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 HMPREF9447_RS06115
arginine rocA: 1-pyrroline-5-carboxylate dehydrogenase HMPREF9447_RS24980
arginine rocD: ornithine aminotransferase HMPREF9447_RS09200
arginine rocE: L-arginine permease
arginine rocF: arginase
cellobiose MFS-glucose: glucose transporter, MFS superfamily HMPREF9447_RS01535 HMPREF9447_RS13045
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component HMPREF9447_RS08975 HMPREF9447_RS01965
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 HMPREF9447_RS01070
citrulline rocA: 1-pyrroline-5-carboxylate dehydrogenase HMPREF9447_RS24980
citrulline rocD: ornithine aminotransferase HMPREF9447_RS09200
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-lactate lctP: D-lactate:H+ symporter LctP or LidP
D-serine cycA: D-serine:H+ symporter CycA
D-serine dsdA: D-serine ammonia-lyase
deoxyinosine adh: acetaldehyde dehydrogenase (not acylating)
deoxyinosine deoB: phosphopentomutase HMPREF9447_RS23160
deoxyribonate atoB: acetyl-CoA C-acetyltransferase
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase HMPREF9447_RS22415
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)
deoxyribose deoP: deoxyribose transporter HMPREF9447_RS00640 HMPREF9447_RS11855
ethanol adh: acetaldehyde dehydrogenase (not acylating)
fumarate dauA: fumarate transporter DauA HMPREF9447_RS12015
galactose galP: galactose:H+ symporter GalP HMPREF9447_RS17330 HMPREF9447_RS24815
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
gluconate gntK: D-gluconate kinase
gluconate gntT: gluconate:H+ symporter GntT
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE)
glucose MFS-glucose: glucose transporter, MFS superfamily HMPREF9447_RS01535 HMPREF9447_RS13045
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter HMPREF9447_RS12810
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate uxuB: D-mannonate dehydrogenase
glycerol dhaD: glycerol dehydrogenase HMPREF9447_RS01780 HMPREF9447_RS12495
glycerol dhaL: dihydroxyacetone:PEP phosphotransferase, subunit L HMPREF9447_RS16105 HMPREF9447_RS18945
glycerol dhaM: dihydroxyacetone:PEP phosphotransferase, subunit M
glycerol glpF: glycerol facilitator glpF HMPREF9447_RS05245
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine permease: L-histidine permease
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase HMPREF9447_RS26600
isoleucine Bap2: L-isoleucine permease Bap2
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase
isoleucine fadA: 2-methylacetoacetyl-CoA thiolase
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase HMPREF9447_RS22415 HMPREF9447_RS12495
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit
isoleucine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC HMPREF9447_RS17830
L-lactate lctO: L-lactate oxidase or 2-monooxygenase
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
L-malate sdlC: L-malate:Na+ symporter SdlC
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 HMPREF9447_RS09650
leucine liuA: isovaleryl-CoA dehydrogenase HMPREF9447_RS26600
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit
leucine liuC: 3-methylglutaconyl-CoA hydratase
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit HMPREF9447_RS06625
leucine liuE: hydroxymethylglutaryl-CoA lyase
leucine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC HMPREF9447_RS17830
lysine amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd)
lysine hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase HMPREF9447_RS09200
lysine lysN: 2-aminoadipate transaminase HMPREF9447_RS08585 HMPREF9447_RS09200
lysine lysP: L-lysine:H+ symporter LysP
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase
maltose malI: maltose transporter HMPREF9447_RS26235
mannitol mt2d: mannitol 2-dehydrogenase HMPREF9447_RS12495 HMPREF9447_RS22415
mannitol PLT5: polyol transporter PLT5
mannose manA: mannose-6-phosphate isomerase HMPREF9447_RS17680 HMPREF9447_RS14700
mannose STP6: mannose:H+ symporter HMPREF9447_RS24815 HMPREF9447_RS01535
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 SMIT1: myo-inositol:Na+ symporter HMPREF9447_RS19290 HMPREF9447_RS17770
myoinositol uxaE: D-tagaturonate epimerase
myoinositol uxuB: D-mannonate dehydrogenase
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagP: N-acetylglucosamine transporter NagP
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 HMPREF9447_RS22415 HMPREF9447_RS04200
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
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 HMPREF9447_RS24980
propionate pccA: propionyl-CoA carboxylase, alpha subunit
propionate prpE: propionyl-CoA synthetase HMPREF9447_RS09225
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabD: succinate semialdehyde dehydrogenase
putrescine gabT: gamma-aminobutyrate transaminase HMPREF9447_RS09200 HMPREF9447_RS22595
putrescine patA: putrescine aminotransferase (PatA/SpuC) HMPREF9447_RS09200 HMPREF9447_RS22595
putrescine patD: gamma-aminobutyraldehyde dehydrogenase
putrescine potB: putrescine ABC transporter, permease component 1 (PotB/PotH) HMPREF9447_RS00535
putrescine potC: putrescine ABC transporter, permease component 2 (PotC/PotI) HMPREF9447_RS00530
putrescine potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) HMPREF9447_RS00525
pyruvate SLC5A8: sodium-coupled pyruvate transporter
serine snatA: L-serine transporter HMPREF9447_RS21505 HMPREF9447_RS05555
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2 HMPREF9447_RS24815 HMPREF9447_RS01535
succinate dauA: succinate:H+ symporter DauA HMPREF9447_RS12015
threonine snatA: L-threonine transporter snatA HMPREF9447_RS21505 HMPREF9447_RS05555
thymidine adh: acetaldehyde dehydrogenase (not acylating)
thymidine deoA: thymidine phosphorylase DeoA HMPREF9447_RS05885
thymidine deoB: phosphopentomutase HMPREF9447_RS23160
trehalose BT2158: periplasmic trehalose 3-dehydrogenase (BT2158) HMPREF9447_RS11325
trehalose klh: 3-ketotrehalose hydrolase HMPREF9447_RS11320
trehalose MFS-glucose: glucose transporter, MFS superfamily HMPREF9447_RS01535 HMPREF9447_RS13045
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 HMPREF9447_RS26600
valine Bap2: L-valine permease Bap2
valine bch: 3-hydroxyisobutyryl-CoA hydrolase
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase
valine mmsA: methylmalonate-semialdehyde dehydrogenase
valine mmsB: 3-hydroxyisobutyrate dehydrogenase
valine pccA: propionyl-CoA carboxylase, alpha subunit
valine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC HMPREF9447_RS17830
xylitol PLT5: xylitol:H+ symporter PLT5 HMPREF9447_RS24815 HMPREF9447_RS01535

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