GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Bacteroides clarus YIT 12056

Found 139 low-confidence and 34 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) BUB52_RS06870
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 snatA: L-alanine symporter SnatA BUB52_RS00350
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose BT0355: L-arabinose:Na+ symporter BUB52_RS14570
arginine gabD: succinate semialdehyde dehydrogenase
arginine gabT: gamma-aminobutyrate transaminase BUB52_RS13360 BUB52_RS04845
arginine patA: putrescine aminotransferase (PatA/SpuC) BUB52_RS13360 BUB52_RS04845
arginine patD: gamma-aminobutyraldehyde dehydrogenase
arginine rocE: L-arginine permease
aspartate dauA: dicarboxylic acid transporter DauA BUB52_RS09955
cellobiose SSS-glucose: Sodium/glucose cotransporter BUB52_RS14570
citrate SLC13A5: citrate:Na+ symporter
citrulline citrullinase: putative citrullinase BUB52_RS08840
citrulline PS417_17590: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline PS417_17595: ABC transporter for L-Citrulline, permease component 1
citrulline PS417_17600: ABC transporter for L-Citrulline, permease component 2
citrulline PS417_17605: ABC transporter for L-Citrulline, ATPase component BUB52_RS04930 BUB52_RS11690
citrulline rocA: 1-pyrroline-5-carboxylate dehydrogenase
citrulline rocD: ornithine aminotransferase BUB52_RS04845 BUB52_RS13360
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) BUB52_RS06870
deoxyinosine deoB: phosphopentomutase BUB52_RS05025
deoxyribonate atoB: acetyl-CoA C-acetyltransferase
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase BUB52_RS00055
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) BUB52_RS06870
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter BUB52_RS08075
ethanol adh: acetaldehyde dehydrogenase (not acylating) BUB52_RS06870
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) BUB52_RS13275 BUB52_RS12985
fucose fucA: L-fuculose-phosphate aldolase FucA
fucose fucI: L-fucose isomerase FucI
fucose fucP: L-fucose:H+ symporter FucP BUB52_RS08075
fucose fucU: L-fucose mutarotase FucU
fumarate dauA: fumarate transporter DauA BUB52_RS09955
galactose galP: galactose:H+ symporter GalP BUB52_RS10060 BUB52_RS08575
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 BUB52_RS08075
glucosamine nagX: transmembrane glucosamine N-acetyltransferase NagX BUB52_RS13780
glucose SSS-glucose: Sodium/glucose cotransporter BUB52_RS14570
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter BUB52_RS06875 BUB52_RS13510
glucuronate exuT: D-glucuronate:H+ symporter ExuT BUB52_RS10345
glucuronate uxuB: D-mannonate dehydrogenase
glutamate gltS: L-glutamate:Na+ symporter GltS
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric)
glycerol glpF: glycerol facilitator glpF
glycerol glpK: glycerol kinase
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine permease: L-histidine permease
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase BUB52_RS07185
isoleucine Bap2: L-isoleucine permease Bap2
isoleucine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit BUB52_RS00230
isoleucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component BUB52_RS00225
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase
isoleucine fadA: 2-methylacetoacetyl-CoA thiolase
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase BUB52_RS00055 BUB52_RS10260
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit BUB52_RS09190
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 bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit BUB52_RS00230
leucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component BUB52_RS00225
leucine leuT: L-leucine:Na+ symporter LeuT BUB52_RS13665
leucine liuA: isovaleryl-CoA dehydrogenase BUB52_RS07185
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit BUB52_RS09190
leucine liuC: 3-methylglutaconyl-CoA hydratase
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit BUB52_RS06235 BUB52_RS09180
leucine liuE: hydroxymethylglutaryl-CoA lyase
lysine amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd)
lysine hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase
lysine lysN: 2-aminoadipate transaminase BUB52_RS14755 BUB52_RS13360
lysine lysP: L-lysine:H+ symporter LysP
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase
maltose malI: maltose transporter BUB52_RS02650
mannitol mt2d: mannitol 2-dehydrogenase BUB52_RS00055 BUB52_RS10260
mannitol PLT5: polyol transporter PLT5 BUB52_RS10060 BUB52_RS08575
mannose gluP: mannose:Na+ symporter BUB52_RS08075
mannose manA: mannose-6-phosphate isomerase BUB52_RS12575 BUB52_RS04025
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 BUB52_RS10060 BUB52_RS08575
myoinositol uxaE: D-tagaturonate epimerase
myoinositol uxuB: D-mannonate dehydrogenase
NAG nagP: N-acetylglucosamine transporter NagP BUB52_RS08075
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 BUB52_RS00055
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
propionate pccA: propionyl-CoA carboxylase, alpha subunit BUB52_RS09190
propionate prpE: propionyl-CoA synthetase BUB52_RS13375
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabD: succinate semialdehyde dehydrogenase
putrescine gabT: gamma-aminobutyrate transaminase BUB52_RS13360 BUB52_RS04845
putrescine patA: putrescine aminotransferase (PatA/SpuC) BUB52_RS13360 BUB52_RS04845
putrescine patD: gamma-aminobutyraldehyde dehydrogenase
putrescine potB: putrescine ABC transporter, permease component 1 (PotB/PotH) BUB52_RS15220
putrescine potC: putrescine ABC transporter, permease component 2 (PotC/PotI) BUB52_RS15215
putrescine potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) BUB52_RS15210
pyruvate SLC5A8: sodium-coupled pyruvate transporter
rhamnose rhaM: L-rhamnose mutarotase
ribose rbsK: ribokinase
ribose rbsU: probable D-ribose transporter RbsU
serine snatA: L-serine transporter BUB52_RS00350
sorbitol sdh: sorbitol dehydrogenase BUB52_RS00055 BUB52_RS10260
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2 BUB52_RS10060 BUB52_RS08575
succinate dauA: succinate:H+ symporter DauA BUB52_RS09955
threonine snatA: L-threonine transporter snatA BUB52_RS00350
thymidine adh: acetaldehyde dehydrogenase (not acylating) BUB52_RS06870
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase BUB52_RS05025
trehalose SSS-glucose: Sodium/glucose cotransporter BUB52_RS14570
trehalose treF: trehalase
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 BUB52_RS07185
valine Bap2: L-valine permease Bap2
valine bch: 3-hydroxyisobutyryl-CoA hydrolase
valine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit BUB52_RS00230
valine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component BUB52_RS00225
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 BUB52_RS09190
xylitol PLT5: xylitol:H+ symporter PLT5 BUB52_RS10060 BUB52_RS08575
xylitol xdhA: xylitol dehydrogenase BUB52_RS00055 BUB52_RS00875

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