GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Collinsella tanakaei YIT 12063

Found 151 low-confidence and 33 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 actP: cation/acetate symporter ActP
alanine cycA: L-alanine symporter CycA
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase HMPREF9452_RS04750
arabinose araE: L-arabinose:H+ symporter
arginine arcC: carbamate kinase HMPREF9452_RS05785
arginine rocA: 1-pyrroline-5-carboxylate dehydrogenase
arginine rocD: ornithine aminotransferase HMPREF9452_RS06405
arginine rocE: L-arginine permease
cellobiose bgl: cellobiase HMPREF9452_RS06170 HMPREF9452_RS09920
citrate acn: aconitase
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component HMPREF9452_RS00665 HMPREF9452_RS08755
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 HMPREF9452_RS00660 HMPREF9452_RS03130
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline arcC: carbamate kinase HMPREF9452_RS05785
citrulline rocA: 1-pyrroline-5-carboxylate dehydrogenase
citrulline rocD: ornithine aminotransferase HMPREF9452_RS06405
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-serine cycA: D-serine:H+ symporter CycA
D-serine dsdA: D-serine ammonia-lyase HMPREF9452_RS00695
deoxyinosine nupB: deoxyinosine ABC transporter, permease component 1 HMPREF9452_RS06105
deoxyribonate aacS: acetoacetyl-CoA synthetase
deoxyribonate atoB: acetyl-CoA C-acetyltransferase
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate garK: glycerate 2-kinase HMPREF9452_RS08875
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoK: deoxyribokinase HMPREF9452_RS05460 HMPREF9452_RS06915
deoxyribose deoP: deoxyribose transporter
fructose 1pfk: 1-phosphofructokinase HMPREF9452_RS00850 HMPREF9452_RS01780
fructose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components HMPREF9452_RS00845 HMPREF9452_RS03530
fucose fucA: L-fuculose-phosphate aldolase FucA HMPREF9452_RS04750
fucose fucK: L-fuculose kinase FucK HMPREF9452_RS04765
fucose fucP: L-fucose:H+ symporter FucP
fumarate dauA: fumarate transporter DauA HMPREF9452_RS10660
galactose galK: galactokinase (-1-phosphate forming) HMPREF9452_RS07000
galactose galP: galactose:H+ symporter GalP
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase HMPREF9452_RS07005
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate kdgK: 2-keto-3-deoxygluconate kinase HMPREF9452_RS08960 HMPREF9452_RS06915
gluconate edd: phosphogluconate dehydratase HMPREF9452_RS05330 HMPREF9452_RS00690
gluconate gntK: D-gluconate kinase
gluconate gntT: gluconate:H+ symporter GntT
glucosamine manX: glucosamine PTS system, EII-AB component ManX HMPREF9452_RS00200 HMPREF9452_RS03890
glucosamine manY: glucosamine PTS system, EII-C component ManY HMPREF9452_RS00205 HMPREF9452_RS04740
glucosamine manZ: glucosamine PTS system, EII-D component ManZ HMPREF9452_RS00210 HMPREF9452_RS04785
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate kdgK: 2-keto-3-deoxygluconate kinase HMPREF9452_RS08960 HMPREF9452_RS06915
glutamate gdhA: glutamate dehydrogenase, NAD-dependent HMPREF9452_RS02805
glycerol glpO: glycerol 3-phosphate oxidase HMPREF9452_RS02725
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
histidine PA5503: L-histidine ABC transporter, ATPase component HMPREF9452_RS03120 HMPREF9452_RS00665
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase
isoleucine epi: methylmalonyl-CoA epimerase
isoleucine fadA: 2-methylacetoacetyl-CoA thiolase
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase HMPREF9452_RS10260 HMPREF9452_RS08900
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 HMPREF9452_RS10230
isoleucine pccB: propionyl-CoA carboxylase, beta subunit
L-malate sdlC: L-malate:Na+ symporter SdlC
lactose gatZ: D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)
leucine aacS: acetoacetyl-CoA synthetase
leucine atoB: acetyl-CoA C-acetyltransferase
leucine liuA: isovaleryl-CoA dehydrogenase
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit HMPREF9452_RS10230
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 HMPREF9452_RS06405
lysine lysN: 2-aminoadipate transaminase HMPREF9452_RS09585 HMPREF9452_RS06405
lysine lysP: L-lysine:H+ symporter LysP
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase
maltose susB: alpha-glucosidase (maltase) HMPREF9452_RS01635
mannitol mt2d: mannitol 2-dehydrogenase HMPREF9452_RS00090 HMPREF9452_RS10260
mannitol PLT5: polyol transporter PLT5
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
myoinositol kdgK: 2-keto-3-deoxygluconate kinase HMPREF9452_RS08960 HMPREF9452_RS06915
myoinositol uxaE: D-tagaturonate epimerase
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 HMPREF9452_RS07760 HMPREF9452_RS10260
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase
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
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 HMPREF9452_RS02730
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 HMPREF9452_RS10230
propionate pccB: propionyl-CoA carboxylase, beta subunit
propionate prpE: propionyl-CoA synthetase
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabD: succinate semialdehyde dehydrogenase HMPREF9452_RS03710 HMPREF9452_RS01590
putrescine gabT: gamma-aminobutyrate transaminase HMPREF9452_RS06405
putrescine patA: putrescine aminotransferase (PatA/SpuC) HMPREF9452_RS06405
putrescine patD: gamma-aminobutyraldehyde dehydrogenase
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate SLC5A8: sodium-coupled pyruvate transporter
rhamnose rhaA: L-rhamnose isomerase
rhamnose rhaB: L-rhamnulokinase HMPREF9452_RS04765
rhamnose rhaD: rhamnulose 1-phosphate aldolase
rhamnose rhaM: L-rhamnose mutarotase
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose fru2-IIA: D-ribose PTS, IIA component HMPREF9452_RS03540
ribose fru2-IIC: D-ribose PTS, IIC component HMPREF9452_RS03530
serine serP: L-serine permease SerP
sorbitol sdh: sorbitol dehydrogenase HMPREF9452_RS08900 HMPREF9452_RS00090
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2
succinate dauA: succinate:H+ symporter DauA HMPREF9452_RS10660
sucrose ams: sucrose hydrolase (invertase) HMPREF9452_RS06920
threonine gloA: glyoxylase I
threonine gloB: hydroxyacylglutathione hydrolase (glyoxalase II) HMPREF9452_RS10995
threonine tdcC: L-threonine:H+ symporter TdcC
threonine tdh: L-threonine 3-dehydrogenase HMPREF9452_RS07580 HMPREF9452_RS03480
threonine tynA: aminoacetone oxidase
thymidine nupG: thymidine permease NupG/XapB
trehalose treF: trehalase
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine aacS: acetoacetyl-CoA synthetase
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
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 HMPREF9452_RS04005
valine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
valine pccA: propionyl-CoA carboxylase, alpha subunit HMPREF9452_RS10230
valine pccB: propionyl-CoA carboxylase, beta subunit
xylitol fruI: xylitol PTS, enzyme IIABC (FruI) HMPREF9452_RS00845 HMPREF9452_RS03530
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase
xylose xylA: xylose isomerase
xylose xylB: xylulokinase
xylose xylT: D-xylose transporter

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