GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Ethanoligenens harbinense YUAN-3

Found 173 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 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
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter
arginine gabD: succinate semialdehyde dehydrogenase ETHHA_RS02955 ETHHA_RS07000
arginine gabT: gamma-aminobutyrate transaminase ETHHA_RS02960 ETHHA_RS11350
arginine patD: gamma-aminobutyraldehyde dehydrogenase ETHHA_RS02955 ETHHA_RS03435
arginine rocE: L-arginine permease
asparagine agcS: Probable asparagine:Na+ symporter AgcS ETHHA_RS02395
asparagine ans: asparaginase
aspartate glt: aspartate:proton symporter Glt
cellobiose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) ETHHA_RS03675
citrate icd: isocitrate dehydrogenase ETHHA_RS04715 ETHHA_RS07010
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component ETHHA_RS11315 ETHHA_RS08700
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 ETHHA_RS11320
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component ETHHA_RS11325
citrulline arcC: carbamate kinase
citrulline gabD: succinate semialdehyde dehydrogenase ETHHA_RS02955 ETHHA_RS07000
citrulline gabT: gamma-aminobutyrate transaminase ETHHA_RS02960 ETHHA_RS11350
citrulline odc: L-ornithine decarboxylase
citrulline patD: gamma-aminobutyraldehyde dehydrogenase ETHHA_RS02955 ETHHA_RS03435
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase ETHHA_RS11355 ETHHA_RS00175
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 ETHHA_RS11310
deoxyinosine deoB: phosphopentomutase ETHHA_RS04555 ETHHA_RS13795
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate aacS: acetoacetyl-CoA synthetase
deoxyribonate atoB: acetyl-CoA C-acetyltransferase
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase ETHHA_RS02170 ETHHA_RS02795
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate garK: glycerate 2-kinase
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoK: deoxyribokinase ETHHA_RS10045
deoxyribose deoP: deoxyribose transporter
fucose aldA: lactaldehyde dehydrogenase ETHHA_RS02955 ETHHA_RS03435
fucose fucA: L-fuculose-phosphate aldolase FucA
fucose fucI: L-fucose isomerase FucI
fucose fucK: L-fuculose kinase FucK
fucose fucP: L-fucose:H+ symporter FucP
fucose fucU: L-fucose mutarotase FucU
fumarate dctA: fumarate:H+ symporter DctA
galactose galK: galactokinase (-1-phosphate forming) ETHHA_RS08975
galactose galP: galactose:H+ symporter GalP
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase ETHHA_RS03860 ETHHA_RS08980
galacturonate eda: 2-keto-3-deoxygluconate 6-phosphate aldolase
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate kdgK: 2-keto-3-deoxygluconate kinase ETHHA_RS10045
galacturonate uxaA: D-altronate dehydratase
galacturonate uxaB: tagaturonate reductase
galacturonate uxaC: D-galacturonate isomerase
gluconate gnd: 6-phosphogluconate dehydrogenase, decarboxylating
gluconate gntK: D-gluconate kinase
gluconate gntT: gluconate:H+ symporter GntT
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) ETHHA_RS03675
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) ETHHA_RS02220
glucose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) ETHHA_RS03675
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate dopDH: 2,5-dioxopentanonate dehydrogenase ETHHA_RS02955 ETHHA_RS03435
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate kdgD: 5-dehydro-4-deoxyglucarate dehydratase ETHHA_RS07190
glucuronate udh: D-glucuronate dehydrogenase
glutamate gltS: L-glutamate:Na+ symporter GltS
glycerol dhaK': dihydroxyacetone kinase, ATP dependent (monomeric)
glycerol glpF: glycerol facilitator glpF
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 ETHHA_RS08700 ETHHA_RS11315
histidine PA5504: L-histidine ABC transporter, permease component ETHHA_RS08695
histidine PA5505: L-histidine ABC transporter, substrate-binding component ETHHA_RS08710
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase ETHHA_RS01345
isoleucine Bap2: L-isoleucine permease Bap2
isoleucine dddA: 3-hydroxypropionate dehydrogenase
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase
isoleucine fadA: 2-methylacetoacetyl-CoA thiolase
isoleucine hpcD: 3-hydroxypropionyl-CoA dehydratase
isoleucine iolA: malonate semialdehyde dehydrogenase (CoA-acylating) ETHHA_RS02955 ETHHA_RS03435
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase ETHHA_RS13355 ETHHA_RS03445
isoleucine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
L-malate sdlC: L-malate:Na+ symporter SdlC
lactose galK: galactokinase (-1-phosphate forming) ETHHA_RS08975
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase ETHHA_RS03860 ETHHA_RS08980
lactose glk: glucokinase ETHHA_RS06780 ETHHA_RS03770
lactose lacE: lactose ABC transporter, substrate-binding component
lactose lacG: lactose ABC transporter, permease component 2 ETHHA_RS03835
lactose lacK: lactose ABC transporter, ATPase component ETHHA_RS04655 ETHHA_RS04015
leucine aacS: acetoacetyl-CoA synthetase
leucine atoB: acetyl-CoA C-acetyltransferase
leucine leuT: L-leucine:Na+ symporter LeuT
leucine liuA: isovaleryl-CoA dehydrogenase ETHHA_RS01345
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit ETHHA_RS12140 ETHHA_RS05110
leucine liuC: 3-methylglutaconyl-CoA hydratase
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit
leucine liuE: hydroxymethylglutaryl-CoA lyase
leucine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC
lysine amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) ETHHA_RS03435 ETHHA_RS02955
lysine hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase ETHHA_RS11350 ETHHA_RS02960
lysine lysN: 2-aminoadipate transaminase ETHHA_RS03080 ETHHA_RS01245
lysine lysP: L-lysine:H+ symporter LysP
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase
maltose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) ETHHA_RS03675
mannose manP: mannose PTS system, EII-CBA components ETHHA_RS02910 ETHHA_RS10040
myoinositol iolB: 5-deoxy-D-glucuronate isomerase
myoinositol iolC: 5-dehydro-2-deoxy-D-gluconate kinase ETHHA_RS10045
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 ETHHA_RS13640
myoinositol iolT: myo-inositol:H+ symporter
myoinositol mmsA: malonate-semialdehyde dehydrogenase ETHHA_RS02955 ETHHA_RS03435
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) ETHHA_RS02220
NAG nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components ETHHA_RS03675
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 ETHHA_RS01340 ETHHA_RS13355
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 ETHHA_RS05550
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 ETHHA_RS02955 ETHHA_RS03435
propionate dddA: 3-hydroxypropionate dehydrogenase
propionate hpcD: 3-hydroxypropionyl-CoA dehydratase
propionate iolA: malonate semialdehyde dehydrogenase (CoA-acylating) ETHHA_RS02955 ETHHA_RS03435
propionate prpE: propionyl-CoA synthetase ETHHA_RS06735
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabD: succinate semialdehyde dehydrogenase ETHHA_RS02955 ETHHA_RS07000
putrescine gabT: gamma-aminobutyrate transaminase ETHHA_RS02960 ETHHA_RS11350
putrescine patD: gamma-aminobutyraldehyde dehydrogenase ETHHA_RS02955 ETHHA_RS03435
putrescine potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) ETHHA_RS02995
pyruvate SLC5A8: sodium-coupled pyruvate transporter
rhamnose aldA: lactaldehyde dehydrogenase ETHHA_RS02955 ETHHA_RS03435
rhamnose LRA1: L-rhamnofuranose dehydrogenase ETHHA_RS02170 ETHHA_RS02795
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase
rhamnose LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsK: ribokinase ETHHA_RS10045
ribose rbsU: probable D-ribose transporter RbsU
serine sdaB: L-serine ammonia-lyase ETHHA_RS11310
serine serP: L-serine permease SerP
sorbitol mtlA: PTS system for polyols, EII-CBA components ETHHA_RS13875
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase ETHHA_RS13355 ETHHA_RS02795
succinate sdc: succinate:Na+ symporter Sdc
threonine dddA: 3-hydroxypropionate dehydrogenase
threonine hpcD: 3-hydroxypropionyl-CoA dehydratase
threonine iolA: malonate semialdehyde dehydrogenase (CoA-acylating) ETHHA_RS02955 ETHHA_RS03435
threonine tdcB: L-threonine dehydratase ETHHA_RS11310
threonine tdcC: L-threonine:H+ symporter TdcC
thymidine deoB: phosphopentomutase ETHHA_RS04555 ETHHA_RS13795
thymidine nupG: thymidine permease NupG/XapB
trehalose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) ETHHA_RS03675
trehalose treF: trehalase ETHHA_RS03800 ETHHA_RS03805
tryptophan tnaA: tryptophanase
tryptophan trpP: energy-coupling factor transporter, tryptophan-specific (S) component TrpP
tyrosine aacS: acetoacetyl-CoA synthetase
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine atoB: acetyl-CoA C-acetyltransferase
tyrosine fahA: fumarylacetoacetate hydrolase ETHHA_RS05550
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase ETHHA_RS01345
valine Bap2: L-valine permease Bap2
valine bch: 3-hydroxyisobutyryl-CoA hydrolase
valine dddA: 3-hydroxypropionate dehydrogenase
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase
valine hpcD: 3-hydroxypropionyl-CoA dehydratase
valine iolA: malonate semialdehyde dehydrogenase (CoA-acylating) ETHHA_RS02955 ETHHA_RS03435
valine mmsA: methylmalonate-semialdehyde dehydrogenase ETHHA_RS02955 ETHHA_RS03435
valine mmsB: 3-hydroxyisobutyrate dehydrogenase
valine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC
xylitol fruI: xylitol PTS, enzyme IIABC (FruI) ETHHA_RS10040 ETHHA_RS02910
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