GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Thermithiobacillus tepidarius DSM 3134

Found 193 low-confidence and 28 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) G579_RS0101050
4-hydroxybenzoate mhpD: 2-hydroxypentadienoate hydratase
4-hydroxybenzoate mhpE: 4-hydroxy-2-oxovalerate aldolase G579_RS0102000
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 G579_RS0110885 G579_RS0101425
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter
arginine rocA: 1-pyrroline-5-carboxylate dehydrogenase
arginine rocD: ornithine aminotransferase G579_RS0105030 G579_RS0114350
arginine rocE: L-arginine permease
arginine rocF: arginase
cellobiose cbp: cellobiose phosphorylase
cellobiose cdt: cellobiose transporter cdt-1/cdt-2
cellobiose glk: glucokinase G579_RS16310
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component G579_RS0111760 G579_RS0108745
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 arcC: carbamate kinase
citrulline rocA: 1-pyrroline-5-carboxylate dehydrogenase
citrulline rocD: ornithine aminotransferase G579_RS0105030 G579_RS0114350
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 G579_RS0111535
deoxyinosine adh: acetaldehyde dehydrogenase (not acylating) G579_RS0101050
deoxyinosine deoB: phosphopentomutase G579_RS0107775
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine deoD: deoxyinosine phosphorylase G579_RS16830
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate aacS: acetoacetyl-CoA synthetase G579_RS0104490 G579_RS0100325
deoxyribonate atoB: acetyl-CoA C-acetyltransferase
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase G579_RS0103215
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) G579_RS0101050
deoxyribose deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter
ethanol adh: acetaldehyde dehydrogenase (not acylating) G579_RS0101050
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) G579_RS0108825 G579_RS0101050
fructose 1pfk: 1-phosphofructokinase
fructose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components
fucose aldA: lactaldehyde dehydrogenase
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
galactose galE: UDP-glucose 4-epimerase G579_RS0111685 G579_RS17890
galactose galP: galactose:H+ symporter GalP
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase G579_RS0102050
galacturonate eda: 2-keto-3-deoxygluconate 6-phosphate aldolase
galacturonate exuT: D-galacturonate transporter ExuT G579_RS15445
galacturonate kdgK: 2-keto-3-deoxygluconate kinase
galacturonate uxaA: D-altronate dehydratase
galacturonate uxaB: tagaturonate reductase
galacturonate uxaC: D-galacturonate isomerase
gluconate gntT: gluconate:H+ symporter GntT
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE)
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) G579_RS0110335
glucose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate garL: 5-dehydro-4-deoxy-D-glucarate aldolase G579_RS0102000
glucuronate garR: tartronate semialdehyde reductase G579_RS0108215
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate udh: D-glucuronate dehydrogenase
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric)
glycerol glpF: glycerol facilitator glpF G579_RS15850
glycerol glpK: glycerol kinase
histidine Ga0059261_1577: L-histidine transporter G579_RS0110050
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase G579_RS15200
histidine hutU: urocanase
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase G579_RS0113460
isoleucine Bap2: L-isoleucine permease Bap2
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase G579_RS0106750
isoleucine epi: methylmalonyl-CoA epimerase
isoleucine fadA: 2-methylacetoacetyl-CoA thiolase
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase G579_RS0106580 G579_RS0103215
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 G579_RS0111780 G579_RS0106615
isoleucine pccB: propionyl-CoA carboxylase, beta subunit
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 galE: UDP-glucose 4-epimerase G579_RS0111685 G579_RS17890
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase G579_RS0102050
lactose glk: glucokinase G579_RS16310
lactose lacP: lactose permease LacP
leucine aacS: acetoacetyl-CoA synthetase G579_RS0104490 G579_RS0100325
leucine atoB: acetyl-CoA C-acetyltransferase
leucine leuT: L-leucine:Na+ symporter LeuT
leucine liuA: isovaleryl-CoA dehydrogenase
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit G579_RS0106615 G579_RS0111780
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 G579_RS0105030 G579_RS0114350
lysine lysN: 2-aminoadipate transaminase G579_RS0106655 G579_RS0105030
lysine lysP: L-lysine:H+ symporter LysP
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase G579_RS0100245
maltose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
maltose susB: alpha-glucosidase (maltase) G579_RS0112575
mannitol mtlA: mannitol phosphotransferase system, EII-CBA components
mannitol mtlD: mannitol-1-phosphate 5-dehydrogenase
mannose manP: mannose PTS system, EII-CBA components
myoinositol iolB: 5-deoxy-D-glucuronate isomerase
myoinositol iolC: 5-dehydro-2-deoxy-D-gluconate kinase
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 G579_RS0107525
myoinositol iolT: myo-inositol:H+ symporter
myoinositol mmsA: malonate-semialdehyde dehydrogenase
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) G579_RS0110335
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 G579_RS0106750
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase
phenylacetate paaH: 3-hydroxyadipyl-CoA dehydrogenase G579_RS0103215 G579_RS0112390
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 G579_RS0104490 G579_RS0100325
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 G579_RS0109740
phenylalanine QDPR: 6,7-dihydropteridine reductase G579_RS0109505
proline CCNA_00435: proline transporter G579_RS0110050
proline put1: proline dehydrogenase
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 G579_RS0111780 G579_RS0106615
propionate pccB: propionyl-CoA carboxylase, beta subunit
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabD: succinate semialdehyde dehydrogenase
putrescine gabT: gamma-aminobutyrate transaminase G579_RS0114350 G579_RS0105030
putrescine patA: putrescine aminotransferase (PatA/SpuC) G579_RS0114350 G579_RS0105030
putrescine patD: gamma-aminobutyraldehyde dehydrogenase
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
rhamnose aldA: lactaldehyde dehydrogenase
rhamnose rhaA: L-rhamnose isomerase
rhamnose rhaB: L-rhamnulokinase
rhamnose rhaD: rhamnulose 1-phosphate aldolase
rhamnose rhaM: L-rhamnose mutarotase
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsK: ribokinase
ribose rbsU: probable D-ribose transporter RbsU
serine sdaB: L-serine ammonia-lyase G579_RS0111535
serine snatA: L-serine transporter G579_RS0110885 G579_RS0101425
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase G579_RS0108835
sucrose scrK: fructokinase
sucrose SUS: sucrose synthase
sucrose sut: sucrose:proton symporter SUT/SUC
threonine adh: acetaldehyde dehydrogenase (not acylating) G579_RS0101050
threonine gcvP: glycine cleavage system, P component (glycine decarboxylase) G579_RS0109675 G579_RS0109680
threonine ltaE: L-threonine aldolase G579_RS0111270
threonine snatA: L-threonine transporter snatA G579_RS0110885 G579_RS0101425
thymidine adh: acetaldehyde dehydrogenase (not acylating) G579_RS0101050
thymidine deoA: thymidine phosphorylase DeoA G579_RS0105015
thymidine deoB: phosphopentomutase G579_RS0107775
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupG: thymidine permease NupG/XapB
trehalose glk: glucokinase G579_RS16310
trehalose PsTP: trehalose phosphorylase
trehalose TRET1: facilitated trehalose transporter Tret1
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase G579_RS0105425
tyrosine aacS: acetoacetyl-CoA synthetase G579_RS0104490 G579_RS0100325
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 Bap2: L-valine permease Bap2
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 G579_RS0108215
valine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
valine pccA: propionyl-CoA carboxylase, alpha subunit G579_RS0111780 G579_RS0106615
valine pccB: propionyl-CoA carboxylase, beta subunit
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase
xylose xylA: xylose isomerase
xylose xylB: xylulokinase G579_RS15355
xylose xylT: D-xylose transporter

Confidence: high confidence medium confidence low confidence

This GapMind analysis is from Apr 09 2024. 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