GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Arcobacter nitrofigilis DSM 7299

Found 157 low-confidence and 47 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
2-oxoglutarate Psest_0084: 2-oxoglutarate TRAP transporter, fused 4TM/12TM components ARNIT_RS06050 ARNIT_RS06360
2-oxoglutarate Psest_0085: 2-oxoglutarate TRAP transporter, solute receptor component ARNIT_RS00085
4-hydroxybenzoate adh: acetaldehyde dehydrogenase (not acylating) ARNIT_RS13950 ARNIT_RS06115
4-hydroxybenzoate mhpD: 2-hydroxypentadienoate hydratase
4-hydroxybenzoate mhpE: 4-hydroxy-2-oxovalerate aldolase ARNIT_RS04745
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 ARNIT_RS03795
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter
arginine gabT: gamma-aminobutyrate transaminase ARNIT_RS06120 ARNIT_RS11930
arginine patA: putrescine aminotransferase (PatA/SpuC) ARNIT_RS11930 ARNIT_RS06120
arginine patD: gamma-aminobutyraldehyde dehydrogenase ARNIT_RS13950 ARNIT_RS05955
arginine rocE: L-arginine permease
asparagine ans: asparaginase ARNIT_RS15665 ARNIT_RS12720
cellobiose bgl: cellobiase
cellobiose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
citrate citT: citrate:succinate antiporter CitT ARNIT_RS02215
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component ARNIT_RS01655 ARNIT_RS05320
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 ARNIT_RS13580 ARNIT_RS01645
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 ARNIT_RS13580 ARNIT_RS16500
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component ARNIT_RS14270
citrulline arcC: carbamate kinase
citrulline rocA: 1-pyrroline-5-carboxylate dehydrogenase ARNIT_RS08940 ARNIT_RS05955
citrulline rocD: ornithine aminotransferase ARNIT_RS13880 ARNIT_RS11930
D-alanine dadA: D-alanine dehydrogenase
D-alanine Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component ARNIT_RS02910
D-alanine Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component ARNIT_RS02895 ARNIT_RS13590
D-serine dsdA: D-serine ammonia-lyase ARNIT_RS02585
D-serine dsdX: D-serine transporter DsdX ARNIT_RS11970
deoxyinosine adh: acetaldehyde dehydrogenase (not acylating) ARNIT_RS13950 ARNIT_RS06115
deoxyinosine deoB: phosphopentomutase
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine deoD: deoxyinosine phosphorylase ARNIT_RS05260
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate aacS: acetoacetyl-CoA synthetase
deoxyribonate atoB: acetyl-CoA C-acetyltransferase ARNIT_RS06730
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase
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) ARNIT_RS13950 ARNIT_RS06115
deoxyribose deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter
ethanol adh: acetaldehyde dehydrogenase (not acylating) ARNIT_RS13950 ARNIT_RS06115
fructose 1pfk: 1-phosphofructokinase
fructose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components
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 galK: galactokinase (-1-phosphate forming)
galactose galP: galactose:H+ symporter GalP
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate kdgD: 5-dehydro-4-deoxyglucarate dehydratase
galacturonate udh: D-galacturonate dehydrogenase
galacturonate uxuL: D-galactaro-1,5-lactonase (UxuL or UxuF)
gluconate gntK: D-gluconate kinase
gluconate gntT: gluconate:H+ symporter GntT
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE)
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) ARNIT_RS03495
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 ARNIT_RS00065
glucuronate udh: D-glucuronate dehydrogenase
glucuronate uxuL: D-glucaro-1,5-lactonase UxuL or UxuF
histidine hutG: N-formiminoglutamate formiminohydrolase ARNIT_RS07020
histidine hutH: histidine ammonia-lyase ARNIT_RS11570
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
histidine PA5503: L-histidine ABC transporter, ATPase component ARNIT_RS05320 ARNIT_RS13775
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase ARNIT_RS06725
isoleucine fadA: 2-methylacetoacetyl-CoA thiolase ARNIT_RS06730 ARNIT_RS06725
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase ARNIT_RS02495 ARNIT_RS11565
isoleucine livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) ARNIT_RS06920 ARNIT_RS08965
isoleucine livM: L-isoleucine ABC transporter, permease component 2 (LivM/BraE) ARNIT_RS08955 ARNIT_RS06930
isoleucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
L-malate sdlC: L-malate:Na+ symporter SdlC ARNIT_RS07760
lactose galK: galactokinase (-1-phosphate forming)
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
lactose glk: glucokinase
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
leucine aacS: acetoacetyl-CoA synthetase
leucine atoB: acetyl-CoA C-acetyltransferase ARNIT_RS06730
leucine liuA: isovaleryl-CoA dehydrogenase
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit ARNIT_RS13965 ARNIT_RS00660
leucine liuC: 3-methylglutaconyl-CoA hydratase ARNIT_RS06725
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit
leucine liuE: hydroxymethylglutaryl-CoA lyase
leucine livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) ARNIT_RS06920 ARNIT_RS08965
leucine livM: L-leucine ABC transporter, permease component 2 (LivM/BraE) ARNIT_RS08955 ARNIT_RS06930
leucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
lysine amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) ARNIT_RS05955 ARNIT_RS00055
lysine hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase ARNIT_RS13880
lysine lysN: 2-aminoadipate transaminase ARNIT_RS10285 ARNIT_RS13880
lysine lysP: L-lysine:H+ symporter LysP
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase ARNIT_RS11485
maltose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
maltose susB: alpha-glucosidase (maltase)
mannitol mtlA: mannitol phosphotransferase system, EII-CBA components
mannitol mtlD: mannitol-1-phosphate 5-dehydrogenase
mannose manA: mannose-6-phosphate isomerase ARNIT_RS01490
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
myoinositol iolT: myo-inositol:H+ symporter
myoinositol mmsA: malonate-semialdehyde dehydrogenase ARNIT_RS04410 ARNIT_RS05955
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) ARNIT_RS03495
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 ARNIT_RS06725
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase
phenylacetate paaH: 3-hydroxyadipyl-CoA dehydrogenase ARNIT_RS06725 ARNIT_RS11565
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase ARNIT_RS06730
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase ARNIT_RS06730
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 atoB: acetyl-CoA C-acetyltransferase ARNIT_RS06730
phenylalanine fahA: fumarylacetoacetate hydrolase
phenylalanine hmgA: homogentisate dioxygenase
phenylalanine HPD: 4-hydroxyphenylpyruvate dioxygenase
phenylalanine livF: L-phenylalanine ABC transporter, ATPase component 1 (LivF) ARNIT_RS08945 ARNIT_RS06940
phenylalanine livG: L-phenylalanine ABC transporter, ATPase component 2 (LivG) ARNIT_RS06935 ARNIT_RS08950
phenylalanine livH: L-phenylalanine ABC transporter, permease component 1 (LivH) ARNIT_RS08960 ARNIT_RS06925
phenylalanine livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK ARNIT_RS08965
phenylalanine livM: L-phenylalanine ABC transporter, permease component 2 (LivM) ARNIT_RS08955 ARNIT_RS06930
phenylalanine maiA: maleylacetoacetate isomerase
phenylalanine PAH: phenylalanine 4-monooxygenase
phenylalanine PCBD: pterin-4-alpha-carbinoalamine dehydratase
phenylalanine QDPR: 6,7-dihydropteridine reductase
proline put1: proline dehydrogenase
proline putA: L-glutamate 5-semialdeyde dehydrogenase ARNIT_RS08940 ARNIT_RS05955
propionate prpE: propionyl-CoA synthetase
putrescine gabT: gamma-aminobutyrate transaminase ARNIT_RS06120 ARNIT_RS11930
putrescine patA: putrescine aminotransferase (PatA/SpuC) ARNIT_RS11930 ARNIT_RS06120
putrescine patD: gamma-aminobutyraldehyde dehydrogenase ARNIT_RS13950 ARNIT_RS05955
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate dctQ: pyruvate TRAP transporter, small permease component ARNIT_RS00985 ARNIT_RS00610
rhamnose LRA1: L-rhamnofuranose dehydrogenase ARNIT_RS02495
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsK: ribokinase
ribose rbsU: probable D-ribose transporter RbsU
serine snatA: L-serine transporter ARNIT_RS09940 ARNIT_RS09155
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase ARNIT_RS02495 ARNIT_RS11565
succinate sdc: succinate:Na+ symporter Sdc ARNIT_RS07760
sucrose scrK: fructokinase
sucrose SUS: sucrose synthase
sucrose sut: sucrose:proton symporter SUT/SUC
threonine snatA: L-threonine transporter snatA ARNIT_RS09940 ARNIT_RS09155
threonine tdcB: L-threonine dehydratase ARNIT_RS02585
threonine tdcE: 2-ketobutyrate formate-lyase
thymidine adh: acetaldehyde dehydrogenase (not acylating) ARNIT_RS13950 ARNIT_RS06115
thymidine deoA: thymidine phosphorylase DeoA ARNIT_RS07045 ARNIT_RS05260
thymidine deoB: phosphopentomutase
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupG: thymidine permease NupG/XapB
trehalose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
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 ARNIT_RS06730
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 ARNIT_RS06725
valine livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) ARNIT_RS06920 ARNIT_RS08965
valine livM: L-valine ABC transporter, permease component 2 (LivM/BraE) ARNIT_RS06930 ARNIT_RS08955
valine mmsA: methylmalonate-semialdehyde dehydrogenase ARNIT_RS04410 ARNIT_RS05955
valine mmsB: 3-hydroxyisobutyrate dehydrogenase ARNIT_RS05135
valine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase
xylose xylA: xylose isomerase
xylose xylB: xylulokinase ARNIT_RS06590
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