GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Desulfobacca acetoxidans DSM 11109

Found 195 low-confidence and 48 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 ald-dh-CoA: acetaldehyde dehydrogenase, acylating
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 acs: acetyl-CoA synthetase, AMP-forming DESAC_RS02235
acetate actP: cation/acetate symporter ActP
alanine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) DESAC_RS01545 DESAC_RS10080
alanine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) DESAC_RS09200 DESAC_RS06200
alanine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) DESAC_RS09195 DESAC_RS10060
alanine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) DESAC_RS06215 DESAC_RS10070
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 DESAC_RS07485 DESAC_RS12910
arginine rocE: L-arginine permease
arginine rocF: arginase DESAC_RS03585
asparagine ans: asparaginase DESAC_RS09770
asparagine glt: aspartate:proton symporter Glt DESAC_RS16845
aspartate glt: aspartate:proton symporter Glt DESAC_RS16845
cellobiose bgl: cellobiase
cellobiose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component DESAC_RS13535 DESAC_RS02355
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 DESAC_RS07485 DESAC_RS12910
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-lactate lctB: electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), small subunit DESAC_RS02720
D-lactate lctC: electron-transfer flavoprotein for D-lactate dehydrogenase (NAD+, ferredoxin), large subunit DESAC_RS02725
D-lactate lctD: D-lactate dehydrogenase (NAD+, ferredoxin), lactate dehydrogenase component DESAC_RS03170
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 DESAC_RS04655
deoxyinosine ald-dh-CoA: acetaldehyde dehydrogenase, acylating
deoxyinosine deoB: phosphopentomutase DESAC_RS01495
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate aacS: acetoacetyl-CoA synthetase DESAC_RS02235
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
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose ald-dh-CoA: acetaldehyde dehydrogenase, acylating
deoxyribose deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter
ethanol ald-dh-CoA: acetaldehyde dehydrogenase, acylating
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) DESAC_RS13435 DESAC_RS12155
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 DESAC_RS02505
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)
galactose galP: galactose:H+ symporter GalP
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase DESAC_RS12010
galactose pgmA: alpha-phosphoglucomutase DESAC_RS06940 DESAC_RS01495
galacturonate eda: 2-keto-3-deoxygluconate 6-phosphate aldolase DESAC_RS12395
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate kdgK: 2-keto-3-deoxygluconate kinase
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)
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) DESAC_RS12260
glucose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate dopDH: 2,5-dioxopentanonate dehydrogenase
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate kdgD: 5-dehydro-4-deoxyglucarate dehydratase DESAC_RS12395
glucuronate udh: D-glucuronate dehydrogenase
glutamate gdhA: glutamate dehydrogenase, NAD-dependent DESAC_RS12140 DESAC_RS09465
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 hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
histidine permease: L-histidine permease
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase DESAC_RS02715
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase DESAC_RS11950 DESAC_RS07880
isoleucine fadA: 2-methylacetoacetyl-CoA thiolase
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase DESAC_RS02730
isoleucine livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) DESAC_RS10080 DESAC_RS07565
isoleucine livM: L-isoleucine ABC transporter, permease component 2 (LivM/BraE) DESAC_RS09195 DESAC_RS01515
isoleucine ofoA: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA DESAC_RS10780
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit DESAC_RS08025
isoleucine pccB: propionyl-CoA carboxylase, beta subunit DESAC_RS14020
L-lactate L-LDH: L-lactate dehydrogenase DESAC_RS00185
L-lactate SfMCT: L-lactate transporter SfMCT DESAC_RS12905
L-malate sdlC: L-malate:Na+ symporter SdlC
lactose galK: galactokinase (-1-phosphate forming)
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase DESAC_RS12010
lactose glk: glucokinase DESAC_RS05210
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
lactose pgmA: alpha-phosphoglucomutase DESAC_RS06940 DESAC_RS01495
leucine aacS: acetoacetyl-CoA synthetase DESAC_RS02235
leucine atoB: acetyl-CoA C-acetyltransferase
leucine liuA: isovaleryl-CoA dehydrogenase DESAC_RS02715
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit DESAC_RS08025
leucine liuC: 3-methylglutaconyl-CoA hydratase
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit DESAC_RS14020
leucine liuE: hydroxymethylglutaryl-CoA lyase
leucine livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) DESAC_RS10080 DESAC_RS07565
leucine livM: L-leucine ABC transporter, permease component 2 (LivM/BraE) DESAC_RS01515 DESAC_RS09195
leucine ofoA: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA DESAC_RS10780
lysine amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd)
lysine hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase DESAC_RS07485 DESAC_RS12910
lysine lysN: 2-aminoadipate transaminase DESAC_RS12075 DESAC_RS03760
lysine lysP: L-lysine:H+ symporter LysP
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase DESAC_RS03170
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
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
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) DESAC_RS12260
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 DESAC_RS07880
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase DESAC_RS14225
phenylacetate paaH: 3-hydroxyadipyl-CoA dehydrogenase DESAC_RS09745 DESAC_RS02730
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 aacS: acetoacetyl-CoA synthetase DESAC_RS02235
phenylalanine atoB: acetyl-CoA C-acetyltransferase
phenylalanine fahA: fumarylacetoacetate hydrolase DESAC_RS12405
phenylalanine hmgA: homogentisate dioxygenase
phenylalanine HPD: 4-hydroxyphenylpyruvate dioxygenase
phenylalanine livF: L-phenylalanine ABC transporter, ATPase component 1 (LivF) DESAC_RS06215 DESAC_RS10070
phenylalanine livH: L-phenylalanine ABC transporter, permease component 1 (LivH) DESAC_RS09200 DESAC_RS06200
phenylalanine livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK
phenylalanine livM: L-phenylalanine ABC transporter, permease component 2 (LivM) DESAC_RS09195 DESAC_RS01515
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 DESAC_RS08025
propionate pccB: propionyl-CoA carboxylase, beta subunit DESAC_RS14020
propionate prpE: propionyl-CoA synthetase DESAC_RS02235
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabD: succinate semialdehyde dehydrogenase DESAC_RS15420
putrescine gabT: gamma-aminobutyrate transaminase DESAC_RS07485 DESAC_RS12335
putrescine patA: putrescine aminotransferase (PatA/SpuC) DESAC_RS07485 DESAC_RS12335
putrescine patD: gamma-aminobutyraldehyde dehydrogenase
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate SLC5A8: sodium-coupled pyruvate transporter
rhamnose LRA1: L-rhamnofuranose dehydrogenase DESAC_RS02730
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase
rhamnose LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase DESAC_RS02730
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsK: ribokinase
ribose rbsU: probable D-ribose transporter RbsU
serine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) DESAC_RS01545 DESAC_RS10080
serine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) DESAC_RS09200 DESAC_RS06200
serine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) DESAC_RS09195 DESAC_RS10060
serine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) DESAC_RS06215 DESAC_RS10070
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase
succinate sdc: succinate:Na+ symporter Sdc
sucrose 1pfk: 1-phosphofructokinase
sucrose ams: sucrose hydrolase (invertase)
sucrose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components
threonine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) DESAC_RS01545 DESAC_RS10080
threonine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) DESAC_RS09200 DESAC_RS06200
threonine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) DESAC_RS09195 DESAC_RS10060
threonine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) DESAC_RS06215 DESAC_RS10070
threonine pccA: propionyl-CoA carboxylase, alpha subunit DESAC_RS08025
threonine pccB: propionyl-CoA carboxylase, beta subunit DESAC_RS14020
threonine tdcE: 2-ketobutyrate formate-lyase
thymidine ald-dh-CoA: acetaldehyde dehydrogenase, acylating
thymidine deoB: phosphopentomutase DESAC_RS01495
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 DESAC_RS02235
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine atoB: acetyl-CoA C-acetyltransferase
tyrosine fahA: fumarylacetoacetate hydrolase DESAC_RS12405
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase DESAC_RS02715
valine bch: 3-hydroxyisobutyryl-CoA hydrolase
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase DESAC_RS07880 DESAC_RS11950
valine livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) DESAC_RS10080 DESAC_RS07565
valine livM: L-valine ABC transporter, permease component 2 (LivM/BraE) DESAC_RS01515 DESAC_RS09195
valine mmsA: methylmalonate-semialdehyde dehydrogenase
valine mmsB: 3-hydroxyisobutyrate dehydrogenase
valine ofoA: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA DESAC_RS10780
valine pccA: propionyl-CoA carboxylase, alpha subunit DESAC_RS08025
valine pccB: propionyl-CoA carboxylase, beta subunit DESAC_RS14020
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
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 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