GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Paucidesulfovibrio gracilis DSM 16080

Found 173 low-confidence and 68 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
2-oxoglutarate kgtP: 2-oxoglutarate:H+ symporter KgtP B5D49_RS00840
4-hydroxybenzoate adh: acetaldehyde dehydrogenase (not acylating) B5D49_RS13965 B5D49_RS04205
4-hydroxybenzoate mhpD: 2-hydroxypentadienoate hydratase
4-hydroxybenzoate mhpE: 4-hydroxy-2-oxovalerate aldolase B5D49_RS04290
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
alanine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) B5D49_RS00095 B5D49_RS04220
alanine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) B5D49_RS00090 B5D49_RS04225
alanine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) B5D49_RS04230 B5D49_RS00085
alanine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) B5D49_RS00080 B5D49_RS00870
alanine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) B5D49_RS04235 B5D49_RS00075
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter
arginine braC: ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC B5D49_RS04220 B5D49_RS00095
arginine braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) B5D49_RS00090 B5D49_RS04225
arginine braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) B5D49_RS00085 B5D49_RS04230
arginine braF: ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) B5D49_RS04215 B5D49_RS00080
arginine rocF: arginase
asparagine glt: aspartate:proton symporter Glt
aspartate glt: aspartate:proton symporter Glt
cellobiose cbp: cellobiose phosphorylase
cellobiose cdt: cellobiose transporter cdt-1/cdt-2
cellobiose glk: glucokinase B5D49_RS04535
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component B5D49_RS04740 B5D49_RS02695
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 B5D49_RS01060 B5D49_RS12105
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 B5D49_RS01060 B5D49_RS02700
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component B5D49_RS02705 B5D49_RS12100
citrulline arcC: carbamate kinase
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase B5D49_RS07870 B5D49_RS10655
D-serine cycA: D-serine:H+ symporter CycA
D-serine dsdA: D-serine ammonia-lyase
deoxyinosine adh: acetaldehyde dehydrogenase (not acylating) B5D49_RS13965 B5D49_RS04205
deoxyinosine deoB: phosphopentomutase B5D49_RS05410 B5D49_RS09285
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine deoD: deoxyinosine phosphorylase B5D49_RS05725
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate atoB: acetyl-CoA C-acetyltransferase B5D49_RS03160
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase B5D49_RS01965
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 adh: acetaldehyde dehydrogenase (not acylating) B5D49_RS13965 B5D49_RS04205
deoxyribose deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter
ethanol adh: acetaldehyde dehydrogenase (not acylating) B5D49_RS13965 B5D49_RS04205
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) B5D49_RS13960 B5D49_RS00550
fructose 1pfk: 1-phosphofructokinase
fructose fba: fructose 1,6-bisphosphate aldolase B5D49_RS09460 B5D49_RS08675
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 fucO: L-lactaldehyde reductase B5D49_RS02515 B5D49_RS02645
fucose fucP: L-fucose:H+ symporter FucP
fucose fucU: L-fucose mutarotase FucU
fumarate dctA: fumarate:H+ symporter DctA
galactose galE: UDP-glucose 4-epimerase B5D49_RS09210 B5D49_RS11915
galactose galK: galactokinase (-1-phosphate forming)
galactose galP: galactose:H+ symporter GalP
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
galacturonate eda: 2-keto-3-deoxygluconate 6-phosphate aldolase
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) B5D49_RS08590
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 B5D49_RS13965 B5D49_RS04205
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate kdgD: 5-dehydro-4-deoxyglucarate dehydratase B5D49_RS05670
glucuronate udh: D-glucuronate dehydrogenase
glutamate dmeA: L-glutamate transporter DmeA B5D49_RS14535
glutamate gdhA: glutamate dehydrogenase, NAD-dependent B5D49_RS05330
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric)
glycerol glpF: glycerol facilitator glpF
glycerol glpK: glycerol kinase
histidine braC: ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC B5D49_RS04220 B5D49_RS00095
histidine braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) B5D49_RS00090 B5D49_RS04225
histidine braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) B5D49_RS00085 B5D49_RS04230
histidine braF: ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) B5D49_RS04215 B5D49_RS00080
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase
isoleucine epi: methylmalonyl-CoA epimerase
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase B5D49_RS01965
isoleucine livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) B5D49_RS00095 B5D49_RS04220
isoleucine mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit B5D49_RS12550 B5D49_RS04650
isoleucine pccB: propionyl-CoA carboxylase, beta subunit
isoleucine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC
L-malate sdlC: L-malate:Na+ symporter SdlC
lactose galE: UDP-glucose 4-epimerase B5D49_RS09210 B5D49_RS11915
lactose galK: galactokinase (-1-phosphate forming)
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
lactose glk: glucokinase B5D49_RS04535
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
leucine atoB: acetyl-CoA C-acetyltransferase B5D49_RS03160
leucine liuA: isovaleryl-CoA dehydrogenase
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit B5D49_RS12550 B5D49_RS04650
leucine liuC: 3-methylglutaconyl-CoA hydratase
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) B5D49_RS00095 B5D49_RS04220
leucine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC
lysine amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) B5D49_RS13965
lysine hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase B5D49_RS03155 B5D49_RS05850
lysine lysP: L-lysine:H+ symporter LysP
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase B5D49_RS10975
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 B5D49_RS04385
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 B5D49_RS13965 B5D49_RS04205
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) B5D49_RS08590
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 B5D49_RS01965
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase B5D49_RS03160
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase B5D49_RS03160
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine atoB: acetyl-CoA C-acetyltransferase B5D49_RS03160
phenylalanine fahA: fumarylacetoacetate hydrolase
phenylalanine hmgA: homogentisate dioxygenase
phenylalanine HPD: 4-hydroxyphenylpyruvate dioxygenase
phenylalanine livF: L-phenylalanine ABC transporter, ATPase component 1 (LivF) B5D49_RS04235 B5D49_RS00075
phenylalanine livH: L-phenylalanine ABC transporter, permease component 1 (LivH) B5D49_RS00090 B5D49_RS04225
phenylalanine livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK B5D49_RS00095 B5D49_RS04220
phenylalanine maiA: maleylacetoacetate isomerase
phenylalanine PAH: phenylalanine 4-monooxygenase
phenylalanine PCBD: pterin-4-alpha-carbinoalamine dehydratase
phenylalanine QDPR: 6,7-dihydropteridine reductase
proline betS: proline transporter BetS B5D49_RS07505 B5D49_RS09365
proline put1: proline dehydrogenase B5D49_RS04205
propionate epi: methylmalonyl-CoA epimerase
propionate lctP: propionate permease B5D49_RS09160
propionate mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
propionate pccA: propionyl-CoA carboxylase, alpha subunit B5D49_RS12550 B5D49_RS04650
propionate pccB: propionyl-CoA carboxylase, beta subunit
putrescine gabD: succinate semialdehyde dehydrogenase B5D49_RS13965 B5D49_RS04205
putrescine gabT: gamma-aminobutyrate transaminase B5D49_RS03155 B5D49_RS14700
putrescine patA: putrescine aminotransferase (PatA/SpuC) B5D49_RS14700 B5D49_RS12615
putrescine patD: gamma-aminobutyraldehyde dehydrogenase B5D49_RS13965 B5D49_RS04205
pyruvate actP: large subunit of pyruvate transporter (actP-like) B5D49_RS08720
pyruvate yjcH: putative small subunit of pyruvate transporter (yjcH-like) B5D49_RS08715
rhamnose fucO: L-lactaldehyde reductase B5D49_RS02515 B5D49_RS02645
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 braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) B5D49_RS00095 B5D49_RS04220
serine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) B5D49_RS00090 B5D49_RS04225
serine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) B5D49_RS04230 B5D49_RS00085
serine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) B5D49_RS00080 B5D49_RS00870
serine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) B5D49_RS04235 B5D49_RS00075
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase B5D49_RS01965
succinate sdc: succinate:Na+ symporter Sdc
sucrose scrK: fructokinase
sucrose SUS: sucrose synthase
sucrose sut: sucrose:proton symporter SUT/SUC
threonine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) B5D49_RS00095 B5D49_RS04220
threonine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) B5D49_RS00090 B5D49_RS04225
threonine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) B5D49_RS04230 B5D49_RS00085
threonine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) B5D49_RS00080 B5D49_RS00870
threonine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) B5D49_RS04235 B5D49_RS00075
threonine gcvP: glycine cleavage system, P component (glycine decarboxylase) B5D49_RS04120 B5D49_RS04115
threonine lpd: dihydrolipoyl dehydrogenase B5D49_RS04110 B5D49_RS13200
thymidine adh: acetaldehyde dehydrogenase (not acylating) B5D49_RS13965 B5D49_RS04205
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase B5D49_RS05410 B5D49_RS09285
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupG: thymidine permease NupG/XapB
trehalose glk: glucokinase B5D49_RS04535
trehalose PsTP: trehalose phosphorylase
trehalose TRET1: facilitated trehalose transporter Tret1
tryptophan tnaA: tryptophanase
tyrosine Ac3H11_1692: L-tyrosine ABC transporter, ATPase component 2 B5D49_RS04235 B5D49_RS00075
tyrosine Ac3H11_1694: L-tyrosine ABC transporter, permease component 2 B5D49_RS04230 B5D49_RS00085
tyrosine Ac3H11_1695: L-tyrosine ABC transporter, permease component 1 B5D49_RS00090 B5D49_RS04225
tyrosine Ac3H11_2396: L-tyrosine ABC transporter, substrate-binding component component B5D49_RS04220
tyrosine atoB: acetyl-CoA C-acetyltransferase B5D49_RS03160
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 livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) B5D49_RS00095 B5D49_RS04220
valine mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
valine mmsA: methylmalonate-semialdehyde dehydrogenase B5D49_RS13965 B5D49_RS04205
valine mmsB: 3-hydroxyisobutyrate dehydrogenase
valine pccA: propionyl-CoA carboxylase, alpha subunit B5D49_RS12550 B5D49_RS04650
valine pccB: propionyl-CoA carboxylase, beta subunit
valine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase B5D49_RS01275
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