GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Desulfotomaculum hydrothermale Lam5

Found 158 low-confidence and 32 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 DESHY_RS07740
2-oxoglutarate Psest_0085: 2-oxoglutarate TRAP transporter, solute receptor component DESHY_RS07730
4-hydroxybenzoate mhpD: 2-hydroxypentadienoate hydratase
4-hydroxybenzoate mhpE: 4-hydroxy-2-oxovalerate aldolase DESHY_RS05105 DESHY_RS05125
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 satP: acetate/proton symporter satP DESHY_RS08995
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase DESHY_RS08325
arabinose araE: L-arabinose:H+ symporter
arginine rocD: ornithine aminotransferase DESHY_RS05040 DESHY_RS02820
arginine rocF: arginase DESHY_RS07005
asparagine ans: asparaginase DESHY_RS03060
cellobiose bgl: cellobiase
cellobiose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
citrate acn: aconitase DESHY_RS05110
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component DESHY_RS02740 DESHY_RS09800
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 DESHY_RS02735 DESHY_RS09795
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 DESHY_RS02735
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component DESHY_RS09790 DESHY_RS02730
citrulline arcC: carbamate kinase
citrulline rocD: ornithine aminotransferase DESHY_RS05040 DESHY_RS02820
D-alanine cycA: D-alanine:H+ symporter CycA DESHY_RS02795
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase DESHY_RS02840 DESHY_RS08495
D-serine cycA: D-serine:H+ symporter CycA DESHY_RS02795
D-serine dsdA: D-serine ammonia-lyase DESHY_RS10075 DESHY_RS08940
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate atoB: acetyl-CoA C-acetyltransferase
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase DESHY_RS00155
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 deoP: deoxyribose transporter
fructose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components DESHY_RS03305
fucose fucA: L-fuculose-phosphate aldolase FucA DESHY_RS08325
fucose fucI: L-fucose isomerase FucI
fucose fucK: L-fuculose kinase FucK
fucose fucO: L-lactaldehyde reductase DESHY_RS12390 DESHY_RS12395
fucose fucP: L-fucose:H+ symporter FucP
fucose fucU: L-fucose mutarotase FucU
fumarate dctA: fumarate:H+ symporter DctA DESHY_RS09640
galactose galK: galactokinase (-1-phosphate forming)
galactose galP: galactose:H+ symporter GalP
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
galactose pgmA: alpha-phosphoglucomutase DESHY_RS03835 DESHY_RS05140
galacturonate eda: 2-keto-3-deoxygluconate 6-phosphate aldolase
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate kdgK: 2-keto-3-deoxygluconate kinase DESHY_RS10060
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 DESHY_RS10055
gluconate gntT: gluconate:H+ symporter GntT
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE)
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing)
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 DESHY_RS11965
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate kdgD: 5-dehydro-4-deoxyglucarate dehydratase
glucuronate udh: D-glucuronate dehydrogenase DESHY_RS03840
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric)
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 DESHY_RS05510 DESHY_RS09800
histidine PA5504: L-histidine ABC transporter, permease component DESHY_RS05515
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase
isoleucine epi: methylmalonyl-CoA epimerase
isoleucine fadA: 2-methylacetoacetyl-CoA thiolase
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase DESHY_RS08375
isoleucine mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit DESHY_RS10455
isoleucine pccB: propionyl-CoA carboxylase, beta subunit
isoleucine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC
L-malate dctA: L-malate:H+ symporter DctA DESHY_RS09640
lactose galK: galactokinase (-1-phosphate forming)
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
lactose glk: glucokinase DESHY_RS02610
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
lactose pgmA: alpha-phosphoglucomutase DESHY_RS03835 DESHY_RS05140
leucine atoB: acetyl-CoA C-acetyltransferase
leucine liuA: isovaleryl-CoA dehydrogenase
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit DESHY_RS10455
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 davD: glutarate semialdehyde dehydrogenase DESHY_RS11965
lysine glaH: glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lysine lhgD: L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
lysine lysP: L-lysine:H+ symporter LysP DESHY_RS02795
lysine patD: 5-aminopentanal dehydrogenase DESHY_RS11965
maltose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
maltose susB: alpha-glucosidase (maltase) DESHY_RS03470
mannitol mt2d: mannitol 2-dehydrogenase DESHY_RS10050 DESHY_RS10045
mannitol PLT5: polyol transporter PLT5
mannose manA: mannose-6-phosphate isomerase DESHY_RS05140
mannose manP: mannose PTS system, EII-CBA components DESHY_RS03305
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 DESHY_RS07910 DESHY_RS10015
myoinositol iolT: myo-inositol:H+ symporter
myoinositol mmsA: malonate-semialdehyde dehydrogenase DESHY_RS11965
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing)
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 DESHY_RS08375
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 aroP: L-phenylalanine:H+ symporter AroP DESHY_RS02795
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
phenylalanine QDPR: 6,7-dihydropteridine reductase
proline putP: proline:Na+ symporter DESHY_RS07830
propionate epi: methylmalonyl-CoA epimerase
propionate lctP: propionate permease DESHY_RS00630 DESHY_RS00625
propionate mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
propionate pccA: propionyl-CoA carboxylase, alpha subunit DESHY_RS10455
propionate pccB: propionyl-CoA carboxylase, beta subunit
putrescine gabD: succinate semialdehyde dehydrogenase DESHY_RS04445 DESHY_RS04365
putrescine patD: gamma-aminobutyraldehyde dehydrogenase DESHY_RS11965
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate SLC5A8: sodium-coupled pyruvate transporter
rhamnose fucO: L-lactaldehyde reductase DESHY_RS12390 DESHY_RS12395
rhamnose LRA1: L-rhamnofuranose dehydrogenase DESHY_RS08375
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 rbsA: D-ribose ABC transporter, ATPase component RbsA DESHY_RS05390 DESHY_RS00685
ribose rbsB: D-ribose ABC transporter, substrate-binding component RbsB DESHY_RS05380
ribose rbsC: D-ribose ABC transporter, permease component RbsC DESHY_RS05385
serine serP: L-serine permease SerP DESHY_RS02795
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2
succinate dctA: succinate:H+ symporter DctA DESHY_RS09640
sucrose ams: sucrose hydrolase (invertase)
sucrose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components DESHY_RS03305
threonine gcvP: glycine cleavage system, P component (glycine decarboxylase) DESHY_RS09765 DESHY_RS09770
threonine tdcC: L-threonine:H+ symporter TdcC
thymidine nupG: thymidine permease NupG/XapB
trehalose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
trehalose treF: trehalase
tryptophan ecfT: energy-coupling factor transporter, transmembrane (T) component DESHY_RS04975
tryptophan trpP: energy-coupling factor transporter, tryptophan-specific (S) component TrpP
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 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 DESHY_RS11965
valine mmsB: 3-hydroxyisobutyrate dehydrogenase
valine pccA: propionyl-CoA carboxylase, alpha subunit DESHY_RS10455
valine pccB: propionyl-CoA carboxylase, beta subunit
valine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC
xylitol PLT5: xylitol:H+ symporter PLT5
xylose xylT: D-xylose transporter
xylose xyrA: xylitol reductase DESHY_RS00120 DESHY_RS00160

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