GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Thiohalomonas denitrificans HLD2

Found 182 low-confidence and 29 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 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
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 BLP65_RS04710 BLP65_RS06860
arginine patA: putrescine aminotransferase (PatA/SpuC) BLP65_RS06860 BLP65_RS05880
arginine patD: gamma-aminobutyraldehyde dehydrogenase BLP65_RS04695 BLP65_RS03760
arginine rocE: L-arginine permease
aspartate glt: aspartate:proton symporter Glt BLP65_RS12395
cellobiose cbp: cellobiose phosphorylase
cellobiose cdt: cellobiose transporter cdt-1/cdt-2
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component BLP65_RS08155 BLP65_RS04495
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 rocD: ornithine aminotransferase BLP65_RS04710 BLP65_RS12310
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 BLP65_RS10115
deoxyinosine deoB: phosphopentomutase BLP65_RS00825
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine deoD: deoxyinosine phosphorylase BLP65_RS09340
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate aacS: acetoacetyl-CoA synthetase
deoxyribonate atoB: acetyl-CoA C-acetyltransferase
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase BLP65_RS11225 BLP65_RS01760
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate garK: glycerate 2-kinase BLP65_RS12535
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter
fructose Slc2a5: fructose:H+ symporter
fucose aldA: lactaldehyde dehydrogenase BLP65_RS04695 BLP65_RS03760
fucose fucA: L-fuculose-phosphate aldolase FucA BLP65_RS07205
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 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 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) BLP65_RS12985
glucose MFS-glucose: glucose transporter, MFS superfamily
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate dopDH: 2,5-dioxopentanonate dehydrogenase BLP65_RS04695 BLP65_RS03760
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate kdgD: 5-dehydro-4-deoxyglucarate dehydratase BLP65_RS05080
glucuronate udh: D-glucuronate dehydrogenase
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric) BLP65_RS10635
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
isoleucine Bap2: L-isoleucine permease Bap2
isoleucine bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit BLP65_RS07270 BLP65_RS06725
isoleucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component BLP65_RS07265
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase
isoleucine fadA: 2-methylacetoacetyl-CoA thiolase
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase BLP65_RS08625
isoleucine prpB: 2-methylisocitrate lyase
isoleucine prpC: 2-methylcitrate synthase BLP65_RS02570
isoleucine prpD: 2-methylcitrate dehydratase
L-lactate lctO: L-lactate oxidase or 2-monooxygenase
L-lactate Shew_2731: L-lactate:Na+ symporter, large component BLP65_RS00650
L-lactate Shew_2732: L-lactate:Na+ symporter, small component BLP65_RS00645
L-malate sdlC: L-malate:Na+ symporter SdlC
lactose galK: galactokinase (-1-phosphate forming)
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
leucine aacS: acetoacetyl-CoA synthetase
leucine atoB: acetyl-CoA C-acetyltransferase
leucine bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit BLP65_RS07270 BLP65_RS06725
leucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component BLP65_RS07265
leucine leuT: L-leucine:Na+ symporter LeuT
leucine liuA: isovaleryl-CoA dehydrogenase
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit BLP65_RS08595 BLP65_RS03235
leucine liuC: 3-methylglutaconyl-CoA hydratase
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit
leucine liuE: hydroxymethylglutaryl-CoA lyase
lysine amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) BLP65_RS04695 BLP65_RS09020
lysine hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase BLP65_RS04710 BLP65_RS06860
lysine lysN: 2-aminoadipate transaminase BLP65_RS00370 BLP65_RS04710
lysine lysP: L-lysine:H+ symporter LysP
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase BLP65_RS12170 BLP65_RS02135
maltose susB: alpha-glucosidase (maltase) BLP65_RS07505
maltose thuE: maltose ABC transporter, substrate-binding component ThuE BLP65_RS09960
maltose thuF: maltose ABC transporter, permease component 1 (ThuF) BLP65_RS09965
maltose thuK: maltose ABC transporter, ATPase component ThuK BLP65_RS09975 BLP65_RS16320
mannitol mt2d: mannitol 2-dehydrogenase BLP65_RS08625
mannitol PLT5: polyol transporter PLT5
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 BLP65_RS10855 BLP65_RS05450
myoinositol iolT: myo-inositol:H+ symporter
myoinositol mmsA: malonate-semialdehyde dehydrogenase BLP65_RS04695
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) BLP65_RS12985
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 BLP65_RS08625
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
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 BLP65_RS06620
phenylalanine QDPR: 6,7-dihydropteridine reductase
propionate prpB: 2-methylisocitrate lyase
propionate prpC: 2-methylcitrate synthase BLP65_RS02570
propionate prpD: 2-methylcitrate dehydratase
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabT: gamma-aminobutyrate transaminase BLP65_RS04710 BLP65_RS06860
putrescine patA: putrescine aminotransferase (PatA/SpuC) BLP65_RS06860 BLP65_RS05880
putrescine patD: gamma-aminobutyraldehyde dehydrogenase BLP65_RS04695 BLP65_RS03760
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate yjcH: putative small subunit of pyruvate transporter (yjcH-like) BLP65_RS00645
rhamnose aldA: lactaldehyde dehydrogenase BLP65_RS04695 BLP65_RS03760
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 BLP65_RS10115
serine snatA: L-serine transporter BLP65_RS02950
sorbitol sdh: sorbitol dehydrogenase BLP65_RS12085 BLP65_RS08625
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2
sucrose thuK: sucrose ABC transporter, ATPase component ThuK BLP65_RS09975 BLP65_RS16320
threonine gcvP: glycine cleavage system, P component (glycine decarboxylase) BLP65_RS08420 BLP65_RS08425
threonine ltaE: L-threonine aldolase BLP65_RS05265
threonine snatA: L-threonine transporter snatA BLP65_RS02950
thymidine deoA: thymidine phosphorylase DeoA BLP65_RS01745
thymidine deoB: phosphopentomutase BLP65_RS00825
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupG: thymidine permease NupG/XapB
trehalose thuE: trehalose ABC transporter, substrate-binding component ThuE BLP65_RS09960
trehalose thuF: trehalose ABC transporter, permease component 1 (ThuF) BLP65_RS09965
trehalose thuK: trehalose ABC transporter, ATPase component ThuK BLP65_RS09975 BLP65_RS16320
trehalose treF: trehalase BLP65_RS11895 BLP65_RS04565
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
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 bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit BLP65_RS07270 BLP65_RS06725
valine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component BLP65_RS07265
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase
valine mmsA: methylmalonate-semialdehyde dehydrogenase BLP65_RS04695
valine mmsB: 3-hydroxyisobutyrate dehydrogenase
valine prpB: 2-methylisocitrate lyase
valine prpC: 2-methylcitrate synthase BLP65_RS02570
valine prpD: 2-methylcitrate dehydratase
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase
xylose xylA: xylose isomerase
xylose xylB: xylulokinase BLP65_RS00585
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