GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Bizionia argentinensis JUB59

Found 130 low-confidence and 34 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 BZARG_RS09955
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
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter
arginine rocE: L-arginine permease
arginine rocF: arginase
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 BZARG_RS11775 BZARG_RS03035
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
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase BZARG_RS06890 BZARG_RS00525
D-lactate lctP: D-lactate:H+ symporter LctP or LidP
D-serine cycA: D-serine:H+ symporter CycA
deoxyinosine deoB: phosphopentomutase BZARG_RS05430
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase BZARG_RS00770 BZARG_RS06770
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 deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) BZARG_RS00900 BZARG_RS01060
fructose 1pfk: 1-phosphofructokinase
fructose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components
fucose aldA: lactaldehyde dehydrogenase BZARG_RS01960 BZARG_RS04795
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
fumarate SLC26dg: fumarate transporter SLC26dg BZARG_RS02285
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) BZARG_RS13990
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 BZARG_RS04795 BZARG_RS01960
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
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric)
glycerol glpF: glycerol facilitator glpF
glycerol glpK: glycerol kinase
histidine permease: L-histidine permease
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase BZARG_RS12915 BZARG_RS01000
isoleucine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit BZARG_RS01255 BZARG_RS02455
isoleucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component BZARG_RS02185 BZARG_RS08985
isoleucine brnQ: L-isoleucine:cation symporter BrnQ/BraZ/BraB BZARG_RS14230
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase BZARG_RS02125 BZARG_RS10395
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase BZARG_RS00770 BZARG_RS06770
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit BZARG_RS05675 BZARG_RS09580
L-lactate lctO: L-lactate oxidase or 2-monooxygenase
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
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 glk: glucokinase
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
leucine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit BZARG_RS01255 BZARG_RS02455
leucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component BZARG_RS02185 BZARG_RS08985
leucine brnQ: L-leucine:Na+ symporter BrnQ/BraB BZARG_RS14230
leucine liuA: isovaleryl-CoA dehydrogenase BZARG_RS12915 BZARG_RS12340
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit BZARG_RS05675 BZARG_RS09580
leucine liuC: 3-methylglutaconyl-CoA hydratase BZARG_RS10395 BZARG_RS02125
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit BZARG_RS01575 BZARG_RS05670
lysine hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase BZARG_RS00030 BZARG_RS05755
lysine lysN: 2-aminoadipate transaminase BZARG_RS05000 BZARG_RS00030
lysine lysP: L-lysine:H+ symporter LysP
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase BZARG_RS00460
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 BZARG_RS12225 BZARG_RS11215
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 BZARG_RS04795 BZARG_RS01960
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) BZARG_RS13990
NAG nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components
phenylacetate paaF: 2,3-dehydroadipyl-CoA hydratase BZARG_RS10395 BZARG_RS02125
phenylacetate paaK: phenylacetate-CoA ligase BZARG_RS10770
phenylacetate paaT: phenylacetate transporter Paa
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
phenylalanine iorAB: phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB
phenylalanine paaF: 2,3-dehydroadipyl-CoA hydratase BZARG_RS10395 BZARG_RS02125
proline betS: proline transporter BetS BZARG_RS01775
propionate pccA: propionyl-CoA carboxylase, alpha subunit BZARG_RS05675 BZARG_RS09580
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabT: gamma-aminobutyrate transaminase BZARG_RS00030 BZARG_RS05755
putrescine patA: putrescine aminotransferase (PatA/SpuC) BZARG_RS00030 BZARG_RS05755
putrescine patD: gamma-aminobutyraldehyde dehydrogenase BZARG_RS01960 BZARG_RS04795
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate SLC5A8: sodium-coupled pyruvate transporter
rhamnose aldA: lactaldehyde dehydrogenase BZARG_RS01960 BZARG_RS04795
rhamnose LRA1: L-rhamnofuranose dehydrogenase BZARG_RS00770 BZARG_RS10915
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 rbsK: ribokinase
ribose rbsU: probable D-ribose transporter RbsU
serine snatA: L-serine transporter BZARG_RS05715
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase BZARG_RS00770 BZARG_RS10915
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 snatA: L-threonine transporter snatA BZARG_RS05715
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase BZARG_RS05430
thymidine nupC: thymidine permease NupC BZARG_RS08060
trehalose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
trehalose treF: trehalase
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase BZARG_RS12915 BZARG_RS01000
valine bch: 3-hydroxyisobutyryl-CoA hydrolase BZARG_RS10395 BZARG_RS02125
valine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit BZARG_RS01255 BZARG_RS02455
valine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component BZARG_RS02185 BZARG_RS08985
valine brnQ: L-valine:cation symporter BrnQ/BraZ/BraB BZARG_RS14230
valine mmsA: methylmalonate-semialdehyde dehydrogenase BZARG_RS04795 BZARG_RS01960
valine mmsB: 3-hydroxyisobutyrate dehydrogenase
valine pccA: propionyl-CoA carboxylase, alpha subunit BZARG_RS05675 BZARG_RS09580
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase BZARG_RS12640
xylose xylA: xylose isomerase
xylose xylB: xylulokinase
xylose xylT: D-xylose transporter

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