GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Desulfovibrio oxyclinae DSM 11498

Found 169 low-confidence and 44 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
2-oxoglutarate kgtP: 2-oxoglutarate:H+ symporter KgtP B149_RS0115480
4-hydroxybenzoate adh: acetaldehyde dehydrogenase (not acylating) B149_RS0113400 B149_RS0108900
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
alanine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) B149_RS0104760 B149_RS0114955
alanine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) B149_RS0104755 B149_RS0114950
alanine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) B149_RS0104745 B149_RS0108680
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 B149_RS0114955 B149_RS0104760
arginine braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) B149_RS0104755 B149_RS0114950
arginine braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) B149_RS0104750 B149_RS0114945
arginine braF: ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) B149_RS0104745 B149_RS0114960
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 B149_RS0104145
citrate SLC13A5: citrate:Na+ symporter B149_RS0102470
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component B149_RS0102055 B149_RS0110340
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 B149_RS0102050 B149_RS0104105
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 B149_RS0104105 B149_RS0101890
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component B149_RS0110330 B149_RS0102045
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 B149_RS0103820 B149_RS0107810
D-serine cycA: D-serine:H+ symporter CycA
D-serine dsdA: D-serine ammonia-lyase
deoxyinosine adh: acetaldehyde dehydrogenase (not acylating) B149_RS0113400 B149_RS0108900
deoxyinosine deoB: phosphopentomutase B149_RS0108005
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
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 adh: acetaldehyde dehydrogenase (not acylating) B149_RS0113400 B149_RS0108900
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter
ethanol adh: acetaldehyde dehydrogenase (not acylating) B149_RS0113400 B149_RS0108900
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) B149_RS0101180 B149_RS0110305
fructose 1pfk: 1-phosphofructokinase
fructose fba: fructose 1,6-bisphosphate aldolase B149_RS0107855 B149_RS0103015
fructose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components
fucose aldA: lactaldehyde dehydrogenase B149_RS0113400 B149_RS0108900
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
galactose galE: UDP-glucose 4-epimerase B149_RS0106470 B149_RS0105880
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 B149_RS0102570
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)
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 B149_RS0113400 B149_RS0108900
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate kdgD: 5-dehydro-4-deoxyglucarate dehydratase B149_RS0102570
glucuronate udh: D-glucuronate dehydrogenase
glutamate dmeA: L-glutamate transporter DmeA B149_RS0114350
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric)
histidine Ac3H11_2554: ABC transporter for L-Histidine, permease component 2 B149_RS0110335 B149_RS0104105
histidine Ac3H11_2555: L-histidine ABC transporter, substrate-binding component 2 B149_RS0110330 B149_RS0104110
histidine Ac3H11_2562: L-histidine ABC transporter, substrate-binding component 1 B149_RS0103610
histidine hutG: N-formiminoglutamate formiminohydrolase B149_RS16365
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase
isoleucine dddA: 3-hydroxypropionate dehydrogenase B149_RS0113405
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase
isoleucine fadA: 2-methylacetoacetyl-CoA thiolase
isoleucine hpcD: 3-hydroxypropionyl-CoA dehydratase
isoleucine iolA: malonate semialdehyde dehydrogenase (CoA-acylating) B149_RS0113400 B149_RS0108900
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase B149_RS0114920
isoleucine livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) B149_RS0104760 B149_RS0114955
isoleucine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC B149_RS0100895
lactose galE: UDP-glucose 4-epimerase B149_RS0106470 B149_RS0105880
lactose galK: galactokinase (-1-phosphate forming)
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
lactose glk: glucokinase B149_RS0104145
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
leucine atoB: acetyl-CoA C-acetyltransferase
leucine liuA: isovaleryl-CoA dehydrogenase
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit B149_RS0111240 B149_RS0102080
leucine liuC: 3-methylglutaconyl-CoA hydratase
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit
leucine liuE: hydroxymethylglutaryl-CoA lyase B149_RS16860
leucine livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) B149_RS0104760 B149_RS0114955
leucine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC B149_RS0100895
lysine amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) B149_RS0113400
lysine hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase B149_RS0110790 B149_RS0115240
lysine lysN: 2-aminoadipate transaminase B149_RS0109030 B149_RS0115315
lysine lysP: L-lysine:H+ symporter LysP
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase B149_RS0107810
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 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 B149_RS0113400 B149_RS0108900
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 B149_RS0114920
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 atoB: acetyl-CoA C-acetyltransferase
phenylalanine fahA: fumarylacetoacetate hydrolase
phenylalanine hmgA: homogentisate dioxygenase
phenylalanine HPD: 4-hydroxyphenylpyruvate dioxygenase
phenylalanine livH: L-phenylalanine ABC transporter, permease component 1 (LivH) B149_RS0104755 B149_RS0114950
phenylalanine livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK B149_RS0104760 B149_RS0114955
phenylalanine maiA: maleylacetoacetate isomerase
phenylalanine PAH: phenylalanine 4-monooxygenase
phenylalanine PCBD: pterin-4-alpha-carbinoalamine dehydratase
phenylalanine QDPR: 6,7-dihydropteridine reductase
proline proW: proline ABC transporter, permease component ProW B149_RS0105520 B149_RS0110015
proline proX: proline ABC transporter, substrate-binding component ProX B149_RS0105515
proline put1: proline dehydrogenase
propionate dddA: 3-hydroxypropionate dehydrogenase B149_RS0113405
propionate hpcD: 3-hydroxypropionyl-CoA dehydratase
propionate iolA: malonate semialdehyde dehydrogenase (CoA-acylating) B149_RS0113400 B149_RS0108900
propionate lctP: propionate permease B149_RS0103815
putrescine gabD: succinate semialdehyde dehydrogenase B149_RS0113400 B149_RS0109050
putrescine gabT: gamma-aminobutyrate transaminase B149_RS0110790 B149_RS0115240
putrescine patA: putrescine aminotransferase (PatA/SpuC) B149_RS0115240 B149_RS0110790
putrescine patD: gamma-aminobutyraldehyde dehydrogenase B149_RS0113400 B149_RS0108900
pyruvate SLC5A8: sodium-coupled pyruvate transporter
rhamnose aldA: lactaldehyde dehydrogenase B149_RS0113400 B149_RS0108900
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) B149_RS0104760 B149_RS0114955
serine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) B149_RS0104755 B149_RS0114950
serine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) B149_RS0104745 B149_RS0108680
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase
sucrose scrK: fructokinase
sucrose SUS: sucrose synthase
sucrose sut: sucrose:proton symporter SUT/SUC
threonine adh: acetaldehyde dehydrogenase (not acylating) B149_RS0113400 B149_RS0108900
threonine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) B149_RS0104760 B149_RS0114955
threonine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) B149_RS0104755 B149_RS0114950
threonine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) B149_RS0104745 B149_RS0108680
threonine gcvP: glycine cleavage system, P component (glycine decarboxylase) B149_RS0110775 B149_RS0110780
thymidine adh: acetaldehyde dehydrogenase (not acylating) B149_RS0113400 B149_RS0108900
thymidine deoB: phosphopentomutase B149_RS0108005
thymidine nupG: thymidine permease NupG/XapB
trehalose glk: glucokinase B149_RS0104145
trehalose PsTP: trehalose phosphorylase
trehalose TRET1: facilitated trehalose transporter Tret1
tryptophan tnaA: tryptophanase
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 bch: 3-hydroxyisobutyryl-CoA hydrolase
valine dddA: 3-hydroxypropionate dehydrogenase B149_RS0113405
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase
valine hpcD: 3-hydroxypropionyl-CoA dehydratase
valine iolA: malonate semialdehyde dehydrogenase (CoA-acylating) B149_RS0113400 B149_RS0108900
valine livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) B149_RS0104760 B149_RS0114955
valine mmsA: methylmalonate-semialdehyde dehydrogenase B149_RS0113400 B149_RS0108900
valine mmsB: 3-hydroxyisobutyrate dehydrogenase B149_RS0109050
valine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC B149_RS0100895
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase B149_RS0110305
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.

Links

Downloads

Related tools

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