GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Desulfobacter vibrioformis DSM 8776

Found 159 low-confidence and 48 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 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 cycA: L-alanine symporter CycA
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase Q366_RS17895
arabinose araE: L-arabinose:H+ symporter
arginine rocE: L-arginine permease
asparagine ans: asparaginase
asparagine glt: aspartate:proton symporter Glt
aspartate glt: aspartate:proton symporter Glt
cellobiose cbp: cellobiose phosphorylase
cellobiose cdt: cellobiose transporter cdt-1/cdt-2
citrate SLC13A5: citrate:Na+ symporter
citrulline arcC: carbamate kinase
citrulline PS417_17590: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline PS417_17595: ABC transporter for L-Citrulline, permease component 1
citrulline PS417_17600: ABC transporter for L-Citrulline, permease component 2
citrulline PS417_17605: ABC transporter for L-Citrulline, ATPase component Q366_RS06940 Q366_RS06100
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase Q366_RS13490 Q366_RS12750
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
deoxyinosine deoB: phosphopentomutase
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine deoD: deoxyinosine phosphorylase Q366_RS07185 Q366_RS03910
deoxyinosine nupC: deoxyinosine:H+ symporter NupC Q366_RS09940
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase Q366_RS02280
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate garK: glycerate 2-kinase Q366_RS03210
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) Q366_RS03850 Q366_RS09470
fructose Slc2a5: fructose:H+ symporter
fucose aldA: lactaldehyde dehydrogenase Q366_RS10385 Q366_RS17050
fucose fucA: L-fuculose-phosphate aldolase FucA Q366_RS17895
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 dctA: fumarate:H+ symporter DctA
galactose galK: galactokinase (-1-phosphate forming)
galactose galP: galactose:H+ symporter GalP
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
galacturonate dopDH: 2,5-dioxopentanonate dehydrogenase Q366_RS13505 Q366_RS17050
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate gci: D-galactarolactone cycloisomerase
galacturonate gli: D-galactarolactone isomerase
galacturonate kdgD: 5-dehydro-4-deoxyglucarate dehydratase
galacturonate udh: D-galacturonate dehydrogenase
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)
glucose MFS-glucose: glucose transporter, MFS superfamily
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate dopDH: 2,5-dioxopentanonate dehydrogenase Q366_RS13505 Q366_RS17050
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
glutamate gltS: L-glutamate:Na+ symporter GltS
glycerol dhaK': dihydroxyacetone kinase, ATP dependent (monomeric)
glycerol glpF: glycerol facilitator glpF
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
histidine permease: L-histidine permease
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase Q366_RS11450 Q366_RS06780
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase Q366_RS18135 Q366_RS07650
isoleucine epi: methylmalonyl-CoA epimerase
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase Q366_RS09470 Q366_RS02355
isoleucine livH: L-isoleucine ABC transporter, permease component 1 (LivH/BraD) Q366_RS13525 Q366_RS04655
isoleucine livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) Q366_RS04660
isoleucine livM: L-isoleucine ABC transporter, permease component 2 (LivM/BraE) Q366_RS04650 Q366_RS13530
isoleucine mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit Q366_RS05475
isoleucine pccB: propionyl-CoA carboxylase, beta subunit Q366_RS09820
isoleucine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC
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 lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
leucine liuA: isovaleryl-CoA dehydrogenase Q366_RS11450 Q366_RS08980
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit Q366_RS05475
leucine liuC: 3-methylglutaconyl-CoA hydratase Q366_RS18135 Q366_RS07650
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit Q366_RS09820
leucine liuE: hydroxymethylglutaryl-CoA lyase
leucine livH: L-leucine ABC transporter, permease component 1 (LivH/BraD) Q366_RS13525 Q366_RS04655
leucine livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) Q366_RS04660
leucine livM: L-leucine ABC transporter, permease component 2 (LivM/BraE) Q366_RS04650 Q366_RS13530
leucine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC
lysine cadA: lysine decarboxylase
lysine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase Q366_RS18135 Q366_RS13010
lysine gcdG: succinyl-CoA:glutarate CoA-transferase
lysine gcdH: glutaryl-CoA dehydrogenase Q366_RS06780 Q366_RS11450
lysine lysP: L-lysine:H+ symporter LysP
lysine patA: cadaverine aminotransferase Q366_RS19250 Q366_RS00665
maltose malA: 6-phospho-alphaglucosidase
maltose malEIICBA: maltose phosphotransferase system, EII-CBA components
mannitol mt2d: mannitol 2-dehydrogenase Q366_RS02280 Q366_RS02355
mannitol PLT5: polyol transporter PLT5
mannose manA: mannose-6-phosphate isomerase Q366_RS11055
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 Q366_RS17050 Q366_RS13505
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 Q366_RS18135 Q366_RS07650
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase Q366_RS18135 Q366_RS07650
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase Q366_RS00870 Q366_RS02505
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase Q366_RS02505 Q366_RS00870
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase Q366_RS07650 Q366_RS18135
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
phenylalanine paaA: phenylacetyl-CoA 1,2-epoxidase, subunit A
phenylalanine paaB: phenylacetyl-CoA 1,2-epoxidase, subunit B
phenylalanine paaC: phenylacetyl-CoA 1,2-epoxidase, subunit C
phenylalanine paaE: phenylacetyl-CoA 1,2-epoxidase, subunit E
phenylalanine paaF: 2,3-dehydroadipyl-CoA hydratase Q366_RS18135 Q366_RS07650
phenylalanine paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase Q366_RS18135 Q366_RS07650
phenylalanine paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase Q366_RS00870 Q366_RS02505
phenylalanine paaJ2: 3-oxoadipyl-CoA thiolase Q366_RS02505 Q366_RS00870
phenylalanine paaZ1: oxepin-CoA hydrolase Q366_RS07650 Q366_RS18135
phenylalanine paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
proline proW: proline ABC transporter, permease component ProW Q366_RS03740
proline put1: proline dehydrogenase Q366_RS04815
propionate epi: methylmalonyl-CoA epimerase
propionate mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
propionate pccA: propionyl-CoA carboxylase, alpha subunit Q366_RS05475
propionate pccB: propionyl-CoA carboxylase, beta subunit Q366_RS09820
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabT: gamma-aminobutyrate transaminase Q366_RS07000 Q366_RS13500
putrescine patA: putrescine aminotransferase (PatA/SpuC) Q366_RS07000 Q366_RS19250
pyruvate dctM: pyruvate TRAP transporter, large permease component Q366_RS17980 Q366_RS12825
pyruvate dctP: pyruvate TRAP transporter, substrate-binding component Q366_RS17970
pyruvate dctQ: pyruvate TRAP transporter, small permease component Q366_RS17975
rhamnose LRA1: L-rhamnofuranose dehydrogenase Q366_RS09470 Q366_RS02280
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase
rhamnose LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase Q366_RS02355
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsK: ribokinase
ribose rbsU: probable D-ribose transporter RbsU
serine sdaB: L-serine ammonia-lyase
serine serP: L-serine permease SerP
sorbitol sdh: sorbitol dehydrogenase Q366_RS02280 Q366_RS09470
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2
sucrose ams: sucrose hydrolase (invertase) Q366_RS08470
sucrose sut: sucrose:proton symporter SUT/SUC
threonine gcvP: glycine cleavage system, P component (glycine decarboxylase) Q366_RS19510 Q366_RS19515
threonine gcvT: glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) Q366_RS19525
threonine ltaE: L-threonine aldolase Q366_RS19665
threonine tdcC: L-threonine:H+ symporter TdcC
thymidine deoA: thymidine phosphorylase DeoA Q366_RS01905
thymidine deoB: phosphopentomutase
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupC: thymidine permease NupC Q366_RS09940
trehalose PsTP: trehalose phosphorylase
trehalose TRET1: facilitated trehalose transporter Tret1
tryptophan tnaA: tryptophanase
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine fahA: fumarylacetoacetate hydrolase Q366_RS17640
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase Q366_RS11450 Q366_RS06780
valine bch: 3-hydroxyisobutyryl-CoA hydrolase Q366_RS18135
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase Q366_RS18135 Q366_RS13010
valine epi: methylmalonyl-CoA epimerase
valine livH: L-valine ABC transporter, permease component 1 (LivH/BraD) Q366_RS13525 Q366_RS04655
valine livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) Q366_RS04660
valine livM: L-valine ABC transporter, permease component 2 (LivM/BraE) Q366_RS04650 Q366_RS13530
valine mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
valine mmsA: methylmalonate-semialdehyde dehydrogenase Q366_RS17050 Q366_RS13505
valine mmsB: 3-hydroxyisobutyrate dehydrogenase
valine pccA: propionyl-CoA carboxylase, alpha subunit Q366_RS05475
valine pccB: propionyl-CoA carboxylase, beta subunit Q366_RS09820
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
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