GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Desulfobulbus mediterraneus DSM 13871

Found 125 low-confidence and 77 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
4-hydroxybenzoate mhpD: 2-hydroxypentadienoate hydratase
4-hydroxybenzoate mhpE: 4-hydroxy-2-oxovalerate aldolase G494_RS0115910
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 G494_RS0103530
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 G494_RS24635 G494_RS0110185
arginine braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) G494_RS0110180 G494_RS0119640
arginine braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) G494_RS0110175 G494_RS0119635
arginine braF: ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) G494_RS0110170 G494_RS0119630
arginine braG: ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) G494_RS0110165 G494_RS0119625
arginine rocA: 1-pyrroline-5-carboxylate dehydrogenase G494_RS0119655 G494_RS0112240
arginine rocD: ornithine aminotransferase G494_RS0108610 G494_RS0103960
asparagine ans: asparaginase G494_RS23895 G494_RS0120045
asparagine dauA: dicarboxylic acid transporter DauA G494_RS22000
aspartate dauA: dicarboxylic acid transporter DauA G494_RS22000
cellobiose cbp: cellobiose phosphorylase
cellobiose cdt: cellobiose transporter cdt-1/cdt-2
citrate SLC13A5: citrate:Na+ symporter G494_RS0112220 G494_RS0114330
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component G494_RS0108320 G494_RS0118635
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 G494_RS0118640 G494_RS0108315
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 G494_RS0112685
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline arcC: carbamate kinase
citrulline rocA: 1-pyrroline-5-carboxylate dehydrogenase G494_RS0119655 G494_RS0112240
citrulline rocD: ornithine aminotransferase G494_RS0108610 G494_RS0103960
D-alanine AZOBR_RS08240: D-alanine ABC transporter, permease component 2 G494_RS0110175 G494_RS0119635
D-alanine AZOBR_RS08245: D-alanine ABC transporter, ATPase component 1 G494_RS0110170 G494_RS0119630
D-alanine AZOBR_RS08250: D-alanine ABC transporter, ATPase component 2 G494_RS0110165 G494_RS0119625
D-alanine AZOBR_RS08260: D-alanine ABC transporter, substrate-binding component G494_RS24635 G494_RS0110185
D-alanine dadA: D-alanine dehydrogenase
D-serine cycA: D-serine:H+ symporter CycA
D-serine dsdA: D-serine ammonia-lyase G494_RS0110775 G494_RS0112930
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter
fructose Slc2a5: fructose:H+ symporter
fucose fucA: L-fuculose-phosphate aldolase FucA G494_RS0100585
fucose fucI: L-fucose isomerase FucI
fucose fucK: L-fuculose kinase FucK
fucose fucO: L-lactaldehyde reductase G494_RS0110865 G494_RS0117660
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 G494_RS0102545
galacturonate dopDH: 2,5-dioxopentanonate dehydrogenase G494_RS0112240 G494_RS0120720
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 gntK: D-gluconate kinase
gluconate gntT: gluconate:H+ symporter GntT
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) G494_RS0109685
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) G494_RS0111590
glucose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) G494_RS0109685
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate garL: 5-dehydro-4-deoxy-D-glucarate aldolase G494_RS0108640
glucuronate garR: tartronate semialdehyde reductase G494_RS0116595 G494_RS0107880
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate udh: D-glucuronate dehydrogenase
glycerol glpF: glycerol facilitator glpF
histidine braC: ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC G494_RS24635 G494_RS0110185
histidine braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) G494_RS0110180 G494_RS0119640
histidine braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) G494_RS0110175 G494_RS0119635
histidine braF: ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) G494_RS0110170 G494_RS0119630
histidine braG: ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) G494_RS0110165 G494_RS0119625
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase G494_RS0109105 G494_RS0107500
isoleucine bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit G494_RS0107605
isoleucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component G494_RS0104020 G494_RS0107600
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase G494_RS0106850 G494_RS0116145
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase G494_RS0109090 G494_RS0103555
isoleucine livH: L-isoleucine ABC transporter, permease component 1 (LivH/BraD) G494_RS0110180 G494_RS0119640
isoleucine livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) G494_RS0110185 G494_RS24635
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit G494_RS0107515
lactose galK: galactokinase (-1-phosphate forming)
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase G494_RS0102545
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
leucine bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit G494_RS0107605
leucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component G494_RS0104020 G494_RS0107600
leucine liuE: hydroxymethylglutaryl-CoA lyase
leucine livH: L-leucine ABC transporter, permease component 1 (LivH/BraD) G494_RS0110180 G494_RS0119640
leucine livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) G494_RS0110185 G494_RS24635
lysine amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) G494_RS0111845 G494_RS0112240
lysine hglS: D-2-hydroxyglutarate synthase
lysine lysN: 2-aminoadipate transaminase G494_RS0100225 G494_RS0117930
lysine lysP: L-lysine:H+ symporter LysP
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase G494_RS0101925 G494_RS0102495
maltose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) G494_RS0109685
maltose susB: alpha-glucosidase (maltase)
mannitol mt2d: mannitol 2-dehydrogenase G494_RS25080 G494_RS0103555
mannitol PLT5: polyol transporter PLT5
mannose manA: mannose-6-phosphate isomerase G494_RS0120230
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
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) G494_RS0111590
NAG nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components G494_RS0109685
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 G494_RS0116145 G494_RS0115915
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase G494_RS0116145 G494_RS0115915
phenylacetate paaH: 3-hydroxyadipyl-CoA dehydrogenase G494_RS0106850 G494_RS0107495
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase G494_RS0107490 G494_RS22310
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase G494_RS0107490 G494_RS22310
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase G494_RS0115915
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine livF: L-phenylalanine ABC transporter, ATPase component 1 (LivF) G494_RS0106710 G494_RS0110165
phenylalanine livH: L-phenylalanine ABC transporter, permease component 1 (LivH) G494_RS0110180 G494_RS0119640
phenylalanine livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK G494_RS0110185 G494_RS24635
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 G494_RS0116145 G494_RS0115915
phenylalanine paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase G494_RS0116145 G494_RS0115915
phenylalanine paaH: 3-hydroxyadipyl-CoA dehydrogenase G494_RS0106850 G494_RS0107495
phenylalanine paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase G494_RS0107490 G494_RS22310
phenylalanine paaJ2: 3-oxoadipyl-CoA thiolase G494_RS0107490 G494_RS22310
phenylalanine paaZ1: oxepin-CoA hydrolase G494_RS0115915
phenylalanine paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
proline proW: proline ABC transporter, permease component ProW G494_RS0105485
proline put1: proline dehydrogenase G494_RS0119655
proline putA: L-glutamate 5-semialdeyde dehydrogenase G494_RS0119655 G494_RS0112240
propionate pccA: propionyl-CoA carboxylase, alpha subunit G494_RS0107515
putrescine gabT: gamma-aminobutyrate transaminase G494_RS0112760 G494_RS0103960
putrescine patA: putrescine aminotransferase (PatA/SpuC) G494_RS0112760 G494_RS0103960
putrescine patD: gamma-aminobutyraldehyde dehydrogenase G494_RS0112240 G494_RS0120720
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate dctP: pyruvate TRAP transporter, substrate-binding component G494_RS0101975 G494_RS0115725
pyruvate dctQ: pyruvate TRAP transporter, small permease component G494_RS23925 G494_RS0101625
rhamnose fucO: L-lactaldehyde reductase G494_RS0110865 G494_RS0117660
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) G494_RS0110185 G494_RS0112100
serine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) G494_RS0110180 G494_RS0119640
serine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) G494_RS0110170 G494_RS0119630
serine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) G494_RS0110165 G494_RS0106710
sorbitol sdh: sorbitol dehydrogenase G494_RS0113960 G494_RS0109090
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2
sucrose sut: sucrose:proton symporter SUT/SUC
threonine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) G494_RS0110185 G494_RS0112100
threonine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) G494_RS0110180 G494_RS0119640
threonine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) G494_RS0110170 G494_RS0119630
threonine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) G494_RS0110165 G494_RS0106710
threonine gcvP: glycine cleavage system, P component (glycine decarboxylase) G494_RS0108195 G494_RS0108190
threonine gcvT: glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) G494_RS0108205
thymidine nupG: thymidine permease NupG/XapB
trehalose treB: trehalose PTS system, EII-BC components TreB
trehalose treC: trehalose-6-phosphate hydrolase
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine Ac3H11_1692: L-tyrosine ABC transporter, ATPase component 2 G494_RS0119625 G494_RS0106710
tyrosine Ac3H11_1694: L-tyrosine ABC transporter, permease component 2 G494_RS0110175 G494_RS0119635
tyrosine Ac3H11_1695: L-tyrosine ABC transporter, permease component 1 G494_RS0110180 G494_RS0119640
tyrosine Ac3H11_2396: L-tyrosine ABC transporter, substrate-binding component component G494_RS24635
tyrosine fahA: fumarylacetoacetate hydrolase
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase G494_RS0109105 G494_RS0107500
valine bch: 3-hydroxyisobutyryl-CoA hydrolase G494_RS0116145
valine bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit G494_RS0107605
valine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component G494_RS0104020 G494_RS0107600
valine livH: L-valine ABC transporter, permease component 1 (LivH/BraD) G494_RS0110180 G494_RS0119640
valine livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) G494_RS0110185 G494_RS24635
valine mmsB: 3-hydroxyisobutyrate dehydrogenase G494_RS0116595 G494_RS0107880
valine pccA: propionyl-CoA carboxylase, alpha subunit G494_RS0107515
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase
xylose xylA: xylose isomerase
xylose xylB: xylulokinase
xylose xylF: ABC transporter for xylose, substrate binding component xylF G494_RS22375
xylose xylG: ABC transporter for xylose, ATP-binding component xylG G494_RS0107325 G494_RS0113385

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