GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Desulfogranum mediterraneum 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 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