GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Desulfarculus baarsii DSM 2075

Found 156 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 mhpE: 4-hydroxy-2-oxovalerate aldolase DEBA_RS04730
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 snatA: L-alanine symporter SnatA DEBA_RS14805
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter
arginine gabD: succinate semialdehyde dehydrogenase DEBA_RS16895
arginine gabT: gamma-aminobutyrate transaminase DEBA_RS03020 DEBA_RS06780
arginine patA: putrescine aminotransferase (PatA/SpuC) DEBA_RS09405 DEBA_RS03020
arginine patD: gamma-aminobutyraldehyde dehydrogenase DEBA_RS16895
arginine rocE: L-arginine permease
asparagine ans: asparaginase DEBA_RS15730
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 DEBA_RS01980
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 DEBA_RS18365 DEBA_RS01005
citrulline rocA: 1-pyrroline-5-carboxylate dehydrogenase DEBA_RS16895
citrulline rocD: ornithine aminotransferase DEBA_RS03020 DEBA_RS06780
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase DEBA_RS07695 DEBA_RS03615
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 DEBA_RS00725
deoxyinosine deoB: phosphopentomutase DEBA_RS13420 DEBA_RS03840
deoxyinosine nupC: deoxyinosine:H+ symporter NupC DEBA_RS08085
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase DEBA_RS00595 DEBA_RS05555
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribose deoK: deoxyribokinase DEBA_RS09665
deoxyribose deoP: deoxyribose transporter
fructose scrK: fructokinase
fructose Slc2a5: fructose:H+ symporter
fucose aldA: lactaldehyde dehydrogenase DEBA_RS16895
fucose fucA: L-fuculose-phosphate aldolase FucA DEBA_RS17280
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 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 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) DEBA_RS01435
glucose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
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
glucuronate garR: tartronate semialdehyde reductase
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate udh: D-glucuronate dehydrogenase DEBA_RS00720
glutamate gdhA: glutamate dehydrogenase, NAD-dependent
glutamate gltS: L-glutamate:Na+ symporter GltS
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric) DEBA_RS15050 DEBA_RS07545
glycerol glpF: glycerol facilitator glpF
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
histidine permease: L-histidine permease
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase DEBA_RS06410 DEBA_RS09720
isoleucine livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) DEBA_RS06500
isoleucine livM: L-isoleucine ABC transporter, permease component 2 (LivM/BraE) DEBA_RS08565 DEBA_RS06510
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit DEBA_RS16260
isoleucine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC DEBA_RS09755
L-lactate L-LDH: L-lactate dehydrogenase DEBA_RS06825
L-lactate SfMCT: L-lactate transporter SfMCT DEBA_RS10590 DEBA_RS11300
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 DEBA_RS01980
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit DEBA_RS16260
leucine liuC: 3-methylglutaconyl-CoA hydratase DEBA_RS06445 DEBA_RS05560
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit DEBA_RS16255 DEBA_RS04420
leucine liuE: hydroxymethylglutaryl-CoA lyase DEBA_RS02165
leucine livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) DEBA_RS06500
leucine livM: L-leucine ABC transporter, permease component 2 (LivM/BraE) DEBA_RS08565 DEBA_RS06510
leucine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC DEBA_RS09755
lysine amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd)
lysine hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase DEBA_RS09405
lysine lysN: 2-aminoadipate transaminase DEBA_RS09890 DEBA_RS09405
lysine lysP: L-lysine:H+ symporter LysP
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase DEBA_RS07695
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 DEBA_RS10490 DEBA_RS18960
myoinositol iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase
myoinositol iolT: myo-inositol:H+ symporter
myoinositol mmsA: malonate-semialdehyde dehydrogenase DEBA_RS16895
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) DEBA_RS01435
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 DEBA_RS06445 DEBA_RS12230
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase DEBA_RS03345 DEBA_RS06445
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase DEBA_RS12235 DEBA_RS09300
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase DEBA_RS12235 DEBA_RS09300
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase DEBA_RS14405 DEBA_RS03345
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine iorB: phenylpyruvate:ferredoxin oxidoreductase, IorB subunit DEBA_RS08770 DEBA_RS04440
phenylalanine livH: L-phenylalanine ABC transporter, permease component 1 (LivH) DEBA_RS15715 DEBA_RS06505
phenylalanine livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK
phenylalanine livM: L-phenylalanine ABC transporter, permease component 2 (LivM) DEBA_RS08565 DEBA_RS15710
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 DEBA_RS06445 DEBA_RS12230
phenylalanine paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase DEBA_RS03345 DEBA_RS06445
phenylalanine paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase DEBA_RS12235 DEBA_RS09300
phenylalanine paaJ2: 3-oxoadipyl-CoA thiolase DEBA_RS12235 DEBA_RS09300
phenylalanine paaZ1: oxepin-CoA hydrolase DEBA_RS14405 DEBA_RS03345
phenylalanine paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
proline proY: proline:H+ symporter
proline put1: proline dehydrogenase
proline putA: L-glutamate 5-semialdeyde dehydrogenase DEBA_RS16895
propionate pccA: propionyl-CoA carboxylase, alpha subunit DEBA_RS16260
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabD: succinate semialdehyde dehydrogenase DEBA_RS16895
putrescine gabT: gamma-aminobutyrate transaminase DEBA_RS03020 DEBA_RS06780
putrescine patA: putrescine aminotransferase (PatA/SpuC) DEBA_RS09405 DEBA_RS03020
putrescine patD: gamma-aminobutyraldehyde dehydrogenase DEBA_RS16895
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate SLC5A8: sodium-coupled pyruvate transporter
rhamnose aldA: lactaldehyde dehydrogenase DEBA_RS16895
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 DEBA_RS09665
ribose rbsU: probable D-ribose transporter RbsU
serine sdaB: L-serine ammonia-lyase DEBA_RS00725
serine snatA: L-serine transporter DEBA_RS14805
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase DEBA_RS14860 DEBA_RS11930
succinate sdc: succinate:Na+ symporter Sdc
sucrose ams: sucrose hydrolase (invertase)
sucrose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
threonine gcvP: glycine cleavage system, P component (glycine decarboxylase)
threonine gcvT: glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase)
threonine ltaE: L-threonine aldolase DEBA_RS15345
threonine snatA: L-threonine transporter snatA DEBA_RS14805
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase DEBA_RS13420 DEBA_RS03840
thymidine nupC: thymidine permease NupC DEBA_RS08085
trehalose glk: glucokinase DEBA_RS01980
trehalose PsTP: trehalose phosphorylase
trehalose TRET1: facilitated trehalose transporter Tret1
tryptophan tnaA: tryptophanase
tryptophan tnaT: tryptophan:Na+ symporter TnaT DEBA_RS00605
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine fahA: fumarylacetoacetate hydrolase DEBA_RS09360
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase DEBA_RS06410 DEBA_RS09720
valine bch: 3-hydroxyisobutyryl-CoA hydrolase DEBA_RS06445 DEBA_RS15115
valine livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) DEBA_RS06500
valine livM: L-valine ABC transporter, permease component 2 (LivM/BraE) DEBA_RS08565 DEBA_RS06510
valine mmsA: methylmalonate-semialdehyde dehydrogenase DEBA_RS16895
valine mmsB: 3-hydroxyisobutyrate dehydrogenase
valine pccA: propionyl-CoA carboxylase, alpha subunit DEBA_RS16260
valine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC DEBA_RS09755
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