GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Maridesulfovibrio zosterae DSM 11974

Found 145 low-confidence and 62 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 H589_RS0110555 H589_RS0111930
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
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase H589_RS0106750
arabinose araE: L-arabinose:H+ symporter H589_RS0105145
arginine rocE: L-arginine permease
arginine rocF: arginase H589_RS0117030
asparagine aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) H589_RS0105870 H589_RS0100760
asparagine aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP H589_RS0105875 H589_RS0112205
asparagine aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) H589_RS0105865
asparagine ans: asparaginase H589_RS0118680
aspartate aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) H589_RS0105870 H589_RS0100760
aspartate aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP H589_RS0105875 H589_RS0112205
aspartate aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) H589_RS0105865
cellobiose bgl: cellobiase
cellobiose glk: glucokinase H589_RS0113290
citrate cit1: citrate:H+ symporter Cit1 H589_RS0108870
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component H589_RS0110275 H589_RS0118135
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 H589_RS0118130 H589_RS0115925
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 H589_RS0105870
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component H589_RS0100435 H589_RS0115910
citrulline arcC: carbamate kinase
D-alanine AZOBR_RS08235: D-alanine ABC transporter, permease component 1 H589_RS0112345 H589_RS0101630
D-alanine AZOBR_RS08240: D-alanine ABC transporter, permease component 2 H589_RS0112350 H589_RS0101625
D-alanine AZOBR_RS08245: D-alanine ABC transporter, ATPase component 1 H589_RS0112355 H589_RS0101640
D-alanine AZOBR_RS08250: D-alanine ABC transporter, ATPase component 2 H589_RS0112360 H589_RS0101620
D-alanine AZOBR_RS08260: D-alanine ABC transporter, substrate-binding component H589_RS0101635 H589_RS0112340
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase H589_RS0110950 H589_RS0105840
D-serine cycA: D-serine:H+ symporter CycA
D-serine dsdA: D-serine ammonia-lyase
deoxyinosine deoB: phosphopentomutase
deoxyinosine nupC: deoxyinosine:H+ symporter NupC H589_RS0118000
deoxyribonate atoB: acetyl-CoA C-acetyltransferase
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter H589_RS19655
deoxyribonate garK: glycerate 2-kinase H589_RS0102230
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoK: deoxyribokinase H589_RS0116170
deoxyribose deoP: deoxyribose transporter
fucose fucA: L-fuculose-phosphate aldolase FucA H589_RS0106750
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 H589_RS0103695 H589_RS0111125
galactose galK: galactokinase (-1-phosphate forming)
galactose galP: galactose:H+ symporter GalP H589_RS0105145
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 gnd: 6-phosphogluconate dehydrogenase, decarboxylating
gluconate gntA: gluconate TRAP transporter, small permease component H589_RS0109225
gluconate gntB: gluconate TRAP transporter, large permease component H589_RS0109230 H589_RS0110060
gluconate gntC: gluconate TRAP transporter, periplasmic solute-binding component H589_RS0113685 H589_RS0109220
gluconate gntK: D-gluconate kinase
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE)
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) H589_RS0103925
glucose glk: glucokinase H589_RS0113290
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate garK: glycerate 2-kinase H589_RS0102230
glucuronate garL: 5-dehydro-4-deoxy-D-glucarate aldolase H589_RS0110555
glucuronate garR: tartronate semialdehyde reductase H589_RS0102830
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate udh: D-glucuronate dehydrogenase
glutamate aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) H589_RS0105870 H589_RS0100760
glutamate aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP H589_RS0105875 H589_RS0112205
glutamate aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) H589_RS0105865
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric) H589_RS0117805
histidine aapM: L-histidine ABC transporter, permease component 2 (AapM) H589_RS0105870 H589_RS0100760
histidine aapP: L-histidine ABC transporter, ATPase component AapP H589_RS0105875 H589_RS0112205
histidine aapQ: L-histidine ABC transporter, permease component 1 (AapQ) H589_RS0105865 H589_RS0115925
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
isoleucine dddA: 3-hydroxypropionate dehydrogenase
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) H589_RS0107295
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase H589_RS0117160 H589_RS0116820
isoleucine livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) H589_RS0112340 H589_RS0101635
isoleucine pco: propanyl-CoA oxidase H589_RS0100550
isoleucine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC
lactose galE: UDP-glucose 4-epimerase H589_RS0103695 H589_RS0111125
lactose galK: galactokinase (-1-phosphate forming)
lactose glk: glucokinase H589_RS0113290
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 H589_RS0114155 H589_RS0104280
leucine liuC: 3-methylglutaconyl-CoA hydratase
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit
leucine liuE: hydroxymethylglutaryl-CoA lyase
leucine livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) H589_RS0112340 H589_RS0101635
leucine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC
lysine davD: glutarate semialdehyde dehydrogenase H589_RS0109990 H589_RS0118155
lysine glaH: glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lysine lhgD: L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) H589_RS0100555
lysine lysP: L-lysine:H+ symporter LysP
lysine patA: cadaverine aminotransferase H589_RS0100395 H589_RS0118050
lysine patD: 5-aminopentanal dehydrogenase H589_RS0109990 H589_RS0102680
maltose glk: glucokinase H589_RS0113290
maltose susB: alpha-glucosidase (maltase) H589_RS0102155 H589_RS0112520
mannitol mt2d: mannitol 2-dehydrogenase H589_RS0110660 H589_RS0108180
mannitol PLT5: polyol transporter PLT5
mannitol scrK: fructokinase H589_RS0116170
mannose manA: mannose-6-phosphate isomerase H589_RS0116375
mannose manP: mannose PTS system, EII-CBA components H589_RS0115575
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 H589_RS0115820
myoinositol iolT: myo-inositol:H+ symporter H589_RS0105145
myoinositol mmsA: malonate-semialdehyde dehydrogenase H589_RS0107295
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) H589_RS0103925
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 H589_RS0116710
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 H589_RS0107120
phenylalanine hmgA: homogentisate dioxygenase
phenylalanine HPD: 4-hydroxyphenylpyruvate dioxygenase
phenylalanine livH: L-phenylalanine ABC transporter, permease component 1 (LivH) H589_RS0112345 H589_RS0101630
phenylalanine livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK H589_RS0112340 H589_RS0101635
phenylalanine maiA: maleylacetoacetate isomerase
phenylalanine PAH: phenylalanine 4-monooxygenase
phenylalanine PCBD: pterin-4-alpha-carbinoalamine dehydratase
phenylalanine QDPR: 6,7-dihydropteridine reductase
proline put1: proline dehydrogenase H589_RS0114955 H589_RS0107295
propionate dddA: 3-hydroxypropionate dehydrogenase
propionate hpcD: 3-hydroxypropionyl-CoA dehydratase
propionate iolA: malonate semialdehyde dehydrogenase (CoA-acylating) H589_RS0107295
propionate pco: propanyl-CoA oxidase H589_RS0100550
propionate putP: propionate transporter; proline:Na+ symporter H589_RS0113975
putrescine gabT: gamma-aminobutyrate transaminase H589_RS0118185 H589_RS0104130
putrescine patA: putrescine aminotransferase (PatA/SpuC) H589_RS0100395 H589_RS0118050
putrescine patD: gamma-aminobutyraldehyde dehydrogenase H589_RS0109990 H589_RS0118155
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate SLC5A8: sodium-coupled pyruvate transporter
rhamnose LRA1: L-rhamnofuranose dehydrogenase H589_RS0116820 H589_RS0116710
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsK: ribokinase H589_RS0116170
ribose rbsU: probable D-ribose transporter RbsU
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase H589_RS0116710
sucrose ams: sucrose hydrolase (invertase)
threonine gcvP: glycine cleavage system, P component (glycine decarboxylase) H589_RS0105190 H589_RS0105195
threonine lpd: dihydrolipoyl dehydrogenase H589_RS0105200 H589_RS0113295
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase
thymidine nupC: thymidine permease NupC H589_RS0118000
trehalose glk: glucokinase H589_RS0113290
trehalose treF: trehalase
tryptophan tnaA: tryptophanase
tyrosine Ac3H11_1692: L-tyrosine ABC transporter, ATPase component 2 H589_RS0101620 H589_RS0112360
tyrosine Ac3H11_1694: L-tyrosine ABC transporter, permease component 2 H589_RS0112350 H589_RS0101625
tyrosine Ac3H11_1695: L-tyrosine ABC transporter, permease component 1 H589_RS0101630 H589_RS0112345
tyrosine Ac3H11_2396: L-tyrosine ABC transporter, substrate-binding component component H589_RS0101635
tyrosine atoB: acetyl-CoA C-acetyltransferase
tyrosine fahA: fumarylacetoacetate hydrolase H589_RS0107120
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
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase
valine hpcD: 3-hydroxypropionyl-CoA dehydratase
valine iolA: malonate semialdehyde dehydrogenase (CoA-acylating) H589_RS0107295
valine livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) H589_RS0112340 H589_RS0101635
valine mmsA: methylmalonate-semialdehyde dehydrogenase H589_RS0107295
valine mmsB: 3-hydroxyisobutyrate dehydrogenase H589_RS0102830
valine pco: propanyl-CoA oxidase H589_RS0100550
valine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC
xylitol fruI: xylitol PTS, enzyme IIABC (FruI) H589_RS0115575
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase H589_RS0109350
xylose xylA: xylose isomerase
xylose xylB: xylulokinase
xylose xylT: D-xylose transporter H589_RS0105145

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