GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Desulfacinum hydrothermale DSM 13146

Found 138 low-confidence and 81 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
2-oxoglutarate Psest_0084: 2-oxoglutarate TRAP transporter, fused 4TM/12TM components B9A12_RS03675 B9A12_RS11345
2-oxoglutarate Psest_0085: 2-oxoglutarate TRAP transporter, solute receptor component B9A12_RS03685 B9A12_RS05495
4-hydroxybenzoate mhpD: 2-hydroxypentadienoate hydratase
4-hydroxybenzoate mhpE: 4-hydroxy-2-oxovalerate aldolase B9A12_RS09645
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
acetate satP: acetate/proton symporter satP B9A12_RS00520
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter
arginine rocE: L-arginine permease
asparagine aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) B9A12_RS06585 B9A12_RS14255
asparagine aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP B9A12_RS06580 B9A12_RS05110
asparagine aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) B9A12_RS06590
asparagine ans: asparaginase B9A12_RS15680
aspartate aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) B9A12_RS06585 B9A12_RS14255
aspartate aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP B9A12_RS06580 B9A12_RS05110
aspartate aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) B9A12_RS06590
cellobiose cbp: cellobiose phosphorylase
cellobiose cdt: cellobiose transporter cdt-1/cdt-2
cellobiose glk: glucokinase B9A12_RS09725
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component B9A12_RS06645 B9A12_RS06580
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 B9A12_RS06650 B9A12_RS14255
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 B9A12_RS05505 B9A12_RS05515
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component B9A12_RS05500
citrulline arcC: carbamate kinase B9A12_RS09075
D-alanine dadA: D-alanine dehydrogenase
D-alanine Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component B9A12_RS06595
D-alanine Pf6N2E2_5403: ABC transporter for D-Alanine, permease component 2 B9A12_RS06590
D-alanine Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component B9A12_RS06580 B9A12_RS05110
D-lactate D-LDH: D-lactate dehydrogenase B9A12_RS01310 B9A12_RS16105
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 B9A12_RS14410 B9A12_RS12145
deoxyinosine deoB: phosphopentomutase B9A12_RS14335 B9A12_RS02180
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine nupC: deoxyinosine:H+ symporter NupC B9A12_RS10760
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase B9A12_RS01145
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
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)) B9A12_RS14125 B9A12_RS02300
fructose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components
fucose fucA: L-fuculose-phosphate aldolase FucA B9A12_RS06170
fucose fucI: L-fucose isomerase FucI
fucose fucK: L-fuculose kinase FucK
fucose fucO: L-lactaldehyde reductase B9A12_RS14125 B9A12_RS14110
fucose fucP: L-fucose:H+ symporter FucP
fucose fucU: L-fucose mutarotase FucU
fumarate dctA: fumarate:H+ symporter DctA
galactose galE: UDP-glucose 4-epimerase B9A12_RS14325 B9A12_RS13160
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 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) B9A12_RS15595
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 B9A12_RS04125
glucuronate garR: tartronate semialdehyde reductase B9A12_RS09090 B9A12_RS07650
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate udh: D-glucuronate dehydrogenase B9A12_RS02675
glutamate aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) B9A12_RS06585 B9A12_RS14255
glutamate aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP B9A12_RS06580 B9A12_RS05110
glutamate aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) B9A12_RS06590
glutamate gdhA: glutamate dehydrogenase, NAD-dependent B9A12_RS09290
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric)
histidine aapM: L-histidine ABC transporter, permease component 2 (AapM) B9A12_RS06585 B9A12_RS10815
histidine aapP: L-histidine ABC transporter, ATPase component AapP B9A12_RS06580 B9A12_RS05110
histidine hutG: N-formiminoglutamate formiminohydrolase B9A12_RS07925
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase B9A12_RS12590 B9A12_RS01200
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase B9A12_RS10305 B9A12_RS12585
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase
isoleucine livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) B9A12_RS14635 B9A12_RS02910
isoleucine livM: L-isoleucine ABC transporter, permease component 2 (LivM/BraE) B9A12_RS14625 B9A12_RS00035
isoleucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit B9A12_RS08335
L-lactate SfMCT: L-lactate transporter SfMCT B9A12_RS00530
L-malate sdlC: L-malate:Na+ symporter SdlC
lactose galE: UDP-glucose 4-epimerase B9A12_RS14325 B9A12_RS13160
lactose galK: galactokinase (-1-phosphate forming)
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
lactose glk: glucokinase B9A12_RS09725
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit B9A12_RS08335
leucine liuC: 3-methylglutaconyl-CoA hydratase B9A12_RS11510 B9A12_RS12585
leucine liuE: hydroxymethylglutaryl-CoA lyase B9A12_RS01900
leucine livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) B9A12_RS14635 B9A12_RS02910
leucine livM: L-leucine ABC transporter, permease component 2 (LivM/BraE) B9A12_RS14625 B9A12_RS00035
leucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
lysine davA: 5-aminovaleramidase B9A12_RS06265
lysine davB: L-lysine 2-monooxygenase
lysine davD: glutarate semialdehyde dehydrogenase B9A12_RS10445 B9A12_RS14640
lysine davT: 5-aminovalerate aminotransferase B9A12_RS03895 B9A12_RS04090
lysine gcdH: glutaryl-CoA dehydrogenase B9A12_RS12590 B9A12_RS03700
lysine lysP: L-lysine:H+ symporter LysP
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
myoinositol iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase
myoinositol iolT: myo-inositol:H+ symporter
myoinositol mmsA: malonate-semialdehyde dehydrogenase B9A12_RS14640 B9A12_RS10445
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) B9A12_RS15595
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 B9A12_RS12585 B9A12_RS11510
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase B9A12_RS01110 B9A12_RS11510
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase B9A12_RS12580 B9A12_RS06945
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase B9A12_RS12580 B9A12_RS06945
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase B9A12_RS01110 B9A12_RS11510
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine livF: L-phenylalanine ABC transporter, ATPase component 1 (LivF) B9A12_RS02930 B9A12_RS14615
phenylalanine livH: L-phenylalanine ABC transporter, permease component 1 (LivH) B9A12_RS14630 B9A12_RS02915
phenylalanine livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK B9A12_RS14635 B9A12_RS00020
phenylalanine livM: L-phenylalanine ABC transporter, permease component 2 (LivM) B9A12_RS14625 B9A12_RS00035
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 B9A12_RS12585 B9A12_RS11510
phenylalanine paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase B9A12_RS01110 B9A12_RS11510
phenylalanine paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase B9A12_RS12580 B9A12_RS06945
phenylalanine paaJ2: 3-oxoadipyl-CoA thiolase B9A12_RS12580 B9A12_RS06945
phenylalanine paaZ1: oxepin-CoA hydrolase B9A12_RS01110 B9A12_RS11510
phenylalanine paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
proline aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) B9A12_RS06585 B9A12_RS14255
proline aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP B9A12_RS06580 B9A12_RS05110
proline aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) B9A12_RS06590
proline put1: proline dehydrogenase B9A12_RS14640 B9A12_RS08080
propionate pccA: propionyl-CoA carboxylase, alpha subunit B9A12_RS08335
propionate prpE: propionyl-CoA synthetase B9A12_RS01105 B9A12_RS03050
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabD: succinate semialdehyde dehydrogenase B9A12_RS10445 B9A12_RS14640
putrescine gabT: gamma-aminobutyrate transaminase B9A12_RS03895 B9A12_RS05520
putrescine patA: putrescine aminotransferase (PatA/SpuC) B9A12_RS05520 B9A12_RS04090
putrescine patD: gamma-aminobutyraldehyde dehydrogenase B9A12_RS10445 B9A12_RS14640
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate dctQ: pyruvate TRAP transporter, small permease component B9A12_RS04310
rhamnose fucO: L-lactaldehyde reductase B9A12_RS14125 B9A12_RS14110
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) B9A12_RS14635 B9A12_RS02910
serine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) B9A12_RS14630 B9A12_RS02915
serine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) B9A12_RS14625 B9A12_RS00035
serine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) B9A12_RS02925 B9A12_RS05165
serine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) B9A12_RS02930 B9A12_RS05170
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase B9A12_RS03625
succinate satP: succinate:H+ symporter SatP B9A12_RS00520
sucrose ams: sucrose hydrolase (invertase)
sucrose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components
threonine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) B9A12_RS14635 B9A12_RS02910
threonine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) B9A12_RS14630 B9A12_RS02915
threonine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) B9A12_RS14625 B9A12_RS00035
threonine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) B9A12_RS02925 B9A12_RS05165
threonine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) B9A12_RS02930 B9A12_RS05170
threonine gcvP: glycine cleavage system, P component (glycine decarboxylase) B9A12_RS15450 B9A12_RS15455
threonine gcvT: glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) B9A12_RS15440 B9A12_RS08090
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase B9A12_RS14335 B9A12_RS02180
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupG: thymidine permease NupG/XapB
trehalose glk: glucokinase B9A12_RS09725
trehalose PsTP: trehalose phosphorylase
trehalose TRET1: facilitated trehalose transporter Tret1
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine fahA: fumarylacetoacetate hydrolase
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase B9A12_RS12590 B9A12_RS01200
valine bch: 3-hydroxyisobutyryl-CoA hydrolase B9A12_RS16900 B9A12_RS11510
valine livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) B9A12_RS14635 B9A12_RS02910
valine livM: L-valine ABC transporter, permease component 2 (LivM/BraE) B9A12_RS14625 B9A12_RS00035
valine mmsA: methylmalonate-semialdehyde dehydrogenase B9A12_RS10445 B9A12_RS14640
valine mmsB: 3-hydroxyisobutyrate dehydrogenase B9A12_RS09090 B9A12_RS07650
valine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
valine pccA: propionyl-CoA carboxylase, alpha subunit B9A12_RS08335
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