GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Desulfacinum infernum DSM 9756

Found 132 low-confidence and 88 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 BUB04_RS10335 BUB04_RS06490
2-oxoglutarate Psest_0085: 2-oxoglutarate TRAP transporter, solute receptor component BUB04_RS05255 BUB04_RS06485
4-hydroxybenzoate mhpD: 2-hydroxypentadienoate hydratase
4-hydroxybenzoate mhpE: 4-hydroxy-2-oxovalerate aldolase BUB04_RS14925 BUB04_RS10320
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 actP: cation/acetate symporter ActP
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) BUB04_RS05925 BUB04_RS13795
asparagine aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP BUB04_RS05930 BUB04_RS14565
asparagine aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) BUB04_RS05920
asparagine ans: asparaginase BUB04_RS04620 BUB04_RS16660
aspartate aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) BUB04_RS05925 BUB04_RS13795
aspartate aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP BUB04_RS05930 BUB04_RS14565
aspartate aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) BUB04_RS05920
cellobiose cbp: cellobiose phosphorylase
cellobiose cdt: cellobiose transporter cdt-1/cdt-2
cellobiose glk: glucokinase BUB04_RS16875
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component BUB04_RS05855 BUB04_RS10875
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 BUB04_RS05850 BUB04_RS13795
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 BUB04_RS06475 BUB04_RS06465
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component BUB04_RS03450
citrulline arcC: carbamate kinase BUB04_RS05565
D-alanine dadA: D-alanine dehydrogenase
D-alanine Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component BUB04_RS05915
D-alanine Pf6N2E2_5403: ABC transporter for D-Alanine, permease component 2 BUB04_RS05920 BUB04_RS12165
D-alanine Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component BUB04_RS05930 BUB04_RS14565
D-lactate D-LDH: D-lactate dehydrogenase BUB04_RS15385 BUB04_RS07455
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 BUB04_RS13615 BUB04_RS01900
deoxyinosine deoB: phosphopentomutase BUB04_RS13695
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine nupC: deoxyinosine:H+ symporter NupC BUB04_RS04420
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribose deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) BUB04_RS10050 BUB04_RS15270
fructose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components
fucose fucA: L-fuculose-phosphate aldolase FucA BUB04_RS08380
fucose fucI: L-fucose isomerase FucI
fucose fucK: L-fuculose kinase FucK
fucose fucO: L-lactaldehyde reductase BUB04_RS10050 BUB04_RS15270
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 BUB04_RS13365 BUB04_RS13705
galactose galK: galactokinase (-1-phosphate forming)
galactose galP: galactose:H+ symporter GalP
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate kdgK: 2-keto-3-deoxygluconate kinase BUB04_RS05935
galacturonate uxaA: D-altronate dehydratase
galacturonate uxaB: tagaturonate reductase
galacturonate uxaC: D-galacturonate isomerase
gluconate edd: phosphogluconate dehydratase BUB04_RS09665
gluconate gntK: D-gluconate kinase BUB04_RS08485
gluconate gntT: gluconate:H+ symporter GntT
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE)
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) BUB04_RS16750
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 BUB04_RS11085
glucuronate garR: tartronate semialdehyde reductase BUB04_RS05580 BUB04_RS01755
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase BUB04_RS07000
glucuronate udh: D-glucuronate dehydrogenase
glutamate aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) BUB04_RS05925 BUB04_RS13795
glutamate aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP BUB04_RS05930 BUB04_RS14565
glutamate aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) BUB04_RS05920
glutamate gdhA: glutamate dehydrogenase, NAD-dependent BUB04_RS09120 BUB04_RS01215
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric)
histidine aapM: L-histidine ABC transporter, permease component 2 (AapM) BUB04_RS05925 BUB04_RS10880
histidine aapP: L-histidine ABC transporter, ATPase component AapP BUB04_RS05930 BUB04_RS14565
histidine hutG: N-formiminoglutamate formiminohydrolase BUB04_RS18635
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase BUB04_RS03730 BUB04_RS01095
isoleucine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit BUB04_RS01335 BUB04_RS01455
isoleucine bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit BUB04_RS01340 BUB04_RS01450
isoleucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component BUB04_RS01345 BUB04_RS07775
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase BUB04_RS07485 BUB04_RS18395
isoleucine livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) BUB04_RS13175 BUB04_RS14530
isoleucine livM: L-isoleucine ABC transporter, permease component 2 (LivM/BraE) BUB04_RS13185 BUB04_RS14540
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit BUB04_RS08790
L-lactate L-LDH: L-lactate dehydrogenase BUB04_RS00940
L-lactate SfMCT: L-lactate transporter SfMCT BUB04_RS12750
L-malate sdlC: L-malate:Na+ symporter SdlC
lactose galE: UDP-glucose 4-epimerase BUB04_RS13365 BUB04_RS13705
lactose galK: galactokinase (-1-phosphate forming)
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
lactose glk: glucokinase BUB04_RS16875
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
leucine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit BUB04_RS01335 BUB04_RS01455
leucine bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit BUB04_RS01340 BUB04_RS01450
leucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component BUB04_RS01345 BUB04_RS07775
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit BUB04_RS08790
leucine liuC: 3-methylglutaconyl-CoA hydratase BUB04_RS07705 BUB04_RS01090
leucine liuE: hydroxymethylglutaryl-CoA lyase BUB04_RS00695
leucine livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) BUB04_RS13175 BUB04_RS14530
leucine livM: L-leucine ABC transporter, permease component 2 (LivM/BraE) BUB04_RS13185 BUB04_RS14540
lysine cadA: lysine decarboxylase
lysine davD: glutarate semialdehyde dehydrogenase BUB04_RS04110 BUB04_RS05780
lysine gcdH: glutaryl-CoA dehydrogenase BUB04_RS03730 BUB04_RS05240
lysine lysP: L-lysine:H+ symporter LysP
lysine patD: 5-aminopentanal dehydrogenase BUB04_RS04110 BUB04_RS05780
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 iolG: myo-inositol 2-dehydrogenase
myoinositol iolM: 2-inosose 4-dehydrogenase
myoinositol iolO: 5-dehydro-L-gluconate epimerase
myoinositol iolT: myo-inositol:H+ symporter
myoinositol kdgK: 2-keto-3-deoxygluconate kinase BUB04_RS05935
myoinositol uxaE: D-tagaturonate epimerase
myoinositol uxuA: D-mannonate dehydratase
myoinositol uxuB: D-mannonate dehydrogenase
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) BUB04_RS16750
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 BUB04_RS03725 BUB04_RS07705
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase BUB04_RS09760 BUB04_RS07705
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase BUB04_RS03720 BUB04_RS17410
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase BUB04_RS03720 BUB04_RS17410
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase BUB04_RS09760 BUB04_RS15240
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine livF: L-phenylalanine ABC transporter, ATPase component 1 (LivF) BUB04_RS02700 BUB04_RS14475
phenylalanine livH: L-phenylalanine ABC transporter, permease component 1 (LivH) BUB04_RS13180 BUB04_RS02685
phenylalanine livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK BUB04_RS13175 BUB04_RS02680
phenylalanine livM: L-phenylalanine ABC transporter, permease component 2 (LivM) BUB04_RS13185 BUB04_RS12270
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 BUB04_RS03725 BUB04_RS07705
phenylalanine paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase BUB04_RS09760 BUB04_RS07705
phenylalanine paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase BUB04_RS03720 BUB04_RS17410
phenylalanine paaJ2: 3-oxoadipyl-CoA thiolase BUB04_RS03720 BUB04_RS17410
phenylalanine paaZ1: oxepin-CoA hydrolase BUB04_RS09760 BUB04_RS15240
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) BUB04_RS05925 BUB04_RS13795
proline aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP BUB04_RS05930 BUB04_RS14565
proline aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) BUB04_RS05920
proline put1: proline dehydrogenase BUB04_RS13170 BUB04_RS16575
propionate pccA: propionyl-CoA carboxylase, alpha subunit BUB04_RS08790
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabD: succinate semialdehyde dehydrogenase BUB04_RS04110 BUB04_RS05780
putrescine gabT: gamma-aminobutyrate transaminase BUB04_RS10885 BUB04_RS02225
putrescine patD: gamma-aminobutyraldehyde dehydrogenase BUB04_RS04110 BUB04_RS05780
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate dctQ: pyruvate TRAP transporter, small permease component BUB04_RS15595
rhamnose fucO: L-lactaldehyde reductase BUB04_RS10050 BUB04_RS15270
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) BUB04_RS13175 BUB04_RS02680
serine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) BUB04_RS13180 BUB04_RS02685
serine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) BUB04_RS13185 BUB04_RS12270
serine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) BUB04_RS02695 BUB04_RS13190
serine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) BUB04_RS02700 BUB04_RS14475
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase BUB04_RS18395 BUB04_RS12055
succinate sdc: succinate:Na+ symporter Sdc
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) BUB04_RS13175 BUB04_RS02680
threonine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) BUB04_RS13180 BUB04_RS02685
threonine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) BUB04_RS13185 BUB04_RS12270
threonine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) BUB04_RS02695 BUB04_RS13190
threonine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) BUB04_RS02700 BUB04_RS14475
threonine gcvP: glycine cleavage system, P component (glycine decarboxylase) BUB04_RS03940 BUB04_RS03935
threonine gcvT: glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) BUB04_RS03950 BUB04_RS16585
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase BUB04_RS13695
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupC: thymidine permease NupC BUB04_RS04420
trehalose glk: glucokinase BUB04_RS16875
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 BUB04_RS03730 BUB04_RS15245
valine bch: 3-hydroxyisobutyryl-CoA hydrolase BUB04_RS13370 BUB04_RS07705
valine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit BUB04_RS01335 BUB04_RS01455
valine bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit BUB04_RS01340 BUB04_RS01450
valine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component BUB04_RS01345 BUB04_RS07775
valine livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) BUB04_RS13175 BUB04_RS14530
valine livM: L-valine ABC transporter, permease component 2 (LivM/BraE) BUB04_RS13185 BUB04_RS14540
valine mmsA: methylmalonate-semialdehyde dehydrogenase BUB04_RS04110 BUB04_RS13170
valine mmsB: 3-hydroxyisobutyrate dehydrogenase BUB04_RS05580 BUB04_RS01755
valine pccA: propionyl-CoA carboxylase, alpha subunit BUB04_RS08790
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