GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Desulfuromusa kysingii DSM 7343

Found 142 low-confidence and 83 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
4-hydroxybenzoate adh: acetaldehyde dehydrogenase (not acylating) BLU87_RS03510 BLU87_RS07020
4-hydroxybenzoate mhpD: 2-hydroxypentadienoate hydratase
4-hydroxybenzoate mhpE: 4-hydroxy-2-oxovalerate aldolase BLU87_RS05665
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 braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) BLU87_RS11835
alanine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) BLU87_RS11830 BLU87_RS12680
alanine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) BLU87_RS11820 BLU87_RS12690
alanine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) BLU87_RS11815 BLU87_RS12695
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase BLU87_RS06340
arabinose araE: L-arabinose:H+ symporter
arginine put1: proline dehydrogenase BLU87_RS12670 BLU87_RS15955
arginine putA: L-glutamate 5-semialdeyde dehydrogenase BLU87_RS05345 BLU87_RS05845
arginine rocE: L-arginine permease
asparagine ans: asparaginase BLU87_RS11585
asparagine yhiT: probable L-asparagine transporter YhiT BLU87_RS04225
aspartate aapJ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ BLU87_RS03900
aspartate aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) BLU87_RS03910 BLU87_RS11125
aspartate aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP BLU87_RS03915 BLU87_RS11120
aspartate aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) BLU87_RS03905
cellobiose bgl: cellobiase
cellobiose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
citrate tctB: citrate/Na+ symporter, small transmembrane component TctB
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component BLU87_RS03915 BLU87_RS11120
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 BLU87_RS09590 BLU87_RS11125
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 BLU87_RS09590
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline citrullinase: putative citrullinase BLU87_RS07975
citrulline put1: proline dehydrogenase BLU87_RS12670 BLU87_RS15955
citrulline putA: L-glutamate 5-semialdeyde dehydrogenase BLU87_RS05345 BLU87_RS05845
D-alanine dadA: D-alanine dehydrogenase
D-alanine Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component BLU87_RS03900
D-alanine Pf6N2E2_5403: ABC transporter for D-Alanine, permease component 2 BLU87_RS03905
D-alanine Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component BLU87_RS03915 BLU87_RS11120
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 BLU87_RS11570 BLU87_RS04710
deoxyinosine adh: acetaldehyde dehydrogenase (not acylating) BLU87_RS03510 BLU87_RS07020
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase BLU87_RS14010
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose adh: acetaldehyde dehydrogenase (not acylating) BLU87_RS03510 BLU87_RS07020
deoxyribose deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter
ethanol adh: acetaldehyde dehydrogenase (not acylating) BLU87_RS03510 BLU87_RS07020
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) BLU87_RS10700 BLU87_RS10015
fructose 1pfk: 1-phosphofructokinase
fructose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components
fucose aldA: lactaldehyde dehydrogenase BLU87_RS07020 BLU87_RS05845
fucose fucA: L-fuculose-phosphate aldolase FucA BLU87_RS06340
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 BLU87_RS06225 BLU87_RS10400
galactose galK: galactokinase (-1-phosphate forming)
galactose galP: galactose:H+ symporter GalP
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase BLU87_RS04510
galactose pgmA: alpha-phosphoglucomutase BLU87_RS10530 BLU87_RS06860
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate gci: D-galactarolactone cycloisomerase
galacturonate gli: D-galactarolactone isomerase
galacturonate kdgD: 5-dehydro-4-deoxyglucarate dehydratase BLU87_RS01645
galacturonate udh: D-galacturonate dehydrogenase
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) BLU87_RS15755
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 gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate kdgD: 5-dehydro-4-deoxyglucarate dehydratase BLU87_RS01645
glucuronate udh: D-glucuronate dehydrogenase
glycerol glpF: glycerol facilitator glpF
histidine aapJ: L-histidine ABC transporter, substrate-binding component AapJ BLU87_RS03900
histidine aapM: L-histidine ABC transporter, permease component 2 (AapM) BLU87_RS03910 BLU87_RS11125
histidine aapP: L-histidine ABC transporter, ATPase component AapP BLU87_RS03915 BLU87_RS11120
histidine aapQ: L-histidine ABC transporter, permease component 1 (AapQ) BLU87_RS03905
histidine hutG: N-formiminoglutamate formiminohydrolase BLU87_RS12445
histidine hutH: histidine ammonia-lyase BLU87_RS00950
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase BLU87_RS11780 BLU87_RS14575
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase BLU87_RS11775 BLU87_RS14565
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase BLU87_RS14010 BLU87_RS00915
isoleucine livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) BLU87_RS11835 BLU87_RS03940
isoleucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit BLU87_RS13655 BLU87_RS06260
isoleucine pccB: propionyl-CoA carboxylase, beta subunit BLU87_RS11655
L-lactate L-LDH: L-lactate dehydrogenase BLU87_RS16460 BLU87_RS11760
lactose galE: UDP-glucose 4-epimerase BLU87_RS06225 BLU87_RS10400
lactose galK: galactokinase (-1-phosphate forming)
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase BLU87_RS04510
lactose glk: glucokinase BLU87_RS12610
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
lactose pgmA: alpha-phosphoglucomutase BLU87_RS10530 BLU87_RS06860
leucine liuA: isovaleryl-CoA dehydrogenase BLU87_RS11780 BLU87_RS14575
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit BLU87_RS13655 BLU87_RS06260
leucine liuC: 3-methylglutaconyl-CoA hydratase BLU87_RS11775 BLU87_RS12270
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) BLU87_RS11835 BLU87_RS03940
leucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
lysine amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) BLU87_RS05845
lysine hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase BLU87_RS01565 BLU87_RS04965
lysine lysN: 2-aminoadipate transaminase BLU87_RS08685 BLU87_RS01565
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 manA: mannose-6-phosphate isomerase BLU87_RS10525 BLU87_RS03630
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 BLU87_RS07850
myoinositol iolT: myo-inositol:H+ symporter
myoinositol mmsA: malonate-semialdehyde dehydrogenase BLU87_RS05845 BLU87_RS07020
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) BLU87_RS15755
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 BLU87_RS11775 BLU87_RS12270
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase BLU87_RS14585 BLU87_RS11775
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase BLU87_RS14570 BLU87_RS04905
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase BLU87_RS14570 BLU87_RS04905
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine livF: L-phenylalanine ABC transporter, ATPase component 1 (LivF) BLU87_RS11815 BLU87_RS12695
phenylalanine livG: L-phenylalanine ABC transporter, ATPase component 2 (LivG) BLU87_RS11820 BLU87_RS12690
phenylalanine livH: L-phenylalanine ABC transporter, permease component 1 (LivH) BLU87_RS11830 BLU87_RS12680
phenylalanine livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK BLU87_RS11835
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 BLU87_RS11775 BLU87_RS12270
phenylalanine paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase BLU87_RS14585 BLU87_RS11775
phenylalanine paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase BLU87_RS14570 BLU87_RS04905
phenylalanine paaJ2: 3-oxoadipyl-CoA thiolase BLU87_RS14570 BLU87_RS04905
phenylalanine paaZ1: oxepin-CoA hydrolase
phenylalanine paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
proline proW: proline ABC transporter, permease component ProW BLU87_RS10690
proline proX: proline ABC transporter, substrate-binding component ProX BLU87_RS10695
proline put1: proline dehydrogenase BLU87_RS12670 BLU87_RS15955
proline putA: L-glutamate 5-semialdeyde dehydrogenase BLU87_RS05345 BLU87_RS05845
propionate pccA: propionyl-CoA carboxylase, alpha subunit BLU87_RS13655 BLU87_RS06260
propionate pccB: propionyl-CoA carboxylase, beta subunit BLU87_RS11655
propionate prpE: propionyl-CoA synthetase BLU87_RS12135 BLU87_RS12405
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabT: gamma-aminobutyrate transaminase BLU87_RS01675 BLU87_RS04965
putrescine patA: putrescine aminotransferase (PatA/SpuC) BLU87_RS01675 BLU87_RS04965
putrescine patD: gamma-aminobutyraldehyde dehydrogenase BLU87_RS07020 BLU87_RS05845
putrescine potA: putrescine ABC transporter, ATPase component (PotA/PotG) BLU87_RS13055 BLU87_RS09610
putrescine potB: putrescine ABC transporter, permease component 1 (PotB/PotH) BLU87_RS13050
putrescine potC: putrescine ABC transporter, permease component 2 (PotC/PotI) BLU87_RS13045
putrescine potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) BLU87_RS13060
pyruvate dctQ: pyruvate TRAP transporter, small permease component BLU87_RS12845 BLU87_RS12825
rhamnose aldA: lactaldehyde dehydrogenase BLU87_RS07020 BLU87_RS05845
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) BLU87_RS11835
serine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) BLU87_RS11830 BLU87_RS12680
serine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) BLU87_RS11820 BLU87_RS12690
serine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) BLU87_RS11815 BLU87_RS12695
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase BLU87_RS14010 BLU87_RS00915
sucrose 1pfk: 1-phosphofructokinase
sucrose ams: sucrose hydrolase (invertase) BLU87_RS09965
sucrose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components
threonine adh: acetaldehyde dehydrogenase (not acylating) BLU87_RS03510 BLU87_RS07020
threonine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) BLU87_RS11835
threonine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) BLU87_RS11830 BLU87_RS12680
threonine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) BLU87_RS11820 BLU87_RS12690
threonine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) BLU87_RS11815 BLU87_RS12695
threonine gcvP: glycine cleavage system, P component (glycine decarboxylase) BLU87_RS06620 BLU87_RS06615
thymidine adh: acetaldehyde dehydrogenase (not acylating) BLU87_RS03510 BLU87_RS07020
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupG: thymidine permease NupG/XapB
trehalose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
trehalose treF: trehalase
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine fahA: fumarylacetoacetate hydrolase BLU87_RS03080
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase BLU87_RS11780 BLU87_RS14575
valine bch: 3-hydroxyisobutyryl-CoA hydrolase BLU87_RS11775
valine livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) BLU87_RS11835 BLU87_RS03940
valine mmsA: methylmalonate-semialdehyde dehydrogenase BLU87_RS05845 BLU87_RS07020
valine mmsB: 3-hydroxyisobutyrate dehydrogenase
valine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
valine pccA: propionyl-CoA carboxylase, alpha subunit BLU87_RS13655 BLU87_RS06260
valine pccB: propionyl-CoA carboxylase, beta subunit BLU87_RS11655
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase BLU87_RS10015
xylose xylA: xylose isomerase
xylose xylB: xylulokinase
xylose xylT: D-xylose transporter

Confidence: high confidence medium confidence low confidence

This GapMind analysis is from Sep 24 2021. 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