GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Denitrovibrio acetiphilus DSM 12809

Found 169 low-confidence and 67 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 DACET_RS06125 DACET_RS05940
2-oxoglutarate Psest_0085: 2-oxoglutarate TRAP transporter, solute receptor component DACET_RS06120
4-hydroxybenzoate adh: acetaldehyde dehydrogenase (not acylating) DACET_RS05370 DACET_RS08150
4-hydroxybenzoate mhpD: 2-hydroxypentadienoate hydratase
4-hydroxybenzoate mhpE: 4-hydroxy-2-oxovalerate aldolase
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) DACET_RS04485 DACET_RS07575
alanine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) DACET_RS04490 DACET_RS07580
alanine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) DACET_RS04495 DACET_RS07585
alanine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) DACET_RS04500 DACET_RS07590
alanine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) DACET_RS04505 DACET_RS07595
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase DACET_RS10645
arabinose araE: L-arabinose:H+ symporter
arginine put1: proline dehydrogenase DACET_RS07565
arginine rocD: ornithine aminotransferase DACET_RS05585 DACET_RS02325
arginine rocE: L-arginine permease
arginine rocF: arginase
asparagine yhiT: probable L-asparagine transporter YhiT DACET_RS06985
aspartate glt: aspartate:proton symporter Glt
cellobiose bgl: cellobiase
cellobiose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component DACET_RS00715 DACET_RS10860
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 DACET_RS10865 DACET_RS00705
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 DACET_RS10865 DACET_RS00705
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline arcC: carbamate kinase
citrulline put1: proline dehydrogenase DACET_RS07565
citrulline rocD: ornithine aminotransferase DACET_RS05585 DACET_RS02325
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase DACET_RS06335
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 DACET_RS11370
deoxyinosine adh: acetaldehyde dehydrogenase (not acylating) DACET_RS05370 DACET_RS08150
deoxyinosine deoB: phosphopentomutase DACET_RS06525
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate aacS: acetoacetyl-CoA synthetase DACET_RS05990
deoxyribonate atoB: acetyl-CoA C-acetyltransferase DACET_RS12670
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase DACET_RS15190
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate garK: glycerate 2-kinase DACET_RS14775
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose adh: acetaldehyde dehydrogenase (not acylating) DACET_RS05370 DACET_RS08150
deoxyribose deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoP: deoxyribose transporter
ethanol adh: acetaldehyde dehydrogenase (not acylating) DACET_RS05370 DACET_RS08150
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) DACET_RS07160 DACET_RS13850
fructose 1pfk: 1-phosphofructokinase
fructose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components
fucose aldA: lactaldehyde dehydrogenase DACET_RS08150 DACET_RS05370
fucose fucA: L-fuculose-phosphate aldolase FucA DACET_RS10645
fucose fucI: L-fucose isomerase FucI
fucose fucK: L-fuculose kinase FucK
fucose fucP: L-fucose:H+ symporter FucP
fumarate dctA: fumarate:H+ symporter DctA
galactose galE: UDP-glucose 4-epimerase DACET_RS02150 DACET_RS12290
galactose galK: galactokinase (-1-phosphate forming)
galactose galP: galactose:H+ symporter GalP
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase DACET_RS02195
galactose pgmA: alpha-phosphoglucomutase DACET_RS13520 DACET_RS14070
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) DACET_RS01275
glucose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate dopDH: 2,5-dioxopentanonate dehydrogenase DACET_RS08150 DACET_RS05370
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate kdgD: 5-dehydro-4-deoxyglucarate dehydratase
glucuronate udh: D-glucuronate dehydrogenase
glutamate gltS: L-glutamate:Na+ symporter GltS
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric)
glycerol glpF: glycerol facilitator glpF
glycerol glpK: glycerol kinase
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
histidine PA5503: L-histidine ABC transporter, ATPase component DACET_RS10485 DACET_RS10860
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase DACET_RS12835 DACET_RS14805
isoleucine fadA: 2-methylacetoacetyl-CoA thiolase DACET_RS12670
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase DACET_RS15190
isoleucine livH: L-isoleucine ABC transporter, permease component 1 (LivH/BraD) DACET_RS04490 DACET_RS07580
isoleucine livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) DACET_RS04485 DACET_RS07575
isoleucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit DACET_RS00335 DACET_RS09735
L-lactate L-LDH: L-lactate dehydrogenase DACET_RS11810
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
L-malate sdlC: L-malate:Na+ symporter SdlC
lactose galE: UDP-glucose 4-epimerase DACET_RS02150 DACET_RS12290
lactose galK: galactokinase (-1-phosphate forming)
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase DACET_RS02195
lactose glk: glucokinase DACET_RS15655
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
lactose pgmA: alpha-phosphoglucomutase DACET_RS13520 DACET_RS14070
leucine aacS: acetoacetyl-CoA synthetase DACET_RS05990
leucine atoB: acetyl-CoA C-acetyltransferase DACET_RS12670
leucine liuA: isovaleryl-CoA dehydrogenase
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit DACET_RS09735 DACET_RS00335
leucine liuC: 3-methylglutaconyl-CoA hydratase DACET_RS14805 DACET_RS14810
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit DACET_RS09160 DACET_RS09740
leucine liuE: hydroxymethylglutaryl-CoA lyase
leucine livH: L-leucine ABC transporter, permease component 1 (LivH/BraD) DACET_RS04490 DACET_RS07580
leucine livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) DACET_RS04485 DACET_RS07575
leucine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
lysine amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) DACET_RS08150
lysine hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase DACET_RS05585
lysine lysN: 2-aminoadipate transaminase DACET_RS01590
lysine lysP: L-lysine:H+ symporter LysP
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase
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 DACET_RS12750
myoinositol iolT: myo-inositol:H+ symporter
myoinositol mmsA: malonate-semialdehyde dehydrogenase DACET_RS08150 DACET_RS05370
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) DACET_RS01275
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 DACET_RS12835 DACET_RS14805
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase DACET_RS12835
phenylacetate paaH: 3-hydroxyadipyl-CoA dehydrogenase DACET_RS15190
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase
phenylacetate paaZ1: oxepin-CoA hydrolase
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylacetate ppa: phenylacetate permease ppa DACET_RS05620 DACET_RS06285
phenylalanine aacS: acetoacetyl-CoA synthetase DACET_RS05990
phenylalanine atoB: acetyl-CoA C-acetyltransferase DACET_RS12670
phenylalanine fahA: fumarylacetoacetate hydrolase
phenylalanine hmgA: homogentisate dioxygenase
phenylalanine HPD: 4-hydroxyphenylpyruvate dioxygenase
phenylalanine livF: L-phenylalanine ABC transporter, ATPase component 1 (LivF) DACET_RS04505 DACET_RS07595
phenylalanine livG: L-phenylalanine ABC transporter, ATPase component 2 (LivG) DACET_RS04500 DACET_RS07590
phenylalanine livH: L-phenylalanine ABC transporter, permease component 1 (LivH) DACET_RS04490 DACET_RS07580
phenylalanine livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK DACET_RS04485 DACET_RS07575
phenylalanine maiA: maleylacetoacetate isomerase
phenylalanine PAH: phenylalanine 4-monooxygenase
phenylalanine PCBD: pterin-4-alpha-carbinoalamine dehydratase
phenylalanine QDPR: 6,7-dihydropteridine reductase
proline proW: proline ABC transporter, permease component ProW DACET_RS10260
proline proX: proline ABC transporter, substrate-binding component ProX DACET_RS10255
proline put1: proline dehydrogenase DACET_RS07565
propionate mctC: propionate:H+ symporter DACET_RS05620 DACET_RS06285
propionate pccA: propionyl-CoA carboxylase, alpha subunit DACET_RS00335 DACET_RS09735
propionate prpE: propionyl-CoA synthetase DACET_RS06270 DACET_RS08205
putrescine gabT: gamma-aminobutyrate transaminase DACET_RS05585 DACET_RS02325
putrescine patA: putrescine aminotransferase (PatA/SpuC) DACET_RS05585 DACET_RS01590
putrescine patD: gamma-aminobutyraldehyde dehydrogenase DACET_RS08150 DACET_RS05370
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
rhamnose aldA: lactaldehyde dehydrogenase DACET_RS08150 DACET_RS05370
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 rbsA: D-ribose ABC transporter, ATPase component RbsA DACET_RS01085 DACET_RS10620
ribose rbsB: D-ribose ABC transporter, substrate-binding component RbsB DACET_RS01095
ribose rbsC: D-ribose ABC transporter, permease component RbsC DACET_RS01090 DACET_RS10625
serine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) DACET_RS04485 DACET_RS07575
serine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) DACET_RS04490 DACET_RS07580
serine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) DACET_RS04495 DACET_RS07585
serine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) DACET_RS04500 DACET_RS07590
serine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) DACET_RS04505 DACET_RS07595
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase DACET_RS15190
sucrose pgmA: alpha-phosphoglucomutase DACET_RS13520 DACET_RS14070
sucrose scrK: fructokinase DACET_RS14850
sucrose sut: sucrose:proton symporter SUT/SUC
threonine braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) DACET_RS04485 DACET_RS07575
threonine braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) DACET_RS04490 DACET_RS07580
threonine braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) DACET_RS04495 DACET_RS07585
threonine braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) DACET_RS04500 DACET_RS07590
threonine braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) DACET_RS04505 DACET_RS07595
threonine pccA: propionyl-CoA carboxylase, alpha subunit DACET_RS00335 DACET_RS09735
threonine tdcE: 2-ketobutyrate formate-lyase
thymidine adh: acetaldehyde dehydrogenase (not acylating) DACET_RS05370 DACET_RS08150
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase DACET_RS06525
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 aacS: acetoacetyl-CoA synthetase DACET_RS05990
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine atoB: acetyl-CoA C-acetyltransferase DACET_RS12670
tyrosine fahA: fumarylacetoacetate hydrolase
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 ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase DACET_RS12835 DACET_RS14805
valine livH: L-valine ABC transporter, permease component 1 (LivH/BraD) DACET_RS04490 DACET_RS07580
valine livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) DACET_RS04485 DACET_RS07575
valine mmsA: methylmalonate-semialdehyde dehydrogenase DACET_RS08150
valine mmsB: 3-hydroxyisobutyrate dehydrogenase
valine ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
valine pccA: propionyl-CoA carboxylase, alpha subunit DACET_RS00335 DACET_RS09735
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