GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Desulfatitalea tepidiphila S28bF

Found 141 low-confidence and 78 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 DFT_RS14610 DFT_RS17540
2-oxoglutarate Psest_0085: 2-oxoglutarate TRAP transporter, solute receptor component DFT_RS14330 DFT_RS17530
4-hydroxybenzoate adh: acetaldehyde dehydrogenase (not acylating) DFT_RS24075 DFT_RS20370
4-hydroxybenzoate mhpD: 2-hydroxypentadienoate hydratase
4-hydroxybenzoate mhpE: 4-hydroxy-2-oxovalerate aldolase DFT_RS14405 DFT_RS12630
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 DFT_RS12380 DFT_RS15495
alanine cycA: L-alanine symporter CycA
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase DFT_RS17450
arabinose araE: L-arabinose:H+ symporter
arginine adiA: arginine decarboxylase (AdiA/SpeA) DFT_RS08620
arginine gabT: gamma-aminobutyrate transaminase DFT_RS09045 DFT_RS06225
arginine patA: putrescine aminotransferase (PatA/SpuC) DFT_RS06225
arginine patD: gamma-aminobutyraldehyde dehydrogenase DFT_RS24075 DFT_RS20370
arginine rocE: L-arginine permease
asparagine ans: asparaginase
asparagine bgtA: aspartate ABC transporter, ATPase component BgtA DFT_RS18645 DFT_RS15800
asparagine bgtB': aspartate ABC transporter, permease component 1 (BgtB) DFT_RS18635
asparagine natF: aspartate ABC transporter, substrate-binding component NatF DFT_RS18630
asparagine natH: aspartate ABC transporter, permease component 2 (NatH) DFT_RS18640
aspartate bgtA: aspartate ABC transporter, ATPase component BgtA DFT_RS18645 DFT_RS15800
aspartate bgtB': aspartate ABC transporter, permease component 1 (BgtB) DFT_RS18635
aspartate natF: aspartate ABC transporter, substrate-binding component NatF DFT_RS18630
aspartate natH: aspartate ABC transporter, permease component 2 (NatH) DFT_RS18640
cellobiose cbp: cellobiose phosphorylase
cellobiose cdt: cellobiose transporter cdt-1/cdt-2
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component DFT_RS18645 DFT_RS18035
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline arcC: carbamate kinase DFT_RS07685
citrulline put1: proline dehydrogenase DFT_RS07180
citrulline putA: L-glutamate 5-semialdeyde dehydrogenase DFT_RS07180 DFT_RS24075
citrulline rocD: ornithine aminotransferase DFT_RS06225
D-alanine dadA: D-alanine dehydrogenase
D-alanine Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component DFT_RS18630
D-alanine Pf6N2E2_5403: ABC transporter for D-Alanine, permease component 2 DFT_RS18635
D-alanine Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component DFT_RS18645 DFT_RS18035
D-lactate D-LDH: D-lactate dehydrogenase DFT_RS18530 DFT_RS07970
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 DFT_RS10560
deoxyinosine adh: acetaldehyde dehydrogenase (not acylating) DFT_RS24075 DFT_RS20370
deoxyinosine deoB: phosphopentomutase DFT_RS07165 DFT_RS11825
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase DFT_RS18780 DFT_RS02160
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribose deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase DFT_RS18780 DFT_RS02160
deoxyribose deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribose drdehyd-alpha: 2-deoxy-D-ribose dehydrogenase, alpha subunit DFT_RS25370 DFT_RS01925
deoxyribose drdehyd-beta: 2-deoxy-D-ribose dehydrogenase, beta subunit
deoxyribose drdehyd-cytc: 2-deoxyribose-D dehydrogenase, cytochrome c component
ethanol adh: acetaldehyde dehydrogenase (not acylating) DFT_RS24075 DFT_RS20370
fructose 1pfk: 1-phosphofructokinase
fructose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components
fucose aldA: lactaldehyde dehydrogenase DFT_RS24075 DFT_RS23425
fucose fucA: L-fuculose-phosphate aldolase FucA DFT_RS17450
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
fumarate dctA: fumarate:H+ symporter DctA
galactose galK: galactokinase (-1-phosphate forming)
galactose galP: galactose:H+ symporter GalP
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
galacturonate dopDH: 2,5-dioxopentanonate dehydrogenase DFT_RS20370 DFT_RS24075
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate gci: D-galactarolactone cycloisomerase
galacturonate gli: D-galactarolactone isomerase
galacturonate kdgD: 5-dehydro-4-deoxyglucarate dehydratase
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)
glucose MFS-glucose: glucose transporter, MFS superfamily
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 DFT_RS14405
glucuronate garR: tartronate semialdehyde reductase DFT_RS08535
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate udh: D-glucuronate dehydrogenase
glutamate dmeA: L-glutamate transporter DmeA DFT_RS21845
glutamate gdhA: glutamate dehydrogenase, NAD-dependent DFT_RS21900 DFT_RS16065
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric) DFT_RS18875
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine hutH: histidine ammonia-lyase DFT_RS25635
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
histidine LAT2: L-histidine transporter DFT_RS21640
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase DFT_RS05355 DFT_RS24355
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase DFT_RS02885 DFT_RS24350
isoleucine livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) DFT_RS01295 DFT_RS20470
isoleucine livM: L-isoleucine ABC transporter, permease component 2 (LivM/BraE) DFT_RS13710 DFT_RS12350
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit DFT_RS17925
isoleucine pccB: propionyl-CoA carboxylase, beta subunit DFT_RS17930 DFT_RS01185
isoleucine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC
L-lactate SfMCT: L-lactate transporter SfMCT DFT_RS16300 DFT_RS03590
L-malate sdlC: L-malate:Na+ symporter SdlC
lactose galK: galactokinase (-1-phosphate forming)
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
leucine aapJ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ DFT_RS18630
leucine aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) DFT_RS18640
leucine aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP DFT_RS18645 DFT_RS14560
leucine aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) DFT_RS18635
leucine liuA: isovaleryl-CoA dehydrogenase DFT_RS24355 DFT_RS22645
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit DFT_RS17925
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit DFT_RS17930 DFT_RS01185
leucine liuE: hydroxymethylglutaryl-CoA lyase DFT_RS17325
leucine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC
lysine davA: 5-aminovaleramidase DFT_RS15930 DFT_RS12360
lysine davB: L-lysine 2-monooxygenase
lysine davT: 5-aminovalerate aminotransferase DFT_RS06225 DFT_RS09045
lysine gcdG: succinyl-CoA:glutarate CoA-transferase DFT_RS15405 DFT_RS07300
lysine gcdH: glutaryl-CoA dehydrogenase DFT_RS22645 DFT_RS05355
lysine lysP: L-lysine:H+ symporter LysP
maltose malA: 6-phospho-alphaglucosidase
maltose malEIICBA: maltose phosphotransferase system, EII-CBA components
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 DFT_RS12615
myoinositol iolE: scyllo-inosose 2-dehydratase
myoinositol iolG: myo-inositol 2-dehydrogenase DFT_RS23660
myoinositol iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase
myoinositol iolT: myo-inositol:H+ symporter
myoinositol mmsA: malonate-semialdehyde dehydrogenase DFT_RS20370 DFT_RS24075
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing)
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 DFT_RS22655 DFT_RS10430
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase DFT_RS09470 DFT_RS20250
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase DFT_RS07080 DFT_RS08640
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase DFT_RS08640 DFT_RS20405
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase DFT_RS09470 DFT_RS20250
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
phenylalanine iorB: phenylpyruvate:ferredoxin oxidoreductase, IorB subunit DFT_RS16840 DFT_RS02870
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 DFT_RS22655 DFT_RS10430
phenylalanine paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase DFT_RS09470 DFT_RS20250
phenylalanine paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase DFT_RS07080 DFT_RS08640
phenylalanine paaJ2: 3-oxoadipyl-CoA thiolase DFT_RS08640 DFT_RS20405
phenylalanine paaZ1: oxepin-CoA hydrolase DFT_RS09470 DFT_RS20250
phenylalanine paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
proline proW: proline ABC transporter, permease component ProW DFT_RS18030
proline put1: proline dehydrogenase DFT_RS07180
proline putA: L-glutamate 5-semialdeyde dehydrogenase DFT_RS07180 DFT_RS24075
propionate pccA: propionyl-CoA carboxylase, alpha subunit DFT_RS17925
propionate pccB: propionyl-CoA carboxylase, beta subunit DFT_RS17930 DFT_RS01185
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabT: gamma-aminobutyrate transaminase DFT_RS09045 DFT_RS06225
putrescine patA: putrescine aminotransferase (PatA/SpuC) DFT_RS06225
putrescine patD: gamma-aminobutyraldehyde dehydrogenase DFT_RS24075 DFT_RS20370
pyruvate dctQ: pyruvate TRAP transporter, small permease component DFT_RS07960 DFT_RS03530
rhamnose LRA1: L-rhamnofuranose dehydrogenase DFT_RS20295 DFT_RS20180
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase DFT_RS22310
rhamnose LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase DFT_RS22290 DFT_RS20445
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsK: ribokinase
ribose rbsU: probable D-ribose transporter RbsU
serine serP: L-serine permease SerP
sorbitol scrK: fructokinase DFT_RS05815 DFT_RS02175
sorbitol sdh: sorbitol dehydrogenase DFT_RS18710 DFT_RS22290
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2
succinate satP: succinate:H+ symporter SatP DFT_RS20960
sucrose ams: sucrose hydrolase (invertase) DFT_RS18935
sucrose MFS-glucose: glucose transporter, MFS superfamily
threonine adh: acetaldehyde dehydrogenase (not acylating) DFT_RS24075 DFT_RS20370
threonine gcvP: glycine cleavage system, P component (glycine decarboxylase) DFT_RS18395 DFT_RS18390
threonine ltaE: L-threonine aldolase DFT_RS00145
threonine tdcC: L-threonine:H+ symporter TdcC
thymidine adh: acetaldehyde dehydrogenase (not acylating) DFT_RS24075 DFT_RS20370
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase DFT_RS07165 DFT_RS11825
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupG: thymidine permease NupG/XapB
trehalose PsTP: trehalose phosphorylase
trehalose TRET1: facilitated trehalose transporter Tret1
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase DFT_RS24520
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine fahA: fumarylacetoacetate hydrolase DFT_RS00595
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase DFT_RS05355 DFT_RS24355
valine bch: 3-hydroxyisobutyryl-CoA hydrolase DFT_RS24350 DFT_RS17915
valine mmsA: methylmalonate-semialdehyde dehydrogenase DFT_RS20370 DFT_RS24075
valine mmsB: 3-hydroxyisobutyrate dehydrogenase DFT_RS08535
valine pccA: propionyl-CoA carboxylase, alpha subunit DFT_RS17925
valine pccB: propionyl-CoA carboxylase, beta subunit DFT_RS17930 DFT_RS01185
valine phtJ: L-valine uptake permease PhtJ DFT_RS04075
valine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase DFT_RS18710
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.

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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