GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Geobacter lovleyi SZ

Found 167 low-confidence and 48 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
2-oxoglutarate kgtP: 2-oxoglutarate:H+ symporter KgtP
4-hydroxybenzoate adh: acetaldehyde dehydrogenase (not acylating) GLOV_RS08400 GLOV_RS13735
4-hydroxybenzoate mhpD: 2-hydroxypentadienoate hydratase
4-hydroxybenzoate mhpE: 4-hydroxy-2-oxovalerate aldolase
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK GLOV_RS04610
4-hydroxybenzoate pobA: 4-hydroxybenzoate 3-monooxygenase
4-hydroxybenzoate praA: protocatechuate 2,3-dioxygenase
4-hydroxybenzoate xylF: 2-hydroxymuconate semialdehyde hydrolase
alanine cycA: L-alanine symporter CycA
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter
arginine gabT: gamma-aminobutyrate transaminase GLOV_RS11140 GLOV_RS00310
arginine patA: putrescine aminotransferase (PatA/SpuC) GLOV_RS11140 GLOV_RS15575
arginine patD: gamma-aminobutyraldehyde dehydrogenase GLOV_RS08400 GLOV_RS13735
arginine rocE: L-arginine permease
asparagine ans: asparaginase
asparagine yhiT: probable L-asparagine transporter YhiT GLOV_RS17505
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 GLOV_RS03485 GLOV_RS10035
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 GLOV_RS03490 GLOV_RS10040
citrulline citrullinase: putative citrullinase GLOV_RS12855
citrulline rocA: 1-pyrroline-5-carboxylate dehydrogenase GLOV_RS13735 GLOV_RS04485
citrulline rocD: ornithine aminotransferase GLOV_RS15575 GLOV_RS00310
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase GLOV_RS02235 GLOV_RS10345
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 GLOV_RS02320
deoxyinosine adh: acetaldehyde dehydrogenase (not acylating) GLOV_RS08400 GLOV_RS13735
deoxyinosine deoB: phosphopentomutase GLOV_RS12510
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine nupC: deoxyinosine:H+ symporter NupC GLOV_RS11815
deoxyribonate atoB: acetyl-CoA C-acetyltransferase
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase GLOV_RS09625
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) GLOV_RS08400 GLOV_RS13735
deoxyribose deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter
ethanol adh: acetaldehyde dehydrogenase (not acylating) GLOV_RS08400 GLOV_RS13735
fructose 1pfk: 1-phosphofructokinase
fructose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components
fucose aldA: lactaldehyde dehydrogenase GLOV_RS13735 GLOV_RS08400
fucose fucA: L-fuculose-phosphate aldolase FucA
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 GLOV_RS04315 GLOV_RS16655
galactose galK: galactokinase (-1-phosphate forming)
galactose galP: galactose:H+ symporter GalP
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase GLOV_RS01960
galactose pgmA: alpha-phosphoglucomutase GLOV_RS16425 GLOV_RS07935
galacturonate dopDH: 2,5-dioxopentanonate dehydrogenase GLOV_RS13735 GLOV_RS08400
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate gci: D-galactarolactone cycloisomerase
galacturonate gli: D-galactarolactone isomerase
galacturonate kdgD: 5-dehydro-4-deoxyglucarate dehydratase GLOV_RS15035
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) GLOV_RS03960 GLOV_RS07470
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 GLOV_RS13735 GLOV_RS08400
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate kdgD: 5-dehydro-4-deoxyglucarate dehydratase GLOV_RS15035
glucuronate udh: D-glucuronate dehydrogenase
glutamate gdhA: glutamate dehydrogenase, NAD-dependent GLOV_RS02780 GLOV_RS03380
glutamate gltS: L-glutamate:Na+ symporter GltS
glycerol glpF: glycerol facilitator glpF GLOV_RS04410
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
histidine permease: L-histidine permease
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase
isoleucine Bap2: L-isoleucine permease Bap2
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase GLOV_RS14360
isoleucine fadA: 2-methylacetoacetyl-CoA thiolase
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase GLOV_RS09625 GLOV_RS10875
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit GLOV_RS07900 GLOV_RS12625
isoleucine pccB: propionyl-CoA carboxylase, beta subunit GLOV_RS09005 GLOV_RS16145
isoleucine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC GLOV_RS11445
L-lactate L-LDH: L-lactate dehydrogenase GLOV_RS08065 GLOV_RS17535
L-lactate SfMCT: L-lactate transporter SfMCT GLOV_RS04605 GLOV_RS13015
lactose galE: UDP-glucose 4-epimerase GLOV_RS04315 GLOV_RS16655
lactose galK: galactokinase (-1-phosphate forming)
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase GLOV_RS01960
lactose glk: glucokinase GLOV_RS06220
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
lactose pgmA: alpha-phosphoglucomutase GLOV_RS16425 GLOV_RS07935
leucine atoB: acetyl-CoA C-acetyltransferase
leucine leuT: L-leucine:Na+ symporter LeuT GLOV_RS13070
leucine liuA: isovaleryl-CoA dehydrogenase
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit GLOV_RS12625 GLOV_RS07900
leucine liuC: 3-methylglutaconyl-CoA hydratase GLOV_RS14360 GLOV_RS06795
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit GLOV_RS09005
leucine liuE: hydroxymethylglutaryl-CoA lyase
leucine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC GLOV_RS11445
lysine davA: 5-aminovaleramidase GLOV_RS17205
lysine davB: L-lysine 2-monooxygenase
lysine davT: 5-aminovalerate aminotransferase GLOV_RS15575 GLOV_RS00310
lysine glaH: glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lysine lhgD: L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) GLOV_RS12590
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 GLOV_RS08245
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 GLOV_RS04670
myoinositol iolT: myo-inositol:H+ symporter
myoinositol mmsA: malonate-semialdehyde dehydrogenase GLOV_RS13735 GLOV_RS08400
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) GLOV_RS03960 GLOV_RS07470
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 GLOV_RS14360
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase GLOV_RS14360
phenylacetate paaH: 3-hydroxyadipyl-CoA dehydrogenase GLOV_RS11935 GLOV_RS09625
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase
phenylacetate paaZ1: oxepin-CoA hydrolase GLOV_RS14360
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylacetate ppa: phenylacetate permease ppa GLOV_RS06890 GLOV_RS06900
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
phenylalanine atoB: acetyl-CoA C-acetyltransferase
phenylalanine fahA: fumarylacetoacetate hydrolase
phenylalanine hmgA: homogentisate dioxygenase
phenylalanine HPD: 4-hydroxyphenylpyruvate dioxygenase
phenylalanine maiA: maleylacetoacetate isomerase
phenylalanine PAH: phenylalanine 4-monooxygenase
phenylalanine PCBD: pterin-4-alpha-carbinoalamine dehydratase
phenylalanine QDPR: 6,7-dihydropteridine reductase
proline proY: proline:H+ symporter
proline put1: proline dehydrogenase
proline putA: L-glutamate 5-semialdeyde dehydrogenase GLOV_RS13735 GLOV_RS04485
propionate mctC: propionate:H+ symporter GLOV_RS06890 GLOV_RS06900
propionate pccA: propionyl-CoA carboxylase, alpha subunit GLOV_RS07900 GLOV_RS12625
propionate pccB: propionyl-CoA carboxylase, beta subunit GLOV_RS09005 GLOV_RS16145
propionate prpE: propionyl-CoA synthetase GLOV_RS16915 GLOV_RS06850
putrescine gabT: gamma-aminobutyrate transaminase GLOV_RS11140 GLOV_RS00310
putrescine patA: putrescine aminotransferase (PatA/SpuC) GLOV_RS11140 GLOV_RS15575
putrescine patD: gamma-aminobutyraldehyde dehydrogenase GLOV_RS08400 GLOV_RS13735
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate mctC: pyruvate symporter MctC GLOV_RS06890 GLOV_RS06900
rhamnose LRA1: L-rhamnofuranose dehydrogenase GLOV_RS10875 GLOV_RS09625
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase
rhamnose LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase GLOV_RS09625 GLOV_RS10875
rhamnose LRA6: 2,4-diketo-3-deoxyrhamnonate hydrolase GLOV_RS17770
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
ribose rbsK: ribokinase
ribose rbsU: probable D-ribose transporter RbsU
serine serP: L-serine permease SerP
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase GLOV_RS09625 GLOV_RS10875
sucrose 1pfk: 1-phosphofructokinase
sucrose ams: sucrose hydrolase (invertase)
sucrose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components
threonine adh: acetaldehyde dehydrogenase (not acylating) GLOV_RS08400 GLOV_RS13735
threonine gcvP: glycine cleavage system, P component (glycine decarboxylase) GLOV_RS13230 GLOV_RS13225
threonine lpd: dihydrolipoyl dehydrogenase GLOV_RS07965 GLOV_RS09845
threonine tdcC: L-threonine:H+ symporter TdcC
thymidine adh: acetaldehyde dehydrogenase (not acylating) GLOV_RS08400 GLOV_RS13735
thymidine deoA: thymidine phosphorylase DeoA GLOV_RS09700
thymidine deoB: phosphopentomutase GLOV_RS12510
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 GLOV_RS09000
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine atoB: acetyl-CoA C-acetyltransferase
tyrosine fahA: fumarylacetoacetate hydrolase
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase
valine Bap2: L-valine permease Bap2
valine bch: 3-hydroxyisobutyryl-CoA hydrolase GLOV_RS14360
valine mmsA: methylmalonate-semialdehyde dehydrogenase GLOV_RS04485 GLOV_RS13735
valine mmsB: 3-hydroxyisobutyrate dehydrogenase GLOV_RS06525
valine pccA: propionyl-CoA carboxylase, alpha subunit GLOV_RS07900 GLOV_RS12625
valine pccB: propionyl-CoA carboxylase, beta subunit GLOV_RS09005 GLOV_RS16145
valine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC GLOV_RS11445
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 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