GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Geobacter daltonii FRC-32

Found 168 low-confidence and 47 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 gcdH: glutaryl-CoA dehydrogenase GEOB_RS10880 GEOB_RS01170
4-hydroxybenzoate hcrA: 4-hydroxybenzoyl-CoA reductase, alpha subunit GEOB_RS00520
4-hydroxybenzoate hcrB: 4-hydroxybenzoyl-CoA reductase, beta subunit
4-hydroxybenzoate hcrC: 4-hydroxybenzoyl-CoA reductase, gamma subunit GEOB_RS00525
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK GEOB_RS01110
4-hydroxybenzoate pimB: 3-oxopimeloyl-CoA:CoA acetyltransferase GEOB_RS00490 GEOB_RS01200
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 rocD: ornithine aminotransferase GEOB_RS05585 GEOB_RS14935
arginine rocE: L-arginine permease
asparagine ans: asparaginase
asparagine yhiT: probable L-asparagine transporter YhiT GEOB_RS11185
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 GEOB_RS03640 GEOB_RS10430
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
citrulline rocD: ornithine aminotransferase GEOB_RS05585 GEOB_RS14935
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase GEOB_RS04150 GEOB_RS17085
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 GEOB_RS03490
deoxyinosine adh: acetaldehyde dehydrogenase (not acylating) GEOB_RS17645 GEOB_RS12935
deoxyinosine deoB: phosphopentomutase GEOB_RS17000 GEOB_RS15160
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine deoD: deoxyinosine phosphorylase GEOB_RS17625
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate garK: glycerate 2-kinase
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose adh: acetaldehyde dehydrogenase (not acylating) GEOB_RS17645 GEOB_RS12935
deoxyribose deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter
ethanol adh: acetaldehyde dehydrogenase (not acylating) GEOB_RS17645 GEOB_RS12935
fructose scrK: fructokinase
fructose Slc2a5: fructose:H+ symporter
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
fumarate sdcL: fumarate:Na+ symporter SdcL GEOB_RS03995
galactose galK: galactokinase (-1-phosphate forming)
galactose galP: galactose:H+ symporter GalP
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase GEOB_RS05025
galactose pgmA: alpha-phosphoglucomutase GEOB_RS15160 GEOB_RS17000
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) GEOB_RS18355
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 GEOB_RS17645 GEOB_RS12935
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate kdgD: 5-dehydro-4-deoxyglucarate dehydratase GEOB_RS05625
glucuronate udh: D-glucuronate dehydrogenase
glutamate gltP: L-glutamate:cation symporter GltP/GltT GEOB_RS02095
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 permease: L-histidine permease
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase GEOB_RS10880 GEOB_RS10905
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase GEOB_RS01210 GEOB_RS15615
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase GEOB_RS12960 GEOB_RS09520
isoleucine livH: L-isoleucine ABC transporter, permease component 1 (LivH/BraD) GEOB_RS13885
isoleucine livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) GEOB_RS13880
isoleucine livM: L-isoleucine ABC transporter, permease component 2 (LivM/BraE) GEOB_RS13890
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit GEOB_RS15185 GEOB_RS17375
isoleucine pccB: propionyl-CoA carboxylase, beta subunit GEOB_RS04165
isoleucine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC
L-lactate SfMCT: L-lactate transporter SfMCT GEOB_RS14155
L-malate sdlC: L-malate:Na+ symporter SdlC GEOB_RS03995
lactose galK: galactokinase (-1-phosphate forming)
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase GEOB_RS05025
lactose glk: glucokinase GEOB_RS14280
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
lactose pgmA: alpha-phosphoglucomutase GEOB_RS15160 GEOB_RS17000
leucine liuA: isovaleryl-CoA dehydrogenase GEOB_RS10880 GEOB_RS10905
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit GEOB_RS17375 GEOB_RS15185
leucine liuC: 3-methylglutaconyl-CoA hydratase GEOB_RS01210 GEOB_RS12040
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit
leucine liuE: hydroxymethylglutaryl-CoA lyase
leucine livH: L-leucine ABC transporter, permease component 1 (LivH/BraD) GEOB_RS13885
leucine livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) GEOB_RS13880
leucine livM: L-leucine ABC transporter, permease component 2 (LivM/BraE) GEOB_RS13890
leucine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC
lysine davA: 5-aminovaleramidase GEOB_RS05490 GEOB_RS11655
lysine davB: L-lysine 2-monooxygenase
lysine davD: glutarate semialdehyde dehydrogenase GEOB_RS17645 GEOB_RS12935
lysine davT: 5-aminovalerate aminotransferase GEOB_RS05585 GEOB_RS14935
lysine gcdG: succinyl-CoA:glutarate CoA-transferase GEOB_RS12030
lysine gcdH: glutaryl-CoA dehydrogenase GEOB_RS10880 GEOB_RS01170
lysine lysP: L-lysine:H+ symporter LysP
maltose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
maltose susB: alpha-glucosidase (maltase) GEOB_RS06075
mannitol mtlA: mannitol phosphotransferase system, EII-CBA components
mannitol mtlD: mannitol-1-phosphate 5-dehydrogenase
mannose manA: mannose-6-phosphate isomerase GEOB_RS09320
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
myoinositol iolT: myo-inositol:H+ symporter
myoinositol mmsA: malonate-semialdehyde dehydrogenase GEOB_RS17645 GEOB_RS12935
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) GEOB_RS18355
NAG nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components
phenylacetate gcdH: glutaryl-CoA dehydrogenase GEOB_RS10880 GEOB_RS01170
phenylacetate padB: phenylacetyl-CoA dehydrogenase, PadB subunit
phenylacetate padC: phenylacetyl-CoA dehydrogenase, PadC subunit GEOB_RS06735 GEOB_RS04315
phenylacetate padD: phenylacetyl-CoA dehydrogenase, PadD subunit
phenylacetate padE: phenylglyoxylate dehydrogenase, gamma subunit
phenylacetate padF: phenylglyoxylate dehydrogenase, delta subunit
phenylacetate padG: phenylglyoxylate dehydrogenase, alpha subunit GEOB_RS13225
phenylacetate padH: phenylglyoxylate dehydrogenase, epsilon subunit GEOB_RS16275
phenylacetate padI: phenylglyoxylate dehydrogenase, beta subunit
phenylacetate pimB: 3-oxopimeloyl-CoA:CoA acetyltransferase GEOB_RS00490 GEOB_RS01200
phenylacetate ppa: phenylacetate permease ppa GEOB_RS11595 GEOB_RS00755
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
phenylalanine gcdH: glutaryl-CoA dehydrogenase GEOB_RS10880 GEOB_RS01170
phenylalanine padB: phenylacetyl-CoA dehydrogenase, PadB subunit
phenylalanine padC: phenylacetyl-CoA dehydrogenase, PadC subunit GEOB_RS06735 GEOB_RS04315
phenylalanine padD: phenylacetyl-CoA dehydrogenase, PadD subunit
phenylalanine padE: phenylglyoxylate dehydrogenase, gamma subunit
phenylalanine padF: phenylglyoxylate dehydrogenase, delta subunit
phenylalanine padG: phenylglyoxylate dehydrogenase, alpha subunit GEOB_RS13225
phenylalanine padH: phenylglyoxylate dehydrogenase, epsilon subunit GEOB_RS16275
phenylalanine padI: phenylglyoxylate dehydrogenase, beta subunit
phenylalanine pimB: 3-oxopimeloyl-CoA:CoA acetyltransferase GEOB_RS00490 GEOB_RS01200
proline proY: proline:H+ symporter
proline put1: proline dehydrogenase GEOB_RS12935
propionate mctC: propionate:H+ symporter GEOB_RS11595 GEOB_RS00850
propionate pccA: propionyl-CoA carboxylase, alpha subunit GEOB_RS15185 GEOB_RS17375
propionate pccB: propionyl-CoA carboxylase, beta subunit GEOB_RS04165
propionate prpE: propionyl-CoA synthetase GEOB_RS00985 GEOB_RS17665
putrescine gabD: succinate semialdehyde dehydrogenase GEOB_RS17645 GEOB_RS12935
putrescine gabT: gamma-aminobutyrate transaminase GEOB_RS14935 GEOB_RS02285
putrescine patA: putrescine aminotransferase (PatA/SpuC) GEOB_RS14935 GEOB_RS05585
putrescine patD: gamma-aminobutyraldehyde dehydrogenase GEOB_RS17645 GEOB_RS12935
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate mctC: pyruvate symporter MctC GEOB_RS11595 GEOB_RS00850
rhamnose LRA1: L-rhamnofuranose dehydrogenase GEOB_RS12960 GEOB_RS00485
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase
rhamnose LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase
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 GEOB_RS12960 GEOB_RS00485
sucrose ams: sucrose hydrolase (invertase)
sucrose ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG)
threonine adh: acetaldehyde dehydrogenase (not acylating) GEOB_RS17645 GEOB_RS12935
threonine gcvP: glycine cleavage system, P component (glycine decarboxylase) GEOB_RS06285 GEOB_RS06290
threonine ltaE: L-threonine aldolase GEOB_RS12980
threonine tdcC: L-threonine:H+ symporter TdcC
thymidine adh: acetaldehyde dehydrogenase (not acylating) GEOB_RS17645 GEOB_RS12935
thymidine deoA: thymidine phosphorylase DeoA GEOB_RS14840
thymidine deoB: phosphopentomutase GEOB_RS17000 GEOB_RS15160
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 GEOB_RS18815 GEOB_RS06075
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine fahA: fumarylacetoacetate hydrolase GEOB_RS07880
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase GEOB_RS10880 GEOB_RS10900
valine bch: 3-hydroxyisobutyryl-CoA hydrolase GEOB_RS12040 GEOB_RS01210
valine livG: L-valine ABC transporter, ATPase component 2 (LivG/BraF) GEOB_RS13895 GEOB_RS08235
valine livH: L-valine ABC transporter, permease component 1 (LivH/BraD) GEOB_RS13885
valine livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) GEOB_RS13880
valine livM: L-valine ABC transporter, permease component 2 (LivM/BraE) GEOB_RS13890
valine mmsA: methylmalonate-semialdehyde dehydrogenase GEOB_RS17645 GEOB_RS12935
valine mmsB: 3-hydroxyisobutyrate dehydrogenase
valine pccA: propionyl-CoA carboxylase, alpha subunit GEOB_RS15185 GEOB_RS17375
valine pccB: propionyl-CoA carboxylase, beta subunit GEOB_RS04165
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
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