GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Geotalea uraniireducens Rf4

Found 156 low-confidence and 54 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) GURA_RS00565 GURA_RS16875
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 TRIC: TRIC-type L-alanine transporter GURA_RS01335
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 GURA_RS09920 GURA_RS00600
arginine patA: putrescine aminotransferase (PatA/SpuC) GURA_RS11390 GURA_RS01135
arginine patD: gamma-aminobutyraldehyde dehydrogenase GURA_RS00565 GURA_RS16875
arginine rocE: L-arginine permease
asparagine ans: asparaginase
asparagine glt: aspartate:proton symporter Glt GURA_RS01960
aspartate glt: aspartate:proton symporter Glt GURA_RS01960
cellobiose cbp: cellobiose phosphorylase GURA_RS22075
cellobiose cdt: cellobiose transporter cdt-1/cdt-2
citrate SLC13A5: citrate:Na+ symporter
citrulline arcC: carbamate kinase
citrulline PS417_17590: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline PS417_17595: ABC transporter for L-Citrulline, permease component 1
citrulline PS417_17600: ABC transporter for L-Citrulline, permease component 2
citrulline PS417_17605: ABC transporter for L-Citrulline, ATPase component GURA_RS05755 GURA_RS19800
citrulline put1: proline dehydrogenase GURA_RS09480
citrulline rocD: ornithine aminotransferase GURA_RS01135 GURA_RS00600
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase GURA_RS11155 GURA_RS03295
D-lactate lctP: D-lactate:H+ symporter LctP or LidP GURA_RS22820
D-serine cycA: D-serine:H+ symporter CycA
D-serine dsdA: D-serine ammonia-lyase GURA_RS20520
deoxyinosine adh: acetaldehyde dehydrogenase (not acylating) GURA_RS00565 GURA_RS16875
deoxyinosine deoB: phosphopentomutase GURA_RS13880
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine deoD: deoxyinosine phosphorylase GURA_RS08055
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase GURA_RS09505 GURA_RS18385
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) GURA_RS00565 GURA_RS16875
deoxyribose deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter
ethanol adh: acetaldehyde dehydrogenase (not acylating) GURA_RS00565 GURA_RS16875
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) GURA_RS12310 GURA_RS06110
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
galactose galK: galactokinase (-1-phosphate forming)
galactose galP: galactose:H+ symporter GalP
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase GURA_RS04350
galacturonate exuT: D-galacturonate transporter ExuT
galacturonate gci: D-galactarolactone cycloisomerase
galacturonate gli: D-galactarolactone isomerase
galacturonate kdgD: 5-dehydro-4-deoxyglucarate dehydratase GURA_RS01175
galacturonate udh: D-galacturonate dehydrogenase GURA_RS11700
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) GURA_RS00610
glucose MFS-glucose: glucose transporter, MFS superfamily
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 GURA_RS01175
glucuronate udh: D-glucuronate dehydrogenase GURA_RS11700
glutamate gltP: L-glutamate:cation symporter GltP/GltT GURA_RS01960
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 GURA_RS15475 GURA_RS15455
isoleucine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit GURA_RS14760 GURA_RS06460
isoleucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component GURA_RS14750 GURA_RS08200
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase GURA_RS15480 GURA_RS08095
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase GURA_RS09505 GURA_RS18385
isoleucine livH: L-isoleucine ABC transporter, permease component 1 (LivH/BraD) GURA_RS10795
isoleucine livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) GURA_RS10805
isoleucine livM: L-isoleucine ABC transporter, permease component 2 (LivM/BraE) GURA_RS10790
isoleucine lpd: branched-chain alpha-ketoacid dehydrogenase, E3 component GURA_RS06450 GURA_RS04270
L-lactate L-LDH: L-lactate dehydrogenase GURA_RS11125
L-lactate lctP: L-lactate:H+ symporter LctP or LidP GURA_RS22820
lactose galK: galactokinase (-1-phosphate forming)
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase GURA_RS04350
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
leucine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit GURA_RS14760 GURA_RS06460
leucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component GURA_RS14750 GURA_RS08200
leucine liuA: isovaleryl-CoA dehydrogenase GURA_RS15475 GURA_RS16870
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit GURA_RS14795 GURA_RS09260
leucine liuC: 3-methylglutaconyl-CoA hydratase GURA_RS15480 GURA_RS08130
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit
leucine liuE: hydroxymethylglutaryl-CoA lyase
leucine livH: L-leucine ABC transporter, permease component 1 (LivH/BraD) GURA_RS10795
leucine livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) GURA_RS10805
leucine livM: L-leucine ABC transporter, permease component 2 (LivM/BraE) GURA_RS10790
leucine lpd: branched-chain alpha-ketoacid dehydrogenase, E3 component GURA_RS06450 GURA_RS04270
lysine davA: 5-aminovaleramidase GURA_RS01040 GURA_RS07345
lysine davB: L-lysine 2-monooxygenase
lysine gcdG: succinyl-CoA:glutarate CoA-transferase
lysine gcdH: glutaryl-CoA dehydrogenase GURA_RS16870 GURA_RS15475
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 manA: mannose-6-phosphate isomerase GURA_RS16640
mannose STP6: mannose:H+ symporter
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 GURA_RS16875 GURA_RS00565
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) GURA_RS00610
NAG nagP: N-acetylglucosamine transporter NagP
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 GURA_RS15480 GURA_RS08130
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase GURA_RS08130 GURA_RS15480
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase GURA_RS08100 GURA_RS15490
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase GURA_RS08100 GURA_RS15490
phenylacetate paaZ1: oxepin-CoA hydrolase
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylacetate ppa: phenylacetate permease ppa GURA_RS06815
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
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 GURA_RS15480 GURA_RS08130
phenylalanine paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase GURA_RS08130 GURA_RS15480
phenylalanine paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase GURA_RS08100 GURA_RS15490
phenylalanine paaJ2: 3-oxoadipyl-CoA thiolase GURA_RS08100 GURA_RS15490
phenylalanine paaZ1: oxepin-CoA hydrolase
phenylalanine paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
proline proY: proline:H+ symporter
proline put1: proline dehydrogenase GURA_RS09480
propionate mctC: propionate:H+ symporter GURA_RS07225
propionate prpE: propionyl-CoA synthetase GURA_RS08185 GURA_RS08015
putrescine gabT: gamma-aminobutyrate transaminase GURA_RS09920 GURA_RS00600
putrescine patA: putrescine aminotransferase (PatA/SpuC) GURA_RS11390 GURA_RS01135
putrescine patD: gamma-aminobutyraldehyde dehydrogenase GURA_RS00565 GURA_RS16875
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate mctC: pyruvate symporter MctC GURA_RS07225
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 snatA: L-serine transporter GURA_RS03275
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase GURA_RS18385 GURA_RS09505
sucrose ams: sucrose hydrolase (invertase)
sucrose MFS-glucose: glucose transporter, MFS superfamily
threonine adh: acetaldehyde dehydrogenase (not acylating) GURA_RS00565 GURA_RS16875
threonine gcvP: glycine cleavage system, P component (glycine decarboxylase) GURA_RS01730 GURA_RS01725
threonine lpd: dihydrolipoyl dehydrogenase GURA_RS06450 GURA_RS04270
threonine snatA: L-threonine transporter snatA GURA_RS03275
thymidine adh: acetaldehyde dehydrogenase (not acylating) GURA_RS00565 GURA_RS16875
thymidine deoA: thymidine phosphorylase DeoA GURA_RS11300
thymidine deoB: phosphopentomutase GURA_RS13880
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
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine fahA: fumarylacetoacetate hydrolase
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase GURA_RS15475 GURA_RS15455
valine bch: 3-hydroxyisobutyryl-CoA hydrolase GURA_RS15480
valine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit GURA_RS14760 GURA_RS06460
valine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component GURA_RS14750 GURA_RS08200
valine livH: L-valine ABC transporter, permease component 1 (LivH/BraD) GURA_RS10795
valine livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) GURA_RS10805
valine livM: L-valine ABC transporter, permease component 2 (LivM/BraE) GURA_RS10790
valine lpd: branched-chain alpha-ketoacid dehydrogenase, E3 component GURA_RS06450 GURA_RS04270
valine mmsA: methylmalonate-semialdehyde dehydrogenase GURA_RS00565 GURA_RS09480
valine mmsB: 3-hydroxyisobutyrate dehydrogenase GURA_RS02990 GURA_RS14275
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