GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Carboxydothermus pertinax Ug1

Found 136 low-confidence and 56 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 mhpD: 2-hydroxypentadienoate hydratase cpu_RS07680
4-hydroxybenzoate mhpE: 4-hydroxy-2-oxovalerate aldolase cpu_RS07670 cpu_RS12435
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK
4-hydroxybenzoate pobA: 4-hydroxybenzoate 3-monooxygenase
4-hydroxybenzoate praA: protocatechuate 2,3-dioxygenase
4-hydroxybenzoate praB: 2-hydroxymuconate 6-semialdehyde dehydrogenase
4-hydroxybenzoate praD: 2-oxohex-3-enedioate decarboxylase cpu_RS07680
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase cpu_RS11835
arabinose araE: L-arabinose:H+ symporter
arginine gabD: succinate semialdehyde dehydrogenase
arginine gabT: gamma-aminobutyrate transaminase cpu_RS12205 cpu_RS11265
arginine patA: putrescine aminotransferase (PatA/SpuC) cpu_RS12205 cpu_RS11265
arginine patD: gamma-aminobutyraldehyde dehydrogenase
arginine rocE: L-arginine permease cpu_RS11915
asparagine ans: asparaginase cpu_RS02715
asparagine glt: aspartate:proton symporter Glt cpu_RS10925
aspartate glt: aspartate:proton symporter Glt cpu_RS10925
cellobiose cbp: cellobiose phosphorylase
cellobiose cdt: cellobiose transporter cdt-1/cdt-2
citrate acn: aconitase cpu_RS04970
citrate cit1: citrate:H+ symporter Cit1 cpu_RS04040
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component cpu_RS09910 cpu_RS09015
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 cpu_RS09905
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline arcC: carbamate kinase
citrulline rocA: 1-pyrroline-5-carboxylate dehydrogenase
citrulline rocD: ornithine aminotransferase cpu_RS12205 cpu_RS05070
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase cpu_RS02910 cpu_RS03150
D-lactate lctP: D-lactate:H+ symporter LctP or LidP cpu_RS02905
D-serine cycA: D-serine:H+ symporter CycA cpu_RS11915
D-serine dsdA: D-serine ammonia-lyase cpu_RS06700 cpu_RS11930
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate aacS: acetoacetyl-CoA synthetase cpu_RS10435 cpu_RS10425
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase cpu_RS09085 cpu_RS11320
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) cpu_RS07830 cpu_RS07370
fructose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components cpu_RS04935
fucose fucA: L-fuculose-phosphate aldolase FucA cpu_RS11835
fucose fucI: L-fucose isomerase FucI
fucose fucK: L-fuculose kinase FucK
fucose fucO: L-lactaldehyde reductase cpu_RS07830 cpu_RS07370
fucose fucP: L-fucose:H+ symporter FucP
fucose fucU: L-fucose mutarotase FucU
galactose galE: UDP-glucose 4-epimerase cpu_RS12715 cpu_RS05430
galactose galK: galactokinase (-1-phosphate forming)
galactose galP: galactose:H+ symporter GalP
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
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 cpu_RS04015
glucosamine glc-kinase: glucosamine kinase cpu_RS00255 cpu_RS09385
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) cpu_RS01780 cpu_RS09410
glucosamine SM_b21216: ABC transporter for D-Glucosamine, ATPase component cpu_RS09405 cpu_RS07620
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
glucuronate garR: tartronate semialdehyde reductase
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate udh: D-glucuronate dehydrogenase
glutamate gltP: L-glutamate:cation symporter GltP/GltT cpu_RS10925
glutamate mcl: (S)-citramalyl-CoA pyruvate-lyase
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric)
histidine hutG: N-formiminoglutamate formiminohydrolase cpu_RS10775
histidine hutH: histidine ammonia-lyase
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
histidine PA5503: L-histidine ABC transporter, ATPase component cpu_RS09015 cpu_RS09910
isoleucine acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase cpu_RS11860 cpu_RS02525
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase cpu_RS10405 cpu_RS10860
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase cpu_RS11320 cpu_RS09085
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit cpu_RS04525 cpu_RS07800
isoleucine pccB: propionyl-CoA carboxylase, beta subunit cpu_RS07795 cpu_RS01750
isoleucine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC
L-lactate lutA: L-lactate dehydrogenase, LutA subunit cpu_RS02930 cpu_RS02915
L-lactate lutB: L-lactate dehydrogenase, LutB subunit cpu_RS02930 cpu_RS06900
L-lactate lutC: L-lactate dehydrogenase, LutC subunit cpu_RS02925 cpu_RS06900
lactose galE: UDP-glucose 4-epimerase cpu_RS12715 cpu_RS05430
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 aacS: acetoacetyl-CoA synthetase cpu_RS10435 cpu_RS10425
leucine liuA: isovaleryl-CoA dehydrogenase cpu_RS02525 cpu_RS11860
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit cpu_RS07800 cpu_RS04525
leucine liuC: 3-methylglutaconyl-CoA hydratase cpu_RS10860 cpu_RS10405
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit cpu_RS07795 cpu_RS01750
leucine liuE: hydroxymethylglutaryl-CoA lyase
leucine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC
lysine amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd)
lysine hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase cpu_RS12205 cpu_RS11265
lysine lysN: 2-aminoadipate transaminase cpu_RS11525 cpu_RS07060
lysine lysP: L-lysine:H+ symporter LysP cpu_RS11915
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase
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 cpu_RS04935
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 cpu_RS04995
myoinositol iolE: scyllo-inosose 2-dehydratase
myoinositol iolG: myo-inositol 2-dehydrogenase
myoinositol iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase cpu_RS06995
myoinositol iolT: myo-inositol:H+ symporter
myoinositol mmsA: malonate-semialdehyde dehydrogenase
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) cpu_RS01780 cpu_RS09410
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 cpu_RS10860 cpu_RS10420
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase cpu_RS10410 cpu_RS10880
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase cpu_RS10410 cpu_RS10880
phenylacetate paaZ1: oxepin-CoA hydrolase cpu_RS12240 cpu_RS10420
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylacetate ppa: phenylacetate permease ppa cpu_RS01670
phenylalanine aroP: L-phenylalanine:H+ symporter AroP cpu_RS11915
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 cpu_RS10860 cpu_RS10420
phenylalanine paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase cpu_RS10410 cpu_RS10880
phenylalanine paaJ2: 3-oxoadipyl-CoA thiolase cpu_RS10410 cpu_RS10880
phenylalanine paaZ1: oxepin-CoA hydrolase cpu_RS12240 cpu_RS10420
phenylalanine paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
proline proY: proline:H+ symporter cpu_RS11915
proline put1: proline dehydrogenase
proline putA: L-glutamate 5-semialdeyde dehydrogenase
propionate pccA: propionyl-CoA carboxylase, alpha subunit cpu_RS04525 cpu_RS07800
propionate pccB: propionyl-CoA carboxylase, beta subunit cpu_RS07795 cpu_RS01750
putrescine gabD: succinate semialdehyde dehydrogenase
putrescine gabT: gamma-aminobutyrate transaminase cpu_RS12205 cpu_RS11265
putrescine patA: putrescine aminotransferase (PatA/SpuC) cpu_RS12205 cpu_RS11265
putrescine patD: gamma-aminobutyraldehyde dehydrogenase
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
rhamnose fucO: L-lactaldehyde reductase cpu_RS07830 cpu_RS07370
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 serP: L-serine permease SerP cpu_RS11915
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase cpu_RS11320
sucrose ams: sucrose hydrolase (invertase)
sucrose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components cpu_RS04935
threonine RR42_RS28305: L-threonine:H+ symporter cpu_RS11915
thymidine nupG: thymidine permease NupG/XapB
trehalose MFS-glucose: glucose transporter, MFS superfamily
trehalose treF: trehalase cpu_RS10755
tryptophan aroP: tryptophan:H+ symporter AroP cpu_RS11915
tryptophan tnaA: tryptophanase
tyrosine aacS: acetoacetyl-CoA synthetase cpu_RS10435 cpu_RS10425
tyrosine aroP: L-tyrosine transporter (AroP/FywP) cpu_RS11915
tyrosine fahA: fumarylacetoacetate hydrolase cpu_RS10025
tyrosine hmgA: homogentisate dioxygenase
tyrosine HPD: 4-hydroxyphenylpyruvate dioxygenase
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase cpu_RS11860 cpu_RS02525
valine bch: 3-hydroxyisobutyryl-CoA hydrolase cpu_RS10420 cpu_RS10860
valine mmsA: methylmalonate-semialdehyde dehydrogenase
valine mmsB: 3-hydroxyisobutyrate dehydrogenase
valine pccA: propionyl-CoA carboxylase, alpha subunit cpu_RS04525 cpu_RS07800
valine pccB: propionyl-CoA carboxylase, beta subunit cpu_RS07795 cpu_RS01750
valine vorC: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC
xylitol fruI: xylitol PTS, enzyme IIABC (FruI) cpu_RS04935
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