GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Aquimarina agarilytica ZC1

Found 135 low-confidence and 31 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
4-hydroxybenzoate mhpE: 4-hydroxy-2-oxovalerate aldolase KQA_RS18655
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
acetate actP: cation/acetate symporter ActP
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter KQA_RS0216875
arginine rocE: L-arginine permease
arginine rocF: arginase
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component KQA_RS0204935 KQA_RS0210450
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
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-lactate D-LDH: D-lactate dehydrogenase KQA_RS0216110 KQA_RS0210485
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
deoxyinosine deoB: phosphopentomutase KQA_RS0215090
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase KQA_RS0216565 KQA_RS0204195
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 deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter KQA_RS0205845
ethanol etoh-dh-nad: ethanol dehydrogenase (NAD(P)) KQA_RS0202490 KQA_RS0216565
fructose 1pfk: 1-phosphofructokinase
fructose fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components
fucose fucD: L-fuconate dehydratase
fucose fucDH: 2-keto-3-deoxy-L-fuconate 4-dehydrogenase KQA_RS0216565 KQA_RS0202100
fucose fuconolactonase: L-fucono-1,5-lactonase KQA_RS0205855
fucose KDF-hydrolase: 2,4-diketo-3-deoxy-L-fuconate hydrolase KQA_RS0201925
fumarate SLC26dg: fumarate transporter SLC26dg KQA_RS0208715
galactose sglS: sodium/galactose cotransporter KQA_RS0206325 KQA_RS0211305
galacturonate PS417_04205: D-galacturonate transporter KQA_RS0206115
galacturonate uxaC: D-galacturonate isomerase
gluconate gntT: gluconate:H+ symporter GntT
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE)
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) KQA_RS0214275
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate uxaC: D-glucuronate isomerase
glucuronate uxuA: D-mannonate dehydratase KQA_RS0206120
glucuronate uxuB: D-mannonate dehydrogenase
glutamate aspA: L-aspartate ammonia-lyase KQA_RS0203105
glycerol glpF: glycerol facilitator glpF KQA_RS0212530
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 KQA_RS0200835 KQA_RS0210620
isoleucine Bap2: L-isoleucine permease Bap2
isoleucine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit KQA_RS0212430
isoleucine bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit KQA_RS0201575 KQA_RS0213230
isoleucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component KQA_RS0205185 KQA_RS0212435
isoleucine ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase KQA_RS0202635 KQA_RS0206355
isoleucine epi: methylmalonyl-CoA epimerase
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase KQA_RS0216565 KQA_RS0204195
isoleucine mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
isoleucine pccA: propionyl-CoA carboxylase, alpha subunit KQA_RS0205450 KQA_RS0217680
L-lactate lctO: L-lactate oxidase or 2-monooxygenase
L-lactate lctP: L-lactate:H+ symporter LctP or LidP
L-malate sdlC: L-malate:Na+ symporter SdlC
lactose lacP: lactose permease LacP
leucine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit KQA_RS0212430
leucine bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit KQA_RS0201575 KQA_RS0213230
leucine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component KQA_RS0205185 KQA_RS0212435
leucine leuT: L-leucine:Na+ symporter LeuT
leucine liuA: isovaleryl-CoA dehydrogenase KQA_RS0210620 KQA_RS0200835
leucine liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit KQA_RS0205450 KQA_RS0217680
leucine liuC: 3-methylglutaconyl-CoA hydratase KQA_RS0202635 KQA_RS0206355
leucine liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit KQA_RS0216515
lysine hglS: D-2-hydroxyglutarate synthase
lysine lat: L-lysine 6-aminotransferase KQA_RS0201990 KQA_RS0210000
lysine lysN: 2-aminoadipate transaminase KQA_RS0205060 KQA_RS0206170
lysine lysP: L-lysine:H+ symporter LysP
lysine ydiJ: (R)-2-hydroxyglutarate dehydrogenase KQA_RS0214315
mannitol mtlA: mannitol phosphotransferase system, EII-CBA components
mannitol mtlD: mannitol-1-phosphate 5-dehydrogenase
mannose manA: mannose-6-phosphate isomerase KQA_RS0206190 KQA_RS0214785
mannose STP6: mannose:H+ symporter KQA_RS0216875
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 iolG: myo-inositol 2-dehydrogenase
myoinositol iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase
myoinositol iolT: myo-inositol:H+ symporter KQA_RS0216875
myoinositol mmsA: malonate-semialdehyde dehydrogenase KQA_RS0203955 KQA_RS0203960
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) KQA_RS0214275
NAG nagP: N-acetylglucosamine transporter NagP KQA_RS0204555
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 paaF: 2,3-dehydroadipyl-CoA hydratase KQA_RS0202635 KQA_RS0206355
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase KQA_RS0202635
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase KQA_RS0206350 KQA_RS0209185
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase KQA_RS0206350 KQA_RS0209185
phenylacetate paaK: phenylacetate-CoA ligase
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
phenylalanine maiA: maleylacetoacetate isomerase
phenylalanine PAH: phenylalanine 4-monooxygenase KQA_RS0210195
phenylalanine PCBD: pterin-4-alpha-carbinoalamine dehydratase
phenylalanine QDPR: 6,7-dihydropteridine reductase
proline proY: proline:H+ symporter
propionate epi: methylmalonyl-CoA epimerase
propionate mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
propionate pccA: propionyl-CoA carboxylase, alpha subunit KQA_RS0205450 KQA_RS0217680
propionate putP: propionate transporter; proline:Na+ symporter
putrescine gabT: gamma-aminobutyrate transaminase KQA_RS0206170 KQA_RS0210000
putrescine patA: putrescine aminotransferase (PatA/SpuC) KQA_RS0201990 KQA_RS0212565
putrescine patD: gamma-aminobutyraldehyde dehydrogenase KQA_RS0203955 KQA_RS0203960
putrescine puuP: putrescine:H+ symporter PuuP/PlaP
pyruvate SLC5A8: sodium-coupled pyruvate transporter
rhamnose aldA: lactaldehyde dehydrogenase KQA_RS0203955 KQA_RS0203960
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 sdaB: L-serine ammonia-lyase
serine serP: L-serine permease SerP
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase KQA_RS0216565 KQA_RS0212070
succinate sdc: succinate:Na+ symporter Sdc
sucrose ams: sucrose hydrolase (invertase)
threonine ltaE: L-threonine aldolase KQA_RS0203930
threonine tdcC: L-threonine:H+ symporter TdcC
thymidine deoA: thymidine phosphorylase DeoA
thymidine deoB: phosphopentomutase KQA_RS0215090
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupC: thymidine permease NupC KQA_RS0205075
trehalose treF: trehalase
tryptophan aroP: tryptophan:H+ symporter AroP
tryptophan tnaA: tryptophanase
tyrosine aroP: L-tyrosine transporter (AroP/FywP)
tyrosine maiA: maleylacetoacetate isomerase
valine acdH: isobutyryl-CoA dehydrogenase KQA_RS0210620 KQA_RS0200835
valine Bap2: L-valine permease Bap2
valine bch: 3-hydroxyisobutyryl-CoA hydrolase KQA_RS0202635
valine bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit KQA_RS0212430
valine bkdB: branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit KQA_RS0201575 KQA_RS0213230
valine bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component KQA_RS0205185 KQA_RS0212435
valine epi: methylmalonyl-CoA epimerase
valine mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
valine mmsA: methylmalonate-semialdehyde dehydrogenase KQA_RS0203955 KQA_RS0203960
valine mmsB: 3-hydroxyisobutyrate dehydrogenase
valine pccA: propionyl-CoA carboxylase, alpha subunit KQA_RS0205450 KQA_RS0217680
xylitol PLT5: xylitol:H+ symporter PLT5 KQA_RS0216875
xylitol xdhA: xylitol dehydrogenase KQA_RS0212070 KQA_RS0203975
xylose xylT: D-xylose transporter KQA_RS0216875

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