GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Pseudomonas stutzeri RCH2

Found 76 low-confidence and 28 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
4-hydroxybenzoate pcaB: 3-carboxymuconate cycloisomerase
4-hydroxybenzoate pcaC: 4-carboxymuconolactone decarboxylase Psest_3069 Psest_1394
4-hydroxybenzoate pcaG: protocatechuate 3,4-dioxygenase, beta subunit
4-hydroxybenzoate pcaH: protocatechuate 3,4-dioxygenase, alpha subunit
4-hydroxybenzoate pcaK: 4-hydroxybenzoate transporter pcaK Psest_2695
4-hydroxybenzoate pobA: 4-hydroxybenzoate 3-monooxygenase
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 Psest_4285 Psest_3653
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component Psest_0139 Psest_0016
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2 Psest_0136 Psest_0018
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 Psest_0137 Psest_0018
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component Psest_0138
citrulline gabT: gamma-aminobutyrate transaminase Psest_4285 Psest_3653
citrulline odc: L-ornithine decarboxylase Psest_3350 Psest_2075
D-serine cycA: D-serine:H+ symporter CycA Psest_1697
D-serine dsdA: D-serine ammonia-lyase Psest_3866
deoxyinosine deoB: phosphopentomutase Psest_0974
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine deoD: deoxyinosine phosphorylase Psest_2642
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase Psest_3522 Psest_1716
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoK: deoxyribokinase
deoxyribose deoP: deoxyribose transporter
fucose aldA: lactaldehyde dehydrogenase Psest_0905 Psest_0375
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 galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
galacturonate exuT: D-galacturonate transporter ExuT
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE)
glucosamine nagB: glucosamine 6-phosphate deaminase (isomerizing) Psest_4349
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
histidine hutG: N-formiminoglutamate formiminohydrolase
histidine hutH: histidine ammonia-lyase Psest_3695
histidine hutI: imidazole-5-propionate hydrolase
histidine hutU: urocanase
lactose galK: galactokinase (-1-phosphate forming)
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
lactose lacP: lactose permease LacP
lysine patA: cadaverine aminotransferase Psest_2719 Psest_4306
lysine patD: 5-aminopentanal dehydrogenase Psest_0905 Psest_2634
mannitol mak: mannose kinase
mannitol mt1d: mannitol 1-dehydrogenase Psest_1276
mannitol PLT5: polyol transporter PLT5
mannose manP: mannose PTS system, EII-CBA components Psest_3353
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 Psest_0333
myoinositol iolT: myo-inositol:H+ symporter
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) Psest_4349
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 Psest_3453
phenylacetate paaF: 2,3-dehydroadipyl-CoA hydratase Psest_2437 Psest_3109
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase Psest_2437 Psest_3109
phenylacetate paaK: phenylacetate-CoA ligase Psest_1335 Psest_4228
phenylacetate paaZ1: oxepin-CoA hydrolase Psest_3109 Psest_2437
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylacetate ppa: phenylacetate permease ppa Psest_2938 Psest_0347
putrescine gabT: gamma-aminobutyrate transaminase Psest_4285 Psest_3653
rhamnose aldA: lactaldehyde dehydrogenase Psest_0905 Psest_0375
rhamnose LRA1: L-rhamnofuranose dehydrogenase Psest_0357 Psest_2081
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA3: L-rhamnonate dehydratase Psest_0377
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
sorbitol mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase Psest_1147 Psest_1716
sucrose ams: sucrose hydrolase (invertase) Psest_0870 Psest_3785
thymidine deoA: thymidine phosphorylase DeoA Psest_3523 Psest_2502
thymidine deoB: phosphopentomutase Psest_0974
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupG: thymidine permease NupG/XapB
tryptophan antA: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA Psest_2699
tryptophan antB: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB Psest_2698
tryptophan antC: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC Psest_2697 Psest_1174
tryptophan kyn: kynureninase
tryptophan kynA: tryptophan 2,3-dioxygenase
tryptophan kynB: kynurenine formamidase
xylitol fruI: xylitol PTS, enzyme IIABC (FruI) Psest_3353
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase Psest_1428
xylose gtsA: xylose ABC transporter, periplasmic substrate-binding component GtsA Psest_1896
xylose gtsB: xylose ABC transporter, permease component 1 GtsB Psest_1897
xylose gtsC: xylose ABC transporter, permease component 2 GtsC Psest_1898
xylose gtsD: xylose ABC transporter, ATPase component GtsD Psest_1899 Psest_0871
xylose xylA: xylose isomerase
xylose xylB: xylulokinase

Confidence: high confidence medium confidence low confidence

This GapMind analysis is from Sep 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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