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 (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