GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Shewanella sp. ANA-3

Found 82 low-confidence and 20 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
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
arginine aguB: N-carbamoylputrescine hydrolase
arginine rocE: L-arginine permease
cellobiose bgl: cellobiase
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component Shewana3_0880 Shewana3_1538
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 Shewana3_0881
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component
citrulline arcC: carbamate kinase
citrulline odc: L-ornithine decarboxylase Shewana3_3871 Shewana3_3682
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-serine dsdA: D-serine ammonia-lyase Shewana3_0359
D-serine dsdX: D-serine transporter DsdX Shewana3_2684
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase Shewana3_2690 Shewana3_0437
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoP: deoxyribose transporter Shewana3_2310
fructose fruP: fructose porter FruP Shewana3_2310 Shewana3_2696
fucose aldA: lactaldehyde dehydrogenase Shewana3_3105 Shewana3_0250
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 Shewana3_2310
fucose fucU: L-fucose mutarotase FucU
galactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
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 gntK: D-gluconate kinase
gluconate gntT: gluconate:H+ symporter GntT Shewana3_2684
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
glucuronate dopDH: 2,5-dioxopentanonate dehydrogenase Shewana3_3092 Shewana3_3105
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate kdgD: 5-dehydro-4-deoxyglucarate dehydratase
glucuronate udh: D-glucuronate dehydrogenase
glycerol glpD: glycerol 3-phosphate dehydrogenase (monomeric) Shewana3_3310
glycerol glpF: glycerol facilitator glpF Shewana3_3064
histidine permease: L-histidine permease
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
lysine davA: 5-aminovaleramidase Shewana3_3642
lysine davB: L-lysine 2-monooxygenase
lysine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase Shewana3_2768 Shewana3_0024
lysine gcdG: succinyl-CoA:glutarate CoA-transferase
lysine gcdH: glutaryl-CoA dehydrogenase Shewana3_1672 Shewana3_2769
lysine lysP: L-lysine:H+ symporter LysP
mannitol mt2d: mannitol 2-dehydrogenase Shewana3_4105 Shewana3_2558
mannitol PLT5: polyol transporter PLT5
mannose gluP: mannose:Na+ symporter Shewana3_2310 Shewana3_2696
mannose man-isomerase: D-mannose isomerase
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 Shewana3_3350
myoinositol iolT: myo-inositol:H+ symporter
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 Shewana3_3010
phenylacetate paaF: 2,3-dehydroadipyl-CoA hydratase Shewana3_2768 Shewana3_0721
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase Shewana3_0721 Shewana3_4123
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase Shewana3_0023 Shewana3_2771
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase Shewana3_0023 Shewana3_2771
phenylacetate paaK: phenylacetate-CoA ligase Shewana3_2386
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase Shewana3_2768 Shewana3_1461
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
pyruvate actP: large subunit of pyruvate transporter (actP-like) Shewana3_1575
pyruvate yjcH: putative small subunit of pyruvate transporter (yjcH-like) Shewana3_1574
rhamnose aldA: lactaldehyde dehydrogenase Shewana3_3105 Shewana3_0250
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 rbsU: probable D-ribose transporter RbsU
sorbitol sdh: sorbitol dehydrogenase Shewana3_2558 Shewana3_4105
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2
trehalose treF: trehalase Shewana3_2311
tryptophan tnaA: tryptophanase
valine acdH: isobutyryl-CoA dehydrogenase Shewana3_2769 Shewana3_1672
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase Shewana3_2768 Shewana3_0024
valine mmsB: 3-hydroxyisobutyrate dehydrogenase Shewana3_2766 Shewana3_2554
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase Shewana3_4105
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 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