GapMind for catabolism of small carbon sources

 

Potential Gaps in catabolism of small carbon sources in Shewanella loihica PV-4

Found 81 low-confidence and 31 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
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose Echvi_1880: L-arabinose:Na+ symporter Shew_2286
arginine gabD: succinate semialdehyde dehydrogenase Shew_3173 Shew_0967
arginine gabT: gamma-aminobutyrate transaminase Shew_3172 Shew_0966
arginine rocE: L-arginine permease
cellobiose bgl: cellobiase
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component Shew_3164 Shew_2402
citrulline AO353_03045: ABC transporter for L-Citrulline, permease component 2
citrulline AO353_03050: ABC transporter for L-Citrulline, permease component 1 Shew_3165
citrulline AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component Shew_3166
citrulline arcC: carbamate kinase
citrulline gabD: succinate semialdehyde dehydrogenase Shew_3173 Shew_0967
citrulline gabT: gamma-aminobutyrate transaminase Shew_3172 Shew_0966
citrulline odc: L-ornithine decarboxylase Shew_3392
D-alanine cycA: D-alanine:H+ symporter CycA
D-alanine dadA: D-alanine dehydrogenase
D-serine cycA: D-serine:H+ symporter CycA
D-serine dsdA: D-serine ammonia-lyase Shew_0293
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase Shew_2863 Shew_1407
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoP: deoxyribose transporter
fructose fruP: fructose porter FruP Shew_1890 Shew_1119
fructose scrK: fructokinase Shew_1428
fucose aldA: lactaldehyde dehydrogenase Shew_0967 Shew_3574
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 Shew_1890
fucose fucU: L-fucose mutarotase FucU
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 Shew_2533
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter
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) Shew_0800
glycerol glpF: glycerol facilitator glpF
histidine permease: L-histidine permease
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric) Shew_3269
lysine davA: 5-aminovaleramidase Shew_0409
lysine davB: L-lysine 2-monooxygenase
lysine davD: glutarate semialdehyde dehydrogenase Shew_3173 Shew_0967
lysine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase Shew_1670 Shew_0019
lysine gcdG: succinyl-CoA:glutarate CoA-transferase
lysine lysP: L-lysine:H+ symporter LysP
mannitol mtlA: mannitol phosphotransferase system, EII-CBA components
mannitol mtlD: mannitol-1-phosphate 5-dehydrogenase
mannose gluP: mannose:Na+ symporter Shew_1890 Shew_1119
mannose manA: mannose-6-phosphate isomerase
mannose mannokinase: D-mannose kinase Shew_1428
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 Shew_0755
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
phenylacetate paaF: 2,3-dehydroadipyl-CoA hydratase Shew_1670 Shew_2864
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase Shew_0540 Shew_2672
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase Shew_0018 Shew_2858
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase Shew_0018 Shew_1667
phenylacetate paaK: phenylacetate-CoA ligase Shew_2188 Shew_3084
phenylacetate paaT: phenylacetate transporter Paa
phenylacetate paaZ1: oxepin-CoA hydrolase Shew_2672 Shew_1670
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine aroP: L-phenylalanine:H+ symporter AroP
putrescine gabD: succinate semialdehyde dehydrogenase Shew_3173 Shew_0967
putrescine gabT: gamma-aminobutyrate transaminase Shew_3172 Shew_0966
putrescine potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) Shew_0973
pyruvate actP: large subunit of pyruvate transporter (actP-like) Shew_2371
pyruvate yjcH: putative small subunit of pyruvate transporter (yjcH-like) Shew_2372
rhamnose aldA: lactaldehyde dehydrogenase Shew_0967 Shew_3574
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 mtlA: PTS system for polyols, EII-CBA components
sorbitol srlD: sorbitol 6-phosphate 2-dehydrogenase Shew_1673 Shew_1603
sucrose ams: sucrose hydrolase (invertase) Shew_1889
trehalose treF: trehalase Shew_1889
tryptophan tnaA: tryptophanase
valine acdH: isobutyryl-CoA dehydrogenase Shew_1669 Shew_2570
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase Shew_1670 Shew_0019
valine mmsB: 3-hydroxyisobutyrate dehydrogenase Shew_1672 Shew_1609
xylitol fruI: xylitol PTS, enzyme IIABC (FruI)
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase Shew_3710
xylose Echvi_1871: sodium/xylose cotransporter Shew_2286 Shew_3270
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, the preprint on GapMind for carbon sources, 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