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 (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