GapMind for catabolism of small carbon sources


Potential Gaps in catabolism of small carbon sources in Chromobacterium vaccinii MWU205

Found 65 low-confidence and 40 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
2-oxoglutarate dctP: 2-oxoglutarate TRAP transporter, solute receptor component DctP VL52_RS19650
2-oxoglutarate dctQ: 2-oxoglutarate TRAP transporter, small permease component DctQ
4-hydroxybenzoate mhpD: 2-hydroxypentadienoate hydratase
4-hydroxybenzoate mhpE: 4-hydroxy-2-oxovalerate aldolase
4-hydroxybenzoate pobA: 4-hydroxybenzoate 3-monooxygenase
4-hydroxybenzoate praA: protocatechuate 2,3-dioxygenase
4-hydroxybenzoate xylF: 2-hydroxymuconate semialdehyde hydrolase VL52_RS11130
arabinose araA: L-arabinose isomerase
arabinose araB: ribulokinase
arabinose araD: L-ribulose-5-phosphate epimerase
arabinose araE: L-arabinose:H+ symporter
cellobiose bgl: cellobiase VL52_RS08440 VL52_RS04915
cellobiose crr: glucose PTS, enzyme IIA VL52_RS01610 VL52_RS06575
citrate SLC13A5: citrate:Na+ symporter
citrulline AO353_03040: ABC transporter for L-Citrulline, ATPase component VL52_RS06130 VL52_RS19750
citrulline aruG: ornithine/arginine N-succinyltransferase subunit AruAII (AruG) VL52_RS15515 VL52_RS15520
D-serine cycA: D-serine:H+ symporter CycA VL52_RS13800 VL52_RS00290
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase VL52_RS17095 VL52_RS01235
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme
deoxyribose deoP: deoxyribose transporter
fructose frcA: fructose ABC transporter, ATPase component FrcA VL52_RS18715 VL52_RS07675
fructose frcC: fructose ABC transporter, permease component FrcC VL52_RS18720
fucose aldA: lactaldehyde dehydrogenase VL52_RS07105 VL52_RS21455
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 VL52_RS04135
fucose fucU: L-fucose mutarotase FucU
galactose galK: galactokinase (-1-phosphate forming)
galactose galP: galactose:H+ symporter GalP
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 gntT: gluconate:H+ symporter GntT
glucosamine gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) VL52_RS06570 VL52_RS01615
glucose crr: glucose PTS, enzyme IIA VL52_RS01610 VL52_RS06575
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter VL52_RS04955
glucuronate exuT: D-glucuronate:H+ symporter ExuT
glucuronate garL: 5-dehydro-4-deoxy-D-glucarate aldolase
glucuronate gci: D-glucaro-1,4-lactone cycloisomerase
glucuronate udh: D-glucuronate dehydrogenase
histidine PA5503: L-histidine ABC transporter, ATPase component VL52_RS00410 VL52_RS19750
histidine PA5505: L-histidine ABC transporter, substrate-binding component VL52_RS07410
isoleucine ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase VL52_RS17095 VL52_RS02940
lactose galK: galactokinase (-1-phosphate forming)
lactose galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
lysine davD: glutarate semialdehyde dehydrogenase VL52_RS20940 VL52_RS07105
lysine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase VL52_RS18865 VL52_RS21030
lysine patA: cadaverine aminotransferase VL52_RS18210 VL52_RS15525
lysine patD: 5-aminopentanal dehydrogenase VL52_RS20940 VL52_RS21455
maltose crr: glucose PTS, enzyme IIA VL52_RS01610 VL52_RS06575
maltose susB: alpha-glucosidase (maltase) VL52_RS03515
mannitol mt2d: mannitol 2-dehydrogenase VL52_RS13400 VL52_RS17095
mannitol PLT5: polyol transporter PLT5
mannose manP: mannose PTS system, EII-CBA components VL52_RS18010 VL52_RS07470
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 VL52_RS05280
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 VL52_RS18865 VL52_RS21030
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase VL52_RS18865 VL52_RS19950
phenylacetate paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase VL52_RS14225 VL52_RS10355
phenylacetate paaJ2: 3-oxoadipyl-CoA thiolase VL52_RS14225 VL52_RS10355
phenylacetate paaK: phenylacetate-CoA ligase VL52_RS11845 VL52_RS00860
phenylacetate paaZ1: oxepin-CoA hydrolase VL52_RS21030 VL52_RS17970
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylalanine PCBD: pterin-4-alpha-carbinoalamine dehydratase VL52_RS07770
propionate lctP: propionate permease VL52_RS18675
rhamnose aldA: lactaldehyde dehydrogenase VL52_RS07105 VL52_RS21455
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 rbsB: D-ribose ABC transporter, substrate-binding component RbsB VL52_RS18725 VL52_RS16360
ribose rbsC: D-ribose ABC transporter, permease component RbsC VL52_RS18720
sorbitol sdh: sorbitol dehydrogenase VL52_RS20160 VL52_RS02940
sorbitol SOT: sorbitol:H+ co-transporter SOT1 or SOT2
sucrose ams: sucrose hydrolase (invertase) VL52_RS03515
sucrose frcA: fructose ABC transporter, ATPase component FrcA VL52_RS18715 VL52_RS07675
sucrose frcC: fructose ABC transporter, permease component FrcC VL52_RS18720
threonine tdcC: L-threonine:H+ symporter TdcC VL52_RS12080
valine acdH: isobutyryl-CoA dehydrogenase VL52_RS21025 VL52_RS19965
valine ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase VL52_RS18865 VL52_RS21030
valine livH: L-valine ABC transporter, permease component 1 (LivH/BraD) VL52_RS15500
valine livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) VL52_RS09675 VL52_RS18885
valine mmsB: 3-hydroxyisobutyrate dehydrogenase VL52_RS21040 VL52_RS18355
xylitol fruI: xylitol PTS, enzyme IIABC (FruI) VL52_RS18010
xylitol x5p-reductase: D-xylulose-5-phosphate 2-reductase VL52_RS13400
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 24 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