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:
- ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
- HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.
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:
- ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
- ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
- HMMer finds a hit (regardless of coverage or other bits).
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:
- our ignorance of proteins' functions,
- omissions in the gene models,
- frame-shift errors in the genome sequence, or
- the organism lacks the pathway.
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