Potential Gaps in catabolism of small carbon sources in Dokdonella koreensis DS-123
Found 135 low-confidence and 19 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 | I596_RS00605 | |
| 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 | | |
| alanine | cycA: L-alanine symporter CycA | | |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arginine | rocD: ornithine aminotransferase | I596_RS12880 | I596_RS03965 |
| arginine | rocE: L-arginine permease | | |
| asparagine | ans: asparaginase | I596_RS02180 | |
| cellobiose | bgl: cellobiase | | |
| cellobiose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
| citrate | SLC13A5: citrate:Na+ symporter | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | I596_RS09325 | I596_RS02480 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | | |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | | |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
| citrulline | citrullinase: putative citrullinase | I596_RS08295 | |
| citrulline | rocD: ornithine aminotransferase | I596_RS12880 | I596_RS03965 |
| D-alanine | cycA: D-alanine:H+ symporter CycA | | |
| D-alanine | dadA: D-alanine dehydrogenase | I596_RS04610 | |
| D-lactate | D-LDH: D-lactate dehydrogenase | I596_RS07265 | I596_RS02995 |
| D-lactate | lctP: D-lactate:H+ symporter LctP or LidP | | |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | I596_RS16215 | I596_RS17335 |
| deoxyinosine | deoB: phosphopentomutase | I596_RS17115 | I596_RS06125 |
| deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyinosine | deoD: deoxyinosine phosphorylase | I596_RS02340 | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | I596_RS02455 | I596_RS09390 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | garK: glycerate 2-kinase | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fructose | 1pfk: 1-phosphofructokinase | | |
| fructose | fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components | | |
| 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 | | |
| fucose | fucU: L-fucose mutarotase FucU | | |
| galactose | galE: UDP-glucose 4-epimerase | I596_RS05190 | I596_RS05165 |
| galactose | galK: galactokinase (-1-phosphate forming) | | |
| galactose | galP: galactose:H+ symporter GalP | | |
| galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| galacturonate | eda: 2-keto-3-deoxygluconate 6-phosphate aldolase | | |
| 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 | gnd: 6-phosphogluconate dehydrogenase, decarboxylating | | |
| gluconate | gntK: D-gluconate kinase | | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | I596_RS14265 | |
| glucose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | dopDH: 2,5-dioxopentanonate dehydrogenase | I596_RS02225 | I596_RS04570 |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
| glucuronate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | I596_RS12675 | |
| glucuronate | udh: D-glucuronate dehydrogenase | | |
| glutamate | gltP: L-glutamate:cation symporter GltP/GltT | I596_RS02910 | |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | | |
| glycerol | glpF: glycerol facilitator glpF | I596_RS00815 | |
| glycerol | glpK: glycerol kinase | | |
| histidine | hutH: histidine ammonia-lyase | I596_RS15860 | I596_RS08810 |
| isoleucine | Bap2: L-isoleucine permease Bap2 | | |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| L-malate | sdlC: L-malate:Na+ symporter SdlC | | |
| lactose | galE: UDP-glucose 4-epimerase | I596_RS05190 | I596_RS05165 |
| lactose | galK: galactokinase (-1-phosphate forming) | | |
| lactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| lactose | glk: glucokinase | | |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | | |
| leucine | leuT: L-leucine:Na+ symporter LeuT | | |
| lysine | hglS: D-2-hydroxyglutarate synthase | | |
| lysine | lat: L-lysine 6-aminotransferase | I596_RS03960 | |
| lysine | lysN: 2-aminoadipate transaminase | I596_RS14430 | I596_RS03960 |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| lysine | ydiJ: (R)-2-hydroxyglutarate dehydrogenase | I596_RS07265 | I596_RS02995 |
| maltose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
| maltose | susB: alpha-glucosidase (maltase) | | |
| mannitol | mtlA: mannitol phosphotransferase system, EII-CBA components | | |
| mannitol | mtlD: mannitol-1-phosphate 5-dehydrogenase | | |
| mannose | manA: mannose-6-phosphate isomerase | I596_RS14730 | |
| mannose | manP: mannose PTS system, EII-CBA components | | |
| myoinositol | iolB: 5-deoxy-D-glucuronate isomerase | | |
| myoinositol | iolC: 5-dehydro-2-deoxy-D-gluconate kinase | I596_RS05395 | |
| 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 | I596_RS11670 | |
| myoinositol | iolT: myo-inositol:H+ symporter | | |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | I596_RS14265 | |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
| 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 | I596_RS12940 | I596_RS04715 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | I596_RS12940 | I596_RS08905 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | I596_RS06325 | I596_RS05370 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | I596_RS06325 | I596_RS05370 |
| phenylacetate | paaK: phenylacetate-CoA ligase | I596_RS07565 | |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | I596_RS04715 | I596_RS08905 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| phenylalanine | PCBD: pterin-4-alpha-carbinoalamine dehydratase | I596_RS12135 | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | I596_RS11280 | |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| putrescine | gabD: succinate semialdehyde dehydrogenase | I596_RS04570 | I596_RS02225 |
| putrescine | gabT: gamma-aminobutyrate transaminase | I596_RS12880 | I596_RS03960 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | I596_RS12880 | I596_RS03960 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | I596_RS04570 | I596_RS02225 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| 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 | | |
| serine | serP: L-serine permease SerP | | |
| sorbitol | mtlA: PTS system for polyols, EII-CBA components | | |
| sorbitol | srlD: sorbitol 6-phosphate 2-dehydrogenase | I596_RS10645 | I596_RS08880 |
| sucrose | scrK: fructokinase | I596_RS05395 | |
| sucrose | SUS: sucrose synthase | | |
| sucrose | sut: sucrose:proton symporter SUT/SUC | | |
| threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | I596_RS15740 | I596_RS03290 |
| threonine | tdcC: L-threonine:H+ symporter TdcC | | |
| thymidine | deoA: thymidine phosphorylase DeoA | | |
| thymidine | deoB: phosphopentomutase | I596_RS17115 | I596_RS06125 |
| thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
| trehalose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
| trehalose | treF: trehalase | I596_RS13870 | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| valine | Bap2: L-valine permease Bap2 | | |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | I596_RS12940 | I596_RS02240 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | I596_RS04725 | I596_RS16190 |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | | |
| 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