Potential Gaps in catabolism of small carbon sources in Pandoraea thiooxydans ATSB16
Found 89 low-confidence and 30 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 4-hydroxybenzoate | hcrA: 4-hydroxybenzoyl-CoA reductase, alpha subunit | PATSB16_RS01635 | |
| 4-hydroxybenzoate | hcrB: 4-hydroxybenzoyl-CoA reductase, beta subunit | | |
| 4-hydroxybenzoate | hcrC: 4-hydroxybenzoyl-CoA reductase, gamma subunit | PATSB16_RS01630 | PATSB16_RS09835 |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arginine | rocE: L-arginine permease | PATSB16_RS09985 | PATSB16_RS06000 |
| asparagine | glt: aspartate:proton symporter Glt | PATSB16_RS13295 | |
| aspartate | glt: aspartate:proton symporter Glt | PATSB16_RS13295 | |
| cellobiose | cbp: cellobiose phosphorylase | PATSB16_RS08730 | |
| cellobiose | cdt: cellobiose transporter cdt-1/cdt-2 | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | PATSB16_RS08600 | PATSB16_RS01415 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | PATSB16_RS13415 | PATSB16_RS08590 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | PATSB16_RS08590 | PATSB16_RS05360 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | PATSB16_RS05365 | PATSB16_RS13420 |
| D-serine | cycA: D-serine:H+ symporter CycA | PATSB16_RS09985 | PATSB16_RS06000 |
| D-serine | dsdA: D-serine ammonia-lyase | PATSB16_RS04845 | PATSB16_RS11890 |
| deoxyinosine | deoB: phosphopentomutase | | |
| deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyinosine | deoD: deoxyinosine phosphorylase | PATSB16_RS06805 | PATSB16_RS00775 |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | PATSB16_RS13335 | PATSB16_RS14520 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | PATSB16_RS03885 | PATSB16_RS06950 |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | PATSB16_RS13335 | PATSB16_RS14520 |
| deoxyribose | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | PATSB16_RS03885 | PATSB16_RS06950 |
| deoxyribose | drdehyd-alpha: 2-deoxy-D-ribose dehydrogenase, alpha subunit | PATSB16_RS15835 | PATSB16_RS09835 |
| deoxyribose | drdehyd-beta: 2-deoxy-D-ribose dehydrogenase, beta subunit | PATSB16_RS15840 | PATSB16_RS09830 |
| deoxyribose | drdehyd-cytc: 2-deoxyribose-D dehydrogenase, cytochrome c component | | |
| deoxyribose | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| fructose | 1pfk: 1-phosphofructokinase | PATSB16_RS11555 | |
| fructose | fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components | | |
| fucose | aldA: lactaldehyde dehydrogenase | PATSB16_RS01930 | PATSB16_RS15895 |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | PATSB16_RS11060 | |
| 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 | 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 | PATSB16_RS03155 | |
| galacturonate | uxaB: tagaturonate reductase | | |
| galacturonate | uxaC: D-galacturonate isomerase | | |
| gluconate | gntK: D-gluconate kinase | | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | PATSB16_RS08790 | PATSB16_RS17855 |
| glucosamine | SLC2A2: glucosamine transporter SLC2A2 | | |
| glucose | MFS-glucose: glucose transporter, MFS superfamily | | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | garL: 5-dehydro-4-deoxy-D-glucarate aldolase | PATSB16_RS08695 | PATSB16_RS05105 |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | PATSB16_RS17565 | |
| glucuronate | udh: D-glucuronate dehydrogenase | | |
| glutamate | gltP: L-glutamate:cation symporter GltP/GltT | PATSB16_RS13295 | |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | PATSB16_RS01245 | |
| glycerol | glpF: glycerol facilitator glpF | PATSB16_RS05410 | PATSB16_RS08815 |
| histidine | permease: L-histidine permease | PATSB16_RS09985 | PATSB16_RS06000 |
| 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 | davT: 5-aminovalerate aminotransferase | PATSB16_RS10400 | PATSB16_RS17895 |
| lysine | lysP: L-lysine:H+ symporter LysP | PATSB16_RS09985 | PATSB16_RS02760 |
| lysine | patA: cadaverine aminotransferase | PATSB16_RS01925 | PATSB16_RS17895 |
| lysine | patD: 5-aminopentanal dehydrogenase | PATSB16_RS14485 | PATSB16_RS01930 |
| maltose | malA: 6-phospho-alphaglucosidase | | |
| maltose | malEIICBA: maltose phosphotransferase system, EII-CBA components | | |
| mannitol | mtlA: mannitol phosphotransferase system, EII-CBA components | | |
| mannitol | mtlD: mannitol-1-phosphate 5-dehydrogenase | | |
| mannose | manA: mannose-6-phosphate isomerase | PATSB16_RS14385 | |
| mannose | manP: mannose PTS system, EII-CBA components | | |
| 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 | PATSB16_RS01565 | |
| myoinositol | iolT: myo-inositol:H+ symporter | | |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | PATSB16_RS08790 | PATSB16_RS17855 |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
| phenylacetate | H281DRAFT_04042: phenylacetate:H+ symporter | PATSB16_RS06000 | PATSB16_RS11290 |
| putrescine | gabT: gamma-aminobutyrate transaminase | PATSB16_RS01925 | PATSB16_RS10730 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | PATSB16_RS01925 | PATSB16_RS17975 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | PATSB16_RS09910 | PATSB16_RS03895 |
| rhamnose | aldA: lactaldehyde dehydrogenase | PATSB16_RS01930 | PATSB16_RS15895 |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | PATSB16_RS13785 | PATSB16_RS11230 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | PATSB16_RS03155 | PATSB16_RS12805 |
| rhamnose | LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase | PATSB16_RS08695 | PATSB16_RS02780 |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsK: ribokinase | | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| sorbitol | mtlA: PTS system for polyols, EII-CBA components | | |
| sorbitol | srlD: sorbitol 6-phosphate 2-dehydrogenase | PATSB16_RS14680 | PATSB16_RS03095 |
| sucrose | ams: sucrose hydrolase (invertase) | | |
| sucrose | MFS-glucose: glucose transporter, MFS superfamily | | |
| threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | PATSB16_RS00990 | PATSB16_RS12765 |
| threonine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | PATSB16_RS00995 | PATSB16_RS05685 |
| threonine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | PATSB16_RS01000 | PATSB16_RS05690 |
| thymidine | deoB: phosphopentomutase | | |
| thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | MFS-glucose: glucose transporter, MFS superfamily | | |
| tryptophan | tnaA: tryptophanase | PATSB16_RS14190 | |
| valine | livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | PATSB16_RS00990 | PATSB16_RS12765 |
| valine | livM: L-valine ABC transporter, permease component 2 (LivM/BraE) | PATSB16_RS01000 | PATSB16_RS12755 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | PATSB16_RS19035 | PATSB16_RS01900 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | PATSB16_RS03530 | PATSB16_RS14020 |
| 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