Potential Gaps in catabolism of small carbon sources in Methylibium petroleiphilum PM1
Found 110 low-confidence and 30 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | kgtP: 2-oxoglutarate:H+ symporter KgtP | MPE_RS16910 | |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| 4-hydroxybenzoate | pobA: 4-hydroxybenzoate 3-monooxygenase | MPE_RS16560 | |
| 4-hydroxybenzoate | praA: protocatechuate 2,3-dioxygenase | | |
| alanine | snatA: L-alanine symporter SnatA | MPE_RS19200 | |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arginine | gabD: succinate semialdehyde dehydrogenase | MPE_RS11735 | MPE_RS09615 |
| arginine | odc: L-ornithine decarboxylase | MPE_RS09695 | |
| cellobiose | cbp: cellobiose phosphorylase | | |
| cellobiose | cdt: cellobiose transporter cdt-1/cdt-2 | | |
| cellobiose | glk: glucokinase | MPE_RS10495 | |
| citrate | SLC13A5: citrate:Na+ symporter | | |
| citrulline | arcC: carbamate kinase | | |
| citrulline | gabD: succinate semialdehyde dehydrogenase | MPE_RS11735 | MPE_RS09615 |
| citrulline | odc: L-ornithine decarboxylase | MPE_RS09695 | |
| D-alanine | cycA: D-alanine:H+ symporter CycA | | |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | MPE_RS19035 | MPE_RS15770 |
| deoxyinosine | deoB: phosphopentomutase | MPE_RS10790 | MPE_RS06385 |
| deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyinosine | deoD: deoxyinosine phosphorylase | | |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | MPE_RS07950 | MPE_RS14735 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribose | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | MPE_RS07950 | MPE_RS14735 |
| deoxyribose | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribose | drdehyd-beta: 2-deoxy-D-ribose dehydrogenase, beta subunit | MPE_RS18320 | MPE_RS14775 |
| deoxyribose | drdehyd-cytc: 2-deoxyribose-D dehydrogenase, cytochrome c component | MPE_RS03770 | |
| 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 | MPE_RS09640 | MPE_RS03155 |
| galactose | galK: galactokinase (-1-phosphate forming) | | |
| galactose | galP: galactose:H+ symporter GalP | | |
| galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| galacturonate | dopDH: 2,5-dioxopentanonate dehydrogenase | MPE_RS11735 | MPE_RS17810 |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | gci: D-galactarolactone cycloisomerase | | |
| galacturonate | gli: D-galactarolactone isomerase | | |
| galacturonate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | MPE_RS12915 | |
| galacturonate | udh: D-galacturonate dehydrogenase | | |
| 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) | MPE_RS02815 | |
| glucose | ptsG-crr: glucose PTS, enzyme II (CBA components, PtsG) | | |
| 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 | MPE_RS00935 | MPE_RS04865 |
| glucuronate | udh: D-glucuronate dehydrogenase | | |
| glucuronate | uxuL: D-glucaro-1,5-lactonase UxuL or UxuF | | |
| glutamate | gdhA: glutamate dehydrogenase, NAD-dependent | MPE_RS18915 | |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | MPE_RS18515 | |
| glycerol | glpF: glycerol facilitator glpF | | |
| histidine | bgtA: L-histidine ABC transporter, ATPase component BgtA | MPE_RS14545 | MPE_RS02235 |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | MPE_RS16960 | MPE_RS16000 |
| lactose | galE: UDP-glucose 4-epimerase | MPE_RS09640 | MPE_RS03155 |
| lactose | galK: galactokinase (-1-phosphate forming) | | |
| lactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| lactose | glk: glucokinase | MPE_RS10495 | |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | | |
| lysine | davD: glutarate semialdehyde dehydrogenase | MPE_RS11735 | MPE_RS01830 |
| lysine | hisP: L-lysine ABC transporter, ATPase component HisP | MPE_RS14545 | MPE_RS02235 |
| lysine | patA: cadaverine aminotransferase | MPE_RS15280 | MPE_RS09620 |
| lysine | patD: 5-aminopentanal dehydrogenase | MPE_RS03015 | MPE_RS11735 |
| 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 | MPE_RS03160 | MPE_RS13770 |
| 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 | MPE_RS01450 | MPE_RS14090 |
| myoinositol | iolT: myo-inositol:H+ symporter | | |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | MPE_RS02815 | |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | ARO10: phenylpyruvate decarboxylase | | |
| phenylalanine | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| proline | davD: glutarate semialdehyde dehydrogenase | MPE_RS11735 | MPE_RS01830 |
| proline | prdA: D-proline reductase, prdA component | | |
| proline | prdB: D-proline reductase, prdB component | | |
| proline | prdC: D-proline reductase, electron transfer component PrdC | | |
| proline | prdF: proline racemase | | |
| propionate | lctP: propionate permease | MPE_RS11145 | |
| putrescine | gabD: succinate semialdehyde dehydrogenase | MPE_RS11735 | MPE_RS09615 |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | MPE_RS14735 | MPE_RS03210 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | | |
| rhamnose | LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase | MPE_RS00935 | MPE_RS04865 |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsK: ribokinase | | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| sorbitol | scrK: fructokinase | MPE_RS10495 | |
| sorbitol | sdh: sorbitol dehydrogenase | MPE_RS08040 | MPE_RS14735 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
| sucrose | scrK: fructokinase | MPE_RS10495 | |
| sucrose | SUS: sucrose synthase | | |
| sucrose | sut: sucrose:proton symporter SUT/SUC | | |
| threonine | snatA: L-threonine transporter snatA | MPE_RS19200 | |
| thymidine | deoA: thymidine phosphorylase DeoA | | |
| thymidine | deoB: phosphopentomutase | MPE_RS10790 | MPE_RS06385 |
| thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | glk: glucokinase | MPE_RS10495 | |
| trehalose | PsTP: trehalose phosphorylase | | |
| trehalose | TRET1: facilitated trehalose transporter Tret1 | | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | MPE_RS16960 | MPE_RS16000 |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | MPE_RS04915 | MPE_RS03005 |
| valine | livH: L-valine ABC transporter, permease component 1 (LivH/BraD) | MPE_RS05630 | MPE_RS18970 |
| valine | livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | MPE_RS09770 | |
| valine | livM: L-valine ABC transporter, permease component 2 (LivM/BraE) | MPE_RS05635 | |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | MPE_RS17810 | MPE_RS09615 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | MPE_RS19000 | MPE_RS04870 |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | MPE_RS21935 | |
| 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