Potential Gaps in catabolism of small carbon sources in Corynebacterium frankenforstense ST18
Found 116 low-confidence and 51 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | csbX: 2-oxoglutarate permease csbX | CFRA_RS07880 | |
| 4-hydroxybenzoate | mhpD: 2-hydroxypentadienoate hydratase | | |
| 4-hydroxybenzoate | mhpE: 4-hydroxy-2-oxovalerate aldolase | | |
| 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 | | |
| arginine | odc: L-ornithine decarboxylase | | |
| arginine | patA: putrescine aminotransferase (PatA/SpuC) | CFRA_RS06140 | CFRA_RS02675 |
| arginine | patD: gamma-aminobutyraldehyde dehydrogenase | CFRA_RS04135 | CFRA_RS05120 |
| arginine | rocE: L-arginine permease | CFRA_RS02685 | CFRA_RS04555 |
| arginine | rocF: arginase | | |
| asparagine | ans: asparaginase | CFRA_RS03160 | CFRA_RS09310 |
| aspartate | glt: aspartate:proton symporter Glt | CFRA_RS00135 | |
| cellobiose | bgl: cellobiase | CFRA_RS01295 | |
| cellobiose | MFS-glucose: glucose transporter, MFS superfamily | CFRA_RS09000 | |
| citrate | cit1: citrate:H+ symporter Cit1 | CFRA_RS09880 | CFRA_RS02540 |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | CFRA_RS06310 | CFRA_RS06995 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | CFRA_RS06305 | CFRA_RS07005 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | CFRA_RS06305 | |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
| citrulline | arcC: carbamate kinase | | |
| citrulline | odc: L-ornithine decarboxylase | | |
| citrulline | patA: putrescine aminotransferase (PatA/SpuC) | CFRA_RS06140 | CFRA_RS02675 |
| citrulline | patD: gamma-aminobutyraldehyde dehydrogenase | CFRA_RS04135 | CFRA_RS05120 |
| D-alanine | cycA: D-alanine:H+ symporter CycA | CFRA_RS04555 | CFRA_RS04345 |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-lactate | D-LDH: D-lactate dehydrogenase | CFRA_RS10585 | CFRA_RS06480 |
| D-lactate | lctP: D-lactate:H+ symporter LctP or LidP | | |
| D-serine | cycA: D-serine:H+ symporter CycA | CFRA_RS04555 | CFRA_RS07890 |
| deoxyinosine | deoB: phosphopentomutase | CFRA_RS01745 | CFRA_RS02915 |
| deoxyribonate | aacS: acetoacetyl-CoA synthetase | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | | |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | garK: glycerate 2-kinase | CFRA_RS07535 | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fructose | 1pfk: 1-phosphofructokinase | CFRA_RS04740 | |
| fucose | aldA: lactaldehyde dehydrogenase | CFRA_RS05120 | CFRA_RS04135 |
| 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 | galK: galactokinase (-1-phosphate forming) | | |
| galactose | galP: galactose:H+ symporter GalP | CFRA_RS09000 | |
| 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 | CFRA_RS08730 | |
| galacturonate | uxaA: D-altronate dehydratase | | |
| galacturonate | uxaB: tagaturonate reductase | | |
| galacturonate | uxaC: D-galacturonate isomerase | CFRA_RS09355 | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucose | MFS-glucose: glucose transporter, MFS superfamily | CFRA_RS09000 | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | eda: 2-keto-3-deoxygluconate 6-phosphate aldolase | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | kdgK: 2-keto-3-deoxygluconate kinase | CFRA_RS08730 | |
| glucuronate | uxaC: D-glucuronate isomerase | CFRA_RS09355 | |
| glucuronate | uxuA: D-mannonate dehydratase | CFRA_RS09375 | |
| glucuronate | uxuB: D-mannonate dehydrogenase | CFRA_RS09360 | CFRA_RS07885 |
| glutamate | gltP: L-glutamate:cation symporter GltP/GltT | CFRA_RS00135 | |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | | |
| glycerol | glpF: glycerol facilitator glpF | | |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | CFRA_RS00375 | |
| histidine | hutH: histidine ammonia-lyase | | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | CFRA_RS00505 | CFRA_RS00485 |
| isoleucine | brnQ: L-isoleucine:cation symporter BrnQ/BraZ/BraB | CFRA_RS08665 | |
| isoleucine | ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase | CFRA_RS04615 | CFRA_RS09015 |
| isoleucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| 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) | | |
| leucine | aacS: acetoacetyl-CoA synthetase | | |
| leucine | brnQ: L-leucine:Na+ symporter BrnQ/BraB | CFRA_RS08665 | |
| leucine | liuA: isovaleryl-CoA dehydrogenase | CFRA_RS00505 | CFRA_RS00360 |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | CFRA_RS02750 | CFRA_RS02740 |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | CFRA_RS04615 | CFRA_RS09015 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | CFRA_RS02790 | CFRA_RS10740 |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
| leucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| lysine | davA: 5-aminovaleramidase | CFRA_RS10480 | |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | davD: glutarate semialdehyde dehydrogenase | CFRA_RS03430 | CFRA_RS02680 |
| lysine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | CFRA_RS04615 | CFRA_RS01685 |
| lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | CFRA_RS00495 | CFRA_RS00355 |
| maltose | malA: 6-phospho-alphaglucosidase | | |
| maltose | malEIICBA: maltose phosphotransferase system, EII-CBA components | CFRA_RS10030 | |
| mannitol | PLT5: polyol transporter PLT5 | CFRA_RS09000 | |
| mannitol | scrK: fructokinase | CFRA_RS02045 | CFRA_RS08730 |
| mannose | manP: mannose PTS system, EII-CBA components | CFRA_RS04735 | |
| 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 | | |
| myoinositol | mmsA: malonate-semialdehyde dehydrogenase | CFRA_RS04135 | CFRA_RS02680 |
| myoinositol | PGA1_c07300: myo-inositol ABC transport, substrate-binding component | CFRA_RS00100 | |
| myoinositol | PGA1_c07310: myo-inositol ABC transporter, permease component | CFRA_RS00105 | |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | CFRA_RS10025 | |
| 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 | CFRA_RS04615 | |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | CFRA_RS04615 | |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | CFRA_RS09020 | CFRA_RS00705 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | CFRA_RS09020 | CFRA_RS00705 |
| phenylacetate | paaK: phenylacetate-CoA ligase | CFRA_RS04620 | CFRA_RS09005 |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | CFRA_RS04615 | |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylacetate | ppa: phenylacetate permease ppa | CFRA_RS03360 | |
| phenylalanine | iorAB: phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB | | |
| phenylalanine | paaA: phenylacetyl-CoA 1,2-epoxidase, subunit A | | |
| phenylalanine | paaB: phenylacetyl-CoA 1,2-epoxidase, subunit B | | |
| phenylalanine | paaC: phenylacetyl-CoA 1,2-epoxidase, subunit C | | |
| phenylalanine | paaE: phenylacetyl-CoA 1,2-epoxidase, subunit E | | |
| phenylalanine | paaF: 2,3-dehydroadipyl-CoA hydratase | CFRA_RS04615 | |
| phenylalanine | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | CFRA_RS04615 | |
| phenylalanine | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | CFRA_RS09020 | CFRA_RS00705 |
| phenylalanine | paaJ2: 3-oxoadipyl-CoA thiolase | CFRA_RS09020 | CFRA_RS00705 |
| phenylalanine | paaZ1: oxepin-CoA hydrolase | CFRA_RS04615 | |
| phenylalanine | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| proline | put1: proline dehydrogenase | | |
| proline | putA: L-glutamate 5-semialdeyde dehydrogenase | CFRA_RS04135 | CFRA_RS03430 |
| propionate | prpE: propionyl-CoA synthetase | CFRA_RS04620 | |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | CFRA_RS06140 | CFRA_RS02675 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | CFRA_RS04135 | CFRA_RS05120 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| rhamnose | aldA: lactaldehyde dehydrogenase | CFRA_RS05120 | CFRA_RS04135 |
| 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 | rbsA: D-ribose ABC transporter, ATPase component RbsA | CFRA_RS00395 | |
| ribose | rbsC: D-ribose ABC transporter, permease component RbsC | CFRA_RS00390 | CFRA_RS00105 |
| sorbitol | scrK: fructokinase | CFRA_RS02045 | CFRA_RS08730 |
| sorbitol | sdh: sorbitol dehydrogenase | CFRA_RS07885 | CFRA_RS09060 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | CFRA_RS09000 | |
| sucrose | 1pfk: 1-phosphofructokinase | CFRA_RS04740 | |
| threonine | ltaE: L-threonine aldolase | CFRA_RS03965 | |
| threonine | RR42_RS28305: L-threonine:H+ symporter | CFRA_RS07890 | CFRA_RS04555 |
| thymidine | deoB: phosphopentomutase | CFRA_RS01745 | CFRA_RS02915 |
| trehalose | PsTP: trehalose phosphorylase | | |
| trehalose | thuE: trehalose ABC transporter, substrate-binding component ThuE | CFRA_RS02865 | |
| trehalose | thuF: trehalose ABC transporter, permease component 1 (ThuF) | | |
| trehalose | thuK: trehalose ABC transporter, ATPase component ThuK | CFRA_RS02870 | CFRA_RS02480 |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aacS: acetoacetyl-CoA synthetase | | |
| tyrosine | fahA: fumarylacetoacetate hydrolase | CFRA_RS06450 | CFRA_RS03775 |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | CFRA_RS00505 | CFRA_RS00485 |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | CFRA_RS03725 | |
| valine | brnQ: L-valine:cation symporter BrnQ/BraZ/BraB | CFRA_RS08665 | |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | CFRA_RS04615 | CFRA_RS01685 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | CFRA_RS03430 | CFRA_RS04135 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | | |
| valine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | CFRA_RS09000 | |
| xylose | xyrA: xylitol reductase | CFRA_RS09095 | CFRA_RS09475 |
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