Potential Gaps in catabolism of small carbon sources in Nocardioides dokdonensis FR1436
Found 95 low-confidence and 70 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | kgtP: 2-oxoglutarate:H+ symporter KgtP | | |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| 4-hydroxybenzoate | pobA: 4-hydroxybenzoate 3-monooxygenase | I601_RS04750 | |
| 4-hydroxybenzoate | praA: protocatechuate 2,3-dioxygenase | | |
| 4-hydroxybenzoate | xylF: 2-hydroxymuconate semialdehyde hydrolase | I601_RS17180 | I601_RS02865 |
| acetate | actP: cation/acetate symporter ActP | I601_RS07725 | I601_RS07700 |
| alanine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | I601_RS18165 | |
| alanine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | I601_RS18185 | I601_RS10450 |
| alanine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | I601_RS18180 | I601_RS05895 |
| 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 | | |
| asparagine | glt: aspartate:proton symporter Glt | I601_RS15970 | |
| aspartate | glt: aspartate:proton symporter Glt | I601_RS15970 | |
| cellobiose | MFS-glucose: glucose transporter, MFS superfamily | | |
| citrate | SLC13A5: citrate:Na+ symporter | I601_RS18080 | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | I601_RS07015 | I601_RS08990 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | | |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | I601_RS08985 | |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
| D-alanine | cycA: D-alanine:H+ symporter CycA | | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| 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 | I601_RS09980 | |
| deoxyinosine | deoB: phosphopentomutase | I601_RS01115 | I601_RS00705 |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | I601_RS09210 | I601_RS02915 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoK: deoxyribokinase | I601_RS02645 | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fructose | 1pfk: 1-phosphofructokinase | I601_RS20105 | I601_RS02165 |
| fucose | aldA: lactaldehyde dehydrogenase | I601_RS01130 | I601_RS12775 |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | I601_RS02650 | |
| 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 | 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 | I601_RS02165 | |
| galacturonate | uxaA: D-altronate dehydratase | | |
| galacturonate | uxaB: tagaturonate reductase | | |
| galacturonate | uxaC: D-galacturonate isomerase | | |
| gluconate | gntT: gluconate:H+ symporter GntT | I601_RS11235 | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | I601_RS09685 | I601_RS05935 |
| 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 | | |
| glucuronate | garR: tartronate semialdehyde reductase | | |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
| glucuronate | udh: D-glucuronate dehydrogenase | | |
| glutamate | gltP: L-glutamate:cation symporter GltP/GltT | I601_RS15970 | |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | I601_RS12605 | I601_RS05700 |
| glycerol | glpF: glycerol facilitator glpF | I601_RS12595 | I601_RS01285 |
| histidine | hutG': N-formylglutamate amidohydrolase | | |
| histidine | natB: L-histidine ABC transporter, substrate-binding component NatB | I601_RS18165 | |
| histidine | natC: L-histidine ABC transporter, permease component 1 (NatC) | I601_RS18180 | |
| histidine | natD: L-histidine ABC transporter, permease component 2 (NatD) | I601_RS18185 | I601_RS10450 |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | I601_RS05880 | I601_RS05205 |
| isoleucine | livH: L-isoleucine ABC transporter, permease component 1 (LivH/BraD) | I601_RS10450 | I601_RS05905 |
| isoleucine | livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | | |
| isoleucine | livM: L-isoleucine ABC transporter, permease component 2 (LivM/BraE) | I601_RS05895 | I601_RS02140 |
| isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | I601_RS00935 | I601_RS06760 |
| L-lactate | Shew_2732: L-lactate:Na+ symporter, small component | I601_RS07705 | |
| lactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | I601_RS05650 | I601_RS13885 |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | I601_RS05880 | I601_RS05205 |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | I601_RS19165 | I601_RS17105 |
| leucine | natB: L-leucine ABC transporter, substrate-binding component NatB | I601_RS18165 | |
| leucine | natC: L-leucine ABC transporter, permease component 1 (NatC) | I601_RS18180 | |
| leucine | natD: L-leucine ABC transporter, permease component 2 (NatD) | I601_RS18185 | I601_RS10450 |
| lysine | cadA: lysine decarboxylase | | |
| lysine | davD: glutarate semialdehyde dehydrogenase | I601_RS05735 | I601_RS14160 |
| lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | I601_RS06545 | I601_RS10415 |
| lysine | gcdH: glutaryl-CoA dehydrogenase | I601_RS02110 | I601_RS10230 |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| lysine | patA: cadaverine aminotransferase | I601_RS15155 | I601_RS01940 |
| maltose | MAL11: maltose permease | | |
| mannitol | mtlD: mannitol-1-phosphate 5-dehydrogenase | | |
| mannose | manA: mannose-6-phosphate isomerase | I601_RS00750 | |
| mannose | manP: mannose PTS system, EII-CBA components | I601_RS12935 | |
| 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 | I601_RS08955 | |
| myoinositol | iolE: scyllo-inosose 2-dehydratase | | |
| myoinositol | iolG: myo-inositol 2-dehydrogenase | | |
| myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | | |
| myoinositol | iolT: myo-inositol:H+ symporter | | |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | I601_RS09685 | I601_RS05935 |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
| phenylacetate | paaF: 2,3-dehydroadipyl-CoA hydratase | I601_RS19165 | I601_RS17105 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | I601_RS10740 | I601_RS11365 |
| phenylacetate | paaK: phenylacetate-CoA ligase | I601_RS05795 | I601_RS04470 |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | I601_RS08400 | I601_RS17105 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | livF: L-phenylalanine ABC transporter, ATPase component 1 (LivF) | I601_RS10465 | I601_RS02130 |
| phenylalanine | livH: L-phenylalanine ABC transporter, permease component 1 (LivH) | I601_RS05905 | I601_RS02135 |
| phenylalanine | livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK | | |
| phenylalanine | livM: L-phenylalanine ABC transporter, permease component 2 (LivM) | I601_RS05895 | I601_RS19355 |
| phenylalanine | paaF: 2,3-dehydroadipyl-CoA hydratase | I601_RS19165 | I601_RS17105 |
| phenylalanine | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | I601_RS10740 | I601_RS11365 |
| phenylalanine | paaK: phenylacetate-CoA ligase | I601_RS05795 | I601_RS04470 |
| phenylalanine | paaZ1: oxepin-CoA hydrolase | I601_RS08400 | I601_RS17105 |
| phenylalanine | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | pad-dh: phenylacetaldehyde dehydrogenase | I601_RS01130 | I601_RS01590 |
| phenylalanine | PPDCalpha: phenylpyruvate decarboxylase, alpha subunit | I601_RS05215 | I601_RS05890 |
| proline | natB: proline ABC transporter, substrate-binding component NatB | I601_RS18165 | |
| proline | natC: proline ABC transporter, permease component 1 (NatC) | I601_RS18180 | |
| proline | natD: proline ABC transporter, permease component 2 (NatD) | I601_RS18185 | I601_RS10450 |
| propionate | mctC: propionate:H+ symporter | I601_RS07725 | I601_RS07700 |
| propionate | pccA: propionyl-CoA carboxylase, alpha subunit | I601_RS00935 | I601_RS06760 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | I601_RS15155 | I601_RS12765 |
| putrescine | potB: putrescine ABC transporter, permease component 1 (PotB/PotH) | I601_RS12745 | I601_RS08925 |
| putrescine | potC: putrescine ABC transporter, permease component 2 (PotC/PotI) | I601_RS12750 | I601_RS08930 |
| putrescine | potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) | | |
| pyruvate | mctC: pyruvate symporter MctC | I601_RS07725 | I601_RS07700 |
| rhamnose | aldA: lactaldehyde dehydrogenase | I601_RS01130 | I601_RS12775 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | | |
| rhamnose | LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase | | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsK: ribokinase | I601_RS02645 | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| serine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | I601_RS18165 | |
| serine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | I601_RS18185 | I601_RS10450 |
| serine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | I601_RS18180 | I601_RS05895 |
| sorbitol | srlD: sorbitol 6-phosphate 2-dehydrogenase | I601_RS11285 | I601_RS17320 |
| sucrose | 1pfk: 1-phosphofructokinase | I601_RS20105 | I601_RS02165 |
| sucrose | ams: sucrose hydrolase (invertase) | I601_RS03405 | I601_RS19190 |
| threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | I601_RS18165 | |
| threonine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | I601_RS18185 | I601_RS10450 |
| threonine | braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) | I601_RS18180 | I601_RS05895 |
| thymidine | deoB: phosphopentomutase | I601_RS01115 | I601_RS00705 |
| trehalose | thuE: trehalose ABC transporter, substrate-binding component ThuE | | |
| trehalose | treF: trehalase | I601_RS03405 | I601_RS15865 |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | Ac3H11_1692: L-tyrosine ABC transporter, ATPase component 2 | I601_RS10465 | I601_RS19345 |
| tyrosine | Ac3H11_1694: L-tyrosine ABC transporter, permease component 2 | I601_RS05895 | |
| tyrosine | Ac3H11_1695: L-tyrosine ABC transporter, permease component 1 | I601_RS05905 | I601_RS02135 |
| tyrosine | Ac3H11_2396: L-tyrosine ABC transporter, substrate-binding component component | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | I601_RS19165 | I601_RS16810 |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | I601_RS05880 | I601_RS05205 |
| valine | livH: L-valine ABC transporter, permease component 1 (LivH/BraD) | I601_RS10450 | I601_RS18185 |
| valine | livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | | |
| valine | livM: L-valine ABC transporter, permease component 2 (LivM/BraE) | I601_RS02140 | I601_RS05895 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | I601_RS07030 | I601_RS05735 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | | |
| valine | pccA: propionyl-CoA carboxylase, alpha subunit | I601_RS00935 | I601_RS06760 |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | I601_RS12935 | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | I601_RS20120 | I601_RS07125 |
| xylose | xylA: xylose isomerase | | |
| xylose | xylB: xylulokinase | I601_RS13290 | |
| 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.
Links
Downloads
Related tools
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