Potential Gaps in catabolism of small carbon sources in Rhodococcus qingshengii djl-6-2
Found 56 low-confidence and 56 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | kgtP: 2-oxoglutarate:H+ symporter KgtP | C1M55_RS18640 | C1M55_RS06055 |
| 4-hydroxybenzoate | pcaF: succinyl-CoA:acetyl-CoA C-succinyltransferase | C1M55_RS26675 | C1M55_RS01065 |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | C1M55_RS13270 | |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | araE: L-arabinose:H+ symporter | C1M55_RS14300 | |
| arginine | artP: L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA | C1M55_RS21985 | C1M55_RS16555 |
| arginine | bgtB: L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) | C1M55_RS30350 | C1M55_RS21980 |
| arginine | kauB: 4-guanidinobutyraldehyde dehydrogenase | C1M55_RS09205 | C1M55_RS09155 |
| aspartate | glt: aspartate:proton symporter Glt | C1M55_RS09240 | C1M55_RS05140 |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | C1M55_RS16555 | C1M55_RS21985 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | C1M55_RS16560 | |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | C1M55_RS21980 | C1M55_RS16560 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
| citrulline | arcC: carbamate kinase | | |
| citrulline | odc: L-ornithine decarboxylase | | |
| D-alanine | dadA: D-alanine dehydrogenase | C1M55_RS07705 | |
| D-lactate | D-LDH: D-lactate dehydrogenase | C1M55_RS25910 | C1M55_RS29255 |
| D-lactate | lctP: D-lactate:H+ symporter LctP or LidP | | |
| D-serine | dsdA: D-serine ammonia-lyase | C1M55_RS21040 | C1M55_RS27535 |
| deoxyinosine | deoB: phosphopentomutase | C1M55_RS10455 | C1M55_RS09595 |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | C1M55_RS03670 | C1M55_RS10010 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | C1M55_RS00110 | |
| deoxyribonate | garK: glycerate 2-kinase | C1M55_RS17755 | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fructose | 1pfk: 1-phosphofructokinase | C1M55_RS13990 | C1M55_RS18150 |
| fucose | aldA: lactaldehyde dehydrogenase | C1M55_RS09205 | C1M55_RS09155 |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | C1M55_RS22410 | |
| 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 | C1M55_RS14300 | |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | gci: D-galactarolactone cycloisomerase | | |
| galacturonate | gli: D-galactarolactone isomerase | | |
| galacturonate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | C1M55_RS13800 | |
| galacturonate | udh: D-galacturonate dehydrogenase | | |
| glucosamine | nagA: N-acetylglucosamine 6-phosphate deacetylase | C1M55_RS19645 | C1M55_RS04725 |
| glucosamine | nagX: transmembrane glucosamine N-acetyltransferase NagX | | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
| glucuronate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | C1M55_RS13800 | |
| glucuronate | udh: D-glucuronate dehydrogenase | | |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | C1M55_RS23170 | C1M55_RS10615 |
| glycerol | glpF: glycerol facilitator glpF | C1M55_RS23180 | C1M55_RS18555 |
| histidine | hutH: histidine ammonia-lyase | C1M55_RS25900 | C1M55_RS25965 |
| isoleucine | livH: L-isoleucine ABC transporter, permease component 1 (LivH/BraD) | C1M55_RS22590 | C1M55_RS16600 |
| isoleucine | livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | | |
| isoleucine | livM: L-isoleucine ABC transporter, permease component 2 (LivM/BraE) | C1M55_RS22585 | C1M55_RS16605 |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | C1M55_RS18785 | C1M55_RS14415 |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | C1M55_RS12340 | C1M55_RS20280 |
| leucine | livH: L-leucine ABC transporter, permease component 1 (LivH/BraD) | C1M55_RS22590 | C1M55_RS16600 |
| leucine | livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | | |
| leucine | livM: L-leucine ABC transporter, permease component 2 (LivM/BraE) | C1M55_RS22585 | C1M55_RS16605 |
| lysine | bgtB: L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) | C1M55_RS30350 | C1M55_RS21980 |
| lysine | davD: glutarate semialdehyde dehydrogenase | C1M55_RS22335 | C1M55_RS03295 |
| lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | C1M55_RS24685 | C1M55_RS30270 |
| lysine | hisP: L-lysine ABC transporter, ATPase component HisP | C1M55_RS13925 | C1M55_RS16555 |
| mannitol | mtlE: polyol ABC transporter, substrate-binding component MtlE/SmoE | C1M55_RS18170 | |
| mannitol | mtlF: polyol ABC transporter, permease component 1 (MtlF/SmoF) | C1M55_RS18165 | |
| mannitol | mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) | C1M55_RS18160 | C1M55_RS20460 |
| mannitol | mtlK: polyol ABC transporter, ATP component MtlK/SmoG | C1M55_RS30235 | C1M55_RS20455 |
| mannose | manP: mannose PTS system, EII-CBA components | C1M55_RS13985 | |
| myoinositol | iolB: 5-deoxy-D-glucuronate isomerase | C1M55_RS10195 | |
| myoinositol | iolE: scyllo-inosose 2-dehydratase | C1M55_RS10185 | |
| myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | C1M55_RS10205 | |
| myoinositol | PGA1_c07300: myo-inositol ABC transport, substrate-binding component | | |
| myoinositol | PGA1_c07310: myo-inositol ABC transporter, permease component | C1M55_RS10270 | |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | C1M55_RS19645 | C1M55_RS04725 |
| phenylacetate | paaF: 2,3-dehydroadipyl-CoA hydratase | C1M55_RS19610 | C1M55_RS12340 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | C1M55_RS27980 | C1M55_RS08860 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | C1M55_RS26675 | C1M55_RS04430 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | C1M55_RS26675 | C1M55_RS04430 |
| phenylacetate | ppa: phenylacetate permease ppa | C1M55_RS22765 | |
| phenylalanine | paaF: 2,3-dehydroadipyl-CoA hydratase | C1M55_RS19610 | C1M55_RS12340 |
| phenylalanine | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | C1M55_RS27980 | C1M55_RS08860 |
| phenylalanine | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | C1M55_RS26675 | C1M55_RS04430 |
| phenylalanine | paaJ2: 3-oxoadipyl-CoA thiolase | C1M55_RS26675 | C1M55_RS04430 |
| phenylalanine | pad-dh: phenylacetaldehyde dehydrogenase | C1M55_RS09205 | C1M55_RS09155 |
| proline | put1: proline dehydrogenase | C1M55_RS23685 | C1M55_RS23680 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | C1M55_RS29020 | C1M55_RS25060 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | | |
| rhamnose | LRA6: 2,4-diketo-3-deoxyrhamnonate hydrolase | C1M55_RS12530 | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| serine | serP: L-serine permease SerP | C1M55_RS22525 | C1M55_RS07700 |
| sorbitol | mtlK: ABC transporter for polyols MtlEFGK, permease component MtlK | C1M55_RS30235 | C1M55_RS18155 |
| sucrose | 1pfk: 1-phosphofructokinase | C1M55_RS13990 | C1M55_RS18150 |
| sucrose | ams: sucrose hydrolase (invertase) | C1M55_RS18885 | |
| threonine | serP1: L-threonine uptake transporter SerP1 | C1M55_RS22525 | C1M55_RS07700 |
| thymidine | deoB: phosphopentomutase | C1M55_RS10455 | C1M55_RS09595 |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| tryptophan | hpaH: anthranilate 3-monooxygenase (hydroxylase), FADH2-dependent | C1M55_RS27390 | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | C1M55_RS19620 | C1M55_RS01960 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | C1M55_RS10170 | C1M55_RS19630 |
| valine | natB: L-valine ABC transporter, substrate-binding component NatB | C1M55_RS16620 | |
| valine | natC: L-valine ABC transporter, permease component 1 (NatC) | | |
| valine | natD: L-valine ABC transporter, permease component 2 (NatD) | C1M55_RS16600 | C1M55_RS07895 |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | | |
| xylitol | xdhA: xylitol dehydrogenase | C1M55_RS18180 | C1M55_RS01525 |
| xylose | xylA: xylose isomerase | | |
| xylose | xylT: D-xylose transporter | C1M55_RS14300 | |
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