Potential Gaps in catabolism of small carbon sources in Actinokineospora bangkokensis 44EHW
Found 80 low-confidence and 69 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | kgtP: 2-oxoglutarate:H+ symporter KgtP | BJP25_RS01360 | BJP25_RS25185 |
| 4-hydroxybenzoate | mhpD: 2-hydroxypentadienoate hydratase | | |
| 4-hydroxybenzoate | mhpE: 4-hydroxy-2-oxovalerate aldolase | BJP25_RS09065 | |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| 4-hydroxybenzoate | pobA: 4-hydroxybenzoate 3-monooxygenase | BJP25_RS05145 | |
| 4-hydroxybenzoate | praA: protocatechuate 2,3-dioxygenase | | |
| 4-hydroxybenzoate | xylF: 2-hydroxymuconate semialdehyde hydrolase | BJP25_RS23505 | BJP25_RS12725 |
| alanine | cycA: L-alanine symporter CycA | BJP25_RS17955 | |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arginine | arcA: arginine deiminase | BJP25_RS00420 | |
| arginine | arcC: carbamate kinase | | |
| arginine | rocE: L-arginine permease | BJP25_RS17955 | |
| aspartate | glt: aspartate:proton symporter Glt | BJP25_RS07375 | BJP25_RS23320 |
| cellobiose | cebE: cellobiose ABC transporter, substrate-binding component CebE | BJP25_RS05955 | |
| citrate | tctB: citrate/Na+ symporter, small transmembrane component TctB | | |
| citrate | tctC: citrate/Na+ symporter, substrate-binding component TctC | BJP25_RS13585 | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | BJP25_RS26340 | BJP25_RS13435 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | BJP25_RS13430 | |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | BJP25_RS02380 | BJP25_RS26345 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
| citrulline | arcC: carbamate kinase | | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-lactate | D-LDH: D-lactate dehydrogenase | BJP25_RS01440 | BJP25_RS26120 |
| D-serine | cycA: D-serine:H+ symporter CycA | BJP25_RS17955 | |
| D-serine | dsdA: D-serine ammonia-lyase | BJP25_RS27980 | BJP25_RS13975 |
| deoxyinosine | bmpA: deoxyinosine ABC transporter, substrate-binding component | BJP25_RS23585 | |
| deoxyinosine | deoB: phosphopentomutase | BJP25_RS23330 | BJP25_RS24100 |
| deoxyinosine | nupB: deoxyinosine ABC transporter, permease component 1 | BJP25_RS23575 | BJP25_RS09275 |
| deoxyinosine | nupC': deoxyinosine ABC transporter, permease component 2 | BJP25_RS23570 | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | BJP25_RS11865 | BJP25_RS10135 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | BJP25_RS25710 | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fructose | 1pfk: 1-phosphofructokinase | BJP25_RS30950 | BJP25_RS26720 |
| fructose | fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components | | |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | BJP25_RS02830 | |
| 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 | pgmA: alpha-phosphoglucomutase | BJP25_RS23050 | BJP25_RS23330 |
| galactose | yjtF: galactose ABC transporter, permease component 2 | BJP25_RS09270 | |
| galactose | ytfQ: galactose ABC transporter, substrate-binding component | BJP25_RS09285 | |
| galactose | ytfT: galactose ABC transporter, permease component 1 | BJP25_RS09275 | BJP25_RS09270 |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | uxaA: D-altronate dehydratase | | |
| galacturonate | uxaB: tagaturonate reductase | | |
| galacturonate | uxaC: D-galacturonate isomerase | | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
| glucose | MFS-glucose: glucose transporter, MFS superfamily | | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | uxaC: D-glucuronate isomerase | | |
| glucuronate | uxuA: D-mannonate dehydratase | | |
| glucuronate | uxuB: D-mannonate dehydrogenase | | |
| glutamate | gluB: L-glutamate ABC transporter, substrate-binding component GluB | BJP25_RS02390 | |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | BJP25_RS23415 | BJP25_RS28580 |
| histidine | hutG': N-formylglutamate amidohydrolase | | |
| histidine | permease: L-histidine permease | BJP25_RS17955 | |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | BJP25_RS26415 | BJP25_RS01660 |
| isoleucine | livJ: L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | BJP25_RS06755 | BJP25_RS32065 |
| isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | BJP25_RS23450 | BJP25_RS22660 |
| L-lactate | lctO: L-lactate oxidase or 2-monooxygenase | BJP25_RS15490 | BJP25_RS19335 |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | BJP25_RS14460 | BJP25_RS31000 |
| lactose | pgmA: alpha-phosphoglucomutase | BJP25_RS23050 | BJP25_RS23330 |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | BJP25_RS26415 | BJP25_RS01660 |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | BJP25_RS21155 | BJP25_RS00950 |
| leucine | livJ: L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | BJP25_RS06755 | BJP25_RS32065 |
| lysine | bcd: butanoyl-CoA dehydrogenase (NAD+, ferredoxin), dehydrogenase subunit | BJP25_RS23200 | BJP25_RS15595 |
| lysine | ctfA: butanoyl-CoA:acetoacetate CoA-transferase, alpha subunit | BJP25_RS10040 | BJP25_RS12280 |
| lysine | ctfB: butanoyl-CoA:acetoacetate CoA-transferase, beta subunit | BJP25_RS10035 | BJP25_RS12285 |
| lysine | etfA: butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfA subunit | BJP25_RS21095 | |
| lysine | etfB: butanoyl-CoA dehydrogenase (NAD+, ferredoxin), etfB subunit | BJP25_RS21100 | |
| lysine | kamA: L-lysine 2,3-aminomutase | BJP25_RS10610 | |
| lysine | kce: (S)-5-amino-3-oxohexanoate cleavage enzyme | BJP25_RS25710 | |
| lysine | lysP: L-lysine:H+ symporter LysP | BJP25_RS17955 | |
| maltose | MAL11: maltose permease | | |
| mannitol | mt2d: mannitol 2-dehydrogenase | BJP25_RS17625 | BJP25_RS26750 |
| mannitol | PLT5: polyol transporter PLT5 | | |
| mannitol | scrK: fructokinase | BJP25_RS17160 | BJP25_RS14845 |
| mannose | manP: mannose PTS system, EII-CBA components | | |
| myoinositol | iolB: 5-deoxy-D-glucuronate isomerase | | |
| myoinositol | iolC: 5-dehydro-2-deoxy-D-gluconate kinase | BJP25_RS14845 | |
| myoinositol | iolD: 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase | | |
| myoinositol | iolE: scyllo-inosose 2-dehydratase | | |
| myoinositol | iolG: myo-inositol 2-dehydrogenase | BJP25_RS07295 | BJP25_RS25385 |
| myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | BJP25_RS30945 | |
| myoinositol | iolT: myo-inositol:H+ symporter | | |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
| phenylacetate | paaF: 2,3-dehydroadipyl-CoA hydratase | BJP25_RS21155 | BJP25_RS29835 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | BJP25_RS29835 | BJP25_RS24615 |
| phenylacetate | ppa: phenylacetate permease ppa | BJP25_RS17090 | BJP25_RS05470 |
| phenylalanine | livF: L-phenylalanine ABC transporter, ATPase component 1 (LivF) | BJP25_RS06775 | BJP25_RS13540 |
| phenylalanine | livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK | BJP25_RS32065 | BJP25_RS06755 |
| phenylalanine | paaF: 2,3-dehydroadipyl-CoA hydratase | BJP25_RS21155 | BJP25_RS29835 |
| phenylalanine | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | BJP25_RS29835 | BJP25_RS24615 |
| phenylalanine | pad-dh: phenylacetaldehyde dehydrogenase | BJP25_RS23515 | BJP25_RS29000 |
| phenylalanine | PPDCalpha: phenylpyruvate decarboxylase, alpha subunit | BJP25_RS26405 | BJP25_RS00495 |
| proline | HSERO_RS00870: proline ABC transporter, substrate-binding component | BJP25_RS32065 | BJP25_RS06755 |
| proline | HSERO_RS00890: proline ABC transporter, permease component 2 | BJP25_RS06765 | |
| proline | HSERO_RS00900: proline ABC transporter, ATPase component 2 | BJP25_RS06775 | BJP25_RS13540 |
| propionate | pccA: propionyl-CoA carboxylase, alpha subunit | BJP25_RS23450 | BJP25_RS22660 |
| putrescine | gabT: gamma-aminobutyrate transaminase | BJP25_RS03910 | BJP25_RS14785 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | BJP25_RS03910 | BJP25_RS19925 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | BJP25_RS23515 | BJP25_RS29000 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| 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 | rbsU: probable D-ribose transporter RbsU | | |
| serine | Ac3H11_1692: L-tyrosine ABC transporter, ATPase component 2 | BJP25_RS06775 | BJP25_RS13540 |
| serine | Ac3H11_1694: L-tyrosine ABC transporter, permease component 2 | BJP25_RS06765 | |
| serine | Ac3H11_1695: L-tyrosine ABC transporter, permease component 1 | BJP25_RS06760 | BJP25_RS13535 |
| serine | Ac3H11_2396: L-tyrosine ABC transporter, substrate-binding component component | BJP25_RS32065 | BJP25_RS06755 |
| sorbitol | mtlF: ABC transporter for polyols MtlEFGK, permease component MtlF | BJP25_RS17635 | BJP25_RS13380 |
| sorbitol | mtlK: ABC transporter for polyols MtlEFGK, permease component MtlK | BJP25_RS22090 | BJP25_RS29960 |
| sorbitol | scrK: fructokinase | BJP25_RS17160 | BJP25_RS14845 |
| sorbitol | sdh: sorbitol dehydrogenase | BJP25_RS30855 | BJP25_RS26750 |
| sucrose | ams: sucrose hydrolase (invertase) | BJP25_RS17525 | BJP25_RS31740 |
| sucrose | MFS-glucose: glucose transporter, MFS superfamily | | |
| threonine | RR42_RS28305: L-threonine:H+ symporter | BJP25_RS17955 | |
| thymidine | deoB: phosphopentomutase | BJP25_RS23330 | BJP25_RS24100 |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | thuE: trehalose ABC transporter, substrate-binding component ThuE | BJP25_RS17540 | |
| trehalose | treF: trehalase | BJP25_RS04700 | BJP25_RS08350 |
| tryptophan | aroP: tryptophan:H+ symporter AroP | BJP25_RS17955 | |
| tyrosine | Ac3H11_1692: L-tyrosine ABC transporter, ATPase component 2 | BJP25_RS06775 | BJP25_RS13540 |
| tyrosine | Ac3H11_1694: L-tyrosine ABC transporter, permease component 2 | BJP25_RS06765 | |
| tyrosine | Ac3H11_1695: L-tyrosine ABC transporter, permease component 1 | BJP25_RS06760 | BJP25_RS13535 |
| tyrosine | Ac3H11_2396: L-tyrosine ABC transporter, substrate-binding component component | BJP25_RS32065 | BJP25_RS06755 |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | BJP25_RS21155 | BJP25_RS24615 |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | BJP25_RS26415 | BJP25_RS01660 |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | BJP25_RS21155 | BJP25_RS29180 |
| valine | livH: L-valine ABC transporter, permease component 1 (LivH/BraD) | BJP25_RS06760 | BJP25_RS28710 |
| valine | livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | BJP25_RS06755 | BJP25_RS32065 |
| valine | livM: L-valine ABC transporter, permease component 2 (LivM/BraE) | BJP25_RS06765 | BJP25_RS13530 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | BJP25_RS03115 | BJP25_RS23515 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | | |
| valine | pccA: propionyl-CoA carboxylase, alpha subunit | BJP25_RS23450 | BJP25_RS22660 |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | | |
| xylitol | xdhA: xylitol dehydrogenase | BJP25_RS17625 | BJP25_RS26750 |
| 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