Potential Gaps in catabolism of small carbon sources in Devosia chinhatensis IPL18
Found 98 low-confidence and 47 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | Psest_0084: 2-oxoglutarate TRAP transporter, fused 4TM/12TM components | VE26_RS13175 | |
| 2-oxoglutarate | Psest_0085: 2-oxoglutarate TRAP transporter, solute receptor component | VE26_RS13170 | |
| 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 | | |
| arabinose | xacD: L-arabinonate dehydratase | VE26_RS06630 | VE26_RS02060 |
| arginine | bgtB: L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) | | |
| arginine | rocD: ornithine aminotransferase | VE26_RS15655 | VE26_RS16375 |
| asparagine | aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) | VE26_RS05290 | VE26_RS15135 |
| asparagine | ans: asparaginase | VE26_RS02905 | |
| aspartate | aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) | VE26_RS05290 | VE26_RS15135 |
| cellobiose | glk: glucokinase | VE26_RS16265 | |
| citrate | tctB: citrate/Na+ symporter, small transmembrane component TctB | | |
| citrate | tctC: citrate/Na+ symporter, substrate-binding component TctC | VE26_RS03640 | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | VE26_RS11055 | VE26_RS05300 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | VE26_RS11070 | VE26_RS15135 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | VE26_RS02425 | VE26_RS15135 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | VE26_RS11060 | |
| citrulline | arcC: carbamate kinase | | |
| citrulline | rocD: ornithine aminotransferase | VE26_RS15655 | VE26_RS16375 |
| D-alanine | dadA: D-alanine dehydrogenase | VE26_RS13165 | |
| D-alanine | Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component | VE26_RS05285 | VE26_RS05305 |
| D-alanine | Pf6N2E2_5403: ABC transporter for D-Alanine, permease component 2 | VE26_RS05290 | |
| D-alanine | Pf6N2E2_5404: ABC transporter for D-Alanine, permease component 1 | VE26_RS05295 | |
| D-alanine | Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component | VE26_RS05300 | VE26_RS02415 |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | VE26_RS11640 | |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
| deoxyribonate | aacS: acetoacetyl-CoA synthetase | VE26_RS12240 | |
| deoxyribonate | atoB: acetyl-CoA C-acetyltransferase | VE26_RS12225 | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | VE26_RS03510 | VE26_RS02030 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| ethanol | etoh-dh-nad: ethanol dehydrogenase (NAD(P)) | VE26_RS04905 | VE26_RS04615 |
| fructose | scrK: fructokinase | VE26_RS12435 | VE26_RS14410 |
| fucose | fucD: L-fuconate dehydratase | VE26_RS12395 | |
| fucose | fucDH: 2-keto-3-deoxy-L-fuconate 4-dehydrogenase | VE26_RS02700 | VE26_RS08300 |
| fucose | fucP: L-fucose:H+ symporter FucP | | |
| galactose | dgoD: D-galactonate dehydratase | VE26_RS06630 | VE26_RS02060 |
| galactose | galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) | VE26_RS06645 | |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | uxaA: D-altronate dehydratase | VE26_RS12395 | |
| galacturonate | uxaB: tagaturonate reductase | | |
| galacturonate | uxaC: D-galacturonate isomerase | VE26_RS00825 | |
| gluconate | gntA: gluconate TRAP transporter, small permease component | VE26_RS03745 | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | | |
| glucose | glk: glucokinase | VE26_RS16265 | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | dctQ: D-glucuronate TRAP transporter, small permease component | VE26_RS11120 | |
| glucuronate | uxaC: D-glucuronate isomerase | VE26_RS00825 | |
| glutamate | aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) | VE26_RS05290 | VE26_RS15135 |
| glycerol | glpF: glycerol facilitator glpF | | |
| histidine | aapQ: L-histidine ABC transporter, permease component 1 (AapQ) | VE26_RS05290 | VE26_RS15135 |
| 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 | | |
| isoleucine | Bap2: L-isoleucine permease Bap2 | | |
| isoleucine | ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase | VE26_RS12230 | VE26_RS17015 |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | VE26_RS04020 | VE26_RS08300 |
| isoleucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| L-malate | sdlC: L-malate:Na+ symporter SdlC | | |
| lactose | dgoD: D-galactonate dehydratase | VE26_RS06630 | VE26_RS02060 |
| lactose | galactonolactonase: galactonolactonase (either 1,4- or 1,5-lactone) | VE26_RS06645 | |
| lactose | glk: glucokinase | VE26_RS16265 | |
| leucine | aacS: acetoacetyl-CoA synthetase | VE26_RS12240 | |
| leucine | aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) | VE26_RS05290 | VE26_RS15135 |
| leucine | atoB: acetyl-CoA C-acetyltransferase | VE26_RS12225 | |
| leucine | liuA: isovaleryl-CoA dehydrogenase | | |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | VE26_RS15970 | VE26_RS07160 |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | VE26_RS12230 | VE26_RS17015 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | VE26_RS15965 | |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
| leucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| lysine | amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) | VE26_RS09925 | VE26_RS04900 |
| lysine | bgtB: L-histidine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) | | |
| lysine | hglS: D-2-hydroxyglutarate synthase | | |
| lysine | lat: L-lysine 6-aminotransferase | VE26_RS15655 | VE26_RS16375 |
| lysine | lysN: 2-aminoadipate transaminase | VE26_RS10245 | VE26_RS16375 |
| lysine | ydiJ: (R)-2-hydroxyglutarate dehydrogenase | VE26_RS01985 | |
| maltose | glk: glucokinase | VE26_RS16265 | |
| mannitol | mtlE: polyol ABC transporter, substrate-binding component MtlE/SmoE | VE26_RS10955 | |
| mannitol | mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) | VE26_RS10965 | VE26_RS02045 |
| mannitol | scrK: fructokinase | VE26_RS12435 | VE26_RS14410 |
| mannose | scrK: fructokinase | VE26_RS12435 | VE26_RS14410 |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
| 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 | VE26_RS12230 | VE26_RS17015 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | | |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | VE26_RS12225 | |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | VE26_RS12225 | |
| phenylacetate | paaK: phenylacetate-CoA ligase | VE26_RS12240 | |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | | |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | aacS: acetoacetyl-CoA synthetase | VE26_RS12240 | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| phenylalanine | atoB: acetyl-CoA C-acetyltransferase | VE26_RS12225 | |
| phenylalanine | hmgA: homogentisate dioxygenase | | |
| phenylalanine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| phenylalanine | maiA: maleylacetoacetate isomerase | | |
| phenylalanine | PAH: phenylalanine 4-monooxygenase | | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | | |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| putrescine | gabT: gamma-aminobutyrate transaminase | VE26_RS15655 | VE26_RS16375 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | VE26_RS15655 | VE26_RS16375 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | VE26_RS04900 | VE26_RS00905 |
| pyruvate | dctM: pyruvate TRAP transporter, large permease component | VE26_RS12445 | VE26_RS03740 |
| pyruvate | dctQ: pyruvate TRAP transporter, small permease component | VE26_RS12440 | |
| serine | sdaB: L-serine ammonia-lyase | VE26_RS11640 | |
| serine | snatA: L-serine transporter | VE26_RS14515 | |
| sorbitol | scrK: fructokinase | VE26_RS12435 | VE26_RS14410 |
| succinate | sdc: succinate:Na+ symporter Sdc | | |
| sucrose | ams: sucrose hydrolase (invertase) | VE26_RS00890 | |
| sucrose | scrK: fructokinase | VE26_RS12435 | VE26_RS14410 |
| threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | VE26_RS01560 | VE26_RS01565 |
| threonine | snatA: L-threonine transporter snatA | VE26_RS14515 | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | glk: glucokinase | VE26_RS16265 | |
| trehalose | treF: trehalase | VE26_RS00890 | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aacS: acetoacetyl-CoA synthetase | VE26_RS12240 | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| tyrosine | atoB: acetyl-CoA C-acetyltransferase | VE26_RS12225 | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | | |
| valine | Bap2: L-valine permease Bap2 | | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | VE26_RS17015 | |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | VE26_RS12230 | VE26_RS17015 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | VE26_RS15650 | VE26_RS09925 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | VE26_RS16205 | VE26_RS08670 |
| valine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | | |
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