Potential Gaps in catabolism of small carbon sources in Amphibacillus jilinensis Y1
Found 124 low-confidence and 41 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 | 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 | praB: 2-hydroxymuconate 6-semialdehyde dehydrogenase | B494_RS0100700 | |
| 4-hydroxybenzoate | praD: 2-oxohex-3-enedioate decarboxylase | | |
| acetate | satP: acetate/proton symporter satP | B494_RS0115245 | |
| arginine | bgtB: L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB) | | |
| arginine | gabD: succinate semialdehyde dehydrogenase | B494_RS0100700 | B494_RS0116705 |
| arginine | gabT: gamma-aminobutyrate transaminase | B494_RS0115200 | B494_RS0116750 |
| arginine | patA: putrescine aminotransferase (PatA/SpuC) | B494_RS0104485 | B494_RS0115200 |
| arginine | patD: gamma-aminobutyraldehyde dehydrogenase | B494_RS0100700 | |
| asparagine | bgtA: aspartate ABC transporter, ATPase component BgtA | B494_RS0107160 | B494_RS0107100 |
| asparagine | natG: aspartate ABC transporter, permease component 1 (NatG) | B494_RS0107170 | B494_RS0107165 |
| aspartate | bgtA: aspartate ABC transporter, ATPase component BgtA | B494_RS0107160 | B494_RS0107100 |
| aspartate | natG: aspartate ABC transporter, permease component 1 (NatG) | B494_RS0107170 | B494_RS0107165 |
| citrate | citM: citrate:cation:H+ symporter CitM | B494_RS0101175 | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | B494_RS0107100 | B494_RS0111290 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | B494_RS0111285 | B494_RS0107095 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | B494_RS0111285 | B494_RS0107165 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
| citrulline | arcC: carbamate kinase | | |
| citrulline | rocA: 1-pyrroline-5-carboxylate dehydrogenase | B494_RS0100700 | |
| citrulline | rocD: ornithine aminotransferase | B494_RS0104485 | B494_RS0115200 |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-alanine | Pf6N2E2_5402: ABC transporter for D-Alanine, substrate-binding component | B494_RS0107175 | |
| D-alanine | Pf6N2E2_5403: ABC transporter for D-Alanine, permease component 2 | B494_RS0107170 | |
| D-alanine | Pf6N2E2_5404: ABC transporter for D-Alanine, permease component 1 | B494_RS0107165 | B494_RS0111285 |
| D-alanine | Pf6N2E2_5405: ABC transporter for D-Alanine, ATPase component | B494_RS0107160 | B494_RS0107100 |
| D-lactate | D-LDH: D-lactate dehydrogenase | B494_RS0113510 | B494_RS0106480 |
| 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 | B494_RS0109190 | |
| deoxyribonate | aacS: acetoacetyl-CoA synthetase | | |
| deoxyribonate | atoB: acetyl-CoA C-acetyltransferase | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | B494_RS0105085 | B494_RS0102850 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fucose | aldA: lactaldehyde dehydrogenase | B494_RS0100700 | |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | | |
| fucose | fucI: L-fucose isomerase FucI | | |
| fucose | fucK: L-fuculose kinase FucK | B494_RS0100515 | |
| fucose | fucP: L-fucose:H+ symporter FucP | | |
| fucose | fucU: L-fucose mutarotase FucU | | |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | B494_RS0100185 | B494_RS0102975 |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | uxuB: D-mannonate dehydrogenase | | |
| glutamate | gdhA: glutamate dehydrogenase, NAD-dependent | B494_RS0104840 | |
| glycerol | glpF: glycerol facilitator glpF | | |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| histidine | PA5503: L-histidine ABC transporter, ATPase component | B494_RS0110605 | B494_RS0102690 |
| histidine | PA5505: L-histidine ABC transporter, substrate-binding component | B494_RS0104990 | B494_RS0110595 |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | | |
| isoleucine | Bap2: L-isoleucine permease Bap2 | | |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | B494_RS0109980 | B494_RS0107460 |
| isoleucine | ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase | | |
| isoleucine | fadA: 2-methylacetoacetyl-CoA thiolase | | |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | B494_RS0107925 | B494_RS0114775 |
| isoleucine | prpB: 2-methylisocitrate lyase | | |
| isoleucine | prpC: 2-methylcitrate synthase | B494_RS0115950 | |
| isoleucine | prpD: 2-methylcitrate dehydratase | | |
| L-lactate | SfMCT: L-lactate transporter SfMCT | B494_RS0111485 | B494_RS0102205 |
| L-malate | sdlC: L-malate:Na+ symporter SdlC | | |
| lactose | lacK: lactose ABC transporter, ATPase component | B494_RS0102070 | B494_RS0102875 |
| leucine | aacS: acetoacetyl-CoA synthetase | | |
| leucine | atoB: acetyl-CoA C-acetyltransferase | | |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | B494_RS0109980 | B494_RS0107460 |
| leucine | leuT: L-leucine:Na+ symporter LeuT | B494_RS0110510 | |
| leucine | liuA: isovaleryl-CoA dehydrogenase | | |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | B494_RS0110105 | |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | | |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | | |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
| lysine | amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) | B494_RS0100700 | |
| lysine | hglS: D-2-hydroxyglutarate synthase | | |
| lysine | lat: L-lysine 6-aminotransferase | B494_RS0115200 | B494_RS0104485 |
| lysine | lysN: 2-aminoadipate transaminase | B494_RS0109555 | B494_RS0116765 |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| lysine | ydiJ: (R)-2-hydroxyglutarate dehydrogenase | | |
| myoinositol | iolG: myo-inositol 2-dehydrogenase | B494_RS0106090 | |
| myoinositol | iolM: 2-inosose 4-dehydrogenase | B494_RS19065 | |
| myoinositol | iolN: 2,4-diketo-inositol hydratase | | |
| myoinositol | iolO: 5-dehydro-L-gluconate epimerase | | |
| myoinositol | iolT: myo-inositol:H+ symporter | | |
| myoinositol | uxaE: D-tagaturonate epimerase | | |
| myoinositol | uxuB: D-mannonate dehydrogenase | | |
| NAG | nagPcb: N-acetylglucosamine phosphotransferase system, EII-CB component NagP | B494_RS0102975 | B494_RS0100185 |
| 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 | | |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | | |
| phenylacetate | paaH: 3-hydroxyadipyl-CoA dehydrogenase | B494_RS0107925 | B494_RS0114775 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | | |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | | |
| phenylacetate | paaK: phenylacetate-CoA ligase | | |
| 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 | | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| phenylalanine | atoB: acetyl-CoA C-acetyltransferase | | |
| phenylalanine | fahA: fumarylacetoacetate hydrolase | | |
| phenylalanine | hmgA: homogentisate dioxygenase | | |
| phenylalanine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| phenylalanine | maiA: maleylacetoacetate isomerase | | |
| phenylalanine | PAH: phenylalanine 4-monooxygenase | | |
| phenylalanine | PCBD: pterin-4-alpha-carbinoalamine dehydratase | | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | | |
| proline | ectP: proline transporter EctP | B494_RS0117175 | |
| proline | put1: proline dehydrogenase | | |
| proline | putA: L-glutamate 5-semialdeyde dehydrogenase | B494_RS0100700 | |
| propionate | prpB: 2-methylisocitrate lyase | | |
| propionate | prpC: 2-methylcitrate synthase | B494_RS0115950 | |
| propionate | prpD: 2-methylcitrate dehydratase | | |
| propionate | prpE: propionyl-CoA synthetase | B494_RS0101085 | |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| putrescine | gabD: succinate semialdehyde dehydrogenase | B494_RS0100700 | B494_RS0116705 |
| putrescine | gabT: gamma-aminobutyrate transaminase | B494_RS0115200 | B494_RS0116750 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | B494_RS0104485 | B494_RS0115200 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | B494_RS0100700 | |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| pyruvate | SLC5A8: sodium-coupled pyruvate transporter | | |
| rhamnose | aldA: lactaldehyde dehydrogenase | B494_RS0100700 | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsA: D-ribose ABC transporter, ATPase component RbsA | B494_RS0103365 | B494_RS0104410 |
| ribose | rbsB: D-ribose ABC transporter, substrate-binding component RbsB | | |
| serine | serP: L-serine permease SerP | | |
| sorbitol | srlB: PTS system for sorbitol SrlABE, EII-A component SrlB | B494_RS0100375 | |
| succinate | satP: succinate:H+ symporter SatP | B494_RS0115245 | |
| threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | B494_RS0111420 | B494_RS0111415 |
| threonine | ltaE: L-threonine aldolase | B494_RS0103805 | |
| threonine | tdcC: L-threonine:H+ symporter TdcC | | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | treC: trehalose-6-phosphate hydrolase | B494_RS0104650 | B494_RS0107005 |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aacS: acetoacetyl-CoA synthetase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| tyrosine | atoB: acetyl-CoA C-acetyltransferase | | |
| tyrosine | fahA: fumarylacetoacetate hydrolase | | |
| 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 | | |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | B494_RS0109980 | B494_RS0107460 |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | | |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | B494_RS0100700 | |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | B494_RS0116445 | |
| valine | prpB: 2-methylisocitrate lyase | | |
| valine | prpC: 2-methylcitrate synthase | B494_RS0115950 | |
| valine | prpD: 2-methylcitrate dehydratase | | |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | B494_RS0102510 | B494_RS0105805 |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | B494_RS0106505 | B494_RS19065 |
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