Potential Gaps in catabolism of small carbon sources in Gracilibacillus halophilus YIM-C55.5
Found 136 low-confidence and 42 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 | adh: acetaldehyde dehydrogenase (not acylating) | J416_RS06115 | J416_RS13265 |
| 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 | | |
| acetate | actP: cation/acetate symporter ActP | J416_RS13350 | |
| alanine | TRIC: TRIC-type L-alanine transporter | J416_RS05020 | |
| arginine | rocA: 1-pyrroline-5-carboxylate dehydrogenase | J416_RS13265 | J416_RS06115 |
| arginine | rocD: ornithine aminotransferase | J416_RS09410 | J416_RS02575 |
| arginine | rocE: L-arginine permease | | |
| arginine | rocF: arginase | | |
| asparagine | ans: asparaginase | J416_RS06415 | |
| asparagine | glt: aspartate:proton symporter Glt | | |
| aspartate | glt: aspartate:proton symporter Glt | | |
| citrate | SLC13A5: citrate:Na+ symporter | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | J416_RS10755 | J416_RS09925 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | J416_RS09920 | J416_RS14400 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | | |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
| citrulline | citrullinase: putative citrullinase | | |
| citrulline | rocA: 1-pyrroline-5-carboxylate dehydrogenase | J416_RS13265 | J416_RS06115 |
| citrulline | rocD: ornithine aminotransferase | J416_RS09410 | J416_RS02575 |
| D-alanine | cycA: D-alanine:H+ symporter CycA | | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-lactate | D-LDH: D-lactate dehydrogenase | J416_RS12685 | J416_RS06485 |
| 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 | J416_RS07585 | |
| deoxyinosine | adh: acetaldehyde dehydrogenase (not acylating) | J416_RS06115 | J416_RS13265 |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | J416_RS11430 | |
| deoxyribonate | aacS: acetoacetyl-CoA synthetase | | |
| deoxyribonate | atoB: acetyl-CoA C-acetyltransferase | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | | |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | adh: acetaldehyde dehydrogenase (not acylating) | J416_RS06115 | J416_RS13265 |
| deoxyribose | deoP: deoxyribose transporter | | |
| ethanol | adh: acetaldehyde dehydrogenase (not acylating) | J416_RS06115 | J416_RS13265 |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | | |
| fucose | fucI: L-fucose isomerase FucI | | |
| fucose | fucK: L-fuculose kinase FucK | J416_RS07600 | |
| fucose | fucU: L-fucose mutarotase FucU | | |
| fucose | HSERO_RS05250: ABC transporter for L-fucose, ATPase component | J416_RS08125 | J416_RS02055 |
| fucose | HSERO_RS05255: ABC transporter for L-fucose, permease component | J416_RS08065 | J416_RS08120 |
| fucose | HSERO_RS05260: ABC transporter for L-fucose, substrate-binding component | J416_RS02075 | |
| fumarate | dctA: fumarate:H+ symporter DctA | | |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | kdgK: 2-keto-3-deoxygluconate kinase | J416_RS09890 | |
| galacturonate | uxaA: D-altronate dehydratase | | |
| galacturonate | uxaB: tagaturonate reductase | | |
| gluconate | gntK: D-gluconate kinase | J416_RS09190 | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | J416_RS04205 | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | kdgK: 2-keto-3-deoxygluconate kinase | J416_RS09890 | |
| glucuronate | uxuA: D-mannonate dehydratase | | |
| glucuronate | uxuB: D-mannonate dehydrogenase | | |
| glutamate | gdhA: glutamate dehydrogenase, NAD-dependent | J416_RS01625 | |
| glutamate | gltS: L-glutamate:Na+ symporter GltS | | |
| 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 | J416_RS12260 | J416_RS01155 |
| histidine | PA5505: L-histidine ABC transporter, substrate-binding component | J416_RS12250 | J416_RS01165 |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | | |
| isoleucine | Bap2: L-isoleucine permease Bap2 | | |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | J416_RS05025 | J416_RS06855 |
| isoleucine | ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase | J416_RS06375 | |
| isoleucine | epi: methylmalonyl-CoA epimerase | J416_RS02200 | |
| isoleucine | fadA: 2-methylacetoacetyl-CoA thiolase | | |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | J416_RS00905 | J416_RS04110 |
| isoleucine | mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components | | |
| isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | J416_RS05135 | |
| isoleucine | pccB: propionyl-CoA carboxylase, beta subunit | | |
| L-lactate | Shew_2732: L-lactate:Na+ symporter, small component | | |
| L-malate | sdlC: L-malate:Na+ symporter SdlC | | |
| lactose | lacK: lactose ABC transporter, ATPase component | J416_RS13975 | J416_RS06505 |
| leucine | aacS: acetoacetyl-CoA synthetase | | |
| leucine | atoB: acetyl-CoA C-acetyltransferase | | |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | J416_RS05025 | J416_RS06855 |
| leucine | leuT: L-leucine:Na+ symporter LeuT | J416_RS12765 | J416_RS03595 |
| leucine | liuA: isovaleryl-CoA dehydrogenase | | |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | J416_RS05135 | |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | J416_RS06375 | |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | | |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
| lysine | amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) | J416_RS13265 | J416_RS11040 |
| lysine | hglS: D-2-hydroxyglutarate synthase | | |
| lysine | lat: L-lysine 6-aminotransferase | J416_RS10720 | |
| lysine | lysN: 2-aminoadipate transaminase | J416_RS04530 | J416_RS10055 |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| lysine | ydiJ: (R)-2-hydroxyglutarate dehydrogenase | | |
| mannose | manP: mannose PTS system, EII-CBA components | J416_RS01580 | |
| myoinositol | iolG: myo-inositol 2-dehydrogenase | | |
| myoinositol | iolM: 2-inosose 4-dehydrogenase | J416_RS08060 | |
| myoinositol | iolN: 2,4-diketo-inositol hydratase | | |
| myoinositol | iolO: 5-dehydro-L-gluconate epimerase | | |
| myoinositol | iolT: myo-inositol:H+ symporter | J416_RS02170 | |
| myoinositol | kdgK: 2-keto-3-deoxygluconate kinase | J416_RS09890 | |
| myoinositol | uxuA: D-mannonate dehydratase | | |
| myoinositol | uxuB: D-mannonate dehydrogenase | | |
| NAG | nagPcb: N-acetylglucosamine phosphotransferase system, EII-CB component NagP | J416_RS04205 | |
| 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 | J416_RS06375 | |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | J416_RS06375 | |
| phenylacetate | paaH: 3-hydroxyadipyl-CoA dehydrogenase | J416_RS11400 | J416_RS00905 |
| 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 | J416_RS10750 | |
| 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 | J416_RS00165 | |
| proline | ectP: proline transporter EctP | J416_RS12915 | J416_RS02880 |
| proline | put1: proline dehydrogenase | | |
| proline | putA: L-glutamate 5-semialdeyde dehydrogenase | J416_RS13265 | J416_RS06115 |
| propionate | epi: methylmalonyl-CoA epimerase | J416_RS02200 | |
| propionate | mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components | | |
| propionate | pccA: propionyl-CoA carboxylase, alpha subunit | J416_RS05135 | |
| propionate | pccB: propionyl-CoA carboxylase, beta subunit | | |
| propionate | prpE: propionyl-CoA synthetase | J416_RS00160 | |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| putrescine | gabD: succinate semialdehyde dehydrogenase | J416_RS13265 | J416_RS11040 |
| putrescine | gabT: gamma-aminobutyrate transaminase | J416_RS10720 | J416_RS10070 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | J416_RS10720 | J416_RS09410 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | J416_RS13265 | J416_RS11040 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| pyruvate | actP: large subunit of pyruvate transporter (actP-like) | J416_RS13350 | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| serine | sdaB: L-serine ammonia-lyase | J416_RS07585 | |
| serine | serP: L-serine permease SerP | | |
| sorbitol | mtlA: PTS system for polyols, EII-CBA components | J416_RS01585 | |
| sorbitol | srlD: sorbitol 6-phosphate 2-dehydrogenase | J416_RS00905 | J416_RS09900 |
| succinate | sdc: succinate:Na+ symporter Sdc | | |
| threonine | tdcC: L-threonine:H+ symporter TdcC | | |
| threonine | tdh: L-threonine 3-dehydrogenase | J416_RS08060 | J416_RS01495 |
| threonine | tynA: aminoacetone oxidase | | |
| thymidine | adh: acetaldehyde dehydrogenase (not acylating) | J416_RS06115 | J416_RS13265 |
| trehalose | treC: trehalose-6-phosphate hydrolase | J416_RS01645 | J416_RS12565 |
| tryptophan | tnaA: tryptophanase | | |
| tryptophan | tnaT: tryptophan:Na+ symporter TnaT | J416_RS12765 | |
| tyrosine | aacS: acetoacetyl-CoA synthetase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| tyrosine | atoB: acetyl-CoA C-acetyltransferase | | |
| tyrosine | fahA: fumarylacetoacetate hydrolase | J416_RS10750 | |
| 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 | J416_RS06375 | |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | J416_RS05025 | J416_RS06855 |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | J416_RS06375 | |
| valine | epi: methylmalonyl-CoA epimerase | J416_RS02200 | |
| valine | mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components | | |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | J416_RS13265 | J416_RS06115 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | J416_RS10445 | |
| valine | pccA: propionyl-CoA carboxylase, alpha subunit | J416_RS05135 | |
| valine | pccB: propionyl-CoA carboxylase, beta subunit | | |
| 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