Potential Gaps in catabolism of small carbon sources in Lentibacillus jeotgali Grbi
Found 88 low-confidence and 46 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | csbX: 2-oxoglutarate permease csbX | ON01_RS14715 | |
| 4-hydroxybenzoate | adh: acetaldehyde dehydrogenase (not acylating) | ON01_RS16395 | ON01_RS16145 |
| 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 | ON01_RS12535 | ON01_RS12555 |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | araE: L-arabinose:H+ symporter | ON01_RS14040 | |
| arginine | rocE: L-arginine permease | | |
| cellobiose | bgl: cellobiase | ON01_RS18600 | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | ON01_RS05305 | ON01_RS02030 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | ON01_RS02040 | ON01_RS05300 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | | |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | ON01_RS05295 | |
| citrulline | arcC: carbamate kinase | ON01_RS06900 | |
| D-alanine | cycA: D-alanine:H+ symporter CycA | | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| deoxyinosine | adh: acetaldehyde dehydrogenase (not acylating) | ON01_RS16395 | ON01_RS16145 |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | ON01_RS17760 | ON01_RS16035 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | ON01_RS03270 | |
| deoxyribose | adh: acetaldehyde dehydrogenase (not acylating) | ON01_RS16395 | ON01_RS16145 |
| deoxyribose | deoP: deoxyribose transporter | | |
| ethanol | adh: acetaldehyde dehydrogenase (not acylating) | ON01_RS16395 | ON01_RS16145 |
| ethanol | etoh-dh-nad: ethanol dehydrogenase (NAD(P)) | ON01_RS02875 | ON01_RS04000 |
| fructose | fba: fructose 1,6-bisphosphate aldolase | ON01_RS15280 | |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | | |
| 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 | ON01_RS14040 | |
| 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) | ON01_RS04430 | ON01_RS14380 |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | | |
| glucuronate | udh: D-glucuronate dehydrogenase | | |
| 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 | ON01_RS16935 | ON01_RS05305 |
| histidine | PA5504: L-histidine ABC transporter, permease component | ON01_RS16940 | |
| histidine | PA5505: L-histidine ABC transporter, substrate-binding component | ON01_RS16945 | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | ON01_RS13295 | ON01_RS09180 |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | ON01_RS10005 | ON01_RS04560 |
| isoleucine | brnQ: L-isoleucine:cation symporter BrnQ/BraZ/BraB | ON01_RS12265 | ON01_RS13125 |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | ON01_RS08625 | ON01_RS06190 |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | | |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | ON01_RS10005 | ON01_RS04560 |
| leucine | brnQ: L-leucine:Na+ symporter BrnQ/BraB | ON01_RS12265 | ON01_RS13125 |
| leucine | liuA: isovaleryl-CoA dehydrogenase | ON01_RS09180 | ON01_RS13295 |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | ON01_RS07520 | ON01_RS09190 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | ON01_RS09205 | ON01_RS09985 |
| lysine | davA: 5-aminovaleramidase | ON01_RS16405 | |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | davD: glutarate semialdehyde dehydrogenase | ON01_RS16145 | ON01_RS14830 |
| lysine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | ON01_RS09200 | ON01_RS06105 |
| lysine | gcdH: glutaryl-CoA dehydrogenase | ON01_RS03670 | ON01_RS13300 |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| mannose | manP: mannose PTS system, EII-CBA components | ON01_RS15425 | |
| myoinositol | iolB: 5-deoxy-D-glucuronate isomerase | | |
| myoinositol | iolC: 5-dehydro-2-deoxy-D-gluconate kinase | ON01_RS05395 | |
| myoinositol | iolD: 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase | | |
| myoinositol | iolE: scyllo-inosose 2-dehydratase | | |
| myoinositol | iolG: myo-inositol 2-dehydrogenase | | |
| myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | | |
| myoinositol | iolT: myo-inositol:H+ symporter | ON01_RS14040 | |
| 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 | ON01_RS06105 | ON01_RS18180 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | ON01_RS06210 | ON01_RS06115 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | ON01_RS06210 | ON01_RS06115 |
| phenylacetate | paaK: phenylacetate-CoA ligase | ON01_RS18170 | ON01_RS06180 |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | ON01_RS06245 | |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylacetate | ppa: phenylacetate permease ppa | ON01_RS12535 | ON01_RS12555 |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | | |
| phenylalanine | fahA: fumarylacetoacetate hydrolase | ON01_RS13850 | |
| 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 | ON01_RS12110 | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | ON01_RS15440 | |
| putrescine | gabT: gamma-aminobutyrate transaminase | ON01_RS14825 | ON01_RS16140 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | ON01_RS15110 | ON01_RS15265 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | ON01_RS04100 | ON01_RS16395 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| pyruvate | mctC: pyruvate symporter MctC | ON01_RS12535 | ON01_RS12555 |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | ON01_RS08625 | ON01_RS15390 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | ON01_RS08060 | ON01_RS05405 |
| rhamnose | LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase | | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsA: D-ribose ABC transporter, ATPase component RbsA | ON01_RS16055 | ON01_RS08915 |
| ribose | rbsB: D-ribose ABC transporter, substrate-binding component RbsB | ON01_RS16065 | |
| ribose | rbsC: D-ribose ABC transporter, permease component RbsC | ON01_RS16060 | |
| serine | serP: L-serine permease SerP | | |
| sorbitol | srlB: PTS system for sorbitol SrlABE, EII-A component SrlB | ON01_RS13950 | |
| sorbitol | srlD: sorbitol 6-phosphate 2-dehydrogenase | ON01_RS06190 | ON01_RS08625 |
| threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | ON01_RS10350 | ON01_RS10355 |
| threonine | tdcC: L-threonine:H+ symporter TdcC | | |
| thymidine | adh: acetaldehyde dehydrogenase (not acylating) | ON01_RS16395 | ON01_RS16145 |
| trehalose | treF: trehalase | ON01_RS02165 | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| tyrosine | fahA: fumarylacetoacetate hydrolase | ON01_RS13850 | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | ON01_RS13295 | ON01_RS09180 |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | ON01_RS06105 | ON01_RS09200 |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | ON01_RS10005 | ON01_RS04560 |
| valine | brnQ: L-valine:cation symporter BrnQ/BraZ/BraB | ON01_RS12265 | ON01_RS13125 |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | ON01_RS09200 | ON01_RS06105 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | ON01_RS06340 | ON01_RS06000 |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | ON01_RS14040 | |
| xylitol | xylB: xylulokinase | ON01_RS05390 | ON01_RS14910 |
| xylose | xylB: xylulokinase | ON01_RS05390 | ON01_RS14910 |
| xylose | xylT: D-xylose transporter | ON01_RS14040 | |
| xylose | xyrA: xylitol reductase | ON01_RS01815 | ON01_RS17050 |
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