Potential Gaps in catabolism of small carbon sources in Listeria fleischmannii LU2006-1
Found 134 low-confidence and 47 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 | xylF: 2-hydroxymuconate semialdehyde hydrolase | | |
| acetate | actP: cation/acetate symporter ActP | | |
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| arginine | arcC: carbamate kinase | | |
| arginine | rocA: 1-pyrroline-5-carboxylate dehydrogenase | LFLEISCH_RS09075 | |
| arginine | rocD: ornithine aminotransferase | LFLEISCH_RS02470 | LFLEISCH_RS13825 |
| arginine | rocE: L-arginine permease | LFLEISCH_RS14130 | LFLEISCH_RS05970 |
| asparagine | ans: asparaginase | LFLEISCH_RS01880 | |
| asparagine | glnP: L-asparagine ABC transporter, fused permease and substrate-binding components GlnP | | |
| aspartate | glt: aspartate:proton symporter Glt | | |
| citrate | acn: aconitase | | |
| citrate | icd: isocitrate dehydrogenase | LFLEISCH_RS01705 | |
| citrate | SLC13A5: citrate:Na+ symporter | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | LFLEISCH_RS11090 | LFLEISCH_RS06145 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | LFLEISCH_RS13085 | LFLEISCH_RS11085 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | LFLEISCH_RS06150 | LFLEISCH_RS13085 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
| citrulline | arcC: carbamate kinase | | |
| citrulline | rocA: 1-pyrroline-5-carboxylate dehydrogenase | LFLEISCH_RS09075 | |
| citrulline | rocD: ornithine aminotransferase | LFLEISCH_RS02470 | LFLEISCH_RS13825 |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| D-lactate | D-LDH: D-lactate dehydrogenase | LFLEISCH_RS13435 | |
| D-serine | dsdA: D-serine ammonia-lyase | LFLEISCH_RS15180 | LFLEISCH_RS01690 |
| deoxyribonate | aacS: acetoacetyl-CoA synthetase | | |
| deoxyribonate | atoB: acetyl-CoA C-acetyltransferase | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | LFLEISCH_RS08200 | |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | garK: glycerate 2-kinase | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | | |
| fucose | fucI: L-fucose isomerase FucI | | |
| fucose | fucK: L-fuculose kinase FucK | LFLEISCH_RS03200 | |
| fucose | fucO: L-lactaldehyde reductase | LFLEISCH_RS03220 | LFLEISCH_RS02850 |
| fucose | fucP: L-fucose:H+ symporter FucP | | |
| fucose | fucU: L-fucose mutarotase FucU | | |
| fumarate | dctA: fumarate:H+ symporter DctA | | |
| galactose | galK: galactokinase (-1-phosphate forming) | | |
| galactose | galP: galactose:H+ symporter GalP | | |
| galactose | galT: UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase | | |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| galacturonate | kdgK: 2-keto-3-deoxygluconate kinase | LFLEISCH_RS06060 | |
| galacturonate | uxaA: D-altronate dehydratase | | |
| galacturonate | uxaB: tagaturonate reductase | | |
| galacturonate | uxaC: D-galacturonate isomerase | | |
| gluconate | gntK: D-gluconate kinase | LFLEISCH_RS03400 | |
| glucosamine | manX: glucosamine PTS system, EII-AB component ManX | LFLEISCH_RS12725 | |
| glucosamine | manY: glucosamine PTS system, EII-C component ManY | LFLEISCH_RS12580 | LFLEISCH_RS12730 |
| glucosamine | manZ: glucosamine PTS system, EII-D component ManZ | LFLEISCH_RS12585 | LFLEISCH_RS03165 |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | kdgK: 2-keto-3-deoxygluconate kinase | LFLEISCH_RS06060 | |
| glucuronate | uxaC: D-glucuronate isomerase | | |
| glucuronate | uxuA: D-mannonate dehydratase | | |
| glucuronate | uxuB: D-mannonate dehydrogenase | | |
| glutamate | aspA: L-aspartate ammonia-lyase | LFLEISCH_RS06570 | |
| glutamate | glnP: L-glutamate ABC transporter, fused permease and substrate-binding components GlnP | | |
| glycerol | dhaD: glycerol dehydrogenase | LFLEISCH_RS04915 | LFLEISCH_RS02220 |
| 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 | LFLEISCH_RS10060 | |
| isoleucine | bcaP: L-isoleucine uptake transporter BcaP/CitA | LFLEISCH_RS03890 | LFLEISCH_RS08975 |
| isoleucine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | LFLEISCH_RS02925 | |
| isoleucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | LFLEISCH_RS09410 | LFLEISCH_RS02915 |
| isoleucine | ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase | LFLEISCH_RS10070 | LFLEISCH_RS07905 |
| isoleucine | epi: methylmalonyl-CoA epimerase | | |
| isoleucine | fadA: 2-methylacetoacetyl-CoA thiolase | LFLEISCH_RS10080 | |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | LFLEISCH_RS10980 | LFLEISCH_RS03535 |
| isoleucine | mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components | | |
| isoleucine | pccA: propionyl-CoA carboxylase, alpha subunit | | |
| L-malate | sdlC: L-malate:Na+ symporter SdlC | | |
| lactose | lacA: galactose-6-phosphate isomerase, lacA subunit | | |
| lactose | lacB: galactose-6-phosphate isomerase, lacB subunit | LFLEISCH_RS12130 | LFLEISCH_RS03045 |
| lactose | lacC: D-tagatose-6-phosphate kinase | LFLEISCH_RS07765 | LFLEISCH_RS04565 |
| lactose | lacIIA: lactose PTS system, EIIA component | LFLEISCH_RS03125 | LFLEISCH_RS12490 |
| lactose | lacIIB: lactose PTS system, EIIB component | LFLEISCH_RS03115 | LFLEISCH_RS12495 |
| lactose | lacIIC: lactose PTS system, EIIC component | LFLEISCH_RS07185 | LFLEISCH_RS11710 |
| leucine | aacS: acetoacetyl-CoA synthetase | | |
| leucine | atoB: acetyl-CoA C-acetyltransferase | | |
| leucine | bcaP: L-leucine uptake transporter BcaP | LFLEISCH_RS03890 | LFLEISCH_RS08975 |
| leucine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | LFLEISCH_RS02925 | |
| leucine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | LFLEISCH_RS09410 | LFLEISCH_RS02915 |
| leucine | liuA: isovaleryl-CoA dehydrogenase | LFLEISCH_RS10060 | |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | | |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | LFLEISCH_RS10075 | |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
| lysine | davA: 5-aminovaleramidase | LFLEISCH_RS10460 | |
| lysine | davB: L-lysine 2-monooxygenase | | |
| lysine | davT: 5-aminovalerate aminotransferase | LFLEISCH_RS02470 | LFLEISCH_RS13825 |
| lysine | glaH: glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD) | | |
| lysine | lhgD: L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) | | |
| maltose | susB: alpha-glucosidase (maltase) | LFLEISCH_RS13400 | LFLEISCH_RS08115 |
| mannose | manA: mannose-6-phosphate isomerase | | |
| myoinositol | iolE: scyllo-inosose 2-dehydratase | | |
| myoinositol | iolG: myo-inositol 2-dehydrogenase | LFLEISCH_RS05175 | LFLEISCH_RS08080 |
| myoinositol | iolJ: 5-dehydro-2-deoxyphosphogluconate aldolase | LFLEISCH_RS11870 | LFLEISCH_RS06505 |
| myoinositol | mmsA: malonate-semialdehyde dehydrogenase | LFLEISCH_RS09075 | |
| NAG | nagPcb: N-acetylglucosamine phosphotransferase system, EII-CB component NagP | | |
| phenylacetate | H281DRAFT_04042: phenylacetate:H+ symporter | LFLEISCH_RS05970 | LFLEISCH_RS14130 |
| 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 | LFLEISCH_RS10070 | LFLEISCH_RS07905 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | LFLEISCH_RS07905 | |
| phenylacetate | paaH: 3-hydroxyadipyl-CoA dehydrogenase | LFLEISCH_RS10980 | LFLEISCH_RS08200 |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | | |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | | |
| phenylacetate | paaK: phenylacetate-CoA ligase | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | LFLEISCH_RS07905 | LFLEISCH_RS10070 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylalanine | aacS: acetoacetyl-CoA synthetase | | |
| phenylalanine | aroP: L-phenylalanine:H+ symporter AroP | LFLEISCH_RS05970 | LFLEISCH_RS14130 |
| 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 | LFLEISCH_RS08815 | |
| proline | opuBA: proline ABC transporter, ATPase component OpuBA/BusAA | LFLEISCH_RS08170 | LFLEISCH_RS08935 |
| proline | put1: proline dehydrogenase | | |
| proline | putA: L-glutamate 5-semialdeyde dehydrogenase | LFLEISCH_RS09075 | |
| propionate | epi: methylmalonyl-CoA epimerase | | |
| propionate | mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components | | |
| propionate | pccA: propionyl-CoA carboxylase, alpha subunit | | |
| propionate | prpE: propionyl-CoA synthetase | | |
| putrescine | gabD: succinate semialdehyde dehydrogenase | LFLEISCH_RS09075 | LFLEISCH_RS02220 |
| putrescine | gabT: gamma-aminobutyrate transaminase | LFLEISCH_RS02470 | LFLEISCH_RS13825 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | LFLEISCH_RS02470 | LFLEISCH_RS07675 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | LFLEISCH_RS09075 | LFLEISCH_RS04500 |
| pyruvate | SLC5A8: sodium-coupled pyruvate transporter | | |
| rhamnose | fucO: L-lactaldehyde reductase | LFLEISCH_RS03220 | LFLEISCH_RS02850 |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsU: probable D-ribose transporter RbsU | LFLEISCH_RS12750 | LFLEISCH_RS12770 |
| serine | serP: L-serine permease SerP | LFLEISCH_RS05970 | LFLEISCH_RS14130 |
| sorbitol | sdh: sorbitol dehydrogenase | LFLEISCH_RS12125 | LFLEISCH_RS12120 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
| succinate | sdc: succinate:Na+ symporter Sdc | | |
| sucrose | ams: sucrose hydrolase (invertase) | LFLEISCH_RS13400 | LFLEISCH_RS08115 |
| threonine | gcvP: glycine cleavage system, P component (glycine decarboxylase) | LFLEISCH_RS06355 | LFLEISCH_RS06360 |
| threonine | gcvT: glycine cleavage system, T component (tetrahydrofolate aminomethyltransferase) | | |
| threonine | ltaE: L-threonine aldolase | LFLEISCH_RS05495 | |
| threonine | serP1: L-threonine uptake transporter SerP1 | LFLEISCH_RS05970 | LFLEISCH_RS14130 |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | treC: trehalose-6-phosphate hydrolase | LFLEISCH_RS13400 | LFLEISCH_RS08115 |
| tryptophan | aroP: tryptophan:H+ symporter AroP | LFLEISCH_RS05970 | LFLEISCH_RS14130 |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aacS: acetoacetyl-CoA synthetase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | LFLEISCH_RS05970 | LFLEISCH_RS14130 |
| 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 | LFLEISCH_RS10060 | |
| valine | bcaP: L-valine uptake transporter BcaP/CitA | LFLEISCH_RS03890 | LFLEISCH_RS08975 |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | | |
| valine | bkdA: branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | LFLEISCH_RS02925 | |
| valine | bkdC: branched-chain alpha-ketoacid dehydrogenase, E2 component | LFLEISCH_RS09410 | LFLEISCH_RS02915 |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | LFLEISCH_RS10070 | LFLEISCH_RS07905 |
| valine | epi: methylmalonyl-CoA epimerase | | |
| valine | mcmA: methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components | | |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | LFLEISCH_RS09075 | |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | LFLEISCH_RS01335 | |
| valine | pccA: propionyl-CoA carboxylase, alpha subunit | | |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | LFLEISCH_RS04560 | |
| xylose | xylA: xylose isomerase | | |
| 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