Potential Gaps in catabolism of small carbon sources in Neiella marina J221
Found 128 low-confidence and 25 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 | CBE68_RS14365 | |
| 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 | CBE68_RS09575 | |
| arabinose | araE: L-arabinose:H+ symporter | CBE68_RS15430 | CBE68_RS06295 |
| arabinose | xacB: L-arabinose 1-dehydrogenase | CBE68_RS16430 | CBE68_RS03625 |
| arabinose | xacC: L-arabinono-1,4-lactonase | CBE68_RS03620 | CBE68_RS16720 |
| arabinose | xacD: L-arabinonate dehydratase | CBE68_RS01310 | |
| arabinose | xacE: 2-dehydro-3-deoxy-L-arabinonate dehydratase | | |
| arginine | rocE: L-arginine permease | | |
| citrate | SLC13A5: citrate:Na+ symporter | CBE68_RS16860 | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | CBE68_RS04845 | CBE68_RS13315 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | | |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | | |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | | |
| citrulline | arcC: carbamate kinase | | |
| citrulline | aruF: ornithine/arginine N-succinyltransferase subunit AruAI (AruF) | CBE68_RS00845 | |
| citrulline | aruG: ornithine/arginine N-succinyltransferase subunit AruAII (AruG) | CBE68_RS00845 | |
| D-alanine | cycA: D-alanine:H+ symporter CycA | | |
| D-alanine | dadA: D-alanine dehydrogenase | | |
| 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 | CBE68_RS11520 | CBE68_RS01305 |
| deoxyribonate | aacS: acetoacetyl-CoA synthetase | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | CBE68_RS17620 | |
| 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 | deoK: deoxyribokinase | CBE68_RS00505 | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fructose | glcP: fructose:H+ symporter GlcP | CBE68_RS06295 | CBE68_RS15430 |
| fucose | aldA: lactaldehyde dehydrogenase | CBE68_RS09400 | CBE68_RS14670 |
| 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 | CBE68_RS15430 | CBE68_RS06295 |
| galacturonate | exuT: D-galacturonate transporter ExuT | CBE68_RS11445 | CBE68_RS01635 |
| galacturonate | uxaA: D-altronate dehydratase | | |
| galacturonate | uxaB: tagaturonate reductase | | |
| galacturonate | uxaC: D-galacturonate isomerase | | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | CBE68_RS17710 | CBE68_RS17695 |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | CBE68_RS06990 | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | CBE68_RS11445 | CBE68_RS01635 |
| glucuronate | uxaC: D-glucuronate isomerase | | |
| glucuronate | uxuA: D-mannonate dehydratase | CBE68_RS09430 | CBE68_RS13110 |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | | |
| glycerol | glpF: glycerol facilitator glpF | CBE68_RS00945 | |
| glycerol | glpK: glycerol kinase | | |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
| histidine | hutH: histidine ammonia-lyase | | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| histidine | permease: L-histidine permease | | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | | |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | CBE68_RS16430 | CBE68_RS17620 |
| isoleucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| isoleucine | prpC: 2-methylcitrate synthase | CBE68_RS08160 | |
| isoleucine | prpD: 2-methylcitrate dehydratase | | |
| L-lactate | lctO: L-lactate oxidase or 2-monooxygenase | | |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | CBE68_RS13045 | CBE68_RS14675 |
| leucine | aacS: acetoacetyl-CoA synthetase | | |
| leucine | liuA: isovaleryl-CoA dehydrogenase | | |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | CBE68_RS00315 | CBE68_RS12635 |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | CBE68_RS15805 | CBE68_RS17495 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | | |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
| leucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| lysine | amaB: L-2-aminoadipate semialdehyde dehydrogenase (AmaB/Pcd) | CBE68_RS09400 | CBE68_RS10815 |
| lysine | hglS: D-2-hydroxyglutarate synthase | | |
| lysine | lat: L-lysine 6-aminotransferase | CBE68_RS00840 | |
| lysine | lysN: 2-aminoadipate transaminase | CBE68_RS00840 | CBE68_RS12435 |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| mannitol | mt2d: mannitol 2-dehydrogenase | CBE68_RS14645 | CBE68_RS18265 |
| mannitol | PLT5: polyol transporter PLT5 | | |
| mannose | manA: mannose-6-phosphate isomerase | CBE68_RS12810 | CBE68_RS18445 |
| mannose | STP6: mannose:H+ symporter | CBE68_RS06295 | CBE68_RS15430 |
| myoinositol | iolG: myo-inositol 2-dehydrogenase | | |
| myoinositol | iolM: 2-inosose 4-dehydrogenase | | |
| myoinositol | iolN: 2,4-diketo-inositol hydratase | | |
| myoinositol | iolO: 5-dehydro-L-gluconate epimerase | | |
| myoinositol | iolT: myo-inositol:H+ symporter | CBE68_RS06295 | CBE68_RS14625 |
| myoinositol | uxaE: D-tagaturonate epimerase | | |
| myoinositol | uxuA: D-mannonate dehydratase | CBE68_RS09430 | CBE68_RS13110 |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | CBE68_RS06990 | |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | CBE68_RS17710 | CBE68_RS17695 |
| 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 | CBE68_RS15805 | CBE68_RS16825 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | CBE68_RS12080 | |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | CBE68_RS17490 | CBE68_RS09895 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | CBE68_RS17490 | CBE68_RS09895 |
| phenylacetate | paaK: phenylacetate-CoA ligase | CBE68_RS03965 | |
| 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 | fahA: fumarylacetoacetate hydrolase | | |
| phenylalanine | hmgA: homogentisate dioxygenase | | |
| phenylalanine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| phenylalanine | maiA: maleylacetoacetate isomerase | CBE68_RS13335 | |
| phenylalanine | PAH: phenylalanine 4-monooxygenase | | |
| propionate | prpC: 2-methylcitrate synthase | CBE68_RS08160 | |
| propionate | prpD: 2-methylcitrate dehydratase | | |
| putrescine | gabD: succinate semialdehyde dehydrogenase | CBE68_RS10135 | CBE68_RS04595 |
| putrescine | gabT: gamma-aminobutyrate transaminase | CBE68_RS00840 | CBE68_RS12435 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | CBE68_RS00840 | CBE68_RS07905 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | CBE68_RS09400 | CBE68_RS14670 |
| pyruvate | dctQ: pyruvate TRAP transporter, small permease component | CBE68_RS10545 | CBE68_RS05015 |
| rhamnose | aldA: lactaldehyde dehydrogenase | CBE68_RS09400 | CBE68_RS14670 |
| rhamnose | rhaA: L-rhamnose isomerase | | |
| rhamnose | rhaB: L-rhamnulokinase | | |
| rhamnose | rhaD: rhamnulose 1-phosphate aldolase | | |
| rhamnose | rhaM: L-rhamnose mutarotase | | |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| ribose | rbsK: ribokinase | CBE68_RS00505 | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| serine | snatA: L-serine transporter | CBE68_RS04590 | |
| sorbitol | sdh: sorbitol dehydrogenase | CBE68_RS14530 | CBE68_RS14645 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | CBE68_RS14625 | CBE68_RS15430 |
| sucrose | ams: sucrose hydrolase (invertase) | | |
| threonine | snatA: L-threonine transporter snatA | CBE68_RS04590 | |
| trehalose | treF: trehalase | CBE68_RS02885 | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aacS: acetoacetyl-CoA synthetase | | |
| tyrosine | aroP: L-tyrosine transporter (AroP/FywP) | | |
| tyrosine | fahA: fumarylacetoacetate hydrolase | | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | CBE68_RS13335 | |
| valine | acdH: isobutyryl-CoA dehydrogenase | | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | CBE68_RS11150 | CBE68_RS12080 |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | CBE68_RS17495 | CBE68_RS15805 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | CBE68_RS15800 | CBE68_RS09400 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | CBE68_RS18105 | |
| valine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| valine | prpC: 2-methylcitrate synthase | CBE68_RS08160 | |
| valine | prpD: 2-methylcitrate dehydratase | | |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | | |
| xylitol | xdhA: xylitol dehydrogenase | CBE68_RS14530 | CBE68_RS18265 |
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