Potential Gaps in catabolism of small carbon sources in Amantichitinum ursilacus IGB-41
Found 83 low-confidence and 45 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | kgtP: 2-oxoglutarate:H+ symporter KgtP | WG78_RS12280 | WG78_RS04330 |
| 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 | WG78_RS05840 | |
| 4-hydroxybenzoate | praA: protocatechuate 2,3-dioxygenase | | |
| 4-hydroxybenzoate | xylF: 2-hydroxymuconate semialdehyde hydrolase | | |
| alanine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | WG78_RS14890 | WG78_RS14725 |
| alanine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | WG78_RS14895 | WG78_RS14720 |
| alanine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | WG78_RS14905 | WG78_RS14710 |
| alanine | braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) | WG78_RS14910 | WG78_RS14705 |
| arginine | braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) | WG78_RS14895 | WG78_RS14720 |
| arginine | braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) | WG78_RS14900 | WG78_RS14715 |
| cellobiose | glk: glucokinase | WG78_RS13930 | WG78_RS21595 |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | WG78_RS16125 | WG78_RS16145 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | WG78_RS08860 | |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | WG78_RS08860 | WG78_RS15275 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | WG78_RS08855 | |
| citrulline | arcC: carbamate kinase | WG78_RS17575 | |
| citrulline | aruF: ornithine/arginine N-succinyltransferase subunit AruAI (AruF) | WG78_RS00585 | |
| citrulline | aruG: ornithine/arginine N-succinyltransferase subunit AruAII (AruG) | WG78_RS00585 | |
| D-lactate | lctP: D-lactate:H+ symporter LctP or LidP | | |
| D-serine | cycA: D-serine:H+ symporter CycA | WG78_RS03005 | |
| D-serine | dsdA: D-serine ammonia-lyase | WG78_RS13285 | |
| deoxyribonate | aacS: acetoacetyl-CoA synthetase | WG78_RS10575 | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | WG78_RS04575 | WG78_RS08820 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoP: deoxyribose transporter | WG78_RS19555 | |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | WG78_RS16620 | |
| fucose | fucI: L-fucose isomerase FucI | | |
| fucose | fucK: L-fuculose kinase FucK | | |
| fucose | fucP: L-fucose:H+ symporter FucP | WG78_RS19555 | |
| fucose | fucU: L-fucose mutarotase FucU | WG78_RS08805 | |
| glucose | glk: glucokinase | WG78_RS13930 | WG78_RS21595 |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | uxuA: D-mannonate dehydratase | WG78_RS15640 | WG78_RS06325 |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | | |
| glycerol | glpF: glycerol facilitator glpF | WG78_RS08050 | |
| histidine | hutG: N-formiminoglutamate formiminohydrolase | | |
| histidine | hutH: histidine ammonia-lyase | WG78_RS05490 | |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | WG78_RS10110 | |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | WG78_RS04575 | WG78_RS08820 |
| isoleucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| isoleucine | prpC: 2-methylcitrate synthase | WG78_RS10345 | |
| isoleucine | prpD: 2-methylcitrate dehydratase | | |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| lactose | glk: glucokinase | WG78_RS13930 | WG78_RS21595 |
| lactose | lacP: lactose permease LacP | | |
| leucine | aacS: acetoacetyl-CoA synthetase | WG78_RS10575 | |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | WG78_RS08300 | WG78_RS18565 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | | |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
| leucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| lysine | glaH: glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD) | | |
| lysine | patA: cadaverine aminotransferase | WG78_RS16665 | WG78_RS06780 |
| lysine | patD: 5-aminopentanal dehydrogenase | WG78_RS16670 | WG78_RS14820 |
| maltose | glk: glucokinase | WG78_RS13930 | WG78_RS21595 |
| mannitol | mt2d: mannitol 2-dehydrogenase | WG78_RS15635 | WG78_RS09690 |
| mannitol | mtlE: polyol ABC transporter, substrate-binding component MtlE/SmoE | WG78_RS09715 | |
| mannitol | mtlF: polyol ABC transporter, permease component 1 (MtlF/SmoF) | WG78_RS09710 | WG78_RS06130 |
| mannitol | mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) | WG78_RS09705 | WG78_RS20150 |
| mannitol | mtlK: polyol ABC transporter, ATP component MtlK/SmoG | WG78_RS07490 | WG78_RS09695 |
| myoinositol | iolG: myo-inositol 2-dehydrogenase | WG78_RS17405 | WG78_RS16575 |
| myoinositol | iolM: 2-inosose 4-dehydrogenase | | |
| myoinositol | iolN: 2,4-diketo-inositol hydratase | | |
| myoinositol | iolO: 5-dehydro-L-gluconate epimerase | WG78_RS21600 | |
| myoinositol | PS417_11885: myo-inositol ABC transporter, substrate-binding component | WG78_RS19940 | WG78_RS15690 |
| myoinositol | PS417_11895: myo-inositol ABC transporter, permease component | WG78_RS19935 | WG78_RS19015 |
| myoinositol | uxaE: D-tagaturonate epimerase | | |
| myoinositol | uxuA: D-mannonate dehydratase | WG78_RS15640 | WG78_RS06325 |
| 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 | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | WG78_RS19070 | WG78_RS04410 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | WG78_RS19070 | WG78_RS04410 |
| phenylacetate | paaK: phenylacetate-CoA ligase | WG78_RS10575 | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | | |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylacetate | ppa: phenylacetate permease ppa | WG78_RS08055 | |
| phenylalanine | aacS: acetoacetyl-CoA synthetase | WG78_RS10575 | |
| phenylalanine | fahA: fumarylacetoacetate hydrolase | WG78_RS08825 | WG78_RS02700 |
| phenylalanine | hmgA: homogentisate dioxygenase | | |
| phenylalanine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| phenylalanine | maiA: maleylacetoacetate isomerase | WG78_RS13310 | |
| phenylalanine | PAH: phenylalanine 4-monooxygenase | | |
| phenylalanine | PCBD: pterin-4-alpha-carbinoalamine dehydratase | WG78_RS08100 | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | WG78_RS20825 | |
| propionate | mctC: propionate:H+ symporter | WG78_RS08055 | |
| propionate | prpC: 2-methylcitrate synthase | WG78_RS10345 | |
| propionate | prpD: 2-methylcitrate dehydratase | | |
| putrescine | potD: putrescine ABC transporter, substrate-binding component (PotD/PotF) | WG78_RS14790 | WG78_RS05425 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | rhaP: L-rhamnose ABC transporter, permease component 1 (RhaP) | WG78_RS08790 | WG78_RS19015 |
| rhamnose | rhaQ: L-rhamnose ABC transporter, permease component 2 (RhaQ) | WG78_RS08785 | WG78_RS19935 |
| rhamnose | rhaS: L-rhamnose ABC transporter, substrate-binding component RhaS | WG78_RS08780 | |
| rhamnose | rhaT': L-rhamnose ABC transporter, ATPase component RhaT | WG78_RS08795 | WG78_RS19930 |
| ribose | rbsB: D-ribose ABC transporter, substrate-binding component RbsB | WG78_RS19940 | WG78_RS15690 |
| sorbitol | sdh: sorbitol dehydrogenase | WG78_RS19235 | WG78_RS09155 |
| sucrose | ams: sucrose hydrolase (invertase) | WG78_RS14610 | WG78_RS20155 |
| threonine | braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) | WG78_RS14890 | WG78_RS14725 |
| threonine | braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) | WG78_RS14895 | WG78_RS14720 |
| threonine | braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) | WG78_RS14905 | WG78_RS14710 |
| threonine | braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) | WG78_RS14910 | WG78_RS14705 |
| trehalose | glk: glucokinase | WG78_RS13930 | WG78_RS21595 |
| tryptophan | aroP: tryptophan:H+ symporter AroP | WG78_RS03005 | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aacS: acetoacetyl-CoA synthetase | WG78_RS10575 | |
| tyrosine | fahA: fumarylacetoacetate hydrolase | WG78_RS08825 | WG78_RS02700 |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | WG78_RS13310 | |
| valine | acdH: isobutyryl-CoA dehydrogenase | WG78_RS10110 | WG78_RS04395 |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | WG78_RS03010 | |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | | |
| valine | livH: L-valine ABC transporter, permease component 1 (LivH/BraD) | WG78_RS14895 | WG78_RS14720 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | WG78_RS07195 | WG78_RS14820 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | WG78_RS18815 | |
| valine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| valine | prpC: 2-methylcitrate synthase | WG78_RS10345 | |
| valine | prpD: 2-methylcitrate dehydratase | | |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | | |
| xylitol | xdhA: xylitol dehydrogenase | WG78_RS08820 | WG78_RS04575 |
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