Potential Gaps in catabolism of small carbon sources in Herbaspirillum aquaticum IEH 4430
Found 41 low-confidence and 44 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 4-hydroxybenzoate | pcaC: 4-carboxymuconolactone decarboxylase | CEJ45_RS16080 | CEJ45_RS21340 |
| 4-hydroxybenzoate | pcaF: succinyl-CoA:acetyl-CoA C-succinyltransferase | CEJ45_RS16030 | CEJ45_RS20030 |
| 4-hydroxybenzoate | pcaH: protocatechuate 3,4-dioxygenase, alpha subunit | CEJ45_RS16095 | |
| alanine | braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) | CEJ45_RS04965 | CEJ45_RS01005 |
| arginine | braC: ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC | CEJ45_RS04945 | CEJ45_RS12295 |
| arginine | braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) | CEJ45_RS04950 | CEJ45_RS11220 |
| arginine | braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) | CEJ45_RS04955 | CEJ45_RS13770 |
| arginine | braF: ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) | CEJ45_RS04960 | CEJ45_RS20105 |
| arginine | braG: ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) | CEJ45_RS04965 | CEJ45_RS22555 |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | CEJ45_RS11345 | CEJ45_RS20430 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | CEJ45_RS11350 | CEJ45_RS20425 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | CEJ45_RS03555 | CEJ45_RS04235 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | CEJ45_RS03560 | CEJ45_RS04230 |
| citrulline | arcC: carbamate kinase | | |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| D-serine | dsdA: D-serine ammonia-lyase | CEJ45_RS14605 | CEJ45_RS07345 |
| deoxyinosine | deoB: phosphopentomutase | | |
| deoxyinosine | deoD: deoxyinosine phosphorylase | | |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | CEJ45_RS11375 | CEJ45_RS04045 |
| deoxyribose | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | CEJ45_RS11375 | CEJ45_RS04045 |
| fructose | frcA: fructose ABC transporter, ATPase component FrcA | CEJ45_RS12010 | CEJ45_RS11935 |
| glucosamine | nagK: N-acetylglucosamine kinase | CEJ45_RS22500 | CEJ45_RS13280 |
| glucosamine | nagX: transmembrane glucosamine N-acetyltransferase NagX | | |
| glucosamine | SMc02869: N-acetylglucosamine ABC transporter, ATPase component | CEJ45_RS13285 | CEJ45_RS16805 |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | uxuL: D-glucaro-1,5-lactonase UxuL or UxuF | CEJ45_RS20965 | CEJ45_RS12040 |
| histidine | hutH: histidine ammonia-lyase | CEJ45_RS23805 | CEJ45_RS19165 |
| histidine | hutI: imidazole-5-propionate hydrolase | | |
| histidine | hutU: urocanase | | |
| histidine | PA5503: L-histidine ABC transporter, ATPase component | CEJ45_RS08870 | CEJ45_RS15200 |
| histidine | PA5504: L-histidine ABC transporter, permease component | CEJ45_RS08865 | |
| histidine | PA5505: L-histidine ABC transporter, substrate-binding component | CEJ45_RS08860 | CEJ45_RS05610 |
| lactose | lacP: lactose permease LacP | | |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| lysine | patA: cadaverine aminotransferase | CEJ45_RS11820 | CEJ45_RS12790 |
| lysine | patD: 5-aminopentanal dehydrogenase | CEJ45_RS11615 | CEJ45_RS01340 |
| maltose | susB: alpha-glucosidase (maltase) | | |
| mannitol | mt2d: mannitol 2-dehydrogenase | CEJ45_RS16800 | CEJ45_RS09195 |
| mannitol | mtlE: polyol ABC transporter, substrate-binding component MtlE/SmoE | CEJ45_RS16825 | |
| mannitol | mtlF: polyol ABC transporter, permease component 1 (MtlF/SmoF) | CEJ45_RS16820 | CEJ45_RS09495 |
| mannitol | mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) | CEJ45_RS16815 | CEJ45_RS09200 |
| mannitol | mtlK: polyol ABC transporter, ATP component MtlK/SmoG | CEJ45_RS16805 | CEJ45_RS13285 |
| mannose | HSERO_RS03640: mannose ABC transporter, ATPase component | CEJ45_RS12010 | CEJ45_RS11935 |
| myoinositol | iolB: 5-deoxy-D-glucuronate isomerase | | |
| myoinositol | iolC: 5-dehydro-2-deoxy-D-gluconate kinase | CEJ45_RS19640 | |
| 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 | CEJ45_RS07755 | CEJ45_RS19640 |
| myoinositol | PS417_11885: myo-inositol ABC transporter, substrate-binding component | CEJ45_RS08035 | |
| myoinositol | PS417_11895: myo-inositol ABC transporter, permease component | CEJ45_RS08045 | CEJ45_RS11930 |
| NAG | nagK: N-acetylglucosamine kinase | CEJ45_RS22500 | CEJ45_RS13280 |
| NAG | SMc02869: N-acetylglucosamine ABC transporter, ATPase component | CEJ45_RS13285 | CEJ45_RS16805 |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylalanine | iorAB: phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB | CEJ45_RS10405 | CEJ45_RS06400 |
| proline | HSERO_RS00890: proline ABC transporter, permease component 2 | CEJ45_RS04955 | CEJ45_RS05575 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | CEJ45_RS11625 | CEJ45_RS12790 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | CEJ45_RS06185 | CEJ45_RS11550 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | CEJ45_RS11695 | CEJ45_RS09675 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | CEJ45_RS14255 | CEJ45_RS20970 |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| serine | braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) | CEJ45_RS04965 | CEJ45_RS01005 |
| sucrose | ams: sucrose hydrolase (invertase) | | |
| threonine | braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) | CEJ45_RS04965 | CEJ45_RS01005 |
| threonine | tdcE: 2-ketobutyrate formate-lyase | | |
| thymidine | deoA: thymidine phosphorylase DeoA | CEJ45_RS15400 | |
| thymidine | deoB: phosphopentomutase | | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | treF: trehalase | CEJ45_RS14360 | |
| tryptophan | antA: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA | CEJ45_RS21365 | CEJ45_RS21470 |
| tryptophan | antB: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB | CEJ45_RS21370 | |
| tryptophan | antC: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC | CEJ45_RS21375 | CEJ45_RS17600 |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | catC: muconolactone isomerase | CEJ45_RS21345 | |
| tryptophan | kyn: kynureninase | | |
| tryptophan | kynA: tryptophan 2,3-dioxygenase | | |
| tryptophan | kynB: kynurenine formamidase | CEJ45_RS11670 | CEJ45_RS17565 |
| tryptophan | pcaF: succinyl-CoA:acetyl-CoA C-succinyltransferase | CEJ45_RS16030 | CEJ45_RS20030 |
| tyrosine | Ac3H11_1694: L-tyrosine ABC transporter, permease component 2 | CEJ45_RS04955 | CEJ45_RS05575 |
| valine | acdH: isobutyryl-CoA dehydrogenase | CEJ45_RS06405 | CEJ45_RS12595 |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | CEJ45_RS14820 | CEJ45_RS16530 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | CEJ45_RS00290 | CEJ45_RS10180 |
| xylose | xylC: xylonolactonase | CEJ45_RS14270 | CEJ45_RS12040 |
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