Potential Gaps in catabolism of small carbon sources in Duganella sacchari Sac-22
Found 55 low-confidence and 43 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| 4-hydroxybenzoate | pobA: 4-hydroxybenzoate 3-monooxygenase | | |
| 4-hydroxybenzoate | praA: protocatechuate 2,3-dioxygenase | | |
| 4-hydroxybenzoate | praC: 2-hydroxymuconate tautomerase | | |
| alanine | cycA: L-alanine symporter CycA | BUA36_RS06065 | BUA36_RS24700 |
| arabinose | araE: L-arabinose:H+ symporter | BUA36_RS18045 | |
| arabinose | xacC: L-arabinono-1,4-lactonase | BUA36_RS22905 | BUA36_RS13650 |
| arabinose | xacD: L-arabinonate dehydratase | BUA36_RS22810 | BUA36_RS22860 |
| arabinose | xacE: 2-dehydro-3-deoxy-L-arabinonate dehydratase | | |
| arginine | astE: succinylglutamate desuccinylase | BUA36_RS14110 | |
| arginine | braC: ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC | BUA36_RS22795 | BUA36_RS27625 |
| arginine | braD: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) | BUA36_RS22500 | |
| arginine | braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) | BUA36_RS22495 | BUA36_RS26915 |
| arginine | braF: ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) | BUA36_RS26915 | BUA36_RS06900 |
| arginine | braG: ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) | BUA36_RS22485 | BUA36_RS26920 |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | BUA36_RS13970 | BUA36_RS10245 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | | |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | BUA36_RS10510 | |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | BUA36_RS10505 | |
| citrulline | arcC: carbamate kinase | | |
| citrulline | aruG: ornithine/arginine N-succinyltransferase subunit AruAII (AruG) | BUA36_RS14090 | BUA36_RS14085 |
| citrulline | astE: succinylglutamate desuccinylase | BUA36_RS14110 | |
| D-alanine | cycA: D-alanine:H+ symporter CycA | BUA36_RS06065 | BUA36_RS24700 |
| D-lactate | lctP: D-lactate:H+ symporter LctP or LidP | | |
| D-serine | cycA: D-serine:H+ symporter CycA | BUA36_RS06065 | BUA36_RS24700 |
| D-serine | dsdA: D-serine ammonia-lyase | BUA36_RS25770 | BUA36_RS18985 |
| deoxyinosine | bmpA: deoxyinosine ABC transporter, substrate-binding component | BUA36_RS13065 | |
| deoxyinosine | nupB: deoxyinosine ABC transporter, permease component 1 | BUA36_RS13075 | |
| deoxyinosine | nupC': deoxyinosine ABC transporter, permease component 2 | BUA36_RS23415 | BUA36_RS13080 |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | BUA36_RS18290 | BUA36_RS17920 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | BUA36_RS08325 | BUA36_RS06120 |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | deoK: deoxyribokinase | | |
| deoxyribose | deoP: deoxyribose transporter | BUA36_RS02040 | BUA36_RS22585 |
| fructose | fruP: fructose porter FruP | BUA36_RS22585 | BUA36_RS02040 |
| fucose | fucD: L-fuconate dehydratase | BUA36_RS13610 | |
| fucose | fucDH: 2-keto-3-deoxy-L-fuconate 4-dehydrogenase | BUA36_RS17920 | BUA36_RS21210 |
| fucose | fuconolactonase: L-fucono-1,5-lactonase | | |
| fucose | fucP: L-fucose:H+ symporter FucP | BUA36_RS02040 | BUA36_RS22585 |
| fucose | fucU: L-fucose mutarotase FucU | | |
| galactose | dgoK: 2-dehydro-3-deoxygalactonokinase | BUA36_RS22915 | |
| gluconate | gntT: gluconate:H+ symporter GntT | | |
| glucosamine | nagX: transmembrane glucosamine N-acetyltransferase NagX | BUA36_RS04775 | BUA36_RS06455 |
| glucosamine | SMc02869: N-acetylglucosamine ABC transporter, ATPase component | BUA36_RS01000 | BUA36_RS20915 |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | BUA36_RS24985 | |
| glutamate | gdhA: glutamate dehydrogenase, NAD-dependent | BUA36_RS14105 | BUA36_RS17675 |
| glutamate | gltP: L-glutamate:cation symporter GltP/GltT | BUA36_RS10900 | BUA36_RS13965 |
| glycerol | glpF: glycerol facilitator glpF | BUA36_RS22040 | |
| histidine | permease: L-histidine permease | BUA36_RS06065 | BUA36_RS24700 |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| lactose | dgoK: 2-dehydro-3-deoxygalactonokinase | BUA36_RS22915 | |
| lactose | lacP: lactose permease LacP | | |
| lysine | davT: 5-aminovalerate aminotransferase | BUA36_RS15745 | BUA36_RS14080 |
| lysine | lysP: L-lysine:H+ symporter LysP | BUA36_RS06065 | BUA36_RS24700 |
| lysine | patA: cadaverine aminotransferase | BUA36_RS14080 | BUA36_RS15745 |
| lysine | patD: 5-aminopentanal dehydrogenase | BUA36_RS24745 | BUA36_RS07090 |
| maltose | susB: alpha-glucosidase (maltase) | BUA36_RS22940 | BUA36_RS17900 |
| mannitol | mt2d: mannitol 2-dehydrogenase | BUA36_RS22870 | BUA36_RS04645 |
| mannitol | PLT5: polyol transporter PLT5 | | |
| mannose | gluP: mannose:Na+ symporter | BUA36_RS22585 | BUA36_RS02040 |
| myoinositol | iolB: 5-deoxy-D-glucuronate isomerase | | |
| myoinositol | iolC: 5-dehydro-2-deoxy-D-gluconate kinase | | |
| 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 | BUA36_RS15190 | |
| myoinositol | iolT: myo-inositol:H+ symporter | | |
| NAG | SMc02869: N-acetylglucosamine ABC transporter, ATPase component | BUA36_RS01000 | BUA36_RS20915 |
| phenylacetate | ppa: phenylacetate permease ppa | BUA36_RS28605 | |
| phenylalanine | iorAB: phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB | BUA36_RS23930 | BUA36_RS23525 |
| propionate | mctC: propionate:H+ symporter | BUA36_RS28605 | |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | BUA36_RS15000 | BUA36_RS13005 |
| 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 | | |
| ribose | rbsU: probable D-ribose transporter RbsU | | |
| sorbitol | sdh: sorbitol dehydrogenase | BUA36_RS21210 | BUA36_RS17920 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | | |
| sucrose | ams: sucrose hydrolase (invertase) | BUA36_RS22940 | |
| threonine | RR42_RS28305: L-threonine:H+ symporter | BUA36_RS06065 | BUA36_RS24700 |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | treF: trehalase | BUA36_RS22940 | |
| tryptophan | hpaH: anthranilate 3-monooxygenase (hydroxylase), FADH2-dependent | BUA36_RS05355 | |
| tryptophan | kynB: kynurenine formamidase | BUA36_RS19530 | BUA36_RS28245 |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| valine | livH: L-valine ABC transporter, permease component 1 (LivH/BraD) | BUA36_RS22500 | BUA36_RS07245 |
| valine | livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | BUA36_RS04095 | BUA36_RS27625 |
| valine | livM: L-valine ABC transporter, permease component 2 (LivM/BraE) | BUA36_RS22495 | BUA36_RS26915 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | BUA36_RS12650 | BUA36_RS20945 |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | | |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | | |
| xylose | kdaD: 2-keto-3-deoxy-D-arabinonate dehydratase | | |
| xylose | xad: D-xylonate dehydratase | BUA36_RS03355 | BUA36_RS22860 |
| xylose | xdh: D-xylose dehydrogenase | BUA36_RS13995 | BUA36_RS17920 |
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