Potential Gaps in catabolism of small carbon sources in Acidovorax sp. GW101-3H11
Found 70 low-confidence and 39 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 2-oxoglutarate | kgtP: 2-oxoglutarate:H+ symporter KgtP | Ac3H11_3022 | |
| 4-hydroxybenzoate | pcaK: 4-hydroxybenzoate transporter pcaK | | |
| alanine | TRIC: TRIC-type L-alanine transporter | Ac3H11_3909 | |
| arginine | braC: ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC | Ac3H11_2396 | Ac3H11_552 |
| arginine | braE: ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) | Ac3H11_1694 | Ac3H11_1938 |
| arginine | braF: ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) | Ac3H11_4630 | Ac3H11_1937 |
| arginine | braG: ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) | Ac3H11_1692 | Ac3H11_1936 |
| cellobiose | bgl: cellobiase | | |
| citrate | tctB: citrate/Na+ symporter, small transmembrane component TctB | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | Ac3H11_4899 | Ac3H11_2553 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | Ac3H11_3200 | Ac3H11_3326 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | Ac3H11_2554 | Ac3H11_3326 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | Ac3H11_2555 | |
| D-alanine | cycA: D-alanine:H+ symporter CycA | | |
| D-lactate | lctP: D-lactate:H+ symporter LctP or LidP | | |
| D-serine | cycA: D-serine:H+ symporter CycA | | |
| deoxyinosine | adh: acetaldehyde dehydrogenase (not acylating) | Ac3H11_4393 | Ac3H11_4184 |
| deoxyinosine | deoB: phosphopentomutase | Ac3H11_444 | |
| deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyinosine | deoD: deoxyinosine phosphorylase | | |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | Ac3H11_493 | Ac3H11_2762 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | | |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | Ac3H11_1929 | |
| deoxyribose | adh: acetaldehyde dehydrogenase (not acylating) | Ac3H11_4393 | Ac3H11_4184 |
| deoxyribose | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| ethanol | adh: acetaldehyde dehydrogenase (not acylating) | Ac3H11_4393 | Ac3H11_4184 |
| fucose | aldA: lactaldehyde dehydrogenase | Ac3H11_1496 | Ac3H11_4393 |
| 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 | | |
| galacturonate | exuT: D-galacturonate transporter ExuT | | |
| glucosamine | nagB: glucosamine 6-phosphate deaminase (isomerizing) | Ac3H11_3072 | |
| glucosamine | SLC2A2: glucosamine transporter SLC2A2 | | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glucuronate | uxuL: D-glucaro-1,5-lactonase UxuL or UxuF | Ac3H11_2337 | Ac3H11_3954 |
| glutamate | gdhA: glutamate dehydrogenase, NAD-dependent | Ac3H11_3282 | Ac3H11_315 |
| glycerol | glpD: glycerol 3-phosphate dehydrogenase (monomeric) | Ac3H11_797 | |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| lactose | lacP: lactose permease LacP | | |
| lactose | lacZ: lactase (homomeric) | | |
| lysine | lysP: L-lysine:H+ symporter LysP | | |
| lysine | patA: cadaverine aminotransferase | Ac3H11_1332 | Ac3H11_4179 |
| lysine | patD: 5-aminopentanal dehydrogenase | Ac3H11_1496 | Ac3H11_1480 |
| maltose | susB: alpha-glucosidase (maltase) | | |
| mannitol | mt2d: mannitol 2-dehydrogenase | Ac3H11_2939 | Ac3H11_3445 |
| mannitol | mtlE: polyol ABC transporter, substrate-binding component MtlE/SmoE | Ac3H11_2944 | |
| mannitol | mtlF: polyol ABC transporter, permease component 1 (MtlF/SmoF) | Ac3H11_2943 | |
| mannitol | mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) | Ac3H11_2942 | Ac3H11_794 |
| mannitol | mtlK: polyol ABC transporter, ATP component MtlK/SmoG | Ac3H11_2941 | Ac3H11_4785 |
| 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 | Ac3H11_658 | |
| myoinositol | iolT: myo-inositol:H+ symporter | | |
| NAG | nagA: N-acetylglucosamine 6-phosphate deacetylase | | |
| NAG | nagB: glucosamine 6-phosphate deaminase (isomerizing) | Ac3H11_3072 | |
| NAG | nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components | | |
| 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 | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | Ac3H11_2719 | Ac3H11_4989 |
| phenylacetate | paaK: phenylacetate-CoA ligase | Ac3H11_4625 | Ac3H11_964 |
| phenylacetate | paaT: phenylacetate transporter Paa | | |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | Ac3H11_3089 | |
| phenylalanine | hmgA: homogentisate dioxygenase | | |
| phenylalanine | PCBD: pterin-4-alpha-carbinoalamine dehydratase | Ac3H11_1679 | |
| phenylalanine | QDPR: 6,7-dihydropteridine reductase | | |
| propionate | putP: propionate transporter; proline:Na+ symporter | | |
| putrescine | gabT: gamma-aminobutyrate transaminase | Ac3H11_4179 | Ac3H11_4342 |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | Ac3H11_4342 | Ac3H11_1332 |
| putrescine | patD: gamma-aminobutyraldehyde dehydrogenase | Ac3H11_1496 | Ac3H11_1486 |
| putrescine | puuP: putrescine:H+ symporter PuuP/PlaP | | |
| rhamnose | aldA: lactaldehyde dehydrogenase | Ac3H11_1496 | Ac3H11_4393 |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | Ac3H11_2257 | Ac3H11_2748 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | Ac3H11_3953 | Ac3H11_600 |
| rhamnose | LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase | Ac3H11_3372 | Ac3H11_1482 |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| sucrose | ams: sucrose hydrolase (invertase) | | |
| threonine | adh: acetaldehyde dehydrogenase (not acylating) | Ac3H11_4393 | Ac3H11_4184 |
| threonine | snatA: L-threonine transporter snatA | Ac3H11_2153 | Ac3H11_817 |
| thymidine | adh: acetaldehyde dehydrogenase (not acylating) | Ac3H11_4393 | Ac3H11_4184 |
| thymidine | deoA: thymidine phosphorylase DeoA | Ac3H11_2202 | Ac3H11_2615 |
| thymidine | deoB: phosphopentomutase | Ac3H11_444 | |
| thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| trehalose | treF: trehalase | | |
| tryptophan | adh: acetaldehyde dehydrogenase (not acylating) | Ac3H11_4393 | Ac3H11_4184 |
| tryptophan | andAa: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin--NAD(+) reductase component AndAa | Ac3H11_214 | Ac3H11_2771 |
| tryptophan | andAb: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin subunit AndAb | Ac3H11_215 | |
| tryptophan | andAc: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AndAc | Ac3H11_217 | |
| tryptophan | andAd: athranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AndAd | Ac3H11_216 | |
| tryptophan | aroP: tryptophan:H+ symporter AroP | | |
| tryptophan | mhpD: 2-hydroxypentadienoate hydratase | Ac3H11_1483 | Ac3H11_4809 |
| tryptophan | praD: 2-oxohex-3-enedioate decarboxylase | Ac3H11_1483 | Ac3H11_4809 |
| tryptophan | xylE: catechol 2,3-dioxygenase | | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| valine | livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | Ac3H11_2396 | Ac3H11_4169 |
| valine | livM: L-valine ABC transporter, permease component 2 (LivM/BraE) | Ac3H11_1694 | Ac3H11_4628 |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | | |
| xylitol | xdhA: xylitol dehydrogenase | Ac3H11_2257 | Ac3H11_1922 |
| xylose | xdh: D-xylose dehydrogenase | Ac3H11_614 | Ac3H11_2257 |
| xylose | xylC: xylonolactonase | Ac3H11_615 | Ac3H11_2081 |
Confidence: high confidence medium confidence low confidence
This GapMind analysis is from Sep 17 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