Potential Gaps in catabolism of small carbon sources in Tatumella morbirosei LMG 23360
Found 90 low-confidence and 29 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 4-hydroxybenzoate | adh: acetaldehyde dehydrogenase (not acylating) | HA49_RS03160 | HA49_RS11040 |
| 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 | | |
| 4-hydroxybenzoate | praA: protocatechuate 2,3-dioxygenase | | |
| 4-hydroxybenzoate | praB: 2-hydroxymuconate 6-semialdehyde dehydrogenase | HA49_RS11065 | HA49_RS12270 |
| 4-hydroxybenzoate | praD: 2-oxohex-3-enedioate decarboxylase | | |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | HA49_RS07785 | HA49_RS09690 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | HA49_RS07790 | HA49_RS01460 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | HA49_RS07795 | HA49_RS01465 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | HA49_RS00950 | HA49_RS18660 |
| citrulline | patA: putrescine aminotransferase (PatA/SpuC) | HA49_RS17650 | HA49_RS00185 |
| D-lactate | lctP: D-lactate:H+ symporter LctP or LidP | | |
| deoxyinosine | adh: acetaldehyde dehydrogenase (not acylating) | HA49_RS03160 | HA49_RS11040 |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
| deoxyribonate | aacS: acetoacetyl-CoA synthetase | HA49_RS05005 | HA49_RS13245 |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | HA49_RS00335 | HA49_RS11495 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | HA49_RS01100 | HA49_RS06310 |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | | |
| deoxyribose | adh: acetaldehyde dehydrogenase (not acylating) | HA49_RS03160 | HA49_RS11040 |
| deoxyribose | deoP: deoxyribose transporter | HA49_RS00365 | |
| ethanol | adh: acetaldehyde dehydrogenase (not acylating) | HA49_RS03160 | HA49_RS11040 |
| galactose | pgmA: alpha-phosphoglucomutase | HA49_RS13070 | HA49_RS20450 |
| galacturonate | exuT: D-galacturonate transporter ExuT | HA49_RS18965 | |
| galacturonate | garD: meso-galactarate dehydratase (L-threo-forming) GarD | | |
| galacturonate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | | |
| galacturonate | udh: D-galacturonate dehydrogenase | | |
| galacturonate | uxuL: D-galactaro-1,5-lactonase (UxuL or UxuF) | HA49_RS18960 | HA49_RS01185 |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | HA49_RS16910 | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | HA49_RS18965 | |
| glucuronate | gci: D-glucaro-1,4-lactone cycloisomerase | | |
| glucuronate | kdgD: 5-dehydro-4-deoxyglucarate dehydratase | | |
| glucuronate | udh: D-glucuronate dehydrogenase | | |
| histidine | hisJ: L-histidine ABC transporter, substrate-binding component HisJ | HA49_RS07800 | HA49_RS00950 |
| histidine | hutH: histidine ammonia-lyase | HA49_RS11630 | |
| isoleucine | acdH: (2S)-2-methylbutanoyl-CoA dehydrogenase | | |
| isoleucine | ivdG: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase | HA49_RS02320 | HA49_RS00355 |
| isoleucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| isoleucine | prpB: 2-methylisocitrate lyase | | |
| isoleucine | prpC: 2-methylcitrate synthase | HA49_RS15410 | |
| isoleucine | prpD: 2-methylcitrate dehydratase | | |
| L-lactate | lctP: L-lactate:H+ symporter LctP or LidP | | |
| lactose | pgmA: alpha-phosphoglucomutase | HA49_RS13070 | HA49_RS20450 |
| leucine | aacS: acetoacetyl-CoA synthetase | HA49_RS05005 | HA49_RS13245 |
| leucine | liuA: isovaleryl-CoA dehydrogenase | | |
| leucine | liuB: 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | HA49_RS20085 | HA49_RS10750 |
| leucine | liuC: 3-methylglutaconyl-CoA hydratase | HA49_RS07935 | HA49_RS16815 |
| leucine | liuD: 3-methylcrotonyl-CoA carboxylase, beta subunit | | |
| leucine | liuE: hydroxymethylglutaryl-CoA lyase | | |
| leucine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| lysine | cadA: lysine decarboxylase | HA49_RS04215 | HA49_RS06950 |
| lysine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | HA49_RS07935 | HA49_RS16815 |
| lysine | gcdG: succinyl-CoA:glutarate CoA-transferase | | |
| lysine | gcdH: glutaryl-CoA dehydrogenase | | |
| lysine | patA: cadaverine aminotransferase | HA49_RS11030 | HA49_RS19635 |
| maltose | susB: alpha-glucosidase (maltase) | HA49_RS03325 | |
| 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 | | |
| myoinositol | iolT: myo-inositol:H+ symporter | HA49_RS12775 | HA49_RS00475 |
| myoinositol | mmsA: malonate-semialdehyde dehydrogenase | HA49_RS12400 | HA49_RS10825 |
| 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 | HA49_RS07935 | HA49_RS16815 |
| phenylacetate | paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase | | |
| phenylacetate | paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase | HA49_RS16820 | HA49_RS07940 |
| phenylacetate | paaJ2: 3-oxoadipyl-CoA thiolase | HA49_RS16820 | HA49_RS07940 |
| phenylacetate | paaK: phenylacetate-CoA ligase | | |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | | |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylacetate | ppa: phenylacetate permease ppa | HA49_RS16185 | HA49_RS05685 |
| phenylalanine | aacS: acetoacetyl-CoA synthetase | HA49_RS05005 | HA49_RS13245 |
| phenylalanine | fahA: fumarylacetoacetate hydrolase | HA49_RS00340 | |
| phenylalanine | hmgA: homogentisate dioxygenase | | |
| phenylalanine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| phenylalanine | maiA: maleylacetoacetate isomerase | | |
| phenylalanine | PAH: phenylalanine 4-monooxygenase | | |
| phenylalanine | PCBD: pterin-4-alpha-carbinoalamine dehydratase | | |
| propionate | prpB: 2-methylisocitrate lyase | | |
| propionate | prpC: 2-methylcitrate synthase | HA49_RS15410 | |
| propionate | prpD: 2-methylcitrate dehydratase | | |
| propionate | prpE: propionyl-CoA synthetase | HA49_RS06615 | |
| putrescine | patA: putrescine aminotransferase (PatA/SpuC) | HA49_RS17650 | HA49_RS00185 |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | HA49_RS04195 | HA49_RS05350 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | | |
| rhamnose | LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase | HA49_RS02320 | HA49_RS00335 |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| serine | serP: L-serine permease SerP | HA49_RS01890 | HA49_RS10315 |
| sorbitol | SOT: sorbitol:H+ co-transporter SOT1 or SOT2 | HA49_RS09585 | HA49_RS12775 |
| sucrose | ams: sucrose hydrolase (invertase) | HA49_RS01070 | HA49_RS01075 |
| threonine | adh: acetaldehyde dehydrogenase (not acylating) | HA49_RS03160 | HA49_RS11040 |
| threonine | serP1: L-threonine uptake transporter SerP1 | HA49_RS01890 | HA49_RS10315 |
| thymidine | adh: acetaldehyde dehydrogenase (not acylating) | HA49_RS03160 | HA49_RS11040 |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| tryptophan | tnaA: tryptophanase | | |
| tyrosine | aacS: acetoacetyl-CoA synthetase | HA49_RS05005 | HA49_RS13245 |
| tyrosine | fahA: fumarylacetoacetate hydrolase | HA49_RS00340 | |
| tyrosine | hmgA: homogentisate dioxygenase | | |
| tyrosine | HPD: 4-hydroxyphenylpyruvate dioxygenase | | |
| tyrosine | maiA: maleylacetoacetate isomerase | | |
| valine | acdH: isobutyryl-CoA dehydrogenase | | |
| valine | bch: 3-hydroxyisobutyryl-CoA hydrolase | | |
| valine | ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase | HA49_RS07935 | HA49_RS16815 |
| valine | mmsA: methylmalonate-semialdehyde dehydrogenase | HA49_RS10825 | HA49_RS11065 |
| valine | mmsB: 3-hydroxyisobutyrate dehydrogenase | | |
| valine | ofo: branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | | |
| valine | prpB: 2-methylisocitrate lyase | | |
| valine | prpC: 2-methylcitrate synthase | HA49_RS15410 | |
| valine | prpD: 2-methylcitrate dehydratase | | |
| xylitol | fruI: xylitol PTS, enzyme IIABC (FruI) | HA49_RS21135 | HA49_RS07395 |
| xylitol | x5p-reductase: D-xylulose-5-phosphate 2-reductase | HA49_RS04190 | |
| xylose | xylA: xylose isomerase | | |
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