Potential Gaps in catabolism of small carbon sources in Pseudomonas fluorescens FW300-N2E3
Found 41 low-confidence and 18 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| arabinose | araA: L-arabinose isomerase | | |
| arabinose | araB: ribulokinase | | |
| arabinose | araD: L-ribulose-5-phosphate epimerase | | |
| arabinose | araE: L-arabinose:H+ symporter | | |
| deoxyinosine | deoB: phosphopentomutase | AO353_05595 | |
| deoxyinosine | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyinosine | nupC: deoxyinosine:H+ symporter NupC | | |
| deoxyribonate | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | AO353_24520 | AO353_21770 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | AO353_29035 | AO353_24515 |
| deoxyribonate | ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme | AO353_07745 | |
| deoxyribose | deoC: deoxyribose-5-phosphate aldolase | | |
| deoxyribose | deoP: deoxyribose transporter | | |
| fucose | aldA: lactaldehyde dehydrogenase | AO353_19510 | AO353_06560 |
| fucose | fucA: L-fuculose-phosphate aldolase FucA | | |
| fucose | fucI: L-fucose isomerase FucI | | |
| fucose | fucK: L-fuculose kinase FucK | | |
| fucose | fucU: L-fucose mutarotase FucU | | |
| fucose | HSERO_RS05255: ABC transporter for L-fucose, permease component | AO353_20825 | AO353_21390 |
| fucose | HSERO_RS05260: ABC transporter for L-fucose, substrate-binding component | | |
| galactose | dgoD: D-galactonate dehydratase | AO353_03420 | |
| galactose | galdh: D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) | AO353_01660 | AO353_23170 |
| galacturonate | udh: D-galacturonate dehydrogenase | AO353_03260 | AO353_06770 |
| galacturonate | uxuL: D-galactaro-1,5-lactonase (UxuL or UxuF) | | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | AO353_08820 | |
| glucuronate | exuT: D-glucuronate:H+ symporter ExuT | | |
| glucuronate | udh: D-glucuronate dehydrogenase | AO353_03260 | AO353_06770 |
| glucuronate | uxuL: D-glucaro-1,5-lactonase UxuL or UxuF | | |
| lactose | klh: periplasmic 3'-ketolactose hydrolase | | |
| lactose | lacA': periplasmic lactose 3-dehydrogenase, LacA subunit | | |
| lactose | lacB': periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB) | AO353_23370 | AO353_18090 |
| lactose | lacC': periplasmic lactose 3-dehydrogenase, LacC subunit | | |
| maltose | susB: alpha-glucosidase (maltase) | AO353_15985 | AO353_22940 |
| mannose | gluP: mannose:Na+ symporter | AO353_25100 | |
| 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 | AO353_25675 | AO353_24830 |
| phenylacetate | paaK: phenylacetate-CoA ligase | AO353_03315 | AO353_03310 |
| phenylacetate | paaZ1: oxepin-CoA hydrolase | AO353_25675 | AO353_03780 |
| phenylacetate | paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase | | |
| phenylacetate | ppa: phenylacetate permease ppa | AO353_01865 | |
| propionate | putP: propionate transporter; proline:Na+ symporter | AO353_12815 | |
| rhamnose | LRA1: L-rhamnofuranose dehydrogenase | AO353_24520 | AO353_21495 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | LRA3: L-rhamnonate dehydratase | AO353_05290 | |
| rhamnose | LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase | AO353_01060 | AO353_20700 |
| rhamnose | rhaT: L-rhamnose:H+ symporter RhaT | | |
| sorbitol | sdh: sorbitol dehydrogenase | AO353_25900 | AO353_01660 |
| thymidine | deoB: phosphopentomutase | AO353_05595 | |
| thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| xylitol | PLT5: xylitol:H+ symporter PLT5 | | |
| xylitol | xdhA: xylitol dehydrogenase | AO353_25145 | AO353_01660 |
| xylose | gtsA: xylose ABC transporter, periplasmic substrate-binding component GtsA | AO353_03395 | |
| xylose | gtsB: xylose ABC transporter, permease component 1 GtsB | AO353_03390 | |
| xylose | gtsC: xylose ABC transporter, permease component 2 GtsC | AO353_03385 | |
| xylose | gtsD: xylose ABC transporter, ATPase component GtsD | AO353_03380 | AO353_25130 |
| xylose | xylA: xylose isomerase | | |
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