Potential Gaps in catabolism of small carbon sources in Burkholderia phytofirmans PsJN
Found 12 low-confidence and 24 medium-confidence steps on the best paths for 62 pathways.
| Pathway | Step | Best candidate | 2nd candidate |
|---|
| 4-hydroxybenzoate | pcaF: succinyl-CoA:acetyl-CoA C-succinyltransferase | BPHYT_RS29385 | BPHYT_RS17345 |
| alanine | cycA: L-alanine symporter CycA | BPHYT_RS15500 | BPHYT_RS07280 |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | BPHYT_RS05495 | BPHYT_RS07685 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | BPHYT_RS07680 | BPHYT_RS05500 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | BPHYT_RS05505 | BPHYT_RS07675 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | BPHYT_RS29525 | BPHYT_RS07735 |
| citrulline | aruG: ornithine/arginine N-succinyltransferase subunit AruAII (AruG) | BPHYT_RS07705 | BPHYT_RS07700 |
| D-serine | cycA: D-serine:H+ symporter CycA | BPHYT_RS15500 | BPHYT_RS21680 |
| D-serine | dsdA: D-serine ammonia-lyase | BPHYT_RS15425 | BPHYT_RS09280 |
| deoxyinosine | deoB: phosphopentomutase | BPHYT_RS14155 | |
| deoxyinosine | deoD: deoxyinosine phosphorylase | | |
| deoxyribose | drdehyd-alpha: 2-deoxy-D-ribose dehydrogenase, alpha subunit | BPHYT_RS24630 | BPHYT_RS32800 |
| deoxyribose | drdehyd-beta: 2-deoxy-D-ribose dehydrogenase, beta subunit | BPHYT_RS24635 | BPHYT_RS32805 |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | BPHYT_RS02745 | |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| lactose | lacP: lactose permease LacP | | |
| lysine | hisM: L-lysine ABC transporter, permease component 1 (HisM) | BPHYT_RS05500 | BPHYT_RS07680 |
| lysine | hisQ: L-lysine ABC transporter, permease component 2 (HisQ) | BPHYT_RS05505 | BPHYT_RS07675 |
| lysine | patA: cadaverine aminotransferase | BPHYT_RS27170 | BPHYT_RS07695 |
| lysine | patD: 5-aminopentanal dehydrogenase | BPHYT_RS09900 | BPHYT_RS25160 |
| maltose | susB: alpha-glucosidase (maltase) | BPHYT_RS33775 | |
| mannitol | mt2d: mannitol 2-dehydrogenase | BPHYT_RS28510 | BPHYT_RS23425 |
| mannitol | mtlE: polyol ABC transporter, substrate-binding component MtlE/SmoE | BPHYT_RS16115 | |
| mannitol | mtlF: polyol ABC transporter, permease component 1 (MtlF/SmoF) | BPHYT_RS16110 | BPHYT_RS35665 |
| mannitol | mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) | BPHYT_RS16105 | BPHYT_RS27970 |
| mannitol | mtlK: polyol ABC transporter, ATP component MtlK/SmoG | BPHYT_RS16095 | BPHYT_RS22760 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| sucrose | ams: sucrose hydrolase (invertase) | BPHYT_RS33775 | |
| threonine | snatA: L-threonine transporter snatA | BPHYT_RS17695 | |
| thymidine | deoA: thymidine phosphorylase DeoA | BPHYT_RS33245 | |
| thymidine | deoB: phosphopentomutase | BPHYT_RS14155 | |
| tryptophan | hpaH: anthranilate 3-monooxygenase (hydroxylase), FADH2-dependent | | |
| valine | livH: L-valine ABC transporter, permease component 1 (LivH/BraD) | BPHYT_RS15605 | BPHYT_RS31740 |
| valine | livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | BPHYT_RS01885 | BPHYT_RS31715 |
| xylitol | PS417_12055: xylitol ABC transporter, substrate-binding component | | |
| xylitol | PS417_12065: xylitol ABC transporter, ATPase component | BPHYT_RS27185 | BPHYT_RS28215 |
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