Potential Gaps in catabolism of small carbon sources in Paraburkholderia atlantica CCGE1002
Found 16 low-confidence and 35 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 | BC1002_RS17450 | BC1002_RS33120 |
| alanine | cycA: L-alanine symporter CycA | BC1002_RS11820 | BC1002_RS33045 |
| citrulline | AO353_03040: ABC transporter for L-Citrulline, ATPase component | BC1002_RS30535 | BC1002_RS03950 |
| citrulline | AO353_03045: ABC transporter for L-Citrulline, permease component 2 | BC1002_RS05545 | BC1002_RS03955 |
| citrulline | AO353_03050: ABC transporter for L-Citrulline, permease component 1 | BC1002_RS03960 | BC1002_RS30525 |
| citrulline | AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component | BC1002_RS17340 | BC1002_RS03965 |
| citrulline | arcC: carbamate kinase | | |
| citrulline | aruG: ornithine/arginine N-succinyltransferase subunit AruAII (AruG) | BC1002_RS05570 | BC1002_RS05565 |
| D-serine | cycA: D-serine:H+ symporter CycA | BC1002_RS33045 | BC1002_RS11820 |
| D-serine | dsdA: D-serine ammonia-lyase | BC1002_RS11650 | BC1002_RS23935 |
| deoxyinosine | deoB: phosphopentomutase | BC1002_RS10435 | |
| 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 | BC1002_RS24635 | BC1002_RS06085 |
| deoxyribonate | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | BC1002_RS32050 | BC1002_RS23405 |
| deoxyribose | deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase | BC1002_RS24635 | BC1002_RS06085 |
| deoxyribose | deoxyribonate-transport: 2-deoxy-D-ribonate transporter | BC1002_RS32050 | BC1002_RS23405 |
| deoxyribose | drdehyd-alpha: 2-deoxy-D-ribose dehydrogenase, alpha subunit | BC1002_RS18825 | BC1002_RS26250 |
| deoxyribose | drdehyd-beta: 2-deoxy-D-ribose dehydrogenase, beta subunit | BC1002_RS18830 | BC1002_RS26245 |
| glucosamine | gamP: glucosamine PTS system, EII-CBA components (GamP/NagE) | BC1002_RS01450 | BC1002_RS27325 |
| glucose-6-P | uhpT: glucose-6-phosphate:phosphate antiporter | | |
| glycerol | glpF: glycerol facilitator glpF | BC1002_RS15325 | BC1002_RS01760 |
| histidine | PA5503: L-histidine ABC transporter, ATPase component | BC1002_RS11085 | BC1002_RS28880 |
| histidine | PA5505: L-histidine ABC transporter, substrate-binding component | BC1002_RS11075 | BC1002_RS01420 |
| lactose | lacP: lactose permease LacP | | |
| lysine | davT: 5-aminovalerate aminotransferase | BC1002_RS05560 | BC1002_RS11895 |
| lysine | hisM: L-lysine ABC transporter, permease component 1 (HisM) | BC1002_RS03955 | BC1002_RS05545 |
| lysine | hisP: L-lysine ABC transporter, ATPase component HisP | BC1002_RS30535 | BC1002_RS05550 |
| lysine | hisQ: L-lysine ABC transporter, permease component 2 (HisQ) | BC1002_RS03960 | BC1002_RS30525 |
| lysine | patA: cadaverine aminotransferase | BC1002_RS05560 | BC1002_RS00965 |
| lysine | patD: 5-aminopentanal dehydrogenase | BC1002_RS30590 | BC1002_RS07840 |
| maltose | susB: alpha-glucosidase (maltase) | BC1002_RS32085 | BC1002_RS25875 |
| mannitol | mt2d: mannitol 2-dehydrogenase | BC1002_RS12485 | BC1002_RS12460 |
| mannitol | mtlE: polyol ABC transporter, substrate-binding component MtlE/SmoE | BC1002_RS12525 | |
| mannitol | mtlF: polyol ABC transporter, permease component 1 (MtlF/SmoF) | BC1002_RS12520 | BC1002_RS23845 |
| mannitol | mtlG: polyol ABC transporter, permease component 2 (MtlG/SmoG) | BC1002_RS12515 | BC1002_RS28095 |
| mannitol | mtlK: polyol ABC transporter, ATP component MtlK/SmoG | BC1002_RS12505 | BC1002_RS21755 |
| rhamnose | LRA2: L-rhamnono-gamma-lactonase | | |
| rhamnose | rhaP: L-rhamnose ABC transporter, permease component 1 (RhaP) | BC1002_RS21100 | BC1002_RS21095 |
| rhamnose | rhaQ: L-rhamnose ABC transporter, permease component 2 (RhaQ) | BC1002_RS21095 | BC1002_RS12465 |
| rhamnose | rhaT': L-rhamnose ABC transporter, ATPase component RhaT | BC1002_RS21105 | BC1002_RS23905 |
| sucrose | ams: sucrose hydrolase (invertase) | BC1002_RS32085 | BC1002_RS25875 |
| threonine | snatA: L-threonine transporter snatA | BC1002_RS13485 | |
| thymidine | deoA: thymidine phosphorylase DeoA | BC1002_RS21615 | |
| thymidine | deoB: phosphopentomutase | BC1002_RS10435 | |
| thymidine | deoC: deoxyribose-5-phosphate aldolase | | |
| thymidine | nupG: thymidine permease NupG/XapB | | |
| valine | livH: L-valine ABC transporter, permease component 1 (LivH/BraD) | BC1002_RS11925 | BC1002_RS34550 |
| valine | livJ: L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | BC1002_RS15500 | BC1002_RS00535 |
| valine | livM: L-valine ABC transporter, permease component 2 (LivM/BraE) | BC1002_RS34545 | BC1002_RS11920 |
Confidence: high confidence medium confidence low confidence
This GapMind analysis is from Apr 09 2024. 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