Finding step levF for D-fructose catabolism in Sporolactobacillus vineae SL153
4 candidates for levF: fructose PTS system (fructose 6-phosphate forming), EII-C component
| Score | Gene | Description | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| med | RH97_RS02400 | PTS mannose/fructose/sorbose transporter subunit IIC | Mannose-specific PTS system component IIC, component of The hexose (glucose and fructose demonstrated) PTS uptake system (characterized) | 68% | 100% | 377.9 | ManM aka EIIC, component of Glucose porter, ManLMN | 83% | 443.0 |
| med | RH97_RS10975 | PTS mannose/fructose/sorbose transporter subunit IIC | mannose permease IIC component (characterized) | 65% | 92% | 329.7 | PTS system sorbose-specific EIIC component; EIIC-Sor; Sorbose permease IIC component | 71% | 370.9 |
| lo | RH97_RS11140 | PTS sugar transporter subunit IIC | mannose permease IIC component (characterized) | 31% | 94% | 129.4 | Putative phosphotransferase system enzyme IIC, component of D-glucosaminate group translocating uptake porter, DgaABCD (IIA-141 aas, IIB-161 aas, IIC-249 aas, and IID-285 aas, respectively) | 45% | 206.1 |
| lo | RH97_RS01730 | PTS sugar transporter subunit IIC | ManM, component of The glucose/mannose/2-deoxyglucose/fructose phosphotransferase systems (phosphorylates without transport), ManLMN (characterized) | 30% | 96% | 120.9 | PTS system, IIC component, component of Fucosyl-α-1,3-N-acetylglucosamine PTS uptake porter, AlfEFG (next to an operon encoding a fucosidase (AlfB) and a transcriptional regulator of the GntR family, AlfR) | 50% | 241.1 |
Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.
GapMind searches the predicted proteins for candidates by using ublast (a fast alternative to protein BLAST) to find similarities to characterized proteins or by using HMMer to find similarities to enzyme models (usually from TIGRFams). For alignments to characterized proteins (from ublast), scores of 44 bits correspond to an expectation value (E) of about 0.001.
Definition of step levF
- Curated sequence CH_088330: mannose permease IIC component. PTS system mannose-specific EIIC component; EII-P-Man; EIIC-Man; Mannose permease IIC component. PTNC aka MANY aka PTSP aka PEL aka B1818, component of The mannose (glucose, 2-deoxyglucose, glucosamine, N-acetylglucosamine, N-acetylmannosamine, mannosamine and fructose) PTS porter/group translocator, ManXYZ (Rephaeli and Saier 1980; Plumbridge 2015). Catalyzes xylose facilitated diffusion in lactobacilli. The order of D-sugar substrate affinities is: glucose > mannose > 2-deoxyglucose > N-acetylglucosamine > glucosamine > N-acetylmannosamine > mannosamine > fructose. mannose-specific PTS enzyme IIC component (EC 2.7.1.191; EC 2.7.1.199; EC 2.7.1.193). mannose-specific PTS enzyme IIC component (EC 2.7.1.191; EC 2.7.1.199; EC 2.7.1.193)
- Curated sequence P26381: PTFC aka LEVF, component of Fructose group translocator, LevDEFG
- Curated sequence Q04GK0: Mannose-specific PTS system component IIC, component of The hexose (glucose and fructose demonstrated) PTS uptake system
- Curated sequence Q5M5W7: ManM, component of The glucose/mannose/2-deoxyglucose/fructose phosphotransferase systems (phosphorylates without transport), ManLMN
Or cluster all characterized levF proteins
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Links
Downloads
Related tools
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