Finding step fruI for sucrose catabolism in Pseudomonas fluorescens GW456-L13
3 candidates for fruI: fructose-specific PTS system (fructose 1-phosphate forming), EI, Hpr, and EII-A components
| Score | Gene | Description | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| hi | PfGW456L13_5075 | Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9) | Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized) | 93% | 100% | 1715.7 | D-trehalose PTS system, I, HPr, and IIA components | 45% | 505.4 |
| med | PfGW456L13_4832 | PTS system, glucose-specific IIA component / Phosphotransferase system, phosphocarrier protein HPr / Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9) | Fructose-specific PTS system, I, HPr, and IIA components (characterized) | 41% | 72% | 458.8 | N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) | 84% | 1364.4 |
| lo | PfGW456L13_953 | FIG001592: Phosphocarrier protein kinase/phosphorylase, nitrogen regulation associated | Fructose-specific PTS system, I, HPr, and IIA components (characterized) | 37% | 58% | 344.7 | Phosphoenolpyruvate-dependent phosphotransferase system; Enzyme I-Ntr; EINtr; Phosphotransferase system, enzyme I; EC 2.7.3.9 | 43% | 585.1 |
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.
Also see fitness data for the candidates
Definition of step fruI
- Curated sequence Q9HY55: Phosphotransferase system transporter enzyme I, FruI, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA
- Curated sequence AZOBR_RS32325: Fructose PTS system (E-I, HPr, and E-IIA components)
- Curated sequence AO353_05485: Fructose-specific PTS system, I, HPr, and IIA components
- Curated sequence P45597: Multiphosphoryl transfer protein; MTP; Triphosphoryl transfer protein; TTP; EC 2.7.3.9
- Curated sequence Pf1N1B4_1146: Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9)
- Curated sequence AO356_07335: Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9)
- Curated sequence GFF780: Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9)
- Curated sequence GFF3291: Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9)
- Comment: Homologs of fruI in other Pseudomonas fluorescens are annotated differently, but are important for fructose utilization, so probably have the same function.
Or cluster all characterized fruI proteins
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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