Overview: Many bacteria take up fructose by a phosphotransferase (PTS) system that forms fructose 1-phosphate; this can be consumed via 1-phosphofructokinase and glycolysis (link). Alternatively, some PTS systems form fructose 6-phosphate, which is a central metabolic intermediate. Fructose can also be taken up directly and then phosphorylated to fructose 6-phosphate, a central metabolic intermediate. Another path is known in Aeromonas hydrophila -- phosphofructomutase converts fructose 1-phosphate (formed by a PTS system) to fructose 6-phosphate (PMID:9579084). This path is not included in GapMind because phosphofructomutase has not been linked to sequence. Also, in eukaryotes, fructose-1,6-bisphosphate aldolase is reported to cleave fructose 1-phosphate to glycerone phosphate and glyceraldehyde (link). This would make 1-phosphofructokinase unnececessary. It's not clear that this occurs in prokaryotes, so this is not listed.
Or see definitions of steps
| Step | Description | Best candidate | 2nd candidate |
|---|---|---|---|
| fruII-ABC | fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components | HMPREF9454_RS08300 | HMPREF9454_RS06610 |
| 1pfk | 1-phosphofructokinase | HMPREF9454_RS08295 | |
| fba | fructose 1,6-bisphosphate aldolase | HMPREF9454_RS06040 | HMPREF9454_RS06615 |
| tpi | triose-phosphate isomerase | HMPREF9454_RS03395 | HMPREF9454_RS03400 |
| Alternative steps: | |||
| araS | fructose ABC transporter, substrate-binding component AraS | ||
| araT | fructose ABC transporter, permease component 2 (AraT) | ||
| araU | fructose ABC transporter, permease component 1 (AraU) | ||
| araV | fructose ABC transporter, ATPase component AraV | HMPREF9454_RS05390 | HMPREF9454_RS00035 |
| BT1758 | fructose transporter | ||
| ffz | fructose facilitator (uniporter) | ||
| frcA | fructose ABC transporter, ATPase component FrcA | ||
| frcB | fructose ABC transporter, substrate-binding component FrcB | ||
| frcC | fructose ABC transporter, permease component FrcC | ||
| frt1 | fructose:H+ symporter Frt1 | ||
| fruA | fructose-specific PTS system (fructose 1-phosphate forming), EII-B'BC components | HMPREF9454_RS08300 | HMPREF9454_RS06610 |
| fruB | fructose-specific PTS system (fructose 1-phosphate forming), Hpr and EII-A components | ||
| fruD | fructose-specific PTS system (fructose 1-phosphate forming), EII-A component | HMPREF9454_RS06605 | |
| fruE | fructose ABC transporter, substrate-binding component FruE | ||
| fruF | fructose ABC transporter, permease component 1 (FruF) | ||
| fruG | fructose ABC transporter, permease component 2 (FruG) | ||
| fruI | fructose-specific PTS system (fructose 1-phosphate forming), EI, Hpr, and EII-A components | HMPREF9454_RS09390 | |
| fruII-A | fructose-specific PTS system (fructose 1-phosphate forming), EII-A component | HMPREF9454_RS08300 | HMPREF9454_RS06605 |
| fruII-B | fructose-specific PTS system (fructose 1-phosphate forming), EII-B component | HMPREF9454_RS08300 | HMPREF9454_RS06610 |
| fruII-C | fructose-specific PTS system (fructose 1-phosphate forming), EII-C component | HMPREF9454_RS06610 | HMPREF9454_RS08300 |
| fruK | fructose ABC transporter, ATPase component FruK | ||
| fruP | fructose porter FruP | HMPREF9454_RS03085 | HMPREF9454_RS06625 |
| ght6 | high-affinity fructose transporter ght6 | ||
| glcP | fructose:H+ symporter GlcP | HMPREF9454_RS09490 | HMPREF9454_RS09235 |
| levD | fructose PTS system (fructose 6-phosphate forming), EII-A component | HMPREF9454_RS07880 | HMPREF9454_RS08335 |
| levDE | fructose PTS system (fructose 6-phosphate forming), EII-AB component | ||
| levE | fructose PTS system (fructose 6-phosphate forming), EII-B component | HMPREF9454_RS07875 | |
| levF | fructose PTS system (fructose 6-phosphate forming), EII-C component | HMPREF9454_RS07870 | |
| levG | fructose PTS system (fructose 6-phosphate forming), EII-D component | HMPREF9454_RS07865 | HMPREF9454_RS10755 |
| scrK | fructokinase | HMPREF9454_RS09110 | HMPREF9454_RS07600 |
| Slc2a5 | fructose:H+ symporter | HMPREF9454_RS09235 | HMPREF9454_RS09490 |
| STP6 | sugar transport protein 6 | ||
| THT2A | fructose THT2A | ||
Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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:
Otherwise, a candidate is "medium confidence" if either:
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:
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