ams, fruII-ABC, 1pfk, fba, tpi
Overview: Sucrose utilization in GapMind is based on MetaCyc pathways sucrose degradation I via sucrose 6-phosphate hydrolase (link), pathway II via sucrose synthase (link), pathway III via invertase (link), and pathway IV via sucrose phosphorylase (link). Pathway V is similar to pathway III and is not reported in prokaryotes, so it is not included. There is no pathway VI. Pathway VII (via sucrose 3-dehydrogenase, link) is too poorly understood to include in GapMind.
Or see definitions of steps
| Step | Description | Best candidate | 2nd candidate |
|---|---|---|---|
| ams | sucrose hydrolase (invertase) | ||
| fruII-ABC | fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components | ||
| 1pfk | 1-phosphofructokinase | ||
| fba | fructose 1,6-bisphosphate aldolase | SULKU_RS03195 | |
| tpi | triose-phosphate isomerase | SULKU_RS01480 | SULKU_RS01475 |
| Alternative steps: | |||
| aglE | sucrose ABC transporter, substrate-binding component AglK | ||
| aglE' | glucose ABC transporter, substrate-binding component (AglE) | ||
| aglF | sucrose ABC transporter, permease component 1 (AglF) | ||
| aglF' | glucose ABC transporter, permease component 1 (AglF) | ||
| aglG | sucrose ABC transporter, permease component 2 (AglG) | ||
| aglG' | glucose ABC transporter, permease component 2 (AglG) | ||
| aglK | sucrose ABC transporter, ATPase component AglK | SULKU_RS05735 | SULKU_RS00635 |
| aglK' | glucose ABC transporter, ATPase component (AglK) | SULKU_RS05735 | SULKU_RS00635 |
| 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 | SULKU_RS05735 | SULKU_RS04275 |
| bglF | glucose PTS, enzyme II (BCA components, BglF) | ||
| BT1758 | fructose transporter | ||
| crr | glucose PTS, enzyme IIA | ||
| cscB | sucrose:H+ symporter CscB | ||
| eda | 2-keto-3-deoxygluconate 6-phosphate aldolase | ||
| edd | phosphogluconate dehydratase | SULKU_RS12160 | |
| ffz | fructose facilitator (uniporter) | ||
| frcA | fructose ABC transporter, ATPase component FrcA | SULKU_RS12645 | |
| 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 | ||
| 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 | ||
| 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 | ||
| fruII-A | fructose-specific PTS system (fructose 1-phosphate forming), EII-A component | ||
| fruII-B | fructose-specific PTS system (fructose 1-phosphate forming), EII-B component | ||
| fruII-C | fructose-specific PTS system (fructose 1-phosphate forming), EII-C component | ||
| fruK | fructose ABC transporter, ATPase component FruK | ||
| fruP | fructose porter FruP | ||
| gadh1 | gluconate 2-dehydrogenase flavoprotein subunit | ||
| gadh2 | gluconate 2-dehydrogenase cytochrome c subunit | ||
| gadh3 | gluconate 2-dehydrogenase subunit 3 | ||
| galU | glucose 1-phosphate uridylyltransferase | SULKU_RS09275 | SULKU_RS13390 |
| gdh | quinoprotein glucose dehydrogenase | ||
| ght6 | high-affinity fructose transporter ght6 | ||
| glcP | fructose:H+ symporter GlcP | ||
| glcS | glucose ABC transporter, substrate-binding component (GlcS) | ||
| glcT | glucose ABC transporter, permease component 1 (GlcT) | ||
| glcU | glucose ABC transporter, permease component 2 (GlcU) | ||
| glcU' | Glucose uptake protein GlcU | ||
| glcV | glucose ABC transporter, ATPase component (GclV) | SULKU_RS05735 | SULKU_RS04275 |
| glk | glucokinase | ||
| gnl | gluconolactonase | ||
| gtsA | glucose ABC transporter, substrate-binding component (GtsA) | ||
| gtsB | glucose ABC transporter, permease component 1 (GtsB) | ||
| gtsC | glucose ABC transporter, permease component 2 (GtsC) | ||
| gtsD | glucose ABC transporter, ATPase component (GtsD) | SULKU_RS05735 | SULKU_RS06960 |
| kguD | 2-keto-6-phosphogluconate reductase | ||
| kguK | 2-ketogluconokinase | ||
| kguT | 2-ketogluconate transporter | ||
| levD | fructose PTS system (fructose 6-phosphate forming), EII-A component | ||
| levDE | fructose PTS system (fructose 6-phosphate forming), EII-AB component | ||
| levE | fructose PTS system (fructose 6-phosphate forming), EII-B component | ||
| levF | fructose PTS system (fructose 6-phosphate forming), EII-C component | ||
| levG | fructose PTS system (fructose 6-phosphate forming), EII-D component | ||
| manX | glucose PTS, enzyme EIIAB | ||
| manY | glucose PTS, enzyme EIIC | ||
| manZ | glucose PTS, enzyme EIID | ||
| MFS-glucose | glucose transporter, MFS superfamily | ||
| mglA | glucose ABC transporter, ATP-binding component (MglA) | SULKU_RS04825 | SULKU_RS13425 |
| mglB | glucose ABC transporter, substrate-binding component | ||
| mglC | glucose ABC transporter, permease component (MglC) | ||
| PAST-A | proton-associated sugar transporter A | ||
| pgmA | alpha-phosphoglucomutase | SULKU_RS10450 | SULKU_RS00525 |
| ptsG | glucose PTS, enzyme IICB | ||
| ptsG-crr | glucose PTS, enzyme II (CBA components, PtsG) | ||
| ptsS | sucrose phosphotransferase enzyme EII-BCA | ||
| sacP | sucrose phosphotransferase enzyme EII-BC | ||
| scrB | sucrose-6-phosphate hydrolase | ||
| scrK | fructokinase | ||
| scrP | sucrose phosphorylase | ||
| scrT | sucrose permease ScrT | ||
| SemiSWEET | Sugar transporter SemiSWEET | ||
| Slc2a5 | fructose:H+ symporter | ||
| SLC45A2 | sucrose transporter | ||
| SLC45A3 | sucrose:H+ symporter | ||
| SLC45A4 | sucrose:H+ symporter | ||
| SSS-glucose | Sodium/glucose cotransporter | ||
| STP6 | sugar transport protein 6 | ||
| SUS | sucrose synthase | ||
| sut | sucrose:proton symporter SUT/SUC | ||
| sut1 | alpha-glucoside permease Sut1 | ||
| SWEET1 | bidirectional sugar transporter SWEET1 | ||
| THT2A | fructose THT2A | ||
| thuE | sucrose ABC transporter, substrate-binding component ThuE | ||
| thuF | sucrose ABC transporter, permease component 1 (ThuF) | ||
| thuG | sucrose ABC transporter, permease component 2 (ThuG) | ||
| thuK | sucrose ABC transporter, ATPase component ThuK | SULKU_RS05735 | SULKU_RS06960 |
| TMT1 | heteromeric sucrose:H+ symporter, TMT1 component | ||
| TMT2 | heteromeric sucrose:H+ symporter, TMT2 component | ||
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