Also see fitness data for the top candidates
Overview: Trehalose degradation is based on MetaCyc pathways I via trehalose-6-phosphate hydrolase (link), II via cytoplasmic trehalase (link), III via trehalose-6-phosphate phosphorylase (link), IV via inverting trehalose phosphorylase (link), V via trehalose phosphorylase (link), VI via periplasmic trehalase (link), as well as trehalose degradation via 3-ketotrehalose (PMID:33657378).
Or see definitions of steps
| Step | Description | Best candidate | 2nd candidate |
|---|---|---|---|
| treEIIA | N-acetylglucosamine phosphotransferase system, EII-A component (Crr/PtsG/YpqE/GamP) | Pf1N1B4_833 | Pf1N1B4_1146 |
| treB | trehalose PTS system, EII-BC components TreB | Pf1N1B4_836 | |
| treC | trehalose-6-phosphate hydrolase | Pf1N1B4_835 | Pf1N1B4_4677 |
| glk | glucokinase | Pf1N1B4_600 | |
| Alternative steps: | |||
| aglE | trehalose ABC transporter, substrate-binding component AglE | ||
| aglE' | glucose ABC transporter, substrate-binding component (AglE) | ||
| aglF | trehalose ABC transporter, permease component 1 (AglF) | ||
| aglF' | glucose ABC transporter, permease component 1 (AglF) | ||
| aglG | trehalose ABC transporter, permease component 2 (AglG) | Pf1N1B4_5114 | Pf1N1B4_594 |
| aglG' | glucose ABC transporter, permease component 2 (AglG) | Pf1N1B4_4011 | Pf1N1B4_594 |
| aglK | trehalose ABC trehalose, ATPase component AglK | Pf1N1B4_5115 | Pf1N1B4_4847 |
| aglK' | glucose ABC transporter, ATPase component (AglK) | Pf1N1B4_4847 | Pf1N1B4_5115 |
| bglF | glucose PTS, enzyme II (BCA components, BglF) | ||
| BT2158 | periplasmic trehalose 3-dehydrogenase (BT2158) | ||
| crr | glucose PTS, enzyme IIA | Pf1N1B4_833 | |
| eda | 2-keto-3-deoxygluconate 6-phosphate aldolase | Pf1N1B4_587 | Pf1N1B4_399 |
| edd | phosphogluconate dehydratase | Pf1N1B4_601 | Pf1N1B4_2303 |
| gadh1 | gluconate 2-dehydrogenase flavoprotein subunit | ||
| gadh2 | gluconate 2-dehydrogenase cytochrome c subunit | ||
| gadh3 | gluconate 2-dehydrogenase subunit 3 | ||
| gdh | quinoprotein glucose dehydrogenase | Pf1N1B4_821 | Pf1N1B4_5582 |
| glcS | glucose ABC transporter, substrate-binding component (GlcS) | ||
| glcT | glucose ABC transporter, permease component 1 (GlcT) | ||
| glcU | glucose ABC transporter, permease component 2 (GlcU) | Pf1N1B4_594 | |
| glcU' | Glucose uptake protein GlcU | ||
| glcV | glucose ABC transporter, ATPase component (GclV) | Pf1N1B4_2538 | Pf1N1B4_4352 |
| gnl | gluconolactonase | Pf1N1B4_4626 | Pf1N1B4_4510 |
| gtsA | glucose ABC transporter, substrate-binding component (GtsA) | Pf1N1B4_596 | |
| gtsB | glucose ABC transporter, permease component 1 (GtsB) | Pf1N1B4_595 | |
| gtsC | glucose ABC transporter, permease component 2 (GtsC) | Pf1N1B4_594 | Pf1N1B4_5114 |
| gtsD | glucose ABC transporter, ATPase component (GtsD) | Pf1N1B4_593 | Pf1N1B4_5115 |
| kguD | 2-keto-6-phosphogluconate reductase | Pf1N1B4_1004 | Pf1N1B4_4763 |
| kguK | 2-ketogluconokinase | Pf1N1B4_4765 | |
| kguT | 2-ketogluconate transporter | Pf1N1B4_4764 | Pf1N1B4_5000 |
| klh | 3-ketotrehalose hydrolase | ||
| lacA | periplasmic trehalose 3-dehydrogenase, LacA subunit | ||
| lacB | periplasmic trehalose 3-dehydrogenase, cytochrome c subunit (LacB) | Pf1N1B4_5765 | |
| lacC | periplasmic trehalose 3-dehydrogenase, LacC subunit | ||
| lpqY | trehalose ABC transporter, substrate-binding lipoprotein component LpqY | ||
| malE2 | trehalose ABC transporter, substrate-binding component MalE2 | ||
| malF | trehalose ABC transporter, permease component 1 (MalF) | ||
| malF1 | trehalose ABC transporter, permease component 1 | ||
| malG | trehalose ABC transporter, permease component 2 (MalG) | Pf1N1B4_5114 | |
| malG1 | trehalose ABC transporter, permease component 2 (MalG1/MalG2) | ||
| malK | trehalose ABC transporter, ATPase component MalK | Pf1N1B4_5115 | Pf1N1B4_593 |
| malX | trehalose ABC transporter, substrate-binding component MalX | ||
| 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) | Pf1N1B4_4286 | Pf1N1B4_410 |
| mglB | glucose ABC transporter, substrate-binding component | Pf1N1B4_4386 | |
| mglC | glucose ABC transporter, permease component (MglC) | Pf1N1B4_4287 | Pf1N1B4_409 |
| PAST-A | proton-associated sugar transporter A | ||
| pgmA | alpha-phosphoglucomutase | Pf1N1B4_4886 | Pf1N1B4_2122 |
| pgmB | beta-phosphoglucomutase | Pf1N1B4_3808 | |
| PsTP | trehalose phosphorylase | ||
| ptsG | glucose PTS, enzyme IICB | ||
| ptsG-crr | glucose PTS, enzyme II (CBA components, PtsG) | ||
| SemiSWEET | Sugar transporter SemiSWEET | ||
| SSS-glucose | Sodium/glucose cotransporter | ||
| SWEET1 | bidirectional sugar transporter SWEET1 | ||
| thuE | trehalose ABC transporter, substrate-binding component ThuE | Pf1N1B4_5112 | |
| thuF | trehalose ABC transporter, permease component 1 (ThuF) | Pf1N1B4_5113 | Pf1N1B4_4849 |
| thuG | trehalose ABC transporter, permease component 2 (ThuG) | Pf1N1B4_5114 | Pf1N1B4_4848 |
| thuK | trehalose ABC transporter, ATPase component ThuK | Pf1N1B4_593 | Pf1N1B4_4847 |
| treF | trehalase | Pf1N1B4_153 | Pf1N1B4_835 |
| treP | trehalose phosphorylase, inverting | ||
| trePP | trehalose-6-phosphate phosphorylase | ||
| treS | trehalose ABC transporter, substrate-binding comopnent TreS | ||
| treT | trehalose ABC transporter, permease component 1 (TreT) | ||
| TRET1 | facilitated trehalose transporter Tret1 | ||
| treU | trehalose ABC transporter, permease component 2 (TreU) | ||
| treV | trehalose ABC transporter, ATPase component TreV | Pf1N1B4_593 | Pf1N1B4_4847 |
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 17 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