Also see fitness data for the top candidates
Overview: The canonical pathway for glucosamine utilization involves glucosamine 6-phosphate as an intermediate, as in N-acetylglucosamine utilization (link). GapMind also includes two other pathways: an oxidative pathway via glucosaminate ammonia-lyase, and a transmembrane transacetylase (NagX) pathway.
Or see definitions of steps
| Step | Description | Best candidate | 2nd candidate |
|---|---|---|---|
| gamP | glucosamine PTS system, EII-CBA components (GamP/NagE) | PfGW456L13_4833 | |
| nagB | glucosamine 6-phosphate deaminase (isomerizing) | PfGW456L13_4831 | PfGW456L13_686 |
| Alternative steps: | |||
| AO353_21710 | glucosaminate ABC transporter, substrate-binding component | ||
| AO353_21715 | glucosaminate ABC transporter, permease component 1 | PfGW456L13_445 | PfGW456L13_3607 |
| AO353_21720 | glucosaminate ABC transporter, permease component 2 | PfGW456L13_445 | PfGW456L13_4636 |
| AO353_21725 | glucosaminate ABC transporter, ATPase component | PfGW456L13_376 | PfGW456L13_876 |
| crr | N-acetylglucosamine phosphotransferase system, EII-A component Crr | PfGW456L13_4832 | |
| gdh | quinoprotein glucose dehydrogenase | PfGW456L13_4805 | PfGW456L13_1173 |
| glc-kinase | glucosamine kinase | PfGW456L13_1890 | |
| glucosaminate-lyase | glucosaminate ammonia-lyase | PfGW456L13_2867 | PfGW456L13_4983 |
| kdgA | 2-keto-3-deoxygluconate-6-phosphate aldolase EC:4.1.2.14 | PfGW456L13_1903 | PfGW456L13_2127 |
| kdgK | 2-keto-3-deoxygluconate kinase | PfGW456L13_2869 | PfGW456L13_2950 |
| manX | glucosamine PTS system, EII-AB component ManX | ||
| manY | glucosamine PTS system, EII-C component ManY | ||
| manZ | glucosamine PTS system, EII-D component ManZ | ||
| nag3 | N-acetylglucosamine transporter nag3/nag4 | ||
| nagA | N-acetylglucosamine 6-phosphate deacetylase | PfGW456L13_4830 | |
| nagEcb | N-acetylglucosamine phosphotransferase system, EII-CB components | PfGW456L13_4833 | |
| nagEcba | N-acetylglucosamine phosphotransferase system, EII-CBA components | PfGW456L13_4833 | |
| nagEIIA | N-acetylglucosamine phosphotransferase system, EII-A component (PtsG/YpqE/GamP) | PfGW456L13_4833 | PfGW456L13_4832 |
| nagF | N-acetylglucosamine phosphotransferase system, E-I, Hpr, and EII-A components (NagF) | PfGW456L13_4832 | PfGW456L13_5075 |
| nagK | N-acetylglucosamine kinase | PfGW456L13_1890 | |
| nagP | N-acetylglucosamine transporter NagP | ||
| nagPcb | N-acetylglucosamine phosphotransferase system, EII-CB component NagP | PfGW456L13_4833 | |
| nagX | transmembrane glucosamine N-acetyltransferase NagX | ||
| ngcE | N-acetylglucosamine ABC transporter, substrate-binding component (NgcE) | ||
| ngcF | N-acetylglucosamine ABC transporter, permease component 1 (NgcF) | ||
| ngcG | N-acetylglucosamine ABC transporter, permease component 2 (NgcG) | ||
| ngt1 | N-acetylglucosamine:H+ symporter Ngt1 | ||
| ptsB | N-acetylglucosamine-specific phosphotransferase system, EII-B component PtsB | ||
| ptsC | N-acetylglucosamine phosphotransferase system, EII-C component PtsC | PfGW456L13_4833 | |
| SLC2A2 | glucosamine transporter SLC2A2 | ||
| SM_b21216 | ABC transporter for D-Glucosamine, ATPase component | PfGW456L13_1897 | PfGW456L13_3039 |
| SM_b21219 | ABC transporter for D-Glucosamine, permease component 1 | PfGW456L13_3040 | |
| SM_b21220 | ABC transporter for D-Glucosamine, permease component 2 | ||
| SM_b21221 | ABC transporter for D-Glucosamine, substrate-binding protein | ||
| SMc02869 | N-acetylglucosamine ABC transporter, ATPase component | PfGW456L13_3039 | PfGW456L13_1897 |
| SMc02871 | N-acetylglucosamine ABC transporter, permease component 2 | PfGW456L13_1896 | |
| SMc02872 | N-acetylglucosamine ABC transporter, permease component 1 | ||
| SMc02873 | N-acetylglucosamine ABC transporter, substrate-binding 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 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