Overview: Glycine biosynthesis in GapMind is based on MetaCyc pathways glycine biosynthesis I from serine (link), III from glyoxylate (link), or IV from threonine (link). Pathway II from methylene-tetrahydrofolate, CO2, and ammonia (link) is not included because it is not clear that bacteria really run this in reverse (although apparently budding yeast can). Glcyine synthiesis by glyXL/glyXS, whose biochemical function is not known, is also represented. Another pathway not listed is the formation of glycine from glycolate as in Pelagibacter (see PMID:23096402). This is an unusual nutritional requirement.
Or see definitions of steps
Step | Description | Best candidate | 2nd candidate |
---|---|---|---|
glyA | serine hydroxymethyltransferase | CPAR_RS07700 | |
Alternative steps: | |||
aceA | isocitrate lyase | ||
agx1 | alanine--glyoxylate aminotransferase | CPAR_RS04855 | CPAR_RS06310 |
gly1 | L-threonine aldolase | CPAR_RS07700 | |
glyXL | putative glycine synthesis enzyme, catalytic component | ||
glyXS | putative glycine synthesis enzyme, ACT domain component |
Confidence: high confidence medium confidence low confidence
? – known gap: despite the lack of a good candidate for this step, this organism (or a related organism) performs the pathway
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.
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