GapMind for Amino acid biosynthesis

 

glycine biosynthesis in Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome

Best path

glyA

Rules

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.

6 steps (4 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
glyA serine hydroxymethyltransferase Ga0074568_11186
Alternative steps:
aceA isocitrate lyase Ga0074568_113968
agx1 alanine--glyoxylate aminotransferase Ga0074568_111984 Ga0074568_11123
gly1 L-threonine aldolase Ga0074568_11186 Ga0074568_111308
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 Apr 09 2024. The underlying query database was built on Apr 09 2024.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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