GapMind for Amino acid biosynthesis


Finding step thrB for L-threonine biosynthesis in Bacteroides thetaiotaomicron VPI-5482

Manual classification of gap: novel
Rationale: This genome does not encode a standard homoserine kinase, but does encode a standard threonine synthase (BT2401). BT2402 is related to phosphoglycerate mutases and is proposed to move phosphate groups to homoserine based on conserved gene order (see TIGR02535). Indeed, BT2402 is required for growth in minimal media unless threonine is provided. However, BT2402 did not complement a thrB- strain of E. coli (Hualan Liu, personal communication). Insertions in BT2402 could be polar on the threonine synthase (which is downstream), but insertions in either orientation seem deficient in growth in minimal media. Overall, the role of BT2402 remains uncertain.

No candidates for thrB: homoserine kinase

GapMind classifies a step as low confidence even if it does not find any candidates. You can still try to find candidates by using Curated BLAST (which searches the 6-frame translation) or by text search of the annotations (which may indicate weak homology, under 30% identity or 50% coverage, that GapMind does not consider). See the links below.

Definition of step thrB

Or cluster all characterized thrB proteins

Known gaps in related organisms

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.



Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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