GapMind for Amino acid biosynthesis


Definition of L-threonine biosynthesis

As text, or see rules and steps

# Threonine biosynthesis in GapMind is based on MetaCyc pathway
# L-threonine biosynthesis (metacyc:HOMOSER-THRESYN-PWY).

import met.steps:homoserine

# ThrB from B. subtilis (uniprot:P04948) can complement a thrB- strain of E. coli (PMC1167255; Bradley Biggs).
thrB	homoserine kinase	EC:	uniprot:P04948

# BT2402 (uniprot:Q8PX04) is required for threonine synthesis (PMC7311316) and belongs to a family
# (TIGR02535) that was proposed replace the missing homoserine kinase. It is
# often encoded next to aspartate kinase and threonine synthase.
# It is related to phosphoglycerate mutases and might transfer phosphate groups
# from a donor such as phosphoenolpyruvate to homoserine.
# This family is also known as ThrB2 (PMC9026213).
# In GapMind, HomK is described separately from ThrB because it probably carries out a different reaction.
homK	putative homoserine phosphotransferase	predicted:Q8PX04

# N515DRAFT_0575 (uniprot:A0A1I2JHD2_9GAMM) from Dyella japonica UNC79MFTsu3.2 is somewhat
# diverged; mutants in this gene are auxotrophic.
thrC	threonine synthase	EC:	uniprot:A0A1I2JHD2_9GAMM

all: homoserine thrB thrC
all: homoserine homK thrC



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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