GapMind for Amino acid biosynthesis

 

Definition of glycine biosynthesis

As text, or see rules and steps

# Glycine biosynthesis in GapMind is based on MetaCyc pathways
# glycine biosynthesis I from serine (metacyc:GLYSYN-PWY),
# III from glyoxylate (metacyc:GLYSYN-ALA-PWY),
# or IV from threonine (metacyc:GLYSYN-THR-PWY).
# Pathway II from methylene-tetrahydrofolate, CO2, and ammonia
# (metacyc:GLYSYN-PWY) is not included because it is not clear that bacteria really
# run this in reverse (although apparently budding yeast can).

# Some methanogens use tetrahydromethanopterin instead of tetrahydrofolate as the folate carrier,
# which is annotated as "Serine hydroxymethyltransferase" but with a different EC number.
glyA	serine hydroxymethyltransferase	EC:2.1.2.1	term:Serine hydroxymethyltransferase

aceA	isocitrate lyase	EC:4.1.3.1
agx1	alanine--glyoxylate aminotransferase	EC:2.6.1.44

gly1	L-threonine aldolase	EC:4.1.2.5	EC:4.1.2.48

# Another pathway not listed is the formation of glycine from glycolate
# as in Pelagibacter (see PMID:23096402). This is an unusual nutritional requirement.

from_serine: glyA

# For biosynthesis from glyoyxlate (pathway III), assume that the glyoxylate is formed from
# isocitrate (an intermediate in the TCA cycle).
via_glyoxylate: aceA agx1

from_threonine: gly1

all: from_serine
all: via_glyoxylate
all: from_threonine

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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