glycine biosynthesis in Pseudomonas putida KT2440

GapMind for Amino acid biosynthesis

glycine biosynthesis in Pseudomonas putida KT2440

Best path

Also see fitness data for the top candidates

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.

all:

from_serine
or via_glyoxylate
or from_threonine
or glyXL and glyXS

from_threonine: gly1
via_glyoxylate: aceA and agx1

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

from_serine: glyA

6 steps (4 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
glyA	serine hydroxymethyltransferase	PP_0322	PP_0671
Alternative steps:
aceA	isocitrate lyase	PP_4116	PP_2334
agx1	alanine--glyoxylate aminotransferase	PP_0817	PP_3361
gly1	L-threonine aldolase	PP_0321	PP_0671
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the original 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

GapMind for Amino acid biosynthesis