GapMind for Amino acid biosynthesis

 

Definition of L-serine biosynthesis

As text, or see rules and steps

# Serine biosynthesis in GapMind is based on MetaCyc pathway
# L-serine biosynthesis I (metacyc:SERSYN-PWY).
# Pathway II (metacyc:PWY-8011) is not included because it is known only in plants.
# Also, MetaCyc states that the gene for the first step (EC 3.1.3.38) is not known.
# (Alkaline phosphatase from E. coli (phoA) is reported to be catalyze this reaction,
# but it has rather broad specificity.)

# BRENDA::Q4JDI4 is misannotated as 3-phosphoglycerate dehydrogenase instead of 3-phosphoglycerate kinase.
# (The curators were notified and report that they have corrected this.)
# CA265_RS09010 (uniprot:A0A1X9ZCD3) from Pedobacter sp. GW460-11-11-14-LB5
# is annotated as 3-phosphoglycerate dehydrogenase
# and has auxotrophic phenotypes. In particular, mutants are partially rescued by glycine or serine.
# Also it is adjacent to the putative serC.
serA	3-phosphoglycerate dehydrogenase	EC:1.1.1.95	uniprot:A0A1X9ZCD3	ignore:BRENDA::Q4JDI4

# MJ0959 (uniprot:Y959_METJA) is phosphoserine transaminase (PMID:17071763)
serC	3-phosphoserine aminotransferase	EC:2.6.1.52	uniprot:Y959_METJA

# CA265_RS22635 (uniprot:A0A1X9ZBA8_9SPHI) is diverged serB and is auxotrophic. It also appears to be fused to 
# diverged serA, but there is another serA in the genome (CA265_RS09010), so
# CA265_RS22635 may not be a functional dehydrogenase.
# Echvi_2777 (uniprot:L0G228_ECHVK) from Echinicola vietnamensis KMM 6221 is a diverged serB and is auxotrophic,
# rescued by serine.
# It is fused to serA and probably provides that activity as well.
# Hits to serA are ignored because of serAB fusions.
# Some curated resources link this EC number to protein phosphatases, or to
# non-specific periplasmic phosphatases, that are unlikely to play a role in serine biosynthesis.
# These are all marked ignore (P60487, Q96GD0, Q3ZBF9, P00634, P0AE22, Q9P376).
# Also, Swiss-Prot annotates RsbX (P17906) and RsbU (P40399) with this EC number, but
# they probably act on proteins.
# I was not able to find evidence that AraL (P94526) is a phosphoserine phosphatase
# (the cited paper PMID:25848029 does not seem to discuss this protein.)
# PMID:25848029 does show that Q9K8N3 and X3MFA4 (A0A1R2PVY2) have this activity.
serB	phosphoserine phosphatase	EC:3.1.3.3	uniprot:A0A1X9ZBA8_9SPHI	uniprot:L0G228_ECHVK	ignore_other:EC 1.1.1.95	ignore:SwissProt::P60487	ignore:SwissProt::Q96GD0	ignore:SwissProt::Q9P376	ignore:SwissProt::Q3ZBF9	ignore:BRENDA::P00634	ignore:SwissProt::P0AE22	ignore:SwissProt::Q9P376	ignore:SwissProt::P17906	ignore:SwissProt::P40399	ignore:SwissProt::P94526	uniprot:Q9K8N3	uniprot:A0A1R2PVY2

all: serA serC serB

Links

Downloads

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 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