Definition of L-cysteine biosynthesis

GapMind for Amino acid biosynthesis

Definition of L-cysteine biosynthesis

# Cysteine biosynthesis in GapMind is based on MetaCyc pathways
# L-cysteine biosynthesis I from serine and sulfide (metacyc:CYSTSYN-PWY),
# II (tRNA-dependent) (metacyc:PWY-6308),
# III from serine and homocysteine (metacyc:HOMOCYSDEGR-PWY),
# V (protein-bound thiocarboxylates) (metacyc:PWY-7289),
# VIII via serine kinase (metacyc:PWY-8009),
# or IX via phosphoserine (metacyc:PWY-8010).
# There is no pathway IV.
# Pathway VI (from serine + methionine) is not included because it is not found in prototrophic bacteria.
# (It is found in H. pylori, which lacks biosynthesis of homocysteine or methionine;
# also, it is a supserset of the reactions in pathway III, from serine and homocysteine.)
# Pathway VII is not included because it requires sulfocysteine, an uncommon precursor.
# GapMind also describes cysteine biosynthesis with O-succinylserine as an intermediate (PMID:28581482),
# instead of O-acetylserine (as in pathway I).

# Desulfovibrios have a somewhat diverged serine O-acetyltransferase.
# DVU0662 (uniprot:Q72EB6_DESVH) and DvMF_2657 (uniprot:B8DIT5_DESVM)
# are both essential which suggests that they are correctly annotated.
cysE	serine acetyltransferase	EC:2.3.1.30	uniprot:Q72EB6_DESVH	uniprot:B8DIT5_DESVM

# E. coli also has cysM (same EC number).
# BRENDA misannotates uniprot:O22682 and uniprot:Q9YBL2 with this activity.
# CH_123612 maybe have this activity but is annotated more vaguely.
cysK	O-acetylserine or O-succinylserine sulfhydrylase	EC:2.5.1.47	ignore:BRENDA::O22682	ignore:BRENDA::Q9YBL2	ignore:CharProtDB::CH_123612

# Cysteine can be formed from serine via O-acetylserine as in pathway I (cysE and cysK),
# via O-succinylserine (SST), or via serine kinase (serK) as in pathway IX.
# For the O-succinylserine pathway, the identity of the O-succinylserine sulfhydrylase is not proven,
# but it is expected to be similar to cysK.
from-serine: cysE cysK

# The EC number for these corresponds to homoserine O-succinyltransferase so do not use that.
SST	serine O-succinyltransferase	term:serine O-succinyltransferase
from-serine: SST cysK

# Q3TWN3 and Q5SK23 are misannotated in BRENDA.
# uniprot:Q9EYM7 may well have this activity (PMID:12101301).
# Human CGL is given this EC number as well by metacyc (metacyc:HS04050-MONOMER),
# but is not expected to form cystathionine from serine + homocysteine.
CBS	cystathionine beta-synthase	EC:4.2.1.22	ignore:BRENDA::Q3TWN3	ignore:BRENDA::Q5SK23	ignore:BRENDA::Q9EYM7	ignore:metacyc::HS04050-MONOMER

# EC:4.4.1.1 includes some other reactions, so it is not used to define CGL.
# uniprot:Q9M1R1 is misannotated in BRENDA.
# SwissProt annotates the cysteine desulfurase DES1 (uniprot:F4K5T2) with this activity, but we did
# not find evidence for it, so it is ignored.
# "MetB" from Helicobacter pylori was originally reported to be a cystathionine gamma-synthase
# (i.e., uniprot:Q1M0P5 in BRENDA), but was later identified as a CGL (PMC2820867), so Q1M0P5 is ignored.
# Similarly, "MetC" from Lactoccus lactis (uniprot:A2RM21) is reported to be a CGL and a cystathionine
# beta-lyase (PMID:10620674); another paper proposed that it is a CBL but did not distinguish between
# the two activities (PMC91783, cited by CharProtDB, which is ignored).
CGL	cystathionine gamma-lyase	term:cystathionine gamma-lyase	term:cystathionine-gamma-lyase	ignore:BRENDA::Q9M1R1	ignore:SwissProt::F4K5T2	ignore:BRENDA::Q1M0P5	ignore:CharProtDB::CH_088676

# In many organisms, the sulfhydryl group of cysteine is used to form homocysteine and methionine, but
# this pathway can also run in reverse.
# GapMind uses a pathway requirement to warn if an organism is modeled as
# synthesizing methionine and cysteine from each other.
from-serine-homocysteine: CBS CGL

sepS	O-phosphoseryl-tRNA ligase	EC:6.1.1.27
pscS	Sep-tRNA:Cys-tRNA synthase	EC:2.5.1.73
# Phosphoserine can be converted to cysteine by
# the tRNA-dependent pathway II (sepS and pscS),
# the protein-bound thiocarboxylate pathway V with the carrier protein cysO,
# or by direct sulfhydrylation (PSSH) as in pathway IX.
from-phosphoserine: sepS pscS

Mt_cysM	CysO-thiocarboxylate-dependent cysteine synthase	EC:2.5.1.113
mec	[CysO sulfur-carrier protein]-S-L-cysteine hydrolase	EC:3.13.1.6

# uniprot:A0A2R3ZBG9 (metacyc:MONOMER-21317) is not reported to be involved in cysteine biosynthesis,
# but it has a similar chemical activity, so similarity to it is ignored.
moeZ	[sulfur carrier protein CysO]--sulfur ligase	curated:metacyc::G185E-7476-MONOMER	ignore:metacyc::MONOMER-21317

cysO	sulfur carrier protein CysO	curated:SwissProt::P9WP33
from-phosphoserine: cysO moeZ Mt_cysM mec 

# BRENDA misannotates Mt_cysM (uniprot:P9WP53) as this.
# Trichomonas cysteine synthase (uniprot:A2GMG5) probably has this activity as well, so similarity to it
# is ignored.
PSSH	O-phosphoserine sulfhydrylase	EC:2.5.1.65	ignore:BRENDA::P9WP53	ignore:BRENDA::A2GMG5

from-phosphoserine: PSSH

serK	serine kinase (ADP-dependent)	EC:2.7.1.226
from-serine: serK PSSH

all: from-serine
import ser.steps:serA serC # serA and serC form phosphoserine
all: serA serC from-phosphoserine
all: from-serine-homocysteine

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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:

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 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 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