GapMind for Amino acid biosynthesis


L-cysteine biosynthesis in Thermomonospora curvata DSM 43183

Best path

serA, serC, cysO, moeZ, Mt_cysM, mec


Overview: Cysteine biosynthesis in GapMind is based on MetaCyc pathways L-cysteine biosynthesis I from serine and sulfide (link), II (tRNA-dependent) (link), III from serine and homocysteine (link), V (protein-bound thiocarboxylates) (link), VIII via serine kinase (link), or IX via phosphoserine (link). 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).

15 steps (12 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
serA 3-phosphoglycerate dehydrogenase TCUR_RS17475 TCUR_RS02200
serC 3-phosphoserine aminotransferase TCUR_RS04095
cysO sulfur carrier protein CysO TCUR_RS03925 TCUR_RS19045
moeZ [sulfur carrier protein CysO]--sulfur ligase TCUR_RS18530 TCUR_RS10500
Mt_cysM CysO-thiocarboxylate-dependent cysteine synthase TCUR_RS19040 TCUR_RS05170
mec [CysO sulfur-carrier protein]-S-L-cysteine hydrolase TCUR_RS19050
Alternative steps:
CBS cystathionine beta-synthase TCUR_RS05170 TCUR_RS19040
CGL cystathionine gamma-lyase TCUR_RS05180 TCUR_RS18805
cysE serine acetyltransferase TCUR_RS07155 TCUR_RS04910
cysK O-acetylserine or O-succinylserine sulfhydrylase TCUR_RS07160 TCUR_RS19040
pscS Sep-tRNA:Cys-tRNA synthase
PSSH O-phosphoserine sulfhydrylase TCUR_RS19040 TCUR_RS05170
sepS O-phosphoseryl-tRNA ligase
serK serine kinase (ADP-dependent)
SST serine O-succinyltransferase TCUR_RS07155

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 Apr 09 2024. The underlying query database was built on Apr 09 2024.



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:

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