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).
Or see definitions of steps
| Step | Description | Best candidate | 2nd candidate |
|---|---|---|---|
| cysE | serine acetyltransferase | METME_RS19670 | METME_RS15610 |
| cysK | O-acetylserine or O-succinylserine sulfhydrylase | METME_RS12000 | METME_RS14025 |
| Alternative steps: | |||
| CBS | cystathionine beta-synthase | METME_RS14025 | METME_RS12000 |
| CGL | cystathionine gamma-lyase | METME_RS03045 | |
| cysO | sulfur carrier protein CysO | ||
| mec | [CysO sulfur-carrier protein]-S-L-cysteine hydrolase | ||
| moeZ | [sulfur carrier protein CysO]--sulfur ligase | METME_RS04045 | |
| Mt_cysM | CysO-thiocarboxylate-dependent cysteine synthase | METME_RS12000 | METME_RS14025 |
| pscS | Sep-tRNA:Cys-tRNA synthase | ||
| PSSH | O-phosphoserine sulfhydrylase | METME_RS12000 | METME_RS14025 |
| sepS | O-phosphoseryl-tRNA ligase | ||
| serA | 3-phosphoglycerate dehydrogenase | METME_RS08655 | METME_RS07460 |
| serC | 3-phosphoserine aminotransferase | METME_RS09445 | METME_RS20000 |
| serK | serine kinase (ADP-dependent) | ||
| SST | serine O-succinyltransferase | ||
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 10 2024. The underlying query database was built on Apr 09 2024.
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:
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