GapMind for Amino acid biosynthesis


L-cysteine biosynthesis in Echinicola vietnamensis KMM 6221, DSM 17526

Best path

cysE?, cysK

Also see fitness data for the top candidates


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 (9 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate Class of gap
cysE? serine acetyltransferase Echvi_0221 Echvi_2964 diverged
cysK O-acetylserine sulfhydrylase Echvi_0220 Echvi_3411  
Alternative steps:
CBS cystathionine beta-synthase Echvi_4660 Echvi_0220  
CGL cystathionine gamma-lyase Echvi_2080 Echvi_1734  
cysO sulfur carrier protein CysO  
mec [CysO sulfur-carrier protein]-S-L-cysteine hydrolase  
moeZ [sulfur carrier protein CysO]--sulfur ligase Echvi_1891  
Mt_cysM CysO-thiocarboxylate-dependent cysteine synthase Echvi_0220 Echvi_4660  
pscS Sep-tRNA:Cys-tRNA synthase  
PSSH O-phosphoserine sulfhydrylase Echvi_0220 Echvi_4660  
sepS O-phosphoseryl-tRNA ligase  
serA 3-phosphoglycerate dehydrogenase Echvi_2777 Echvi_3936  
serC 3-phosphoserine aminotransferase  
serK serine kinase (ADP-dependent)  
SST serine O-succinyltransferase Echvi_3285  

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 Aug 03 2021. The underlying query database was built on Aug 03 2021.



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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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