GapMind for Amino acid biosynthesis

 

L-cysteine biosynthesis in Desulfitobacterium hafniense DCB-2

Best path

cysE, cysK

Rules

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 (10 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
cysE serine acetyltransferase DHAF_RS02065 DHAF_RS22870
cysK O-acetylserine or O-succinylserine sulfhydrylase DHAF_RS05770 DHAF_RS05755
Alternative steps:
CBS cystathionine beta-synthase DHAF_RS05770
CGL cystathionine gamma-lyase DHAF_RS06925 DHAF_RS05755
cysO sulfur carrier protein CysO
mec [CysO sulfur-carrier protein]-S-L-cysteine hydrolase DHAF_RS20490
moeZ [sulfur carrier protein CysO]--sulfur ligase DHAF_RS20495
Mt_cysM CysO-thiocarboxylate-dependent cysteine synthase DHAF_RS05770
pscS Sep-tRNA:Cys-tRNA synthase
PSSH O-phosphoserine sulfhydrylase DHAF_RS05770
sepS O-phosphoseryl-tRNA ligase
serA 3-phosphoglycerate dehydrogenase DHAF_RS22855 DHAF_RS10340
serC 3-phosphoserine aminotransferase DHAF_RS22860 DHAF_RS24160
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 09 2024. The underlying query database was built on Apr 09 2024.

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 (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