GapMind for Amino acid biosynthesis

 

L-cysteine biosynthesis in Magnetospirillum magneticum AMB-1

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 AMB_RS09365 AMB_RS15270
cysK O-acetylserine sulfhydrylase AMB_RS01005 AMB_RS06615
Alternative steps:
CBS cystathionine beta-synthase AMB_RS01005 AMB_RS06615
CGL cystathionine gamma-lyase AMB_RS01005 AMB_RS21365
cysO sulfur carrier protein CysO
mec [CysO sulfur-carrier protein]-S-L-cysteine hydrolase
moeZ [sulfur carrier protein CysO]--sulfur ligase AMB_RS01000
Mt_cysM CysO-thiocarboxylate-dependent cysteine synthase AMB_RS01005 AMB_RS09340
pscS Sep-tRNA:Cys-tRNA synthase
PSSH O-phosphoserine sulfhydrylase AMB_RS01005 AMB_RS09340
sepS O-phosphoseryl-tRNA ligase
serA 3-phosphoglycerate dehydrogenase AMB_RS16130 AMB_RS00685
serC 3-phosphoserine aminotransferase AMB_RS16135 AMB_RS22510
serK serine kinase (ADP-dependent)
SST serine O-succinyltransferase AMB_RS20100

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.

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