Finding step CGL for L-cysteine biosynthesis in Methanococcus maripaludis C5
No candidates for CGL: cystathionine gamma-lyase
GapMind classifies a step as low confidence even if it does not find any candidates. You can still try to find candidates by using Curated BLAST (which searches the 6-frame translation) or by text search of the annotations (which may indicate weak homology, under 30% identity or 50% coverage, that GapMind does not consider). See the links below.
Definition of step CGL
- Curated proteins matching cystathionine gamma-lyase
- Curated proteins matching cystathionine-gamma-lyase
- Ignore hits to Q9M1R1 when looking for 'other' hits (cystathionine gamma-lyase (EC 4.4.1.1). L-cysteine desulfhydrase; AtL-CDes1; L-CDes1; AtLCD; EC 4.4.1.28)
- Ignore hits to F4K5T2 when looking for 'other' hits (L-cysteine desulfidase (EC 4.4.1.28). Bifunctional cystathionine gamma-lyase/cysteine synthase; Beta-substituted Ala synthase 4;3; ARAth-Bsas4;3; L-cysteine desulfhydrase 1; DES1; O-acetylserine (thiol)-lyase; OASTL; Protein CS-LIKE; EC 2.5.1.47; EC 4.4.1.1)
- Ignore hits to Q1M0P5 when looking for 'other' hits (Cystathionine gamma-synthase; CGS; O-succinylhomoserine (thiol)-lyase; EC 2.5.1.48. cystathionine gamma-synthase (EC 2.5.1.48))
- Ignore hits to CH_088676 when looking for 'other' hits (cystathionine beta-lyase; EC 4.4.1.8)
- Comment: EC 4.4.1.1 includes some other reactions, so it is not used to define CGL. Q9M1R1 is misannotated in BRENDA. SwissProt annotates the cysteine desulfurase DES1 (F4K5T2) with this activity, but we did not find evidence for it, so it is ignored. "MetB" from Helicobacter pylori was originally reported to be a cystathionine gamma-synthase (i.e., Q1M0P5 in BRENDA), but was later identified as a CGL (PMC2820867), so Q1M0P5 is ignored. Similarly, "MetC" from Lactoccus lactis (A2RM21) is reported to be a CGL and a cystathionine beta-lyase (PMID:10620674); another paper proposed that it is a CBL but did not distinguish between the two activities (PMC91783, cited by CharProtDB, which is ignored).
Or cluster all characterized CGL proteins
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.
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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:
- ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
- HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.
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:
- ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
- ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
- HMMer finds a hit (regardless of coverage or other bits).
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:
- our ignorance of proteins' functions,
- omissions in the gene models,
- frame-shift errors in the genome sequence, or
- the organism lacks the pathway.
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