Finding step serA for L-serine biosynthesis in Chlorobaculum tepidum TLS
Classification of gap: spurious
Rationale: Although serA was not found in the annotated proteins, it was found when analyzing the six-frame translation of the genome. This is often due to a missing gene call, but it could be due to an error in the genome sequence.
No candidates for serA: 3-phosphoglycerate dehydrogenase
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 serA
- Curated proteins or TIGRFams with EC 1.1.1.95 (search)
- UniProt sequence A0A1X9ZCD3: SubName: Full=3-phosphoglycerate dehydrogenase {ECO:0000313|EMBL:ARS42937.1};
- UniProt sequence Q6LWW6: RecName: Full=D-3-phosphoglycerate dehydrogenase {ECO:0000256|RuleBase:RU363003}; EC=1.1.1.95 {ECO:0000256|RuleBase:RU363003};
- Ignore hits to Q4JDI4 when looking for 'other' hits (phosphoglycerate kinase (EC 2.7.2.3))
- Ignore hits to HP_RS05420-MONOMER when looking for 'other' hits (cinnamyl-alcohol dehydrogenase (EC 1.1.1.2; EC 1.1.1.95; EC 1.1.1.195))
- Ignore hits to SGL_RS08600-MONOMER when looking for 'other' hits (glycerate dehydrogenase (EC 1.1.1.29))
- Predicted: UniProt sequence A0A374I5P9: RecName: Full=D-3-phosphoglycerate dehydrogenase {ECO:0000256|ARBA:ARBA00021582}; EC=1.1.1.399 {ECO:0000256|ARBA:ARBA00013001}; EC=1.1.1.95 {ECO:0000256|ARBA:ARBA00013143}; AltName: Full=2-oxoglutarate reductase {ECO:0000256|ARBA:ARBA00030455};
- UniProt sequence Q5JGC4: SubName: Full=D-3-phosphoglycerate dehydrogenase {ECO:0000313|EMBL:BAD86155.1};
- Comment: BRENDA::Q4JDI4 is misannotated as 3-phosphoglycerate dehydrogenase instead of 3-phosphoglycerate kinase. (The curators were notified and report that they have corrected this.) CA265_RS09010 (A0A1X9ZCD3) from Pedobacter sp. GW460-11-11-14-LB5 is annotated as 3-phosphoglycerate dehydrogenase and has auxotrophic phenotypes. In particular, mutants are partially rescued by glycine or serine. Also it is adjacent to the putative serC. MMP1588 (Q6LWW6) was identified as the serA of Methanococcus (PMC1797378). Ignore link_RS05420-MONOMER which has this EC but has a different function. Ignore similarity to sll1908 (link_RS08600-MONOMER) which seems likely to be serA but was proposed (without experimental evidence) to be hydroxpyruvate reductase. In Roseburia faecis, the putative serA (A0A374I5P9) is diverged but is similar to the serA part of Echvi_2777 and is conserved next to serC and DUF1015 (putative serB). In Thermococcus kodakarensis, TK1966 (Q5JGC4) is the 3-phosphoglycerate dehydrogenase (PMC5120207).
Or cluster all characterized serA 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