Finding step serB for L-serine biosynthesis in Phaeobacter inhibens BS107
3 candidates for serB: phosphoserine phosphatase
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
GapMind searches the predicted proteins for candidates by using ublast (a fast alternative to protein BLAST) to find similarities to characterized proteins or by using HMMer to find similarities to enzyme models (usually from TIGRFams). For alignments to characterized proteins (from ublast), scores of 44 bits correspond to an expectation value (E) of about 0.001.
Also see fitness data for the candidates
Definition of step serB
- Curated proteins or TIGRFams with EC 3.1.3.3 (search)
- UniProt sequence A0A1X9ZBA8_9SPHI: RecName: Full=2-oxoglutarate reductase {ECO:0000256|ARBA:ARBA00016905}; EC=1.1.1.399 {ECO:0000256|ARBA:ARBA00013001}; EC=3.1.3.3 {ECO:0000256|ARBA:ARBA00012640}; AltName: Full=D-3-phosphoglycerate dehydrogenase {ECO:0000256|ARBA:ARBA00021582}; AltName: Full=O-phosphoserine phosphohydrolase {ECO:0000256|ARBA:ARBA00013466};
- UniProt sequence L0G228_ECHVK: RecName: Full=2-oxoglutarate reductase {ECO:0000256|ARBA:ARBA00016905}; EC=1.1.1.399 {ECO:0000256|ARBA:ARBA00013001}; EC=1.1.1.95 {ECO:0000256|ARBA:ARBA00013143}; EC=3.1.3.3 {ECO:0000256|ARBA:ARBA00012640}; AltName: Full=D-3-phosphoglycerate dehydrogenase {ECO:0000256|ARBA:ARBA00021582}; AltName: Full=O-phosphoserine phosphohydrolase {ECO:0000256|ARBA:ARBA00013466};
- Ignore hits to items matching EC 1.1.1.95 when looking for 'other' hits
- Ignore hits to P60487 when looking for 'other' hits (pyridoxal phosphatase (EC 3.1.3.74). Pyridoxal phosphate phosphatase; PLP phosphatase; Chronophin; EC 3.1.3.3; EC 3.1.3.74)
- Ignore hits to Q96GD0 when looking for 'other' hits (pyridoxal phosphatase (EC 3.1.3.74). Pyridoxal phosphate phosphatase; PLP phosphatase; Chronophin; EC 3.1.3.3; EC 3.1.3.74)
- Ignore hits to Q9P376 when looking for 'other' hits (CTD phosphatase Fcp1; EC 3.1.3.3. RNA polymerase II subunit A C-terminal domain phosphatase; CTD phosphatase fcp1; EC 3.1.3.16)
- Ignore hits to Q3ZBF9 when looking for 'other' hits (Pyridoxal phosphate phosphatase; PLP phosphatase; Chronophin; EC 3.1.3.3; EC 3.1.3.74)
- Ignore hits to P00634 when looking for 'other' hits (alkaline phosphatase (EC 3.1.3.1). alkaline phosphatase (EC 3.1.3.1; EC 3.1.3.75; EC 3.1.3.41; EC 3.1.3.74; EC 3.1.3.99; EC 3.1.3.5; EC 3.1.3.6; EC 3.1.3.89; EC 3.1.3.91; EC 3.1.3.60; EC 3.1.3.15; EC 3.1.3.102; EC 3.1.3.2; EC 3.1.3.11; EC 3.1.3.20; EC 3.1.3.19; EC 3.1.3.3; EC 3.6.1.25; EC 3.6.1.1; EC 3.1.3.58; EC 3.1.3.9; EC 3.1.3.23; EC 3.1.3.38; EC 3.1.3.18; EC 3.1.3.68; EC 3.9.1.1). alkaline phosphatase (EC 3.1.3.1; EC 3.1.3.75; EC 3.1.3.41; EC 3.1.3.74; EC 3.1.3.99; EC 3.1.3.5; EC 3.1.3.6; EC 3.1.3.89; EC 3.1.3.91; EC 3.1.3.60; EC 3.1.3.15; EC 3.1.3.102; EC 3.1.3.2; EC 3.1.3.11; EC 3.1.3.20; EC 3.1.3.19; EC 3.1.3.3; EC 3.6.1.25; EC 3.6.1.1; EC 3.1.3.58; EC 3.1.3.23; EC 3.1.3.38; EC 3.1.3.18; EC 3.1.3.68; EC 3.9.1.1))
- Ignore hits to P0AE22 when looking for 'other' hits (acid phosphatase (EC 3.1.3.2). class B acid phosphatase; EC 3.1.3.2. Class B acid phosphatase; CBAP; EC 3.1.3.2. acid phosphatase / phosphotransferase (EC 3.1.3.2; EC 3.1.3.31; EC 3.1.3.5; EC 3.1.3.6; EC 3.1.3.89; EC 3.1.3.34; EC 3.1.3.3). acid phosphatase / phosphotransferase (EC 3.1.3.2; EC 3.1.3.31; EC 3.1.3.5; EC 3.1.3.6; EC 3.1.3.89; EC 3.1.3.34; EC 3.1.3.3))
- Ignore hits to Q9P376 when looking for 'other' hits (CTD phosphatase Fcp1; EC 3.1.3.3. RNA polymerase II subunit A C-terminal domain phosphatase; CTD phosphatase fcp1; EC 3.1.3.16)
- Ignore hits to P17906 when looking for 'other' hits (Phosphoserine phosphatase RsbX; Sigma-B negative effector; EC 3.1.3.3)
- Ignore hits to P40399 when looking for 'other' hits (Phosphoserine phosphatase RsbU; Sigma factor SigB regulation protein RsbU; EC 3.1.3.3)
- Ignore hits to P94526 when looking for 'other' hits (Sugar-phosphatase AraL; Arabinose operon protein AraL; Phosphoserine phosphatase; EC 3.1.3.23; EC 3.1.3.3)
- UniProt sequence Q9K8N3: SubName: Full=BH2972 protein {ECO:0000313|EMBL:BAB06691.1};
- UniProt sequence A0A1R2PVY2: RecName: Full=O-phosphoserine phosphohydrolase {ECO:0000256|ARBA:ARBA00013466}; EC=3.1.3.3 {ECO:0000256|ARBA:ARBA00012640}; AltName: Full=Phosphoserine phosphatase {ECO:0000256|ARBA:ARBA00015196};
- Comment: CA265_RS22635 (A0A1X9ZBA8_9SPHI) is diverged serB and is auxotrophic. It also appears to be fused to diverged serA, but there is another serA in the genome (CA265_RS09010), so CA265_RS22635 may not be a functional dehydrogenase. Echvi_2777 (L0G228_ECHVK) from Echinicola vietnamensis KMM 6221 is a diverged serB and is auxotrophic, rescued by serine. It is fused to serA and probably provides that activity as well. Hits to serA are ignored because of serAB fusions. Some curated resources link this EC number to protein phosphatases, or to non-specific periplasmic phosphatases, that are unlikely to play a role in serine biosynthesis. These are all marked ignore (P60487, Q96GD0, Q3ZBF9, P00634, P0AE22, Q9P376). Also, Swiss-Prot annotates RsbX (P17906) and RsbU (P40399) with this EC number, but they probably act on proteins. I was not able to find evidence that AraL (P94526) is a phosphoserine phosphatase (the cited paper PMID:25848029 does not seem to discuss this protein.) PMID:25848029 does show that Q9K8N3 and X3MFA4 (A0A1R2PVY2) have this activity.
Or cluster all characterized serB proteins
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:
- 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 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