GapMind for Amino acid biosynthesis

 

Finding step serB for L-serine biosynthesis in Pseudomonas stutzeri RCH2

4 candidates for serB: phosphoserine phosphatase

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
hi Psest_2327 phosphoserine phosphatase/homoserine phosphotransferase bifunctional protein Phosphoserine phosphatase; PSP; PSPase; EC 3.1.3.3 (characterized) 92% 86% 379.4
hi Psest_2327 phosphoserine phosphatase/homoserine phosphotransferase bifunctional protein thrH: phosphoserine phosphatase/homoserine phosphotransferase bifunctional protein (EC 3.1.3.3) (TIGR02137) 100% 386.5
hi Psest_0489 phosphoserine phosphatase SerB phosphoserine phosphatase (EC 3.1.3.3) (characterized) 41% 93% 254.6
hi Psest_0489 phosphoserine phosphatase SerB serB: phosphoserine phosphatase SerB (EC 3.1.3.3) (TIGR00338) 100% 263.3
lo Psest_3873 Phosphoglycerate dehydrogenase and related dehydrogenases 2-oxoglutarate reductase; EC 1.1.1.399; EC 1.1.1.95; EC 3.1.3.3 (characterized, see rationale) 56% 64% 448.7 Hydroxypyruvate reductase; HPR; EC 1.1.1.81 36% 175.6
lo Psest_3864 HAD-superfamily subfamily IB hydrolase, TIGR01490 Phosphoserine phosphatase SerB1; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized) 33% 70% 96.7 Histidinol-phosphatase (EC:3.1.3.15) 100% 444.9

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

Also see fitness data for the candidates

Definition of step serB

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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