GapMind for catabolism of small carbon sources

 

D-serine catabolism in Pseudomonas simiae WCS417

Best path

cycA, dsdA

Also see fitness data for the top candidates

Rules

Overview: D-serine degradation in GapMind is based on the MetaCyc pathway (link)

3 steps (3 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
cycA D-serine:H+ symporter CycA PS417_14545 PS417_05405
dsdA D-serine ammonia-lyase PS417_12925 PS417_01110
Alternative steps:
dsdX D-serine transporter DsdX PS417_21980 PS417_23605

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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 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.

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