GapMind for catabolism of small carbon sources

 

D-alanine catabolism in Pseudomonas simiae WCS417

Best path

Pf6N2E2_5402, Pf6N2E2_5403, Pf6N2E2_5404, Pf6N2E2_5405, dadA

Also see fitness data for the top candidates

Rules

Overview: GapMind describes D-alanine catabolism via D-alanine dehydrogenase, which forms pyruvate. This reaction is part of the MetaCyc pathway for L-alanine catabolism via D-alanine (link). In principle, D-alanine might also be catabolized via racemization to L-alanine and transamination to pyruvate, but this is not described here.

12 steps (11 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
Pf6N2E2_5402 ABC transporter for D-Alanine, substrate-binding component PS417_04900 PS417_23345
Pf6N2E2_5403 ABC transporter for D-Alanine, permease component 2 PS417_04905
Pf6N2E2_5404 ABC transporter for D-Alanine, permease component 1 PS417_04910 PS417_05550
Pf6N2E2_5405 ABC transporter for D-Alanine, ATPase component PS417_04915 PS417_26115
dadA D-alanine dehydrogenase PS417_27705 PS417_26560
Alternative steps:
AZOBR_RS08235 D-alanine ABC transporter, permease component 1 PS417_02660 PS417_06610
AZOBR_RS08240 D-alanine ABC transporter, permease component 2 PS417_06605 PS417_02665
AZOBR_RS08245 D-alanine ABC transporter, ATPase component 1 PS417_06600 PS417_16795
AZOBR_RS08250 D-alanine ABC transporter, ATPase component 2 PS417_06595 PS417_02675
AZOBR_RS08260 D-alanine ABC transporter, substrate-binding component PS417_02655 PS417_06615
cycA D-alanine:H+ symporter CycA PS417_05405 PS417_14545
mctP D-alanine transporter MctP

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 (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:

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. 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:

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