GapMind for catabolism of small carbon sources

 

D-alanine catabolism in Pseudomonas putida KT2440

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 PP_1297
Pf6N2E2_5403 ABC transporter for D-Alanine, permease component 2 PP_1298
Pf6N2E2_5404 ABC transporter for D-Alanine, permease component 1 PP_1299 PP_1069
Pf6N2E2_5405 ABC transporter for D-Alanine, ATPase component PP_1300 PP_3597
dadA D-alanine dehydrogenase PP_5270 PP_4434
Alternative steps:
AZOBR_RS08235 D-alanine ABC transporter, permease component 1 PP_4866 PP_1140
AZOBR_RS08240 D-alanine ABC transporter, permease component 2 PP_1139 PP_4865
AZOBR_RS08245 D-alanine ABC transporter, ATPase component 1 PP_4864 PP_1138
AZOBR_RS08250 D-alanine ABC transporter, ATPase component 2 PP_4863 PP_1137
AZOBR_RS08260 D-alanine ABC transporter, substrate-binding component PP_4867 PP_1141
cycA D-alanine:H+ symporter CycA PP_1059 PP_4840
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 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, 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