GapMind for catabolism of small carbon sources

 

D-alanine catabolism in Paraburkholderia phymatum STM815

Best path

mctP, dadA

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 (12 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
mctP D-alanine transporter MctP BPHY_RS19670 BPHY_RS10730
dadA D-alanine dehydrogenase BPHY_RS03860 BPHY_RS23650
Alternative steps:
AZOBR_RS08235 D-alanine ABC transporter, permease component 1 BPHY_RS02955 BPHY_RS11455
AZOBR_RS08240 D-alanine ABC transporter, permease component 2 BPHY_RS02960
AZOBR_RS08245 D-alanine ABC transporter, ATPase component 1 BPHY_RS02965 BPHY_RS15490
AZOBR_RS08250 D-alanine ABC transporter, ATPase component 2 BPHY_RS02970 BPHY_RS15485
AZOBR_RS08260 D-alanine ABC transporter, substrate-binding component BPHY_RS00550 BPHY_RS15375
cycA D-alanine:H+ symporter CycA BPHY_RS03010 BPHY_RS31005
Pf6N2E2_5402 ABC transporter for D-Alanine, substrate-binding component BPHY_RS29405
Pf6N2E2_5403 ABC transporter for D-Alanine, permease component 2 BPHY_RS13050
Pf6N2E2_5404 ABC transporter for D-Alanine, permease component 1 BPHY_RS33255 BPHY_RS13045
Pf6N2E2_5405 ABC transporter for D-Alanine, ATPase component BPHY_RS13040 BPHY_RS27405

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 Apr 09 2024. 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:

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