GapMind for catabolism of small carbon sources

 

L-alanine catabolism in Pseudomonas simiae WCS417

Best path

braC, braD, braE, braF, braG

Also see fitness data for the top candidates

Rules

Overview: GapMind describes L-alanine uptake only. No enzymatic steps are represented because L-alanine is a single transamination reaction away from pyruvate, which is a central metabolic intermediate. (L-alanine can also be converted to pyruvate by alanine dehydrogenase or by by alanine racemase and D-alanine dehydrogenase, link).

15 steps (10 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
braC L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) PS417_06615 PS417_02655
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) PS417_06610 PS417_02660
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) PS417_06605 PS417_02665
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) PS417_06600 PS417_17675
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) PS417_06595 PS417_02675
Alternative steps:
AAP1 L-alanine permease AAP1
AAP24 L-alanine transporter AAP24
alsT L-alanine symporter AlsT/DagA PS417_28135
cycA L-alanine symporter CycA PS417_05405 PS417_14545
metP sodium-dependent methionine/alanine transporter, large subunit MetP
metS sodium-dependent methionine/alanine transporter, small subunit MetS
SLC1A4 L-alanine symporter SLC1A4 PS417_21500
SLC38A3 L-alanine symporter SLC38A3
snatA L-alanine symporter SnatA PS417_02925
TRIC TRIC-type L-alanine transporter PS417_02455

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