GapMind for catabolism of small carbon sources

 

L-alanine catabolism in Cupriavidus basilensis 4G11

Best path

cycA

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 (9 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
cycA L-alanine symporter CycA RR42_RS28305 RR42_RS14635
Alternative steps:
AAP1 L-alanine permease AAP1
AAP24 L-alanine transporter AAP24
alsT L-alanine symporter AlsT/DagA
braC L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) RR42_RS14425 RR42_RS20120
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) RR42_RS14420 RR42_RS16975
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) RR42_RS14415 RR42_RS16970
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) RR42_RS29450 RR42_RS14410
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) RR42_RS14405 RR42_RS16960
metP sodium-dependent methionine/alanine transporter, large subunit MetP
metS sodium-dependent methionine/alanine transporter, small subunit MetS
SLC1A4 L-alanine symporter SLC1A4 RR42_RS33745
SLC38A3 L-alanine symporter SLC38A3
snatA L-alanine symporter SnatA RR42_RS18900
TRIC TRIC-type L-alanine transporter RR42_RS30380 RR42_RS04305

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:

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