GapMind for catabolism of small carbon sources

 

L-alanine catabolism in Klebsiella michiganensis M5al

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 BWI76_RS02700 BWI76_RS01140
Alternative steps:
AAP1 L-alanine permease AAP1
AAP24 L-alanine transporter AAP24
alsT L-alanine symporter AlsT/DagA BWI76_RS04265
braC L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) BWI76_RS26350 BWI76_RS26365
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) BWI76_RS26345 BWI76_RS07280
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) BWI76_RS26340 BWI76_RS07275
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) BWI76_RS26335 BWI76_RS05980
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) BWI76_RS26330 BWI76_RS05975
metP sodium-dependent methionine/alanine transporter, large subunit MetP
metS sodium-dependent methionine/alanine transporter, small subunit MetS
SLC1A4 L-alanine symporter SLC1A4
SLC38A3 L-alanine symporter SLC38A3
snatA L-alanine symporter SnatA BWI76_RS17245
TRIC TRIC-type L-alanine transporter BWI76_RS27405 BWI76_RS05160

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