GapMind for catabolism of small carbon sources

 

Definition of L-serine catabolism

As rules and steps, or see full text

Rules

Overview: L-serine degradation in GapMind is based on the MetaCyc pathway (link)

Steps

braC: L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB)

braD: L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD)

braE: L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC)

braF: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA)

braG: L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE)

Ac3H11_2396: L-tyrosine ABC transporter, substrate-binding component component

Ac3H11_1695: L-tyrosine ABC transporter, permease component 1

Ac3H11_1694: L-tyrosine ABC transporter, permease component 2

Ac3H11_1693: L-tyrosine ABC transporter, ATPase component 1

Ac3H11_1692: L-tyrosine ABC transporter, ATPase component 2

serP: L-serine permease SerP

dlsT: L-serine transporter DlsT

sdaC: L-serine transporter:H+ symporter sdaC

AAP1: L-serine transporter AAP1

sstT: L-serine:Na+ symporter SstT

snatA: L-serine transporter

sdaB: L-serine ammonia-lyase

sdhA: FeS-containing L-serine dehydratase, alpha subunit

sdhB: FeS-containing L-serine dehydratase, beta subunit

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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