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 (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