GapMind for catabolism of small carbon sources


L-serine catabolism in Pseudomonas fluorescens FW300-N2E2

Best path

braC, braD, braE, braF, braG, sdaB

Also see fitness data for the top candidates


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

19 steps (16 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) Pf6N2E2_2921 Pf6N2E2_3580
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) Pf6N2E2_2923 Pf6N2E2_3579
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) Pf6N2E2_2924 Pf6N2E2_3578
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) Pf6N2E2_2925 Pf6N2E2_1433
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) Pf6N2E2_2926 Pf6N2E2_3576
sdaB L-serine ammonia-lyase Pf6N2E2_5557 Pf6N2E2_4685
Alternative steps:
AAP1 L-serine transporter AAP1
Ac3H11_1692 L-tyrosine ABC transporter, ATPase component 2 Pf6N2E2_2926 Pf6N2E2_3576
Ac3H11_1693 L-tyrosine ABC transporter, ATPase component 1 Pf6N2E2_2925 Pf6N2E2_3577
Ac3H11_1694 L-tyrosine ABC transporter, permease component 2 Pf6N2E2_2924 Pf6N2E2_3578
Ac3H11_1695 L-tyrosine ABC transporter, permease component 1 Pf6N2E2_3579 Pf6N2E2_2923
Ac3H11_2396 L-tyrosine ABC transporter, substrate-binding component component Pf6N2E2_3580 Pf6N2E2_2921
dlsT L-serine transporter DlsT
sdaC L-serine transporter:H+ symporter sdaC Pf6N2E2_563
sdhA FeS-containing L-serine dehydratase, alpha subunit Pf6N2E2_4685 Pf6N2E2_5557
sdhB FeS-containing L-serine dehydratase, beta subunit
serP L-serine permease SerP Pf6N2E2_5459 Pf6N2E2_5633
snatA L-serine transporter Pf6N2E2_3525
sstT L-serine:Na+ symporter SstT Pf6N2E2_2230

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.



Related tools

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