GapMind for catabolism of small carbon sources

 

L-serine catabolism in Phaeobacter inhibens BS107

Best path

snatA, sdaB

Also see fitness data for the top candidates

Rules

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

19 steps (10 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
snatA L-serine transporter PGA1_c19770
sdaB L-serine ammonia-lyase PGA1_c23770 PGA1_c04590
Alternative steps:
AAP1 L-serine transporter AAP1
Ac3H11_1692 L-tyrosine ABC transporter, ATPase component 2 PGA1_c02620 PGA1_c32560
Ac3H11_1693 L-tyrosine ABC transporter, ATPase component 1 PGA1_c32620 PGA1_c02610
Ac3H11_1694 L-tyrosine ABC transporter, permease component 2 PGA1_c32580
Ac3H11_1695 L-tyrosine ABC transporter, permease component 1 PGA1_c02590
Ac3H11_2396 L-tyrosine ABC transporter, substrate-binding component component
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) PGA1_c15940 PGA1_c02590
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) PGA1_c15910 PGA1_c02610
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) PGA1_c15920 PGA1_c02620
dlsT L-serine transporter DlsT
sdaC L-serine transporter:H+ symporter sdaC
sdhA FeS-containing L-serine dehydratase, alpha subunit PGA1_c23770
sdhB FeS-containing L-serine dehydratase, beta subunit
serP L-serine permease SerP
sstT L-serine:Na+ symporter SstT

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, the preprint on GapMind for carbon sources, 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