GapMind for catabolism of small carbon sources

 

L-serine catabolism in Echinicola vietnamensis KMM 6221, DSM 17526

Best path

serP, 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 (7 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
serP L-serine permease SerP
sdaB L-serine ammonia-lyase Echvi_0600 Echvi_2833
Alternative steps:
AAP1 L-serine transporter AAP1
Ac3H11_1692 L-tyrosine ABC transporter, ATPase component 2 Echvi_1333 Echvi_2909
Ac3H11_1693 L-tyrosine ABC transporter, ATPase component 1 Echvi_1333 Echvi_4539
Ac3H11_1694 L-tyrosine ABC transporter, permease component 2
Ac3H11_1695 L-tyrosine ABC transporter, permease component 1
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)
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) Echvi_1333 Echvi_1022
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) Echvi_1333 Echvi_2909
dlsT L-serine transporter DlsT
sdaC L-serine transporter:H+ symporter sdaC
sdhA FeS-containing L-serine dehydratase, alpha subunit Echvi_0600
sdhB FeS-containing L-serine dehydratase, beta subunit Echvi_2833
snatA L-serine transporter
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