GapMind for catabolism of small carbon sources

 

L-serine catabolism in Pseudomonas simiae WCS417

Best path

braC, braD, braE, braF, braG, 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 (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) PS417_06615 PS417_02655
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) PS417_06610 PS417_02660
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) PS417_06605 PS417_02665
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) PS417_06600 PS417_17675
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) PS417_06595 PS417_02675
sdaB L-serine ammonia-lyase PS417_22365 PS417_05075
Alternative steps:
AAP1 L-serine transporter AAP1
Ac3H11_1692 L-tyrosine ABC transporter, ATPase component 2 PS417_06595 PS417_02675
Ac3H11_1693 L-tyrosine ABC transporter, ATPase component 1 PS417_06600 PS417_02670
Ac3H11_1694 L-tyrosine ABC transporter, permease component 2 PS417_06605 PS417_02665
Ac3H11_1695 L-tyrosine ABC transporter, permease component 1 PS417_02660 PS417_06610
Ac3H11_2396 L-tyrosine ABC transporter, substrate-binding component component PS417_02655 PS417_06615
dlsT L-serine transporter DlsT
sdaC L-serine transporter:H+ symporter sdaC PS417_05070 PS417_14995
sdhA FeS-containing L-serine dehydratase, alpha subunit PS417_05075 PS417_26310
sdhB FeS-containing L-serine dehydratase, beta subunit
serP L-serine permease SerP PS417_14545 PS417_23700
snatA L-serine transporter PS417_02925
sstT L-serine:Na+ symporter SstT PS417_10435

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 (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 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