GapMind for catabolism of small carbon sources

 

L-serine catabolism in Pseudomonas putida KT2440

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) PP_1141 PP_4867
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) PP_1140 PP_4866
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) PP_1139 PP_4865
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) PP_1138 PP_4864
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) PP_1137 PP_4863
sdaB L-serine ammonia-lyase PP_0987 PP_3144
Alternative steps:
AAP1 L-serine transporter AAP1
Ac3H11_1692 L-tyrosine ABC transporter, ATPase component 2 PP_1137 PP_4863
Ac3H11_1693 L-tyrosine ABC transporter, ATPase component 1 PP_1138 PP_2767
Ac3H11_1694 L-tyrosine ABC transporter, permease component 2 PP_1139 PP_4865
Ac3H11_1695 L-tyrosine ABC transporter, permease component 1 PP_4866 PP_1140
Ac3H11_2396 L-tyrosine ABC transporter, substrate-binding component component PP_4867 PP_1141
dlsT L-serine transporter DlsT
sdaC L-serine transporter:H+ symporter sdaC PP_3589
sdhA FeS-containing L-serine dehydratase, alpha subunit PP_0297 PP_0987
sdhB FeS-containing L-serine dehydratase, beta subunit
serP L-serine permease SerP PP_4840 PP_5031
snatA L-serine transporter PP_4825
sstT L-serine:Na+ symporter SstT PP_2443

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