GapMind for catabolism of small carbon sources

 

L-serine catabolism in Pseudomonas fluorescens FW300-N2E3

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) AO353_17125 AO353_13340
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) AO353_17120 AO353_13345
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) AO353_17115 AO353_13350
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) AO353_17110 AO353_13530
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) AO353_17105 AO353_13360
sdaB L-serine ammonia-lyase AO353_15500 AO353_03505
Alternative steps:
AAP1 L-serine transporter AAP1
Ac3H11_1692 L-tyrosine ABC transporter, ATPase component 2 AO353_17105 AO353_13360
Ac3H11_1693 L-tyrosine ABC transporter, ATPase component 1 AO353_17110 AO353_13355
Ac3H11_1694 L-tyrosine ABC transporter, permease component 2 AO353_17115 AO353_13350
Ac3H11_1695 L-tyrosine ABC transporter, permease component 1 AO353_13345 AO353_17120
Ac3H11_2396 L-tyrosine ABC transporter, substrate-binding component component AO353_13340 AO353_17125
dlsT L-serine transporter DlsT
sdaC L-serine transporter:H+ symporter sdaC AO353_15495 AO353_21595
sdhA FeS-containing L-serine dehydratase, alpha subunit AO353_15500 AO353_07775
sdhB FeS-containing L-serine dehydratase, beta subunit
serP L-serine permease SerP AO353_25190 AO353_05965
snatA L-serine transporter AO353_13635
sstT L-serine:Na+ symporter SstT AO353_20105

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, 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