GapMind for catabolism of small carbon sources

 

L-serine catabolism in Dinoroseobacter shibae DFL-12

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 (12 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
snatA L-serine transporter Dshi_1348
sdaB L-serine ammonia-lyase Dshi_5008 Dshi_0888
Alternative steps:
AAP1 L-serine transporter AAP1
Ac3H11_1692 L-tyrosine ABC transporter, ATPase component 2 Dshi_0381 Dshi_1520
Ac3H11_1693 L-tyrosine ABC transporter, ATPase component 1 Dshi_0375 Dshi_1981
Ac3H11_1694 L-tyrosine ABC transporter, permease component 2 Dshi_1978
Ac3H11_1695 L-tyrosine ABC transporter, permease component 1 Dshi_2696 Dshi_0861
Ac3H11_2396 L-tyrosine ABC transporter, substrate-binding component component
braC L-alanine/L-serine/L-threonine ABC transporter, substrate binding protein (BraC/NatB) Dshi_1977
braD L-alanine/L-serine/L-threonine ABC transporter, permease component 1 (BraD/NatD) Dshi_1518 Dshi_1979
braE L-alanine/L-serine/L-threonine ABC transporter, permease component 2 (BraE/NatC) Dshi_1978
braF L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 1 (BraF/NatA) Dshi_1521 Dshi_1981
braG L-alanine/L-serine/L-threonine ABC transporter, ATP-binding component 2 (BraG/NatE) Dshi_1520 Dshi_1980
dlsT L-serine transporter DlsT
sdaC L-serine transporter:H+ symporter sdaC
sdhA FeS-containing L-serine dehydratase, alpha subunit Dshi_5008
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 (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