GapMind for catabolism of small carbon sources

 

Finding step aldox-small for D-xylose catabolism in Pseudomonas fluorescens FW300-N1B4

4 candidates for aldox-small: (glycol)aldehyde oxidoreductase, small subunit

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other-bits
med Pf1N1B4_4870 Isoquinoline 1-oxidoreductase alpha subunit (EC 1.3.99.16) Glyceraldehyde dehydrogenase small chain; Glyceraldehyde dehydrogenase subunit C; Glyceraldehyde dehydrogenase subunit gamma; EC 1.2.99.8 (characterized) 43% 91% 120.9 vanillin dehydrogenase, iorA-like component 59% 184.9
med Pf1N1B4_4583 Isoquinoline 1-oxidoreductase alpha subunit (EC 1.3.99.16) glycolaldehyde oxidoreductase small subunit (characterized) 42% 91% 113.2 nicotine dehydrogenase β subunit (EC 1.5.99.4) 60% 183.7
lo Pf1N1B4_3853 Xanthine dehydrogenase iron-sulfur subunit (EC 1.17.1.4) / Xanthine dehydrogenase, FAD binding subunit (EC 1.17.1.4) glycolaldehyde oxidoreductase small subunit (characterized) 36% 82% 110.5 Xanthine dehydrogenase (EC 1.17.1.4) 93% 911.8
lo Pf1N1B4_465 Isoquinoline 1-oxidoreductase alpha subunit (EC 1.3.99.16) Glyceraldehyde dehydrogenase small chain; Glyceraldehyde dehydrogenase subunit C; Glyceraldehyde dehydrogenase subunit gamma; EC 1.2.99.8 (characterized) 37% 91% 109 isoquinoline 1-oxidoreductase subunit α (EC 1.3.99.16) 56% 175.6

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

Also see fitness data for the candidates

Definition of step aldox-small

Or cluster all characterized aldox-small proteins

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