GapMind for catabolism of small carbon sources

 

Finding step treV for trehalose catabolism in Pseudomonas fluorescens FW300-N1B4

4 candidates for treV: trehalose ABC transporter, ATPase component TreV

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
med Pf1N1B4_593 Glucose ABC transporter, ATP-binding subunit (EC 3.6.3.-) TreV, component of Trehalose porter (characterized) 44% 92% 251.1 ABC transporter for D-Galactose and D-Glucose, ATPase component 96% 734.9
med Pf1N1B4_4847 Various polyols ABC transporter, ATP-binding component TreV, component of Trehalose porter (characterized) 51% 73% 241.1 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 95% 686.8
med Pf1N1B4_3027 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1) TreV, component of Trehalose porter (characterized) 43% 86% 235 Uncharacterized ABC transporter ATP-binding protein YdcT 67% 438.7
med Pf1N1B4_3974 ABC transporter, ATP-binding protein TreV, component of Trehalose porter (characterized) 42% 84% 229.2 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 47% 273.5

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 treV

Or cluster all characterized treV 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, 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