GapMind for catabolism of small carbon sources

 

Finding step kgtP for 2-oxoglutarate (alpha-ketoglutarate) catabolism in Pseudomonas fluorescens FW300-N1B4

5 candidates for kgtP: 2-oxoglutarate:H+ symporter KgtP

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
hi Pf1N1B4_686 Dicarboxylate MFS transporter Alpha-ketoglutarate permease, MFS superfamily (characterized) 94% 100% 830.9 Citrate:H+ symporter 34% 242.7
hi Pf1N1B4_5606 Alpha-ketoglutarate permease Alpha-ketoglutarate permease of the major facilitator superfamily protein (characterized, see rationale) 56% 95% 493 Inner membrane metabolite transport protein YhjE 33% 232.6
lo Pf1N1B4_5961 Major facilitator superfamily transporter Alpha-ketoglutarate permease of the major facilitator superfamily protein (characterized, see rationale) 36% 77% 220.7 Acetate/haloacid transporter, Dehp2, with a possible atypical topology 70% 786.6
lo Pf1N1B4_5977 Transporter, MFS superfamily Alpha-ketoglutarate permease of the major facilitator superfamily protein (characterized, see rationale) 33% 91% 214.2 Fosfomycin resistance protein AbaF; Acinetobacter baumannii fosfomycin efflux 78% 691.4
lo Pf1N1B4_180 L-Proline/Glycine betaine transporter ProP alpha-ketoglutarate permease (MHS family) (characterized) 32% 99% 202.6 Inner membrane metabolite transport protein YhjE 43% 349.4

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 kgtP

Or cluster all characterized kgtP proteins

This GapMind analysis is from Aug 02 2021. The underlying query database was built on Aug 02 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