GapMind for catabolism of small carbon sources

 

Finding step lysP for L-lysine catabolism in Pseudomonas fluorescens FW300-N1B4

5 candidates for lysP: L-lysine:H+ symporter LysP

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
med Pf1N1B4_801 D-serine/D-alanine/glycine transporter Lysine permease LysP (characterized) 40% 90% 314.7 L-alanine and D-alanine permease 96% 912.5
lo Pf1N1B4_1639 transport permease protein of gamma-aminobutyrate The lysine specific transporter, LysP of 488 aas and 12 TMSs (characterized) 37% 90% 300.4 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 72% 631.3
lo Pf1N1B4_1580 Histidine transport protein (permease) Lysine permease LysP (characterized) 36% 87% 290.4 histidine permease 95% 885.2
lo Pf1N1B4_3559 Aromatic amino acid transport protein AroP lysine-specific permease (characterized) 34% 71% 246.5 L-tyrosine transporter 96% 903.3
lo Pf1N1B4_5139 Gamma-aminobutyrate permease Probable lysine/arginine permease CAN3; Basic amino acids permease CAN3 (characterized) 31% 78% 217.2 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 69% 635.2

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 lysP

Or cluster all characterized lysP 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