GapMind for catabolism of small carbon sources

 

Finding step lysP for L-lysine catabolism in Pseudomonas fluorescens GW456-L13

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

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
med PfGW456L13_3211 Arginine permease RocE lysine-specific permease (characterized) 43% 93% 399.8 Amino-acid permease RocE 54% 541.6
lo PfGW456L13_4790 D-serine/D-alanine/glycine transporter The lysine specific transporter, LysP of 488 aas and 12 TMSs (characterized) 39% 94% 316.6 L-alanine and D-alanine permease 96% 906.0
lo PfGW456L13_375 transport permease protein of gamma-aminobutyrate lysine-specific permease (characterized) 34% 93% 280.8 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 73% 636.7
lo PfGW456L13_4291 Aromatic amino acid transport protein AroP Lysine/arginine permease CAN1; Basic amino acids permease CAN1 (characterized) 34% 81% 268.1 L-tyrosine transporter 74% 705.3
lo PfGW456L13_4400 Aromatic amino acid transport protein AroP Probable lysine/arginine permease CAN2; Basic amino acids permease CAN2 (characterized) 32% 81% 242.7 L-tyrosine transporter 93% 887.9

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

GapMind searches the predicted proteins for candidates by using ublast (a fast alternative to protein BLAST) to find similarities to characterized proteins or by using HMMer to find similarities to enzyme models (usually from TIGRFams). For alignments to characterized proteins (from ublast), scores of 44 bits correspond to an expectation value (E) of about 0.001.

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 (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