GapMind for catabolism of small carbon sources


Finding step hisM for L-lysine catabolism in Burkholderia phytofirmans PsJN

5 candidates for hisM: L-lysine ABC transporter, permease component 1 (HisM)

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
med BPHYT_RS05500 histidine/lysine/arginine/ornithine ABC transporter permease HisM Histidine transport system permease protein HisM (characterized) 70% 99% 338.2 ABC transporter for L-Arginine, permease component 1 75% 370.2
med BPHYT_RS07680 histidine/lysine/arginine/ornithine ABC transporter permease HisM ABC transporter for L-Lysine, permease component 2 (characterized) 66% 100% 323.9 ABC transporter for L-Arginine, permease component 1 100% 473.4
med BPHYT_RS24010 ABC transporter permease ABC transporter for L-Lysine, permease component 2 (characterized) 42% 97% 178.7 NocM aka ATU6025 aka AGR_PTI_65, component of Nopaline porter 50% 230.3
lo BPHYT_RS21915 ABC transporter permease Amino acid (Lysine/arginine/ornithine/histidine/octopine) ABC transporter membrane protein, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) 37% 97% 144.1 ABC transporter for L-Histidine, permease component 1 80% 357.1
lo BPHYT_RS13290 cysteine ABC transporter permease Histidine transport system permease protein HisM (characterized) 34% 94% 126.3 L-cystine transport system permease protein YecS 53% 215.7

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 hisM

Or cluster all characterized hisM 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