GapMind for catabolism of small carbon sources

 

Finding step artM for L-arginine catabolism in Klebsiella michiganensis M5al

5 candidates for artM: L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM)

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
hi BWI76_RS20325 histidine/lysine/arginine/ornithine ABC transporter permease HisM Histidine transport system permease protein HisM (characterized) 94% 100% 448.7
hi BWI76_RS09505 arginine transporter permease subunit ArtM Arginine ABC transporter permease protein ArtM (characterized) 91% 100% 411 NocM aka ATU6025 aka AGR_PTI_65, component of Nopaline porter 39% 157.5
hi BWI76_RS19230 polar amino acid ABC transporter inner membrane subunit AotP aka AotM aka PA0890, component of Arginine/ornithine (but not lysine) porter (characterized) 43% 96% 184.5
med BWI76_RS07585 polar amino acid ABC transporter inner membrane subunit L-Arginine ABC transporter, permease protein AotM (characterized) 36% 92% 131.3 Probable amino-acid permease protein YxeN 31% 110.2
lo BWI76_RS16800 amino acid ABC transporter permease AotP aka AotM aka PA0890, component of Arginine/ornithine (but not lysine) porter (characterized) 32% 95% 131.3 Basic amino acid uptake transporter, BgtAB 36% 154.5

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 artM

Or cluster all characterized artM 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