GapMind for catabolism of small carbon sources

 

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

5 candidates for rocE: L-arginine permease

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
med BWI76_RS06025 amino acid transporter Amino-acid permease RocE (characterized) 49% 98% 486.1 S-Methylmethionine permease, MmuP 94% 892.9
med BWI76_RS19685 lysine transporter Amino-acid permease RocE (characterized) 40% 97% 379 lysine-specific permease 93% 934.5
lo BWI76_RS04870 aromatic amino acid transporter AroP Amino-acid permease RocE (characterized) 36% 95% 308.1 Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan 94% 864.4
lo BWI76_RS06245 proline-specific permease ProY Amino-acid permease RocE (characterized) 35% 98% 305.8 Proline-specific permease (ProY) 95% 876.7
lo BWI76_RS07360 phenylalanine transporter arginine permease (characterized) 35% 81% 271.6 Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs 89% 818.5

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 rocE

Or cluster all characterized rocE 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, 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