Annotation: NCBI__GCF_001484605.1:WP_240484381.1
Length: 473 amino acids
Source: GCF_001484605.1 in NCBI
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|---|---|---|---|---|---|---|---|---|
| L-arginine catabolism | rocE | med | Amino-acid permease RocE (characterized) | 52% | 95% | 485 | S-Methylmethionine permease, MmuP | 56% | 545.8 |
| L-lysine catabolism | lysP | med | lysine-specific permease (characterized) | 43% | 93% | 365.2 | S-Methylmethionine permease, MmuP | 56% | 545.8 |
| L-histidine catabolism | permease | lo | histidine permease (characterized) | 38% | 93% | 320.5 | S-Methylmethionine permease, MmuP | 56% | 545.8 |
| L-tryptophan catabolism | TAT | lo | tryptophan permease (characterized) | 33% | 77% | 233.4 | S-Methylmethionine permease, MmuP | 56% | 545.8 |
| L-isoleucine catabolism | Bap2 | lo | Leu/Val/Ile amino-acid permease; Branched-chain amino-acid permease 2 (characterized) | 30% | 67% | 207.2 | S-Methylmethionine permease, MmuP | 56% | 545.8 |
| L-valine catabolism | Bap2 | lo | Leu/Val/Ile amino-acid permease; Branched-chain amino-acid permease 2 (characterized) | 30% | 67% | 207.2 | S-Methylmethionine permease, MmuP | 56% | 545.8 |
View WP_240484381.1 at NCBI
Find papers: PaperBLAST
Find functional residues: SitesBLAST
Search for conserved domains
Find the best match in UniProt
Compare to protein structures
Predict transmenbrane helices: Phobius
Predict protein localization: PSORTb
Find homologs in fast.genomics
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MTLDATPAGHAPVQPGLRRSMGTRHLVMIAMGGVIGSGLFLSSGYTISQAGPLGAVLAYL VGAFVVYLVMACLGELAIAYPVSGAFHIYAARSIGPATGFATAWLYWLCWAVAIGSEFTA SGLLMQRWFPDVDVWIWCLIFAAVLFGFNAVSARFFGESEFWFAIIKVGAIIGLIVLGGA ALFGFRPLSDGGSHPFLFENFNTAGGLFPNGFTGVLVTVLAVFYAFSGSELIGVAAGETK DPATSIPKAMRTTVIRLLIFFVGAIAVIAATIPYNEVGLDESPFVTVFSAIGIPFAADIM NFVIITALLSAGNSGLFSCARMLYSLADEGHAPQAFRRLTRRGIPLIALSVSMVGGIASL ISSVVAPETVYLVLVSVAGFAVVGVWMSITASHFFHRRAFVRNGGDVGALAYKAPLFPLV PILAFTLCVISLVGIALDPNQVAALYFGIPFVAACYVYFYFRHGRKRPTAAVQ
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
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:
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:
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