Annotation: NCBI__GCF_000225705.1:WP_009140725.1
Length: 386 amino acids
Source: GCF_000225705.1 in NCBI
Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
---|---|---|---|---|---|---|---|---|---|
L-fucose catabolism | fucO | lo | L-lactaldehyde reductase (EC 1.1.1.77) (characterized) | 37% | 99% | 226.5 | methanol dehydrogenase (EC 1.1.1.244) | 39% | 233.0 |
L-rhamnose catabolism | fucO | lo | L-lactaldehyde reductase (EC 1.1.1.77) (characterized) | 37% | 99% | 226.5 | methanol dehydrogenase (EC 1.1.1.244) | 39% | 233.0 |
L-threonine catabolism | tdh | lo | L-threonine dehydrogenase (EC 1.1.1.103) (characterized) | 37% | 100% | 226.5 | methanol dehydrogenase (EC 1.1.1.244) | 39% | 233.0 |
glycerol catabolism | dhaD | lo | alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized) | 33% | 93% | 195.3 | methanol dehydrogenase (EC 1.1.1.244) | 39% | 233.0 |
View WP_009140725.1 at NCBI
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Predict transmenbrane helices: Phobius
Predict protein localization: PSORTb
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MASIEARSFLMPGKIVYGEGALGQAAPSMAQMGEKALIVTDAMMVKLGNLARLTQALEGE GIGFSVYDGINSEPVDKMVEEGVRRFKDDGCDFMVALGGGSPIDTMKAIAMCAASGEKIA AFMGRPYCGPVCPMVAIPTTAGTGSEATQFTIITDTENDVKMLISGAPLIPALAIVDPVF TLTAPASVTAATGVDALCHAIEAYTSRKAQPLSQVFALSAAKRIFANLDVCVEEPDNIEA RTQMSLAATEAGVAFNNASVTLIHGMSRPIGAVFHVPHGLSNAMLMKVCFDFALDGAYDR FAEVARACGLSASDDDAAAARGLMEGIDDLLTRIKIPTLVEFGVDSDAFTAAIDKMAADA EASGSPANTIKPVSQGDMRAMYRSLI
This GapMind analysis is from Sep 24 2021. 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