Annotation: FitnessBrowser__azobra:AZOBR_RS25335
Length: 365 amino acids
Source: azobra in FitnessBrowser
Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
---|---|---|---|---|---|---|---|---|---|
L-fucose catabolism | SM_b21106 | med | ABC transporter for L-Fucose, ATPase component (characterized) | 43% | 97% | 266.5 | MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] | 46% | 258.1 |
sucrose catabolism | thuK | med | ABC transporter (characterized, see rationale) | 41% | 98% | 256.5 | ABC transporter for L-Fucose, ATPase component | 43% | 266.5 |
xylitol catabolism | HSERO_RS17020 | med | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 43% | 85% | 253.4 | ABC transporter for L-Fucose, ATPase component | 43% | 266.5 |
View AZOBR_RS25335 at FitnessBrowser
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Find functional residues: SitesBLAST
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Predict transmenbrane helices: Phobius
Predict protein localization: PSORTb
Find homologs in fast.genomics
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MSAPQTLVPLALDRLAKRYGTAPPALAALSLEVAGGELLGLVGPSGCGKTTALRLIAGLT PASGGRVLVGGRDITALPAHARGIGLVFQNYALFPHMTAADNVAFGLRMRGLPAAERHAR TAEALAMVRLSHLGGRKPRALSGGQQQRVALARALAIRPNLLLLDEPLSNLDAGLRAELL AEIRTLQRRLGITALFVTHDQGEALAVCDRIAVLRDGRLEQVGTPREVHDRPASGFVAGF VGRTNRIPAERLAGGALRVGGTLLPALADGPAGPVDLFVRPHRIRVGAAGGAGGLPAVLR GTAFLGDRIALSLEAGGAPVTVDWPVEAAPPAPGPALTPGETVALSWDPADMAVFAATRP ADAPP
This GapMind analysis is from Sep 17 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