Annotation: NCBI__GCF_000319285.1:WP_007671746.1
Length: 281 amino acids
Source: GCF_000319285.1 in NCBI
Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
---|---|---|---|---|---|---|---|---|---|
trehalose catabolism | thuG | lo | ABC-type transporter, integral membrane subunit, component of Trehalose porter. Also binds sucrose (Boucher and Noll, 2011). Induced by glucose and trehalose. Directly regulated by trehalose-responsive regulator TreR (characterized) | 33% | 96% | 133.7 | ABC-type glycerol 3-phosphate transporter (EC 7.6.2.10) | 88% | 493.4 |
lactose catabolism | lacG | lo | ABC transporter for Lactose, permease component 2 (characterized) | 30% | 96% | 122.9 | ABC-type glycerol 3-phosphate transporter (EC 7.6.2.10) | 88% | 493.4 |
View WP_007671746.1 at NCBI
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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
Fitness BLAST: loading...
MIENRRGLTIFSHTILILGIAAILFPLYVAFVAATLDNEAVFATPMTLIPGTHLWENLKN IWVNGVGANSAPFWLMLLNSFIMAFSITVGKIAVSMLSAFAIVWFRFPLRNLFFWMIFIT LMLPVEVRIFPTVDVIANLKLMDSYTGLTLPLMASATATFLFRQFFMTLPDELMEAARID GASPMRFFRDIVLPLSKTNLAALFVITFIYGWNQYLWPLLIVSDPALGTAVAGIKGMISV GEGSTQWNQVMAAMLLTLIPPVVIVLVMQRAFVRGLVDSEK
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