Annotation: NCBI__GCF_000010725.1:WP_012976505.1
Length: 176 amino acids
Source: GCF_000010725.1 in NCBI
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|---|---|---|---|---|---|---|---|---|
| L-arabinose catabolism | aldox-small | med | glycolaldehyde oxidoreductase small subunit (characterized) | 48% | 90% | 154.1 | NdhB (EC 1.5.99.4) | 56% | 177.9 |
| D-xylose catabolism | aldox-small | med | glycolaldehyde oxidoreductase small subunit (characterized) | 48% | 90% | 154.1 | NdhB (EC 1.5.99.4) | 56% | 177.9 |
| 4-hydroxybenzoate catabolism | hcrC | med | 4-hydroxybenzoyl-CoA reductase HbaB subunit (EC 1.3.7.9) (characterized) | 50% | 90% | 147.5 | NdhB (EC 1.5.99.4) | 56% | 177.9 |
| 2-deoxy-D-ribose catabolism | drdehyd-alpha | lo | 2-deoxy-D-ribose dehydrogenase α subunit (characterized) | 36% | 83% | 84.7 | NdhB (EC 1.5.99.4) | 56% | 177.9 |
View WP_012976505.1 at NCBI
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MPPLKSTSALTAETRHAVSIVLNGKPRTGHAHPRLLLSDFLRHELGAHGTRVGCEHGVCG ACTVRIDGVAARACLTLAVQADGRRIDTVEGLAETNEGRMTALQEAFRRHHALQCGFCTA GILMSLTDYLGRNPKPTEEELRDMLSGHLCRCTGYAGIVRAVMEVTGQTMKEVSHV
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