Annotation: NCBI__GCF_001971705.1:WP_168170946.1
Length: 290 amino acids
Source: GCF_001971705.1 in NCBI
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|---|---|---|---|---|---|---|---|---|
| L-valine catabolism | mmsB | lo | 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) (characterized) | 38% | 91% | 169.9 | 2-(hydroxymethyl)glutarate dehydrogenase; EC 1.1.1.291 | 38% | 184.1 |
| D-glucuronate catabolism | garR | lo | 2-hydroxy-3-oxopropionate reductase; EC 1.1.1.60; Tartronate semialdehyde reductase; TSAR (uncharacterized) | 37% | 84% | 138.3 | 2-(hydroxymethyl)glutarate dehydrogenase; EC 1.1.1.291 | 38% | 184.1 |
| D-gluconate catabolism | gnd | lo | phosphogluconate dehydrogenase (NAD+-dependent, decarboxylating) (EC 1.1.1.343) (characterized) | 33% | 63% | 92.8 | 2-(hydroxymethyl)glutarate dehydrogenase; EC 1.1.1.291 | 38% | 184.1 |
View WP_168170946.1 at NCBI
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Find functional residues: SitesBLAST
Search for conserved domains
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Predict transmenbrane helices: Phobius
Predict protein localization: PSORTb
Find homologs in fast.genomics
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MSSLGFIGLGSMGGPMAKNLVSADHDLTAYDLDDDALEAISDAGATAATSTADAVEGAEV VFLSLPGPDNVAAVVDEIEADLEAGSILVDLTTSTPGTTEAIANRLADRDIDVLGAPVSG GSSGADAGTLSIIVGGDEAVFEACEPLFEVIGSDVFHVGDGVGHGHAVKLLNNYLSNIAL LATSEAVILGDAAGLDRQTLVDVFSVSSGRNSANQDKIPNYVLTGEYDMGFKIGLMEKDM RLLSEFAGEQQVPMLLGHLTRDLAGYAKTKKGFDSDMTRVYDFLEEFMLE
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