Annotation: NCBI__GCF_000559025.1:WP_024888811.1
Length: 255 amino acids
Source: GCF_000559025.1 in NCBI
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|---|---|---|---|---|---|---|---|---|
| L-fucose catabolism | fucDH | lo | Short-chain alcohol dehydrogenase protein (characterized, see rationale) | 34% | 100% | 129.8 | N-acylmannosamine 1-dehydrogenase (EC 1.1.1.233) | 38% | 159.1 |
| D-xylose catabolism | DKDP-dehydrog | lo | SDR family oxidoreductase (characterized, see rationale) | 33% | 100% | 128.3 | N-acylmannosamine 1-dehydrogenase (EC 1.1.1.233) | 38% | 159.1 |
| D-sorbitol (glucitol) catabolism | srlD | lo | Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized) | 32% | 96% | 117.9 | N-acylmannosamine 1-dehydrogenase (EC 1.1.1.233) | 38% | 159.1 |
| L-isoleucine catabolism | ivdG | lo | GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized) | 30% | 99% | 100.5 | N-acylmannosamine 1-dehydrogenase (EC 1.1.1.233) | 38% | 159.1 |
View WP_024888811.1 at NCBI
Find papers: PaperBLAST
Find functional residues: SitesBLAST
Search for conserved domains
Find the best match in UniProt
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Predict transmenbrane helices: Phobius
Predict protein localization: PSORTb
Find homologs in fast.genomics
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MSDASMPSQAAPFAGRVAIVTGAASGIGRATVELLHRQGARIVAVGRGGNVEALARDGIV PVVADVAQETSAALAVETALERFGRLDILVNNAGIIINRPVAEMSLEEWNRVLAVNATGA FLFSRAAMRPMMAAGSGAIVNIGSYACYQSFAGIAAYAASKGALAQLTRTLALEAIGHGI RVNAVGSGDAVTNITNAIQPDGQAYLAQHGRKAPIGRAARPEEIAEVAAFLASDKASYIV GAVVMADGGMSVAIP
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