Annotation: NCBI__GCF_003010955.1:WP_106709989.1
Length: 255 amino acids
Source: GCF_003010955.1 in NCBI
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|---|---|---|---|---|---|---|---|---|
| L-fucose catabolism | fucDH | lo | Short-chain dehydrogenase/reductase SDR (characterized, see rationale) | 39% | 100% | 164.9 | 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase LinX; 2,5-DDOL dehydrogenase; EC 1.1.1.- | 41% | 188.0 |
| D-xylose catabolism | DKDP-dehydrog | lo | SDR family oxidoreductase (characterized, see rationale) | 36% | 98% | 152.9 | 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase LinX; 2,5-DDOL dehydrogenase; EC 1.1.1.- | 41% | 188.0 |
| L-rhamnose catabolism | LRA1 | lo | L-rhamnose-1-dehydrogenase ( EC 1.1.1.173) (characterized) | 38% | 97% | 141 | 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase LinX; 2,5-DDOL dehydrogenase; EC 1.1.1.- | 41% | 188.0 |
| L-fucose catabolism | fdh | lo | Short-chain dehydrogenase (characterized, see rationale) | 31% | 97% | 98.2 | 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase LinX; 2,5-DDOL dehydrogenase; EC 1.1.1.- | 41% | 188.0 |
View WP_106709989.1 at NCBI
Find papers: PaperBLAST
Find functional residues: SitesBLAST
Search for conserved domains
Find the best match in UniProt
Compare to protein structures
Predict transmenbrane helices: Phobius
Predict protein localization: PSORTb
Find homologs in fast.genomics
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MAGRLAGKVAIVSGGATGMGGAASKLFAAEGAKVAIVDRNEQAAAATVAEIEAVGGVAAY FVADVSDEVQVQKAVAGTAQKFGNVTVLFNHAGTIVIKPFLETTLEEWDWLHAVNVRSMY LMTRAVIPQMLDAGGGSIVCTSSISAVAATPMEVLYDTTKGACHMFARAIAVEFRDRNIR CNAVCPGFIRTPHGLREVDELQKRGVDVSDEAMTAAQGRIGEPEEVARAALFLASDEASF ITGTHLFVDNGFTAI
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