Annotation: NCBI__GCF_001580365.1:WP_062736059.1
Length: 377 amino acids
Source: GCF_001580365.1 in NCBI
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|---|---|---|---|---|---|---|---|---|
| D-galacturonate catabolism | garD | hi | L-talarate dehydratase (EC 4.2.1.156); galactarate dehydratase (EC 4.2.1.42) (characterized) | 66% | 93% | 513.1 | dehydratase involved in L-fucose catabolism | 37% | 235.3 |
| D-galactose catabolism | dgoD | lo | galactonate dehydratase [EC: 4.2.1.6] (characterized) | 30% | 88% | 127.9 | L-talarate dehydratase (EC 4.2.1.156); galactarate dehydratase (EC 4.2.1.42) | 66% | 513.1 |
| lactose catabolism | dgoD | lo | galactonate dehydratase [EC: 4.2.1.6] (characterized) | 30% | 88% | 127.9 | L-talarate dehydratase (EC 4.2.1.156); galactarate dehydratase (EC 4.2.1.42) | 66% | 513.1 |
| L-fucose catabolism | fucD | lo | L-fuconate dehydratase; FucD; EC 4.2.1.68 (characterized) | 33% | 57% | 118.6 | L-talarate dehydratase (EC 4.2.1.156); galactarate dehydratase (EC 4.2.1.42) | 66% | 513.1 |
View WP_062736059.1 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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MTYTPDAVRHLQLSTVTLPLSTPISDAKVFTGRQRPMTEVVFLVAEITTEQGHSGVGFSY SKRAGGPAQYAHAKEVAEGLIGEDPSDIAKVYDKLLWAGASVGRSGVATQALAAIDVALW DLKAKRAGLPLAKLLGAHRDSVRTYNTSGGFLQASLEEVKDRATASLEAGIGGIKIKVGL PDSAEDLRRVAGVREHIGAGVPLMVDANQQWDRATALRMGRRLEEFDLTWIEEPLDAYDA EGHARLTAALDTPIATGEMLASVAEHVRLIEARSCDIIQPDAPRVGGITQFLRLAALADQ RGLDLAPHFAMEIHLHLAAAYPREPWVEHFDWLDPLFEERLETRDGRMLVPSRPGLGITL SEQARAWTTDSAGFGTA
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