Annotation: NCBI__GCF_000152985.1:WP_009779318.1
Length: 538 amino acids
Source: GCF_000152985.1 in NCBI
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|---|---|---|---|---|---|---|---|---|
| D-galacturonate catabolism | uxaA | hi | Altronate dehydratase (EC 4.2.1.7) (characterized) | 54% | 100% | 607.8 | D-arabinoate dehydratase (EC 4.2.1.5); also involved in L-fucose catabolism | 40% | 239.2 |
| D-galacturonate catabolism | garD | lo | Galactarate dehydratase (EC 4.2.1.42) (characterized) | 36% | 68% | 209.1 | Altronate dehydratase (EC 4.2.1.7) | 54% | 607.8 |
| L-fucose catabolism | fucD | lo | L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized) | 32% | 75% | 155.2 | Altronate dehydratase (EC 4.2.1.7) | 54% | 607.8 |
| L-rhamnose catabolism | LRA3 | lo | L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized) | 32% | 75% | 155.2 | Altronate dehydratase (EC 4.2.1.7) | 54% | 607.8 |
View WP_009779318.1 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
Fitness BLAST: loading...
MKSKLIKVHPDDNVAVALVDLFAGDVVEFEGQSLKILTDSKAKHKIALVNLKADDPIFMY GVLVGKALSAIDVGGLLTTENVKHEANSVSQKTETTSWTAPDISKWKDRTFMGYHREDGQ VGTQNVWLFFPLVFCENRNIELLKDVFEKELSFHKASKQRQLLRNLINGAPEDTAVAEIE EEQAIFDNIEVKFITHQGGCGGIRQDSVSLSKLLAGYVNNPNVAGATVLSLGCQNLQIDI FKNALAEKSAAIKKPVLIYEQQQEGTVDEMLAKIIKDSFEGIKKANQIKRQPAPISKLKM GLECGGSDGFSGISANPALGYASDILAAVGGSPILSEFPELCGVEQELVNRCVSDEDAER FMHLMKAYEKSAVDAGSGFDMNPSPGNIKDGLITDAMKSAGAAKKGGTSPIQAILDYGEY VTKPGLNLLCTPGNDVESTTAMVGSGASVVVFTTGLGTPTGNPIAPVLKVASNSTLARRM PDIIDIDSGAVIRGEKTIEEMGEEILEHVIQVASGEVQSKADALGQDDFIPWKRGVSL
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