Annotation: NCBI__GCF_000010525.1:WP_012173137.1
Length: 309 amino acids
Source: GCF_000010525.1 in NCBI
Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
---|---|---|---|---|---|---|---|---|---|
L-tyrosine biosynthesis | pre-dehydr | hi | Cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase (characterized, see rationale) | 66% | 98% | 399.4 | |||
L-tyrosine biosynthesis | aro-dehydr | hi | Cyclohexadienyl dehydrogenase; Arogenate dehydrogenase; ADH; Prephenate dehydrogenase; PDH; EC 1.3.1.43; EC 1.3.1.12 (characterized) | 44% | 96% | 243.4 | |||
L-proline biosynthesis | proC | lo | Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized) | 31% | 65% | 63.5 | prephenate dehydrogenase (EC 1.3.1.12) | 65% | 325.9 |
View WP_012173137.1 at NCBI
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Find functional residues: SitesBLAST
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Predict transmenbrane helices: Phobius
Predict protein localization: PSORTb
Find homologs in fast.genomics
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MSAPLVGRLAIIGAGLIGSSVARAVREKGLAGTVVVADRDAGVRARVRELGFADEVPETA AEAVADADIVIVCVPVGASGAVAAEIGPALKPGAILSDVGSVKAAVVEQMAPHVPAHAHL VPAHPVAGTEFSGPDAGFASLFENRWCIVTPVADADPAAVERLSVLWSGMGANVETMSPQ HHDLVLAITSHLPHLIAYNIVGTAADLEQTLTSEVIKFSAGGFRDFTRIAASDPTMWRDV FLYNREAVLEMLGRFTEDLTALQRAIRYGDGQTLFDHFTRTRAIRRSIIEQGQETAAPDF GRHLVAAKK
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.
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