Finding step pre-dehydr for L-tyrosine biosynthesis in Thiohalospira halophila DSM 15071 HL 3
Classification of gap: spurious
Rationale: Although pre-dehydr was not found in the annotated proteins, it was found when analyzing the six-frame translation of the genome. This is often due to a missing gene call, but it could be due to an error in the genome sequence.
No candidates for pre-dehydr: prephenate dehydrogenase
GapMind classifies a step as low confidence even if it does not find any candidates. You can still try to find candidates by using Curated BLAST (which searches the 6-frame translation) or by text search of the annotations (which may indicate weak homology, under 30% identity or 50% coverage, that GapMind does not consider). See the links below.
Definition of step pre-dehydr
- Curated proteins or TIGRFams with EC 1.3.1.12 (search)
- Curated proteins or TIGRFams with EC 1.3.1.13 (search)
- UniProt sequence Q8A0T8_BACTN: SubName: Full=Chorismate mutase/prephenate dehydratase (TyrA) {ECO:0000313|EMBL:AAO79038.1};
- Curated sequence 209400: prephenate and/or arogenate dehydrogenase
- UniProt sequence D8IR44_HERSS: SubName: Full=Prephenate dehydrogenase protein {ECO:0000313|EMBL:ADJ65170.1}; EC=1.3.1.12 {ECO:0000313|EMBL:ADJ65170.1};
- UniProt sequence A0A1L6J750: SubName: Full=Prephenate dehydrogenase {ECO:0000313|EMBL:PJI88995.1};
- Ignore hits to items matching EC 1.3.1.78 when looking for 'other' hits
- Ignore hits to items matching EC 1.3.1.43 when looking for 'other' hits
- Ignore hits to items matching EC 1.3.1.78 when looking for 'other' hits
- UniProt sequence D4GXG3: SubName: Full=Prephenate dehydrogenase {ECO:0000313|EMBL:ADE03239.1}; EC=1.3.1.12 {ECO:0000313|EMBL:ADE03239.1};
- Ignore hits to P06959 when looking for 'other' hits (pyruvate dehydrogenase system (EC 1.2.1.104); prephenate dehydrogenase (EC 1.3.1.12); dihydrolipoyllysine-residue acetyltransferase (EC 2.3.1.12). pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2. dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex; EC 2.3.1.12. pyruvate dehydrogenase, E2 subunit (EC 2.3.1.12). pyruvate dehydrogenase E2 subunit (EC 2.3.1.12))
- UniProt sequence Q92MG1: SubName: Full=Cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase {ECO:0000313|EMBL:CAC47240.1};
- Predicted: UniProt sequence E1QE65: SubName: Full=Prephenate dehydrogenase {ECO:0000313|EMBL:ADK83851.1};
- Predicted: UniProt sequence A9A228: SubName: Full=Prephenate dehydrogenase {ECO:0000313|EMBL:ABX12441.1};
- Comment: prephenate dehydrogenase and arogenate dehydrogenase are difficult to distinguish. 1.3.1.12 and 1.3.1.13 vary by NAD(P)H cofactor. BT3933 (Q8A0T8_BACTN), DVU0464 (Q72EV4_DESVH), HSERO_RS18425 (D8IR44_HERSS), and Ga0059261_2298 (A0A1L6J750) are auxotrophic and have prephenate dehydrogenase domains (PF02153), but their specificity is unclear. HVO_1312 (D4GXG3) is auxotrophic for tyrosine and is probably a prephenate dehydrogenase (PMC4300041). P06959 is misannotated in BRENDA and is ignored. Ac3H11_2575 (A0A162F6L0) has auxotrophic phenotypes but its specificity is unclear. Q92MG1 was confirmed by binding tyrosine in a crystal structure (PDB:4wji). In Desulfarculus, the enzyme is a bit diverged (E1QE65), but has conserved tyrosine binding residues and is in a conserved operon with aromatic amino acid biosynthesis genes. In Nitrosopumilus maritimus, NMAR_RS02920 (A9A228) is diverged but is in a conserved operon with chorismate synthase.
Or cluster all characterized pre-dehydr proteins
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.
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About GapMind
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:
- ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
- HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.
where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").
Otherwise, a candidate is "medium confidence" if either:
- ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
- ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
- HMMer finds a hit (regardless of coverage or other bits).
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:
- our ignorance of proteins' functions,
- omissions in the gene models,
- frame-shift errors in the genome sequence, or
- the organism lacks the pathway.
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