Finding step pre-dehydr for L-tyrosine biosynthesis in Desulfarculus baarsii DSM 2075
2 candidates for pre-dehydr: prephenate dehydrogenase
Confidence: high confidence medium confidence low confidence
? – known gap: despite the lack of a good candidate for this step, this organism (or a related organism) performs the pathway
GapMind searches the predicted proteins for candidates by using ublast (a fast alternative to protein BLAST) to find similarities to characterized proteins or by using HMMer to find similarities to enzyme models (usually from TIGRFams). For alignments to characterized proteins (from ublast), scores of 44 bits correspond to an expectation value (E) of about 0.001.
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