L-tyrosine biosynthesis
Analysis of pathway tyr in 35 genomes
| Genome | Best path |
|---|
| Acidovorax sp. GW101-3H11 | cmutase, pre-dehydr, tyrB |
| Azospirillum brasilense Sp245 | cmutase, pre-dehydr, tyrB |
| Bacteroides thetaiotaomicron VPI-5482 | cmutase, pre-dehydr, tyrB |
| Burkholderia phytofirmans PsJN | cmutase, pre-dehydr, tyrB |
| Caulobacter crescentus NA1000 | cmutase, pre-dehydr, tyrB |
| Cupriavidus basilensis 4G11 | cmutase, pre-dehydr, tyrB |
| Dechlorosoma suillum PS | cmutase, pre-dehydr, tyrB |
| Desulfovibrio vulgaris Hildenborough | cmutase, pre-dehydr, tyrB |
| Desulfovibrio vulgaris Miyazaki F | cmutase, pre-dehydr, tyrB |
| Dinoroseobacter shibae DFL-12 | cmutase, pre-dehydr, tyrB |
| Dyella japonica UNC79MFTsu3.2 | PAH |
| Echinicola vietnamensis KMM 6221, DSM 17526 | PAH |
| Escherichia coli BW25113 | cmutase, pre-dehydr, tyrB |
| Herbaspirillum seropedicae SmR1 | cmutase, pre-dehydr, tyrB |
| Klebsiella michiganensis M5al | cmutase, pre-dehydr, tyrB |
| Magnetospirillum magneticum AMB-1 | cmutase, pre-dehydr, tyrB |
| Marinobacter adhaerens HP15 | cmutase, pre-dehydr, tyrB |
| Paraburkholderia bryophila 376MFSha3.1 | cmutase, pre-dehydr, tyrB |
| Pedobacter sp. GW460-11-11-14-LB5 | cmutase, pre-dehydr, tyrB |
| Phaeobacter inhibens BS107 | cmutase, pre-dehydr, tyrB |
| Pseudomonas fluorescens FW300-N1B4 | cmutase, pre-dehydr, tyrB |
| Pseudomonas fluorescens FW300-N2C3 | cmutase, pre-dehydr, tyrB |
| Pseudomonas fluorescens FW300-N2E2 | cmutase, pre-dehydr, tyrB |
| Pseudomonas fluorescens FW300-N2E3 | cmutase, pre-dehydr, tyrB |
| Pseudomonas fluorescens GW456-L13 | cmutase, pre-dehydr, tyrB |
| Pseudomonas putida KT2440 | cmutase, pre-dehydr, tyrB |
| Pseudomonas simiae WCS417 | cmutase, pre-dehydr, tyrB |
| Pseudomonas stutzeri RCH2 | cmutase, pre-dehydr, tyrB |
| Shewanella amazonensis SB2B | cmutase, pre-dehydr, tyrB |
| Shewanella loihica PV-4 | cmutase, pre-dehydr, tyrB |
| Shewanella oneidensis MR-1 | cmutase, pre-dehydr, tyrB |
| Shewanella sp. ANA-3 | cmutase, pre-dehydr, tyrB |
| Sinorhizobium meliloti 1021 | cmutase, pre-dehydr, tyrB |
| Sphingomonas koreensis DSMZ 15582 | cmutase, pre-dehydr, tyrB |
| Synechococcus elongatus PCC 7942 | cmutase, ptransferase, aro-dehydr |
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
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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