GapMind for Amino acid biosynthesis

 

Finding step tyrB for L-tyrosine biosynthesis in Rhodomicrobium vannielii ATCC 17100

5 candidates for tyrB: tyrosine aminotransferase

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
hi RVAN_RS06420 pyridoxal phosphate-dependent aminotransferase Aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.79 (characterized) 71% 100% 575.5
med RVAN_RS16195 LL-diaminopimelate aminotransferase aspartate transaminase (EC 2.6.1.1) (characterized) 42% 94% 326.2 alanine-glyoxylate transaminase (EC 2.6.1.44) 53% 417.9
lo RVAN_RS15315 histidinol-phosphate transaminase Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized) 40% 97% 246.1 histidinol-phosphate aminotransferase [EC:2.6.1.9] 53% 379.0
lo RVAN_RS01125 branched-chain amino acid aminotransferase branched-chain-amino-acid aminotransferase; EC 2.6.1.42 (characterized) 39% 96% 196.4 Branched-chain amino acid aminotransferase (EC 2.6.1.42) 43% 235.0
lo RVAN_RS11970 aspartate aminotransferase family protein Beta-phenylalanine transaminase; Aromatic beta-amino acid aminotransferase; Beta-phenylalanine aminotransferase; VpAT; EC 2.6.1.- (characterized) 32% 68% 112.8 acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] 63% 480.3

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 tyrB

Or cluster all characterized tyrB proteins

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:

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:

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