GapMind for Amino acid biosynthesis

 

Finding step dapE for L-lysine biosynthesis in Haloglycomyces albus DSM 45210

5 candidates for dapE: succinyl-diaminopimelate desuccinylase

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
hi HALAL_RS0100600 succinyl-diaminopimelate desuccinylase succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) (characterized) 55% 98% 384.8
hi HALAL_RS0100600 succinyl-diaminopimelate desuccinylase dapE: succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) (TIGR01900) 99% 499.8
lo HALAL_RS0104400 amidohydrolase Predicted dapE by GapMind curators (no experimental data) 35% 97% 225.3 N-acyl-aliphatic-L-amino acid amidohydrolase (EC 3.5.1.14) 39% 250.8
lo HALAL_RS0106245 M20 family metallopeptidase Predicted dapE by GapMind curators (no experimental data) 33% 96% 194.1 N-acyl-aliphatic-L-amino acid amidohydrolase (EC 3.5.1.14) 36% 225.3
lo HALAL_RS0114865 M20/M25/M40 family metallo-hydrolase Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized) 30% 55% 79.3 N-acyl-aliphatic-L-amino acid amidohydrolase (EC 3.5.1.14) 56% 483.0
lo HALAL_RS0101215 dipeptidase Succinyl-diaminopimelate desuccinylase 2; SDAP desuccinylase 2; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase 2 (uncharacterized) 32% 50% 79.3 Cysteinylglycine-S-conjugate dipeptidase; Thiol precursor dipeptidase; EC 3.4.13.23 35% 250.0

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 dapE

Or cluster all characterized dapE 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:

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