GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Desulfovibrio vulgaris Miyazaki F

Best path

asp-kinase, asd, dapA, dapB, DAPtransferase, dapF, lysA

Also see fitness data for the top candidates

Rules

Overview: Lysine biosynthesis in GapMind is based on MetaCyc pathways L-lysine biosynthesis I via diaminopimelate (DAP) and succinylated intermediates (link), II with DAP and acetylated intermediates (link), III with DAP and no blocking group (link), V via 2-aminoadipate and LysW carrier protein (link), and VI with DAP aminotransferase (link). Most of these pathways involve tetrahydrodipicolinate and meso-diaminopimelate, with variations in how the amino group is introduced. Pathway V instead involves L-2-aminoadipate and LysW-attached intermediates. Lysine biosynthesis IV (link), via 2-aminoadipate and saccharopine, is only reported to occur in eukaryotes and is not described here.

25 steps (20 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase DvMF_0276
asd aspartate semi-aldehyde dehydrogenase DvMF_2382
dapA 4-hydroxy-tetrahydrodipicolinate synthase DvMF_0562
dapB 4-hydroxy-tetrahydrodipicolinate reductase DvMF_0450
DAPtransferase L,L-diaminopimelate aminotransferase DvMF_0361 DvMF_1411
dapF diaminopimelate epimerase DvMF_0561
lysA diaminopimelate decarboxylase DvMF_0353 DvMF_1010
Alternative steps:
dapC N-succinyldiaminopimelate aminotransferase DvMF_3149 DvMF_1715
dapD tetrahydrodipicolinate succinylase DvMF_0674
dapE succinyl-diaminopimelate desuccinylase
dapH tetrahydrodipicolinate acetyltransferase DvMF_1901 DvMF_1896
dapL N-acetyl-diaminopimelate deacetylase DvMF_1012
dapX acetyl-diaminopimelate aminotransferase DvMF_2204 DvMF_1564
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase DvMF_1791 DvMF_2612
hicdh homo-isocitrate dehydrogenase DvMF_1739 DvMF_1794
lysJ [LysW]-2-aminoadipate semialdehyde transaminase / [LysW]-glutamate semialdehyde transaminase DvMF_3149 DvMF_0516
lysK [LysW]-lysine hydrolase / [LysW]-ornithine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase DvMF_3003 DvMF_2204
lysT homoaconitase large subunit DvMF_1792 DvMF_3021
lysU homoaconitase small subunit DvMF_1793 DvMF_3021
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase / [LysW]-glutamylphosphate reductase DvMF_1717
lysZ [LysW]-2-aminoadipate 6-kinase / [LysW]-glutamate kinase DvMF_0306

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 Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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