GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Dyella japonica UNC79MFTsu3.2

Best path

asp-kinase, asd, dapA, dapB, dapD, dapC, dapE, dapF, lysA

Also see fitness data for the top candidates


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 (19 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase N515DRAFT_4002
asd aspartate semi-aldehyde dehydrogenase N515DRAFT_0109
dapA 4-hydroxy-tetrahydrodipicolinate synthase N515DRAFT_1147 N515DRAFT_0955
dapB 4-hydroxy-tetrahydrodipicolinate reductase N515DRAFT_2721 N515DRAFT_2152
dapD tetrahydrodipicolinate succinylase N515DRAFT_0740
dapC N-succinyldiaminopimelate aminotransferase N515DRAFT_1430 N515DRAFT_3308
dapE succinyl-diaminopimelate desuccinylase N515DRAFT_0745 N515DRAFT_3767
dapF diaminopimelate epimerase N515DRAFT_3112
lysA diaminopimelate decarboxylase N515DRAFT_4002 N515DRAFT_2124
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase N515DRAFT_0740 N515DRAFT_4259
dapL N-acetyl-diaminopimelate deacetylase N515DRAFT_3530
DAPtransferase L,L-diaminopimelate aminotransferase
dapX acetyl-diaminopimelate aminotransferase N515DRAFT_1410
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase N515DRAFT_0574
hicdh homo-isocitrate dehydrogenase N515DRAFT_1138 N515DRAFT_0570
lysJ [LysW]-2-aminoadipate semialdehyde transaminase N515DRAFT_3308 N515DRAFT_3307
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase N515DRAFT_0006 N515DRAFT_3308
lysT homoaconitase large subunit N515DRAFT_0572
lysU homoaconitase small subunit N515DRAFT_0571 N515DRAFT_1419
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase N515DRAFT_3769
lysZ [LysW]-2-aminoadipate 6-kinase

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:

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