GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Marinobacter adhaerens HP15

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 HP15_1320 HP15_3856
asd aspartate semi-aldehyde dehydrogenase HP15_1831
dapA 4-hydroxy-tetrahydrodipicolinate synthase HP15_2027
dapB 4-hydroxy-tetrahydrodipicolinate reductase HP15_3079
dapD tetrahydrodipicolinate succinylase HP15_1160
dapC N-succinyldiaminopimelate aminotransferase HP15_1162 HP15_1361
dapE succinyl-diaminopimelate desuccinylase HP15_1159
dapF diaminopimelate epimerase HP15_248
lysA diaminopimelate decarboxylase HP15_247
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase
dapL N-acetyl-diaminopimelate deacetylase
DAPtransferase L,L-diaminopimelate aminotransferase HP15_1371 HP15_814
dapX acetyl-diaminopimelate aminotransferase HP15_1371 HP15_814
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase HP15_538
hicdh homo-isocitrate dehydrogenase HP15_1832 HP15_817
lysJ [LysW]-2-aminoadipate semialdehyde transaminase HP15_3042 HP15_3708
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase HP15_1371 HP15_3708
lysT homoaconitase large subunit HP15_1834 HP15_2599
lysU homoaconitase small subunit HP15_2598 HP15_1833
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase HP15_352
lysZ [LysW]-2-aminoadipate 6-kinase HP15_3317

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