GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Pseudomonas simiae WCS417

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 (20 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase PS417_21655
asd aspartate semi-aldehyde dehydrogenase PS417_18580 PS417_18575
dapA 4-hydroxy-tetrahydrodipicolinate synthase PS417_07165 PS417_14640
dapB 4-hydroxy-tetrahydrodipicolinate reductase PS417_24050
dapD tetrahydrodipicolinate succinylase PS417_06180
dapC N-succinyldiaminopimelate aminotransferase PS417_06195 PS417_21710
dapE succinyl-diaminopimelate desuccinylase PS417_06155 PS417_18910
dapF diaminopimelate epimerase PS417_27585 PS417_15365
lysA diaminopimelate decarboxylase PS417_27580
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase PS417_25075 PS417_08205
dapL N-acetyl-diaminopimelate deacetylase PS417_19495
DAPtransferase L,L-diaminopimelate aminotransferase PS417_21975 PS417_13545
dapX acetyl-diaminopimelate aminotransferase PS417_19025 PS417_13545
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase
hicdh homo-isocitrate dehydrogenase PS417_16525 PS417_18585
lysJ [LysW]-2-aminoadipate semialdehyde transaminase PS417_21710 PS417_08025
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase PS417_23355 PS417_19025
lysT homoaconitase large subunit PS417_18600 PS417_09410
lysU homoaconitase small subunit PS417_18595 PS417_09415
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase PS417_25660
lysZ [LysW]-2-aminoadipate 6-kinase PS417_27790

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.



Related tools

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