GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Pseudomonas fluorescens GW456-L13

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 PfGW456L13_1981
asd aspartate semi-aldehyde dehydrogenase PfGW456L13_3944 PfGW456L13_3943
dapA 4-hydroxy-tetrahydrodipicolinate synthase PfGW456L13_3142 PfGW456L13_4507
dapB 4-hydroxy-tetrahydrodipicolinate reductase PfGW456L13_5101
dapD tetrahydrodipicolinate succinylase PfGW456L13_4716
dapC N-succinyldiaminopimelate aminotransferase PfGW456L13_4713 PfGW456L13_1971
dapE succinyl-diaminopimelate desuccinylase PfGW456L13_4721
dapF diaminopimelate epimerase PfGW456L13_844 PfGW456L13_2444
lysA diaminopimelate decarboxylase PfGW456L13_845 PfGW456L13_5067
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase PfGW456L13_4374 PfGW456L13_4875
dapL N-acetyl-diaminopimelate deacetylase
DAPtransferase L,L-diaminopimelate aminotransferase PfGW456L13_1928 PfGW456L13_3206
dapX acetyl-diaminopimelate aminotransferase PfGW456L13_3206 PfGW456L13_2943
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase PfGW456L13_2506
hicdh homo-isocitrate dehydrogenase PfGW456L13_2643 PfGW456L13_3945
lysJ [LysW]-2-aminoadipate semialdehyde transaminase PfGW456L13_1971 PfGW456L13_4910
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase PfGW456L13_4982 PfGW456L13_494
lysT homoaconitase large subunit PfGW456L13_3948 PfGW456L13_3592
lysU homoaconitase small subunit PfGW456L13_3947 PfGW456L13_3593
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase PfGW456L13_1233
lysZ [LysW]-2-aminoadipate 6-kinase PfGW456L13_793

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