GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Pseudomonas fluorescens FW300-N1B4

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 Pf1N1B4_3451
asd aspartate semi-aldehyde dehydrogenase Pf1N1B4_11 Pf1N1B4_10
dapA 4-hydroxy-tetrahydrodipicolinate synthase Pf1N1B4_3332 Pf1N1B4_5813
dapB 4-hydroxy-tetrahydrodipicolinate reductase Pf1N1B4_1174
dapD tetrahydrodipicolinate succinylase Pf1N1B4_3077
dapC N-succinyldiaminopimelate aminotransferase Pf1N1B4_3080 Pf1N1B4_3440
dapE succinyl-diaminopimelate desuccinylase Pf1N1B4_3071
dapF diaminopimelate epimerase Pf1N1B4_2173
lysA diaminopimelate decarboxylase Pf1N1B4_2174
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase Pf1N1B4_867 Pf1N1B4_1226
dapL N-acetyl-diaminopimelate deacetylase
DAPtransferase L,L-diaminopimelate aminotransferase Pf1N1B4_555 Pf1N1B4_5070
dapX acetyl-diaminopimelate aminotransferase Pf1N1B4_5070 Pf1N1B4_4425
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase
hicdh homo-isocitrate dehydrogenase Pf1N1B4_4052 Pf1N1B4_4412
lysJ [LysW]-2-aminoadipate semialdehyde transaminase Pf1N1B4_3440 Pf1N1B4_2980
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase Pf1N1B4_1045 Pf1N1B4_4425
lysT homoaconitase large subunit Pf1N1B4_15
lysU homoaconitase small subunit Pf1N1B4_14 Pf1N1B4_3888
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase Pf1N1B4_2559
lysZ [LysW]-2-aminoadipate 6-kinase Pf1N1B4_2121

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