GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Phaeobacter inhibens BS107

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 PGA1_c23510
asd aspartate semi-aldehyde dehydrogenase PGA1_c31480
dapA 4-hydroxy-tetrahydrodipicolinate synthase PGA1_c28930
dapB 4-hydroxy-tetrahydrodipicolinate reductase PGA1_c32920
dapD tetrahydrodipicolinate succinylase PGA1_c36310
dapC N-succinyldiaminopimelate aminotransferase PGA1_c36150 PGA1_c24230
dapE succinyl-diaminopimelate desuccinylase PGA1_c36420 PGA1_c07830
dapF diaminopimelate epimerase PGA1_c33950
lysA diaminopimelate decarboxylase PGA1_c03470 PGA1_c13710
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase PGA1_c36310 PGA1_c17690
dapL N-acetyl-diaminopimelate deacetylase PGA1_c10160 PGA1_c10150
DAPtransferase L,L-diaminopimelate aminotransferase PGA1_c33280 PGA1_c21250
dapX acetyl-diaminopimelate aminotransferase PGA1_c21250 PGA1_c20300
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase PGA1_c26470 PGA1_c16460
hicdh homo-isocitrate dehydrogenase PGA1_c17990 PGA1_c29830
lysJ [LysW]-2-aminoadipate semialdehyde transaminase PGA1_c24230 PGA1_c28750
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase PGA1_c21250 PGA1_c24230
lysT homoaconitase large subunit
lysU homoaconitase small subunit PGA1_c29790 PGA1_c18830
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase PGA1_c17050
lysZ [LysW]-2-aminoadipate 6-kinase PGA1_c02050

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