GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Leptospirillum ferrooxidans C2-3

Best path

asp-kinase, asd, dapA, dapB, DAPtransferase, dapF, lysA


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 (17 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase LFE_RS05800
asd aspartate semi-aldehyde dehydrogenase LFE_RS12725
dapA 4-hydroxy-tetrahydrodipicolinate synthase LFE_RS10840
dapB 4-hydroxy-tetrahydrodipicolinate reductase LFE_RS10835
DAPtransferase L,L-diaminopimelate aminotransferase LFE_RS01525 LFE_RS05775
dapF diaminopimelate epimerase LFE_RS01230
lysA diaminopimelate decarboxylase LFE_RS10850
Alternative steps:
dapC N-succinyldiaminopimelate aminotransferase LFE_RS06190 LFE_RS10875
dapD tetrahydrodipicolinate succinylase
dapE succinyl-diaminopimelate desuccinylase
dapH tetrahydrodipicolinate acetyltransferase
dapL N-acetyl-diaminopimelate deacetylase
dapX acetyl-diaminopimelate aminotransferase LFE_RS07250
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase LFE_RS12735 LFE_RS12460
hicdh homo-isocitrate dehydrogenase LFE_RS08995 LFE_RS03940
lysJ [LysW]-2-aminoadipate semialdehyde transaminase LFE_RS10875 LFE_RS08300
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase LFE_RS07250 LFE_RS10875
lysT homoaconitase large subunit LFE_RS09315
lysU homoaconitase small subunit LFE_RS09315 LFE_RS04105
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase LFE_RS11070
lysZ [LysW]-2-aminoadipate 6-kinase LFE_RS01600

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