GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Azospirillum brasilense Sp245

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 (21 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase AZOBR_RS18890 AZOBR_RS07835
asd aspartate semi-aldehyde dehydrogenase AZOBR_RS13975 AZOBR_RS14735
dapA 4-hydroxy-tetrahydrodipicolinate synthase AZOBR_RS08420 AZOBR_RS27060
dapB 4-hydroxy-tetrahydrodipicolinate reductase AZOBR_RS01580
dapD tetrahydrodipicolinate succinylase AZOBR_RS03475
dapC N-succinyldiaminopimelate aminotransferase AZOBR_RS19025 AZOBR_RS02295
dapE succinyl-diaminopimelate desuccinylase AZOBR_RS03470 AZOBR_RS18740
dapF diaminopimelate epimerase AZOBR_RS14160
lysA diaminopimelate decarboxylase AZOBR_RS16945 AZOBR_RS00105
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase AZOBR_RS03475 AZOBR_RS05825
dapL N-acetyl-diaminopimelate deacetylase AZOBR_RS25660 AZOBR_RS32390
DAPtransferase L,L-diaminopimelate aminotransferase AZOBR_RS07830 AZOBR_RS20195
dapX acetyl-diaminopimelate aminotransferase AZOBR_RS24065 AZOBR_RS12970
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase AZOBR_RS05495 AZOBR_RS04265
hicdh homo-isocitrate dehydrogenase AZOBR_RS11025 AZOBR_RS14130
lysJ [LysW]-2-aminoadipate semialdehyde transaminase AZOBR_RS19590 AZOBR_RS19025
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase AZOBR_RS12970 AZOBR_RS19630
lysT homoaconitase large subunit AZOBR_RS27815 AZOBR_RS15565
lysU homoaconitase small subunit AZOBR_RS14135 AZOBR_RS27810
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase AZOBR_RS07795
lysZ [LysW]-2-aminoadipate 6-kinase AZOBR_RS03285

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