GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Bradyrhizobium sp. BTAi1

Best path

asp-kinase, asd, dapA, dapB, dapD, dapC, dapE, 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 (21 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase BBTA_RS35575
asd aspartate semi-aldehyde dehydrogenase BBTA_RS01660 BBTA_RS20400
dapA 4-hydroxy-tetrahydrodipicolinate synthase BBTA_RS21995 BBTA_RS29715
dapB 4-hydroxy-tetrahydrodipicolinate reductase BBTA_RS00945
dapD tetrahydrodipicolinate succinylase BBTA_RS34305
dapC N-succinyldiaminopimelate aminotransferase BBTA_RS08495 BBTA_RS03550
dapE succinyl-diaminopimelate desuccinylase BBTA_RS34310 BBTA_RS20040
dapF diaminopimelate epimerase BBTA_RS01775
lysA diaminopimelate decarboxylase BBTA_RS05430 BBTA_RS06365
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase BBTA_RS34305 BBTA_RS24450
dapL N-acetyl-diaminopimelate deacetylase BBTA_RS13925 BBTA_RS21455
DAPtransferase L,L-diaminopimelate aminotransferase BBTA_RS18710 BBTA_RS00625
dapX acetyl-diaminopimelate aminotransferase BBTA_RS05880 BBTA_RS08385
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase BBTA_RS27445 BBTA_RS28270
hicdh homo-isocitrate dehydrogenase BBTA_RS13055 BBTA_RS13420
lysJ [LysW]-2-aminoadipate semialdehyde transaminase BBTA_RS03550 BBTA_RS19410
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase BBTA_RS05880 BBTA_RS08385
lysT homoaconitase large subunit BBTA_RS01730 BBTA_RS28040
lysU homoaconitase small subunit BBTA_RS28045 BBTA_RS01695
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase BBTA_RS05450
lysZ [LysW]-2-aminoadipate 6-kinase BBTA_RS34290

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.



Related tools

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