GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Sinorhizobium medicae WSM419

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 (20 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase SMED_RS12535 SMED_RS07290
asd aspartate semi-aldehyde dehydrogenase SMED_RS15960
dapA 4-hydroxy-tetrahydrodipicolinate synthase SMED_RS19990 SMED_RS03350
dapB 4-hydroxy-tetrahydrodipicolinate reductase SMED_RS16930
dapD tetrahydrodipicolinate succinylase SMED_RS00335
dapC N-succinyldiaminopimelate aminotransferase SMED_RS13120 SMED_RS00640
dapE succinyl-diaminopimelate desuccinylase SMED_RS00300 SMED_RS27795
dapF diaminopimelate epimerase SMED_RS15520
lysA diaminopimelate decarboxylase SMED_RS12710 SMED_RS13885
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase SMED_RS00335 SMED_RS23990
dapL N-acetyl-diaminopimelate deacetylase SMED_RS00865 SMED_RS12880
DAPtransferase L,L-diaminopimelate aminotransferase SMED_RS07295 SMED_RS15855
dapX acetyl-diaminopimelate aminotransferase SMED_RS11150 SMED_RS15855
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase SMED_RS03570
hicdh homo-isocitrate dehydrogenase SMED_RS27775 SMED_RS15945
lysJ [LysW]-2-aminoadipate semialdehyde transaminase SMED_RS00640 SMED_RS23385
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase SMED_RS15855 SMED_RS11150
lysT homoaconitase large subunit SMED_RS15355
lysU homoaconitase small subunit SMED_RS15195 SMED_RS01825
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase
lysZ [LysW]-2-aminoadipate 6-kinase SMED_RS00365

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