GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Hyphomicrobium sulfonivorans WDL6

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 APY04_RS10130
asd aspartate semi-aldehyde dehydrogenase APY04_RS12025
dapA 4-hydroxy-tetrahydrodipicolinate synthase APY04_RS01430
dapB 4-hydroxy-tetrahydrodipicolinate reductase APY04_RS12050
dapD tetrahydrodipicolinate succinylase APY04_RS09380
dapC N-succinyldiaminopimelate aminotransferase APY04_RS16355 APY04_RS02685
dapE succinyl-diaminopimelate desuccinylase APY04_RS09365 APY04_RS02660
dapF diaminopimelate epimerase APY04_RS11995
lysA diaminopimelate decarboxylase APY04_RS09415
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase APY04_RS09380 APY04_RS03255
dapL N-acetyl-diaminopimelate deacetylase
DAPtransferase L,L-diaminopimelate aminotransferase APY04_RS08645
dapX acetyl-diaminopimelate aminotransferase APY04_RS08820 APY04_RS05760
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase APY04_RS10505 APY04_RS01725
hicdh homo-isocitrate dehydrogenase APY04_RS12035
lysJ [LysW]-2-aminoadipate semialdehyde transaminase APY04_RS02685 APY04_RS00380
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase APY04_RS08820 APY04_RS02685
lysT homoaconitase large subunit APY04_RS12100
lysU homoaconitase small subunit APY04_RS11885
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase APY04_RS07575
lysY [LysW]-2-aminoadipate 6-phosphate reductase
lysZ [LysW]-2-aminoadipate 6-kinase APY04_RS03310

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