GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Rhodomicrobium vannielii ATCC 17100

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 RVAN_RS13760
asd aspartate semi-aldehyde dehydrogenase RVAN_RS17470
dapA 4-hydroxy-tetrahydrodipicolinate synthase RVAN_RS13320
dapB 4-hydroxy-tetrahydrodipicolinate reductase RVAN_RS03360
dapD tetrahydrodipicolinate succinylase RVAN_RS15655
dapC N-succinyldiaminopimelate aminotransferase RVAN_RS14850 RVAN_RS11970
dapE succinyl-diaminopimelate desuccinylase RVAN_RS15670 RVAN_RS00495
dapF diaminopimelate epimerase RVAN_RS11340
lysA diaminopimelate decarboxylase RVAN_RS12135
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase RVAN_RS15655 RVAN_RS20970
dapL N-acetyl-diaminopimelate deacetylase
DAPtransferase L,L-diaminopimelate aminotransferase RVAN_RS16195 RVAN_RS17170
dapX acetyl-diaminopimelate aminotransferase RVAN_RS06420 RVAN_RS17170
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase RVAN_RS05675 RVAN_RS08440
hicdh homo-isocitrate dehydrogenase RVAN_RS16155
lysJ [LysW]-2-aminoadipate semialdehyde transaminase RVAN_RS15510 RVAN_RS11970
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase RVAN_RS06420 RVAN_RS15510
lysT homoaconitase large subunit RVAN_RS16815
lysU homoaconitase small subunit RVAN_RS13190
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase RVAN_RS16225
lysZ [LysW]-2-aminoadipate 6-kinase RVAN_RS07930

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