GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Rhodanobacter denitrificans FW104-10B01

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 LRK54_RS12625
asd aspartate semi-aldehyde dehydrogenase LRK54_RS01715
dapA 4-hydroxy-tetrahydrodipicolinate synthase LRK54_RS15085
dapB 4-hydroxy-tetrahydrodipicolinate reductase LRK54_RS17985 LRK54_RS11300
dapD tetrahydrodipicolinate succinylase LRK54_RS14255
dapC N-succinyldiaminopimelate aminotransferase LRK54_RS00400 LRK54_RS06590
dapE succinyl-diaminopimelate desuccinylase LRK54_RS14270 LRK54_RS05355
dapF diaminopimelate epimerase LRK54_RS08545
lysA diaminopimelate decarboxylase LRK54_RS12625 LRK54_RS11485
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase LRK54_RS14255
dapL N-acetyl-diaminopimelate deacetylase LRK54_RS08005
DAPtransferase L,L-diaminopimelate aminotransferase
dapX acetyl-diaminopimelate aminotransferase LRK54_RS00830
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase LRK54_RS10345
hicdh homo-isocitrate dehydrogenase LRK54_RS15050 LRK54_RS10325
lysJ [LysW]-2-aminoadipate semialdehyde transaminase LRK54_RS06590 LRK54_RS06580
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase LRK54_RS00725 LRK54_RS04500
lysT homoaconitase large subunit LRK54_RS07375 LRK54_RS10335
lysU homoaconitase small subunit LRK54_RS10330 LRK54_RS07370
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase LRK54_RS12005
lysY [LysW]-2-aminoadipate 6-phosphate reductase LRK54_RS02385
lysZ [LysW]-2-aminoadipate 6-kinase

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