GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Crocosphaera subtropica ATCC 51142

Best path

asp-kinase, asd, dapA, dapB, DAPtransferase, 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 (19 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase CCE_RS21240
asd aspartate semi-aldehyde dehydrogenase CCE_RS01390
dapA 4-hydroxy-tetrahydrodipicolinate synthase CCE_RS01395
dapB 4-hydroxy-tetrahydrodipicolinate reductase CCE_RS13860
DAPtransferase L,L-diaminopimelate aminotransferase CCE_RS12335 CCE_RS04895
dapF diaminopimelate epimerase CCE_RS19580
lysA diaminopimelate decarboxylase CCE_RS06375
Alternative steps:
dapC N-succinyldiaminopimelate aminotransferase CCE_RS13585 CCE_RS14630
dapD tetrahydrodipicolinate succinylase
dapE succinyl-diaminopimelate desuccinylase
dapH tetrahydrodipicolinate acetyltransferase CCE_RS07575 CCE_RS07210
dapL N-acetyl-diaminopimelate deacetylase CCE_RS08990 CCE_RS17765
dapX acetyl-diaminopimelate aminotransferase CCE_RS12755
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase CCE_RS02635 CCE_RS18945
hicdh homo-isocitrate dehydrogenase CCE_RS17080 CCE_RS15150
lysJ [LysW]-2-aminoadipate semialdehyde transaminase CCE_RS14630 CCE_RS00820
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase CCE_RS12755 CCE_RS14630
lysT homoaconitase large subunit CCE_RS15510
lysU homoaconitase small subunit CCE_RS21575
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase CCE_RS00320
lysZ [LysW]-2-aminoadipate 6-kinase CCE_RS15245

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