GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Billgrantia desiderata SP1

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 BZY95_RS07285 BZY95_RS20540
asd aspartate semi-aldehyde dehydrogenase BZY95_RS04435
dapA 4-hydroxy-tetrahydrodipicolinate synthase BZY95_RS18815 BZY95_RS14805
dapB 4-hydroxy-tetrahydrodipicolinate reductase BZY95_RS13640
dapD tetrahydrodipicolinate succinylase BZY95_RS07625
dapC N-succinyldiaminopimelate aminotransferase BZY95_RS07615 BZY95_RS01045
dapE succinyl-diaminopimelate desuccinylase BZY95_RS07630 BZY95_RS02550
dapF diaminopimelate epimerase BZY95_RS20450
lysA diaminopimelate decarboxylase BZY95_RS20455
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase BZY95_RS18610 BZY95_RS04320
dapL N-acetyl-diaminopimelate deacetylase BZY95_RS04885 BZY95_RS05965
DAPtransferase L,L-diaminopimelate aminotransferase BZY95_RS13490 BZY95_RS07615
dapX acetyl-diaminopimelate aminotransferase BZY95_RS13490
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase
hicdh homo-isocitrate dehydrogenase BZY95_RS15605 BZY95_RS12740
lysJ [LysW]-2-aminoadipate semialdehyde transaminase BZY95_RS01045 BZY95_RS15480
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase BZY95_RS15480 BZY95_RS16860
lysT homoaconitase large subunit BZY95_RS01750 BZY95_RS04400
lysU homoaconitase small subunit BZY95_RS01750 BZY95_RS04405
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase BZY95_RS12275
lysZ [LysW]-2-aminoadipate 6-kinase BZY95_RS05700

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