GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Thioalkalivibrio paradoxus ARh 1

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 (20 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase THITH_RS09080 THITH_RS04655
asd aspartate semi-aldehyde dehydrogenase THITH_RS10440
dapA 4-hydroxy-tetrahydrodipicolinate synthase THITH_RS02525
dapB 4-hydroxy-tetrahydrodipicolinate reductase THITH_RS12640
DAPtransferase L,L-diaminopimelate aminotransferase THITH_RS04650 THITH_RS11500
dapF diaminopimelate epimerase THITH_RS00485
lysA diaminopimelate decarboxylase THITH_RS00475
Alternative steps:
dapC N-succinyldiaminopimelate aminotransferase THITH_RS07035 THITH_RS07685
dapD tetrahydrodipicolinate succinylase THITH_RS07030
dapE succinyl-diaminopimelate desuccinylase THITH_RS06740
dapH tetrahydrodipicolinate acetyltransferase THITH_RS07030
dapL N-acetyl-diaminopimelate deacetylase
dapX acetyl-diaminopimelate aminotransferase THITH_RS08315 THITH_RS11500
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase THITH_RS03540
hicdh homo-isocitrate dehydrogenase THITH_RS08480 THITH_RS10445
lysJ [LysW]-2-aminoadipate semialdehyde transaminase THITH_RS02435 THITH_RS09650
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase THITH_RS08315 THITH_RS09650
lysT homoaconitase large subunit THITH_RS10455
lysU homoaconitase small subunit THITH_RS10450
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase THITH_RS02465
lysZ [LysW]-2-aminoadipate 6-kinase THITH_RS15215

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