GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Thiomicrospira cyclica ALM1

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 THICY_RS02560
asd aspartate semi-aldehyde dehydrogenase THICY_RS03170
dapA 4-hydroxy-tetrahydrodipicolinate synthase THICY_RS04315
dapB 4-hydroxy-tetrahydrodipicolinate reductase THICY_RS05380
dapD tetrahydrodipicolinate succinylase THICY_RS05675
dapC N-succinyldiaminopimelate aminotransferase THICY_RS04230 THICY_RS06630
dapE succinyl-diaminopimelate desuccinylase THICY_RS05685
dapF diaminopimelate epimerase THICY_RS01900
lysA diaminopimelate decarboxylase THICY_RS00790
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase THICY_RS05675
dapL N-acetyl-diaminopimelate deacetylase
DAPtransferase L,L-diaminopimelate aminotransferase THICY_RS03700 THICY_RS07300
dapX acetyl-diaminopimelate aminotransferase THICY_RS07300
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase THICY_RS01160
hicdh homo-isocitrate dehydrogenase THICY_RS03160
lysJ [LysW]-2-aminoadipate semialdehyde transaminase THICY_RS06630 THICY_RS03115
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase THICY_RS07300 THICY_RS06630
lysT homoaconitase large subunit THICY_RS03150
lysU homoaconitase small subunit THICY_RS03155
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase THICY_RS00905
lysZ [LysW]-2-aminoadipate 6-kinase THICY_RS01430

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