GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Desulfatibacillum aliphaticivorans DSM 15576

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 G491_RS0122000 G491_RS0110795
asd aspartate semi-aldehyde dehydrogenase G491_RS0103640
dapA 4-hydroxy-tetrahydrodipicolinate synthase G491_RS0114125
dapB 4-hydroxy-tetrahydrodipicolinate reductase G491_RS0112980
DAPtransferase L,L-diaminopimelate aminotransferase G491_RS0128560 G491_RS0108285
dapF diaminopimelate epimerase G491_RS0128565
lysA diaminopimelate decarboxylase G491_RS0128570
Alternative steps:
dapC N-succinyldiaminopimelate aminotransferase G491_RS0110520 G491_RS0128595
dapD tetrahydrodipicolinate succinylase
dapE succinyl-diaminopimelate desuccinylase G491_RS0121380
dapH tetrahydrodipicolinate acetyltransferase G491_RS0101995 G491_RS0101875
dapL N-acetyl-diaminopimelate deacetylase
dapX acetyl-diaminopimelate aminotransferase G491_RS0110270 G491_RS0105965
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase G491_RS0101035 G491_RS0107090
hicdh homo-isocitrate dehydrogenase G491_RS0111940 G491_RS0123945
lysJ [LysW]-2-aminoadipate semialdehyde transaminase G491_RS0128595 G491_RS0122010
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase G491_RS0110270 G491_RS0128595
lysT homoaconitase large subunit G491_RS0105155 G491_RS0116380
lysU homoaconitase small subunit G491_RS0105160 G491_RS0116380
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase G491_RS0104245
lysZ [LysW]-2-aminoadipate 6-kinase G491_RS0128600

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