GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Stenotrophomonas chelatiphaga DSM 21508

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 ABB28_RS02115 ABB28_RS00495
asd aspartate semi-aldehyde dehydrogenase ABB28_RS15230
dapA 4-hydroxy-tetrahydrodipicolinate synthase ABB28_RS11735
dapB 4-hydroxy-tetrahydrodipicolinate reductase ABB28_RS13580
dapD tetrahydrodipicolinate succinylase ABB28_RS06515
dapC N-succinyldiaminopimelate aminotransferase ABB28_RS00660 ABB28_RS13775
dapE succinyl-diaminopimelate desuccinylase ABB28_RS06525
dapF diaminopimelate epimerase ABB28_RS12205
lysA diaminopimelate decarboxylase ABB28_RS02115 ABB28_RS00495
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase ABB28_RS18455 ABB28_RS06515
dapL N-acetyl-diaminopimelate deacetylase ABB28_RS14300
DAPtransferase L,L-diaminopimelate aminotransferase ABB28_RS12185
dapX acetyl-diaminopimelate aminotransferase ABB28_RS01035 ABB28_RS11865
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase ABB28_RS14490
hicdh homo-isocitrate dehydrogenase ABB28_RS01900 ABB28_RS14510
lysJ [LysW]-2-aminoadipate semialdehyde transaminase ABB28_RS13775 ABB28_RS05895
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase ABB28_RS13775 ABB28_RS11865
lysT homoaconitase large subunit ABB28_RS14500
lysU homoaconitase small subunit ABB28_RS14505 ABB28_RS16850
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase ABB28_RS15365
lysZ [LysW]-2-aminoadipate 6-kinase

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