GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Stutzerimonas stutzeri A1501

Best path

asp-kinase, asd, dapA, dapB, dapD, dapC, dapE, dapF, lysA

Rules

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 PST_RS00920 PST_RS06980
asd aspartate semi-aldehyde dehydrogenase PST_RS08995 PST_RS09000
dapA 4-hydroxy-tetrahydrodipicolinate synthase PST_RS13990
dapB 4-hydroxy-tetrahydrodipicolinate reductase PST_RS16695
dapD tetrahydrodipicolinate succinylase PST_RS14235
dapC N-succinyldiaminopimelate aminotransferase PST_RS14215 PST_RS11800
dapE succinyl-diaminopimelate desuccinylase PST_RS13495
dapF diaminopimelate epimerase PST_RS02630
lysA diaminopimelate decarboxylase PST_RS02635 PST_RS05085
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase PST_RS15265 PST_RS17340
dapL N-acetyl-diaminopimelate deacetylase
DAPtransferase L,L-diaminopimelate aminotransferase PST_RS14215 PST_RS16510
dapX acetyl-diaminopimelate aminotransferase PST_RS16510
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase PST_RS06890 PST_RS16260
hicdh homo-isocitrate dehydrogenase PST_RS11590 PST_RS08990
lysJ [LysW]-2-aminoadipate semialdehyde transaminase PST_RS08350 PST_RS00235
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase PST_RS03780 PST_RS11765
lysT homoaconitase large subunit PST_RS08980
lysU homoaconitase small subunit PST_RS08985
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase PST_RS03850
lysZ [LysW]-2-aminoadipate 6-kinase PST_RS02420

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