GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Persephonella marina EX-H1

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 (21 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase PERMA_RS08105
asd aspartate semi-aldehyde dehydrogenase PERMA_RS01855
dapA 4-hydroxy-tetrahydrodipicolinate synthase PERMA_RS00285
dapB 4-hydroxy-tetrahydrodipicolinate reductase PERMA_RS02245
dapD tetrahydrodipicolinate succinylase PERMA_RS00580
dapC N-succinyldiaminopimelate aminotransferase PERMA_RS03815 PERMA_RS00880
dapE succinyl-diaminopimelate desuccinylase PERMA_RS01365 PERMA_RS00125
dapF diaminopimelate epimerase PERMA_RS05075
lysA diaminopimelate decarboxylase PERMA_RS06885 PERMA_RS04400
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase PERMA_RS00580
dapL N-acetyl-diaminopimelate deacetylase PERMA_RS00225
DAPtransferase L,L-diaminopimelate aminotransferase PERMA_RS09210 PERMA_RS03815
dapX acetyl-diaminopimelate aminotransferase PERMA_RS00810 PERMA_RS04795
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase PERMA_RS04545 PERMA_RS05365
hicdh homo-isocitrate dehydrogenase PERMA_RS01925
lysJ [LysW]-2-aminoadipate semialdehyde transaminase PERMA_RS05260 PERMA_RS00880
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase PERMA_RS00810 PERMA_RS00880
lysT homoaconitase large subunit PERMA_RS08515
lysU homoaconitase small subunit PERMA_RS02530
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase PERMA_RS02140
lysZ [LysW]-2-aminoadipate 6-kinase PERMA_RS07520

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