GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Malonomonas rubra DSM 5091

Best path

asp-kinase, asd, dapA, dapB, DAPtransferase, 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 (19 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase BUB13_RS05490
asd aspartate semi-aldehyde dehydrogenase BUB13_RS15225
dapA 4-hydroxy-tetrahydrodipicolinate synthase BUB13_RS15165
dapB 4-hydroxy-tetrahydrodipicolinate reductase BUB13_RS15170
DAPtransferase L,L-diaminopimelate aminotransferase BUB13_RS15180 BUB13_RS10290
dapF diaminopimelate epimerase BUB13_RS06345
lysA diaminopimelate decarboxylase BUB13_RS00270
Alternative steps:
dapC N-succinyldiaminopimelate aminotransferase BUB13_RS14345 BUB13_RS15120
dapD tetrahydrodipicolinate succinylase
dapE succinyl-diaminopimelate desuccinylase BUB13_RS13610
dapH tetrahydrodipicolinate acetyltransferase BUB13_RS00175 BUB13_RS03930
dapL N-acetyl-diaminopimelate deacetylase
dapX acetyl-diaminopimelate aminotransferase BUB13_RS10290
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase BUB13_RS17220 BUB13_RS02535
hicdh homo-isocitrate dehydrogenase BUB13_RS02510
lysJ [LysW]-2-aminoadipate semialdehyde transaminase BUB13_RS15120 BUB13_RS08945
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase BUB13_RS15120 BUB13_RS10290
lysT homoaconitase large subunit BUB13_RS02530 BUB13_RS11705
lysU homoaconitase small subunit BUB13_RS02525 BUB13_RS11700
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase BUB13_RS02485
lysZ [LysW]-2-aminoadipate 6-kinase BUB13_RS15115

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