GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Beijerinckia mobilis UQM 1969

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 (19 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase DL88_RS06715
asd aspartate semi-aldehyde dehydrogenase DL88_RS14650
dapA 4-hydroxy-tetrahydrodipicolinate synthase DL88_RS11880
dapB 4-hydroxy-tetrahydrodipicolinate reductase DL88_RS04015
dapD tetrahydrodipicolinate succinylase DL88_RS03220
dapC N-succinyldiaminopimelate aminotransferase DL88_RS09605 DL88_RS02255
dapE succinyl-diaminopimelate desuccinylase DL88_RS03205
dapF diaminopimelate epimerase DL88_RS02960
lysA diaminopimelate decarboxylase DL88_RS02275 DL88_RS08220
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase DL88_RS03220
dapL N-acetyl-diaminopimelate deacetylase
DAPtransferase L,L-diaminopimelate aminotransferase DL88_RS07410
dapX acetyl-diaminopimelate aminotransferase DL88_RS07410 DL88_RS07560
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase DL88_RS00795 DL88_RS01170
hicdh homo-isocitrate dehydrogenase DL88_RS14665
lysJ [LysW]-2-aminoadipate semialdehyde transaminase DL88_RS04220 DL88_RS02255
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase DL88_RS07410 DL88_RS02255
lysT homoaconitase large subunit DL88_RS12350
lysU homoaconitase small subunit DL88_RS07250
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase
lysZ [LysW]-2-aminoadipate 6-kinase DL88_RS03260

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