GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Chlorobaculum tepidum TLS

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 (20 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase AYT24_RS09170 AYT24_RS00470
asd aspartate semi-aldehyde dehydrogenase AYT24_RS08720
dapA 4-hydroxy-tetrahydrodipicolinate synthase AYT24_RS07325
dapB 4-hydroxy-tetrahydrodipicolinate reductase AYT24_RS08370
DAPtransferase L,L-diaminopimelate aminotransferase AYT24_RS05620
dapF diaminopimelate epimerase AYT24_RS09125
lysA diaminopimelate decarboxylase AYT24_RS06210 AYT24_RS00470
Alternative steps:
dapC N-succinyldiaminopimelate aminotransferase AYT24_RS00350 AYT24_RS01790
dapD tetrahydrodipicolinate succinylase AYT24_RS10240
dapE succinyl-diaminopimelate desuccinylase
dapH tetrahydrodipicolinate acetyltransferase AYT24_RS10240 AYT24_RS08590
dapL N-acetyl-diaminopimelate deacetylase AYT24_RS04830
dapX acetyl-diaminopimelate aminotransferase AYT24_RS04440 AYT24_RS06260
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase AYT24_RS06910 AYT24_RS02865
hicdh homo-isocitrate dehydrogenase AYT24_RS02880
lysJ [LysW]-2-aminoadipate semialdehyde transaminase AYT24_RS01790 AYT24_RS09480
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase AYT24_RS04440 AYT24_RS00535
lysT homoaconitase large subunit AYT24_RS02875
lysU homoaconitase small subunit AYT24_RS02870
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase AYT24_RS05055
lysZ [LysW]-2-aminoadipate 6-kinase AYT24_RS05065

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