GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Thermodesulforhabdus norvegica DSM 9990

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 BM091_RS02160
asd aspartate semi-aldehyde dehydrogenase BM091_RS03255
dapA 4-hydroxy-tetrahydrodipicolinate synthase BM091_RS13075
dapB 4-hydroxy-tetrahydrodipicolinate reductase BM091_RS13070
DAPtransferase L,L-diaminopimelate aminotransferase BM091_RS13065 BM091_RS02590
dapF diaminopimelate epimerase BM091_RS13080
lysA diaminopimelate decarboxylase BM091_RS13085
Alternative steps:
dapC N-succinyldiaminopimelate aminotransferase BM091_RS08375 BM091_RS13110
dapD tetrahydrodipicolinate succinylase
dapE succinyl-diaminopimelate desuccinylase BM091_RS01610
dapH tetrahydrodipicolinate acetyltransferase
dapL N-acetyl-diaminopimelate deacetylase BM091_RS08955
dapX acetyl-diaminopimelate aminotransferase BM091_RS00080 BM091_RS08615
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase BM091_RS02350 BM091_RS05055
hicdh homo-isocitrate dehydrogenase BM091_RS05950 BM091_RS03260
lysJ [LysW]-2-aminoadipate semialdehyde transaminase BM091_RS13110 BM091_RS09360
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase BM091_RS00080 BM091_RS09360
lysT homoaconitase large subunit BM091_RS03270
lysU homoaconitase small subunit BM091_RS03265 BM091_RS00015
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase BM091_RS00090
lysZ [LysW]-2-aminoadipate 6-kinase BM091_RS13115

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