GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Thioalkalivibrio halophilus HL17

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 (18 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase B1A74_RS00670 B1A74_RS05210
asd aspartate semi-aldehyde dehydrogenase B1A74_RS00505
dapA 4-hydroxy-tetrahydrodipicolinate synthase B1A74_RS11445
dapB 4-hydroxy-tetrahydrodipicolinate reductase B1A74_RS02460
DAPtransferase L,L-diaminopimelate aminotransferase B1A74_RS05205 B1A74_RS03745
dapF diaminopimelate epimerase B1A74_RS05715
lysA diaminopimelate decarboxylase B1A74_RS05725 B1A74_RS00275
Alternative steps:
dapC N-succinyldiaminopimelate aminotransferase B1A74_RS04935 B1A74_RS01035
dapD tetrahydrodipicolinate succinylase B1A74_RS04940
dapE succinyl-diaminopimelate desuccinylase
dapH tetrahydrodipicolinate acetyltransferase B1A74_RS04940
dapL N-acetyl-diaminopimelate deacetylase
dapX acetyl-diaminopimelate aminotransferase B1A74_RS03745
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase
hicdh homo-isocitrate dehydrogenase B1A74_RS03635 B1A74_RS00510
lysJ [LysW]-2-aminoadipate semialdehyde transaminase B1A74_RS04885 B1A74_RS11130
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase B1A74_RS03745 B1A74_RS04885
lysT homoaconitase large subunit B1A74_RS00520
lysU homoaconitase small subunit B1A74_RS00515 B1A74_RS03615
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase B1A74_RS11375
lysZ [LysW]-2-aminoadipate 6-kinase B1A74_RS13185

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