GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Dechloromonas agitata is5

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 (20 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase K420_RS0111660 K420_RS0113745
asd aspartate semi-aldehyde dehydrogenase K420_RS0100500
dapA 4-hydroxy-tetrahydrodipicolinate synthase K420_RS0109365
dapB 4-hydroxy-tetrahydrodipicolinate reductase K420_RS0100185
dapD tetrahydrodipicolinate succinylase K420_RS0114015
dapC N-succinyldiaminopimelate aminotransferase K420_RS0114010 K420_RS0116250
dapE succinyl-diaminopimelate desuccinylase K420_RS0114025
dapF diaminopimelate epimerase K420_RS0103245
lysA diaminopimelate decarboxylase K420_RS0103165 K420_RS0115885
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase K420_RS0114015
dapL N-acetyl-diaminopimelate deacetylase K420_RS0103985
DAPtransferase L,L-diaminopimelate aminotransferase K420_RS0101285 K420_RS0114010
dapX acetyl-diaminopimelate aminotransferase K420_RS0101285
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase K420_RS0116785
hicdh homo-isocitrate dehydrogenase K420_RS0117015 K420_RS0100505
lysJ [LysW]-2-aminoadipate semialdehyde transaminase K420_RS0110205 K420_RS21080
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase K420_RS21080 K420_RS0101285
lysT homoaconitase large subunit K420_RS0100520
lysU homoaconitase small subunit K420_RS0100510
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase
lysZ [LysW]-2-aminoadipate 6-kinase K420_RS0107980

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