GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Desulfogranum mediterraneum DSM 13871

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 G494_RS0110505 G494_RS0115930
asd aspartate semi-aldehyde dehydrogenase G494_RS0117695
dapA 4-hydroxy-tetrahydrodipicolinate synthase G494_RS0108640
dapB 4-hydroxy-tetrahydrodipicolinate reductase G494_RS0108645
DAPtransferase L,L-diaminopimelate aminotransferase G494_RS0104850 G494_RS22980
dapF diaminopimelate epimerase G494_RS0108635
lysA diaminopimelate decarboxylase G494_RS0107965 G494_RS22485
Alternative steps:
dapC N-succinyldiaminopimelate aminotransferase G494_RS0110515 G494_RS0108610
dapD tetrahydrodipicolinate succinylase
dapE succinyl-diaminopimelate desuccinylase G494_RS0119225
dapH tetrahydrodipicolinate acetyltransferase G494_RS28000 G494_RS28005
dapL N-acetyl-diaminopimelate deacetylase G494_RS0120915 G494_RS24250
dapX acetyl-diaminopimelate aminotransferase G494_RS0117930 G494_RS24990
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase G494_RS0115910 G494_RS0110500
hicdh homo-isocitrate dehydrogenase G494_RS0113985 G494_RS0117705
lysJ [LysW]-2-aminoadipate semialdehyde transaminase G494_RS0108610 G494_RS0104195
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase G494_RS0100225 G494_RS0117930
lysT homoaconitase large subunit G494_RS0100215
lysU homoaconitase small subunit G494_RS0100220 G494_RS0118470
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase G494_RS0111675
lysZ [LysW]-2-aminoadipate 6-kinase G494_RS0108605

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