GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Pelobacter propionicus DSM 2379

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 PPRO_RS11225 PPRO_RS06410
asd aspartate semi-aldehyde dehydrogenase PPRO_RS00225 PPRO_RS00230
dapA 4-hydroxy-tetrahydrodipicolinate synthase PPRO_RS15225
dapB 4-hydroxy-tetrahydrodipicolinate reductase PPRO_RS20635 PPRO_RS16245
DAPtransferase L,L-diaminopimelate aminotransferase PPRO_RS20630
dapF diaminopimelate epimerase PPRO_RS16980
lysA diaminopimelate decarboxylase PPRO_RS09900
Alternative steps:
dapC N-succinyldiaminopimelate aminotransferase PPRO_RS03600 PPRO_RS15790
dapD tetrahydrodipicolinate succinylase
dapE succinyl-diaminopimelate desuccinylase
dapH tetrahydrodipicolinate acetyltransferase PPRO_RS14255 PPRO_RS02450
dapL N-acetyl-diaminopimelate deacetylase PPRO_RS12020
dapX acetyl-diaminopimelate aminotransferase PPRO_RS10870 PPRO_RS04680
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase PPRO_RS17245 PPRO_RS02335
hicdh homo-isocitrate dehydrogenase PPRO_RS00220 PPRO_RS02210
lysJ [LysW]-2-aminoadipate semialdehyde transaminase PPRO_RS15790 PPRO_RS13180
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase PPRO_RS10870 PPRO_RS02765
lysT homoaconitase large subunit PPRO_RS09555
lysU homoaconitase small subunit PPRO_RS09560
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase PPRO_RS15305
lysZ [LysW]-2-aminoadipate 6-kinase PPRO_RS15795

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