GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Ferroglobus placidus DSM 10642

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 FERP_RS04025
asd aspartate semi-aldehyde dehydrogenase FERP_RS05625
dapA 4-hydroxy-tetrahydrodipicolinate synthase FERP_RS06365
dapB 4-hydroxy-tetrahydrodipicolinate reductase FERP_RS10190
DAPtransferase L,L-diaminopimelate aminotransferase FERP_RS04050 FERP_RS12225
dapF diaminopimelate epimerase FERP_RS10505
lysA diaminopimelate decarboxylase FERP_RS04045
Alternative steps:
dapC N-succinyldiaminopimelate aminotransferase FERP_RS11050 FERP_RS01920
dapD tetrahydrodipicolinate succinylase
dapE succinyl-diaminopimelate desuccinylase FERP_RS07195
dapH tetrahydrodipicolinate acetyltransferase FERP_RS11890 FERP_RS11875
dapL N-acetyl-diaminopimelate deacetylase
dapX acetyl-diaminopimelate aminotransferase FERP_RS02970 FERP_RS05975
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase FERP_RS07010 FERP_RS11450
hicdh homo-isocitrate dehydrogenase FERP_RS04315 FERP_RS10670
lysJ [LysW]-2-aminoadipate semialdehyde transaminase FERP_RS01920 FERP_RS08870
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase FERP_RS12225 FERP_RS05975
lysT homoaconitase large subunit FERP_RS03495 FERP_RS12430
lysU homoaconitase small subunit FERP_RS10665 FERP_RS07425
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase FERP_RS10895
lysY [LysW]-2-aminoadipate 6-phosphate reductase FERP_RS04630
lysZ [LysW]-2-aminoadipate 6-kinase FERP_RS11200

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