GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Denitrovibrio acetiphilus DSM 12809

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 DACET_RS07120 DACET_RS07130
asd aspartate semi-aldehyde dehydrogenase DACET_RS08625
dapA 4-hydroxy-tetrahydrodipicolinate synthase DACET_RS12560
dapB 4-hydroxy-tetrahydrodipicolinate reductase DACET_RS12565
DAPtransferase L,L-diaminopimelate aminotransferase DACET_RS00020
dapF diaminopimelate epimerase DACET_RS12555
lysA diaminopimelate decarboxylase DACET_RS12550 DACET_RS04015
Alternative steps:
dapC N-succinyldiaminopimelate aminotransferase DACET_RS12185 DACET_RS01590
dapD tetrahydrodipicolinate succinylase
dapE succinyl-diaminopimelate desuccinylase
dapH tetrahydrodipicolinate acetyltransferase DACET_RS14315 DACET_RS07200
dapL N-acetyl-diaminopimelate deacetylase DACET_RS04255
dapX acetyl-diaminopimelate aminotransferase DACET_RS00570
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase DACET_RS05300 DACET_RS02375
hicdh homo-isocitrate dehydrogenase DACET_RS07555
lysJ [LysW]-2-aminoadipate semialdehyde transaminase DACET_RS01590 DACET_RS02325
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase DACET_RS01590
lysT homoaconitase large subunit DACET_RS14210
lysU homoaconitase small subunit DACET_RS14205
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase DACET_RS02320
lysZ [LysW]-2-aminoadipate 6-kinase DACET_RS02235

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