GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Ammonifex degensii KC4

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 (18 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase ADEG_RS04495 ADEG_RS04485
asd aspartate semi-aldehyde dehydrogenase ADEG_RS01750
dapA 4-hydroxy-tetrahydrodipicolinate synthase ADEG_RS01755
dapB 4-hydroxy-tetrahydrodipicolinate reductase ADEG_RS01735
DAPtransferase L,L-diaminopimelate aminotransferase ADEG_RS06975 ADEG_RS06970
dapF diaminopimelate epimerase ADEG_RS06980
lysA diaminopimelate decarboxylase ADEG_RS06585
Alternative steps:
dapC N-succinyldiaminopimelate aminotransferase ADEG_RS00045 ADEG_RS09245
dapD tetrahydrodipicolinate succinylase
dapE succinyl-diaminopimelate desuccinylase
dapH tetrahydrodipicolinate acetyltransferase ADEG_RS02020 ADEG_RS10500
dapL N-acetyl-diaminopimelate deacetylase
dapX acetyl-diaminopimelate aminotransferase ADEG_RS00220 ADEG_RS06970
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase ADEG_RS05565 ADEG_RS01145
hicdh homo-isocitrate dehydrogenase ADEG_RS05580 ADEG_RS09915
lysJ [LysW]-2-aminoadipate semialdehyde transaminase ADEG_RS09245 ADEG_RS07165
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase ADEG_RS06970 ADEG_RS00220
lysT homoaconitase large subunit ADEG_RS05570 ADEG_RS01150
lysU homoaconitase small subunit ADEG_RS01155 ADEG_RS05575
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase ADEG_RS09260
lysZ [LysW]-2-aminoadipate 6-kinase ADEG_RS09250

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