GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Frankia alni ACN14a

Best path

asp-kinase, asd, dapA, dapB, dapD, dapC, dapE, 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 (21 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase FRAAL_RS02615 FRAAL_RS30325
asd aspartate semi-aldehyde dehydrogenase FRAAL_RS02610 FRAAL_RS10540
dapA 4-hydroxy-tetrahydrodipicolinate synthase FRAAL_RS24990
dapB 4-hydroxy-tetrahydrodipicolinate reductase FRAAL_RS25050
dapD tetrahydrodipicolinate succinylase FRAAL_RS26705
dapC N-succinyldiaminopimelate aminotransferase FRAAL_RS00525 FRAAL_RS35345
dapE succinyl-diaminopimelate desuccinylase FRAAL_RS26700 FRAAL_RS20340
dapF diaminopimelate epimerase FRAAL_RS24850
lysA diaminopimelate decarboxylase FRAAL_RS25920 FRAAL_RS28015
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase FRAAL_RS26705 FRAAL_RS05445
dapL N-acetyl-diaminopimelate deacetylase FRAAL_RS21035 FRAAL_RS05255
DAPtransferase L,L-diaminopimelate aminotransferase FRAAL_RS04605 FRAAL_RS26455
dapX acetyl-diaminopimelate aminotransferase FRAAL_RS04605 FRAAL_RS26455
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase FRAAL_RS29760 FRAAL_RS20370
hicdh homo-isocitrate dehydrogenase FRAAL_RS25450
lysJ [LysW]-2-aminoadipate semialdehyde transaminase FRAAL_RS22695 FRAAL_RS28020
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase FRAAL_RS04605 FRAAL_RS18885
lysT homoaconitase large subunit FRAAL_RS25385
lysU homoaconitase small subunit FRAAL_RS25380 FRAAL_RS08975
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase FRAAL_RS22710
lysZ [LysW]-2-aminoadipate 6-kinase FRAAL_RS22700

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