GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Sphingomonas koreensis DSMZ 15582

Best path

asp-kinase, asd, dapA, dapB, dapD, dapC, dapE, dapF, lysA

Also see fitness data for the top candidates


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 Ga0059261_2519
asd aspartate semi-aldehyde dehydrogenase Ga0059261_4003
dapA 4-hydroxy-tetrahydrodipicolinate synthase Ga0059261_0213
dapB 4-hydroxy-tetrahydrodipicolinate reductase Ga0059261_2545
dapD tetrahydrodipicolinate succinylase Ga0059261_1374
dapC N-succinyldiaminopimelate aminotransferase Ga0059261_2265 Ga0059261_3205
dapE succinyl-diaminopimelate desuccinylase Ga0059261_0797 Ga0059261_1675
dapF diaminopimelate epimerase Ga0059261_2394
lysA diaminopimelate decarboxylase Ga0059261_2051 Ga0059261_4188
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase Ga0059261_1374 Ga0059261_3115
dapL N-acetyl-diaminopimelate deacetylase Ga0059261_2769 Ga0059261_3185
DAPtransferase L,L-diaminopimelate aminotransferase Ga0059261_1288 Ga0059261_2226
dapX acetyl-diaminopimelate aminotransferase Ga0059261_2226 Ga0059261_1288
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase
hicdh homo-isocitrate dehydrogenase Ga0059261_3190
lysJ [LysW]-2-aminoadipate semialdehyde transaminase / [LysW]-glutamate semialdehyde transaminase Ga0059261_3205 Ga0059261_3674
lysK [LysW]-lysine hydrolase / [LysW]-ornithine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase Ga0059261_2226 Ga0059261_4131
lysT homoaconitase large subunit Ga0059261_4223
lysU homoaconitase small subunit Ga0059261_4225
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase / [LysW]-glutamylphosphate reductase
lysZ [LysW]-2-aminoadipate 6-kinase / [LysW]-glutamate kinase Ga0059261_2530

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 Aug 03 2021. The underlying query database was built on Aug 03 2021.



Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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