GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Synechococcus elongatus PCC 7942

Best path

asp-kinase, asd, dapA, dapB, DAPtransferase, dapF, lysA

Also see fitness data for the top candidates

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 Synpcc7942_1001
asd aspartate semi-aldehyde dehydrogenase Synpcc7942_1848
dapA 4-hydroxy-tetrahydrodipicolinate synthase Synpcc7942_1847
dapB 4-hydroxy-tetrahydrodipicolinate reductase Synpcc7942_2136
DAPtransferase L,L-diaminopimelate aminotransferase Synpcc7942_0853 Synpcc7942_1794
dapF diaminopimelate epimerase Synpcc7942_1927
lysA diaminopimelate decarboxylase Synpcc7942_0262
Alternative steps:
dapC N-succinyldiaminopimelate aminotransferase Synpcc7942_0191 Synpcc7942_0943
dapD tetrahydrodipicolinate succinylase
dapE succinyl-diaminopimelate desuccinylase
dapH tetrahydrodipicolinate acetyltransferase Synpcc7942_0931 Synpcc7942_1961
dapL N-acetyl-diaminopimelate deacetylase Synpcc7942_0256 Synpcc7942_1971
dapX acetyl-diaminopimelate aminotransferase Synpcc7942_2545
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase Synpcc7942_1410 Synpcc7942_0428
hicdh homo-isocitrate dehydrogenase Synpcc7942_1719 Synpcc7942_1505
lysJ [LysW]-2-aminoadipate semialdehyde transaminase / [LysW]-glutamate semialdehyde transaminase Synpcc7942_0943 Synpcc7942_0031
lysK [LysW]-lysine hydrolase / [LysW]-ornithine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase Synpcc7942_2545 Synpcc7942_0943
lysT homoaconitase large subunit Synpcc7942_1898
lysU homoaconitase small subunit Synpcc7942_2548
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase / [LysW]-glutamylphosphate reductase Synpcc7942_1433
lysZ [LysW]-2-aminoadipate 6-kinase / [LysW]-glutamate kinase Synpcc7942_1496

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.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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