GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Brevundimonas sp. GW460-12-10-14-LB2

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 (20 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase A4249_RS14490 A4249_RS00005
asd aspartate semi-aldehyde dehydrogenase A4249_RS12690 A4249_RS12345
dapA 4-hydroxy-tetrahydrodipicolinate synthase A4249_RS05475
dapB 4-hydroxy-tetrahydrodipicolinate reductase A4249_RS13645
dapD tetrahydrodipicolinate succinylase A4249_RS12955
dapC N-succinyldiaminopimelate aminotransferase A4249_RS10080 A4249_RS11925
dapE succinyl-diaminopimelate desuccinylase A4249_RS11970
dapF diaminopimelate epimerase A4249_RS13290
lysA diaminopimelate decarboxylase A4249_RS12545
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase A4249_RS12955 A4249_RS17085
dapL N-acetyl-diaminopimelate deacetylase A4249_RS11980
DAPtransferase L,L-diaminopimelate aminotransferase A4249_RS02425
dapX acetyl-diaminopimelate aminotransferase A4249_RS04680 A4249_RS02425
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase A4249_RS10010
hicdh homo-isocitrate dehydrogenase A4249_RS09995
lysJ [LysW]-2-aminoadipate semialdehyde transaminase A4249_RS11925
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase A4249_RS04680 A4249_RS13775
lysT homoaconitase large subunit A4249_RS10005
lysU homoaconitase small subunit A4249_RS10000 A4249_RS12770
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase
lysZ [LysW]-2-aminoadipate 6-kinase A4249_RS12965

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