GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Acidovorax sp. GW101-3H11

Best path

asp-kinase, asd, dapA, dapB, dapD, dapC, dapE, 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 (20 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase Ac3H11_4087
asd aspartate semi-aldehyde dehydrogenase Ac3H11_1530
dapA 4-hydroxy-tetrahydrodipicolinate synthase Ac3H11_277 Ac3H11_1501
dapB 4-hydroxy-tetrahydrodipicolinate reductase Ac3H11_686
dapD tetrahydrodipicolinate succinylase Ac3H11_2296
dapC N-succinyldiaminopimelate aminotransferase Ac3H11_2295 Ac3H11_2573
dapE succinyl-diaminopimelate desuccinylase Ac3H11_2298
dapF diaminopimelate epimerase Ac3H11_1993
lysA diaminopimelate decarboxylase Ac3H11_3862
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase Ac3H11_2296 Ac3H11_1394
dapL N-acetyl-diaminopimelate deacetylase Ac3H11_4520 Ac3H11_3202
DAPtransferase L,L-diaminopimelate aminotransferase Ac3H11_3720 Ac3H11_2295
dapX acetyl-diaminopimelate aminotransferase Ac3H11_1602 Ac3H11_3135
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase Ac3H11_530
hicdh homo-isocitrate dehydrogenase Ac3H11_2377 Ac3H11_1528
lysJ [LysW]-2-aminoadipate semialdehyde transaminase Ac3H11_1332 Ac3H11_4179
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase Ac3H11_1602 Ac3H11_4179
lysT homoaconitase large subunit Ac3H11_1525
lysU homoaconitase small subunit Ac3H11_1527
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase
lysZ [LysW]-2-aminoadipate 6-kinase Ac3H11_1907

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