GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Methylotuvimicrobium alcaliphilum 20Z

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 (22 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase MEALZ_RS13830 MEALZ_RS15850
asd aspartate semi-aldehyde dehydrogenase MEALZ_RS17275
dapA 4-hydroxy-tetrahydrodipicolinate synthase MEALZ_RS08685 MEALZ_RS12755
dapB 4-hydroxy-tetrahydrodipicolinate reductase MEALZ_RS09225
dapD tetrahydrodipicolinate succinylase MEALZ_RS06140
dapC N-succinyldiaminopimelate aminotransferase MEALZ_RS06145 MEALZ_RS12225
dapE succinyl-diaminopimelate desuccinylase MEALZ_RS06120
dapF diaminopimelate epimerase MEALZ_RS06025
lysA diaminopimelate decarboxylase MEALZ_RS06030 MEALZ_RS13200
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase MEALZ_RS06140 MEALZ_RS13500
dapL N-acetyl-diaminopimelate deacetylase MEALZ_RS17455 MEALZ_RS19530
DAPtransferase L,L-diaminopimelate aminotransferase MEALZ_RS07605 MEALZ_RS06145
dapX acetyl-diaminopimelate aminotransferase MEALZ_RS04285 MEALZ_RS13915
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase MEALZ_RS16175 MEALZ_RS07345
hicdh homo-isocitrate dehydrogenase MEALZ_RS14775 MEALZ_RS07340
lysJ [LysW]-2-aminoadipate semialdehyde transaminase MEALZ_RS08805 MEALZ_RS15150
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase MEALZ_RS04285 MEALZ_RS08805
lysT homoaconitase large subunit MEALZ_RS17290
lysU homoaconitase small subunit MEALZ_RS17285
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase MEALZ_RS11865
lysY [LysW]-2-aminoadipate 6-phosphate reductase MEALZ_RS02690
lysZ [LysW]-2-aminoadipate 6-kinase MEALZ_RS00695

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