GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Hydrogenovibrio kuenenii DSM 12350

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 N745_RS0108245 N745_RS0100475
asd aspartate semi-aldehyde dehydrogenase N745_RS0107250
dapA 4-hydroxy-tetrahydrodipicolinate synthase N745_RS0103530
dapB 4-hydroxy-tetrahydrodipicolinate reductase N745_RS0107820
dapD tetrahydrodipicolinate succinylase N745_RS0105720
dapC N-succinyldiaminopimelate aminotransferase N745_RS0105245 N745_RS0102880
dapE succinyl-diaminopimelate desuccinylase N745_RS0105730
dapF diaminopimelate epimerase N745_RS0109145
lysA diaminopimelate decarboxylase N745_RS0101695
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase
dapL N-acetyl-diaminopimelate deacetylase N745_RS0101910
DAPtransferase L,L-diaminopimelate aminotransferase N745_RS0105535 N745_RS0102095
dapX acetyl-diaminopimelate aminotransferase N745_RS0102095 N745_RS0109485
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase N745_RS0103395
hicdh homo-isocitrate dehydrogenase N745_RS0107265
lysJ [LysW]-2-aminoadipate semialdehyde transaminase N745_RS0102985 N745_RS0101915
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase N745_RS0102095 N745_RS0102985
lysT homoaconitase large subunit N745_RS0107275
lysU homoaconitase small subunit N745_RS0107270
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase N745_RS0101490
lysZ [LysW]-2-aminoadipate 6-kinase N745_RS0109470

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