GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Alkalihalobacterium alkalinitrilicum DSM 22532

Best path

asp-kinase, asd, dapA, dapB, DAPtransferase, 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 (21 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase BK574_RS11150 BK574_RS26660
asd aspartate semi-aldehyde dehydrogenase BK574_RS26655
dapA 4-hydroxy-tetrahydrodipicolinate synthase BK574_RS09525 BK574_RS26665
dapB 4-hydroxy-tetrahydrodipicolinate reductase BK574_RS09805
DAPtransferase L,L-diaminopimelate aminotransferase BK574_RS14765 BK574_RS16655
dapF diaminopimelate epimerase BK574_RS21170
lysA diaminopimelate decarboxylase BK574_RS10540
Alternative steps:
dapC N-succinyldiaminopimelate aminotransferase BK574_RS13850 BK574_RS23575
dapD tetrahydrodipicolinate succinylase BK574_RS25375
dapE succinyl-diaminopimelate desuccinylase BK574_RS00560 BK574_RS25360
dapH tetrahydrodipicolinate acetyltransferase BK574_RS25375 BK574_RS17925
dapL N-acetyl-diaminopimelate deacetylase BK574_RS25385 BK574_RS14330
dapX acetyl-diaminopimelate aminotransferase BK574_RS21330 BK574_RS15655
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase BK574_RS22745 BK574_RS02120
hicdh homo-isocitrate dehydrogenase BK574_RS22385 BK574_RS22750
lysJ [LysW]-2-aminoadipate semialdehyde transaminase BK574_RS23575 BK574_RS07925
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase BK574_RS09735 BK574_RS15655
lysT homoaconitase large subunit BK574_RS22755 BK574_RS03580
lysU homoaconitase small subunit BK574_RS22760 BK574_RS00360
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase BK574_RS23560
lysZ [LysW]-2-aminoadipate 6-kinase BK574_RS23570

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