GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Klebsiella variicola At-22

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 (21 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase KVAR_RS21890 KVAR_RS25005
asd aspartate semi-aldehyde dehydrogenase KVAR_RS01495 KVAR_RS12625
dapA 4-hydroxy-tetrahydrodipicolinate synthase KVAR_RS06260 KVAR_RS13450
dapB 4-hydroxy-tetrahydrodipicolinate reductase KVAR_RS21680
dapD tetrahydrodipicolinate succinylase KVAR_RS20940
dapC N-succinyldiaminopimelate aminotransferase KVAR_RS01765 KVAR_RS17055
dapE succinyl-diaminopimelate desuccinylase KVAR_RS06295 KVAR_RS15665
dapF diaminopimelate epimerase KVAR_RS24650 KVAR_RS11945
lysA diaminopimelate decarboxylase KVAR_RS04100 KVAR_RS24120
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase KVAR_RS20940 KVAR_RS19605
dapL N-acetyl-diaminopimelate deacetylase KVAR_RS11965 KVAR_RS10890
DAPtransferase L,L-diaminopimelate aminotransferase KVAR_RS06645 KVAR_RS14595
dapX acetyl-diaminopimelate aminotransferase KVAR_RS20445 KVAR_RS08425
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase KVAR_RS08025 KVAR_RS21445
hicdh homo-isocitrate dehydrogenase KVAR_RS16030 KVAR_RS16670
lysJ [LysW]-2-aminoadipate semialdehyde transaminase KVAR_RS15350 KVAR_RS14225
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase KVAR_RS08425 KVAR_RS20445
lysT homoaconitase large subunit KVAR_RS21455
lysU homoaconitase small subunit KVAR_RS21460
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase KVAR_RS24955
lysZ [LysW]-2-aminoadipate 6-kinase KVAR_RS24950

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