GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Allochromatium vinosum DSM 180

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 ALVIN_RS05455
asd aspartate semi-aldehyde dehydrogenase ALVIN_RS07955
dapA 4-hydroxy-tetrahydrodipicolinate synthase ALVIN_RS12050
dapB 4-hydroxy-tetrahydrodipicolinate reductase ALVIN_RS09200
dapD tetrahydrodipicolinate succinylase ALVIN_RS02045
dapC N-succinyldiaminopimelate aminotransferase ALVIN_RS02040 ALVIN_RS09870
dapE succinyl-diaminopimelate desuccinylase ALVIN_RS02050 ALVIN_RS14120
dapF diaminopimelate epimerase ALVIN_RS10415
lysA diaminopimelate decarboxylase ALVIN_RS10405 ALVIN_RS08985
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase ALVIN_RS02045 ALVIN_RS04275
dapL N-acetyl-diaminopimelate deacetylase
DAPtransferase L,L-diaminopimelate aminotransferase ALVIN_RS10590 ALVIN_RS01795
dapX acetyl-diaminopimelate aminotransferase ALVIN_RS01795 ALVIN_RS11365
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase ALVIN_RS07410 ALVIN_RS01770
hicdh homo-isocitrate dehydrogenase ALVIN_RS11055 ALVIN_RS07960
lysJ [LysW]-2-aminoadipate semialdehyde transaminase ALVIN_RS09555 ALVIN_RS00500
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase ALVIN_RS01795 ALVIN_RS09555
lysT homoaconitase large subunit ALVIN_RS07970
lysU homoaconitase small subunit ALVIN_RS07965
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase ALVIN_RS00525
lysZ [LysW]-2-aminoadipate 6-kinase ALVIN_RS14940

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 Jul 25 2024. The underlying query database was built on Jul 25 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