GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Azoarcus olearius BH72

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 AZO_RS15630 AZO_RS10510
asd aspartate semi-aldehyde dehydrogenase AZO_RS05290
dapA 4-hydroxy-tetrahydrodipicolinate synthase AZO_RS05565
dapB 4-hydroxy-tetrahydrodipicolinate reductase AZO_RS12990
dapD tetrahydrodipicolinate succinylase AZO_RS10125
dapC N-succinyldiaminopimelate aminotransferase AZO_RS10120 AZO_RS05410
dapE succinyl-diaminopimelate desuccinylase AZO_RS10135
dapF diaminopimelate epimerase AZO_RS02990
lysA diaminopimelate decarboxylase AZO_RS18340 AZO_RS16320
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase AZO_RS10125 AZO_RS02770
dapL N-acetyl-diaminopimelate deacetylase AZO_RS01055 AZO_RS08110
DAPtransferase L,L-diaminopimelate aminotransferase AZO_RS10120
dapX acetyl-diaminopimelate aminotransferase AZO_RS04130
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase AZO_RS02775 AZO_RS15865
hicdh homo-isocitrate dehydrogenase AZO_RS05825 AZO_RS05285
lysJ [LysW]-2-aminoadipate semialdehyde transaminase AZO_RS11060 AZO_RS06045
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase AZO_RS04250 AZO_RS06045
lysT homoaconitase large subunit AZO_RS05275
lysU homoaconitase small subunit AZO_RS05280 AZO_RS07750
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase
lysZ [LysW]-2-aminoadipate 6-kinase AZO_RS16300

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