GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Herbaspirillum autotrophicum IAM 14942

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 AKL27_RS10445 AKL27_RS07710
asd aspartate semi-aldehyde dehydrogenase AKL27_RS11950
dapA 4-hydroxy-tetrahydrodipicolinate synthase AKL27_RS11850 AKL27_RS23055
dapB 4-hydroxy-tetrahydrodipicolinate reductase AKL27_RS05675
dapD tetrahydrodipicolinate succinylase AKL27_RS10340
dapC N-succinyldiaminopimelate aminotransferase AKL27_RS10335 AKL27_RS16295
dapE succinyl-diaminopimelate desuccinylase AKL27_RS10350 AKL27_RS00570
dapF diaminopimelate epimerase AKL27_RS19585
lysA diaminopimelate decarboxylase AKL27_RS04710
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase AKL27_RS10340 AKL27_RS09730
dapL N-acetyl-diaminopimelate deacetylase AKL27_RS21565 AKL27_RS16025
DAPtransferase L,L-diaminopimelate aminotransferase AKL27_RS06830 AKL27_RS10335
dapX acetyl-diaminopimelate aminotransferase AKL27_RS13975 AKL27_RS22635
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase AKL27_RS18725
hicdh homo-isocitrate dehydrogenase AKL27_RS03045 AKL27_RS14815
lysJ [LysW]-2-aminoadipate semialdehyde transaminase AKL27_RS02370 AKL27_RS12160
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase AKL27_RS13975 AKL27_RS13385
lysT homoaconitase large subunit AKL27_RS11970
lysU homoaconitase small subunit AKL27_RS11960 AKL27_RS06545
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase AKL27_RS21690
lysZ [LysW]-2-aminoadipate 6-kinase AKL27_RS19545

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