GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Pyrolobus fumarii 1A

Best path

hcs, lysT, lysU, hicdh, lysN, lysW, lysX, lysZ, lysY, lysJ, lysK

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 (16 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
hcs homocitrate synthase PYRFU_RS09715 PYRFU_RS08315
lysT homoaconitase large subunit PYRFU_RS09265 PYRFU_RS00315
lysU homoaconitase small subunit PYRFU_RS07965 PYRFU_RS03665
hicdh homo-isocitrate dehydrogenase PYRFU_RS09335 PYRFU_RS05270
lysN 2-aminoadipate:2-oxoglutarate aminotransferase PYRFU_RS08035 PYRFU_RS08855
lysW 2-aminoadipate/glutamate carrier protein PYRFU_RS03640
lysX 2-aminoadipate-LysW ligase PYRFU_RS03645 PYRFU_RS03725
lysZ [LysW]-2-aminoadipate 6-kinase PYRFU_RS01990
lysY [LysW]-2-aminoadipate 6-phosphate reductase PYRFU_RS03735
lysJ [LysW]-2-aminoadipate semialdehyde transaminase PYRFU_RS08855 PYRFU_RS06770
lysK [LysW]-lysine hydrolase PYRFU_RS08530
Alternative steps:
asd aspartate semi-aldehyde dehydrogenase PYRFU_RS04350
asp-kinase aspartate kinase PYRFU_RS06440
dapA 4-hydroxy-tetrahydrodipicolinate synthase
dapB 4-hydroxy-tetrahydrodipicolinate reductase
dapC N-succinyldiaminopimelate aminotransferase PYRFU_RS03405 PYRFU_RS08855
dapD tetrahydrodipicolinate succinylase
dapE succinyl-diaminopimelate desuccinylase
dapF diaminopimelate epimerase
dapH tetrahydrodipicolinate acetyltransferase PYRFU_RS08065
dapL N-acetyl-diaminopimelate deacetylase
DAPtransferase L,L-diaminopimelate aminotransferase
dapX acetyl-diaminopimelate aminotransferase PYRFU_RS02975
ddh meso-diaminopimelate D-dehydrogenase
lysA diaminopimelate decarboxylase

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