GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Nocardioides dokdonensis FR1436

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 I601_RS07580
asd aspartate semi-aldehyde dehydrogenase I601_RS07585
dapA 4-hydroxy-tetrahydrodipicolinate synthase I601_RS14320
dapB 4-hydroxy-tetrahydrodipicolinate reductase I601_RS12970
dapD tetrahydrodipicolinate succinylase I601_RS10660
dapC N-succinyldiaminopimelate aminotransferase I601_RS03480 I601_RS10620
dapE succinyl-diaminopimelate desuccinylase I601_RS10720 I601_RS16550
dapF diaminopimelate epimerase I601_RS09350
lysA diaminopimelate decarboxylase I601_RS19520
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase I601_RS20780 I601_RS10400
dapL N-acetyl-diaminopimelate deacetylase I601_RS01200
DAPtransferase L,L-diaminopimelate aminotransferase I601_RS10620 I601_RS04645
dapX acetyl-diaminopimelate aminotransferase
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase I601_RS12185
hicdh homo-isocitrate dehydrogenase I601_RS07050 I601_RS12170
lysJ [LysW]-2-aminoadipate semialdehyde transaminase I601_RS15155 I601_RS01940
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase I601_RS12155 I601_RS14155
lysT homoaconitase large subunit I601_RS12295
lysU homoaconitase small subunit I601_RS12300 I601_RS17670
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase I601_RS15140
lysZ [LysW]-2-aminoadipate 6-kinase I601_RS15150

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