GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Sinorhizobium fredii NGR234

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 NGR_RS24435 NGR_RS18270
asd aspartate semi-aldehyde dehydrogenase NGR_RS27725
dapA 4-hydroxy-tetrahydrodipicolinate synthase NGR_RS15385 NGR_RS24340
dapB 4-hydroxy-tetrahydrodipicolinate reductase NGR_RS28555
dapD tetrahydrodipicolinate succinylase NGR_RS11705
dapC N-succinyldiaminopimelate aminotransferase NGR_RS25010 NGR_RS12135
dapE succinyl-diaminopimelate desuccinylase NGR_RS11670 NGR_RS03100
dapF diaminopimelate epimerase NGR_RS27260
lysA diaminopimelate decarboxylase NGR_RS24630 NGR_RS25770
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase NGR_RS23345 NGR_RS11705
dapL N-acetyl-diaminopimelate deacetylase NGR_RS30500 NGR_RS24810
DAPtransferase L,L-diaminopimelate aminotransferase NGR_RS18265 NGR_RS22550
dapX acetyl-diaminopimelate aminotransferase NGR_RS22550 NGR_RS27605
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase NGR_RS15630
hicdh homo-isocitrate dehydrogenase NGR_RS14410 NGR_RS03190
lysJ [LysW]-2-aminoadipate semialdehyde transaminase NGR_RS12135 NGR_RS26550
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase NGR_RS27605 NGR_RS01505
lysT homoaconitase large subunit NGR_RS26830
lysU homoaconitase small subunit NGR_RS26920 NGR_RS03745
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase
lysZ [LysW]-2-aminoadipate 6-kinase NGR_RS11740

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