GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Rhizobium leguminosarum WSM1325

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 RLEG_RS18890
asd aspartate semi-aldehyde dehydrogenase RLEG_RS20950
dapA 4-hydroxy-tetrahydrodipicolinate synthase RLEG_RS24005 RLEG_RS05610
dapB 4-hydroxy-tetrahydrodipicolinate reductase RLEG_RS22035 RLEG_RS12605
dapD tetrahydrodipicolinate succinylase RLEG_RS00395
dapC N-succinyldiaminopimelate aminotransferase RLEG_RS17220 RLEG_RS00940
dapE succinyl-diaminopimelate desuccinylase RLEG_RS00390 RLEG_RS24935
dapF diaminopimelate epimerase RLEG_RS20150
lysA diaminopimelate decarboxylase RLEG_RS19110 RLEG_RS18215
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase RLEG_RS00395 RLEG_RS24070
dapL N-acetyl-diaminopimelate deacetylase RLEG_RS19295 RLEG_RS26770
DAPtransferase L,L-diaminopimelate aminotransferase RLEG_RS08595 RLEG_RS34460
dapX acetyl-diaminopimelate aminotransferase RLEG_RS14800 RLEG_RS34460
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase RLEG_RS05790
hicdh homo-isocitrate dehydrogenase RLEG_RS24915 RLEG_RS20910
lysJ [LysW]-2-aminoadipate semialdehyde transaminase RLEG_RS00940 RLEG_RS19395
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase RLEG_RS14800 RLEG_RS34460
lysT homoaconitase large subunit RLEG_RS20205
lysU homoaconitase small subunit RLEG_RS20900 RLEG_RS20100
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase
lysZ [LysW]-2-aminoadipate 6-kinase RLEG_RS00430

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