GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Rhizobium etli CFN 42

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 (19 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase RHE_RS19210
asd aspartate semi-aldehyde dehydrogenase RHE_RS20960
dapA 4-hydroxy-tetrahydrodipicolinate synthase RHE_RS28505 RHE_RS07055
dapB 4-hydroxy-tetrahydrodipicolinate reductase RHE_RS00865 RHE_RS13275
dapD tetrahydrodipicolinate succinylase RHE_RS02120
dapC N-succinyldiaminopimelate aminotransferase RHE_RS17655 RHE_RS02610
dapE succinyl-diaminopimelate desuccinylase RHE_RS02115 RHE_RS28175
dapF diaminopimelate epimerase RHE_RS20220
lysA diaminopimelate decarboxylase RHE_RS19415 RHE_RS18555
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase RHE_RS03800 RHE_RS02120
dapL N-acetyl-diaminopimelate deacetylase RHE_RS19600 RHE_RS22870
DAPtransferase L,L-diaminopimelate aminotransferase RHE_RS09590 RHE_RS30015
dapX acetyl-diaminopimelate aminotransferase RHE_RS15340 RHE_RS23780
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase RHE_RS07245
hicdh homo-isocitrate dehydrogenase RHE_RS28195 RHE_RS20920
lysJ [LysW]-2-aminoadipate semialdehyde transaminase RHE_RS02610 RHE_RS19705
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase RHE_RS15340 RHE_RS23780
lysT homoaconitase large subunit
lysU homoaconitase small subunit RHE_RS20910 RHE_RS20170
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase
lysZ [LysW]-2-aminoadipate 6-kinase RHE_RS02170

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