GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Methanothermobacter thermautotrophicus Delta H

Best path

asp-kinase, asd, dapA?, dapB, DAPtransferase, 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 (17 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate Class of gap
asp-kinase aspartate kinase MTH_RS03770  
asd aspartate semi-aldehyde dehydrogenase MTH_RS03755  
dapA? 4-hydroxy-tetrahydrodipicolinate synthase spurious
dapB 4-hydroxy-tetrahydrodipicolinate reductase MTH_RS03760  
DAPtransferase L,L-diaminopimelate aminotransferase MTH_RS00260 MTH_RS09075  
dapF diaminopimelate epimerase MTH_RS06370  
lysA diaminopimelate decarboxylase MTH_RS06375  
Alternative steps:
dapC N-succinyldiaminopimelate aminotransferase MTH_RS07670 MTH_RS06385  
dapD tetrahydrodipicolinate succinylase  
dapE succinyl-diaminopimelate desuccinylase  
dapH tetrahydrodipicolinate acetyltransferase MTH_RS07605  
dapL N-acetyl-diaminopimelate deacetylase  
dapX acetyl-diaminopimelate aminotransferase MTH_RS09075  
ddh meso-diaminopimelate D-dehydrogenase  
hcs homocitrate synthase MTH_RS07810 MTH_RS07070  
hicdh homo-isocitrate dehydrogenase MTH_RS00845 MTH_RS06640  
lysJ [LysW]-2-aminoadipate semialdehyde transaminase MTH_RS06385 MTH_RS01035  
lysK [LysW]-lysine hydrolase  
lysN 2-aminoadipate:2-oxoglutarate aminotransferase MTH_RS09075 MTH_RS06385  
lysT homoaconitase large subunit MTH_RS07815 MTH_RS06630  
lysU homoaconitase small subunit MTH_RS06635 MTH_RS03905  
lysW 2-aminoadipate/glutamate carrier protein  
lysX 2-aminoadipate-LysW ligase  
lysY [LysW]-2-aminoadipate 6-phosphate reductase MTH_RS03985  
lysZ [LysW]-2-aminoadipate 6-kinase MTH_RS00840  

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