GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Methanosarcina mazei Go1

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 (19 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate Known gap?
asp-kinase aspartate kinase MM_RS07335  
asd aspartate semi-aldehyde dehydrogenase MM_RS08365  
dapA 4-hydroxy-tetrahydrodipicolinate synthase MM_RS06220  
dapB 4-hydroxy-tetrahydrodipicolinate reductase MM_RS06225  
DAPtransferase L,L-diaminopimelate aminotransferase MM_RS13715 MM_RS12280  
dapF? diaminopimelate epimerase known gap
lysA diaminopimelate decarboxylase MM_RS09770  
Alternative steps:
dapC N-succinyldiaminopimelate aminotransferase MM_RS15105 MM_RS01350  
dapD tetrahydrodipicolinate succinylase  
dapE succinyl-diaminopimelate desuccinylase  
dapH tetrahydrodipicolinate acetyltransferase MM_RS05980 MM_RS10940  
dapL N-acetyl-diaminopimelate deacetylase MM_RS11540  
dapX acetyl-diaminopimelate aminotransferase MM_RS10585 MM_RS12280  
ddh meso-diaminopimelate D-dehydrogenase  
hcs homocitrate synthase MM_RS14445 MM_RS06665  
hicdh homo-isocitrate dehydrogenase MM_RS03355 MM_RS05215  
lysJ [LysW]-2-aminoadipate semialdehyde transaminase MM_RS07280 MM_RS00255  
lysK [LysW]-lysine hydrolase  
lysN 2-aminoadipate:2-oxoglutarate aminotransferase MM_RS01335 MM_RS12280  
lysT homoaconitase large subunit MM_RS02210 MM_RS12305  
lysU homoaconitase small subunit MM_RS03370 MM_RS07690  
lysW 2-aminoadipate/glutamate carrier protein  
lysX 2-aminoadipate-LysW ligase MM_RS00550  
lysY [LysW]-2-aminoadipate 6-phosphate reductase MM_RS02550  
lysZ [LysW]-2-aminoadipate 6-kinase MM_RS06315  

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