GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Methylococcus capsulatus Bath

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 MCA_RS01930 MCA_RS02965
asd aspartate semi-aldehyde dehydrogenase MCA_RS10095
dapA 4-hydroxy-tetrahydrodipicolinate synthase MCA_RS03315
dapB 4-hydroxy-tetrahydrodipicolinate reductase MCA_RS09110
dapD tetrahydrodipicolinate succinylase MCA_RS07330
dapC N-succinyldiaminopimelate aminotransferase MCA_RS07335 MCA_RS06985
dapE succinyl-diaminopimelate desuccinylase MCA_RS07660 MCA_RS10200
dapF diaminopimelate epimerase MCA_RS04230
lysA diaminopimelate decarboxylase MCA_RS04225
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase MCA_RS07330 MCA_RS07015
dapL N-acetyl-diaminopimelate deacetylase
DAPtransferase L,L-diaminopimelate aminotransferase MCA_RS02970 MCA_RS10050
dapX acetyl-diaminopimelate aminotransferase MCA_RS10785 MCA_RS10050
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase MCA_RS01250 MCA_RS11135
hicdh homo-isocitrate dehydrogenase MCA_RS15060 MCA_RS10100
lysJ [LysW]-2-aminoadipate semialdehyde transaminase MCA_RS10180 MCA_RS04000
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase MCA_RS10785 MCA_RS14695
lysT homoaconitase large subunit MCA_RS10110
lysU homoaconitase small subunit MCA_RS10105
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase MCA_RS03455
lysZ [LysW]-2-aminoadipate 6-kinase MCA_RS13615

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