GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Dehalococcoides mccartyi 195

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 (18 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase DET_RS08340 DET_RS06220
asd aspartate semi-aldehyde dehydrogenase DET_RS05055
dapA 4-hydroxy-tetrahydrodipicolinate synthase DET_RS05060
dapB 4-hydroxy-tetrahydrodipicolinate reductase DET_RS05050
DAPtransferase L,L-diaminopimelate aminotransferase DET_RS03860 DET_RS06870
dapF diaminopimelate epimerase DET_RS03865
lysA diaminopimelate decarboxylase DET_RS02855
Alternative steps:
dapC N-succinyldiaminopimelate aminotransferase DET_RS03175 DET_RS06460
dapD tetrahydrodipicolinate succinylase
dapE succinyl-diaminopimelate desuccinylase
dapH tetrahydrodipicolinate acetyltransferase DET_RS08125
dapL N-acetyl-diaminopimelate deacetylase
dapX acetyl-diaminopimelate aminotransferase DET_RS06870 DET_RS03860
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase DET_RS04320 DET_RS08245
hicdh homo-isocitrate dehydrogenase DET_RS02445 DET_RS04285
lysJ [LysW]-2-aminoadipate semialdehyde transaminase DET_RS06460
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase DET_RS06870 DET_RS06460
lysT homoaconitase large subunit DET_RS04300 DET_RS02435
lysU homoaconitase small subunit DET_RS04290 DET_RS02440
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase DET_RS08305
lysZ [LysW]-2-aminoadipate 6-kinase DET_RS06455

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 Jul 25 2024. The underlying query database was built on Jul 25 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