GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Bacteroides thetaiotaomicron VPI-5482

Best path

asp-kinase, asd, dapA, dapB, DAPtransferase, dapF, lysA

Also see fitness data for the top candidates

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 BT2403 BT1375
asd aspartate semi-aldehyde dehydrogenase BT3636
dapA 4-hydroxy-tetrahydrodipicolinate synthase BT0895
dapB 4-hydroxy-tetrahydrodipicolinate reductase BT3320
DAPtransferase L,L-diaminopimelate aminotransferase BT0547 BT3935
dapF diaminopimelate epimerase BT0548
lysA diaminopimelate decarboxylase BT1374
Alternative steps:
dapC N-succinyldiaminopimelate aminotransferase BT1153 BT3758
dapD tetrahydrodipicolinate succinylase
dapE succinyl-diaminopimelate desuccinylase
dapH tetrahydrodipicolinate acetyltransferase BT0521 BT2943
dapL N-acetyl-diaminopimelate deacetylase
dapX acetyl-diaminopimelate aminotransferase BT2415 BT3720
ddh meso-diaminopimelate D-dehydrogenase BT1979
hcs homocitrate synthase BT1861 BT1858
hicdh homo-isocitrate dehydrogenase BT2071 BT1857
lysJ [LysW]-2-aminoadipate semialdehyde transaminase / [LysW]-glutamate semialdehyde transaminase BT3758 BT1442
lysK [LysW]-lysine hydrolase / [LysW]-ornithine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase BT2415 BT3375
lysT homoaconitase large subunit BT1860
lysU homoaconitase small subunit BT1859
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase BT1474
lysY [LysW]-2-aminoadipate 6-phosphate reductase / [LysW]-glutamylphosphate reductase BT3759
lysZ [LysW]-2-aminoadipate 6-kinase / [LysW]-glutamate kinase BT3395

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 Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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