GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Desulfovibrio vulgaris Hildenborough

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
asp-kinase aspartate kinase DVU1913
asd aspartate semi-aldehyde dehydrogenase DVU3048
dapA 4-hydroxy-tetrahydrodipicolinate synthase DVU1868
dapB 4-hydroxy-tetrahydrodipicolinate reductase DVU1609
DAPtransferase L,L-diaminopimelate aminotransferase DVU1655 DVU0891
dapF diaminopimelate epimerase DVU1867
lysA diaminopimelate decarboxylase DVU1647 DVU2566
Alternative steps:
dapC N-succinyldiaminopimelate aminotransferase DVU2347 DVU0494
dapD tetrahydrodipicolinate succinylase
dapE succinyl-diaminopimelate desuccinylase
dapH tetrahydrodipicolinate acetyltransferase DVU0340 DVU0347
dapL N-acetyl-diaminopimelate deacetylase DVU2568
dapX acetyl-diaminopimelate aminotransferase DVU3223 DVU0392
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase DVU2981 DVUA0016
hicdh homo-isocitrate dehydrogenase DVU0477 DVU2985
lysJ [LysW]-2-aminoadipate semialdehyde transaminase / [LysW]-glutamate semialdehyde transaminase DVU2347 DVU3168
lysK [LysW]-lysine hydrolase / [LysW]-ornithine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase DVU2364 DVU3223
lysT homoaconitase large subunit DVU2982 DVU1064
lysU homoaconitase small subunit DVU2983 DVU1064
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase / [LysW]-glutamylphosphate reductase DVU0492
lysZ [LysW]-2-aminoadipate 6-kinase / [LysW]-glutamate kinase DVU1466

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