GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Burkholderia phytofirmans PsJN

Best path

asp-kinase, asd, dapA, dapB, dapD, dapC, dapE, 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 BPHYT_RS12410
asd aspartate semi-aldehyde dehydrogenase BPHYT_RS33895
dapA 4-hydroxy-tetrahydrodipicolinate synthase BPHYT_RS30940 BPHYT_RS12615
dapB 4-hydroxy-tetrahydrodipicolinate reductase BPHYT_RS16800
dapD tetrahydrodipicolinate succinylase BPHYT_RS12190
dapC N-succinyldiaminopimelate aminotransferase BPHYT_RS12185 BPHYT_RS14915
dapE succinyl-diaminopimelate desuccinylase BPHYT_RS12200 BPHYT_RS11720
dapF diaminopimelate epimerase BPHYT_RS01665
lysA diaminopimelate decarboxylase BPHYT_RS35090 BPHYT_RS17930
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase BPHYT_RS12190 BPHYT_RS12655
dapL N-acetyl-diaminopimelate deacetylase BPHYT_RS17305 BPHYT_RS07500
DAPtransferase L,L-diaminopimelate aminotransferase BPHYT_RS27000 BPHYT_RS03565
dapX acetyl-diaminopimelate aminotransferase BPHYT_RS15405 BPHYT_RS27000
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase BPHYT_RS06570 BPHYT_RS13280
hicdh homo-isocitrate dehydrogenase BPHYT_RS15730 BPHYT_RS30235
lysJ [LysW]-2-aminoadipate semialdehyde transaminase / [LysW]-glutamate semialdehyde transaminase BPHYT_RS07695 BPHYT_RS22435
lysK [LysW]-lysine hydrolase / [LysW]-ornithine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase BPHYT_RS05965 BPHYT_RS22435
lysT homoaconitase large subunit BPHYT_RS13520 BPHYT_RS23060
lysU homoaconitase small subunit BPHYT_RS33905 BPHYT_RS13515
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase / [LysW]-glutamylphosphate reductase
lysZ [LysW]-2-aminoadipate 6-kinase / [LysW]-glutamate kinase BPHYT_RS01610

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 (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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, 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