GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Paraburkholderia bryophila 376MFSha3.1

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 H281DRAFT_00550
asd aspartate semi-aldehyde dehydrogenase H281DRAFT_06071
dapA 4-hydroxy-tetrahydrodipicolinate synthase H281DRAFT_01195 H281DRAFT_01829
dapB 4-hydroxy-tetrahydrodipicolinate reductase H281DRAFT_06318
dapD tetrahydrodipicolinate succinylase H281DRAFT_00599
dapC N-succinyldiaminopimelate aminotransferase H281DRAFT_00600 H281DRAFT_03926
dapE succinyl-diaminopimelate desuccinylase H281DRAFT_00597 H281DRAFT_04940
dapF diaminopimelate epimerase H281DRAFT_02200
lysA diaminopimelate decarboxylase H281DRAFT_05606
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase H281DRAFT_01622 H281DRAFT_00599
dapL N-acetyl-diaminopimelate deacetylase H281DRAFT_01513 H281DRAFT_06512
DAPtransferase L,L-diaminopimelate aminotransferase H281DRAFT_04693 H281DRAFT_02907
dapX acetyl-diaminopimelate aminotransferase H281DRAFT_04024 H281DRAFT_02907
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase H281DRAFT_04556 H281DRAFT_00385
hicdh homo-isocitrate dehydrogenase H281DRAFT_04085 H281DRAFT_06345
lysJ [LysW]-2-aminoadipate semialdehyde transaminase / [LysW]-glutamate semialdehyde transaminase H281DRAFT_04057 H281DRAFT_06478
lysK [LysW]-lysine hydrolase / [LysW]-ornithine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase H281DRAFT_00271 H281DRAFT_03179
lysT homoaconitase large subunit H281DRAFT_02541 H281DRAFT_05063
lysU homoaconitase small subunit H281DRAFT_06073 H281DRAFT_02540
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 H281DRAFT_02211

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