GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome

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 Ga0074568_112978
asd aspartate semi-aldehyde dehydrogenase Ga0074568_112421
dapA 4-hydroxy-tetrahydrodipicolinate synthase Ga0074568_112419
dapB 4-hydroxy-tetrahydrodipicolinate reductase Ga0074568_114678
DAPtransferase L,L-diaminopimelate aminotransferase Ga0074568_115036 Ga0074568_112520
dapF diaminopimelate epimerase Ga0074568_111813
lysA diaminopimelate decarboxylase Ga0074568_11429
Alternative steps:
dapC N-succinyldiaminopimelate aminotransferase Ga0074568_115169 Ga0074568_11197
dapD tetrahydrodipicolinate succinylase
dapE succinyl-diaminopimelate desuccinylase
dapH tetrahydrodipicolinate acetyltransferase Ga0074568_113737 Ga0074568_112449
dapL N-acetyl-diaminopimelate deacetylase Ga0074568_111084 Ga0074568_114615
dapX acetyl-diaminopimelate aminotransferase Ga0074568_11123 Ga0074568_112746
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase Ga0074568_11628 Ga0074568_114539
hicdh homo-isocitrate dehydrogenase Ga0074568_113826 Ga0074568_112996
lysJ [LysW]-2-aminoadipate semialdehyde transaminase Ga0074568_11197 Ga0074568_1194
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase Ga0074568_112746 Ga0074568_11123
lysT homoaconitase large subunit Ga0074568_11108
lysU homoaconitase small subunit Ga0074568_111960
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase Ga0074568_1143
lysZ [LysW]-2-aminoadipate 6-kinase

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 Apr 09 2024. The underlying query database was built on Apr 09 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