GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Methylocapsa acidiphila B2

Best path

asp-kinase, asd, dapA, dapB, dapD, dapC, dapE, 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 METAC_RS0111830
asd aspartate semi-aldehyde dehydrogenase METAC_RS0113665
dapA 4-hydroxy-tetrahydrodipicolinate synthase METAC_RS0119080
dapB 4-hydroxy-tetrahydrodipicolinate reductase METAC_RS0118120
dapD tetrahydrodipicolinate succinylase METAC_RS0110905
dapC N-succinyldiaminopimelate aminotransferase METAC_RS0102515 METAC_RS0109860
dapE succinyl-diaminopimelate desuccinylase METAC_RS0105125
dapF diaminopimelate epimerase METAC_RS0115680
lysA diaminopimelate decarboxylase METAC_RS0110950 METAC_RS0120605
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase METAC_RS0110905
dapL N-acetyl-diaminopimelate deacetylase
DAPtransferase L,L-diaminopimelate aminotransferase
dapX acetyl-diaminopimelate aminotransferase METAC_RS0118105 METAC_RS0104560
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase METAC_RS23590 METAC_RS0107285
hicdh homo-isocitrate dehydrogenase METAC_RS0113685
lysJ [LysW]-2-aminoadipate semialdehyde transaminase METAC_RS0109860 METAC_RS0116010
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase METAC_RS0118105 METAC_RS23925
lysT homoaconitase large subunit METAC_RS0109580
lysU homoaconitase small subunit METAC_RS0120650 METAC_RS0113690
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase METAC_RS0121250
lysY [LysW]-2-aminoadipate 6-phosphate reductase
lysZ [LysW]-2-aminoadipate 6-kinase METAC_RS0102300

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