GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Magnetospirillum magneticum AMB-1

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 (20 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase AMB_RS08140
asd aspartate semi-aldehyde dehydrogenase AMB_RS03035
dapA 4-hydroxy-tetrahydrodipicolinate synthase AMB_RS12805 AMB_RS11575
dapB 4-hydroxy-tetrahydrodipicolinate reductase AMB_RS22745
dapD tetrahydrodipicolinate succinylase AMB_RS19595
dapC N-succinyldiaminopimelate aminotransferase AMB_RS16135 AMB_RS01605
dapE succinyl-diaminopimelate desuccinylase AMB_RS19600 AMB_RS11990
dapF diaminopimelate epimerase AMB_RS01095
lysA diaminopimelate decarboxylase AMB_RS22725 AMB_RS07020
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase AMB_RS19595 AMB_RS00270
dapL N-acetyl-diaminopimelate deacetylase
DAPtransferase L,L-diaminopimelate aminotransferase AMB_RS18860 AMB_RS00825
dapX acetyl-diaminopimelate aminotransferase AMB_RS02875 AMB_RS07030
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase AMB_RS07875 AMB_RS17765
hicdh homo-isocitrate dehydrogenase AMB_RS16020 AMB_RS20570
lysJ [LysW]-2-aminoadipate semialdehyde transaminase / [LysW]-glutamate semialdehyde transaminase AMB_RS01605 AMB_RS04150
lysK [LysW]-lysine hydrolase / [LysW]-ornithine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase AMB_RS02875 AMB_RS01605
lysT homoaconitase large subunit AMB_RS20560
lysU homoaconitase small subunit AMB_RS20565 AMB_RS18485
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase / [LysW]-glutamylphosphate reductase AMB_RS09075
lysZ [LysW]-2-aminoadipate 6-kinase / [LysW]-glutamate kinase AMB_RS22045

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