GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Pseudomonas stutzeri RCH2

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 (21 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase Psest_4094 Psest_2988
asd aspartate semi-aldehyde dehydrogenase Psest_2588 Psest_2587
dapA 4-hydroxy-tetrahydrodipicolinate synthase Psest_1515
dapB 4-hydroxy-tetrahydrodipicolinate reductase Psest_0966
dapD tetrahydrodipicolinate succinylase Psest_1465
dapC N-succinyldiaminopimelate aminotransferase Psest_1470 Psest_1983
dapE succinyl-diaminopimelate desuccinylase Psest_1618
dapF diaminopimelate epimerase Psest_3765
lysA diaminopimelate decarboxylase Psest_3764
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase Psest_0465 Psest_3139
dapL N-acetyl-diaminopimelate deacetylase Psest_1585
DAPtransferase L,L-diaminopimelate aminotransferase Psest_1917 Psest_1470
dapX acetyl-diaminopimelate aminotransferase Psest_1004 Psest_1268
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase Psest_1056
hicdh homo-isocitrate dehydrogenase Psest_2024 Psest_2589
lysJ [LysW]-2-aminoadipate semialdehyde transaminase / [LysW]-glutamate semialdehyde transaminase Psest_2719 Psest_3653
lysK [LysW]-lysine hydrolase / [LysW]-ornithine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase Psest_3653 Psest_1990
lysT homoaconitase large subunit Psest_2591
lysU homoaconitase small subunit Psest_2590
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase / [LysW]-glutamylphosphate reductase Psest_3639
lysZ [LysW]-2-aminoadipate 6-kinase / [LysW]-glutamate kinase Psest_3807

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 paper from 2022 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