GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Echinicola vietnamensis KMM 6221, DSM 17526

Manual classification of gap: novel
Rationale: This organism probably uses succinylated intermediates, as Echvi_3551 is a good candidate for the succinyltransferase DapD. But the aminotransferase and the desuccinylase cannot be found. Alternatively, Echvi_0124 could be a diverged diamopimelate aminotransferase.

Best path

asp-kinase, asd, dapA, dapB, DAPtransferase?, 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 Echvi_2000 Echvi_1218
asd aspartate semi-aldehyde dehydrogenase Echvi_0713
dapA 4-hydroxy-tetrahydrodipicolinate synthase Echvi_3959 Echvi_3953
dapB 4-hydroxy-tetrahydrodipicolinate reductase Echvi_2395
DAPtransferase? L,L-diaminopimelate aminotransferase Echvi_0124 Echvi_0656
dapF diaminopimelate epimerase Echvi_1430
lysA diaminopimelate decarboxylase Echvi_1295
Alternative steps:
dapC? N-succinyldiaminopimelate aminotransferase Echvi_3848 Echvi_0577
dapD tetrahydrodipicolinate succinylase Echvi_3551
dapE? succinyl-diaminopimelate desuccinylase
dapH? tetrahydrodipicolinate acetyltransferase Echvi_3551 Echvi_0942
dapL? N-acetyl-diaminopimelate deacetylase Echvi_0302 Echvi_1427
dapX? acetyl-diaminopimelate aminotransferase Echvi_0675
ddh? meso-diaminopimelate D-dehydrogenase
hcs? homocitrate synthase Echvi_3833 Echvi_2061
hicdh? homo-isocitrate dehydrogenase Echvi_4068 Echvi_2062
lysJ? [LysW]-2-aminoadipate semialdehyde transaminase / [LysW]-glutamate semialdehyde transaminase Echvi_3848 Echvi_2919
lysK? [LysW]-lysine hydrolase / [LysW]-ornithine hydrolase
lysN? 2-aminoadipate:2-oxoglutarate aminotransferase Echvi_0675 Echvi_3848
lysT? homoaconitase large subunit Echvi_2531 Echvi_2059
lysU? homoaconitase small subunit Echvi_2060 Echvi_4039
lysW? 2-aminoadipate/glutamate carrier protein
lysX? 2-aminoadipate-LysW ligase
lysY? [LysW]-2-aminoadipate 6-phosphate reductase / [LysW]-glutamylphosphate reductase Echvi_3847
lysZ? [LysW]-2-aminoadipate 6-kinase / [LysW]-glutamate kinase Echvi_3850

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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