GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Pseudomonas putida KT2440

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 PP_4473
asd aspartate semi-aldehyde dehydrogenase PP_1989 PP_1992
dapA 4-hydroxy-tetrahydrodipicolinate synthase PP_1257 PP_1237
dapB 4-hydroxy-tetrahydrodipicolinate reductase PP_4725
dapD tetrahydrodipicolinate succinylase PP_1530
dapC N-succinyldiaminopimelate aminotransferase PP_1588 PP_1768
dapE succinyl-diaminopimelate desuccinylase PP_1525 PP_3571
dapF diaminopimelate epimerase PP_5228 PP_3790
lysA diaminopimelate decarboxylase PP_5227 PP_2077
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase PP_3134 PP_5163
dapL N-acetyl-diaminopimelate deacetylase PP_2704
DAPtransferase L,L-diaminopimelate aminotransferase PP_0817 PP_3786
dapX acetyl-diaminopimelate aminotransferase PP_3721 PP_4692
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase PP_1791
hicdh homo-isocitrate dehydrogenase PP_4011 PP_1988
lysJ [LysW]-2-aminoadipate semialdehyde transaminase / [LysW]-glutamate semialdehyde transaminase PP_4481 PP_4223
lysK [LysW]-lysine hydrolase / [LysW]-ornithine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase PP_4108 PP_0214
lysT homoaconitase large subunit PP_1985
lysU homoaconitase small subunit PP_1986
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase / [LysW]-glutamylphosphate reductase PP_0432
lysZ [LysW]-2-aminoadipate 6-kinase / [LysW]-glutamate kinase PP_5289

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.

Links

Downloads

Related tools

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