GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Amycolatopsis halophila YIM 93223

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 (21 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase AMYHA_RS05000
asd aspartate semi-aldehyde dehydrogenase AMYHA_RS05005
dapA 4-hydroxy-tetrahydrodipicolinate synthase AMYHA_RS16680 AMYHA_RS13055
dapB 4-hydroxy-tetrahydrodipicolinate reductase AMYHA_RS16735
dapD tetrahydrodipicolinate succinylase AMYHA_RS24955
dapC N-succinyldiaminopimelate aminotransferase AMYHA_RS06245 AMYHA_RS24965
dapE succinyl-diaminopimelate desuccinylase AMYHA_RS24945 AMYHA_RS25250
dapF diaminopimelate epimerase AMYHA_RS18225
lysA diaminopimelate decarboxylase AMYHA_RS22275 AMYHA_RS06045
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase AMYHA_RS17140 AMYHA_RS17410
dapL N-acetyl-diaminopimelate deacetylase AMYHA_RS25250
DAPtransferase L,L-diaminopimelate aminotransferase AMYHA_RS24965 AMYHA_RS01585
dapX acetyl-diaminopimelate aminotransferase AMYHA_RS01030 AMYHA_RS03915
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase AMYHA_RS20250
hicdh homo-isocitrate dehydrogenase AMYHA_RS20255
lysJ [LysW]-2-aminoadipate semialdehyde transaminase AMYHA_RS15990 AMYHA_RS17620
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase AMYHA_RS01030 AMYHA_RS07330
lysT homoaconitase large subunit AMYHA_RS18810 AMYHA_RS20130
lysU homoaconitase small subunit AMYHA_RS18810 AMYHA_RS20125
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase AMYHA_RS16005
lysZ [LysW]-2-aminoadipate 6-kinase AMYHA_RS15995

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 Jul 26 2024. The underlying query database was built on Jul 25 2024.

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:

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