GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Geotalea uraniireducens Rf4

Best path

asp-kinase, asd, dapA, dapB, DAPtransferase, 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 (18 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase GURA_RS11775 GURA_RS11050
asd aspartate semi-aldehyde dehydrogenase GURA_RS05295 GURA_RS05300
dapA 4-hydroxy-tetrahydrodipicolinate synthase GURA_RS01175
dapB 4-hydroxy-tetrahydrodipicolinate reductase GURA_RS01180
DAPtransferase L,L-diaminopimelate aminotransferase GURA_RS01195
dapF diaminopimelate epimerase GURA_RS19900
lysA diaminopimelate decarboxylase GURA_RS01170
Alternative steps:
dapC N-succinyldiaminopimelate aminotransferase GURA_RS01135 GURA_RS04390
dapD tetrahydrodipicolinate succinylase
dapE succinyl-diaminopimelate desuccinylase
dapH tetrahydrodipicolinate acetyltransferase GURA_RS20785 GURA_RS08630
dapL N-acetyl-diaminopimelate deacetylase
dapX acetyl-diaminopimelate aminotransferase GURA_RS12735
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase GURA_RS17150 GURA_RS18920
hicdh homo-isocitrate dehydrogenase GURA_RS05290
lysJ [LysW]-2-aminoadipate semialdehyde transaminase GURA_RS01135 GURA_RS00600
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase GURA_RS12735 GURA_RS00600
lysT homoaconitase large subunit GURA_RS18890 GURA_RS06455
lysU homoaconitase small subunit GURA_RS06455 GURA_RS18885
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase GURA_RS05320
lysZ [LysW]-2-aminoadipate 6-kinase GURA_RS01130

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 Apr 09 2024. The underlying query database was built on Apr 09 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