GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Sulfurivirga caldicuralii DSM 17737

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 (20 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase BUQ81_RS06570 BUQ81_RS04880
asd aspartate semi-aldehyde dehydrogenase BUQ81_RS03695
dapA 4-hydroxy-tetrahydrodipicolinate synthase BUQ81_RS04725
dapB 4-hydroxy-tetrahydrodipicolinate reductase BUQ81_RS02825
dapD tetrahydrodipicolinate succinylase BUQ81_RS03940
dapC N-succinyldiaminopimelate aminotransferase BUQ81_RS05095 BUQ81_RS02435
dapE succinyl-diaminopimelate desuccinylase BUQ81_RS03950
dapF diaminopimelate epimerase BUQ81_RS06655
lysA diaminopimelate decarboxylase BUQ81_RS06980 BUQ81_RS07475
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase BUQ81_RS03940 BUQ81_RS06110
dapL N-acetyl-diaminopimelate deacetylase
DAPtransferase L,L-diaminopimelate aminotransferase BUQ81_RS04875 BUQ81_RS07000
dapX acetyl-diaminopimelate aminotransferase BUQ81_RS07000
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase BUQ81_RS06155
hicdh homo-isocitrate dehydrogenase BUQ81_RS04500 BUQ81_RS03680
lysJ [LysW]-2-aminoadipate semialdehyde transaminase BUQ81_RS02435 BUQ81_RS04050
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase BUQ81_RS07000 BUQ81_RS04050
lysT homoaconitase large subunit BUQ81_RS03670
lysU homoaconitase small subunit BUQ81_RS03675
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase BUQ81_RS07205
lysZ [LysW]-2-aminoadipate 6-kinase BUQ81_RS01510

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