GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Azospirillum sp. B510

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 AZL_RS00615 AZL_RS05775
asd aspartate semi-aldehyde dehydrogenase AZL_RS12765 AZL_RS07565
dapA 4-hydroxy-tetrahydrodipicolinate synthase AZL_RS07425 AZL_RS23055
dapB 4-hydroxy-tetrahydrodipicolinate reductase AZL_RS27725
dapD tetrahydrodipicolinate succinylase AZL_RS02690
dapC N-succinyldiaminopimelate aminotransferase AZL_RS25025 AZL_RS02205
dapE succinyl-diaminopimelate desuccinylase AZL_RS02685 AZL_RS31045
dapF diaminopimelate epimerase AZL_RS04715
lysA diaminopimelate decarboxylase AZL_RS27915 AZL_RS03275
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase AZL_RS02690 AZL_RS15905
dapL N-acetyl-diaminopimelate deacetylase AZL_RS00880
DAPtransferase L,L-diaminopimelate aminotransferase AZL_RS05770 AZL_RS12610
dapX acetyl-diaminopimelate aminotransferase AZL_RS01020 AZL_RS12610
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase AZL_RS03450 AZL_RS12885
hicdh homo-isocitrate dehydrogenase AZL_RS08920 AZL_RS26200
lysJ [LysW]-2-aminoadipate semialdehyde transaminase AZL_RS24705 AZL_RS02205
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase AZL_RS01020 AZL_RS24705
lysT homoaconitase large subunit AZL_RS12740 AZL_RS26840
lysU homoaconitase small subunit AZL_RS04735 AZL_RS13010
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase AZL_RS15610
lysZ [LysW]-2-aminoadipate 6-kinase AZL_RS02775

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