GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Azorhizobium caulinodans ORS 571

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 AZC_RS23020 AZC_RS09580
asd aspartate semi-aldehyde dehydrogenase AZC_RS19225
dapA 4-hydroxy-tetrahydrodipicolinate synthase AZC_RS06400 AZC_RS00890
dapB 4-hydroxy-tetrahydrodipicolinate reductase AZC_RS00790
dapD tetrahydrodipicolinate succinylase AZC_RS01075
dapC N-succinyldiaminopimelate aminotransferase AZC_RS05045 AZC_RS20660
dapE succinyl-diaminopimelate desuccinylase AZC_RS02805 AZC_RS01015
dapF diaminopimelate epimerase AZC_RS19115
lysA diaminopimelate decarboxylase AZC_RS23865 AZC_RS01695
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase AZC_RS01075 AZC_RS17795
dapL N-acetyl-diaminopimelate deacetylase AZC_RS11380 AZC_RS10745
DAPtransferase L,L-diaminopimelate aminotransferase AZC_RS09575 AZC_RS02835
dapX acetyl-diaminopimelate aminotransferase AZC_RS02835 AZC_RS16160
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase AZC_RS17440 AZC_RS18230
hicdh homo-isocitrate dehydrogenase AZC_RS01545
lysJ [LysW]-2-aminoadipate semialdehyde transaminase AZC_RS20660 AZC_RS08540
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase AZC_RS16160 AZC_RS02835
lysT homoaconitase large subunit AZC_RS20820 AZC_RS10900
lysU homoaconitase small subunit AZC_RS20805 AZC_RS10905
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase AZC_RS12990 AZC_RS05165
lysZ [LysW]-2-aminoadipate 6-kinase AZC_RS03585

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.

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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