GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Sulfurihydrogenibium azorense Az-Fu1

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 SULAZ_RS07315
asd aspartate semi-aldehyde dehydrogenase SULAZ_RS08120
dapA 4-hydroxy-tetrahydrodipicolinate synthase SULAZ_RS00705
dapB 4-hydroxy-tetrahydrodipicolinate reductase SULAZ_RS07200
dapD tetrahydrodipicolinate succinylase SULAZ_RS08405
dapC N-succinyldiaminopimelate aminotransferase SULAZ_RS07135 SULAZ_RS03325
dapE succinyl-diaminopimelate desuccinylase SULAZ_RS03830
dapF diaminopimelate epimerase SULAZ_RS04740
lysA diaminopimelate decarboxylase SULAZ_RS01920
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase SULAZ_RS08405 SULAZ_RS01670
dapL N-acetyl-diaminopimelate deacetylase
DAPtransferase L,L-diaminopimelate aminotransferase SULAZ_RS05275 SULAZ_RS07135
dapX acetyl-diaminopimelate aminotransferase SULAZ_RS01475
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase SULAZ_RS03750 SULAZ_RS07270
hicdh homo-isocitrate dehydrogenase SULAZ_RS02550 SULAZ_RS01325
lysJ [LysW]-2-aminoadipate semialdehyde transaminase SULAZ_RS04620 SULAZ_RS03325
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase SULAZ_RS01475 SULAZ_RS04620
lysT homoaconitase large subunit SULAZ_RS03795
lysU homoaconitase small subunit SULAZ_RS07575
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase SULAZ_RS02150
lysZ [LysW]-2-aminoadipate 6-kinase SULAZ_RS07475

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