GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Desulfacinum infernum DSM 9756

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 BUB04_RS10965 BUB04_RS09005
asd aspartate semi-aldehyde dehydrogenase BUB04_RS15000
dapA 4-hydroxy-tetrahydrodipicolinate synthase BUB04_RS11085
dapB 4-hydroxy-tetrahydrodipicolinate reductase BUB04_RS11090
DAPtransferase L,L-diaminopimelate aminotransferase BUB04_RS11095 BUB04_RS09000
dapF diaminopimelate epimerase BUB04_RS11080
lysA diaminopimelate decarboxylase BUB04_RS11075
Alternative steps:
dapC N-succinyldiaminopimelate aminotransferase BUB04_RS01670 BUB04_RS11050
dapD tetrahydrodipicolinate succinylase
dapE succinyl-diaminopimelate desuccinylase
dapH tetrahydrodipicolinate acetyltransferase BUB04_RS12775 BUB04_RS20020
dapL N-acetyl-diaminopimelate deacetylase
dapX acetyl-diaminopimelate aminotransferase BUB04_RS02665 BUB04_RS00280
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase BUB04_RS10320 BUB04_RS14925
hicdh homo-isocitrate dehydrogenase BUB04_RS07005 BUB04_RS09920
lysJ [LysW]-2-aminoadipate semialdehyde transaminase BUB04_RS11050 BUB04_RS10885
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase BUB04_RS02665 BUB04_RS02225
lysT homoaconitase large subunit BUB04_RS06990 BUB04_RS15010
lysU homoaconitase small subunit BUB04_RS15005 BUB04_RS06995
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase BUB04_RS02655
lysZ [LysW]-2-aminoadipate 6-kinase BUB04_RS11045

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