GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Nitriliruptor alkaliphilus DSM 45188

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 (19 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase NITAL_RS03510
asd aspartate semi-aldehyde dehydrogenase NITAL_RS03505
dapA 4-hydroxy-tetrahydrodipicolinate synthase NITAL_RS12925 NITAL_RS14020
dapB 4-hydroxy-tetrahydrodipicolinate reductase NITAL_RS12855
dapD tetrahydrodipicolinate succinylase NITAL_RS11720
dapC N-succinyldiaminopimelate aminotransferase NITAL_RS17575 NITAL_RS21545
dapE succinyl-diaminopimelate desuccinylase NITAL_RS11715 NITAL_RS25895
dapF diaminopimelate epimerase NITAL_RS13175
lysA diaminopimelate decarboxylase NITAL_RS10480
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase NITAL_RS01230 NITAL_RS29125
dapL N-acetyl-diaminopimelate deacetylase
DAPtransferase L,L-diaminopimelate aminotransferase NITAL_RS11740 NITAL_RS17580
dapX acetyl-diaminopimelate aminotransferase NITAL_RS17580 NITAL_RS21545
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase NITAL_RS11500 NITAL_RS11655
hicdh homo-isocitrate dehydrogenase NITAL_RS11625
lysJ [LysW]-2-aminoadipate semialdehyde transaminase NITAL_RS16995 NITAL_RS04820
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase NITAL_RS17580 NITAL_RS00620
lysT homoaconitase large subunit NITAL_RS17280
lysU homoaconitase small subunit NITAL_RS17280 NITAL_RS11515
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase NITAL_RS16980
lysZ [LysW]-2-aminoadipate 6-kinase

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