GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Thiothrix lacustris DSM 21227

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 Q394_RS0102305 Q394_RS0109355
asd aspartate semi-aldehyde dehydrogenase Q394_RS0107450 Q394_RS0115260
dapA 4-hydroxy-tetrahydrodipicolinate synthase Q394_RS0113940 Q394_RS0112085
dapB 4-hydroxy-tetrahydrodipicolinate reductase Q394_RS0102825
dapD tetrahydrodipicolinate succinylase Q394_RS0111475
dapC N-succinyldiaminopimelate aminotransferase Q394_RS0111480 Q394_RS0108430
dapE succinyl-diaminopimelate desuccinylase Q394_RS0109740
dapF diaminopimelate epimerase Q394_RS0110665
lysA diaminopimelate decarboxylase Q394_RS0107235
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase Q394_RS0111475
dapL N-acetyl-diaminopimelate deacetylase Q394_RS0101535
DAPtransferase L,L-diaminopimelate aminotransferase Q394_RS0109350 Q394_RS0111480
dapX acetyl-diaminopimelate aminotransferase Q394_RS0100140 Q394_RS0109310
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase Q394_RS0111610
hicdh homo-isocitrate dehydrogenase Q394_RS0114485 Q394_RS0115255
lysJ [LysW]-2-aminoadipate semialdehyde transaminase Q394_RS0113995 Q394_RS0104770
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase Q394_RS0100140 Q394_RS0113995
lysT homoaconitase large subunit Q394_RS0115245
lysU homoaconitase small subunit Q394_RS0115250
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase Q394_RS0116805
lysZ [LysW]-2-aminoadipate 6-kinase Q394_RS0100450

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