GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Methylocystis bryophila S285

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 B1812_RS16990
asd aspartate semi-aldehyde dehydrogenase B1812_RS15710
dapA 4-hydroxy-tetrahydrodipicolinate synthase B1812_RS00335 B1812_RS13730
dapB 4-hydroxy-tetrahydrodipicolinate reductase B1812_RS08615
dapD tetrahydrodipicolinate succinylase B1812_RS02260
dapC N-succinyldiaminopimelate aminotransferase B1812_RS08285 B1812_RS12405
dapE succinyl-diaminopimelate desuccinylase B1812_RS02270
dapF diaminopimelate epimerase B1812_RS00195
lysA diaminopimelate decarboxylase B1812_RS04965 B1812_RS06935
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase B1812_RS02260 B1812_RS20330
dapL N-acetyl-diaminopimelate deacetylase
DAPtransferase L,L-diaminopimelate aminotransferase B1812_RS20525 B1812_RS18690
dapX acetyl-diaminopimelate aminotransferase B1812_RS18690 B1812_RS19415
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase B1812_RS07870 B1812_RS03420
hicdh homo-isocitrate dehydrogenase B1812_RS12270
lysJ [LysW]-2-aminoadipate semialdehyde transaminase B1812_RS21480 B1812_RS09075
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase B1812_RS18690 B1812_RS21480
lysT homoaconitase large subunit B1812_RS09105
lysU homoaconitase small subunit B1812_RS09105 B1812_RS12650
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase B1812_RS01100
lysY [LysW]-2-aminoadipate 6-phosphate reductase
lysZ [LysW]-2-aminoadipate 6-kinase B1812_RS13860

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