GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Cupriavidus basilensis FW507-4G11

Best path

asp-kinase, asd, dapA, dapB, dapD, dapC, dapE, dapF, lysA

Also see fitness data for the top candidates

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 RR42_RS06370 RR42_RS12540
asd aspartate semi-aldehyde dehydrogenase RR42_RS14380
dapA 4-hydroxy-tetrahydrodipicolinate synthase RR42_RS06250 RR42_RS17475
dapB 4-hydroxy-tetrahydrodipicolinate reductase RR42_RS17550 RR42_RS18515
dapD tetrahydrodipicolinate succinylase RR42_RS11935
dapC N-succinyldiaminopimelate aminotransferase RR42_RS11930 RR42_RS04455
dapE succinyl-diaminopimelate desuccinylase RR42_RS11950 RR42_RS07840
dapF diaminopimelate epimerase RR42_RS01250
lysA diaminopimelate decarboxylase RR42_RS19050
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase RR42_RS11935 RR42_RS06325
dapL N-acetyl-diaminopimelate deacetylase RR42_RS18215 RR42_RS00390
DAPtransferase L,L-diaminopimelate aminotransferase RR42_RS28540 RR42_RS35305
dapX acetyl-diaminopimelate aminotransferase RR42_RS35305 RR42_RS15580
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase RR42_RS05465 RR42_RS21205
hicdh homo-isocitrate dehydrogenase RR42_RS22955 RR42_RS17135
lysJ [LysW]-2-aminoadipate semialdehyde transaminase RR42_RS26240 RR42_RS21370
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase RR42_RS35305 RR42_RS21370
lysT homoaconitase large subunit RR42_RS21085 RR42_RS01530
lysU homoaconitase small subunit RR42_RS21080 RR42_RS01535
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase
lysZ [LysW]-2-aminoadipate 6-kinase RR42_RS01125

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