GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Rhodospirillum rubrum ATCC 11170

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 (22 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase RRU_RS03870 RRU_RS12480
asd aspartate semi-aldehyde dehydrogenase RRU_RS06260
dapA 4-hydroxy-tetrahydrodipicolinate synthase RRU_RS09675 RRU_RS17285
dapB 4-hydroxy-tetrahydrodipicolinate reductase RRU_RS00795
dapD tetrahydrodipicolinate succinylase RRU_RS17975
dapC N-succinyldiaminopimelate aminotransferase RRU_RS05760 RRU_RS16910
dapE succinyl-diaminopimelate desuccinylase RRU_RS17980
dapF diaminopimelate epimerase RRU_RS06195
lysA diaminopimelate decarboxylase RRU_RS02090 RRU_RS08785
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase RRU_RS17975
dapL N-acetyl-diaminopimelate deacetylase RRU_RS09420 RRU_RS14810
DAPtransferase L,L-diaminopimelate aminotransferase RRU_RS12485 RRU_RS05925
dapX acetyl-diaminopimelate aminotransferase RRU_RS05925
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase RRU_RS11745 RRU_RS03625
hicdh homo-isocitrate dehydrogenase RRU_RS06235
lysJ [LysW]-2-aminoadipate semialdehyde transaminase RRU_RS16910 RRU_RS05985
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase RRU_RS05925 RRU_RS15510
lysT homoaconitase large subunit RRU_RS06225
lysU homoaconitase small subunit RRU_RS06230 RRU_RS18140
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase RRU_RS14275
lysY [LysW]-2-aminoadipate 6-phosphate reductase RRU_RS12535
lysZ [LysW]-2-aminoadipate 6-kinase RRU_RS17280

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