GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Paraburkholderia phymatum STM815

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 BPHY_RS07060 BPHY_RS04720
asd aspartate semi-aldehyde dehydrogenase BPHY_RS21980
dapA 4-hydroxy-tetrahydrodipicolinate synthase BPHY_RS07270 BPHY_RS34160
dapB 4-hydroxy-tetrahydrodipicolinate reductase BPHY_RS13145
dapD tetrahydrodipicolinate succinylase BPHY_RS06845
dapC N-succinyldiaminopimelate aminotransferase BPHY_RS06840 BPHY_RS03730
dapE succinyl-diaminopimelate desuccinylase BPHY_RS06855 BPHY_RS30215
dapF diaminopimelate epimerase BPHY_RS00375
lysA diaminopimelate decarboxylase BPHY_RS14245
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase BPHY_RS06845 BPHY_RS24700
dapL N-acetyl-diaminopimelate deacetylase BPHY_RS09280 BPHY_RS13625
DAPtransferase L,L-diaminopimelate aminotransferase BPHY_RS03085 BPHY_RS06840
dapX acetyl-diaminopimelate aminotransferase BPHY_RS03085 BPHY_RS10105
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase BPHY_RS38190 BPHY_RS10290
hicdh homo-isocitrate dehydrogenase BPHY_RS02835 BPHY_RS21975
lysJ [LysW]-2-aminoadipate semialdehyde transaminase BPHY_RS09090 BPHY_RS23215
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase BPHY_RS24335 BPHY_RS10775
lysT homoaconitase large subunit BPHY_RS30890 BPHY_RS21960
lysU homoaconitase small subunit BPHY_RS21970 BPHY_RS34220
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase BPHY_RS29720
lysY [LysW]-2-aminoadipate 6-phosphate reductase
lysZ [LysW]-2-aminoadipate 6-kinase BPHY_RS00320

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