GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Paraburkholderia atlantica CCGE1002

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 BC1002_RS09065 BC1002_RS06830
asd aspartate semi-aldehyde dehydrogenase BC1002_RS25770
dapA 4-hydroxy-tetrahydrodipicolinate synthase BC1002_RS09275 BC1002_RS17520
dapB 4-hydroxy-tetrahydrodipicolinate reductase BC1002_RS13220
dapD tetrahydrodipicolinate succinylase BC1002_RS08850
dapC N-succinyldiaminopimelate aminotransferase BC1002_RS08845 BC1002_RS11180
dapE succinyl-diaminopimelate desuccinylase BC1002_RS08860 BC1002_RS29665
dapF diaminopimelate epimerase BC1002_RS00340
lysA diaminopimelate decarboxylase BC1002_RS24900 BC1002_RS14320
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase BC1002_RS22860 BC1002_RS08850
dapL N-acetyl-diaminopimelate deacetylase BC1002_RS30620 BC1002_RS13705
DAPtransferase L,L-diaminopimelate aminotransferase BC1002_RS20095 BC1002_RS34115
dapX acetyl-diaminopimelate aminotransferase BC1002_RS20095 BC1002_RS34115
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase BC1002_RS33980 BC1002_RS04680
hicdh homo-isocitrate dehydrogenase BC1002_RS12040 BC1002_RS22640
lysJ [LysW]-2-aminoadipate semialdehyde transaminase BC1002_RS05560 BC1002_RS11895
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase BC1002_RS04170 BC1002_RS26415
lysT homoaconitase large subunit BC1002_RS21590 BC1002_RS25750
lysU homoaconitase small subunit BC1002_RS25760 BC1002_RS21590
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase
lysZ [LysW]-2-aminoadipate 6-kinase BC1002_RS00285

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