GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Polaromonas naphthalenivorans CJ2

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 PNAP_RS14430
asd aspartate semi-aldehyde dehydrogenase PNAP_RS15215
dapA 4-hydroxy-tetrahydrodipicolinate synthase PNAP_RS05990 PNAP_RS07970
dapB 4-hydroxy-tetrahydrodipicolinate reductase PNAP_RS18935
dapD tetrahydrodipicolinate succinylase PNAP_RS09070
dapC N-succinyldiaminopimelate aminotransferase PNAP_RS09075 PNAP_RS13945
dapE succinyl-diaminopimelate desuccinylase PNAP_RS09060
dapF diaminopimelate epimerase PNAP_RS17155
lysA diaminopimelate decarboxylase PNAP_RS03315
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase PNAP_RS09070 PNAP_RS15640
dapL N-acetyl-diaminopimelate deacetylase PNAP_RS03225 PNAP_RS06250
DAPtransferase L,L-diaminopimelate aminotransferase PNAP_RS09075
dapX acetyl-diaminopimelate aminotransferase PNAP_RS14575 PNAP_RS07075
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase PNAP_RS11555 PNAP_RS08600
hicdh homo-isocitrate dehydrogenase PNAP_RS09675 PNAP_RS15210
lysJ [LysW]-2-aminoadipate semialdehyde transaminase PNAP_RS15060 PNAP_RS13135
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase PNAP_RS13135 PNAP_RS01975
lysT homoaconitase large subunit PNAP_RS15200
lysU homoaconitase small subunit PNAP_RS15205
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase
lysZ [LysW]-2-aminoadipate 6-kinase PNAP_RS17375

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