GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Pseudomonas benzenivorans DSM 8628

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 BLS63_RS19300
asd aspartate semi-aldehyde dehydrogenase BLS63_RS07405 BLS63_RS07410
dapA 4-hydroxy-tetrahydrodipicolinate synthase BLS63_RS06945 BLS63_RS10000
dapB 4-hydroxy-tetrahydrodipicolinate reductase BLS63_RS14380
dapD tetrahydrodipicolinate succinylase BLS63_RS09325
dapC N-succinyldiaminopimelate aminotransferase BLS63_RS09340 BLS63_RS19255
dapE succinyl-diaminopimelate desuccinylase BLS63_RS09295 BLS63_RS08535
dapF diaminopimelate epimerase BLS63_RS11455
lysA diaminopimelate decarboxylase BLS63_RS11450 BLS63_RS22540
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase BLS63_RS08805 BLS63_RS05005
dapL N-acetyl-diaminopimelate deacetylase
DAPtransferase L,L-diaminopimelate aminotransferase BLS63_RS00825 BLS63_RS09340
dapX acetyl-diaminopimelate aminotransferase BLS63_RS09835
ddh meso-diaminopimelate D-dehydrogenase BLS63_RS17785
hcs homocitrate synthase BLS63_RS12035 BLS63_RS25765
hicdh homo-isocitrate dehydrogenase BLS63_RS01575 BLS63_RS07400
lysJ [LysW]-2-aminoadipate semialdehyde transaminase BLS63_RS19255 BLS63_RS07545
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase BLS63_RS01095 BLS63_RS09835
lysT homoaconitase large subunit BLS63_RS07390 BLS63_RS00030
lysU homoaconitase small subunit BLS63_RS07395 BLS63_RS00675
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase BLS63_RS25835
lysZ [LysW]-2-aminoadipate 6-kinase BLS63_RS18950

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