GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Steroidobacter denitrificans DSM 18526

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 ACG33_RS07605 ACG33_RS08530
asd aspartate semi-aldehyde dehydrogenase ACG33_RS10380
dapA 4-hydroxy-tetrahydrodipicolinate synthase ACG33_RS09080
dapB 4-hydroxy-tetrahydrodipicolinate reductase ACG33_RS06815
dapD tetrahydrodipicolinate succinylase ACG33_RS09700
dapC N-succinyldiaminopimelate aminotransferase ACG33_RS09695 ACG33_RS07085
dapE succinyl-diaminopimelate desuccinylase ACG33_RS09725
dapF diaminopimelate epimerase ACG33_RS14780
lysA diaminopimelate decarboxylase ACG33_RS07605 ACG33_RS06180
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase ACG33_RS09700 ACG33_RS04720
dapL N-acetyl-diaminopimelate deacetylase
DAPtransferase L,L-diaminopimelate aminotransferase ACG33_RS07200 ACG33_RS09695
dapX acetyl-diaminopimelate aminotransferase ACG33_RS07200
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase ACG33_RS15040
hicdh homo-isocitrate dehydrogenase ACG33_RS02935 ACG33_RS08110
lysJ [LysW]-2-aminoadipate semialdehyde transaminase ACG33_RS14145 ACG33_RS02865
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase ACG33_RS07200 ACG33_RS14145
lysT homoaconitase large subunit ACG33_RS08100
lysU homoaconitase small subunit ACG33_RS08105 ACG33_RS08210
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase ACG33_RS14140
lysZ [LysW]-2-aminoadipate 6-kinase ACG33_RS14155

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