GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Methylohalobius crimeensis 10Ki

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 (22 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase H035_RS0101685 H035_RS0106110
asd aspartate semi-aldehyde dehydrogenase H035_RS0104810
dapA 4-hydroxy-tetrahydrodipicolinate synthase H035_RS0112360
dapB 4-hydroxy-tetrahydrodipicolinate reductase H035_RS0115830
dapD tetrahydrodipicolinate succinylase H035_RS0112230
dapC N-succinyldiaminopimelate aminotransferase H035_RS0112235 H035_RS0104740
dapE succinyl-diaminopimelate desuccinylase H035_RS0112220
dapF diaminopimelate epimerase H035_RS0111940
lysA diaminopimelate decarboxylase H035_RS0111945
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase H035_RS0112230 H035_RS0117045
dapL N-acetyl-diaminopimelate deacetylase H035_RS0104000
DAPtransferase L,L-diaminopimelate aminotransferase H035_RS0111195 H035_RS0108005
dapX acetyl-diaminopimelate aminotransferase H035_RS0116640 H035_RS0108005
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase H035_RS0101200 H035_RS0104410
hicdh homo-isocitrate dehydrogenase H035_RS0105365 H035_RS0110400
lysJ [LysW]-2-aminoadipate semialdehyde transaminase H035_RS0106595 H035_RS0104615
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase H035_RS0116640 H035_RS0106595
lysT homoaconitase large subunit H035_RS0101725 H035_RS0104795
lysU homoaconitase small subunit H035_RS0101725 H035_RS0104800
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase H035_RS0108665
lysY [LysW]-2-aminoadipate 6-phosphate reductase H035_RS0106115
lysZ [LysW]-2-aminoadipate 6-kinase H035_RS0106980

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