GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Thermocrinis albus DSM 14484

Best path

asp-kinase, asd, dapA, dapB, DAPtransferase, 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 (17 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase THAL_RS01760
asd aspartate semi-aldehyde dehydrogenase THAL_RS07710
dapA 4-hydroxy-tetrahydrodipicolinate synthase THAL_RS00255
dapB 4-hydroxy-tetrahydrodipicolinate reductase THAL_RS05130
DAPtransferase L,L-diaminopimelate aminotransferase THAL_RS07720 THAL_RS00345
dapF diaminopimelate epimerase THAL_RS06550
lysA diaminopimelate decarboxylase THAL_RS04195 THAL_RS01725
Alternative steps:
dapC N-succinyldiaminopimelate aminotransferase THAL_RS01365 THAL_RS04470
dapD tetrahydrodipicolinate succinylase
dapE succinyl-diaminopimelate desuccinylase
dapH tetrahydrodipicolinate acetyltransferase
dapL N-acetyl-diaminopimelate deacetylase
dapX acetyl-diaminopimelate aminotransferase THAL_RS00165 THAL_RS02360
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase THAL_RS05225 THAL_RS02075
hicdh homo-isocitrate dehydrogenase THAL_RS03255 THAL_RS02960
lysJ [LysW]-2-aminoadipate semialdehyde transaminase THAL_RS01365 THAL_RS02335
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase THAL_RS00165 THAL_RS01365
lysT homoaconitase large subunit THAL_RS03450 THAL_RS04270
lysU homoaconitase small subunit THAL_RS07500 THAL_RS03450
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase THAL_RS02425
lysZ [LysW]-2-aminoadipate 6-kinase THAL_RS03390

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