GapMind for Amino acid biosynthesis


L-lysine biosynthesis in Thioalkalivibrio thiocyanodenitrificans ARhD 1

Best path

asp-kinase, asd, dapA, dapB, dapD, dapC, dapE, dapF, lysA


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 THITHI_RS0100065 THITHI_RS0101700
asd aspartate semi-aldehyde dehydrogenase THITHI_RS0100270
dapA 4-hydroxy-tetrahydrodipicolinate synthase THITHI_RS0115020
dapB 4-hydroxy-tetrahydrodipicolinate reductase THITHI_RS0115800
dapD tetrahydrodipicolinate succinylase THITHI_RS0100680
dapC N-succinyldiaminopimelate aminotransferase THITHI_RS0100675 THITHI_RS0102405
dapE succinyl-diaminopimelate desuccinylase THITHI_RS0100690
dapF diaminopimelate epimerase THITHI_RS0111255
lysA diaminopimelate decarboxylase THITHI_RS0111230
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase THITHI_RS0100680
dapL N-acetyl-diaminopimelate deacetylase
DAPtransferase L,L-diaminopimelate aminotransferase THITHI_RS0101695 THITHI_RS0100675
dapX acetyl-diaminopimelate aminotransferase THITHI_RS0103675 THITHI_RS0102270
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase THITHI_RS0105090
hicdh homo-isocitrate dehydrogenase THITHI_RS0103320 THITHI_RS0100275
lysJ [LysW]-2-aminoadipate semialdehyde transaminase THITHI_RS0106505 THITHI_RS0103415
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase THITHI_RS0103675 THITHI_RS0106505
lysT homoaconitase large subunit THITHI_RS0100290
lysU homoaconitase small subunit THITHI_RS0100280
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase THITHI_RS0108020
lysY [LysW]-2-aminoadipate 6-phosphate reductase THITHI_RS0106205
lysZ [LysW]-2-aminoadipate 6-kinase THITHI_RS0112025

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