GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Teredinibacter turnerae T7901

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 TERTU_RS12405 TERTU_RS14960
asd aspartate semi-aldehyde dehydrogenase TERTU_RS11080
dapA 4-hydroxy-tetrahydrodipicolinate synthase TERTU_RS04310
dapB 4-hydroxy-tetrahydrodipicolinate reductase TERTU_RS14585
dapD tetrahydrodipicolinate succinylase TERTU_RS04405
dapC N-succinyldiaminopimelate aminotransferase TERTU_RS04420 TERTU_RS12145
dapE succinyl-diaminopimelate desuccinylase TERTU_RS04400 TERTU_RS01675
dapF diaminopimelate epimerase TERTU_RS18530
lysA diaminopimelate decarboxylase TERTU_RS18525
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase TERTU_RS09625 TERTU_RS01810
dapL N-acetyl-diaminopimelate deacetylase TERTU_RS17805
DAPtransferase L,L-diaminopimelate aminotransferase TERTU_RS04420
dapX acetyl-diaminopimelate aminotransferase
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase TERTU_RS07045 TERTU_RS15140
hicdh homo-isocitrate dehydrogenase TERTU_RS11085
lysJ [LysW]-2-aminoadipate semialdehyde transaminase TERTU_RS03190 TERTU_RS17800
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase TERTU_RS09270 TERTU_RS14970
lysT homoaconitase large subunit TERTU_RS11095
lysU homoaconitase small subunit TERTU_RS11090 TERTU_RS13710
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase TERTU_RS13580
lysZ [LysW]-2-aminoadipate 6-kinase TERTU_RS00830

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