GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Rhizorhabdus wittichii RW1

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 (21 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase SWIT_RS22745
asd aspartate semi-aldehyde dehydrogenase SWIT_RS13495
dapA 4-hydroxy-tetrahydrodipicolinate synthase SWIT_RS02620
dapB 4-hydroxy-tetrahydrodipicolinate reductase SWIT_RS01025
dapD tetrahydrodipicolinate succinylase SWIT_RS14730
dapC N-succinyldiaminopimelate aminotransferase SWIT_RS23660 SWIT_RS07135
dapE succinyl-diaminopimelate desuccinylase SWIT_RS18305 SWIT_RS21760
dapF diaminopimelate epimerase SWIT_RS14815
lysA diaminopimelate decarboxylase SWIT_RS14485 SWIT_RS07570
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase SWIT_RS04040 SWIT_RS14730
dapL N-acetyl-diaminopimelate deacetylase SWIT_RS17340 SWIT_RS21760
DAPtransferase L,L-diaminopimelate aminotransferase SWIT_RS04400 SWIT_RS21110
dapX acetyl-diaminopimelate aminotransferase SWIT_RS17960 SWIT_RS21110
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase SWIT_RS02860
hicdh homo-isocitrate dehydrogenase SWIT_RS22700
lysJ [LysW]-2-aminoadipate semialdehyde transaminase SWIT_RS07135 SWIT_RS21305
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase SWIT_RS17960 SWIT_RS21305
lysT homoaconitase large subunit SWIT_RS23765 SWIT_RS21880
lysU homoaconitase small subunit SWIT_RS23775 SWIT_RS11715
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase SWIT_RS00480
lysZ [LysW]-2-aminoadipate 6-kinase SWIT_RS14725

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 Jul 25 2024. The underlying query database was built on Jul 25 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