GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Thermithiobacillus tepidarius DSM 3134

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 G579_RS0113315
asd aspartate semi-aldehyde dehydrogenase G579_RS0104295
dapA 4-hydroxy-tetrahydrodipicolinate synthase G579_RS0105155
dapB 4-hydroxy-tetrahydrodipicolinate reductase G579_RS0111205
dapD tetrahydrodipicolinate succinylase G579_RS0110035
dapC N-succinyldiaminopimelate aminotransferase G579_RS0110040 G579_RS0110080
dapE succinyl-diaminopimelate desuccinylase G579_RS0110020
dapF diaminopimelate epimerase G579_RS0110750
lysA diaminopimelate decarboxylase G579_RS0110770 G579_RS0101995
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase G579_RS0110035 G579_RS19655
dapL N-acetyl-diaminopimelate deacetylase
DAPtransferase L,L-diaminopimelate aminotransferase G579_RS0109030 G579_RS0110040
dapX acetyl-diaminopimelate aminotransferase G579_RS0106655
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase G579_RS0102250
hicdh homo-isocitrate dehydrogenase G579_RS0113640 G579_RS0104300
lysJ [LysW]-2-aminoadipate semialdehyde transaminase G579_RS0105030 G579_RS0111395
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase G579_RS0106655 G579_RS0105030
lysT homoaconitase large subunit G579_RS0113635 G579_RS15645
lysU homoaconitase small subunit G579_RS0113635 G579_RS0103425
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase G579_RS0113080
lysZ [LysW]-2-aminoadipate 6-kinase G579_RS0110705

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.

Links

Downloads

Related tools

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