GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Acidithiobacillus ferrooxidans ATCC 23270

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 AFE_RS01935
asd aspartate semi-aldehyde dehydrogenase AFE_RS09570
dapA 4-hydroxy-tetrahydrodipicolinate synthase AFE_RS10835
dapB 4-hydroxy-tetrahydrodipicolinate reductase AFE_RS12220
dapD tetrahydrodipicolinate succinylase AFE_RS08445
dapC N-succinyldiaminopimelate aminotransferase AFE_RS08450 AFE_RS04200
dapE succinyl-diaminopimelate desuccinylase AFE_RS08440
dapF diaminopimelate epimerase AFE_RS12595
lysA diaminopimelate decarboxylase AFE_RS15025 AFE_RS06870
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase AFE_RS08445 AFE_RS07035
dapL N-acetyl-diaminopimelate deacetylase
DAPtransferase L,L-diaminopimelate aminotransferase AFE_RS02230 AFE_RS08450
dapX acetyl-diaminopimelate aminotransferase AFE_RS09345
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase AFE_RS07040 AFE_RS11900
hicdh homo-isocitrate dehydrogenase AFE_RS02000 AFE_RS09575
lysJ [LysW]-2-aminoadipate semialdehyde transaminase AFE_RS15145 AFE_RS01930
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase AFE_RS09345 AFE_RS01930
lysT homoaconitase large subunit AFE_RS01995 AFE_RS02935
lysU homoaconitase small subunit AFE_RS01995 AFE_RS02940
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase AFE_RS14090
lysZ [LysW]-2-aminoadipate 6-kinase AFE_RS01205

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