GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Halorhodospira halophila SL1

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 HHAL_RS08325
asd aspartate semi-aldehyde dehydrogenase HHAL_RS09120
dapA 4-hydroxy-tetrahydrodipicolinate synthase HHAL_RS11105
dapB 4-hydroxy-tetrahydrodipicolinate reductase HHAL_RS07455
dapD tetrahydrodipicolinate succinylase HHAL_RS07435
dapC N-succinyldiaminopimelate aminotransferase HHAL_RS07430 HHAL_RS02900
dapE succinyl-diaminopimelate desuccinylase HHAL_RS07440 HHAL_RS07580
dapF diaminopimelate epimerase HHAL_RS06110
lysA diaminopimelate decarboxylase HHAL_RS06105 HHAL_RS07885
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase HHAL_RS07435 HHAL_RS00465
dapL N-acetyl-diaminopimelate deacetylase
DAPtransferase L,L-diaminopimelate aminotransferase HHAL_RS00665 HHAL_RS07430
dapX acetyl-diaminopimelate aminotransferase HHAL_RS02760 HHAL_RS09970
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase HHAL_RS01440 HHAL_RS03550
hicdh homo-isocitrate dehydrogenase HHAL_RS09130 HHAL_RS04205
lysJ [LysW]-2-aminoadipate semialdehyde transaminase HHAL_RS03740 HHAL_RS04195
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase HHAL_RS02760 HHAL_RS04195
lysT homoaconitase large subunit HHAL_RS09140 HHAL_RS07115
lysU homoaconitase small subunit HHAL_RS09135 HHAL_RS07115
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase HHAL_RS04505
lysZ [LysW]-2-aminoadipate 6-kinase HHAL_RS11595 HHAL_RS09315

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