GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Paucidesulfovibrio gracilis DSM 16080

Best path

asp-kinase, asd, dapA, dapB, DAPtransferase, 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 (19 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase B5D49_RS06950
asd aspartate semi-aldehyde dehydrogenase B5D49_RS04345
dapA 4-hydroxy-tetrahydrodipicolinate synthase B5D49_RS05670
dapB 4-hydroxy-tetrahydrodipicolinate reductase B5D49_RS06675
DAPtransferase L,L-diaminopimelate aminotransferase B5D49_RS06010 B5D49_RS04590
dapF diaminopimelate epimerase B5D49_RS14405
lysA diaminopimelate decarboxylase B5D49_RS05965
Alternative steps:
dapC N-succinyldiaminopimelate aminotransferase B5D49_RS05850 B5D49_RS02330
dapD tetrahydrodipicolinate succinylase
dapE succinyl-diaminopimelate desuccinylase B5D49_RS03165
dapH tetrahydrodipicolinate acetyltransferase B5D49_RS12800 B5D49_RS15105
dapL N-acetyl-diaminopimelate deacetylase
dapX acetyl-diaminopimelate aminotransferase B5D49_RS13990 B5D49_RS10555
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase B5D49_RS04290 B5D49_RS06945
hicdh homo-isocitrate dehydrogenase B5D49_RS00920 B5D49_RS04305
lysJ [LysW]-2-aminoadipate semialdehyde transaminase B5D49_RS05850 B5D49_RS12615
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase B5D49_RS08760 B5D49_RS03155
lysT homoaconitase large subunit B5D49_RS04295 B5D49_RS07960
lysU homoaconitase small subunit B5D49_RS04300 B5D49_RS07960
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase B5D49_RS10720
lysZ [LysW]-2-aminoadipate 6-kinase B5D49_RS02490

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