GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Cereibacter sphaeroides ATCC 17029

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 RSPH17029_RS02525
asd aspartate semi-aldehyde dehydrogenase RSPH17029_RS00225
dapA 4-hydroxy-tetrahydrodipicolinate synthase RSPH17029_RS15385 RSPH17029_RS12825
dapB 4-hydroxy-tetrahydrodipicolinate reductase RSPH17029_RS13960
dapD tetrahydrodipicolinate succinylase RSPH17029_RS14085
dapC N-succinyldiaminopimelate aminotransferase RSPH17029_RS00100 RSPH17029_RS03665
dapE succinyl-diaminopimelate desuccinylase RSPH17029_RS14070 RSPH17029_RS02055
dapF diaminopimelate epimerase RSPH17029_RS13090
lysA diaminopimelate decarboxylase RSPH17029_RS12035
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase RSPH17029_RS14085 RSPH17029_RS18710
dapL N-acetyl-diaminopimelate deacetylase RSPH17029_RS07865
DAPtransferase L,L-diaminopimelate aminotransferase RSPH17029_RS12225 RSPH17029_RS00745
dapX acetyl-diaminopimelate aminotransferase RSPH17029_RS15545 RSPH17029_RS12225
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase RSPH17029_RS10985 RSPH17029_RS05125
hicdh homo-isocitrate dehydrogenase RSPH17029_RS15285 RSPH17029_RS15290
lysJ [LysW]-2-aminoadipate semialdehyde transaminase RSPH17029_RS04315 RSPH17029_RS03665
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase RSPH17029_RS15545 RSPH17029_RS12225
lysT homoaconitase large subunit
lysU homoaconitase small subunit RSPH17029_RS12720 RSPH17029_RS02300
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase RSPH17029_RS08060
lysZ [LysW]-2-aminoadipate 6-kinase RSPH17029_RS13770

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