Manual classification of gap: novel
Rationale: This organism probably uses succinylated intermediates, as Echvi_3551 is a good candidate for the succinyltransferase DapD. But the aminotransferase and the desuccinylase cannot be found. Alternatively, Echvi_0124 could be a diverged diamopimelate aminotransferase.
asp-kinase, asd, dapA, dapB, DAPtransferase?, dapF, lysA
Also see fitness data for the top candidates
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.
Or see definitions of steps
Step | Description | Best candidate | 2nd candidate |
---|---|---|---|
asp-kinase | aspartate kinase | Echvi_2000 | Echvi_1218 |
asd | aspartate semi-aldehyde dehydrogenase | Echvi_0713 | |
dapA | 4-hydroxy-tetrahydrodipicolinate synthase | Echvi_3959 | Echvi_3953 |
dapB | 4-hydroxy-tetrahydrodipicolinate reductase | Echvi_2395 | |
DAPtransferase? | L,L-diaminopimelate aminotransferase | Echvi_0124 | Echvi_0656 |
dapF | diaminopimelate epimerase | Echvi_1430 | |
lysA | diaminopimelate decarboxylase | Echvi_1295 | |
Alternative steps: | |||
dapC? | N-succinyldiaminopimelate aminotransferase | Echvi_3848 | Echvi_0577 |
dapD | tetrahydrodipicolinate succinylase | Echvi_3551 | |
dapE? | succinyl-diaminopimelate desuccinylase | ||
dapH? | tetrahydrodipicolinate acetyltransferase | Echvi_3551 | Echvi_0942 |
dapL? | N-acetyl-diaminopimelate deacetylase | Echvi_0302 | Echvi_1427 |
dapX? | acetyl-diaminopimelate aminotransferase | Echvi_0675 | |
ddh? | meso-diaminopimelate D-dehydrogenase | ||
hcs? | homocitrate synthase | Echvi_3833 | Echvi_2061 |
hicdh? | homo-isocitrate dehydrogenase | Echvi_4068 | Echvi_2062 |
lysJ? | [LysW]-2-aminoadipate semialdehyde transaminase / [LysW]-glutamate semialdehyde transaminase | Echvi_3848 | Echvi_2919 |
lysK? | [LysW]-lysine hydrolase / [LysW]-ornithine hydrolase | ||
lysN? | 2-aminoadipate:2-oxoglutarate aminotransferase | Echvi_0675 | Echvi_3848 |
lysT? | homoaconitase large subunit | Echvi_2531 | Echvi_2059 |
lysU? | homoaconitase small subunit | Echvi_2060 | Echvi_4039 |
lysW? | 2-aminoadipate/glutamate carrier protein | ||
lysX? | 2-aminoadipate-LysW ligase | ||
lysY? | [LysW]-2-aminoadipate 6-phosphate reductase / [LysW]-glutamylphosphate reductase | Echvi_3847 | |
lysZ? | [LysW]-2-aminoadipate 6-kinase / [LysW]-glutamate kinase | Echvi_3850 |
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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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:
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