GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Hydrogenophaga taeniospiralis NBRC 102512

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 HTA01S_RS18935
asd aspartate semi-aldehyde dehydrogenase HTA01S_RS17205
dapA 4-hydroxy-tetrahydrodipicolinate synthase HTA01S_RS01180 HTA01S_RS16140
dapB 4-hydroxy-tetrahydrodipicolinate reductase HTA01S_RS05675
dapD tetrahydrodipicolinate succinylase HTA01S_RS08370
dapC N-succinyldiaminopimelate aminotransferase HTA01S_RS08365 HTA01S_RS02950
dapE succinyl-diaminopimelate desuccinylase HTA01S_RS08380
dapF diaminopimelate epimerase HTA01S_RS04230
lysA diaminopimelate decarboxylase HTA01S_RS18050
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase HTA01S_RS08370
dapL N-acetyl-diaminopimelate deacetylase HTA01S_RS19765 HTA01S_RS02420
DAPtransferase L,L-diaminopimelate aminotransferase HTA01S_RS08365
dapX acetyl-diaminopimelate aminotransferase HTA01S_RS18800 HTA01S_RS07580
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase HTA01S_RS15315 HTA01S_RS07390
hicdh homo-isocitrate dehydrogenase HTA01S_RS08575 HTA01S_RS00995
lysJ [LysW]-2-aminoadipate semialdehyde transaminase HTA01S_RS17425 HTA01S_RS18580
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase HTA01S_RS18580 HTA01S_RS10480
lysT homoaconitase large subunit HTA01S_RS17225
lysU homoaconitase small subunit HTA01S_RS17215
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase
lysZ [LysW]-2-aminoadipate 6-kinase HTA01S_RS04745

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