GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Acidimicrobium ferrooxidans DSM 10331

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 (21 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase AFER_RS00570
asd aspartate semi-aldehyde dehydrogenase AFER_RS00575
dapA 4-hydroxy-tetrahydrodipicolinate synthase AFER_RS03320
dapB 4-hydroxy-tetrahydrodipicolinate reductase AFER_RS03315
dapD tetrahydrodipicolinate succinylase AFER_RS12270
dapC N-succinyldiaminopimelate aminotransferase AFER_RS07930 AFER_RS10005
dapE succinyl-diaminopimelate desuccinylase AFER_RS03395 AFER_RS10310
dapF diaminopimelate epimerase AFER_RS03375
lysA diaminopimelate decarboxylase AFER_RS09365
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase AFER_RS12270 AFER_RS05510
dapL N-acetyl-diaminopimelate deacetylase AFER_RS10310
DAPtransferase L,L-diaminopimelate aminotransferase AFER_RS07925 AFER_RS04835
dapX acetyl-diaminopimelate aminotransferase AFER_RS07925
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase AFER_RS07915 AFER_RS07960
hicdh homo-isocitrate dehydrogenase AFER_RS09725 AFER_RS10270
lysJ [LysW]-2-aminoadipate semialdehyde transaminase AFER_RS08610 AFER_RS04845
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase AFER_RS07925 AFER_RS03605
lysT homoaconitase large subunit AFER_RS07940 AFER_RS07275
lysU homoaconitase small subunit AFER_RS07935
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase AFER_RS08625
lysZ [LysW]-2-aminoadipate 6-kinase AFER_RS12430

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 Jul 25 2024. The underlying query database was built on Jul 25 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