GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Chlorobium phaeobacteroides BS1

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 (20 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase Cphamn1_0299 Cphamn1_2445
asd aspartate semi-aldehyde dehydrogenase Cphamn1_2183
dapA 4-hydroxy-tetrahydrodipicolinate synthase Cphamn1_0593
dapB 4-hydroxy-tetrahydrodipicolinate reductase Cphamn1_2084
DAPtransferase L,L-diaminopimelate aminotransferase Cphamn1_1267 Cphamn1_1781
dapF diaminopimelate epimerase Cphamn1_0304
lysA diaminopimelate decarboxylase Cphamn1_0976 Cphamn1_2445
Alternative steps:
dapC N-succinyldiaminopimelate aminotransferase Cphamn1_1568 Cphamn1_0638
dapD tetrahydrodipicolinate succinylase Cphamn1_0020
dapE succinyl-diaminopimelate desuccinylase
dapH tetrahydrodipicolinate acetyltransferase Cphamn1_0020
dapL N-acetyl-diaminopimelate deacetylase Cphamn1_1324
dapX acetyl-diaminopimelate aminotransferase Cphamn1_1110 Cphamn1_1781
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase Cphamn1_1747 Cphamn1_1721
hicdh homo-isocitrate dehydrogenase Cphamn1_1720
lysJ [LysW]-2-aminoadipate semialdehyde transaminase Cphamn1_0202 Cphamn1_0638
lysK [LysW]-lysine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase Cphamn1_1110 Cphamn1_0638
lysT homoaconitase large subunit Cphamn1_1722
lysU homoaconitase small subunit Cphamn1_1723 Cphamn1_2466
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase Cphamn1_1337
lysZ [LysW]-2-aminoadipate 6-kinase Cphamn1_1335

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