L-lysine biosynthesis in Phyllobacterium brassicacearum STM 196

GapMind for Amino acid biosynthesis

L-lysine biosynthesis in Phyllobacterium brassicacearum STM 196

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.

all:

meso-DAP and lysA
or lysW-pathway

lysW-pathway: hcs, lysT, lysU, hicdh, lysN, lysW, lysX, lysZ, lysY, lysJ and lysK

Comment: 2-oxoglutarate and acetyl-CoA are converted to homocysteine, homoaconitate and then 2-oxoadipate (by hcs-lysTU-hicdh), an aminotransferase (lysN) forms L-2-aminoadipate, lysX ligates 2-aminoadipate to lysW, lysZYJ convert LysW-aminoadipate to LysW-lysine, and lysK releases lysine.

meso-DAP:

aspartate-semialdehyde, dapA, dapB, dapD, dapC, dapE and dapF
or aspartate-semialdehyde, dapA, dapB, dapH, dapX, dapL and dapF
or aspartate-semialdehyde, dapA, dapB and ddh
or aspartate-semialdehyde, dapA, dapB, DAPtransferase and dapF
Comment: (S)-2,3,4,5-tetrahydrodipicolinate is formed from aspartate semialdehyde by dapAB. In pathway I (dapDCE), it is succinylated, transaminated, and desuccinyulated, to L,L-DAP, and then the epimerase dapF forms meso-DAP. Pathway II (dapHXL) is similar but with acetylated intermediates. In pathway III, tetrahydrodipicolinate is reductively aminated to meso-DAP in one step, by ddh. In pathway VI, an aminotransferase (DAPtransferase) forms L,L-DAP.

aspartate-semialdehyde: asp-kinase and asd

25 steps (21 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
asp-kinase	aspartate kinase	CU102_RS10560
asd	aspartate semi-aldehyde dehydrogenase	CU102_RS19305
dapA	4-hydroxy-tetrahydrodipicolinate synthase	CU102_RS04995	CU102_RS15345
dapB	4-hydroxy-tetrahydrodipicolinate reductase	CU102_RS17880
dapD	tetrahydrodipicolinate succinylase	CU102_RS13305
dapC	N-succinyldiaminopimelate aminotransferase	CU102_RS09935	CU102_RS14190
dapE	succinyl-diaminopimelate desuccinylase	CU102_RS13315	CU102_RS09815
dapF	diaminopimelate epimerase	CU102_RS19150
lysA	diaminopimelate decarboxylase	CU102_RS10315	CU102_RS29060
Alternative steps:
dapH	tetrahydrodipicolinate acetyltransferase	CU102_RS13305	CU102_RS16285
dapL	N-acetyl-diaminopimelate deacetylase	CU102_RS10055	CU102_RS09815
DAPtransferase	L,L-diaminopimelate aminotransferase	CU102_RS16215	CU102_RS03165
dapX	acetyl-diaminopimelate aminotransferase	CU102_RS03165	CU102_RS23675
ddh	meso-diaminopimelate D-dehydrogenase
hcs	homocitrate synthase	CU102_RS15545
hicdh	homo-isocitrate dehydrogenase	CU102_RS21110	CU102_RS20945
lysJ	[LysW]-2-aminoadipate semialdehyde transaminase	CU102_RS14190	CU102_RS07845
lysK	[LysW]-lysine hydrolase
lysN	2-aminoadipate:2-oxoglutarate aminotransferase	CU102_RS03165	CU102_RS07230
lysT	homoaconitase large subunit	CU102_RS19045
lysU	homoaconitase small subunit	CU102_RS22605	CU102_RS19205
lysW	2-aminoadipate/glutamate carrier protein
lysX	2-aminoadipate-LysW ligase	CU102_RS11365
lysY	[LysW]-2-aminoadipate 6-phosphate reductase
lysZ	[LysW]-2-aminoadipate 6-kinase	CU102_RS13275

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 26 2024. The underlying query database was built on Jul 25 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the original publication.

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

GapMind for Amino acid biosynthesis