GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis in Herbaspirillum seropedicae SmR1

Best path

asp-kinase, asd, dapA, dapB, dapD, dapC, dapE, dapF, lysA

Also see fitness data for the top candidates

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 HSERO_RS10695
asd aspartate semi-aldehyde dehydrogenase HSERO_RS16495
dapA 4-hydroxy-tetrahydrodipicolinate synthase HSERO_RS06450 HSERO_RS16395
dapB 4-hydroxy-tetrahydrodipicolinate reductase HSERO_RS03030
dapD tetrahydrodipicolinate succinylase HSERO_RS10800
dapC N-succinyldiaminopimelate aminotransferase HSERO_RS10805 HSERO_RS18435
dapE succinyl-diaminopimelate desuccinylase HSERO_RS10790 HSERO_RS16100
dapF diaminopimelate epimerase HSERO_RS21455
lysA diaminopimelate decarboxylase HSERO_RS00950 HSERO_RS13690
Alternative steps:
dapH tetrahydrodipicolinate acetyltransferase HSERO_RS21030 HSERO_RS10800
dapL N-acetyl-diaminopimelate deacetylase HSERO_RS04135 HSERO_RS05715
DAPtransferase L,L-diaminopimelate aminotransferase HSERO_RS12800 HSERO_RS10805
dapX acetyl-diaminopimelate aminotransferase HSERO_RS17885 HSERO_RS15115
ddh meso-diaminopimelate D-dehydrogenase
hcs homocitrate synthase HSERO_RS14210 HSERO_RS17185
hicdh homo-isocitrate dehydrogenase HSERO_RS07015 HSERO_RS07390
lysJ [LysW]-2-aminoadipate semialdehyde transaminase / [LysW]-glutamate semialdehyde transaminase HSERO_RS16670 HSERO_RS05420
lysK [LysW]-lysine hydrolase / [LysW]-ornithine hydrolase
lysN 2-aminoadipate:2-oxoglutarate aminotransferase HSERO_RS05420 HSERO_RS09050
lysT homoaconitase large subunit HSERO_RS16515
lysU homoaconitase small subunit HSERO_RS16505 HSERO_RS14940
lysW 2-aminoadipate/glutamate carrier protein
lysX 2-aminoadipate-LysW ligase
lysY [LysW]-2-aminoadipate 6-phosphate reductase / [LysW]-glutamylphosphate reductase HSERO_RS19210
lysZ [LysW]-2-aminoadipate 6-kinase / [LysW]-glutamate kinase HSERO_RS21495

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.

Links

Downloads

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:

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the 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