GapMind for Amino acid biosynthesis


Potential Gaps in Amino acid biosynthesis in Haloferax volcanii DS2

Found 1 low-confidence and 21 medium-confidence steps on the best paths for 18 pathways.

Pathway Step Best candidate 2nd candidate
arg argX: glutamate--LysW ligase C498_RS17890
arg lysJ: [LysW]-glutamate-semialdehyde aminotransferase C498_RS17875 C498_RS02300
arg lysK: [LysW]-ornithine hydrolase C498_RS12835 C498_RS17870
arg lysZ: [LysW]-glutamate kinase C498_RS17880
chorismate aroD: 3-dehydroquinate dehydratase C498_RS15190 C498_RS15185
chorismate asp-kinase: aspartate kinase C498_RS17705
his hisN: histidinol-phosphate phosphatase C498_RS17535 C498_RS02145
lys asp-kinase: aspartate kinase C498_RS17705
lys dapC: N-succinyldiaminopimelate aminotransferase C498_RS08325 C498_RS17875
lys dapD: tetrahydrodipicolinate succinylase C498_RS12820
lys dapE: succinyl-diaminopimelate desuccinylase C498_RS00930 C498_RS01700
met asp-kinase: aspartate kinase C498_RS17705
met hom: homoserine dehydrogenase C498_RS16345 C498_RS15195
met split_metE_1: vitamin B12-independent methionine synthase, folate-binding component C498_RS08730
met split_metE_2: vitamin B12-independent methionine synthase, catalytic component C498_RS08725
pro argX: glutamate--LysW ligase C498_RS17890
pro lysJ: [LysW]-glutamate-semialdehyde aminotransferase C498_RS17875 C498_RS02300
pro lysK: [LysW]-ornithine hydrolase C498_RS12835 C498_RS17870
pro lysZ: [LysW]-glutamate kinase C498_RS17880
ser serC: 3-phosphoserine aminotransferase C498_RS08325 C498_RS08375
thr asp-kinase: aspartate kinase C498_RS17705
thr hom: homoserine dehydrogenase C498_RS16345 C498_RS15195

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