Potential Gaps in Amino acid biosynthesis in Thermus aquaticus YT-1

GapMind for Amino acid biosynthesis

Potential Gaps in Amino acid biosynthesis in Thermus aquaticus YT-1

Found 1 low-confidence and 8 medium-confidence steps on the best paths for 18 pathways. 1 of 9 gaps have been classified.

Pathway	Step	Best candidate	2nd candidate	Class of gap
arg	carA: carbamoyl phosphate synthase subunit alpha			spurious
arg	lysK: [LysW]-ornithine hydrolase	BVI061214_RS03250	BVI061214_RS04800
arg	lysZ: [LysW]-glutamate kinase	BVI061214_RS04210	BVI061214_RS02685
chorismate	aroB: 3-dehydroquinate synthase	BVI061214_RS06225
his	hisC: histidinol-phosphate aminotransferase	BVI061214_RS06950	BVI061214_RS10030
met	B12-reactivation-domain: MetH reactivation domain	BVI061214_RS08750
phe	aro-dehydratase: arogenate dehydratase	BVI061214_RS11665
ser	serC: 3-phosphoserine aminotransferase	BVI061214_RS08670	BVI061214_RS04695
tyr	pre-dehydr: prephenate dehydrogenase	BVI061214_RS07370

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

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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:

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 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 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