Potential Gaps in Amino acid biosynthesis in Thermodesulforhabdus norvegica DSM 9990

GapMind for Amino acid biosynthesis

Potential Gaps in Amino acid biosynthesis in Thermodesulforhabdus norvegica DSM 9990

Found 2 low-confidence and 7 medium-confidence steps on the best paths for 18 pathways.

Pathway	Step	Best candidate	2nd candidate
his	hisI: phosphoribosyl-ATP pyrophosphatase	BM091_RS02930	BM091_RS07235
his	hisN: histidinol-phosphate phosphatase	BM091_RS12655	BM091_RS00250
met	asd-S-perS: putative persulfide forming protein	BM091_RS02260
met	mesB: Methylcobalamin:homocysteine methyltransferase MesB	BM091_RS04305
phe	aro-dehydratase: arogenate dehydratase	BM091_RS03430	BM091_RS06270
ser	serB: phosphoserine phosphatase	BM091_RS09805
thr	homK: putative homoserine phosphotransferase	BM091_RS02580
trp	PRAI: phosphoribosylanthranilate isomerase	BM091_RS05045	BM091_RS08350
tyr	pre-dehydr: prephenate dehydrogenase	BM091_RS08660	BM091_RS03430

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 10 2024. The underlying query database was built on Apr 09 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