GapMind for Amino acid biosynthesis


Potential Gaps in Amino acid biosynthesis in Acidimicrobium ferrooxidans DSM 10331

Found 2 low-confidence and 13 medium-confidence steps on the best paths for 18 pathways.

Pathway Step Best candidate 2nd candidate
asn aspS2: aspartyl-tRNA(Asp/Asn) synthetase AFER_RS02725
chorismate aroB: 3-dehydroquinate synthase AFER_RS08885
chorismate aroL: shikimate kinase AFER_RS01155
his hisA: 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase AFER_RS05670 AFER_RS05665
his hisI: phosphoribosyl-ATP pyrophosphatase AFER_RS05690 AFER_RS08245
his hisN: histidinol-phosphate phosphatase AFER_RS01810 AFER_RS05680
ile leuD: 3-isopropylmalate dehydaratase / citramalate isomerase, small subunit AFER_RS07935 AFER_RS07275
leu leuD: 3-isopropylmalate dehydaratase / citramalate isomerase, small subunit AFER_RS07935 AFER_RS07275
met hom_kinase: homoserine kinase AFER_RS03340 AFER_RS01155
met metB: cystathionine gamma-synthase AFER_RS07735
met metC: cystathionine beta-lyase AFER_RS07735 AFER_RS10005
phe preph-dehydratase: prephenate dehydratase AFER_RS00495
ser serB: phosphoserine phosphatase AFER_RS09950 AFER_RS04610
thr thrB: homoserine kinase AFER_RS03340 AFER_RS01155
tyr pre-dehydr: prephenate dehydrogenase AFER_RS11020

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