GapMind for Amino acid biosynthesis


Potential Gaps in Amino acid biosynthesis in Pyrolobus fumarii 1A

Found 6 low-confidence and 30 medium-confidence steps on the best paths for 18 pathways. 1 of 36 gaps have been classified.

Pathway Step Best candidate 2nd candidate Class of gap
arg argH: argininosuccinate lyase PYRFU_RS03710 PYRFU_RS04310  
arg lysK: [LysW]-ornithine hydrolase PYRFU_RS08530  
asn aspS2: aspartyl-tRNA(Asp/Asn) synthetase PYRFU_RS03160  
chorismate aroA: 3-phosphoshikimate 1-carboxyvinyltransferase PYRFU_RS00635  
chorismate aroB: 3-dehydroquinate synthase PYRFU_RS07225  
chorismate aroD: 3-dehydroquinate dehydratase PYRFU_RS04235  
cys serC: 3-phosphoserine aminotransferase PYRFU_RS03405  
his hisA: 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase PYRFU_RS07130 PYRFU_RS07125  
his hisN: histidinol-phosphate phosphatase PYRFU_RS08460  
ile ilvE: isoleucine transaminase PYRFU_RS08035  
ile ilvH: acetolactate/acetohydroxybutanoate synthase regulatory subunit PYRFU_RS08325  
leu ilvE: leucine transaminase PYRFU_RS08035  
leu ilvH: acetolactate/acetohydroxybutanoate synthase regulatory subunit PYRFU_RS08325  
lys hicdh: homo-isocitrate dehydrogenase PYRFU_RS09335 PYRFU_RS05270  
lys lysK: [LysW]-lysine hydrolase PYRFU_RS08530  
lys lysN: 2-aminoadipate:2-oxoglutarate aminotransferase PYRFU_RS08035 PYRFU_RS08855  
lys lysU: homoaconitase small subunit PYRFU_RS07965 PYRFU_RS03665  
met hom: homoserine dehydrogenase PYRFU_RS06440  
met metB: cystathionine gamma-synthase PYRFU_RS03465  
met metC: cystathionine beta-lyase PYRFU_RS03465  
met split_metE_1: vitamin B12-independent methionine synthase, folate-binding component PYRFU_RS09465  
met split_metE_2: vitamin B12-independent methionine synthase, catalytic component PYRFU_RS01495  
phe aro-dehydratase: arogenate dehydratase PYRFU_RS06195  
phe ptransferase: prephenate aminotransferase PYRFU_RS02975  
pro cyclodeaminase: ornithine cyclodeaminase PYRFU_RS04150  
pro lysK: [LysW]-ornithine hydrolase PYRFU_RS08530  
ser serB: phosphoserine phosphatase  
ser serC: 3-phosphoserine aminotransferase PYRFU_RS03405  
thr hom: homoserine dehydrogenase PYRFU_RS06440  
trp IGPS: indole-3-glycerol phosphate synthase PYRFU_RS06835  
trp PRAI: phosphoribosylanthranilate isomerase PYRFU_RS07130 PYRFU_RS03015  
trp trpA: indoleglycerol phosphate aldolase spurious
tyr pre-dehydr: prephenate dehydrogenase PYRFU_RS07240  
tyr tyrB: tyrosine aminotransferase PYRFU_RS08035 PYRFU_RS02975  
val ilvE: valine transaminase PYRFU_RS08035  
val ilvH: acetolactate/acetohydroxybutanoate synthase regulatory subunit PYRFU_RS08325  

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