This research will examine the protein bifunctional phosphoglucose/phosphomannose isomerase of the archaea Pyrobaculum aerophilum
Keywords: Pyrobaculum aerophilum, enzyme
Catalyzes isomerization of glucose-6-phosphate and mannose-6-phosphate with equal catalytic efficiency.
Pyrobaculum aerophilum - facultatively aerobic nitrate-reducing hyperthermophilic archaea. This organism has a number of interesting features. For example, computational analysis of the genome has confirmed experiments showing that P. aerophilum (and possibly all crenarchaea) do not have 5' untranslated regions of mRNA and thus do not appear to use a mechanism based on the ribosome binding site to initiate translation at the 5'-end.[1] Pyrobaculum aerophilum got its name from the Greek noun "aer" (air) and the Greek adjective "philos" (loving). It was found that optimal growth conditions are achieved at 100°C and pH 7.0[2].
wget 'https://www.uniprot.org/uniprot/?query=proteome:up000002439&format=txt&compress=yes' -O UP000002439.swiss.gz
wget 'https://www.uniprot.org/uniprot/?query=proteome:up000001694&format=txt&compress=yes' -O UP000001694.swiss.gz
The reference proteome of archaea Pyrobaculum aerophilum was chosen for comparison, Thermoproteus neutrophilus proteome was taken as a control. (a related strain that is capable of producing hydrogen sulfide)..
Number of proteins in the proteome: 2590 (в swiss-prot:315). Described 12,16%
BUSCO: C:96.5%[S:96.3%,D:0.2%],F:0.2%,M:3.2%,n:404 thermoproteales_odb10. Therefore, 96.5% complete.
CPD is close to standard (slightly higher)
Number of proteins in the proteome: 1965 (в swiss-prot:148). Described 7,53%
BUSCO: C:95.8%[S:95.5%,D:0.2%],F:0.2%,M:4%,n:404 thermoproteales_odb10. Therefore, 95.8% complete.
CPD standard
annotation:(type:transmem) AND organism:"Pyrobaculum aerophilum (strain ATCC 51768 / DSM 7523 / JCM 9630 / CIP 104966 / NBRC 100827 / IM2) [178306]" AND proteome:up000002439
Number of transmembrane proteins: 475 (fraction in proteome: 18,34%)
ec:* AND organism:"Pyrobaculum aerophilum (strain ATCC 51768 / DSM 7523 / JCM 9630 / CIP 104966 / NBRC 100827 / IM2) [178306]" AND proteome:up000002439
Number of enzymes:336 (fraction in proteome:12,97%)
ec:1* AND organism:"Pyrobaculum aerophilum (strain ATCC 51768 / DSM 7523 / JCM 9630 / CIP 104966 / NBRC 100827 / IM2) [178306]" AND proteome:up000002439
Number of oxidoreductases: 48 (fraction in proteome:1,85%)
annotation:(type:transmem) AND organism:"Pyrobaculum neutrophilum (strain DSM 2338 / JCM 9278 / NBRC 100436 / V24Sta) (Thermoproteus neutrophilus) [444157]" AND proteome:up000001694
Number of transmembrane proteins:318 (fraction in proteome:16,18%)
ec:* AND organism:"Pyrobaculum neutrophilum (strain DSM 2338 / JCM 9278 / NBRC 100436 / V24Sta) (Thermoproteus neutrophilus) [444157]" AND proteome:up000001694
Number of enzymes:336 (fraction in proteome:17%)
ec:1* AND organism:"Pyrobaculum neutrophilum (strain DSM 2338 / JCM 9278 / NBRC 100436 / V24Sta) (Thermoproteus neutrophilus) [444157]" AND proteome:up000001694
Number of oxidoreductases: 51(2,6%)
From the above data, we can see that the proportion of oxidoreductases in Thermoproteus neutrophilus, which is capable of forming hydrogen sulfide,is still greater than in Pyrobaculum aerophilum (H2S synthesis involves oxidoreductases). We can assume that the percentage of oxidoreductases does not differ significantly because Pyrobaculum aerophilum uses the mechanism of nitrogen reduction in the process of life activity..
zcat UP000002439.swiss | seqret -filter 'swiss::stdin:*[1:1]' | grep -v "^>" | uniq
zcat UP000001694.swiss | seqret -filter 'swiss::stdin:*[1:1]' | grep -v "^>" | uniq
As a result of running the program, we were able to establish that in both cases all proteins start with methionine (M). This is due to the fact that the AUG triplet is a start codon and encodes methionine. It should be noted that in prokaryotes it is read as formylmethionine..