Category:TeamPurple

The paper identifies the emergence of new ribonucleoside-diphosphate reductase alpha subunits (NrdA) and thioredoxins after E.coli was infected with some other bacteriophages. New enzymes were found in the Enterobacteria phages T5 and T6 but not T7

Pubmed article describes the redox potential determined by experimental evidence. The molecule is able to donate electrons to Nitrogen and can accept electrons from pyruvate.

Using BLASTP, there was a match that met the required threshold to the phage known as moonbeam (AIW03471). The BlastP hit has a query coverage of 54%, E-value of 5e-179 and 40% identity. The match was closely related to the well known Tape Measure Protein that has been found to contribute to the length of phage tails. This gene was also found to be highly conserved in double stranded DNA based phages and would always be preceding two other genes involved in tail formation which are commonly referred to as "gene G" and "gene T", homologs from phage Lambda. (PMID:8065255) These genes are found in Troll as genes "Troll_92" and "Troll_93" and are found upstream of the tape measure protein "Troll_94". It was also found that there was a conserved frame shift within these gene sets that consistently occurs while still maintaining the integrity of the gene functions. Finally, by comparing the sequences of other dsDNA phage has shown that the tape measure protein gene that been conserved through a common ancestor.(PMID:15469818)

Focused blastp result with e-value 4e-31, query coverage 88%, and identity 41% identifies Escherichia coli str. K-12 dihydrofolate reductase as a homolog for this gene product. Dihydrofolate reductase activity of E. coli K-12 DHFR was found by performing a direct dihydrofolate reductase assay. Conserved residues for the gene product in E. coli (e.g. Ala-7, Phe-31, Leu-54, etc.) had identical residue matches in Troll.

The tape measure protein is commonly found within dsDNA phage that contributes to the length of the viral tails. The researchers in the source did specific sequencing analysis to identify the various genes involved in phage tail genes, specifically in bacteriophage P2. (fig 1. pg. 1463) Researchers identified the gene (Gene H) through by utilizing common ORFs found within the sequences and comparing cleaved sites from mutated sequences.(fig. 3 pg. 1464-1465)Function of the gene was also found through experimental recombination to knock down the genes and determining the outcome of the viral structures by comparing sequences to other well known phage.(PMID:1531648)

HHPred shows a match with flavodoxin in the Bacterium Desulfovibrio desulfuricans with probability 100.0, e-value 3.5E-29, p value 1E-33. The structure was determined in PMID:19465766, and linked to the family of flavodoxin proteins. The function of these was determined in PMID:8694750

Flavodoxins are proteins that accept electrons from pyruvate and donate electrons to nitrogen in oxidation reduction pathways. PMID:8694750. Blastp showed the presence of conserved regions in the Flavodoxin family of proteins. Given the conservation of the protein and the match with several other proteins, it can be inferred that the protein has a similar structure and function to flavodoxin found in other organisms.

Blastp to azotobacter vinelandii shows e value of 2e-11. Compositional matrix adjustment. 32% identity, 50% positives.

linked Pubmed article describes the redox potential determined by experimental evidence. The molecule is able to donate electrons to Nitrogen and can accept electrons from pyruvate.

HHPred shows a match with flavodoxin in the Bacterium Desulfovibrio desulfuricans with probability 100.0, e-value 3.5E-29, p value 1E-33.

Flavodoxins are proteins that bind flavin mononucleotide(FMN) and are used in electron transfer pathways and redox potentials. PMID:8694750.

Blastp showed the presence of conserved regions in the Flavodoxin family of proteins. Given the conservation of the protein and the match with several other proteins, it can be inferred that the protein has a similar structure and function to flavodoxin found in other organisms.

Blastp to azotobacter vinelandii has e value of 2e-11. Compositional matrix adjustment. 32% identity, 50% positives

PMID:8694750: The article describes the function of a flavodoxin protein in Azotobacter vinelandii as an electron carrier and donor in redox pathways. The article experimentally determined that the protein contains acid-labile iron and

sulphide and molybdenum pterin cofactor (Moco)redox centers.

GO:0009457 is obsolete because it represents a class of gene products. It was replaced by GO:0009055.