Usage 1U04 - pdb structure Q8U3D2 - UniProt ascension PF Systematic name NP_ NCBI protein ascension We know of relatives in Aquifex aeolicus and Methanocaldococcus jannaschii We also know that the Piwi domain is detectable. Is the Methanopyrus kandleri version a 4-domain Argonaute?
Analysis strategy Protein or DNA sequence? Data source What should we look for ? Search method Alignment method Visualization
Piwi domain in Prokaryotes
Analysis Protein - select PF0537 from UCSC Archaeal Browser Data source - Non-redundant Protein Database What should we look for? –include a positive and a negative (4 domain and 3 domain) Search method - Blastp Alignment method - ClustalW Visualization
In class exercises What is the closest bacterial example of a 4- domain Argonaute ? (not counting Aquifex aeolicus) What is the GC content of PF0537 ?