Learn how to use public databases to collect information about a protein sequence

In this video, Martin Aslett demonstrates how to use public databases to collect information about a protein sequence. These pieces of information will assist us in inferring the potential function of a protein.

In this video, you will learn how, using online searches of resources such as Interpro, Pfam and Phobius, evidence of a protein’s likely function may be accumulated.

Notice that the web interface of Interpro that appears in the video is not the same as the one currently accessible online. This is not a problem since the same query boxes and output information will be displayed.

For this example we will use a Salmonella enterica protein. You can find the protein sequence below.

>NP_456741.1 hypothetical protein STY2412 MMTYIWWSLPLTLAVFFAARRLAAHFKMPLLNPLLVAMVVIIPFLLLTGIPYEHYFKGSEVLNDLLQPAV VALAYPLYEQLHQIRARWKSIISICFVGSLVAMITGTSVALLMGATPEIAASVLPKSVTTPIAMAVGGSI GGIPAISAVCVIFVGILGAVFGHTLLNAMHIRTKAARGLAMGTASHALGTARCAELDYQEGAFSSLALVI CGIITSLVAPFLFPLILAVMR 

To get the most from this step, we recommend that you try to replicate the steps. You can do so by pausing the video and performing the tasks in your internet browser or you can watch it first and replicate the steps later.