This webpage contains the supplementary information for the paper "Markov Random Fields Reveal an N-terminal Beta Propeller Motif as Part of a Bacterial Hybrid 2-component Sensor System" by Matt Menke, Bonnie Berge, and Lenore Cowen, submitted.

This file contains all YYY proteins in pfam (version) annotated with the twin 7-bladed SMURF template. For each protein, it provides Uniprot ID, SMURF raw score, SMURF estimated p-value, and the best scoring SMURF parse of the two putative propellers. Lowercase residues represent the template, uppercase are the UNIPROT sequence.
7-7 twin propeller template

Here are the files for the other twin propeller templates:
6-6 twin propeller template
6-7 twin propeller template
6-8 twin propeller template
7-6 twin propeller template
7-8 twin propeller template
8-6 twin propeller template
8-7 twin propeller template
8-8 twin propeller template

Top 1000 high-scoring putative propellers according to each of SMURF's 6- and 7-bladed templates.
Note: unlike the previous results, these were run using HMMER's null2 correction, which adjusts the final score so as not to give high scores to long low-complexity regions placed in insertion states. Option to enable this will be added to the website within a day or two:
6-bladed
7-bladed

Top 100 high-scoring putative propellers according to SMURF that HMMer scores with an E-value above 0.1:
6-bladed
7-bladed

Pairwise beta-residue pair frequency tables. Values are percents of total number of beta-residue pairs. Note that residue order is ignored, so the table is symmetric:
Buried
Exposed

Pairwise beta-residue pair log score tables. These are just the natural logs of the above tables, after normilization by residue background frequency:
Buried
Exposed

Species distribution of Y_Y_Y motifs: Key: # species, # sequences, # regions Top-level breakdown Phylum Proteobacteria Phylum Bacteroidetes

In addition, you can check the SMURF score for your favorite protein sequence using the SMURF webserver.