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profile velvet hidden markov model  (InterPro Inc)
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InterPro Inc profile velvet hidden markov model
Comparison of the three characteristic motifs of velvet domains among the 21 major clades. The alignment of velvet domains was performed against the profile hidden <t>Markov</t> model of velvet domain <t>PF11754</t> with 243 residues <t>(</t> <t>https://www.ebi.ac.uk/interpro/entry/pfam/PF11754/</t> ) and then subjected to WebLogo ( https://weblogo.threeplusone.com/ ) to generate sequence logos. In the logo, the total stack height represents the information content of residues at that position. The relative height of each residue in the stack is proportional to its frequency at the position, and the residues were sorted so that the most common one was on the top of the stack. The full sequence logos of velvet domains are provided in Fig. S4. The residues are colored according to their chemical properties, of which polar ones G, S, T, Y, and C are in green; neutral ones Q and N are in purple; basic ones K, R, and H are in blue; acidic ones D and E are in red; and hydrophobic ones A, V, L, I, P, W, F, and M are in black. The black balls at the bottom indicate the consensus dominant residues in the 21 clades, and the red balls indicate the other conserved residues revealed by the ConSurf analysis.
Profile Velvet Hidden Markov Model, supplied by InterPro Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Comparison of the three characteristic motifs of velvet domains among the 21 major clades. The alignment of velvet domains was performed against the profile hidden Markov model of velvet domain PF11754 with 243 residues ( https://www.ebi.ac.uk/interpro/entry/pfam/PF11754/ ) and then subjected to WebLogo ( https://weblogo.threeplusone.com/ ) to generate sequence logos. In the logo, the total stack height represents the information content of residues at that position. The relative height of each residue in the stack is proportional to its frequency at the position, and the residues were sorted so that the most common one was on the top of the stack. The full sequence logos of velvet domains are provided in Fig. S4. The residues are colored according to their chemical properties, of which polar ones G, S, T, Y, and C are in green; neutral ones Q and N are in purple; basic ones K, R, and H are in blue; acidic ones D and E are in red; and hydrophobic ones A, V, L, I, P, W, F, and M are in black. The black balls at the bottom indicate the consensus dominant residues in the 21 clades, and the red balls indicate the other conserved residues revealed by the ConSurf analysis.

Journal: Microbiology Spectrum

Article Title: Phylogenomics analysis of velvet regulators in the fungal kingdom

doi: 10.1128/spectrum.03717-23

Figure Lengend Snippet: Comparison of the three characteristic motifs of velvet domains among the 21 major clades. The alignment of velvet domains was performed against the profile hidden Markov model of velvet domain PF11754 with 243 residues ( https://www.ebi.ac.uk/interpro/entry/pfam/PF11754/ ) and then subjected to WebLogo ( https://weblogo.threeplusone.com/ ) to generate sequence logos. In the logo, the total stack height represents the information content of residues at that position. The relative height of each residue in the stack is proportional to its frequency at the position, and the residues were sorted so that the most common one was on the top of the stack. The full sequence logos of velvet domains are provided in Fig. S4. The residues are colored according to their chemical properties, of which polar ones G, S, T, Y, and C are in green; neutral ones Q and N are in purple; basic ones K, R, and H are in blue; acidic ones D and E are in red; and hydrophobic ones A, V, L, I, P, W, F, and M are in black. The black balls at the bottom indicate the consensus dominant residues in the 21 clades, and the red balls indicate the other conserved residues revealed by the ConSurf analysis.

Article Snippet: First, multiple alignments of protein sequences within each clade were constructed using HMMER 3.1 ( http://hmmer.org/ ) against the profile velvet hidden Markov model ( https://www.ebi.ac.uk/interpro/entry/pfam/PF11754/ ) in InterPro ( ).

Techniques: Comparison, Sequencing, Residue