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Structure-guided alignment constructed with homologous sequences using Cn3D (top) and neighbor-joining tree based on the score of aligned residues from homologous sequences using CDTree (bottom).
No full text<p>Structure-guided alignment constructed with homologous sequences using Cn3D (top) and neighbor-joining tree based on the score of aligned residues from homologous sequences using CDTree (bottom).</p
Percent-identity scale.
No full text<p>The horizontal line gives the percent identity between query and subject sequences, and the boxes gives the resources and tools that can be used for functional inference.</p
PIRSF (A,B), COG (C,D), and Pfam (E,F) input and results.
No full text<p>(A) The fasta sequence of query protein with UniProt accession O67940 from <i>Aquifex aeolicus</i> is scanned against PIR's curated family database. (The query is searched against the full-length and domain hidden Markov models for manually curated PIRSFs. If a match is found, the matched regions and statistics are displayed). (B) The query hits the PIRSF family PIRSF006779. The output provides family details; statistical data for full-length proteins, composite domains, and a pairwise alignment of query with the consensus sequence of the PIRSF. (C) The fasta sequence of query protein with UniProt accession O67940 from <i>Aquifex aeolicus</i> is scanned against the database of clusters of orthologous groups. COG compares protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of orthologous/co-orthologous proteins from at least three lineages. (D) The query hits COG1912. The output provides the family details: statistical score, reciprocal best hits, and members of the family. (E) The fasta sequence of query protein with UniProt accession O67940 from <i>Aquifex aeolicus</i> is scanned against the Pfam domain database. The Pfam database is a large collection of domain families, each represented by multiple sequence alignments and hidden Markov models (HMMs). (F) The query hits Pfam family PF01887.</p
Ten-step procedure for comparative analysis of protein structures and sequences to infer biological function.
No full text<p>Ten-step procedure for comparative analysis of protein structures and sequences to infer biological function.</p
SCOP output.
No full text<p>1RQP is used since our query protein O67940 from <i>Aquifex aeolicus</i> does not have a solved structure. The results indicate that the N-terminal and C-terminal domains of 1RQP belong to two SCOP superfamilies. (The SCOP database provides a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known).</p
Ligplot for 1RQP.
No full text<p>SAM-binding residues. Dashed green lines indicate hydrogen bonds, and the half-moon indicates van der Waals interactions. (Ligplot is a program for automatically plotting protein–ligand interactions provided as part of the PDBsum database, which is a Web-based database of summaries and analyses of all PDB structures).</p
Pairwise alignment between query sequence <i>O67940_ AQUAE</i> and 2Q6O (top) and 1RQP (bottom).
No full text<p>(Top) Query aligns end-to-end without any long gaps with a sequence identity of 32%. (Bottom) Query aligns end-to-end but with three regions of gaps, the most significant being a 23-residue region in 1RQP residues 92–116. The sequence identity of query with 1RQP is 26%.</p
Additional file 1: of Ridge regression estimated linear probability model predictions of O-glycosylation in proteins with structural and sequence data
No full textEstimation dataset. (XLSX 1187 kb
VAST output.
No full text<p>Since our query protein O67940 from <i>Aquifex aeolicus</i> does not have a solved structure, 1RQP is used as a query. The only non-redundant structural neighbor that provides functional annotation is 2Q6O, indicated by a pink box.</p
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