Journal: Microbiome

Article Title: A multi-source domain annotation pipeline for quantitative metagenomic and metatranscriptomic functional profiling

doi: 10.1186/s40168-018-0532-2

Figure Lengend Snippet: Read annotations of the Puerto Rico Rainforest MG dataset obtained with InterProScan and MetaCLADE. a Domain annotation of the five tools: Pfam (yellow), Gene3D (blue), TIGRFAM (purple), PRINTS&ProSite (orange) and MetaCLADE (green). The Venn diagram representing the number of reads annotated by one or several tools is reported. b Distribution of species originating CCMs used to annotate the dataset with MetaCLADE. c Distributions of E values associated to the sets of domains identified in an exclusive manner by each tool. For instance, for MetaCLADE, we considered 37,811 domains (see a ). E values are plotted on the x -axis using a − log10 scale. d Distribution of E values associated to all domains identified by MetaCLADE. As in c , E values are plotted on the x -axis using a − log10 scale

Article Snippet: ORF sequences have been annotated by EBI based on five different domain databases found in InterPro [ ]: Pfam [ ], TIGRFAM [ ], Gene3D [ ] and PRINTS & ProSite [ , ].

Techniques:

Journal: BMC Bioinformatics

Article Title: Predicting active site residue annotations in the Pfam database

doi: 10.1186/1471-2105-8-298

Figure Lengend Snippet: A Venn diagram comparing the number of UniProtKB sequences that contain a Pfam active site to the number of sequences that match an active site PROSITE pattern.

Article Snippet: InterPro annotates PROSITE matches in UniProtKB/TrEMBL as 'true' if a sequence match to a PROSITE pattern is confirmed by eMotif, and 'unknown' if it is not.

Techniques:

Journal: BMC Bioinformatics

Article Title: Predicting active site residue annotations in the Pfam database

doi: 10.1186/1471-2105-8-298

Figure Lengend Snippet: Comparison of sequences matching an active site PROSITE pattern with the manual annotation of these sequences by PROSITE

Article Snippet: InterPro annotates PROSITE matches in UniProtKB/TrEMBL as 'true' if a sequence match to a PROSITE pattern is confirmed by eMotif, and 'unknown' if it is not.

Techniques: Comparison

Journal: BMC Bioinformatics

Article Title: Linear array of conserved sequence motifs to discriminate protein subfamilies: study on pyridine nucleotide-disulfide reductases

doi: 10.1186/1471-2105-8-96

Figure Lengend Snippet: Tree of the sequence relationship among 44 selected PNDR members . Class I, class II, and the proposed class III and class IV segregate in 4 different central branches. The tree was obtained using neighbor-joining analysis of a subset of 44 random selected proteins sequences, using the distance matrix of the MSA built with ClustalX. The tree was visualized by TreeView software.

Article Snippet: Considering that only a small proportion of the proteins clusterized as PNDR class I and PNDR class II in InterPro have a PROSITE's PNDR active site signature, a revision of this superfamily classes was performed.

Techniques: Sequencing, Software

Journal: BMC Bioinformatics

Article Title: Linear array of conserved sequence motifs to discriminate protein subfamilies: study on pyridine nucleotide-disulfide reductases

doi: 10.1186/1471-2105-8-96

Figure Lengend Snippet: Linear array of conserved motifs in PNDR family . A diagram for each initial protein cluster is presented in MAST-style. Blocks with known function are depicted in color as follows: (blue) NADH-binding site; (green) FAD-binding sites; (yellow, orange and red) disulfide redox active sites for class I, II and III, respectively. The common blocks between different clusters are shown encircled, and a total of 24 different blocks are included. Names at the left indicate the 11 initial protein groups and at the right the 4 final clusters. The scheme does not represent the real length of the sequences.

Article Snippet: Considering that only a small proportion of the proteins clusterized as PNDR class I and PNDR class II in InterPro have a PROSITE's PNDR active site signature, a revision of this superfamily classes was performed.

Techniques: Binding Assay

Journal: BMC Bioinformatics

Article Title: Linear array of conserved sequence motifs to discriminate protein subfamilies: study on pyridine nucleotide-disulfide reductases

doi: 10.1186/1471-2105-8-96

Figure Lengend Snippet: NDH-2 conserved region around the CxxC motif . (A) MSA displayed as LOGO representation of a 78 PNDR class IV subset with putative Cu(II)-reductase activity. ( B) Derived motifs signature written in PROSITE pattern form. The shadowed blocks represent conserved regions with putative functional assignment. Grey, cyan, yellow and magenta colors correspond to: the second FAD, Cu(I), Cu(II) and quinone binding motifs, respectively.

Article Snippet: Considering that only a small proportion of the proteins clusterized as PNDR class I and PNDR class II in InterPro have a PROSITE's PNDR active site signature, a revision of this superfamily classes was performed.

Techniques: Activity Assay, Derivative Assay, Functional Assay, Binding Assay

Journal: Genome Biology

Article Title: Genome cartography through domain annotation

doi:

Figure Lengend Snippet: A key to the databases mentioned in this article

Article Snippet: InterPro , http://www.ebi.ac.uk/interpro/ , Proteome analysis database based on Pfam, SMART, Prosite, PRINTS.

Techniques: Generated, Comparison, Sequencing, Software, Construct, Microarray