Protein domains and architectural innovation in plant-associated Proteobacteria. by Studholme, D, Downie, J, Preston, G

“…We clustered completely-sequenced proteomes of prokaryotes on the basis of their protein domain content, as defined by Pfam (release 16.0). This revealed that, although there was a correlation between phylogeny and domain content, other factors also have an influence. …”

Protein domains and architectural innovation in plant-associated Proteobacteria

“…We clustered completely-sequenced proteomes of prokaryotes on the basis of their protein domain content, as defined by Pfam (release 16.0). This revealed that, although there was a correlation between phylogeny and domain content, other factors also have an influence. …”

Essential Conditions for the Full Synergy of Probability of Occurrence Distributions by Rubem P. Mondaini, Simão C. de Albuquerque Neto

“…Some applications of the techniques introduced here are applied to protein domain families (Pfam databases, versions 27.0 and 35.0). The results will show evidence of their usefulness for testing the classification work performed with methods of alignment that are used by expert biologists.…”
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Genome-wide identification of CaARR-Bs transcription factor gene family in pepper and their expression patterns under salinity stress by Rana M. Alshegaihi, Salha Mesfer Alshamrani

“…CaARRs-B proteins had a typical conserved domain, including AAR-like (pfam: PF00072) and Myb DNA binding (pfam: PF00249) domains. …”
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Catalase Gene Family in Durum Wheat: Genome-Wide Analysis and Expression Profiling in Response to Multiple Abiotic Stress Conditions by Mouna Ghorbel, Ikram Zribi, Malek Besbes, Nouha Bouali, Faiçal Brini

“…Two conserved domains (pfam00199 and pfam06628) are also present in all identified proteins, which have different subcellular localizations: peroxisome and mitochondrion. …”
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Computer-based characterization of primate endogenous retrovirus in human genome project by Chow, Jia Long

“…Daripada pangkalan data Pfam, bahagian gag mempunyai gen yang kod untuk protein gag p10, gag p24, dan jejari zink. …”
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Structures of replication initiation proteins from staphylococcal antibiotic resistance plasmids reveal protein asymmetry and flexibility are necessary for replication by Carr, S, Phillips, S, Thomas, C

“…These structures are the first examples of the Rep_trans Pfam family providing insights into the replication of numerous antibiotic resistance plasmids from Gram-positive bacteria, Gram-negative phage and the mobilisation of DNA by conjugative transposons.…”

Genome-Wide Identification and Expression Analysis of Catalase Gene Families in <i>Triticeae</i> by Mouna Ghorbel, Ikram Zribi, Najla Haddaji, Arif Jamal Siddiqui, Nouha Bouali, Faiçal Brini

“…In fact, our analysis showed that the identified genes harbor the following two conserved domains: a catalase domain (pfam00199) and a catalase-related domain (pfam06628). …”
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The Flo Adhesin Family by Ronnie G. Willaert, Yeseren Kayacan, Bart Devreese

“…Finally, we identified from Pfam database datamining yeasts that could express Flo adhesins and are encountered in human infections and their adhesin architectures. …”
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Recrafting the neighbor-joining method by Pedersen Christian NS, Fagerberg Rolf, Brodal Gerth S, Mailund Thomas, Phillips Derek

“…We empirically evaluate the performance of our algoritms on distance matrices obtained from the Pfam collection of alignments. The experiments indicate that the running time of our algorithms evolve as Θ(<it>n</it>²) on the examined instance collection. …”
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Genomic comparison of Planktothrix agardhii isolates from a Lake Erie embayment by Katelyn M. McKindles, R. Michael McKay, George S. Bullerjahn

“…These novel isolates were processed for genomic sequencing, where reads were used to generate scaffolds and contigs which were annotated with DIAMOND BLAST hit, Pfam, and GO. Analyses include whole genome alignment to generate phylogenetic trees and comparison of genetic rearrangements between isolates. …”
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Genomic comparison of Planktothrix agardhii isolates from a Lake Erie embayment. by Katelyn M McKindles, R Michael McKay, George S Bullerjahn

“…These novel isolates were processed for genomic sequencing, where reads were used to generate scaffolds and contigs which were annotated with DIAMOND BLAST hit, Pfam, and GO. Analyses include whole genome alignment to generate phylogenetic trees and comparison of genetic rearrangements between isolates. …”
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Metallopeptidases of Toxoplasma gondii: in silico identification and gene expression by Escotte-Binet Sandie, Huguenin Antoine, Aubert Dominique, Martin Anne-Pascaline, Kaltenbach Matthieu, Florent Isabelle, Villena Isabelle

“…In the present study, we screened the T. gondii database using PFAM motifs specific for metallopeptidases in association with the MEROPS peptidase Database (release 10.0). …”
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Foldy: An open-source web application for interactive protein structure analysis. by Jacob B Roberts, Alberto A Nava, Allison N Pearson, Matthew R Incha, Luis E Valencia, Melody Ma, Abhay Rao, Jay D Keasling

“…Foldy enables scientists to predict the structure of proteins and complexes up to 6000 amino acids with AlphaFold, visualize Pfam annotations, and dock ligands with AutoDock Vina and DiffDock. …”
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MtnK, methylthioribose kinase, is a starvation-induced protein in Bacillus subtilis by Tse Jane KS, Krogh Susanne, Mulard Laurence, Sekowska Agnieszka, Danchin Antoine

“…We finally show that this enzyme is part of the family Pfam 01633 (choline kinases) which belongs to a large cluster of orthologs comprizing antibiotic aminoglycoside kinases and protein serine/threonine kinases.…”
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The Neuronal and Peripheral Expressed Membrane-Bound UNC93A Respond to Nutrient Availability in Mice by Mikaela M. Ceder, Emilia Lekholm, Sofie V. Hellsten, Emelie Perland, Robert Fredriksson

“…Many transporters such as the solute carriers belonging to the Major facilitator superfamily Pfam clan are orphans in that their tissue and cellular localization as well as substrate profile and function are still unknown. …”
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MarFERReT, an open-source, version-controlled reference library of marine microbial eukaryote functional genes by R. D. Groussman, S. Blaskowski, S. N. Coesel, E. V. Armbrust

“…Version 1.1 of MarFERReT contains reference sequences from 800 marine eukaryotic genomes and transcriptomes, covering 453 species- and strain-level taxa, totaling nearly 28 million protein sequences with associated NCBI and PR2 Taxonomy identifiers and Pfam functional annotations. The MarFERReT project repository hosts containerized build scripts, documentation on installation and use case examples, and information on new versions of MarFERReT.…”
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QSalignWeb: A Server to Predict and Analyze Protein Quaternary Structure by Sucharita Dey, Jaime Prilusky, Emmanuel D. Levy

“…Given a user-uploaded structure, the sequence is extracted and used to search homologs based on sequence similarity and PFAM domain architecture. If structural conservation is detected between a homolog and the user-uploaded QS, physiological relevance is inferred. …”
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Connecting genomic islands across prokaryotic and phage genomes via protein families by Reem Aldaihani, Lenwood S. Heath

“…We combined the large data set from the IslandViewer4 database with protein families from Pfam while implementing a comprehensive strategy to identify patterns making use of HMMER, BLAST, and MUSCLE. we also implemented Python programs that link the analysis into a single pipeline. …”
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Towards the Exploration and Evolution of Insulin-like Venoms in Actiniaria (<i>Sea anemones</i>) by Alonso Delgado, Kyle S. Sozanski, Marymegan Daly

“…We sourced data for 34 species of <i>Sea anemones</i> and found sequences belonging to two venom families which have Insulin PFAM annotations. Our findings show that both families have undergone duplication events. …”
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