Development of an RNA interference (RNAi) gene knockdown protocol in the anaerobic gut fungus Pecoramyces ruminantium strain C1A by Shelby S. Calkins, Nicole C. Elledge, Katherine E. Mueller, Stephen M. Marek, MB Couger, Mostafa S. Elshahed, Noha H. Youssef

“…As well, significant differential up-regulation of the gene encoding NAD-dependent 2-hydroxyacid dehydrogenase (Pfam00389) in siRNA-treated C1A cultures was observed, which could possibly compensate for loss of D-LDH as an electron sink mechanism in C1A. …”
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Genome-wide identification and expression analysis of fibrillin (FBN) gene family in tomato (Solanum lycopersicum L.) by Huiru Sun, Min Ren, Jianing Zhang

“…Methods In this study, 14 FBN genes were identified in tomato genome by Pfam and Hmmer 3.0 software. ExPASy, MEGA 6.0, MEME, GSDS, TBtools, PlantCARE and so on were used for physical and chemical properties analysis, phylogenetic analysis, gene structure and conserved motifs analysis, collinearity analysis and cis-acting element analysis of FBN family genes in tomato. …”
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Genome-wide identification and expression analysis of the EXO70 gene family in grape (Vitis vinifera L) by Han Wang, Zong-Huan Ma, Juan Mao, Bai-Hong Chen

“…All of VvEXO70s had the conserved pfam03081 domain which maybe necessary for interacting with other proteins. …”
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Structural and Functional Disparities within the Human Gut Virome in Terms of Genome Topology and Representative Genome Selection by Werner P. Veldsman, Chao Yang, Zhenmiao Zhang, Yufen Huang, Debajyoti Chowdhury, Lu Zhang

“…Using Oxford Nanopore long reads for viral genome assembly coupled with Illumina short-read polishing, we showed that circular and linear virus genomes differ remarkably in terms of genome quality, GC skew, transfer RNA gene frequency, structural variant frequency, cross-reference functional annotation (COG, KEGG, Pfam, and TIGRfam), state-of-the-art marker-based classification, and phage–host interaction. …”
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Amino acid permease RcAAP1 increases the uptake and phloem translocation of an L-valine-phenazine-1-carboxylic acid conjugate by Yongxin Xiao, Ciyin Hu, Tom Hsiang, Junkai Li

“…Subsequently, expression of RcAAP1 in yeast cells increased the L-Val-PCA uptake (0.36 μmol/107 cells), which was 2.1-fold higher than the control (0.17 μmol/107 cells). Pfam analysis suggested RcAAP1 with its 11 transmembrane domains belongs to the amino acid transporter family. …”
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Role of bZIP Transcription Factors in Response to NaCl Stress in <i>Tamarix ramosissima</i> under Exogenous Potassium (K⁺) by Yahui Chen, Min Zhang, Dezong Sui, Jiang Jiang, Lei Wang

“…The results revealed that under NaCl stress with additional KCl applied treatments at 0 h, 48 h, and 168 h, based on Pfam protein domain prediction and physicochemical property analysis, we identified 20 related <i>bZIP</i> genes. …”
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DAKS1, a Kunitz Scaffold Peptide from the Venom Gland of <i>Deinagkistrodon acutus</i> Prevents Carotid-Artery and Middle-Cerebral-Artery Thrombosis via Targeting Factor XIa by Zhiping Jia, Yunyang Liu, Xiaoru Ji, Yizheng Zheng, Zhengyang Li, Shuai Jiang, Hongjin Li, Yi Kong

“…In the present study, we developed SBPs from the venom gland of <i>Deinagkistrodon acutus</i> (<i>D. acutus</i>) by combining transcriptome sequencing and Pfam annotation. To that end, 10 Kunitz peptides were discovered from the venom gland of <i>D. acutus</i>, and most of which peptides exhibited Factor XIa (FXIa) inhibitory activity. …”
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Genome-wide identification and expression analysis of the AUX/IAA gene family in turnip (Brassica rapa ssp. rapa) by Huanwen Xu, Yu Liu, Shengmei Zhang, Deju Shui, Zhewen Xia, Ji Sun

“…Results We performed a comprehensive genome-wide analysis and found 89 AUX/IAA genes in turnip based on the conserved AUX/IAA domain (pfam02309). Phylogenetic analysis of AUX/IAA genes from turnip, Arabidopsis, and cabbage revealed that these genes cluster into six subgroups (A1, A2, A3, A4, B1, and B2). …”
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Full-Length Transcriptome Sequencing and RNA-Seq Analysis Offer Insights into Terpenoid Biosynthesis in <i>Blumea balsamifera</i> (L.) DC. by Zhigang Ju, Lin Liang, Yaqiang Zheng, Hongxi Shi, Wenxuan Zhao, Wei Sun, Yuxin Pang

“…Among these highly accurate transcripts, 59,958 (92.18%) transcripts were successfully annotated using NR, eggNOG, Swissprot, KEGG, KOG, COG, Pfam, and GO databases. Finally, a total of 56 differently expressed genes (DEGs) involved in terpenoid biosynthesis were identified, including 38 terpenoid backbone genes and 18 TPSs, which provide a significant amount of genetic information for <i>B. balsamifera</i>. …”
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Genome-Wide Analysis of LysM-Containing Gene Family in Wheat: Structural and Phylogenetic Analysis during Development and Defense by Zheng Chen, Zijie Shen, Da Zhao, Lei Xu, Lijun Zhang, Quan Zou

“…Approximately 4000 proteins with the lysin motif (Pfam PF01476) are found in prokaryotes and eukaryotes. …”
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Genome-Wide Identification of lncRNA and mRNA for Diagnosing Type 2 Diabetes in Saudi Arabia by Albogami S

“…Coding potential was analyzed using coding–noncoding indices, the coding potential calculator, and PFAM, and the lncRNA function was predicted using Pearson’s correlation. …”
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Genome-Wide Analysis of MYB Transcription Factors in the Wheat Genome and Their Roles in Salt Stress Response by Selvakumar Sukumaran, Johanna Lethin, Xin Liu, Justyna Pelc, Peng Zeng, Sameer Hassan, Henrik Aronsson

“…Thus, we used the Chinese spring wheat genome assembled by the International Wheat Genome Sequencing Consortium to identify putative MYB proteins (719 in total). Protein families (PFAM) analysis of the MYB sequences identified 28 combinations of 16 domains in the encoded proteins. …”
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Interactions between C8orf37 and FAM161A, Two Ciliary Proteins Essential for Photoreceptor Survival by Yu Liu, Jinjun Chen, Rachel Sager, Erika Sasaki, Huaiyu Hu

“…Furthermore, interaction domain mapping assays identified that the N-terminal region of C8orf37 and amino acid residues 341-517 within the PFAM UPF0564 domain of FAM161A were critical for C8orf37–FAM161A interaction. …”
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Systematic Identification of Protein Targets of Sub5 Using <i>Saccharomyces cerevisiae</i> Proteome Microarrays by Pramod Shah, Chien-Sheng Chen

“…In total, 11 actin-associated proteins were identified in the protein targets of Sub5. Protein family (PFAM) enrichment anal-ysis shows protein domain enriched in actin binding, i.e., “Cytoskeletal-regulatory complex EF hand (helix E-loop-helix F motif)”. …”
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Phylogenetic classification of natural product biosynthetic gene clusters based on regulatory mechanisms by Alberto C. Rodriguez-Sanchez, Luz A. Gónzalez-Salazar, Lorena Rodriguez-Orduña, Ándres Cumsille, Agustina Undabarrena, Agustina Undabarrena, Beatriz Camara, Nelly Sélem-Mojica, Cuauhtemoc Licona-Cassani, Cuauhtemoc Licona-Cassani

“…We utilized Hidden Markov Models from the Pfam database to retrieve regulatory elements, such as histidine kinases and transcription factors, from BGCs in the MIBiG database, focusing on actinobacterial strains from three distinct environments: oligotrophic basins, rainforests, and marine environments. …”
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Iso-seq and RNA-seq profiling of Fenneropenaeus penicillatus: Unravelling the signaling pathway and genes involved in the ovarian development by Kianann Tan, Peng Xu, Leong-Seng Lim, Chunhong Nie, Karsoon Tan, Ya Peng, Xiaohui Cai, Xueyu Yan, Youhou Xu, Kit Yue Kwan

“…This study utilized CPC, CPAT, PLEK, and pfam, to predict the numbers of long non-coding RNAs (lncRNAs). …”
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RNA-sequencing of methyl-jasmonate treated turmeric (Curcuma longa) reveals novel protease inhibitor transcripts by Chan, Seow Neng, Abu Bakar, Norliza, Mahmood, Mahmmod Basher, Ho, Chai Ling, Shaharuddin, Noor Azmi

“…Sequence annotation and homology search were performed onto several protein databases such as Uniprot, Pfam, GO and KEGG which resulted in around 50% of the transcripts showed similarity hits to known proteins. …”
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Basic Characteristics of Flower Transcriptome Data and Derived Novel EST-SSR Markers of <i>Luculia yunnanensis</i>, an Endangered Species Endemic to Yunnan, Southwestern China by Yao Zhang, Xi Liu, Yuying Li, Xiongfang Liu, Hong Ma, Suping Qu, Zhenghong Li

“…The results showed that 98,389 unigenes were obtained from the <i>L. yunnanensis</i> flower transcriptome, all of which were aligned with sequences in public databases. Nr, Nt, Pfam, KOG/COG, Swiss-Prot, KEGG, and GO annotated 31,859, 13,853, 22,684, 10,947, 21,416, 9722, and 23,390 unigenes, respectively. …”
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Protein domains provide a new layer of information for classifying human variations in rare diseases by Mélanie Corcuff, Marc Garibal, Jean-Pierre Desvignes, Céline Guien, Coralie Grattepanche, Gwenaëlle Collod-Béroud, Estelle Ménoret, David Salgado, Christophe Béroud, Christophe Béroud

“…To improve the classification of human missense variants using protein domains information, we developed the DOLPHIN system (https://dolphin.mmg-gbit.eu).Methods: We used Pfam alignments of eukaryotes to define DOLPHIN scores to identify protein domain residues and variants that have a significant impact. …”
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Transcriptomic Differences between Free-Living and Parasitic <i>Chilodonella uncinata</i> (Alveolata, Ciliophora) by Xialian Bu, Weishan Zhao, Ming Li, Wenxiang Li, Shangong Wu, Hong Zou, Guitang Wang

“…These DEGs were identified through BLAST with NCBI-nr, Swiss-Port, and Pfam databases and then annotated by GO enrichment and KEGG pathway analysis. …”
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