UDP-glucose pyrophosphorylase: genome-wide identification, expression and functional analyses in Gossypium hirsutum by Zhongyang Xu, Jiasen He, Muhammad Tehseen Azhar, Zhen Zhang, Senmiao Fan, Xiao Jiang, Tingting Jia, Haihong Shang, Youlu Yuan

“…In this study, a total of 66 UDP-glucose pyrophosphorylase (UGP) (EC 2.7.7.9) genes were identified from the genomes of four cotton species, which are the members of Pfam glycosyltransferase family (PF01702) and catalyze the reaction between glucose-1-phosphate and UTP to produce UDPG. …”
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Transcriptomic and Metabolomic Profiling Provides Insights into Flavonoid Biosynthesis and Flower Coloring in <i>Loropetalum chinense</i> and <i>Loropetalum chinense</i> var. <i>ru... by Xia Zhang, Li Zhang, Damao Zhang, Yang Liu, Ling Lin, Xingyao Xiong, Donglin Zhang, Ming Sun, Ming Cai, Xiaoying Yu, Yanlin Li

“…Among them, 52,851 transcripts were annotated in the seven databases of NR, KOG, GO, NT, Pfam, Swiss-Port, and KEGG. Combined with NGS analyses, the DETs involved in flavonoids and anthocyanins contributed greatest to the flower coloring. …”
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Comparative transcriptome analysis provides novel insights into molecular response of salt-tolerant and sensitive polyembryonic mango genotypes to salinity stress at seedling stage by Nusrat Perveen, M. R. Dinesh, M. Sankaran, K. V. Ravishankar, Hara Gopal Krishnajee, Vageeshbabu S. Hanur, Saud Alamri, Mahipal Singh Kesawat, Mohammad Irfan

“…In total, 7169 unigenes annotated against all the five public databases, including NR, NT, PFAM, KOG, Swissport, KEGG and GO. Further, maximum number of differentially expressed genes were found between MT and MC (2106) followed by MT vs TT (1158) and TT and TC (587). …”
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TinoTranscriptDB: A Database of Transcripts and Microsatellite Markers of <i>Tinospora cordifolia</i>, an Important Medicinal Plant by Rakesh Singh, Ajay Kumar Mahato, Akshay Singh, Rajesh Kumar, Amit K. Singh, Sundeep Kumar, Soma S. Marla, Ashok Kumar, Nagendra K. Singh

“…We annotated 26,716 (62%) of the total transcripts successfully from National Center for Biotechnology Information non-redundant protein (NCBI-NR), gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Swiss-Prot, and Pfam databases. This database contains information of 2620 perfect simple sequence repeats (P-SSRs) with a relative abundance of 340.12 (loci/Mb), and relative density of 6309.29 (bp/Mb). …”
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Multi-Species Transcriptome Assemblies of Cultivated and Wild Lentils (<i>Lens</i> sp.) Provide a First Glimpse at the Lentil Pangenome by Juan J. Gutierrez-Gonzalez, Pedro García, Carlos Polanco, Ana Isabel González, Francisca Vaquero, Francisco Javier Vences, Marcelino Pérez de la Vega, Luis E. Sáenz de Miera

“…The different pan-transcriptome clusters were also screened for Pfam-domain enrichment. The present study has a high novelty, as it is the first pan-transcriptome analysis using six wild species in addition to cultivated species. …”
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Transcriptome analysis and gene expression analysis related to salinity-alkalinity and low temperature adaptation of Triplophysa yarkandensis by Xuejing Zhang, Tai Wang, Dongdong Zhai, Dongdong Zhai, Hongyan Liu, Hongyan Liu, Fei Xiong, Fei Xiong, Ying Wang, Ying Wang

“…Nine major international gene annotation databases (NR, COG, egg_NOG, TrEMBL, Pfam, KOG, Swiss prot, KEGG and Gene Ontology) were utilized to annotate unigenes. …”
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MiR-142-5p/FAM134B Axis Manipulates ER-Phagy to Control PRRSV Replication by Kaifeng Guan, Qiuju Su, Kailin Kuang, Xiangge Meng, Xiang Zhou, Xiang Zhou, Bang Liu, Bang Liu, Bang Liu

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Sucrose metabolism analysis in a high sucrose sugarcane mutant clone at a mature stage in contrast to low sucrose parental clone through the transcriptomic approach by Qaisar Khan, Ying Qin, Dao-Jun Guo, Jiao-Yun Chen, Xu-Peng Zeng, Amir Mahmood, Li-Tao Yang, Qiang Liang, Xiu-Peng Song, Yong-Xiu Xing, Yang-Rui Li

“…Results A total of 100, 262 differentially expressed genes were obtained, and 69, 637 (69.46%) got annotation in public databases COG, GO, KEGG, KOG, Pfam, eggNOG, NR, and Swiss-Prot. The SPS5 gene was significantly up-regulated in the maturing internodes of GXB9 and downregulated in B9. …”
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Investigation of dirigent like domains from bacterial genomes by Merlin Bardin, Pierre Rousselot-Pailley, Thierry Tron, Viviane Robert

“…Analyzes of structural and functional genomic data led to the identification of the Pfam PF03018 domain as characteristic of DIR proteins. …”
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Complete genome sequence analysis of Edwardsiella tarda SC002 from hatchlings of Siamese crocodile by Muhammad Nafees Ur Rehman, Farman Ullah Dawar, Jifeng Zeng, Jifeng Zeng, Lixia Fan, Wei Feng, Mengqi Wang, Nuo Yang, Guiying Guo, Jiping Zheng, Jiping Zheng

“…In addition, the coding genes of assembled genome were successfully annotated against eight general databases (NR = 3,618/3,734, COG = 2,947/3,734, KEGG = 3,485/3,734, SWISS-PROT = 2,787/3,734, GO = 2,648/3,734, Pfam = 2,648/3,734, CAZy = 130/3,734, and TCDB = 637/3,734) and four pathogenicity-related databases (ARDB = 11/3,734, CARD = 142/3,734, PHI = 538/3,734, and VFDB = 315/3,734). …”
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IurV, Encoded by ORF VCA0231, Is Involved in the Regulation of Iron Uptake Genes in <i>Vibrio cholerae</i> by Bernardo Sachman-Ruiz, José Antonio Ibarra, Paulina Estrada-de los Santos, Alexia Torres Muñoz, Begoña Giménez, Juan Carlos Salazar, Víctor Antonio García-Angulo

“…In addition, a genomic neighborhood analysis with the Enzyme Function Initiative tools detected many Pfam families involved in iron homeostasis genetically associated with VCA0231. …”
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Systematical Screening of Intracellular Protein Targets of Polyphemusin-I Using <i>Escherichia coli</i> Proteome Microarrays by Pramod Shah, Chien-Sheng Chen

“…In accordance to GO enrichment analysis, protein families (PFAM) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enrichment analysis also showed significant enrichment in nucleic acid terms. …”
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Full-length transcriptome sequencing and comparative transcriptome analysis of Eriocheir sinensis in response to infection by the microsporidian Hepatospora eriocheir by Libo Hou, Mengdi Wang, Lei Zhu, Mingxiao Ning, Jingxiu Bi, Jie Du, Xianghui Kong, Wei Gu, Qingguo Meng

“…In addition, 74,732 unigenes were mapped to at least one of the following databases: Non-Redundant Protein Sequence Database (NR), Gene Ontology (GO), Kyoto Encyclopaedia of Genes and Genomes (KEGG), KEGG Orthology (KO) and Protein family (Pfam). In addition, 6696 transcription factors (TFs), 28,458 long non-coding RNAs (lncRNAs) and 94,230 mRNA-miRNA pairs were identified. …”
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Genomic Analysis of <i>LEA</i> Genes in <i>Carica papaya</i> and Insight into Lineage-Specific Family Evolution in Brassicales by Zhi Zou, Jingyuan Guo, Yujiao Zheng, Yanhua Xiao, Anping Guo

“…A total of 28 members were identified from the papaya genome, which belong to eight families with defined Pfam domains, i.e., LEA_1 (3), LEA_2 (4), LEA_3 (5), LEA_4 (5), LEA_5 (2), LEA_6 (2), DHN (4), and SMP (3). …”
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Transcriptome analysis of megalurothrips usitatus (Bagnall) identifies olfactory genes with ligands binding characteristics of MusiOBP1 and MusiCSP1 by Zhaoyang Li, Weiyi Chen, Xiaoshuang Wang, Wen Sang, Huipeng Pan, Shaukat Ali, Liangde Tang, Jianhui Wu

“…A total of 56,669 unigenes were annotated using GO, NR, Pfam, eggNOG, SwissProt, and KEGG. The number of differentially expressed genes between pupae and nymphs, males and nymphs, and females and nymphs were 10,498, 9,235, and 10,964, respectively. …”
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Genome Assembly of a Relict Arabian Species of <i>Daphnia</i> O. F. Müller (Crustacea: Cladocera) Adapted to the Desert Life by Waleed Hamza, Khaled M. Hazzouri, Naganeeswaran Sudalaimuthuasari, Khaled M. A. Amiri, Anna N. Neretina, Shamma E. S. Al Neyadi, Alexey A. Kotov

“…Interestingly, the population expansion in its diversity occurred during the megadrought climate around 100 Ka ago, reflecting the adaptive feature of the species to arid and drought-affected environments. Moreover, the PFAM comparative analysis highlights the presence of the important domain SOSS complex subunit C in <i>D. arabica</i>, which is missing in all other studied species of <i>Daphnia</i>. …”
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Screening and isolation of cold-adapted cellulose degrading bacterium: A candidate for straw degradation and De novo genome sequencing analysis by Zhigang He, Baopeng Ding, Qurban Ali, Huiyu Liu, Ying Zhao, Xiujuan Wang, Yingzuo Han, Huan Dong, Praveen Kumar Divvela, Yinghua Juan

“…The results showed that the low-temperature (10°C) and high-efficiency cellulose-degrading bacterium Bacillus subtilis K1 was 4,060,823 bp in genome size, containing 4,213 genes, with 3,665, 3,656, 2,755, 3,240, 1,261, 3,336 and 4,003 genes annotated in the non-redundant protein sequence database (NR), Pfam, clusters of orthologous groups of proteins (COGs), Genome Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Annotation databases, respectively. …”
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Detection and Typing of Plasmids in Acinetobacter baumannii Using rep Genes Encoding Replication Initiation Proteins by Margaret M. C. Lam, Jonathan Koong, Kathryn E. Holt, Ruth M. Hall, Mehrad Hamidian

“…Plasmids were separated into 3 groups based on the Pfam domains of the encoded replication initiation (Rep) protein and a fourth group that lack an identifiable Rep protein. …”
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Marine prebiotics mediate decolonization of Pseudomonas aeruginosa from gut by inhibiting secreted virulence factor interactions with mucins and enriching Bacteroides population by Rajendra Prasad Janapatla, Anna Dudek, Chyi-Liang Chen, Chih-Hsien Chuang, Kun-Yi Chien, Ye Feng, Yuan-Ming Yeh, Yi-Hsin Wang, Hsin-Ju Chang, Yuan-Chuan Lee, Cheng-Hsun Chiu

“…Lectin like activity at the N-terminal of TpsA due to a conserved hemagglutinin domain (Pfam identifier [ID] PF05860) mediates binding to mucins that carry multiple fucosylated glycans. …”
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Transcriptomic dissection of termite gut microbiota following entomopathogenic fungal infection by Ya-ling Tang, Ya-ling Tang, Yun-hui Kong, Sheng Qin, Sheng Qin, Austin Merchant, Ji-zhe Shi, Xu-guo Zhou, Mu-wang Li, Mu-wang Li, Qian Wang

“…As a result, 142531 transcripts and 73608 unigenes were obtained, and unigenes were annotated following NR, NT, KO, Swiss-Prot, PFAM, GO, and KOG databases. Among them, a total of 3,814 differentially expressed genes (DEGs) were identified between M. robertsii infected termites with or without antibiotics treatment. …”
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