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For: Mudgal R, Sandhya S, Chandra N, Srinivasan N. De-DUFing the DUFs: Deciphering distant evolutionary relationships of Domains of Unknown Function using sensitive homology detection methods. Biol Direct 2015;10:38. [PMID: 26228684 PMCID: PMC4520260 DOI: 10.1186/s13062-015-0069-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 07/20/2015] [Indexed: 12/23/2022]  Open
Number Cited by Other Article(s)
1
Grossman AS, Mucci NC, Kauffman SJ, Rafi J, Goodrich-Blair H. Bioinformatic discovery of type 11 secretion system (T11SS) cargo across the Proteobacteria. Microb Genom 2025;11. [PMID: 40397007 DOI: 10.1099/mgen.0.001406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2025]  Open
2
Li J, Xia R, Huang WC, Gu J, Li M. DUF99 family proteins are novel endonucleases that cleave deoxyuridine on DNA substrates. J Biol Chem 2024;300:107901. [PMID: 39426726 PMCID: PMC11585767 DOI: 10.1016/j.jbc.2024.107901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 10/09/2024] [Accepted: 10/12/2024] [Indexed: 10/21/2024]  Open
3
Yang J, Sun N, Wang W, Zhang R, Sun S, Li B, Shi Y, Zeng J, Jia S. Genomic analysis and mechanisms exploration of a stress tolerance and high-yield pullulan producing strain. Front Genet 2024;15:1469600. [PMID: 39371418 PMCID: PMC11449735 DOI: 10.3389/fgene.2024.1469600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Accepted: 09/10/2024] [Indexed: 10/08/2024]  Open
4
Lu X, Li Y, Akhtar M, Liu C, Ma T, Min W, Bai X, She Y, Chen L, Tian L, Li P, Luo C. A DUF966 gene family member OsDSR3 positively regulates alkali stress tolerance in rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024;343:112072. [PMID: 38513731 DOI: 10.1016/j.plantsci.2024.112072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 03/03/2024] [Accepted: 03/18/2024] [Indexed: 03/23/2024]
5
Luo C, Akhtar M, Min W, Bai X, Ma T, Liu C. Domain of unknown function (DUF) proteins in plants: function and perspective. PROTOPLASMA 2024;261:397-410. [PMID: 38158398 DOI: 10.1007/s00709-023-01917-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 12/08/2023] [Indexed: 01/03/2024]
6
de Oliveira Silva YR, Zheng D, Peters SC, Fisher OS. Stabilization of a Cu-binding site by a highly conserved tryptophan residue. J Inorg Biochem 2024;253:112501. [PMID: 38342077 DOI: 10.1016/j.jinorgbio.2024.112501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/13/2024]
7
Guo S, Lv L, Zhao Y, Wang J, Lu X, Zhang M, Wang R, Zhang Y, Guo X. Using High-Throughput Phenotyping Analysis to Decipher the Phenotypic Components and Genetic Architecture of Maize Seedling Salt Tolerance. Genes (Basel) 2023;14:1771. [PMID: 37761911 PMCID: PMC10530905 DOI: 10.3390/genes14091771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/29/2023]  Open
8
KDF1 Novel Variant Causes Unique Dental and Oral Epithelial Defects. Int J Mol Sci 2022;23:ijms232012465. [PMID: 36293320 PMCID: PMC9604338 DOI: 10.3390/ijms232012465] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/15/2022] [Accepted: 10/16/2022] [Indexed: 11/18/2022]  Open
9
Wang X, Li J, Sun J, Gu S, Wang J, Su C, Li Y, Ma D, Zhao M, Chen W. Mining Beneficial Genes for Salt Tolerance From a Core Collection of Rice Landraces at the Seedling Stage Through Genome-Wide Association Mapping. FRONTIERS IN PLANT SCIENCE 2022;13:847863. [PMID: 35557725 PMCID: PMC9087808 DOI: 10.3389/fpls.2022.847863] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 04/08/2022] [Indexed: 06/15/2023]
10
Tian X, Niu X, Chang Z, Zhang X, Wang R, Yang Q, Li G. DUF1005 Family Identification, Evolution Analysis in Plants, and Primary Root Elongation Regulation of CiDUF1005 From Caragana intermedia. Front Genet 2022;13:807293. [PMID: 35422842 PMCID: PMC9001952 DOI: 10.3389/fgene.2022.807293] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 02/08/2022] [Indexed: 11/13/2022]  Open
11
Kader MA, Ahammed A, Khan MS, Ashik SAA, Islam MS, Hossain MU. Hypothetical protein predicted to be tumor suppressor: a protein functional analysis. Genomics Inform 2022;20:e6. [PMID: 35399005 PMCID: PMC9002001 DOI: 10.5808/gi.21073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 01/08/2022] [Indexed: 12/22/2022]  Open
12
Kumar G, Srinivasan N, Sandhya S. Profiles of Natural and Designed Protein-Like Sequences Effectively Bridge Protein Sequence Gaps: Implications in Distant Homology Detection. Methods Mol Biol 2022;2449:149-167. [PMID: 35507261 DOI: 10.1007/978-1-0716-2095-3_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
13
Ying S. Genome-Wide Identification and Transcriptional Analysis of Arabidopsis DUF506 Gene Family. Int J Mol Sci 2021;22:11442. [PMID: 34768874 PMCID: PMC8583954 DOI: 10.3390/ijms222111442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/14/2021] [Accepted: 10/21/2021] [Indexed: 11/16/2022]  Open
14
TIM29 is required for enhanced stem cell activity during regeneration in the flatworm Macrostomum lignano. Sci Rep 2021;11:1166. [PMID: 33441924 PMCID: PMC7806878 DOI: 10.1038/s41598-020-80682-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 12/10/2020] [Indexed: 01/29/2023]  Open
15
Welkos S, Blanco I, Okaro U, Chua J, DeShazer D. A DUF4148 family protein produced inside RAW264.7 cells is a critical Burkholderia pseudomallei virulence factor. Virulence 2020;11:1041-1058. [PMID: 32835600 PMCID: PMC7549894 DOI: 10.1080/21505594.2020.1806675] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 07/24/2020] [Accepted: 07/27/2020] [Indexed: 11/12/2022]  Open
16
Rahman A, Susmi TF, Yasmin F, Karim ME, Hossain MU. Functional annotation of an ecologically important protein from Chloroflexus aurantiacus involved in polyhydroxyalkanoates (PHA) biosynthetic pathway. SN APPLIED SCIENCES 2020. [DOI: 10.1007/s42452-020-03598-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]  Open
17
Short, Rich, and Powerful: a New Family of Arginine-Rich Small Proteins Have Outsized Impact in Agrobacterium tumefaciens. J Bacteriol 2020;202:JB.00450-20. [PMID: 32839178 DOI: 10.1128/jb.00450-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
18
Arginine-Rich Small Proteins with a Domain of Unknown Function, DUF1127, Play a Role in Phosphate and Carbon Metabolism of Agrobacterium tumefaciens. J Bacteriol 2020;202:JB.00309-20. [PMID: 33093235 DOI: 10.1128/jb.00309-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 07/21/2020] [Indexed: 02/06/2023]  Open
19
Wang L, Wang M, Shi X, Yang J, Qian C, Liu Q, Zong L, Liu X, Zhu Z, Tang D, Zhang X. Investigation into archaeal extremophilic lifestyles through comparative proteogenomic analysis. J Biomol Struct Dyn 2020;39:7080-7092. [PMID: 32820705 DOI: 10.1080/07391102.2020.1808531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
20
Yang Q, Niu X, Tian X, Zhang X, Cong J, Wang R, Zhang G, Li G. Comprehensive genomic analysis of the DUF4228 gene family in land plants and expression profiling of ATDUF4228 under abiotic stresses. BMC Genomics 2020;21:12. [PMID: 31900112 PMCID: PMC6942412 DOI: 10.1186/s12864-019-6389-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 12/12/2019] [Indexed: 01/24/2023]  Open
21
Lv M, Hou D, Zhang L, Fan J, Li C, Chen W, Sun Y, Dong Y, Xu J, Cai L, Gao X, Zhu J, Huang Z, Xu Z, Li L. Molecular characterization and function analysis of the rice OsDUF1191 family. BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2019.1684843] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]  Open
22
Adam S, Klein A, Surup F, Koehnke J. The structure of CgnJ, a domain of unknown function protein from the crocagin gene cluster. Acta Crystallogr F Struct Biol Commun 2019;75:205-211. [PMID: 30839296 PMCID: PMC6404859 DOI: 10.1107/s2053230x19000712] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 01/16/2019] [Indexed: 12/28/2022]  Open
23
Bhagavat R, Sankar S, Srinivasan N, Chandra N. An Augmented Pocketome: Detection and Analysis of Small-Molecule Binding Pockets in Proteins of Known 3D Structure. Structure 2019. [PMID: 29514079 DOI: 10.1016/j.str.2018.02.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
24
Engqvist MKM. Correlating enzyme annotations with a large set of microbial growth temperatures reveals metabolic adaptations to growth at diverse temperatures. BMC Microbiol 2018;18:177. [PMID: 30400856 PMCID: PMC6219164 DOI: 10.1186/s12866-018-1320-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 10/16/2018] [Indexed: 12/15/2022]  Open
25
Kumar G, Mudgal R, Srinivasan N, Sandhya S. Use of designed sequences in protein structure recognition. Biol Direct 2018;13:8. [PMID: 29776380 PMCID: PMC5960202 DOI: 10.1186/s13062-018-0209-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 04/18/2018] [Indexed: 12/13/2022]  Open
26
Aučynaitė A, Rutkienė R, Gasparavičiūtė R, Meškys R, Urbonavičius J. A gene encoding a DUF523 domain protein is involved in the conversion of 2-thiouracil into uracil. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018;10:49-56. [PMID: 29194984 DOI: 10.1111/1758-2229.12605] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 11/17/2017] [Accepted: 11/19/2017] [Indexed: 06/07/2023]
27
Burkhart BJ, Schwalen CJ, Mann G, Naismith JH, Mitchell DA. YcaO-Dependent Posttranslational Amide Activation: Biosynthesis, Structure, and Function. Chem Rev 2017;117:5389-5456. [PMID: 28256131 DOI: 10.1021/acs.chemrev.6b00623] [Citation(s) in RCA: 150] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
28
Yang Y, Yoo CG, Guo HB, Rottmann W, Winkeler KA, Collins CM, Gunter LE, Jawdy SS, Yang X, Guo H, Pu Y, Ragauskas AJ, Tuskan GA, Chen JG. Overexpression of a Domain of Unknown Function 266-containing protein results in high cellulose content, reduced recalcitrance, and enhanced plant growth in the bioenergy crop Populus. BIOTECHNOLOGY FOR BIOFUELS 2017;10:74. [PMID: 28344649 PMCID: PMC5364563 DOI: 10.1186/s13068-017-0760-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 03/18/2017] [Indexed: 05/17/2023]
29
Yang SQ, Li WQ, Miao H, Gan PF, Qiao L, Chang YL, Shi CH, Chen KM. REL2, A Gene Encoding An Unknown Function Protein which Contains DUF630 and DUF632 Domains Controls Leaf Rolling in Rice. RICE (NEW YORK, N.Y.) 2016;9:37. [PMID: 27473144 PMCID: PMC4967057 DOI: 10.1186/s12284-016-0105-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 07/07/2016] [Indexed: 05/20/2023]
30
Wong TY, Kuo J. A new drug design strategy: Killing drug resistant bacteria by deactivating their hypothetical genes. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART C, ENVIRONMENTAL CARCINOGENESIS & ECOTOXICOLOGY REVIEWS 2016;34:276-292. [PMID: 27901648 DOI: 10.1080/10590501.2016.1236605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
31
Yang J, Suzuki M, McCarty DR. Essential role of conserved DUF177A protein in plastid 23S rRNA accumulation and plant embryogenesis. JOURNAL OF EXPERIMENTAL BOTANY 2016;67:5447-5460. [PMID: 27574185 PMCID: PMC5049393 DOI: 10.1093/jxb/erw311] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
32
Lobb B, Doxey AC. Novel function discovery through sequence and structural data mining. Curr Opin Struct Biol 2016;38:53-61. [DOI: 10.1016/j.sbi.2016.05.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Revised: 05/17/2016] [Accepted: 05/24/2016] [Indexed: 01/30/2023]
33
Sandhya S, Mudgal R, Kumar G, Sowdhamini R, Srinivasan N. Protein sequence design and its applications. Curr Opin Struct Biol 2016;37:71-80. [PMID: 26773478 DOI: 10.1016/j.sbi.2015.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 12/07/2015] [Accepted: 12/15/2015] [Indexed: 01/14/2023]
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