Multiple Sequence Alignment of Small Heat Shock Protein 1 Orthologs
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Fecha
Publicador:
Consejo Nacional de Investigaciones Científicas y Técnicas
Fecha de depósito:
28/11/2024
Fecha de creación:
05/06/2024-10/06/2024
Clasificación temática
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Resumen
The curated dataset comprises 474 protein sequences, of which 199 are from invertebrates and 275 from vertebrates. During the curation process and after applying coverage and identity filters, no sequences from other kingdoms, including Plantae, Fungi, Eubacteria and Protista, remained in the dataset. Among the vertebrates, the dataset includes 88 mammals, 124 fish, 26 birds, 26 reptiles, and 11 amphibians. The MSA analysis shows that the ACD is highly conserved in length, with an average of 77.0 ± 0.5 amino acids, while the NTR (88.8 ± 18.3) is longer and more variable compared to the CTR (34.7 ± 8.4). The CTR lengths are similar between vertebrates (32.1 ± 8.1) and invertebrates (38.2 ± 7.5). In contrast, the NTR shows greater length variability between vertebrates (99.5 ± 16.6) and invertebrates (74.0 ± 6.5). This difference is due to a low-complexity region of variable length present in vertebrates, known as the inserted segment in human HSPB1.
Métodos
Homologous protein sequences were recruited from Uniprot KB database with Uniprot BLASTp, using the canonical human HSPB1 (UniProt ID P04792) as query. To ensure a comprehensive dataset, additional sequences were sourced by filtering according to specific taxonomic groups. The recruitment process focused on major kingdoms: Animalia, Plantae, Eubacteria, Fungi, and Protista. After recruitment, an initial filtering step was applied to remove sequences that were partial, hypothetical, or contained indeterminate residues. Duplicated sequences were also eliminated to avoid redundancy. The remaining sequences were aligned and then filtered based on percentage identity and sequence coverage. A threshold of 30% identity and 40% coverage was applied. From the resulting dataset, all HSPB1 sequences were manually curated to compile a set of orthologs HSPB1 sequences for subsequent analysis. The importance of working with proteins coded by orthologs genes is related to studying the evolutionary history of the product of a single gene, ensuring that these are the same protein in different organisms and, consequently, they perform the same function. Dataset characterization Two subsets were generated from the orthologs dataset, one for vertebrates and another for invertebrates. The three sequence datasets (the complete set, the vertebrate subset, and the invertebrate subset) were aligned using Clustal Omega within UGENE.
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