The CATH database of protein domain structures (http://www.biochem.ucl.ac.uk/bsm/cath/) currently contains 43,229 domains classified into 1467 superfamilies and 5107 sequence families. Each structural family is expanded with sequence relatives from GenBank and completed genomes, using a variety of efficient sequence search protocols and reliable thresholds. This extended CATH protein family database contains 616,470 domain sequences classified into 23,876 sequence families. This results in the significant expansion of the CATH HMM model library to include models built from the CATH sequence relatives, giving a 10% increase in coverage for detecting remote homologues. An improved Dictionary of Homologous superfamilies (DHS) (http://www.biochem.ucl.ac.uk/bsm/dhs/) containing specific sequence, structural and functional information for each superfamily in CATH considerably assists manual validation of homologues. Information on sequence relatives in CATH superfamilies, GenBank and completed genomes is presented in the CATH associated DHS and Gene3D resources. Domain partnership information can be obtained from Gene3D (http://www.biochem.ucl.ac.uk/bsm/cath/Gene3D/). A new CATH server has been implemented (http://www.biochem.ucl.ac.uk/cgi-bin/cath/CathServer.pl) providing automatic classification of newly determined sequences and structures using a suite of rapid sequence and structure comparison methods. The statistical significance of matches is assessed and links are provided to the putative superfamily or fold group to which the query sequence or structure is assigned.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC539978 | PMC |
| http://dx.doi.org/10.1093/nar/gki024 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Identification of a pathogenic SDHD mutation in a Chinese family with hereditary head and neck paraganglioma: implications for genetic counseling and management.
World J Surg Oncol
January 2025
Department of Otorhinolaryngology Head and Neck Surgery, Beijing Tiantan Hospital, Capital Medical University, No. 119, South Fourth Ring Road West, Fengtai District, Beijing, 100070, China.
Background: This study aims to identify a pathogenic SDHD mutation associated with hereditary head and neck paraganglioma (HNPGL) in a Chinese family and to explore its implications for genetic counseling.
Methods: The study involved a family with 15 members spanning three generations. A 31-year-old patient (II-4) was diagnosed with a left parotid gland tumor and a right carotid body tumor, while both the father and elder sister had right carotid body tumors, and the third sister had bilateral carotid body tumors.
Genome-wide identification and expression analysis of the WRKY gene family in Mikania micrantha.
BMC Genomics
January 2025
College of Biological Science and Food Engineering, Southwest Forestry University, Kunming, Yunnan Province, 650224, China.
Background: WRKY transcription factors (TFs) regulate plant responses to environmental stimuli and development, including flowering. Despite extensive research on different species, their role in the invasive plant Mikania micrantha remains to be explored. The aim of this study was to identify and analyze WRKY genes in M.
View Article and Find Full Text PDFThe curated Lactobacillus acidophilus NCFM genome provides insights into strain specificity and microevolution.
BMC Genomics
January 2025
Department of Food, Bioprocessing, & Nutrition Sciences, North Carolina State University, Raleigh, NC, USA.
Background: The advent of next generation sequencing technologies has enabled a surge in the number of whole genome sequences in public databases, and our understanding of the composition and evolution of bacterial genomes. Besides model organisms and pathogens, some attention has been dedicated to industrial bacteria, notably members of the Lactobacillaceae family that are commonly studied and formulated as probiotic bacteria. Of particular interest is Lactobacillus acidophilus NCFM, an extensively studied strain that has been widely commercialized for decades and is being used for the delivery of vaccines and therapeutics.
View Article and Find Full Text PDFBuilding a growing genomic repository for maternal and fetal health through the PING Consortium.
Pediatr Res
January 2025
Center for Genetic Medicine, Children's National Research Institute, Washington, DC, USA.
Background: Prenatally transmitted viruses can cause severe damage to the developing brain. There is unexplained variability in prenatal brain injury and postnatal neurodevelopmental outcomes, suggesting disease modifiers. Of note, prenatal Zika infection can cause a spectrum of neurodevelopmental disorders, including congenital Zika syndrome.
View Article and Find Full Text PDFThe prognostic impact of 1q21 gain/amplification in newly diagnosed multiple myeloma: a retrospective study based on a single center in China.
Ann Hematol
January 2025
Department of Hematology, Beijing Chaoyang Hospital, Myeloma Research Center of Beijing, Capital Medical University, Gongtinanlu No 8, Chaoyang District, Beijing, 100020, China.
1q21gain/amp is the most common in patients with multiple myeloma. However, there is limited research on the prognostic heterogeneity of 1q21+, and the prognostic of the 1q21 copy remains controversial. In this study, we primarily conducted a retrospective analysis of the prognostic significance of 1q21 gain/amp in 375 newly diagnosed multiple myeloma patients.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!