PIR SuperFamily
Names
More detailed information about this field from each metasource.
PIR SuperFamily
metasource: Fairsharing.org
version: FAIRsharing.org: PIRSF; PIR SuperFamily; DOI: https://doi.org/10.25504/FAIRsharing.vssch2; Last edited: June 15, 2021, 1:42 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
PIRSF
metasource: Fairsharing.org
version: FAIRsharing.org: PIRSF; PIR SuperFamily; DOI: https://doi.org/10.25504/FAIRsharing.vssch2; Last edited: June 15, 2021, 1:42 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
PIRSF whole-protein classification database
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:07.993116
pirsf
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:07.993116
Names
More detailed information about this field from each metasource.
PIR SuperFamily
metasource: Fairsharing.orgversion: FAIRsharing.org: PIRSF; PIR SuperFamily; DOI: https://doi.org/10.25504/FAIRsharing.vssch2; Last edited: June 15, 2021, 1:42 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
PIRSF
metasource: Fairsharing.orgversion: FAIRsharing.org: PIRSF; PIR SuperFamily; DOI: https://doi.org/10.25504/FAIRsharing.vssch2; Last edited: June 15, 2021, 1:42 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
PIRSF whole-protein classification database
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:07.993116
pirsf
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:07.993116
Other names: PIRSF, PIRSF whole-protein classification database, pirsf
Names
More detailed information about this field from each metasource.
PIR SuperFamily
metasource: Fairsharing.orgversion: FAIRsharing.org: PIRSF; PIR SuperFamily; DOI: https://doi.org/10.25504/FAIRsharing.vssch2; Last edited: June 15, 2021, 1:42 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
PIRSF
metasource: Fairsharing.orgversion: FAIRsharing.org: PIRSF; PIR SuperFamily; DOI: https://doi.org/10.25504/FAIRsharing.vssch2; Last edited: June 15, 2021, 1:42 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
PIRSF whole-protein classification database
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:07.993116
pirsf
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:07.993116
The PIR SuperFamily concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships.
Description
More detailed information about this field from each metasource.
The PIR SuperFamily concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships.
metasource: Fairsharing.orgversion: FAIRsharing.org: PIRSF; PIR SuperFamily; DOI: https://doi.org/10.25504/FAIRsharing.vssch2; Last edited: June 15, 2021, 1:42 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
The PIRSF is a network system of protein classification that reflects evolutionary relationships of full-length proteins and domains. The PIRSF classification system accommodates a flexible number of levels that reflect varying degrees of sequence conservation from superfamily to subfamily levels, allowing improved protein annotation, more accurate extraction of conserved functional residues, and classification of distantly related orphan proteins. The primary PIRSF classification unit is the homeomorphic family, whose members are both homologous (evolved from a common ancestor) and homeomorphic (sharing full-length sequence similarity and a common domain architecture). The PIRSF database consists of two data sets, preliminary clusters and curated families. PIRSF families are curated systematically based on literature review and integrative sequence and functional analysis, including sequence and structure similarity, domain architecture, functional association, genome context, and phyletic pattern. The results of classification and expert annotation are summarized in PIRSF family reports with graphical viewers for taxonomic distribution, domain architecture, family hierarchy, and multiple alignment and phylogenetic tree. The PIRSF system provides a comprehensive resource for bioinformatics analysis and comparative studies of protein function and evolution. Domain searches allow identification of evolutionarily related protein families sharing domains or structural folds. Functional convergence and functional divergence are revealed by the relationships between protein classification and curated family functions. The taxonomic distribution allows the identification of lineage-specific or broadly conserved protein families and can reveal horizontal gene transfer. PIRSF is accessible from the web site at http://pir.georgetown.edu/pirsf/ for report retrieval and sequence classification, and the data sets can be downloaded at ftp://ftp.pir.georgetown.edu/pir_databases/pirsf/dagfiles/.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships. The classification system is based on whole proteins rather than on the component domains therefore, it allows annotation of generic biochemical and specific biological functions, as well as classification of proteins without well-defined domains.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:07.993116
Webpage:
https://proteininformationresource.org/pirwww/dbinfo/pirsf.shtmlWebpage
More detailed information about this field from each metasource.
https://proteininformationresource.org/pirwww/dbinfo/pirsf.shtml
metasource: Fairsharing.orgversion: FAIRsharing.org: PIRSF; PIR SuperFamily; DOI: https://doi.org/10.25504/FAIRsharing.vssch2; Last edited: June 15, 2021, 1:42 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
http://pir.georgetown.edu/pirsf/
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
http://pir.georgetown.edu/pirwww/dbinfo/pirsf.shtml
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:07.993116
Licence:
Name: Open Data Commons (ODC) Public Domain Dedication and Licence (PDDL) 1.0Licence name
More detailed information about this field from each metasource.
Open Data Commons (ODC) Public Domain Dedication and Licence (PDDL) 1.0
metasource: Fairsharing.orgversion: FAIRsharing.org: PIRSF; PIR SuperFamily; DOI: https://doi.org/10.25504/FAIRsharing.vssch2; Last edited: June 15, 2021, 1:42 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
URL: http://opendatacommons.org/licenses/pddl/1.0/
Licence URL
More detailed information about this field from each metasource.
http://opendatacommons.org/licenses/pddl/1.0/
metasource: Fairsharing.orgversion: FAIRsharing.org: PIRSF; PIR SuperFamily; DOI: https://doi.org/10.25504/FAIRsharing.vssch2; Last edited: June 15, 2021, 1:42 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
PIRSF: family classification system at the Protein Information Resource
PMID: 14681371
metasource: Fairsharing.org
version: FAIRsharing.org: PIRSF; PIR SuperFamily; DOI: https://doi.org/10.25504/FAIRsharing.vssch2; Last edited: June 15, 2021, 1:42 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
http://dx.doi.org/10.1093/nar/gkh097
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:07.993116
Publications
More detailed information about this field from each metasource.
PIRSF: family classification system at the Protein Information Resource
PMID: 14681371
metasource: Fairsharing.org
version: FAIRsharing.org: PIRSF; PIR SuperFamily; DOI: https://doi.org/10.25504/FAIRsharing.vssch2; Last edited: June 15, 2021, 1:42 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
http://dx.doi.org/10.1093/nar/gkh097
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:07.993116
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PIRSF: family classification system at the Protein Information Resource
PubMed citations: 107.
107 articles citing: PIRSF: family classification system at the Protein Information Resource
Loci underlying leaf agronomic traits identified by re-sequencing celery accessions based on an assembled genome. PMID:35784787
Chromosome-scale genome assembly of an important medicinal plant honeysuckle. PMID:35610245
Metagenome-assembled genomes of phytoplankton microbiomes from the Arctic and Atlantic Oceans. PMID:35484634
Genome-Wide Survey and Development of the First Microsatellite Markers Database (AnCorDB) in Anemone coronaria L. PMID:35328546
Host-microbiome protein-protein interactions capture disease-relevant pathways. PMID:35246229
Unraveling the Genome Sequence of Plant Growth Promoting Aspergillus niger (CSR3) Provides Insight into the Synthesis of Secondary Metabolites and Its Comparative Genomics. PMID:35205861
Chromosome-level genome assembly of Bactrocera dorsalis reveals its adaptation and invasion mechanisms. PMID:35017661
Genomic Insights Into the Archaea Inhabiting an Australian Radioactive Legacy Site. PMID:34737728
Putative LysM Effectors Contribute to Fungal Lifestyle. PMID:33808705
"Mind the Gap": Hi-C Technology Boosts Contiguity of the Globe Artichoke Genome in Low-Recombination Regions. PMID:32817122
A structural UGDH variant associated with standard Munchkin cats. PMID:32605545
Whole genome resequencing of four Italian sweet pepper landraces provides insights on sequence variation in genes of agronomic value. PMID:32514106
A High-Quality Genome Sequence of Model Legume Lotus japonicus (MG-20) Provides Insights into the Evolution of Root Nodule Symbiosis. PMID:32365501
NAD+ biosynthesis in bacteria is controlled by global carbon/nitrogen levels via PII signaling. PMID:32179648
A specific fungal transcription factor controls effector gene expression and orchestrates the establishment of the necrotrophic pathogen lifestyle on wheat. PMID:31685928
Differential gene expression and gene ontologies associated with increasing water-stress in leaf and root transcriptomes of perennial ryegrass (Lolium perenne). PMID:31361773
Environmental conditions shape the nature of a minimal bacterial genome. PMID:31308405
Comparative genomics sheds light on the predatory lifestyle of accipitrids and owls. PMID:30783131
Genomic Signals of Adaptation towards Mutualism and Sociality in Two Ambrosia Beetle Complexes. PMID:30583535
Draft genome sequence of Bacillus amyloliquefaciens subsp. plantarum strain Fito_F321, an endophyte microorganism from Vitis vinifera with biocontrol potential. PMID:30410642
Analysis of impact metrics for the Protein Data Bank. PMID:30325351
HMMER web server: 2018 update. PMID:29905871
Redefining the ancestral origins of the interleukin-1 superfamily. PMID:29559685
Identification of the Autochaperone Domain in the Type Va Secretion System (T5aSS): Prevalent Feature of Autotransporters with a β-Helical Passenger. PMID:29375499
Genomic assessment in Lactobacillus plantarum links the butyrogenic pathway with glutamine metabolism. PMID:29162929
Genome reconstruction in Cynara cardunculus taxa gains access to chromosome-scale DNA variation. PMID:28717205
APRICOT: an integrated computational pipeline for the sequence-based identification and characterization of RNA-binding proteins. PMID:28334975
Decay of Sexual Trait Genes in an Asexual Parasitoid Wasp. PMID:28172869
Protein Bioinformatics Databases and Resources. PMID:28150231
The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. PMID:28053160
InterPro in 2017-beyond protein family and domain annotations. PMID:27899635
Conservation in Mammals of Genes Associated with Aggression-Related Behavioral Phenotypes in Honey Bees. PMID:27359102
The Ensembl gene annotation system. PMID:27337980
BLAST-based structural annotation of protein residues using Protein Data Bank. PMID:26810894
Insight into the Salivary Gland Transcriptome of Lygus lineolaris (Palisot de Beauvois). PMID:26789269
Kiwifruit Information Resource (KIR): a comparative platform for kiwifruit genomics. PMID:26656885
The PFP and ESG protein function prediction methods in 2014: effect of database updates and ensemble approaches. PMID:26380077
Assessing the Metabolic Diversity of Streptococcus from a Protein Domain Point of View. PMID:26366735
Orthology for comparative genomics in the mouse genome database. PMID:26223881
HMMER web server: 2015 update. PMID:25943547
FR database 1.0: a resource focused on fruit development and ripening. PMID:25725058
UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches. PMID:25398609
Complete genome sequence of the Radiation-Resistant bacterium Rubrobacter radiotolerans RSPS-4. PMID:25197483
A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE). PMID:24667251
Finding the missing honey bee genes: lessons learned from a genome upgrade. PMID:24479613
Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data. PMID:24467687
InterProScan 5: genome-scale protein function classification. PMID:24451626
Developmental gene discovery in a hemimetabolous insect: de novo assembly and annotation of a transcriptome for the cricket Gryllus bimaculatus. PMID:23671567
Structural and functional studies of S-adenosyl-L-methionine binding proteins: a ligand-centric approach. PMID:23617634
ASGARD: an open-access database of annotated transcriptomes for emerging model arthropod species. PMID:23180770
Subcellular localization of extracytoplasmic proteins in monoderm bacteria: rational secretomics-based strategy for genomic and proteomic analyses. PMID:22912771
GFam: a platform for automatic annotation of gene families. PMID:22790981
Structure-function analysis of human TYW2 enzyme required for the biosynthesis of a highly modified Wybutosine (yW) base in phenylalanine-tRNA. PMID:22761755
ProtoNet 6.0: organizing 10 million protein sequences in a compact hierarchical family tree. PMID:22121228
clusterMaker: a multi-algorithm clustering plugin for Cytoscape. PMID:22070249
Quantitative proteomics of Spodoptera frugiperda cells during growth and baculovirus infection. PMID:22039490
The InterPro BioMart: federated query and web service access to the InterPro Resource. PMID:21785143
Dr. PIAS: an integrative system for assessing the druggability of protein-protein interactions. PMID:21303559
In silico characterization of thermostable lipases. PMID:21153672
A tutorial on protein ontology resources for proteomic studies. PMID:21082429
PRIDB: a Protein-RNA interface database. PMID:21071426
Protein Bioinformatics Infrastructure for the Integration and Analysis of Multiple High-Throughput "omics" Data. PMID:20369061
From protein sequences to 3D-structures and beyond: the example of the UniProt knowledgebase. PMID:20043185
Comprehensive in silico prediction and analysis of chlamydial outer membrane proteins reflects evolution and life style of the Chlamydiae. PMID:20040079
GeMMA: functional subfamily classification within superfamilies of predicted protein structural domains. PMID:19923231
The Universal Protein Resource (UniProt) in 2010. PMID:19843607
Significant speedup of database searches with HMMs by search space reduction with PSSM family models. PMID:19828575
FIGfams: yet another set of protein families. PMID:19762480
Comparative genomics of protoploid Saccharomycetaceae. PMID:19525356
ProGMap: an integrated annotation resource for protein orthology. PMID:19494185
PIRSF family classification system for protein functional and evolutionary analysis. PMID:19455212
TGF-beta signaling proteins and the Protein Ontology. PMID:19426460
Protein function annotation by homology-based inference. PMID:19226439
SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny. PMID:19036790
Génolevures: protein families and synteny among complete hemiascomycetous yeast proteomes and genomes. PMID:19015150
FastBLAST: homology relationships for millions of proteins. PMID:18974889
HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot. PMID:18849571
Automatically extracting functionally equivalent proteins from SwissProt. PMID:18838004
The Universal Protein Resource (UniProt) 2009. PMID:18836194
Structure-guided comparative analysis of proteins: principles, tools, and applications for predicting function. PMID:18818720
Standards and ontologies for functional genomics 2. PMID:18629185
The RAST Server: rapid annotations using subsystems technology. PMID:18261238
In silico characterization of proteins: UniProt, InterPro and Integr8. PMID:18219596
Framework for a protein ontology. PMID:18047702
The universal protein resource (UniProt). PMID:18045787
Identification of sensory and signal-transducing domains in two-component signaling systems. PMID:17628134
New developments in the InterPro database. PMID:17202162
The Universal Protein Resource (UniProt). PMID:17142230
AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system. PMID:16855290
Quantitative assessment of dictionary-based protein named entity tagging. PMID:16799122
Conservation of intrinsic disorder in protein domains and families: I. A database of conserved predicted disordered regions. PMID:16602695
Integrating protein structures and precomputed genealogies in the Magnum database: examples with cellular retinoid binding proteins. PMID:16504077
Phytome: a platform for plant comparative genomics. PMID:16381967
Genolevures complete genomes provide data and tools for comparative genomics of hemiascomycetous yeasts. PMID:16381905
DynGO: a tool for visualizing and mining of Gene Ontology and its associations. PMID:16091147
InterProScan: protein domains identifier. PMID:15980438
Plant protein annotation in the UniProt Knowledgebase. PMID:15888679
Human neuroglobin protein in cerebrospinal fluid. PMID:15730566
Large scale hierarchical clustering of protein sequences. PMID:15663796
The PEDANT genome database in 2005. PMID:15608204
The PANTHER database of protein families, subfamilies, functions and pathways. PMID:15608197
The SBASE domain sequence resource, release 12: prediction of protein domain-architecture using support vector machines. PMID:15608182
InterPro, progress and status in 2005. PMID:15608177
The Universal Protein Resource (UniProt). PMID:15608167
Update on genome completion and annotations: Protein Information Resource. PMID:15588483
Interaction profile-based protein classification of death domain. PMID:15189571
UniProt: the Universal Protein knowledgebase. PMID:14681372 - http://dx.doi.org/10.1093/nar/gkh097
Tags:
Tags
More detailed information about this field from each metasource.
molecular structure
metasource: Fairsharing.org
version: FAIRsharing.org: PIRSF; PIR SuperFamily; DOI: https://doi.org/10.25504/FAIRsharing.vssch2; Last edited: June 15, 2021, 1:42 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
protein
metasource: Fairsharing.org
version: FAIRsharing.org: PIRSF; PIR SuperFamily; DOI: https://doi.org/10.25504/FAIRsharing.vssch2; Last edited: June 15, 2021, 1:42 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
sequence cluster
metasource: Fairsharing.org
version: FAIRsharing.org: PIRSF; PIR SuperFamily; DOI: https://doi.org/10.25504/FAIRsharing.vssch2; Last edited: June 15, 2021, 1:42 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
structure
metasource: Fairsharing.org
version: FAIRsharing.org: PIRSF; PIR SuperFamily; DOI: https://doi.org/10.25504/FAIRsharing.vssch2; Last edited: June 15, 2021, 1:42 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
protein sequence databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
protein domain databases; protein classification
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
sequence analysis
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:07.993116
gene and protein families
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:07.993116
Tags
More detailed information about this field from each metasource.
molecular structure
metasource: Fairsharing.orgversion: FAIRsharing.org: PIRSF; PIR SuperFamily; DOI: https://doi.org/10.25504/FAIRsharing.vssch2; Last edited: June 15, 2021, 1:42 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
protein
metasource: Fairsharing.orgversion: FAIRsharing.org: PIRSF; PIR SuperFamily; DOI: https://doi.org/10.25504/FAIRsharing.vssch2; Last edited: June 15, 2021, 1:42 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
sequence cluster
metasource: Fairsharing.orgversion: FAIRsharing.org: PIRSF; PIR SuperFamily; DOI: https://doi.org/10.25504/FAIRsharing.vssch2; Last edited: June 15, 2021, 1:42 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
structure
metasource: Fairsharing.orgversion: FAIRsharing.org: PIRSF; PIR SuperFamily; DOI: https://doi.org/10.25504/FAIRsharing.vssch2; Last edited: June 15, 2021, 1:42 p.m.; Last accessed: Jan 03 2022 7:09 p.m.
protein sequence databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
protein domain databases; protein classification
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
sequence analysis
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:07.993116
gene and protein families
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:27:07.993116
molecular structure protein sequence cluster structure protein sequence protein domains and classification sequence analysis gene and protein families
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