A freely accessible reference database for transport protein research, which provides structural, functional, mechanistic, evolutionary and disease/medical information about transporters from organisms of all types. TCDB is the only transport protein classification database adopted by the International Union of Biochemistry and Molecular Biology (IUBMB). It consists of more than 10 000 non-redundant transport systems with more than 11 000 reference citations, classified into over 1000 transporter families. Transporters in TCDB can be single or multi-component systems, categorized in a functional/phylogenetic hierarchical system of classes, subclasses, families, subfamilies and transport systems. TCDB also includes updated software designed to analyze the distinctive features of transport proteins, extending its usefulness.
Provides annotations for predicted transporters across sequenced genomes. TransportDB serves the membrane transporter annotation of 2777 complete genomes, comprising 2557 eubacteria, 164 archaea and 56 eukaryota. The database currently contains 860252 individual transporters, classified into 168 distinct families of transporters. In terms of each class of transporter, the database currently includes 457183 ATP-Dependent transport proteins, 32952 phosphotransferase system, 318233 secondary transporters, 29874 ion channels, 3273 outer membrane porins and 18731 unclassified transporter proteins. TransportDB also incorporates analysis tools that enable users to query the database on a number of levels.
Contains information gathered from the literature and from public databases available on the internet for more than a thousand transmembrane proteins. TOPDB collects details of various experiments that were carried out to learn about the topology of particular transmembrane proteins.
Combines experimental data regarding mineral composition of mutant and wild-type strains. PlantsT provides extensive information on motifs and domains, detailed information contributed by individual experts in their respective fields, and descriptive information drawn directly from the literature. It incorporates a unique user annotation and review feature aimed at acquiring expert annotation directly from the plant biology community. Graphical displays of insertion location, protein sequence motifs and domains, mineral fingerprints, trees and alignments are provided, as well as complete text and XML versions of the information.
Contains mentions of ATP Binding Cassette (ABC) protein mutations extracted from the literature using the MutMiner automated data mining method. The MutMiner pipeline was designed to recognize any mention of amino acid substitution occurring in text, including natural and experimental mutations found in genotypic or protein in vitro studies. Mutations were extracted from the full-text version of PubMed papers resulting from keyword searches for various ABC proteins.
A public resource devoted to the ATP-binding Cassette (ABC) transporters encoded by completely sequenced prokaryotic genomes. Querying the database allows to easily retrieve ABC transporter repertories and related data. Additional query tools have been developed for the analysis of the ABC family from both functional and evolutionary perspectives.
Provides detailed, experimentally verified, annotation of the topology of α-helical transmembrane proteins. ExTopoDB is a database which is an up to date collection of experimentally verified topological information for α-helical transmembrane proteins. Compared to similar data sets, it contains the largest number of proteins with topology information derived from 1833 studies. Even for common entries, ExTopoDB holds a larger number of experiments for each entry, as most information was gathered from the literature. This web server also provides an analysis showing the increase in the prediction performance using topological data from ExTopoDB.
A resource designed for scientists, who look for a convenient way to access data about individual plant membrane proteins and membrane protein families. Currently, ARAMEMNON provides membrane protein data of nine plant species.
A user-friendly collaborative resource dedicated to the precise classification and annotation of yeast transporters. YTPdb exploits an evolution of the MediaWiki web engine used for popular collaborative databases like Wikipedia, allowing every registered user to edit the data in a user-friendly manner. Proteins in YTPdb are classified on the basis of functional criteria such as subcellular location or their substrate compounds.
Provides a biological trace elements database. dbTEU includes all known transporters and user proteins (excluding metal-binding chaperones and regulators) for five trace elements: Cu, Mo, Ni, Co and Se, in more than 700 sequenced organisms across the three domains of life. Approximately 16 500 proteins are stored in the database. In addition, this resource offers multiple search and browse options, such as BLAST homology searches. It also allows compilation of sets of trace element utilization proteins in individual organisms.
A database of electrophysiological experimental data documenting potential (human ether-a-go-go-related gene (hERG) channel inhibitory actions and the action potentials duration (APD)-prolongation activities of chemical compounds. hERGAPDbase aims to provide useful information for chemical and pharmacological scientists and enable easy access to electrophysiological experimental data on chemical compounds. The database provides links to MEDLINE entries for accessing abstracts of scientific papers related to the experimental data through click using the PMID.
A database of protein sequences of transporters of the model legume Medicago truncatula. Both automated search and manual curation were performed in identifying candidate protein sequences. Extensive annotations referring to each protein were generated, including basic protein function, genome locus, sequence annotations as well as transmembrane segment. A chromosome distribution map, text-based and BLAST search tools against known sequences of M.truncatula and known 3D structures of transporters were also created. A user-friendly web interface and regular updates make database valuable to researchers in related fields.
A manually curated central repository that stores formatted information on the substrates of transporters. In total, 37608 transporters with 15075 substrates from 884 organisms were curated from UniProt functional annotation. A unique feature of TSdb is that all the substrates are mapped to identifiers from the KEGG Ligand compound database. Thus, TSdb links current metabolic pathway schema with compound transporter systems via the shared compounds in the pathways.
A web-accessible, relational database of manually annotated biochemical, functional, and pharmacological data reported on GAT1 - the most intensely studied GABA transporter isoform. This database and its web interface will facilitate knowledge dissemination on this important member of the neurotransmitter:sodium symporter family of transporters.
Dr. Yashwanth Subbannayya obtained his M.Sc. degree in Medical Biochemistry from Manipal University. He qualified the competitive CSIR-UGC National Eligibility Test and joined the Institute of Bioinformatics, Bangalore as a UGC Junior Research Fellow. As part of his Ph.D. work, he studied the molecular mechanisms of gastric cancer in clinical specimens using quantitative proteomic technologies. This study, the results of which were published in Cancer Biology and Therapy, yielded a novel therapeutic target for gastric cancer- CAMKK2. Further, he also studied the serum proteome of gastric cancer patients and developed assays for potential markers using the revolutionary multiple reaction monitoring approach. The results of this study were published in Journal of Proteomics. In addition to his research work, he also trained extensively in sample preparation for mass spectrometry, fractionation techniques and gained expertise in quantitative proteomic techniques and data analysis. In addition, he also trained extensively in various validation platforms including immunohistochemsitry, multiple reaction monitoring and Western blot. He has also worked as a curator for several biological databases including NetPath, Human Protein Reference Database (HPRD) and Breast cancer database. His work in various research projects have yielded him 23 publications either as lead author or co-author in peer reviewed journals. He is a reviewer for the journal Proteomics.
Dr. Yashwanth Subbannayya joined the YU-IOB Center for Systems Biology and Molecular Medicine in June, 2015. During the initial period, his job consisted of assisting other personnel of the university in the establishment of YU-IOB Center for Systems Biology and Molecular Medicine. He was also involved in training of Ph.D. students in biological aspects. After the establishment of the center, he trained in cell culture techniques and metabolomics analysis. At YU-IOB CSBMM, he is studying the molecular mechanisms in various cancers including oral cancer. In addition, he is studying the molecular mechanisms as well as the metabolic constituents of traditional medicine formulations using mass spectrometry technologies. In June 2016, he convened the national symposium “Genomics in clinical practice: Future of precision medicine” held at Yenepoya University on June 1 and 2, 2016. The resource persons included 16 individuals from various academic organizations as well as industry. The symposium was attended by 218 participants from 24 institutions around India. He is a member of the Scientific Review Board of Yenepoya Research Centre where he facilitates timely scientific review of research projects.