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The complexity, challenges and benefits of comparing two transporter classification systems in TCDB and Pfam
2015
Briefings in Bioinformatics
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Two such databases are the Transporter Classification Database (TCDB) and the Protein family (Pfam) database. ...
As part of a long-term endeavor to improve consistency between the two classification systems, we have compared transporter annotations in the two databases to understand the rationale for differences ...
The examples presented in this contribution illustrate the complexity of comparing two resources such as TCDB and Pfam. ...
doi:10.1093/bib/bbu053
pmid:25614388
pmcid:PMC4570203
fatcat:srhthuisb5e55jrehtayyauqly
The Transporter Classification Database (TCDB): 2021 update
2020
Nucleic Acids Research
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TCDB is the only transport protein classification database adopted by the International Union of Biochemistry and Molecular Biology (IUBMB) and now (October 1, 2020) consists of 20 653 proteins classified ...
The Transporter Classification Database (TCDB; tcdb.org) is a freely accessible reference resource, which provides functional, structural, mechanistic, medical and biotechnological information about transporters ...
ACKNOWLEDGEMENTS We thank all professionals and students in the Saier Laboratory who contributed to the advances reported in this TCDB update. ...
doi:10.1093/nar/gkaa1004
pmid:33170213
fatcat:sfljvj5g4nbuhmbidp5gr4x2pa
Genomic Inventory and Transcriptional Analysis of Medicago truncatula Transporters
2009
Plant Physiology
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To initiate and support systematic characterization of transporters in the model legume Medicago truncatula, we identified 3,830 transporters and classified 2,673 of these into 113 families and 146 subfamilies ...
The data presented here are a unique resource for the selection and functional characterization of legume transporters. ...
In the following paragraphs, we discuss some of these genes in the context of what is known about transport and transporters in the two types of symbiosis. ...
doi:10.1104/pp.109.148684
pmid:20023147
pmcid:PMC2832251
fatcat:oqsc4enrnjcqxc7wdcpeujr4na
Harvesting of Prebiotic Fructooligosaccharides by Nonbeneficial Human Gut Bacteria
2020
mSphere
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In this study, we established a new strategy to profile the specificity of oligosaccharide transporters, combining microbiomics, genetic locus and strain engineering, and state-of-the art metabolomics. ...
Based on these developments, we identified and characterized, at the molecular level, a fructooligosaccharide transporting phosphotransferase system, which constitutes a biomarker of diet and gut pathology ...
For transporter classification, we recommend the continued use of the TCDB, which is a mine of information for these proteins, but with caution with respect to the level of classification. ...
doi:10.1128/msphere.00771-19
pmid:31915220
pmcid:PMC6952197
fatcat:xc25dpfmafftvb6gd5humrl64a
TportHMM: Predicting the substrate class of transmembrane transport proteins using profile Hidden Markov Models
2020
2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
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We compare these approaches with the state-of-the-art, TrSSP and TranCEP. iii ...
Abstract TportHMM : Predicting the substrate class of transmembrane transport proteins using profile Hidden Markov Models Shiva Shamloo Transporters make up a large proportion of proteins in a cell, and ...
Protein Sequence Analysis The transporters are classified into families based on the transporter classification (TC) system. ...
doi:10.1109/bibm49941.2020.9313229
fatcat:dvj4sef7ozhkxofi26vdndqh6y
Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control
2011
Genome Biology
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This document has been made available through IUScholarWorks repository, a service of the Indiana University Libraries. ...
Copyrights on documents in IUScholarWorks are held by their respective rights holder(s). Contact iusw@indiana.edu for more information. ...
(TCDB) [49, 50] , a functional/phylogenetic system of classification. ...
doi:10.1186/gb-2011-12-10-r100
pmid:22004680
pmcid:PMC3341644
fatcat:tuma36hrrbgy5hjviwsgeorjia
Exploring the transportome of the biosurfactant producing yeast Starmerella bombicola
2022
BMC Genomics
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Doing this, we could experimentally confirm the transporters participating in the efflux of medium chain fatty alcohols, particularly decanol and undecanol, and identify a second sophorolipid transporter ...
We conducted an analysis of this family by creating deletion mutants to understand their role in the export of hydrophobic compounds, antibiotics and sophorolipids. ...
Fig. 3 3 Fig. 3 Transporter (super) family distribution of predicted transporters of S. bombicola in comparison with S. cerevisiae, S. pombe and C. neoformans according to the TCDB classification system ...
doi:10.1186/s12864-021-08177-x
pmid:34998388
pmcid:PMC8742932
fatcat:7acwxaztyrajbm52fbp5ihcsfu
Protein Structure Annotation Resources
[chapter]
2014
Msphere
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Therefore, to maximize the amount of information garnered from the genes, proteins, and structures we do study, annotations are captured in the hopes that they may apply to similar (homologous) proteins ...
Since the 3-D structure of proteins are ultimately responsible for most actions in the cell, this review will focus on protein structure annotation resources that aim to explain a ...
Acknowledgments The authors are grateful to B. Coimbatore Narayanan, G. Gabanyi ...
doi:10.1007/978-1-4939-2230-7_1
pmid:25502191
pmcid:PMC5586544
fatcat:n4wrlx7rtvfy7mya7w457ppwca
A statistical model for improved membrane protein expression using sequence-derived features
2018
Journal of Biological Chemistry
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IMP expression levels are currently unpredictable, which renders the pursuit of IMPs for structural and biophysical characterization challenging and inefficient. ...
The heterologous expression of integral membrane proteins (IMPs) remains a major bottleneck in the characterization of this important protein class. ...
Acknowledgements We thank Daniel Daley and Thomas Miller's group for discussion, Yaser Abu-Mostafa and Yisong Yue for guidance regarding machine learning, Niles Pierce for providing NUPACK source code ...
doi:10.1074/jbc.ra117.001052
pmid:29378850
fatcat:dbmoezphdbcx5p6p3ybyrunrye
Decoding sequence-level information to predict membrane protein expression
[article]
2017
bioRxiv
pre-print
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IMP expression levels are currently unpredictable, which renders the pursuit of IMPs for structural and biophysical characterization challenging and inefficient. ...
The expression of integral membrane proteins (IMPs) remains a major bottleneck in the characterization of this important protein class. ...
The Transporter Classification Database (TCDB): recent advances. Nucleic 854 Acids Res. 44,
Fig. 1
Fig. 1 . 1 Training performance. ...
doi:10.1101/098673
fatcat:qiiaksp4hfb2db6oxatk6lidly
Comparative Genomics and Transcriptomics Analyses Reveal Divergent Lifestyle Features of Nematode Endoparasitic Fungus Hirsutella minnesotensis
2014
Genome Biology and Evolution
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Data deposition: The Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession JPUM00000000 for Hirsutella minnesotensis. ...
This research was jointly supported by Key Project in the National Natural Science Foundation grant (31430071) of China and 973 Program (2013CB127506). ...
Acknowledgments The authors thank Dr Lijun Ma at University of Massachusetts Amherst, USA for the valuable suggestions and discussions. ...
doi:10.1093/gbe/evu241
pmid:25359922
pmcid:PMC4255773
fatcat:rg7wdnzc5ravlgokpaeijm3ggu
Use of Bioinformatics Tools in Different Spheres of Life Sciences
2014
Journal of Data Mining in Genomics & Proteomics
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Acknowledgment Authors thank Higher Education Commission (HEC), Pakistan, for funding their research work and apologise to all those colleagues whose work could not be discussed here due to space constraints ...
The Transporters Classification Database (TCDB) is a collection of membrane transporters [58] . ...
It uses an internationally approved Transport Classification (TC) system for the classification of protein, which is similar to that of Enzyme Commission (EC). ...
doi:10.4172/2153-0602.1000158
fatcat:m5ziueg3ifaobfnovyguaqlixa
Endophytic Life Strategies Decoded by Genome and Transcriptome Analyses of the Mutualistic Root Symbiont Piriformospora indica
2011
PLoS Pathogens
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Our findings provide a significant advance in understanding development of biotrophic plant symbionts and suggest a series of incremental shifts along the continuum from saprotrophy towards biotrophy in ...
Extensive comparative analysis of the P. indica genome with other Basidiomycota and Ascomycota fungi that have diverse lifestyle strategies identified features typically associated with both, biotrophism ...
Andrei Lupas for his support in the elucidation of the DELD family.
Author Contributions ...
doi:10.1371/journal.ppat.1002290
pmid:22022265
pmcid:PMC3192844
fatcat:32vzsgsu6jfjhnvjtspaemqoca
Strategies for Wheat Stripe Rust Pathogenicity Identified by Transcriptome Sequencing
2013
PLoS ONE
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More than 400 genes encoding secreted proteins which constitute candidate effectors were identified from the haustorial transcriptome, with two thirds of these up-regulated in this tissue compared to germinated ...
454pyrosequencing data and used as reference for digital gene expression analysis to compare the germinated uredinospores and haustoria transcriptomes based on Illumina RNAseq data. ...
Acknowledgments We thank Dr Colin Wellings and Prof. Robert Park (University of Sydney, Cobbitty) for the stripe rust strain and help with pathology. ...
doi:10.1371/journal.pone.0067150
pmid:23840606
pmcid:PMC3694141
fatcat:3tqu7lkqufhixgtiekdingbiky
The Human Microbiome Project
2007
Nature
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The list will be augmented by in vivo culture of a human fecal microbiota in gnotobiotic mice. ...
Our distal gut is the highest density natural bacterial ecosystem known, the most comprehensively surveyed to date, and the most highly represented in pure culture. ...
analyzed based on the classification schemes in TC-DB (http://tcdb.ucsd.edu/tcdb/); families of paralogous genes in a given genome constructed by pairwise searching of ORFs against themselves using BLASTP ...
doi:10.1038/nature06244
pmid:17943116
pmcid:PMC3709439
fatcat:6zrucnfzvrga5mwgmdekoyokfa
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