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The complexity, challenges and benefits of comparing two transporter classification systems in TCDB and Pfam

Zachary Chiang, Ake Vastermark, Marco Punta, Penelope C. Coggill, Jaina Mistry, Robert D. Finn, Milton H. Saier
2015 Briefings in Bioinformatics  
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

Milton H Saier, Vamsee S Reddy, Gabriel Moreno-Hagelsieb, Kevin J Hendargo, Yichi Zhang, Vasu Iddamsetty, Katie Jing Kay Lam, Nuo Tian, Steven Russum, Jianing Wang, Arturo Medrano-Soto
2020 Nucleic Acids Research  
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

V. A. Benedito, H. Li, X. Dai, M. Wandrey, J. He, R. Kaundal, I. Torres-Jerez, S. K. Gomez, M. J. Harrison, Y. Tang, P. X. Zhao, M. K. Udvardi
2009 Plant Physiology  
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

Zhi Wang, Alexandra S. Tauzin, Elisabeth Laville, Pietro Tedesco, Fabien Létisse, Nicolas Terrapon, Pascale Lepercq, Myriam Mercade, Gabrielle Potocki-Veronese, Vincent B. Young
2020 mSphere  
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

Shiva Shamloo, Qing Ye, Gregory Butler
2020 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)  
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

Robert S Coyne, Linda Hannick, Dhanasekaran Shanmugam, Jessica B Hostetler, Daniel Brami, Vinita S Joardar, Justin Johnson, Diana Radune, Irtisha Singh, Jonathan H Badger, Ujjwal Kumar, Milton Saier (+17 others)
2011 Genome Biology  
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

Silke Claus, Sylwia Jezierska, Liam D. H. Elbourne, Inge Van Bogaert
2022 BMC Genomics  
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]

Margaret J. Gabanyi, Helen M. Berman
2014 Msphere  
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

Shyam M. Saladi, Nauman Javed, Axel Müller, William M. Clemons
2018 Journal of Biological Chemistry  
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]

Shyam M Saladi, Nauman Javed, Axel Mueller, William M Clemons
2017 bioRxiv   pre-print
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

Yiling Lai, Keke Liu, Xinyu Zhang, Xiaoling Zhang, Kuan Li, Niuniu Wang, Chi Shu, Yunpeng Wu, Chengshu Wang, Kathryn E. Bushley, Meichun Xiang, Xingzhong Liu
2014 Genome Biology and Evolution  
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

Muhammad Aamer Mehmood
2014 Journal of Data Mining in Genomics & Proteomics  
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

Alga Zuccaro, Urs Lahrmann, Ulrich Güldener, Gregor Langen, Stefanie Pfiffi, Dagmar Biedenkopf, Philip Wong, Birgit Samans, Carolin Grimm, Magdalena Basiewicz, Claude Murat, Francis Martin (+2 others)
2011 PLoS Pathogens  
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

Diana P. Garnica, Narayana M. Upadhyaya, Peter N. Dodds, John P. Rathjen, Mikhail V. Matz
2013 PLoS ONE  
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

Peter J. Turnbaugh, Ruth E. Ley, Micah Hamady, Claire M. Fraser-Liggett, Rob Knight, Jeffrey I. Gordon
2007 Nature  
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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