ReviewJournal of molecular microbiology and biotechnology2011
Phylogenetic characterization of transport protein superfamilies: superiority of SuperfamilyTree programs over those based on multiple alignments.
Review in Journal of molecular microbiology and biotechnology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
34 citing papers in PubMed, 50 citations in OpenAlex.
- A trimeric architecture reveals the glucitol PTS transporter as a distinct superfamily.Communications biology · 2026Article
- Unveiling Specificity, Redundancy, and Promiscuity of FiveInternational journal of molecular sciences · 2026Article
- A putative auxin efflux carrier FgAec1 contributes to the pathogenicity of Fusarium graminearum.BMC biology · 2025Article
- Substrate recognition and transport mechanism of the PIN-FORMED auxin exporters.Trends in biochemical sciences · 2023Review
- The Physiological Function and Potential Role of the Ubiquitous NaInternational journal of molecular sciences · 2022Review
- Article
- The ups and downs of elevator-type di-/tricarboxylate membrane transporters.The FEBS journal · 2022Article
- Characterization and expression profiling of PIN auxin efflux transporters reveal their role in developmental and abiotic stress conditions in rice.Frontiers in plant science · 2022Article
- The evolutionary history of topological variations in the CPA/AT transporters.PLoS computational biology · 2021Article
- Article
- SLC9 Gene Family: Function, Expression, and Regulation.Comprehensive Physiology · 2018Review
- Article
- Bioinformatic characterization of the Anoctamin Superfamily of Ca2+-activated ion channels and lipid scramblases.PloS one · 2018Article
- Characterization of the Tetraspan Junctional Complex (4JC) superfamily.Biochimica et biophysica acta. Biomembranes · 2017Article
- Pathophysiology of Intestinal NaCellular and molecular gastroenterology and hepatology · 2017Article
- The Membrane Attack Complex/Perforin Superfamily.Journal of molecular microbiology and biotechnology · 2017Article
- Expression and functional analysis of two NhaD type antiporters from the halotolerant and alkaliphilic Halomonas sp. Y2.Extremophiles : life under extreme conditions · 2016Article
- The bacterial dicarboxylate transporter VcINDY uses a two-domain elevator-type mechanism.Nature structural & molecular biology · 2016Article
- The Transporter Classification Database (TCDB): recent advances.Nucleic acids research · 2016Article
- Properties and Phylogeny of 76 Families of Bacterial and Eukaryotic Organellar Outer Membrane Pore-Forming Proteins.PloS one · 2016Article
Corrections and comments
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
Abstract
Transport proteins function in the translocation of ions, solutes and macromolecules across cellular and organellar membranes. These integral membrane proteins fall into >600 families as tabulated in the Transporter Classification Database (www.tcdb.org). Recent studies, some of which are reported here, define distant phylogenetic relationships between families with the creation of superfamilies. Several of these are analyzed using a novel set of programs designed to allow reliable prediction of phylogenetic trees when sequence divergence is too great to allow the use of multiple alignments. These new programs, called SuperfamilyTree1 and 2 (SFT1 and 2), allow display of protein and family relationships, respectively, based on thousands of comparative BLAST scores rather than multiple alignments. Superfamilies analyzed include: (1) Aerolysins, (2) RTX Toxins, (3) Defensins, (4) Ion Transporters, (5) Bile/Arsenite/Riboflavin Transporters, (6) Cation:Proton Antiporters, and (7) the Glucose/Fructose/Lactose superfamily within the prokaryotic phosphoenol pyruvate-dependent Phosphotransferase System. In addition to defining the phylogenetic relationships of the proteins and families within these seven superfamilies, evidence is provided showing that the SFT programs outperform programs that are based on multiple alignments whenever sequence divergence of superfamily members is extensive. The SFT programs should be applicable to virtually any superfamily of proteins or nucleic acids.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.