scholarly journals Searching for remote homologs of CAML among eukaryotes

Traffic ◽  
2020 ◽  
Vol 21 (10) ◽  
pp. 647-658
Author(s):  
Nica Borgese
Keyword(s):  
Remote Homologs

scholarly journals A general model of G protein-coupled receptor sequences and its application to detect remote homologs

2006 ◽  
Vol 15 (3) ◽  
pp. 509-521 ◽  
Author(s):  
Markus Wistrand ◽  
Lukas Käll ◽  
Erik L.L. Sonnhammer
Keyword(s):  
G Protein ◽  
General Model ◽  
G Protein Coupled Receptor ◽  
Remote Homologs ◽  
G Protein Coupled

scholarly journals Detection of novel recombinases in bacteriophage genomes unveils Rad52, Rad51 and Gp2.5 remote homologs

2010 ◽  
Vol 38 (12) ◽  
pp. 3952-3962 ◽  
Author(s):  
Anne Lopes ◽  
Jihane Amarir-Bouhram ◽  
Guilhem Faure ◽  
Marie-Agnès Petit ◽  
Raphaël Guerois
Keyword(s):  
Remote Homologs

scholarly journals Graph Theory-Based Sequence Descriptors as Remote Homology Predictors

Biomolecules ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 26 ◽  
Author(s):  
Guillermin Agüero-Chapin ◽  
Deborah Galpert ◽  
Reinaldo Molina-Ruiz ◽  
Evys Ancede-Gallardo ◽  
Gisselle Pérez-Machado ◽  
...  
Keyword(s):  
Graph Theory ◽  
Scale Up ◽  
Twilight Zone ◽  
Classification Problems ◽  
Homology Detection ◽  
Remote Homology ◽  
Alignment Free ◽  
Remote Homologs ◽  
Friendly Graphical User Interface ◽  
Remote Homology Detection

Alignment-free (AF) methodologies have increased in popularity in the last decades as alternative tools to alignment-based (AB) algorithms for performing comparative sequence analyses. They have been especially useful to detect remote homologs within the twilight zone of highly diverse gene/protein families and superfamilies. The most popular alignment-free methodologies, as well as their applications to classification problems, have been described in previous reviews. Despite a new set of graph theory-derived sequence/structural descriptors that have been gaining relevance in the detection of remote homology, they have been omitted as AF predictors when the topic is addressed. Here, we first go over the most popular AF approaches used for detecting homology signals within the twilight zone and then bring out the state-of-the-art tools encoding graph theory-derived sequence/structure descriptors and their success for identifying remote homologs. We also highlight the tendency of integrating AF features/measures with the AB ones, either into the same prediction model or by assembling the predictions from different algorithms using voting/weighting strategies, for improving the detection of remote signals. Lastly, we briefly discuss the efforts made to scale up AB and AF features/measures for the comparison of multiple genomes and proteomes. Alongside the achieved experiences in remote homology detection by both the most popular AF tools and other less known ones, we provide our own using the graphical–numerical methodologies, MARCH-INSIDE, TI2BioP, and ProtDCal. We also present a new Python-based tool (SeqDivA) with a friendly graphical user interface (GUI) for delimiting the twilight zone by using several similar criteria.

scholarly journals Powerful Sequence Similarity Search Methods and In-Depth Manual Analyses Can Identify Remote Homologs in Many Apparently "Orphan" Viral Proteins

2013 ◽  
Vol 88 (1) ◽  
pp. 10-20 ◽  
Author(s):  
D. B. Kuchibhatla ◽  
W. A. Sherman ◽  
B. Y. W. Chung ◽  
S. Cook ◽  
G. Schneider ◽  
...  
Keyword(s):  
Similarity Search ◽  
Sequence Similarity ◽  
Viral Proteins ◽  
Sequence Similarity Search ◽  
Search Methods ◽  
Remote Homologs

scholarly journals Rush Hour of LATs towards Their Transport Cycle

Membranes ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 602
Author(s):  
Adrià Nicolàs-Aragó ◽  
Joana Fort ◽  
Manuel Palacín ◽  
Ekaitz Errasti-Murugarren
Keyword(s):  
Plasma Membrane ◽  
Amino Acid ◽  
Structural Biology ◽  
Amino Acid Transporters ◽  
Functional Information ◽  
Cationic Amino Acid ◽  
Substrate Interaction ◽  
Transport Cycle ◽  
Remote Homologs ◽  
Molecular Bases

The mammalian SLC7 family comprises the L-amino acid transporters (LATs) and the cationic amino acid transporters (CATs). The relevance of these transporters is highlighted by their involvement in several human pathologies, including inherited rare diseases and acquired diseases, such as cancer. In the last four years, several crystal or cryo-EM structures of LATs and CATs have been solved. These structures have started to fill our knowledge gap that previously was based on the structural biology of remote homologs of the amino acid–polyamine–organocation (APC) transporters. This review recovers this structural and functional information to start generating the molecular bases of the transport cycle of LATs. Special attention is given to the known transporter conformations within the transport cycle and the molecular bases for substrate interaction and translocation, including the asymmetric interaction of substrates at both sides of the plasma membrane.

scholarly journals Master Blaster: an approach to sensitive identification of remotely related proteins

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Chintalapati Janaki ◽  
Venkatraman S. Gowri ◽  
Narayanaswamy Srinivasan
Keyword(s):  
Evolutionary Divergence ◽  
Homology Detection ◽  
Homologous Proteins ◽  
Scoring Matrices ◽  
A Genome ◽  
Successful Approach ◽  
Family Connections ◽  
And Function ◽  
Related Proteins ◽  
Remote Homologs

AbstractGenome sequencing projects unearth sequences of all the protein sequences encoded in a genome. As the first step, homology detection is employed to obtain clues to structure and function of these proteins. However, high evolutionary divergence between homologous proteins challenges our ability to detect distant relationships. In the past, an approach involving multiple Position Specific Scoring Matrices (PSSMs) was found to be more effective than traditional single PSSMs. Cascaded search is another successful approach where hits of a search are queried to detect more homologues. We propose a protocol, ‘Master Blaster’, which combines the principles adopted in these two approaches to enhance our ability to detect remote homologues even further. Assessment of the approach was performed using known relationships available in the SCOP70 database, and the results were compared against that of PSI-BLAST and HHblits, a hidden Markov model-based method. Compared to PSI-BLAST, Master Blaster resulted in 10% improvement with respect to detection of cross superfamily connections, nearly 35% improvement in cross family and more than 80% improvement in intra family connections. From the results it was observed that HHblits is more sensitive in detecting remote homologues compared to Master Blaster. However, there are true hits from 46-folds for which Master Blaster reported homologs that are not reported by HHblits even using the optimal parameters indicating that for detecting remote homologues, use of multiple methods employing a combination of different approaches can be more effective in detecting remote homologs. Master Blaster stand-alone code is available for download in the supplementary archive.

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