Searching across hundreds of databases
Biogenesis of lysosome-related organelle complex-1 (BLOC-1) is one of the four multi-subunit complexes implicated in sorting cargo to lysosome-related organelles, as loss of function of any of these complexes causes Hermansky-Pudlak syndrome. Eight subunits of BLOC-1 interact with each other and with many other proteins. Identifying new interactors of BLOC-1 will increase understanding of its mechanism of action, and studies in model organisms are useful for finding such interactors. PSI-BLAST searches identify homologues in diverse model organisms, but there are significant gaps for BLOC-1, with none of its eight subunits found in Saccharomyces cerevisiae. Here we use more sensitive searches to identify distant homologues for three BLOC-1 subunits in S. cerevisiae: Blos1, snapin and cappuccino (cno). Published data on protein interactions show that in yeast these are likely to form a complex with three other proteins. One of these is the yeast homologue of the previously uncharacterized KxDL protein, which also interacts with Blos1 and cno in higher eukaryotes, suggesting that KxDL proteins are key interactors with BLOC-1.
Pubmed ID: 21159114 RIS Download
Publication data is provided by the National Library of Medicine ® and PubMed ®. Data is retrieved from PubMed ® on a weekly schedule. For terms and conditions see the National Library of Medicine Terms and Conditions.
A platform that integrates a great variety of tools for protein sequence analysis. Many tools are developed in-house, and serveral public tools are offered with extended functionality. Most frequently used tools HHpred Sensitive protein homology detection and structure prediction by HMM-HMM-comparison. Starting from a query sequence, HHpred builds a multiple sequence alignment using HHblits and turns it into a profile HMM. This is then compared it with a database of HMMs representing proteins with known structure (e.g. PDB, SCOP) or annotated protein families (e.g. PFAM, SMART, CDD, COGs, KOGs). The output is a list of closest homologs with alignments. HHpred can also build 3d homology models using the identified templates in the PDB database. It can optimize template picking and query-template alignments for homology modeling. The HHblits software is part of the open source package HHsuite. HHblits Remote homology detection method based on iterative HMM-HMM comparison. HHblits can build high-quality MSAs starting from single sequences or from MSAs. It transforms these into a query HMM and iteratively searches through uniprot20 or nr20 databases by adding significantly similar sequences from the previous search to the updated query HMM for the next search iteration. Compared to PSI-BLAST, HHblits is faster, up to twice as sensitive and produces more accurate alignments. The HHblits software is part of the open source package HHsuite. Quick2d Quick2D gives you an overview of secondary structure features like alpha-helices, extended beta-sheets, coiled coils, transmembrane helices and disorder regions. Predictions by PSIPRED, JNET, Prof(Rost), Prof(Ouali), Coils, MEMSAT2, HMMTOP, DISOPRED2 and VSL2. Modeller A Program for Comparative Protein Structure Modelling by Satisfaction of Spatial Restraints. Coils/PCoils This server compares a single sequence (COILS) or a sequence alignment (PCOILS) to a database of known coiled-coils and derives a similarity score. The program then calculates the probability that the sequence will adopt a coiled-coil conformation. PSI-Blast Search with an amino acid sequence against protein databases for locally similar sequences. Similar to ProteinBLAST but more sensitive. PSI-BLAST first performs a BLAST search and builds an alignment from the best local hits. This alignment is then used as a query for the next round of search. After each successive round the search alignment is updated.
View all literature mentionsThe SciCrunch Infrastructure was developed as a cooperative data platform to be used by diverse communities in making data more FAIR.
scicrunch.org
