ArticleProtein science : a publication of the Protein Society2002
Sequence conserved for subcellular localization.
Article in Protein science : a publication of the Protein Society, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
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64 citing papers in PubMed.
- Developing SCL2205: a protein sequence-based spatial modelling dataset for the protein language model frontier.Bioinformatics (Oxford, England) · 2026Article
- Ayu: a machine intelligence tool for identification of extracellular proteins in the marine secretome.Nature communications · 2025Article
- Wheat E3 ligasePhysiology and molecular biology of plants : an international journal of functional plant biology · 2025Article
- A Review for Artificial Intelligence Based Protein Subcellular Localization.Biomolecules · 2024Review
- Protein Sorting Prediction.Methods in molecular biology (Clifton, N.J.) · 2024Article
- HAR_Locator: a novel protein subcellular location prediction model of immunohistochemistry images based on hybrid attention modules and residual units.Frontiers in molecular biosciences · 2023Article
- Spectrum of Protein Location in Proteomes Captures Evolutionary Relationship Between Species.Journal of molecular evolution · 2021Article
- GP4: an integrated Gram-Positive Protein Prediction Pipeline for subcellular localization mimicking bacterial sorting.Briefings in bioinformatics · 2021Article
- Embeddings from deep learning transfer GO annotations beyond homology.Scientific reports · 2021Article
- Computational methods for protein localization prediction.Computational and structural biotechnology journal · 2021Review
- A Methodology to Study Pseudogenized lincRNAs.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Alternatively Splicing Interactomes Identify Novel Isoform-Specific Partners for NSD2.Frontiers in cell and developmental biology · 2021Article
- Bird Eye View of Protein Subcellular Localization Prediction.Life (Basel, Switzerland) · 2020Review
- Use of Chou's 5-steps rule to predict the subcellular localization of gram-negative and gram-positive bacterial proteins by multi-label learning based on gene ontology annotation and profile alignment.Journal of integrative bioinformatics · 2020Article
- MIC_Locator: a novel image-based protein subcellular location multi-label prediction model based on multi-scale monogenic signal representation and intensity encoding strategy.BMC bioinformatics · 2019Article
- A Brief History of Protein Sorting Prediction.The protein journal · 2019Review
- Subcellular stoichiogenomics reveal cell evolution and electrostatic interaction mechanisms in cytoskeleton.BMC genomics · 2018Article
- The plasma membrane proteome of Medicago truncatula roots as modified by arbuscular mycorrhizal symbiosis.Mycorrhiza · 2018Article
- Sparse regressions for predicting and interpreting subcellular localization of multi-label proteins.BMC bioinformatics · 2016Article
- Predicting Subcellular Localization of Apoptosis Proteins Combining GO Features of Homologous Proteins and Distance Weighted KNN Classifier.BioMed research international · 2016Article
4 more citing papers are in PubMed but not listed here.
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2 authors.
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Abstract
The more proteins diverged in sequence, the more difficult it becomes for bioinformatics to infer similarities of protein function and structure from sequence. The precise thresholds used in automated genome annotations depend on the particular aspect of protein function transferred by homology. Here, we presented the first large-scale analysis of the relation between sequence similarity and identity in subcellular localization. Three results stood out: (1) The subcellular compartment is generally more conserved than what might have been expected given that short sequence motifs like nuclear localization signals can alter the native compartment; (2) the sequence conservation of localization is similar between different compartments; and (3) it is similar to the conservation of structure and enzymatic activity. In particular, we found the transition between the regions of conserved and nonconserved localization to be very sharp, although the thresholds for conservation were less well defined than for structure and enzymatic activity. We found that a simple measure for sequence similarity accounting for pairwise sequence identity and alignment length, the HSSP distance, distinguished accurately between protein pairs of identical and different localizations. In fact, BLAST expectation values outperformed the HSSP distance only for alignments in the subtwilight zone. We succeeded in slightly improving the accuracy of inferring localization through homology by fine tuning the thresholds. Finally, we applied our results to the entire SWISS-PROT database and five entirely sequenced eukaryotes.
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