Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

Sequence conserved for subcellular localization.

Rajesh Nair1, Burkhard Rost

  • 1Columbia University Bioinformatics Center (CUBIC), Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA.

Protein Science : a Publication of the Protein Society
|November 21, 2002
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Adoption, consistency, and usability of NICE vs EAU guidelines in low- and intermediate-risk NMIBC: a cross-sectional survey of UK urologists.

BJU international·2026
Same author

Expect the Unexpected: Frequency, Predictors, and Survival Impact of Pathological Upstaging from Non-Muscle-Invasive to Muscle-Invasive Bladder Cancer Following Radical Cystectomy.

Cancers·2026
Same author

Current state of electronic problems lists in primary care: a rapid scoping review.

Family practice·2026
Same author

Nephroureterectomy for upper tract urothelial carcinoma recurrence in bladder cancer patients treated with radical cystectomy: a multicentric propensity score matched analysis on predictors, practice patterns and survival outcomes.

World journal of urology·2026
Same author

10-yr Outcomes of Senior Clinical Fellowship in Robot-assisted Radical Cystectomy (RARC) with focus on Intracorporeal Ileal Conduit Urinary Diversion: Aggregated Learning Curve Assessment and Achievement of the EAU-Robotic Urology Section (ERUS) RARC Curriculum.

European urology open science·2026
Same author

Robot-assisted simple cystectomy for benign disease with medium-term follow-up: a case series.

Therapeutic advances in urology·2026
Same journal

Macromolecular crowding inhibits degradation of alpha-synuclein amyloid fibrils induced by cathepsins and MMP9.

Protein science : a publication of the Protein Society·2026
Same journal

Sequence-encoded differences in the conformational ensembles of CITED transcriptional activation domains impact coactivator binding.

Protein science : a publication of the Protein Society·2026
Same journal

The phospholipid biosynthesis enzyme PlsB contains three distinct domains for membrane association, lysophosphatidic acid synthesis, and dimerization.

Protein science : a publication of the Protein Society·2026
Same journal

Structural basis of ligand selectivity in FAD/NAD(P)H-dependent dehydrogenases: insights from trypanothione reductase and type II NADH dehydrogenase.

Protein science : a publication of the Protein Society·2026
Same journal

Achieving protease substrate-specific inhibition by mAb dual functional selections.

Protein science : a publication of the Protein Society·2026
Same journal

How important are quantum mechanical effects in controlling biological functions: Enzymes, electron transfer and bird navigation.

Protein science : a publication of the Protein Society·2026
See all related articles

Protein sequence similarity accurately predicts subcellular localization, even with low sequence identity. Bioinformatics tools can improve predictions by fine-tuning thresholds for inferring protein function and location.

Area of Science:

  • Computational Biology
  • Bioinformatics
  • Proteomics

Background:

  • Inferring protein function and structure from sequence similarity becomes challenging as sequences diverge.
  • Automated genome annotation thresholds vary depending on the specific protein function being transferred via homology.

Purpose of the Study:

  • To conduct the first large-scale analysis of the relationship between sequence similarity and protein subcellular localization.
  • To evaluate the accuracy of different sequence similarity measures in predicting protein localization.

Main Methods:

  • Analyzed the correlation between sequence similarity (identity and alignment length) and subcellular localization across large protein datasets.
  • Compared the performance of HSSP distance and BLAST expectation values for predicting localization.

Related Experiment Videos

  • Fine-tuned prediction thresholds to improve accuracy.

    • Main Results:

    • Subcellular localization is generally more conserved than anticipated, with short motifs capable of altering native compartments.
    • Sequence conservation of localization is consistent across different cellular compartments and comparable to structure and enzymatic activity conservation.
    • HSSP distance accurately distinguished between identical and different localizations; BLAST expectation values were superior only in specific low-similarity ranges.

    Conclusions:

    • Protein sequence similarity is a reliable indicator of subcellular localization, with a sharp transition between conserved and non-conserved regions.
    • Fine-tuning thresholds can enhance the accuracy of inferring protein localization through homology.
    • The findings were validated across the SWISS-PROT database and five fully sequenced eukaryotes.