Understanding Cuticulome.org
Learn how to browse the database, interpret protein records, filter and download datasets, use miniBLAST, run the Cuticular Protein Classifier, understand standardized nomenclature, and contribute new annotations.
Overview
Cuticulome.org compiles curated information on arthropod cuticular proteins, including protein sequences, protein family assignments, species information, functional annotations, and supporting references.
The goal of Cuticulome.org is to centralize cuticular protein information across arthropod species to support comparative studies, sequence searches, family classification, functional annotation, and broader cuticle biology analyses.
Database structure
The database is organized around curated cuticular protein records linked to species information, standardized protein names, protein family assignments, source publications, and functional annotations.
Protein information
Field
Cuticular protein
Description
Cuticulome.org standardized name of the cuticular protein. The standardized name is only used for consistency on this platform.
Field
Protein family
Description
Cuticular protein family or group to which the protein belongs, such as CPR, CPAP, CPF, CPFL, Tweedle, CPG, CPH, or other cuticular-related families.
Field
Species
Description
Species associated with the protein record, including a standardized species code used internally by the database.
Field
Protein sequence
Description
Amino acid sequence used for browsing, FASTA downloads, miniBLAST, and classifier support.
Field
Function-defined status
Description
Indicates whether the protein is associated with at least one curated functional annotation entry.
| Field | Description |
|---|---|
| Cuticular protein | Cuticulome.org standardized name of the cuticular protein. The standardized name is only used for consistency on this platform. |
| Protein family | Cuticular protein family or group to which the protein belongs, such as CPR, CPAP, CPF, CPFL, Tweedle, CPG, CPH, or other cuticular-related families. |
| Species | Species associated with the protein record, including a standardized species code used internally by the database. |
| Protein sequence | Amino acid sequence used for browsing, FASTA downloads, miniBLAST, and classifier support. |
| Function-defined status | Indicates whether the protein is associated with at least one curated functional annotation entry. |
Functional annotation information
Field
Expression timing
Description
Expression-related details from the source annotation.
Field
Defined function
Description
Curated functional description associated with the protein.
Field
Molecular function
Description
Molecular-level functional annotation.
Field
Biological process
Description
Biological process or broader functional context.
Field
Reference
Description
Source publication or curated reference supporting the annotation.
| Field | Description |
|---|---|
| Expression timing | Expression-related details from the source annotation. |
| Defined function | Curated functional description associated with the protein. |
| Molecular function | Molecular-level functional annotation. |
| Biological process | Biological process or broader functional context. |
| Reference | Source publication or curated reference supporting the annotation. |
Protein Families
The Protein Families page summarizes cuticular protein families represented in Cuticulome.org.
Protein families are not limited to only cuticular protein families, but also include families directly associated with cuticular proteins or cuticle function, such as Yellow, chitinases, and other cuticle-related groups.
Each family also includes a section titled Cuticular proteins with defined functions. This section displays representative function-defined proteins from that family.
Open Protein FamiliesDownloads
The Downloads page is essentially a custom dataset builder. Users can filter the database to create a tailored dataset, then download matching proteins as FASTA or metadata as CSV for downstream implementation and analyses.
Available filters
Field
Search proteins
Description
Search by protein name, accession, species, species code, or protein family.
Field
Function or expression keyword
Description
Search curated function, expression timing, tissue, biological process, or molecular function.
Field
Protein family
Description
Restrict the dataset to a selected cuticular protein family.
Field
Function status
Description
Download all proteins, only function-defined proteins, or proteins lacking defined function.
| Field | Description |
|---|---|
| Search proteins | Search by protein name, accession, species, species code, or protein family. |
| Function or expression keyword | Search curated function, expression timing, tissue, biological process, or molecular function. |
| Protein family | Restrict the dataset to a selected cuticular protein family. |
| Function status | Download all proteins, only function-defined proteins, or proteins lacking defined function. |
Download formats
Download FASTA for downstream sequence analysis. CSV is available for metadata inspection, filtering in spreadsheets, and dataset documentation.
miniBLAST
The miniBLAST tool allows users to compare a protein sequence against all protein sequences currently available in Cuticulome.org.
Paste an amino acid sequence into the input box and run miniBLAST. The input can be in FASTA format containing a header, or as a simple amino acid sequence.
Field
Status
Description
Indicates whether the matching protein is function-defined in Cuticulome.org.
Field
Protein
Description
Standardized Cuticulome.org protein name, linked to the individual protein record.
Field
% Identity
Description
Percentage identity between the query and matched protein over the aligned region.
Field
Query coverage
Description
Percentage of the query sequence covered by the alignment.
Field
Alignment length
Description
Length of the BLAST alignment.
Field
E-value
Description
BLAST expectation value. Lower values indicate stronger matches.
Field
Bit score
Description
BLAST score. Higher values generally indicate stronger matches.
| Field | Description |
|---|---|
| Status | Indicates whether the matching protein is function-defined in Cuticulome.org. |
| Protein | Standardized Cuticulome.org protein name, linked to the individual protein record. |
| % Identity | Percentage identity between the query and matched protein over the aligned region. |
| Query coverage | Percentage of the query sequence covered by the alignment. |
| Alignment length | Length of the BLAST alignment. |
| E-value | BLAST expectation value. Lower values indicate stronger matches. |
| Bit score | BLAST score. Higher values generally indicate stronger matches. |
The results table can be downloaded as a CSV file for further inspection.
Open miniBLASTCuticular Protein Classifier
The Cuticular Protein Classifier allows users to query a protein sequence and assess whether it resembles one of the defined cuticular protein families represented in Cuticulome.org.
This tool uses the current Cuticulome.org HMM classifier models and reports the best supported cuticular protein family classification, along with confidence, interpretation, best HMM hit, and all detected HMM hits.
Paste an amino acid sequence into the input box, then run the classifier. The input can be in FASTA format containing a header, or as a simple amino acid sequence.
Field
Prediction
Description
The most likely cuticular protein family based on classifier evidence.
Field
Confidence
Description
A confidence category based on HMM evidence and supporting classifier logic.
Field
Best HMM hit
Description
The strongest HMM match, including model, E-value, bit score, model coverage, and query coverage.
| Field | Description |
|---|---|
| Prediction | The most likely cuticular protein family based on classifier evidence. |
| Confidence | A confidence category based on HMM evidence and supporting classifier logic. |
| Best HMM hit | The strongest HMM match, including model, E-value, bit score, model coverage, and query coverage. |
Families covered
- CPR, including RR-1 and RR-2 subclassification.
- CPAP, including CPAP1 and CPAP3 subclassification.
- CPF / CPFL.
- CPT / Tweedle.
- CPG / CPH.
- CPLCA / CPLCG / CPLCP / CPLCW.
- CPCFC.
Important note
The classifier is intended as a screening and annotation-support tool, not as absolute proof of protein identity or biological function. A strong classifier result can support family assignment, but users should still seek additional evidence such as domain structure, phylogenetic analysis, species context, and literature support.
Nomenclature standard
The challenge
Historically, scientists have not had a unified way of naming cuticular proteins in arthropods. This has led to inconsistent naming conventions across different research groups and publications.
For example, related proteins might appear in the literature using formats such as Dmel_CPR1, apme_cpr1, or MpCpr1. This inconsistency can make cross-species comparisons more difficult.
Our solution
To improve consistency and database searchability, Cuticulome.org standardizes protein names using the following format:
Xxx_ProteinName
- First letter: capitalized genus initial.
- Second and third letters: lowercase species initials.
- Underscore: separator.
- Protein name: original protein designation.
Examples
Species
Drosophila melanogaster
Old nomenclature
Dmel_CPR1, DMCPR1
Standardized name
Dme_CPR1
Species
Myzus persicae
Old nomenclature
MpCpr1, mp-cpr1
Standardized name
Mpe_CPR1
Species
Apis mellifera
Old nomenclature
apme_cpr1, AmCPR1
Standardized name
Ame_CPR1
| Species | Old nomenclature | Standardized name |
|---|---|---|
| Drosophila melanogaster | Dmel_CPR1, DMCPR1 | Dme_CPR1 |
| Myzus persicae | MpCpr1, mp-cpr1 | Mpe_CPR1 |
| Apis mellifera | apme_cpr1, AmCPR1 | Ame_CPR1 |
Exceptions to nomenclature
The three-letter species prefix system can lead to naming conflicts between different species. For example, Heliothis virescens and Heortia vitessoides would both generate the same prefix. To avoid ambiguity, the full genus name is added as an additional prefix when such conflicts occur.
Species
Heliothis virescens
Ambiguous standardized name
Hvi_ProteinName
Conflict-resolved name
Heliothis_Hvi_ProteinName
Species
Heortia vitessoides
Ambiguous standardized name
Hvi_ProteinName
Conflict-resolved name
Heortia_Hvi_ProteinName
| Species | Ambiguous standardized name | Conflict-resolved name |
|---|---|---|
| Heliothis virescens | Hvi_ProteinName | Heliothis_Hvi_ProteinName |
| Heortia vitessoides | Hvi_ProteinName | Heortia_Hvi_ProteinName |
Important notes
- Cuticulome.org is not attempting to officially rename proteins. The standardization applies only within the database for consistency and searchability.
- Previous nomenclatures are preserved.
- Users can search for proteins using standardized Cuticulome.org names or common alternatives.
Contributing
If you have identified a missing protein or published new findings on arthropod cuticular proteins, please visit the submission page to contribute to the database.
All submissions are reviewed by the Cuticulome.org curators before being added to ensure data quality, consistency, and appropriate documentation.
For large batches of newly identified proteins, species-level datasets, or functional annotations, please contact the Cuticulome.org team directly rather than submitting entries one by one.
Questions or feedback
For questions, suggestions, corrections, collaborations, or to report issues with Cuticulome.org, please visit the contact page.
Contact us