Conserved positions in expansin homologues

Version 1.1

Lohoff, Caroline, 2020, "Conserved positions in expansin homologues", https://doi.org/10.18419/DARUS-735, DaRUS, V1, UNF:6:HemykMznkJ0tyrf89mswkg== [fileUNF]

Learn about Data Citation Standards.

Contact Owner

Dataset Metrics

220 Downloads

Description	Conserved positions in the N- and C-terminal expansin domains of different groups from the Expansin Engineering Database (occurring in at least 70% of the annotated sequence entries). The expansin domains were annotated using hmmscan (from the HMMER software suite) against all sequence entries in the Expansin Engineering Database.
Subject	Medicine, Health and Life Sciences
Keyword	conservation analysis
Related Publication	Lohoff C., Buchholz P. C. F., Le Roes-Hill M. & Pleiss J. (2020). The Expansin Engineering Database: a navigation and classification tool for expansins and homologues. Proteins: Structure, Function, and Bioinformatics 89:2.doi: 10.1002/prot.26001
License/Data Use Agreement	CC BY 4.0

Filter by

	1 to 2 of 2 Files	Original Format Archival Format (.tab)
	Conserved_amino_acids_in_C-terminal_domain.tab Tabular Data - 7.3 KB Published Apr 9, 2020 119 Downloads 8 Variables, 85 Observations UNF:6:CE90w0ai1+p+rVxLddj0OA== Conserved positions in the C-terminal expansin domain with standard numbering according to PDB entry 4FER (Bacillus subtilis EXLX1, first column). The amino acids and their occurrence in % are given for different groups of sequences: (Bacteria (column 2), Fungi (column 3), EXPA (Expansin A, column 4), EXPB (Expansin B, column 5), EXLA (Expansin-like A, column 6), EXLB (Expansin-like B, column 7). The last column indicates the assumed biochemical function of the respective amino acids.	Preview "Conserved_amino_acids_in_C-terminal_domain.tab" Access File File Access Public Download Options Tab-Separated Values (Original File Format) Tab-Delimited RData Download Metadata DDI Codebook v2 Data File Citation Download EndNote XML Download RIS Download BibTeX
	Conserved_amino_acids_in_N-terminal_domain.tab Tabular Data - 9.8 KB Published Apr 9, 2020 101 Downloads 8 Variables, 123 Observations UNF:6:ztPrC1aaxgvhz6A2pKE7oA== Conserved positions in the N-terminal expansin domain with standard numbering according to PDB entry 4FER (Bacillus subtilis EXLX1, first column). The amino acids and their occurrence in % are given for different groups of sequences: (Bacteria (column 2), Fungi (column 3), EXPA (Expansin A, column 4), EXPB (Expansin B, column 5), EXLA (Expansin-like A, column 6), EXLB (Expansin-like B, column 7). The last column indicates the assumed biochemical function of the respective amino acids or a known sequence motif.	Preview "Conserved_amino_acids_in_N-terminal_domain.tab" Access File File Access Public Download Options Tab-Separated Values (Original File Format) Tab-Delimited RData Download Metadata DDI Codebook v2 Data File Citation Download EndNote XML Download RIS Download BibTeX

Citation Metadata

Persistent Identifier	doi:10.18419/DARUS-735
Publication Date	2020-04-09
Title	Conserved positions in expansin homologues
Author	Lohoff, Carolinehttps://ror.org/04vnq7t77
Point of Contact	Use email button above to contact. Pleiss, Jürgen (Universität Stuttgart)
Description	Conserved positions in the N- and C-terminal expansin domains of different groups from the Expansin Engineering Database (occurring in at least 70% of the annotated sequence entries). The expansin domains were annotated using hmmscan (from the HMMER software suite) against all sequence entries in the Expansin Engineering Database.
Subject	Medicine, Health and Life Sciences
Keyword	conservation analysis
Related Publication	Lohoff C., Buchholz P. C. F., Le Roes-Hill M. & Pleiss J. (2020). The Expansin Engineering Database: a navigation and classification tool for expansins and homologues. Proteins: Structure, Function, and Bioinformatics 89:2. doi 10.1002/prot.26001 https://doi.org/10.1002/prot.26001
Language	English
Depositor	Buchholz, Patrick C. F.
Deposit Date	2020-03-10
Related Dataset	Lohoff, Caroline, 2020, "Profile hidden Markov models of the ExED", doi:10.18419/darus-623, DaRUS
Data Source	Expansin Engineering Database (https://exed.biocatnet.de/); PDB (doi: 10.2210/pdb4FER/pdb); Georgelis N, Tabuchi A, Nikolaidis N, Cosgrove DJ. Structure-function analysis of the bacterial expansin EXLX1. J Biol Chem. 2011;286:16814-16823. doi:10.1074/jbc.M111.225037; Yennawar NH, Li AC, Dudzinski DM, Tabuchi A, Cosgrove DJ. Crystal structure and activities of EXPB1 (Zea m 1), a β-expansin and group-1 pollen allergen from maize. Proc Natl Acad Sci U S A. 2006;103:14664-14671. doi:10.1073/pnas.0605979103

Process Metadata

Processing Methods	hmmscan (HMMER) ; Parameters: domain-based score; minimal hit length; maximal ratio of bias over domain-based score
Method Parameters	domain-based score : 35 minimal hit length : 60 maximal ratio of bias over domain-based score [%] : 10
Software	HMMER Version: 3.1b2 (http://www.hmmer.org)

Dataset Terms

License/Data Use Agreement

Our Community Norms as well as good scientific practices expect that proper credit is given via citation. Please use the data citation shown on the dataset page.

Creative Commons Attribution 4.0 International License. CC BY 4.0

Dataset Version	Summary	Version Note	Contributors	Published on
No records found.

Edit File

This file has already been deleted (or replaced) in the current version. It may not be edited.

Restrict Access

Restricting limits access to published files. People who want to use the restricted files can request access by default. If you disable request access, you must add information about access to the Terms of Access field.

Learn about restricting files and dataset access in the User Guide.

Request Access

Enable access request

You must enable request access or add terms of access to restrict file access.

Terms of Access for Restricted Files

Save Changes

Edit Embargo

The selected file or files have already been published. Contact an administrator to change the embargo date or reason of the file or files.

Edit Retention Period

The selected file or files have already been published. Contact an administrator to change the retention period date or reason of the file or files.

Delete Files

The file will be deleted after you click on the Delete button.

Files will not be removed from previously published versions of the dataset.

Select File(s)

Please select one or more files.

Share Dataset

Share this dataset on your favorite social media networks.

Continue

Dataset Citations

Citations for this dataset are retrieved from Crossref via DataCite using Make Data Count standards. For more information about dataset metrics, please refer to the User Guide.

Sorry, no citations were found.

Inaccessible Files Selected

The selected file(s) may not be downloaded because you have not been granted access or the file(s) have a retention period that has expired or the files can only be transferred via Globus.

Ineligible Files Selected

The selected file(s) may not be transferred because you have not been granted access or the file(s) have a retention period that has expired or the files are not Globus accessible.

Download Options

The files selected are too large to download as a ZIP.

You can select individual files that are below the 1.9 GB download limit from the files table, or use the Data Access API for programmatic access to the files.

Select File(s)

Please select a file or files to be downloaded.

Inaccessible Files Selected

The selected file(s) may not be downloaded because you have not been granted access or the file(s) have a retention period that has expired.

Click Continue to download the files you have access to download.

Ineligible Files Selected

Some file(s) cannot be transferred. (They are restricted, embargoed, with an expired retention period, or not Globus accessible.)

Click Continue to transfer the elligible files.

Delete Dataset

Are you sure you want to delete this dataset and all of its files? You cannot undelete this dataset.

Delete Draft Version

Are you sure you want to delete this draft version? Files will be reverted to the most recently published version. You cannot undelete this draft.

Unpublished Dataset Preview URL

Preview URL can only be used with unpublished versions of datasets.

Unpublished Dataset Preview URL

Are you sure you want to disable the Preview URL? If you have shared the Preview URL with others they will no longer be able to use it to access your unpublished dataset.

Delete Files

The file(s) will be deleted after you click on the Delete button.

Files will not be removed from previously published versions of the dataset.

Compute

This dataset contains restricted files you may not compute on because you have not been granted access.

Deaccession Dataset

Are you sure you want to deaccession? This is permanent and the selected version(s) will no longer be viewable by the public.

Deaccession Dataset

Are you sure you want to deaccession this dataset? This is permanent an it will no longer be viewable by the public.

Version Differences Details

Please select two versions to view the differences.

Version Differences Details

Version:
Last Updated:

Select File(s)

Please select a file or files for access request.

Select File(s)

Embargoed files cannot be accessed. Please select an unembargoed file or files for your access request.

Edit Tags

Select existing file tags or create new tags to describe your files. Each file can have more than one tag.

Request Access

You need to Log In to request access.

Dataset Terms

Please confirm and/or complete the information needed below in order to request access to files in this dataset.

This dataset is made available under the following terms. Please confirm and/or complete the information needed below in order to continue.

License/Data Use Agreement

Our Community Norms as well as good scientific practices expect that proper credit is given via citation. Please use the data citation shown on the dataset page.

Creative Commons Attribution 4.0 International License. CC BY 4.0

Preview Guestbook

Upon downloading files the guestbook asks for the following information.

Guestbook Name

Collected Data

Account Information

Package File Download

Use the Download URL in a Wget command or a download manager to download this package file. Download via web browser is not recommended. User Guide - Downloading a Dataverse Package via URL

Download URL

https://darus.uni-stuttgart.de/api/access/datafile/

Compute Batch

Clear Batch

Dataset	Persistent Identifier	Change Compute Batch

Compute Batch

Submit for Review

Please use the publication checklist for authors ( https://www.izus.uni-stuttgart.de/en/fokus/darus/publication/ ) to ensure publication readiness. You will not be able to make changes to this dataset while it is in review.

Publish Dataset

Are you sure you want to republish this dataset?

Select if this is a minor or major version update.

Minor Release (1.2)

Major Release (2.0)

Version Note

Publish Dataset

This dataset cannot be published until Expansin Engineering Database is published by its administrator.

Publish Dataset

This dataset cannot be published until Expansin Engineering Database and Bioinformatics are published.

Return to Author

Return this dataset to contributor for modification. The reason for return entered below will be sent by email to the author.

Add/Edit a Version Note

Enter the reason this version was created. To learn more about Version Notes, visit the Version Notes section of the User Guide.

Version Note

Styled Citation