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

22 Downloads

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

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 12 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 Access File File Access Public Download Options Tab-Separated Values (Original File Format) Tab-Delimited RData Download Metadata Variable Metadata Data File Citation EndNote XML RIS BibTeX Explore Options View Data
	Conserved_amino_acids_in_N-terminal_domain.tab Tabular Data - 9.8 KB Published Apr 9, 2020 10 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 Access File File Access Public Download Options Tab-Separated Values (Original File Format) Tab-Delimited RData Download Metadata Variable Metadata Data File Citation EndNote XML RIS BibTeX Explore Options View Data

Citation Metadata

Dataset Persistent ID	doi:10.18419/darus-735
Publication Date	2020-04-09
Title	Conserved positions in expansin homologues
Author	Lohoff, Caroline (Universität Stuttgart)
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 Datasets	Lohoff, Caroline, 2020, "Profile hidden Markov models of the ExED", doi:10.18419/darus-623, DaRUS
Data Sources	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)

Waiver

Our Community Norms as well as good scientific practices expect that proper credit is given via citation. Please use the data citation above, generated by the Dataverse.

CC BY - "Attribution" Creative Commons CC BY Attribution 4.0 International icon

Guestbook

No guestbook is assigned to this dataset, you will not be prompted to provide any information on file download.

Dataset	Summary	Contributors	Published
No records found.

Edit File

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

Restrict Files and Add Dataset Terms of Access

Restricting limits access to published files. You can add or edit Terms of Access for the dataset, and allow people to Request Access to restricted files.

Terms of Access

Request Access

Enable access request

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.

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.

Restricted Files Selected

The restricted file(s) selected may not be downloaded because you have not been granted access.

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.

Restricted Files Selected

The restricted file(s) selected may not be downloaded because you have not been granted access.

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

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 Private URL

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

Unpublished Dataset Private URL

Are you sure you want to disable the Private URL? If you have shared the Private 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? The selected version(s) will no longer be viewable by the public.

Deaccession Dataset

Are you sure you want to deaccession this dataset? 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.

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 to this file.

???file.mapData.unpublished.header???

???file.mapData.unpublished.message???

Dataset Terms

Please confirm and/or complete the information needed below in order to continue.

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/

Request Access

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

Compute Batch

Clear Batch

Dataset	Dataset Persistent ID

Compute Batch

Submit for Review

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)

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.