Conserved positions in expansin homologues

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

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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
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	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 16 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 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 15 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 Variable Metadata Data File Citation EndNote XML RIS BibTeX Explore Options View Data

Citation Metadata

Persistent Identifier	doi:10.18419/darus-735
Publication Date	2020-04-09
Title	Conserved positions in expansin homologues
Author	Lohoff, Caroline (Universität Stuttgart)
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)

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