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1 to 10 of 56 Results

Update_2_Centroids_USEARCH.tab Jan 30, 2020 - Query sequences for the update of the ExED Tabular Data - 505 B - 1 Variables, 25 Observations - UNF:6:eFcDsa8udm3F11lB7M2q6w== Tabular file with headers: sequence identifier from the Expansin Engineering Database (1st column) and NCBI accession.version (2nd column). This file lists the sequence accessions used in the first update of the ExED.
Update_2_Centroids_USEARCH.fasta Jan 30, 2020 - Query sequences for the update of the ExED Unknown - 6.5 KB - MD5: 5ae0036abf33f3585e5629a8337b7039 Seed (query) sequences for the first update of the ExED (USEARCH centroid sequences). Protein sequences are given in FASTA format with one line per sequence. Headers correspond to sequence identifiers of the Expansin Engineering Database.
Update_1_Seed_sequences_Hfams_1-25.fasta Jan 30, 2020 - Query sequences for the update of the ExED Unknown - 8.7 KB - MD5: 4f5de838715758c51a8cf33de96da0e8 Seed (query) sequences for the initial setup of the ExED. Protein sequences are given in FASTA format. Headers correspond to sequence identifiers in the style of UniprotKB.
Templates.tab Dec 1, 2021 - Profile hidden Markov model for PETase homologues Tabular Data - 255 B - 3 Variables, 12 Observations - UNF:6:AEjnqfOrnimO5Q2xFDkQDw== Uniprot identifiers, PDB identifiers, and PDB chains used for the structure-guided multiple sequence alignment by T-COFFEE
Taxonomic_analysis.tab Apr 9, 2020 - Occurrence of expansins in the tree of life Tabular Data - 4.0 KB - 6 Variables, 90 Observations - UNF:6:eK0oQia4QiaiEO0m1BJFeA== Tabular comparison between the occurrences of expansins in different taxa as reported in the Expansin Engineering Database (ExED) and Chase et al. (2020): Name of the taxonomic superkingdom; Name of the (major) taxonomic group reported in Chase et al. 2020; Lineage contains ex...
Supplements01-1.xlsx Sep 30, 2019 - The modular structure of alpha/beta-hydrolases: similarity of the N- and C-terminal domains to other proteins MS Excel Spreadsheet - 49.3 KB - MD5: 16212d43120787f58882868243783bbf This file contains the data of the Dali analysis with the additional N- and C-terminal module of the indicated proteins. Column A-H show the result from the Dali analysis. All found structures were additionally analyzed by PyMOL to determine whether they belong to the α/β-hydrola...
Sfams_123_210-300_90_50.graphml Jan 30, 2020 - GraphML files for protein sequence networks of expansin homologues GraphML Network Data - 85.9 MB - MD5: 6b7c3ee5702bf65837900503ef335e54 Protein sequence network for N-terminal expansin domains from the bacterial, fungal, and plant superfamily from the Expansin Engineering Database, for sequences with length between 210 and 300 residues.The GraphML file contains representative nodes (clustered by 0.9 in USEARCH/ U...
Sfam_123_Cdomain_90_60.graphml Jan 30, 2020 - GraphML files for protein sequence networks of expansin homologues GraphML Network Data - 20.8 MB - MD5: 1bcf30f501153632979c2e032fe5a497 Protein sequence network for C-terminal expansin domains from the bacterial, fungal, and plant superfamily from the Expansin Engineering Database. The GraphML file contains representative nodes (clustered by 0.9 in USEARCH/ UCLUST) connected by at least 60% pairwise sequence iden...
Sfam13_09_60sim.graphml Dec 1, 2021 - GraphML files for sequence networks of PETases and PURases GraphML Network Data - 16.2 KB - MD5: e93342540254b2c25b2826343947b22b Protein sequence network for PURase homologues from LED superfamily 13. Edges were selected at a threshold of 60% pairwise sequence identity.
Sfam11_09_60sim.graphml Dec 1, 2021 - GraphML files for sequence networks of PETases and PURases GraphML Network Data - 557.2 KB - MD5: 7cd626f025e5d7a0a253281649894b7f Protein sequence network for PURase homologues from LED superfamily 11. Edges were selected at a threshold of 60% pairwise sequence identity.

Update_2_Centroids_USEARCH.tab

Jan 30, 2020 - Query sequences for the update of the ExED

Tabular Data - 505 B - 1 Variables, 25 Observations -

Tabular file with headers: sequence identifier from the Expansin Engineering Database (1st column) and NCBI accession.version (2nd column). This file lists the sequence accessions used in the first update of the ExED.

Update_2_Centroids_USEARCH.fasta

Jan 30, 2020 - Query sequences for the update of the ExED

Unknown - 6.5 KB -

Seed (query) sequences for the first update of the ExED (USEARCH centroid sequences). Protein sequences are given in FASTA format with one line per sequence. Headers correspond to sequence identifiers of the Expansin Engineering Database.

Update_1_Seed_sequences_Hfams_1-25.fasta

Jan 30, 2020 - Query sequences for the update of the ExED

Unknown - 8.7 KB -

Seed (query) sequences for the initial setup of the ExED. Protein sequences are given in FASTA format. Headers correspond to sequence identifiers in the style of UniprotKB.

Templates.tab

Dec 1, 2021 - Profile hidden Markov model for PETase homologues

Tabular Data - 255 B - 3 Variables, 12 Observations -

Uniprot identifiers, PDB identifiers, and PDB chains used for the structure-guided multiple sequence alignment by T-COFFEE

Taxonomic_analysis.tab

Apr 9, 2020 - Occurrence of expansins in the tree of life

Tabular Data - 4.0 KB - 6 Variables, 90 Observations -

Tabular comparison between the occurrences of expansins in different taxa as reported in the Expansin Engineering Database (ExED) and Chase et al. (2020): Name of the taxonomic superkingdom; Name of the (major) taxonomic group reported in Chase et al. 2020; Lineage contains ex...

Supplements01-1.xlsx

Sep 30, 2019 - The modular structure of alpha/beta-hydrolases: similarity of the N- and C-terminal domains to other proteins

MS Excel Spreadsheet - 49.3 KB -

This file contains the data of the Dali analysis with the additional N- and C-terminal module of the indicated proteins. Column A-H show the result from the Dali analysis. All found structures were additionally analyzed by PyMOL to determine whether they belong to the α/β-hydrola...

Sfams_123_210-300_90_50.graphml

Jan 30, 2020 - GraphML files for protein sequence networks of expansin homologues

GraphML Network Data - 85.9 MB -

Protein sequence network for N-terminal expansin domains from the bacterial, fungal, and plant superfamily from the Expansin Engineering Database, for sequences with length between 210 and 300 residues.The GraphML file contains representative nodes (clustered by 0.9 in USEARCH/ U...

Sfam_123_Cdomain_90_60.graphml

Jan 30, 2020 - GraphML files for protein sequence networks of expansin homologues

GraphML Network Data - 20.8 MB -

Protein sequence network for C-terminal expansin domains from the bacterial, fungal, and plant superfamily from the Expansin Engineering Database. The GraphML file contains representative nodes (clustered by 0.9 in USEARCH/ UCLUST) connected by at least 60% pairwise sequence iden...

Sfam13_09_60sim.graphml

Dec 1, 2021 - GraphML files for sequence networks of PETases and PURases

GraphML Network Data - 16.2 KB -

Protein sequence network for PURase homologues from LED superfamily 13. Edges were selected at a threshold of 60% pairwise sequence identity.

Sfam11_09_60sim.graphml

Dec 1, 2021 - GraphML files for sequence networks of PETases and PURases

GraphML Network Data - 557.2 KB -

Protein sequence network for PURase homologues from LED superfamily 11. Edges were selected at a threshold of 60% pairwise sequence identity.

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