Institute of Biochemistry

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1,221 to 1,230 of 1,292 Results

Reference_alignment_ELYSs.stockholm Jun 1, 2020 - Profile hidden Markov models of the Glycoside Hydrolase 19 Engineering Database Unknown - 419.3 KB - MD5: 88e1f79860f29df5626599bd48cfcff3 Stockholm alignment for the profile hidden Markov model of the endolysin superfamily
Seed_sequences.fasta Jun 1, 2020 - Seed sequences for the Glycoside Hydrolase 19 Engineering Database Unknown - 20.3 KB - MD5: 1961bf93199d823fa0fb953e5e120100 FASTA headers comprise (from left to right): number of the seed sequence; sequence identifier (sid) in the GH19ED database; protein identifier (pid) in the GH19ED database; Uniprot or NCBI accession.
CHITs_60_percent_identity_cutoff.graphml Jun 1, 2020 - GraphML files for protein sequence networks of glycoside hydrolase 19 homologues GraphML Network Data - 14.3 MB - MD5: a314980fa659092d23cfda60fb45929a Protein sequence network for the chitinase domains from the Glycoside Hydrolase 19 Engineering Database. The GraphML file contains representative nodes (clustered by 90% in USEARCH) connected by at least 60% pairwise sequence identity (edge weights derived from Needleman-Wunsch alignments).
ELYSs_60_percent_identity_cutoff.graphml Jun 1, 2020 - GraphML files for protein sequence networks of glycoside hydrolase 19 homologues GraphML Network Data - 5.6 MB - MD5: f255b9e12d219a65533643ae3b529282 Protein sequence network for the endolysin domains from the Glycoside Hydrolase 19 Engineering Database. The GraphML file contains representative nodes (clustered by 90% in USEARCH) connected by at least 60% pairwise sequence identity (edge weights derived from Needleman-Wunsch alignments).
GH19_40_percent_identity_cutoff.graphml Jun 1, 2020 - GraphML files for protein sequence networks of glycoside hydrolase 19 homologues GraphML Network Data - 72.1 MB - MD5: 1ef54be08ab8b4dbe1f5b4a0407fac75 Protein sequence network for representative GH19 domains (corresponding to Pfam’s GH19 profile HMM: PF00182) from the Glycoside Hydrolase 19 Engineering Database. The GraphML file contains representative nodes (clustered by 90% in USEARCH) connected by at least 40% pairwise sequence identity (edge weights derived from Needleman-Wunsch alignments).
Conserved_amino_acids_in_C-terminal_domain.tab Apr 9, 2020 - Conserved positions in expansin homologues Tabular Data - 7.3 KB - 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-lik...
Conserved_amino_acids_in_N-terminal_domain.tab Apr 9, 2020 - Conserved positions in expansin homologues Tabular Data - 9.8 KB - 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-lik...
hits_aa.fasta Apr 9, 2020 - Expansin homologues in actinobacterial genomes from South Africa Unknown - 1.3 KB - MD5: 00f8e0957e042214a2c935343fae28f9 FASTA file of protein sequences (amino acid symbols). The numbers in the headers correspond to the hits mentioned in the Supporting Information file from Lohoff et al. 2020.
hits_nt.fasta Apr 9, 2020 - Expansin homologues in actinobacterial genomes from South Africa Unknown - 4.0 KB - MD5: 7dbd7e182fdf07bf4bd300fbd68ed0a4 FASTA file of nucleic acid sequences. The numbers in the headers correspond to the hits mentioned in the Supporting Information file from Lohoff et al. 2020.
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 expansin genes after Chase et al. 2020 (Yes or No); Lineage contains ex...

Reference_alignment_ELYSs.stockholm

Jun 1, 2020 - Profile hidden Markov models of the Glycoside Hydrolase 19 Engineering Database

Unknown - 419.3 KB -

Stockholm alignment for the profile hidden Markov model of the endolysin superfamily

Seed_sequences.fasta

Jun 1, 2020 - Seed sequences for the Glycoside Hydrolase 19 Engineering Database

Unknown - 20.3 KB -

FASTA headers comprise (from left to right): number of the seed sequence; sequence identifier (sid) in the GH19ED database; protein identifier (pid) in the GH19ED database; Uniprot or NCBI accession.

CHITs_60_percent_identity_cutoff.graphml

Jun 1, 2020 - GraphML files for protein sequence networks of glycoside hydrolase 19 homologues

GraphML Network Data - 14.3 MB -

Protein sequence network for the chitinase domains from the Glycoside Hydrolase 19 Engineering Database. The GraphML file contains representative nodes (clustered by 90% in USEARCH) connected by at least 60% pairwise sequence identity (edge weights derived from Needleman-Wunsch alignments).

ELYSs_60_percent_identity_cutoff.graphml

Jun 1, 2020 - GraphML files for protein sequence networks of glycoside hydrolase 19 homologues

GraphML Network Data - 5.6 MB -

Protein sequence network for the endolysin domains from the Glycoside Hydrolase 19 Engineering Database. The GraphML file contains representative nodes (clustered by 90% in USEARCH) connected by at least 60% pairwise sequence identity (edge weights derived from Needleman-Wunsch alignments).

GH19_40_percent_identity_cutoff.graphml

Jun 1, 2020 - GraphML files for protein sequence networks of glycoside hydrolase 19 homologues

GraphML Network Data - 72.1 MB -

Protein sequence network for representative GH19 domains (corresponding to Pfam’s GH19 profile HMM: PF00182) from the Glycoside Hydrolase 19 Engineering Database. The GraphML file contains representative nodes (clustered by 90% in USEARCH) connected by at least 40% pairwise sequence identity (edge weights derived from Needleman-Wunsch alignments).

Conserved_amino_acids_in_C-terminal_domain.tab

Apr 9, 2020 - Conserved positions in expansin homologues

Tabular Data - 7.3 KB - 8 Variables, 85 Observations -

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-lik...

Conserved_amino_acids_in_N-terminal_domain.tab

Apr 9, 2020 - Conserved positions in expansin homologues

Tabular Data - 9.8 KB - 8 Variables, 123 Observations -

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-lik...

hits_aa.fasta

Apr 9, 2020 - Expansin homologues in actinobacterial genomes from South Africa

Unknown - 1.3 KB -

FASTA file of protein sequences (amino acid symbols). The numbers in the headers correspond to the hits mentioned in the Supporting Information file from Lohoff et al. 2020.

hits_nt.fasta

Apr 9, 2020 - Expansin homologues in actinobacterial genomes from South Africa

Unknown - 4.0 KB -

FASTA file of nucleic acid sequences. The numbers in the headers correspond to the hits mentioned in the Supporting Information file from Lohoff et al. 2020.

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 expansin genes after Chase et al. 2020 (Yes or No); Lineage contains ex...

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