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41 to 50 of 66 Results
Consensus sequences of arylsulfatases and phosphonate monoester hydrolases
May 12, 2021 - Bioinformatics
Buchholz, Patrick C. F., 2021, "Consensus sequences of arylsulfatases and phosphonate monoester hydrolases", https://doi.org/10.18419/darus-1838, DaRUS, V1
A multiple sequence alignment was constructed by Clustal Omega for the 95 protein sequences annotated as homologues of arylsulfatases and the 85 protein sequences annotated as homologues of phosphonate monoester hydrolases, respectively. The HMMER software suite was used to deriv...
Protein sequences of arylsulfatases, phosphonate monoester hydrolases, and reconstructed ancestors
May 3, 2021 - Bioinformatics
Heberlein, Magdalena, 2021, "Protein sequences of arylsulfatases, phosphonate monoester hydrolases, and reconstructed ancestors", https://doi.org/10.18419/darus-1801, DaRUS, V1
Protein sequences were derived from a maximum-likelihood phylogenetic tree for arylsulfatases and phosphonate monoester hydrolases, including a selection of reconstructed ancestral sequences.
GraphML file for homologues and reconstructed ancestors of arylsulfatases and phosphonate monoester hydrolases
May 3, 2021 - Bioinformatics
Buchholz, Patrick C. F., 2021, "GraphML file for homologues and reconstructed ancestors of arylsulfatases and phosphonate monoester hydrolases", https://doi.org/10.18419/darus-817, DaRUS, V1
Protein sequence network for homologues of arylsulfatases and phosphonate monoester hydrolases, including reconstructed ancestral sequences from a maximum-likelihood phylogenetic tree.
Data related to "Structural and biochemical insight into the mechanism of dual CpG site binding and methylation by DNMT3A"
Data related to "Structural and biochemical insight into the mechanism of dual CpG site binding and methylation by DNMT3A"
Apr 12, 2021 - Amplicon based bisulfite NGS data
Jeltsch, Albert; Bashtrykov, Pavel; Adam, Sabrina; Kunert, Stefan, 2021, "Data related to "Structural and biochemical insight into the mechanism of dual CpG site binding and methylation by DNMT3A"", https://doi.org/10.18419/darus-1781, DaRUS, V1
Methylation of substrate libraries Single-stranded DNA oligonucleotides used for generation of double stranded substrates with different distance between CpG sites were obtained from IDT. Sixteen single-stranded oligonucleotides were pooled in equimolar amounts and the second str...
Deep enzymology data related to Dukatz et al.: Complex DNA sequence readout mechanisms of the DNMT3B DNA methyltransferase.
Deep enzymology data related to Dukatz et al.: Complex DNA sequence readout mechanisms of the DNMT3B DNA methyltransferase.
Sep 1, 2020 - Amplicon based bisulfite NGS data
Jeltsch, Albert; Bashtrykov, Pavel; Dukatz, Michael; Adam, Sabrina, 2020, "Deep enzymology data related to Dukatz et al.: Complex DNA sequence readout mechanisms of the DNMT3B DNA methyltransferase.", https://doi.org/10.18419/darus-815, DaRUS, V3
Experimental procedures: Libraries of double stranded DNA substrates with CpG, CpH or CpN sites in randomized sequence context were methlyated by DNMT3B. Reactions were stopped by shock freezing in liquid nitrogen, then treated with proteinase K for 2 hours. Afterwards, the DNA w...
Expansin domains in CBM63 sequences
Jun 16, 2020 - Expansin Engineering Database
Lohoff, Caroline, 2020, "Expansin domains in CBM63 sequences", https://doi.org/10.18419/darus-625, DaRUS, V2, UNF:6:p+wfgXpfeyT0/kJm49wLTA== [fileUNF]
The occurrence of N- and C-terminal expansin domains in CBM63 sequences from the CAZy database. Protein sequences are represented by NCBI accessions. Expansin domains were annotated with the hmmscan command from the HMMER software package. The hits were filtered by a minimal doma...
Profile hidden Markov models of the Glycoside Hydrolase 19 Engineering Database
Jun 1, 2020 - Glycoside Hydrolase 19 Engineering Database
Orlando, Marco, 2020, "Profile hidden Markov models of the Glycoside Hydrolase 19 Engineering Database", https://doi.org/10.18419/darus-803, DaRUS, V1
A starting alignment was built if other sequences with a known PDB structure were available, by performing a GH19 domain structure-based alignment generated through the mmaker command implemented in ChimeraX. Other seed sequences in the same superfamily were added to this fixed s...
Seed sequences for the Glycoside Hydrolase 19 Engineering Database
Jun 1, 2020 - Glycoside Hydrolase 19 Engineering Database
Orlando, Marco, 2020, "Seed sequences for the Glycoside Hydrolase 19 Engineering Database", https://doi.org/10.18419/darus-804, DaRUS, V1
Query sequences for the individual BLAST searches used to initialize the Glycoside Hydrolase 19 Engineering Database (GH19ED, https://gh19ed.biocatnet.de/).
GraphML files for protein sequence networks of glycoside hydrolase 19 homologues
Jun 1, 2020 - Glycoside Hydrolase 19 Engineering Database
Orlando, Marco, 2020, "GraphML files for protein sequence networks of glycoside hydrolase 19 homologues", https://doi.org/10.18419/darus-802, DaRUS, V1
GraphML files for undirected weighted graphs with nodes that represent protein sequences of glycoside hydrolase 19 homologues. Protein sequences were clustered by a threshold of 90% sequence identity to derive representative sequences. Pairwise sequence identity between two seque...
Glycoside Hydrolase 19 Engineering Database(Universität Stuttgart)
May 18, 2020Bioinformatics
Supporting information and original files for bioinformatic investigations using the Glycoside Hydrolase 19 Engineering Database (https://gh19ed.biocatnet.de/)
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