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21 to 30 of 77 Results

AS_PMH_ancestors.fasta May 3, 2021 - Protein sequences of arylsulfatases, phosphonate monoester hydrolases, and reconstructed ancestors Unknown - 126.7 KB - MD5: 997793d158069bf670672467978a1688 FASTA file for 238 protein sequences
GraphML file for homologues and reconstructed ancestors of arylsulfatases and phosphonate monoester hydrolases May 3, 2021 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.
AS_PMH_ancestors.graphml May 3, 2021 - GraphML file for homologues and reconstructed ancestors of arylsulfatases and phosphonate monoester hydrolases GraphML Network Data - 2.2 MB - MD5: db9ccb4159a785f02c2e3ae2135d321f GraphML formatted file for an undirected graph (network) containing 238 nodes connected by 28,203 edges.
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...
CBM63_expansin_domains_score20.tab Jun 16, 2020 - Expansin domains in CBM63 sequences Tabular Data - 8.4 KB - 1 Variables, 567 Observations - UNF:6:i7aLIL6weIF8nhTjUBKf+g== Tabular file with headers: CBM63 with both domains (1st column), CBM63 with N-terminal domain (2nd column), CBM63 with C-terminal domain (3rd column). The expansin domains were annotated using a minimal domain-based score of 20.
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...
CHITs.hmm Jun 1, 2020 - Profile hidden Markov models of the Glycoside Hydrolase 19 Engineering Database Unknown - 110.9 KB - MD5: 9c4c77ebc1b7f7a3c4c4f9bf713aa7fe Profile hidden Markov model in HMMER format for the chitinase superfamily
ELYSs.hmm Jun 1, 2020 - Profile hidden Markov models of the Glycoside Hydrolase 19 Engineering Database Unknown - 81.4 KB - MD5: 61d6a4adfde821f447d18458a00e7667 Profile hidden Markov model in HMMER format for the endolysin superfamily
Reference_alignment_CHITs.aln Jun 1, 2020 - Profile hidden Markov models of the Glycoside Hydrolase 19 Engineering Database Unknown - 15.9 KB - MD5: 1de23a931f1988e2e26fa21ca210605c Clustal alignment for the profile hidden Markov model of the chitinase superfamily
Reference_alignment_CHITs.stockholm Jun 1, 2020 - Profile hidden Markov models of the Glycoside Hydrolase 19 Engineering Database Unknown - 18.2 KB - MD5: 116056d1f562c17e3a2b0ebe8714d0fe Stockholm alignment for the profile hidden Markov model of the chitinase superfamily

AS_PMH_ancestors.fasta

May 3, 2021 - Protein sequences of arylsulfatases, phosphonate monoester hydrolases, and reconstructed ancestors

Unknown - 126.7 KB -

FASTA file for 238 protein sequences

GraphML file for homologues and reconstructed ancestors of arylsulfatases and phosphonate monoester hydrolases

May 3, 2021

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.

AS_PMH_ancestors.graphml

May 3, 2021 - GraphML file for homologues and reconstructed ancestors of arylsulfatases and phosphonate monoester hydrolases

GraphML Network Data - 2.2 MB -

GraphML formatted file for an undirected graph (network) containing 238 nodes connected by 28,203 edges.

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...

CBM63_expansin_domains_score20.tab

Jun 16, 2020 - Expansin domains in CBM63 sequences

Tabular Data - 8.4 KB - 1 Variables, 567 Observations -

Tabular file with headers: CBM63 with both domains (1st column), CBM63 with N-terminal domain (2nd column), CBM63 with C-terminal domain (3rd column). The expansin domains were annotated using a minimal domain-based score of 20.

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...

CHITs.hmm

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

Unknown - 110.9 KB -

Profile hidden Markov model in HMMER format for the chitinase superfamily

ELYSs.hmm

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

Unknown - 81.4 KB -

Profile hidden Markov model in HMMER format for the endolysin superfamily

Reference_alignment_CHITs.aln

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

Unknown - 15.9 KB -

Clustal alignment for the profile hidden Markov model of the chitinase superfamily

Reference_alignment_CHITs.stockholm

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

Unknown - 18.2 KB -

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

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