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Part 1: Document Description
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Citation |
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Title: |
Profile hidden Markov models of the Glycoside Hydrolase 19 Engineering Database |
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Identification Number: |
doi:10.18419/darus-803 |
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Distributor: |
DaRUS |
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Date of Distribution: |
2020-06-01 |
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Version: |
1 |
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Bibliographic Citation: |
Orlando, Marco, 2020, "Profile hidden Markov models of the Glycoside Hydrolase 19 Engineering Database", https://doi.org/10.18419/darus-803, DaRUS, V1 |
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Citation |
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Title: |
Profile hidden Markov models of the Glycoside Hydrolase 19 Engineering Database |
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Identification Number: |
doi:10.18419/darus-803 |
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Authoring Entity: |
Orlando, Marco (University of Milano Bicocca) |
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Grant Number: |
031B0571A |
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Grant Number: |
EXC2075 |
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Distributor: |
DaRUS |
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Access Authority: |
Pleiss, Jürgen |
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Depositor: |
Buchholz, Patrick C. F. |
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Date of Deposit: |
2020-05-11 |
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Holdings Information: |
https://doi.org/10.18419/darus-803 |
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Study Scope |
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Keywords: |
Medicine, Health and Life Sciences, profile hidden Markov model, protein sequence, multiple sequence alignment, amino acid sequence |
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Abstract: |
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 structural alignment by the use of “--add” flag option available in MAFFT. If no other structures were available rather than the reference, a sequence-based alignment with other seeds was created with MAFFT “L-INS-i” strategy, improved by adding information of up to 600 close homologues obtained from a search in Uniprot non-redundant Uniref50 database using a restrictive E-value threshold of 10<sup>-20</sup>. The obtained alignments were manually cut with respect to the length of the GH19 domain of the reference structure and used to generate the new superfamily-specific profile HMMs. |
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Methodology and Processing |
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Sources Statement |
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Data Sources: |
Uniref50 database (Uniprot) <a href="ftp://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref50">ftp://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref50</a> |
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<a href="https://gh19ed.biocatnet.de/">https://gh19ed.biocatnet.de/</a> |
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Data Access |
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Other Study Description Materials |
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Related Publications |
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Citation |
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Title: |
Orlando M, Buchholz PCF, Lotti M, Pleiss J (2020) Large-scale exploration of sequences, substrate specificity and evolution in glycoside hydrolase family 19: the GH19 Engineering Database (submitted) |
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Bibliographic Citation: |
Orlando M, Buchholz PCF, Lotti M, Pleiss J (2020) Large-scale exploration of sequences, substrate specificity and evolution in glycoside hydrolase family 19: the GH19 Engineering Database (submitted) |
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Label: |
CHITs.hmm |
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Text: |
Profile hidden Markov model in HMMER format for the chitinase superfamily |
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Notes: |
application/octet-stream |
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Label: |
ELYSs.hmm |
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Text: |
Profile hidden Markov model in HMMER format for the endolysin superfamily |
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Notes: |
application/octet-stream |
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Label: |
Reference_alignment_CHITs.aln |
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Text: |
Clustal alignment for the profile hidden Markov model of the chitinase superfamily |
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Notes: |
application/octet-stream |
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Label: |
Reference_alignment_CHITs.stockholm |
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Text: |
Stockholm alignment for the profile hidden Markov model of the chitinase superfamily |
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Notes: |
application/octet-stream |
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Label: |
Reference_alignment_ELYSs.aln |
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Text: |
Clustal alignment for the profile hidden Markov model of the endolysin superfamily |
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Notes: |
application/octet-stream |
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Label: |
Reference_alignment_ELYSs.stockholm |
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Text: |
Stockholm alignment for the profile hidden Markov model of the endolysin superfamily |
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Notes: |
application/octet-stream |