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Part 1: Document Description
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Citation |
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Title: |
Profile hidden Markov model for PETase homologues |
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Identification Number: |
doi:10.18419/darus-2055 |
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Distributor: |
DaRUS |
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Date of Distribution: |
2021-12-01 |
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Version: |
1 |
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Bibliographic Citation: |
Buchholz, Patrick C. F., 2021, "Profile hidden Markov model for PETase homologues", https://doi.org/10.18419/darus-2055, DaRUS, V1, UNF:6:AEjnqfOrnimO5Q2xFDkQDw== [fileUNF] |
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Citation |
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Title: |
Profile hidden Markov model for PETase homologues |
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Identification Number: |
doi:10.18419/darus-2055 |
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Authoring Entity: |
Buchholz, Patrick C. F. (Universität Stuttgart) |
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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: |
2021-06-28 |
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Holdings Information: |
https://doi.org/10.18419/darus-2055 |
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Study Scope |
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Keywords: |
Medicine, Health and Life Sciences, Profile HMM, Hidden Markov Model, Protein Sequence, Multiple Sequence Alignment, Amino Acid Sequence |
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Abstract: |
Sixteen protein sequences for enzymes with known activity against polyethylene terephthalate (PET) were clustered using CD-HIT to derive a reduced set of twelve centroid sequences. These twelve protein sequences were aligned in a structure-guided multiple sequence alignment by T-COFFEE. A profile hidden Markov model (HMM) was derived from this multiple sequence alignment by HMMER. |
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Notes: |
The profile HMM was trimmed by selecting alignment columns that corresponded to the region between amino acid positions 32 and 274 in the PETase from <i>Ideonella sakaiensis</i> (IsPETase, Uniprot identifier <a href="https://www.uniprot.org/uniprot/A0A0K8P6T7" target="_blank">A0A0K8P6T7</a>) |
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Methodology and Processing |
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Sources Statement |
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Data Sources: |
<a href="http://pmbd.genome-mining.cn/home/" target="_blank">PMBD: a Plastics Microbial Biodegradation Database</a> |
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<br>Zhiqiang Gan, Houjin Zhang, PMBD: a Comprehensive Plastics Microbial Biodegradation Database, Database, Volume 2019, 2019, baz119, <a href="https://doi.org/10.1093/database/baz119">DOI: 10.1093/database/baz119</a> |
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<br><a href="https://www.uniprot.org/" target="_blank">Uniprot</a> |
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<br><a href="https://www.rcsb.org/" target="_blank">Protein Data Bank (PDB)</a> |
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Data Access |
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Other Study Description Materials |
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File Description--f64709 |
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File: Templates.tab |
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Notes: |
UNF:6:AEjnqfOrnimO5Q2xFDkQDw== |
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List of Variables: | |
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Variables |
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f64709 Location: |
Variable Format: character Notes: UNF:6:vh87jWWCcRBCUjTKuxv1Zw== |
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f64709 Location: |
Variable Format: character Notes: UNF:6:Sya4aHN31kB4/xnC4GZ1mw== |
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f64709 Location: |
Variable Format: character Notes: UNF:6:0Y67DOi4/re37jeY8N5YoA== |
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Label: |
PET_09_tcoffee.aln |
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Text: |
Multiple sequence alignment in Clustal format. |
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Notes: |
application/octet-stream |
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Label: |
PET_09_tcoffee.hmm |
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Text: |
Profile hidden Markov model in HMMER3 format |
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Notes: |
application/octet-stream |
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Label: |
PET_09_tcoffee.sto |
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Text: |
Multiple sequence alignment in Stockholm format with reference columns: The trimmed alignment region is marked by an 'x' in lines starting with #=GC RF |
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Notes: |
application/octet-stream |