Preliminary phylogenetic and plasmid data for microbial laccase, fluorinase, dehalogenase, and glycyl radical enzymes
Data files
Apr 26, 2023 version files 4.41 MB
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fluorinase.figTree
15.28 KB
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fluoroacetatedehalogenase.figTree
281.60 KB
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ft_lcced10.treefile
1.20 MB
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ft_lcced11.treefile
88.51 KB
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ft_lcced12.treefile
964.01 KB
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ft_lcced14.treefile
318.53 KB
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ft_lcced15.treefile
158.65 KB
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ft_lcced8.treefile
866.05 KB
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ft_lcced9.treefile
515.85 KB
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README.md
958 B
Mar 28, 2024 version files 4.65 MB
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CotA_laccase_nco.gb
10.83 KB
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CueO_laccase_nco.gb
10.84 KB
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fluorinase_GGKncbi_c2.fa.treefile
19.44 KB
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fluorinase.figTree
15.28 KB
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fluoroacetatedehalogenase.figTree
281.60 KB
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ft_fpm_laccase_supertree.treefile
74.89 KB
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ft_lcced10.treefile
1.20 MB
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ft_lcced11.treefile
88.51 KB
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ft_lcced12.treefile
964.01 KB
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ft_lcced14.treefile
318.53 KB
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ft_lcced15.treefile
158.65 KB
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ft_lcced8.treefile
866.05 KB
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ft_lcced9.treefile
515.85 KB
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islA-in-pet-28a-n-term-histag.gb
13.08 KB
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islB-in-pet-28a-n-term-histag.gb
11.11 KB
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MulticopperOxidase_laccase_nco_nosignalpeptide.gb
10.71 KB
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profile_laccase_supertree.fa.treefile
82.63 KB
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README.md
1.07 KB
Abstract
This dataset includes preliminary raw data associated with Berkeley's Superfund Project 3, 2022-2024, investigating microbial enzymatic degradation of halogenated contaminants in situ. These initial data include uncurated FastTree and maximum likelihood treefiles for various bacterial laccases sourced from the LccED (Graff et al 2020), fluorinases, and dehalogenases; plasmid maps for laccase and glycyl radical enzyme expression; and various scripts/notebooks (in Python) used for data curation and visualization.
README: Preliminary SRP Pr.3 (2022-2024) data
This dataset includes preliminary phylogenetic analyses of publicly-available sequences for laccase, fluorinase, and fluoroacetate dehalogenase enzymes. It also contains plasmid maps for expression of bacterial laccases and select glycyl radical enzymes.
Description of the data and file structure
All treefiles are provided in either newick (.treefile) or nexus (.FigTree) format.
FastTree generated files contain an 'ft_' prefix and the corresponding laccase subfamily number as deposited/curated on the LccED (Graff et al 2020).
ML trees are generated using IQ-Tree (Minh et al 2020).
Plasmids are provided in GenBank (.gb) file format.
Sharing/Access information
N/A; all preliminary data.
Code/Software
All scripts and notebooks are in python/jupyter. These are used for FASTA file renaming/cleanup (notebooks) and subsequent visualization of newick treefiles as taxonomically-annoted nexus files (script modified from original author, Dr. L. Thiberio Rangel). See inline comments for additional detail.