Abstract:
:Provalidator is a web-based tool that facilitates the design and validation of generalized profiles of protein families in prokaryotes. This tool combines the nearly full automation of profile building with a search for family members in all available databases. The tool is useful for assigning a given protein to a specific family, and is also useful for genome mining in annotated prokaryotic genomes. The tool is freely available at http://www.bactregulators.org. As proof of concept we constructed a profile that best defines the MerR family of transcriptional regulators. The profile created includes functional residues that are part of the helix-turn-helix DNA binding domain and accessory elements defined as wings 1 and 2, suggesting that members of the MerR family of regulators may exhibit conserved 3D structure in the region that defines the family profile. The profile defined for MerR was used to search for members of this family in the Swiss-Prot and TrEMBL databases, and also to identify members of the family in the genome of Pseudomonas putida. One of these identified regulators was found to be involved in zinc tolerance, showing the usefulness of identifying family members and assigning phenotypes.
journal_name
Environ Microbiol Repjournal_title
Environmental microbiology reportsauthors
Molina-Henares AJ,Godoy P,Duque E,Ramos JLdoi
10.1111/j.1758-2229.2009.00067.xsubject
Has Abstractpub_date
2009-12-01 00:00:00pages
518-23issue
6issn
1758-2229journal_volume
1pub_type
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journal_title:Environmental microbiology reports
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pub_type: 杂志文章,评审
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journal_title:Environmental microbiology reports
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journal_title:Environmental microbiology reports
pub_type: 杂志文章
doi:10.1111/j.1758-2229.2010.00150.x
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journal_title:Environmental microbiology reports
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更新日期:2018-08-01 00:00:00
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journal_title:Environmental microbiology reports
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journal_title:Environmental microbiology reports
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journal_title:Environmental microbiology reports
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journal_title:Environmental microbiology reports
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journal_title:Environmental microbiology reports
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journal_title:Environmental microbiology reports
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