Dataset Information

The Lactamase Engineering Database: a critical survey of TEM sequences in public databases.

ABSTRACT: BACKGROUND: TEM beta-lactamases are the main cause for resistance against beta-lactam antibiotics. Sequence information about TEM beta-lactamases is mainly found in the NCBI peptide database and TEM mutation table at http://www.lahey.org/Studies/temtable.asp. While the TEM mutation table is manually curated by experts in the lactamase field, who guarantee reliable and consistent information, the rapidly growing sequence and annotation information from the NCBI peptide database is sometimes inconsistent. Therefore, the Lactamase Engineering Database has been developed to collect the TEM beta-lactamase sequences from the NCBI peptide database and the TEM mutation table, systematically compare sequence information and naming, identify inconsistencies, and thus provide a versatile tool for reconciliation of data and for an investigation of the sequence-function relationship. DESCRIPTION: The LacED currently provides 2399 sequence entries and 37 structure entries. Sequence information on 150 different TEM beta-lactamases was derived from the TEM mutation table which provides a unique number to each protein classified as TEM beta-lactamase. 293 TEM-like proteins were found in the NCBI protein database, but only 113 TEM beta-lactamase were common to both data sets. The 180 TEM beta-lactamases from the NCBI protein database which have not yet been assigned to a TEM number fall in three classes: (1) 89 proteins from microbial organisms and 35 proteins from cloning or expression vectors had a new mutation profile; (2) 55 proteins had inconsistent annotation in terms of TEM assignment or reported mutation profile; (3) 39 proteins are fragments. The LacED is web accessible at http://www.LacED.uni-stuttgart.de and contains multisequence alignments, structure information and reconciled annotation of TEM beta-lactamases. The LacED is weekly updated and supplies all data for download. CONCLUSION: The Lactamase Engineering Database enables a systematic analysis of TEM beta-lactamase sequence and annotation data from different data sources, and thus provides a valuable tool to identify inconsistencies in sequences from the NCBI peptide database, to detect TEM beta-lactamases with a novel mutation profile, and to identify new amino acid positions at which mutations can occur.

SUBMITTER: Thai QK

PROVIDER: S-EPMC2742552 | biostudies-literature | 2009

REPOSITORIES: biostudies-literature

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The Lactamase Engineering Database: a critical survey of TEM sequences in public databases.

Thai Quan Ke QK Bös Fabian F Pleiss Jürgen J

BMC genomics 20090821

<h4>Background</h4>TEM beta-lactamases are the main cause for resistance against beta-lactam antibiotics. Sequence information about TEM beta-lactamases is mainly found in the NCBI peptide database and TEM mutation table at http://www.lahey.org/Studies/temtable.asp. While the TEM mutation table is manually curated by experts in the lactamase field, who guarantee reliable and consistent information, the rapidly growing sequence and annotation information from the NCBI peptide database is sometime ...[more]

PMID: 19698099

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Project description:BACKGROUND: SHV ?-lactamases confer resistance to a broad range of antibiotics by accumulating mutations. The number of SHV variants is steadily increasing. 117 SHV variants have been assigned in the SHV mutation table (http://www.lahey.org/Studies/). Besides, information about SHV ?-lactamases can be found in the rapidly growing NCBI protein database. The SHV ?-Lactamase Engineering Database (SHVED) has been developed to collect the SHV ?-lactamase sequences from the NCBI protein database and the SHV mutation table. It serves as a tool for the detection and reconciliation of inconsistencies, and for the identification of new SHV variants and amino acid substitutions. DESCRIPTION: The SHVED contains 200 protein entries with distinct sequences and 20 crystal structures. 83 protein sequences are included in the both the SHV mutation table and the NCBI protein database, while 35 and 82 protein sequences are only in the SHV mutation table and the NCBI protein database, respectively. Of these 82 sequences, 41 originate from microbial sources, and 22 of them are full-length sequences that harbour a mutation profile which has not been classified yet in the SHV mutation table. 27 protein entries from the NCBI protein database were found to have an inconsistency in SHV name identification. These inconsistencies were reconciled using information from the SHV mutation table and stored in the SHVED.The SHVED is accessible at http://www.LacED.uni-stuttgart.de/classA/SHVED/. It provides sequences, structures, and a multisequence alignment of SHV ?-lactamases with the corrected annotation. Amino acid substitutions at each position are also provided. The SHVED is updated monthly and supplies all data for download. CONCLUSIONS: The SHV ?-Lactamase Engineering Database (SHVED) contains information about SHV variants with reconciled annotation. It serves as a tool for detection of inconsistencies in the NCBI protein database, helps to identify new mutations resulting in new SHV variants, and thus supports the investigation of sequence-function relationships of SHV ?-lactamases.

Dataset Information

The Lactamase Engineering Database: a critical survey of TEM sequences in public databases.

Publications

The Lactamase Engineering Database: a critical survey of TEM sequences in public databases.

Similar Datasets

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