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Integration of bioinformatics to biodegradation.

Arora PK, Bae H - Biol Proced Online (2014)

Bottom Line: The present review describes development of various bioinformatics tools that may be applied in the field of biodegradation.Several databases, including the University of Minnesota Biocatalysis/Biodegradation database (UM-BBD), a database of biodegradative oxygenases (OxDBase), Biodegradation Network-Molecular Biology Database (Bionemo) MetaCyc, and BioCyc have been developed to enable access to information related to biochemistry and genetics of microbial degradation.Furthermore, the whole genomes of several potential degrading bacteria have been sequenced and annotated using bioinformatics tools.

View Article: PubMed Central - HTML - PubMed

Affiliation: School of Biotechnology, Yeungnam University, Gyeongsan 712-749, Republic of Korea.

ABSTRACT
Bioinformatics and biodegradation are two primary scientific fields in applied microbiology and biotechnology. The present review describes development of various bioinformatics tools that may be applied in the field of biodegradation. Several databases, including the University of Minnesota Biocatalysis/Biodegradation database (UM-BBD), a database of biodegradative oxygenases (OxDBase), Biodegradation Network-Molecular Biology Database (Bionemo) MetaCyc, and BioCyc have been developed to enable access to information related to biochemistry and genetics of microbial degradation. In addition, several bioinformatics tools for predicting toxicity and biodegradation of chemicals have been developed. Furthermore, the whole genomes of several potential degrading bacteria have been sequenced and annotated using bioinformatics tools.

No MeSH data available.


Related in: MedlinePlus

2-Nitrobenzoic Acid Pathway Map at the UM-BBD (http://umbbd.ethz.ch/onb/onb_map.html).
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Related In: Results  -  Collection

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Figure 1: 2-Nitrobenzoic Acid Pathway Map at the UM-BBD (http://umbbd.ethz.ch/onb/onb_map.html).

Mentions: The UM-BBD is a well-known database in the field of biodegradation that is freely available at http://umbbd.ethz.ch/. This database provides information pertaining to multiple fields of interest including microbes, biotransformation rules, enzymes, genes and reactions involved in microbial degradation [11]. This database mainly focuses on the metabolic pathways of xenobiotic compounds which are available in text as well as graphic formats. Pathways represent multisteps enzymatic reactions in a series initiating from the starting compound and proceeds via the formation of intermediates. There is a diversity of the bacteria that can degrade a chemical compound via different pathways. All known pathways for a single compound are included in the UM-BBD metabolic pathway page (known as pathway map) of a particular compound with the information of the bacteria and enzymes involved in the degradation of that compound. FigureĀ 1 represents the UM-BBD pathway map of 2-nitrobenzoic acid where two bacterial degradation pathways are present. Both pathways were initiated with the formation of 2-hydroxylaminobenzoic acid that further degraded via two different pathways in different bacteria. Currently, the UM-BBD database comprises (i) 219 microbial degradation pathways; (ii) 1503 chemical reactions; (iii) 993 enzymes; (iv) 543 microbes; (v) 250 biotransformation rules; (vi) 50 functional groups; (vii) 76 reactions of naphthalene 1, 2- dioxygenase and (viii) 109 reactions of toluene dioxygenase. This database is cross linked to several others including ExPASy, BRENDA, Enzyme and NCBI to provide information describing genes and enzymes involved in the degradation of xenobiotic compounds [11].


Integration of bioinformatics to biodegradation.

Arora PK, Bae H - Biol Proced Online (2014)

2-Nitrobenzoic Acid Pathway Map at the UM-BBD (http://umbbd.ethz.ch/onb/onb_map.html).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4012781&req=5

Figure 1: 2-Nitrobenzoic Acid Pathway Map at the UM-BBD (http://umbbd.ethz.ch/onb/onb_map.html).
Mentions: The UM-BBD is a well-known database in the field of biodegradation that is freely available at http://umbbd.ethz.ch/. This database provides information pertaining to multiple fields of interest including microbes, biotransformation rules, enzymes, genes and reactions involved in microbial degradation [11]. This database mainly focuses on the metabolic pathways of xenobiotic compounds which are available in text as well as graphic formats. Pathways represent multisteps enzymatic reactions in a series initiating from the starting compound and proceeds via the formation of intermediates. There is a diversity of the bacteria that can degrade a chemical compound via different pathways. All known pathways for a single compound are included in the UM-BBD metabolic pathway page (known as pathway map) of a particular compound with the information of the bacteria and enzymes involved in the degradation of that compound. FigureĀ 1 represents the UM-BBD pathway map of 2-nitrobenzoic acid where two bacterial degradation pathways are present. Both pathways were initiated with the formation of 2-hydroxylaminobenzoic acid that further degraded via two different pathways in different bacteria. Currently, the UM-BBD database comprises (i) 219 microbial degradation pathways; (ii) 1503 chemical reactions; (iii) 993 enzymes; (iv) 543 microbes; (v) 250 biotransformation rules; (vi) 50 functional groups; (vii) 76 reactions of naphthalene 1, 2- dioxygenase and (viii) 109 reactions of toluene dioxygenase. This database is cross linked to several others including ExPASy, BRENDA, Enzyme and NCBI to provide information describing genes and enzymes involved in the degradation of xenobiotic compounds [11].

Bottom Line: The present review describes development of various bioinformatics tools that may be applied in the field of biodegradation.Several databases, including the University of Minnesota Biocatalysis/Biodegradation database (UM-BBD), a database of biodegradative oxygenases (OxDBase), Biodegradation Network-Molecular Biology Database (Bionemo) MetaCyc, and BioCyc have been developed to enable access to information related to biochemistry and genetics of microbial degradation.Furthermore, the whole genomes of several potential degrading bacteria have been sequenced and annotated using bioinformatics tools.

View Article: PubMed Central - HTML - PubMed

Affiliation: School of Biotechnology, Yeungnam University, Gyeongsan 712-749, Republic of Korea.

ABSTRACT
Bioinformatics and biodegradation are two primary scientific fields in applied microbiology and biotechnology. The present review describes development of various bioinformatics tools that may be applied in the field of biodegradation. Several databases, including the University of Minnesota Biocatalysis/Biodegradation database (UM-BBD), a database of biodegradative oxygenases (OxDBase), Biodegradation Network-Molecular Biology Database (Bionemo) MetaCyc, and BioCyc have been developed to enable access to information related to biochemistry and genetics of microbial degradation. In addition, several bioinformatics tools for predicting toxicity and biodegradation of chemicals have been developed. Furthermore, the whole genomes of several potential degrading bacteria have been sequenced and annotated using bioinformatics tools.

No MeSH data available.


Related in: MedlinePlus