CPSIR-CM: A database for structural properties of proteins identified in cyanobacterial C1 metabolism

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• 作者：P. Chellapandi ; ^{pchellapandi@gmail.com} ; M. Mohamed Khaja Hussain ; R. Prathiviraj
• 关键词：Cyanobacteria ; Protein structure ; Text mining ; Methylotrophy ; Bioremediation ; C1 compounds ; Database ; Homology models
• 刊名：Algal Research
• 出版年：2017
• 出版时间：March 2017
• 年：2017
• 卷：22
• 期：Complete
• 页码：135-139
• 全文大小：726 K
• 卷排序：22

文摘

Cyanobacteria are free-living photoautotrophic organisms that are able to degrade aliphatic and aromatic hydrocarbons in anoxic environments. Structural and biochemical information of a complete set of proteome for cyanobacterial C1 metabolism is not yet available in the public domain databases. Hence, we developed a database “Cyanobacterial Protein Structure Information Resource for C1 metabolism (CPSIR-CM)” with detailed structural and metabolic information of cyanobacterial proteins involved in C1 assimilation systems. A text mining approach was employed to identify the cyanobacterial proteins, which are responsible in mediating C1 metabolism. Standard computational prediction programs were used for accurately annotating the structural characteristics of proteins. This database structure was organized for 13 major metabolic pathways of C1 utilization systems. We incorporated structural information of 317 proteins showing significant modeling score and proper query coverage in our database. Home page of this database displays the lists of cyanobacterial C1 metabolism with a detailed summary. The first page describes the enzymes present in individual metabolism of different cyanobacterial genomes. Structural features, functional and metabolic information on each protein entry is available on the second page. A search engine on our database can access search forms as NCBI identifier and enzyme name. A user-friendly visualization tool is inbuilt to analyze three-dimensional structure of our homology models integrated in this database. This database record provides a support to decipher the structural and functional roles of cyanobacterial proteins in C1 metabolism. It also affords guidance for experimental setups to exploit the cyanobacteria in bioremediation applications. This resource can be accessible in online through the URL: http://www.pchellapandi.com/CPSIR/home.pl.