Korean BioInformation Center (KOBIC), KRIBB, Daejeon 305-806, Korea.
BMC Genomics. 2009 Dec 3;10 Suppl 3(Suppl 3):S18. doi: 10.1186/1471-2164-10-S3-S18.
Pseudomonas putida KT2440 (P. putida KT2440) is a highly versatile saprophytic soil bacterium. It is a certified bio-safety host for transferring foreign genes. Therefore, the bacterium is used as a model organism for genetic and physiological studies and for the development of biotechnological applications. In order to provide a more systematic application of the organism, we have constructed a protein-protein interaction (PPI) network analysis system of P. putida KT2440.
PutidaNET is a comprehensive interaction database and server of P. putida KT2440 which is generated from three protein-protein interaction (PPI) methods. We used PSIMAP (Protein Structural Interactome MAP), PEIMAP (Protein Experimental Interactome MAP), and Domain-domain interactions using iPfam. PutidaNET contains 3,254 proteins, and 82,019 possible interactions consisting of 61,011 (PSIMAP), 4,293 (PEIMAP), and 30,043 (iPfam) interaction pairs except for self interaction. Also, we performed a case study by integrating a protein interaction network and experimental 1-DE/MS-MS analysis data P. putida. We found that 1) major functional modules are involved in various metabolic pathways and ribosomes, and 2) existing PPI sub-networks that are specific to succinate or benzoate metabolism are not in the center as predicted.
We introduce the PutidaNET which provides predicted interaction partners and functional analyses such as physicochemical properties, KEGG pathway assignment, and Gene Ontology mapping of P. putida KT2440 PutidaNET is freely available at http://sequenceome.kobic.kr/PutidaNET.
恶臭假单胞菌 KT2440（P. putida KT2440）是一种用途广泛的腐生土壤细菌。它是一种经过认证的生物安全宿主，可用于转移外源基因。因此，该细菌被用作遗传和生理研究以及生物技术应用开发的模式生物。为了更系统地应用该生物体，我们构建了恶臭假单胞菌 KT2440 的蛋白质-蛋白质相互作用（PPI）网络分析系统。
PutidaNET 是一个综合的恶臭假单胞菌 KT2440 相互作用数据库和服务器，它是由三种蛋白质-蛋白质相互作用（PPI）方法生成的。我们使用了 PSIMAP（蛋白质结构相互作用图）、PEIMAP（蛋白质实验相互作用图）和使用 iPfam 的结构域-结构域相互作用。PutidaNET 包含 3254 个蛋白质和 82019 个可能的相互作用，包括 61011 个（PSIMAP）、4293 个（PEIMAP）和 30043 个（iPfam）相互作用对，除了自相互作用。此外，我们通过整合蛋白质相互作用网络和恶臭假单胞菌的实验 1-DE/MS-MS 分析数据进行了案例研究。我们发现：1）主要功能模块涉及各种代谢途径和核糖体；2）预测中位于中心位置的与琥珀酸盐或苯甲酸盐代谢相关的特定 PPI 子网络并不存在。
我们介绍了 PutidaNET，它提供了恶臭假单胞菌 KT2440 的预测相互作用伙伴和功能分析，如理化性质、KEGG 途径分配和基因本体论映射。PutidaNET 可在 http://sequenceome.kobic.kr/PutidaNET 上免费获得。
