cessive NO production by iNOS is responsible for hyporesponsiveness to NA and hypotension in endotoxaemia. In this study, we demonstrated that both aortic iNOS expression and serum NO level were significantly increased in late endotoxaemia. A large amount of NO produced by iNOS may cause desensitization of a1-adrenoceptor, deactivation of NA, and inhibition of RhoA/ROK pathway via a Ca2+-desensitization mechanism. Here, we showed that both activity of RhoA and phosphorylation of MYPT1 at Thr696 and Thr850 were decreased at 4 h and 6 h after LPS, indicating that in late endotoxaemia, the high-output NO production by iNOS could inhibit RhoA/ROK pathway and lead to vascular hyporeactivity, systemic hypotension, and organ dysfunction. Thus, our in vivo data further confirmed that in late endotoxaemia, the RhoA/ ROK pathway could participate in the pathogenesis of vascular hyporeactivity accompanied with endotoxaemic shock. Taken together, this study demonstrated that the injection of rats with LPS induced a biphasic hypotension and a decreased pressor response to NA. Importantly, an increased RhoA activity may compensate vascular reactivity in early endotoxaemia ex vivo, while in late endotoxaemia, the large production of NO by iNOS inhibiting RhoA activity leads to vascular hyporeactivity in vivo and ex vivo. Therefore, both RhoA/ROK and iNOS/NO pathways play important roles in regulation of vascular reactivity and blood pressure in endotoxaemic rats. We propose that a combination of using NO/cGMP pathway inhibitors and specific RhoA activators could be a novel therapeutic strategy in the vascular hyporeactivity associated with endotoxaemic shock. ~~ ~~ Proteins that belong to the same family- exemplified by significant sequence similarity – are evolutionarily related and share similar three dimensional structures and function. Two proteins are said to be remote or distant homologues, if the sequence identity among them is poor, owing to evolutionary divergence, but they share common fold and function. Detection of such distant relationships between proteins from sequence information alone, amongst a wide range of unrelated sequences having poor sequence identity, remains a challenging task. It is also crucial to understand how dissimilar sequences can adopt similar structure and SB 203580 site function which will aid in inferring the evolutionary aspects of proteins. As the 26243621 protein sequence space is very vast and is continuously expanding, as compared to structural space, detecting such distant relationships is still a pivotal task in the field of computational biology. Considerable efforts are required to establish distant relationships amongst proteins. In order to detect such relationships amongst proteins, many search methods can be employed like sequence to sequence, sequence to profile and profile to profile comparisons. Sequencebased approaches basically employ HMMs, profiles, 11358331 templates, intermediate sequences and machine-learning tools to detect true relationships. Structure-based methods perform relatively better as structures are conserved better than sequences. Some of the methods like consensus-based approaches have been found to be highly successful as evident in Sequence Searches for Remote Homology Detection recent editions of the CASP experiment, where accuracy had increased when different methods were combined 
to generate a consensus. Although many of these methods are very powerful in homology detection, yet the coverage of complete s