Figure 2

Tracing back from the AS matrix by integrating the evolutionary coupling information. In query q, the coupled position of i is k _q (i)_, and that of i-1 is k _q (i − 1). In template t, the coupled position of j is k _t (j)_, and that of j-1 is k _t (j − 1). M _q (i) is the corresponding position in template t matched to position i in q during the original tracing-back. M _t (j) is the corresponding position in query q matched to position j in t during the original tracing-back. Additional EC scores are added into the corresponding elements in the AS matrix as shown in the figure so that the correct tracing back is performed.