A simple HMMer profile HMM model visualized by HHMVE. S: start state, N: N-terminal insertion state, B: beginning state of the core of HMM, M: matching state (square), D: deletion state (yellow circle), I: insertion state (pink diamond), E: ending state of the core of HMM, J: jump state from E to B to allow domain duplication, C: C-terminal insertion state, T: terminal state. This example model has three M states (M1-3), three D states (D1-3), and two I states (I1-2). Squares (M states) and diamonds (N, I, C, J states) are emission states that can generate symbols according to emission probabilities. Circles (S, B, D, E, T) states are dummy states that do not generate symbols. The connectivity (directed edge) between two states denotes a possible transition. The number associated with an edge is the transition probability. The connectivity between B, M, D, I, E states is similar as the traditional profile HMM  except that B can jump to any M states and M states can jump to E. These new connectivity allows the local alignment with respect to HMM.
Dai and Cheng BMC Genomics 2008 9(Suppl 1):S8 doi:10.1186/1471-2164-9-S1-S8