Fig. 4. Comparison of the experimentally determined and predicted topology of band 3. Band 3 is a polytopic membrane protein that has an N-terminal cytosolic domain. In the diagram, the TM domain is represented as a rectangle and the number of predicted TM domains is indicated for each. The topology of band 3 has been extensively experimentally characterized (Popov et al., 1997; Tanner, 1997; Ota et al., 1998a). Three types of prediction methods are represented: the hydropathy index (Kyte and Doolittle, 1982); the Dense Alignment Surface (DAS) method (Cserzo et al., 1997); and two hidden Markov model (HMM) methods, TMHMM (Tusnady and Simon, 1998; Tusnady and Simon, 2001) and HMMTOP (Sonnhammer et al., 1998). For reference, the location of the first and tenth TM domains of the experimentally determined topology are indicated by vertical dotted lines.