There is preliminary experimental evidence indicating that the major 
outer-membrane protein (MOMP) of Chlamydia is a porin. We tested this hypothesis 
for the MOMP of the mouse pneumonitis serovar of Chlamydia trachomatis using two 
secondary structure prediction methods. First, an algorithm that calculates the 
mean hydrophobicity of one side of putative beta-strands predicted the positions 
of 16 transmembrane segments, a structure common to known porins. Second, outer 
loops typical of porins were assigned using an artificial neural network trained 
to predict the topology of bacterial outer-membrane proteins with a predominance 
of beta-strands. A topology model based on these results locates the four 
variable domains (VDs) of the MOMP on the outer loops and the five constant 
domains on beta-strands and the periplasmic turns. This model is consistent with 
genetic analysis and immunological and biochemical data that indicate the VDs 
are surface exposed. Furthermore, it shows significant homology with the 
consensus porin model of the program FORESST, which contrasts a proposed 
secondary structure against a data set of 349 proteins of known structure. 
Analysis of the MOMP of other chlamydial species corroborated our predicted 
model.