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We show, using dot matrix comparisons and statistical analysis of sequence alignments, that seven sequenced sigma factors, E.coli sigma-70 and sigma-32, B.subtilis sigma-43 and sigma-29, phage SP01 gene products 28 and 34i and phage T4 gene product 55, comprise a homologous family of proteins. Sigma-70, sigma-32, and sigma-43 each have two copies of a sequence similar to the helix-turn-helix DNA binding motif seen in CRP, and lambda repressor and cro proteins. B.subtilis sigma-29, SP01 gp28, and SP01 gp34 have at least one copy similar to this sequence. We propose that a second sequence, conserved in all seven proteins i s the core RNA polymerase binding site. A third region, present only in sigma-70 and sigma-43, may also be involved in interaction with core. Available mutational evidence supports our model for sigma factor structure …