Strong sequence similarity has been reported among WrbA (the Trp repressor-binding protein of Escherichia coli); Ycp4, a protein of unknown function from the budding yeast Saccharomyces cerevisiae; P25, the pap1-dependent protein of the fission yeast Schizosaccharomyces pombe; and the translation product of a partial cDNA sequence from rice seedling root (Oryza sativa, locus Ricr02421a; here referred to as RicR). Further homology search with the profile method indicates that all the above sequences are related to the flavodoxin family and, in turn, allows detection of the recently proposed flavodoxin-like proteins from E. coli, MioC and the hypothetical protein YihB. We discuss sequence conservation with reference to the known 3-dimensional structures of flavodoxins. Conserved sequence and hydrophobicity patterns, as well as residue-pair interaction potentials, strongly support the hypothesis that these proteins share the alpha/beta twisted open-sheet fold typical of flavodoxins, with an additional alpha/beta unit in the WrbA family. On the basis of the proposed structural homology, we discuss the details of the putative FMN-binding sites. Our analysis also suggests that the helix-turn-helix motif we identified previously in the C-terminal region of the WrbA family is unlikely to reflect a DNA-binding function of this new protein family.