1. VARTAK, N.B., REIZER, J., REIZER, A., GRIPP, J.T., GROISMAN, E.A.,
WU, L.-F., TOMICH, J.M. AND SAIER, M.H.
Sequence and evolution of the fruR protein of Salmonella typhimurium -
a pleiotropic transcriptional regulatory protein possessing both activator
and repressor functions which is homologous to the periplasmic ribose-
RES.MICROBIOL. 142(9) 951-963 (1991).
2. WEICKERT, M.J. AND ADHYA, S.
A family of bacterial regulators homologous to gal and lac repressors.
J.BIOL.CHEM. 267(22) 15869-15874 (1992).
Numerous bacterial transcription regulatory proteins bind DNA via a
helix-turn-helix (HTH) motif. These proteins are very diverse, but for
convenience may be grouped into subfamilies on the basis of sequence
similarity. One such family groups together a range of proteins, including
ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR,
rbtR and scrR [1-2]. Within this family, the HTH motif is situated towards
HTHLACI is a 2-element fingerprint that provides a signature for the HTH
motif of the lacI bacterial regulatory proteins. The fingerprint was
derived from an initial alignment of 6 sequences: the motifs completely
encompass the HTH motif (cf. PROSITE pattern HTH_LACI_FAMILY (PS00356)).
Two iterations on OWL21.1 were required to reach convergence, at which
point a true set comprising 22 sequences was identified. The raffinose
operon, which is not detected by the PROSITE pattern, is similarly not
identified by the fingerprint, as it matches strongly only with the second
motif. The fingerprint also fails to identify the Agrobacterium opnR
protein, which lacks a significant match with the first motif.
An update on SPTR37_9f identified a true set of 64 sequences.