TABLE 3.

Putative RRs with no clear DNA-binding motif

ORFaLength (amino acids)Identity to CheY (%)bConserved residuecKnown or possible identityd% Identity/similarityePossible SK partnerf
D12D13D57T87Y106K109
VF092343920.9XXXXUnpaired
VF105415726.4XXXXXVF1053
VF168936823.3XXXXExpMg32/53Unpaired
VF183037623.3XXXCheB35/54VF1831 (CheA)
VF183312265.1XXXXXXCheY68/86VF1831 (CheA)
VF187930632.6XXXXXCheVh30/55VF1831 (CheA)
VFA021638224.8XXXUnpaired
VFA060833424.0XXXXUnpaired
VFA069829825.6XXXXXCheVh28/53Unpaired
VFA073226722.5XXXXXVFA0733
VFA079533123.3XXXXUnpaired
VFA080231327.1XXXXXCheVh31/53Unpaired
VFA101229924.8XXXXUnpaired
VFA101757223.3XXXXXVFA1016
VFA102450521.7XXXXSypEiVFA1025 (SypF)
  • a ORFs are designated VF if located on chromosome 1 and VFA if found on chromosome 2.

  • b Percent identity to E. coli CheY protein calculated by determining the number of identical residues per ClustalW alignment (76) and dividing by the number of amino acids in the shorter sequence.

  • c Presence (X) of amino acid residues conserved within REC domains of RR proteins (numbers shown represent placement within E. coli CheY).

  • d Possible identities were assigned to proteins whose e-values to the indicated E. coli (or alternative species, where indicated) gene were more significant than e−20, per BLAST analysis (1, 67).

  • e Per BLAST alignment (bl2seq) using the Blosum 62 matrix across the length of the V. fischeri protein (28, 75).

  • f Identified as SK based on the presence of conserved histidine (H box) motifs by rpsBLAST analysis (44); putative homology, based on parameters outlined in footnote d, is indicated in parentheses.

  • g Compared to Erwinia carotovora sequence (2).

  • h Compared to Bacillus subtilis sequence (22).

  • i SypE has been previously named (90).