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Table 3 NarL binding sites with questionable annotations

From: MotifAdjuster: a tool for computational reassessment of transcription factor binding site annotations

Gene ID Gene name BS Lit. Occ. Shift Strand Adj. BS
b0904 focA AATAAAT [63] 1 +1 Reverse TATTTAT
b0904 focA ATAATGC [63] 1 +1 Forward TAATGCT
b0904 focA ATATCAA [63] 1 +1 Forward TATCAAT
b0904 focA CAACTCA [63] 1 +1 Forward AACTCAT
b0904 focA CATTAAT [63] 1 +1 Reverse TATTAAT
b0904 focA GATCGAT [63] 1 +1 Reverse TATCGAT
b0904 focA GTAATTA [63] 1 +1 Forward TAATTAT
b0904 focA TATCGGT [63] 1 +1 Reverse TACCGAT
b0904 focA TTACTCC [63] 1 +1 Forward TACTCCG
b1223 narK CACTGTA [64] 0 - - -
b1224 narG TAGGAAT [64] 1 +1 Reverse AATTCCT
b4070 nrfA TGTGGTT [65] 1 +1 Reverse TAACCAC
b4123 dcuB ATGTTAT [66] 0 - - -
  1. Annotated NarL BSs for which MotifAdjuster proposes either to shift the BS or to remove it from the data set. Columns 1 to 3 contain gene ID, gene name, and the BS (as stored in the database). Column 4 indicates the original literature related to this BS. The following three columns (5 through 7) comprise the three possible adjustments suggested by MotifAdjuster, removal, shift, and strand orientation (relative to the target gene). In column 5, a value of 0 indicates that the BS is proposed for removal, and in column 6, a positive (negative) value denotes a shift of the BS to the right (left). Finally, column 8 provides the adjusted BS. Interestingly, we find that the two BSs that are proposed to be removed are not mentioned in the original literature, and in 10 of the 11 cases, the shifted BS is consistent with the BS published in the original literature. In addition, MotifAdjuster also proposes to switch the BS strand in six of the 11 cases.