Table 2 52 unique biologically significant weight matrices. Listed are the matrix's identifier (column 1), consensus sequence (column 2), regulon size (column 3), and annotation (column 4). The matrices are sub-divided into categories according to the means by which they were identified: by comparison to documented regulatory mechanisms, by inspecting the operons in a matrix's regulon for related functions, and by examining the matrix's matches for positional biases. If a matrix was identified by several means, all listings for the matrix except the first in the top-most category are marked with pluses. Where applicable, the statistical significance – log10 P is reported in (), and entries in a category are sorted according to significance.
From: Genome wide identification of regulatory motifs in Bacillus subtilis
Weight matrix | Consensus sequence | Regulon size | Annotation |
|---|---|---|---|
Documented regulatory mechanisms | |||
DBTBS database[28] | |||
Sigma factors[20] | |||
WM1 | N7TTGAN19TATAATAN6 | 1141 | σA, housekeeping |
WM118 | [G/T]GTTTAN13 [A/C]GGGAA [G/T] | 8 | σB, general stress response |
WM11 | NTGAAACNTTTN12CGTAT [A/T] | 16 | σW, antimicrobial resistance |
WM212 | TGGCA [C/T]N4CTTGCAT | 5 | σL', levanase and amino acid catabolism |
Miscellanous | |||
WM2 | AANNAGGGTGGTACCGCGNN | 24 | T-box, alternate transcription termination regulation of aminoacyl-tRNA synthetases [27] |
WM22 | [A/T]AAN [A/C]GAACNN [A/T]NGTTCNNTTN | 29 | LexA, SOS response [36] |
WM71 | NT [A/T]TGTAN10ACA [A/T]AN | 111 | TnrA, pleiotropic regulator involved in global nitrogen regulation [37] |
WM317 | [A/T]TGTAA [A/G]CG [C/T]TT [A/T]N [A/T] | 54 | CcpA, carbon catabolite repression [59] |
WM298 | NTAATN20ATTAN | 27 | YccG-YccH (3.4) |
WM259 | TGCGN10CGCA | 5 | YclK-YclJ (3.3) |
Novel predictions | |||
Regulons which operons have highly related functions | |||
Identified by detailed manual inspection | |||
WM171 | TGGGN11GGGA | 2 | Sec-dependent protein export machinery |
WM116 | AATTC [A/T]N28 [A/T]GAATT | 4 | Cell lysis |
WM266 | TGGACAN3GCAGA | 3 | Extracellular proteins |
WM304 | AGTGTN15AGACT | 4 | Transport |
WM69 | TATCTN4 [A/T]TCGAGA | 5 | Transport |
WM233 | NGGGAN3TGCGG | 7 | Antimicrobial resistance |
WM290 | NTTGAN16TGTTAN3T | 18 | DNA synthesis and repair |
WM47 | A [A/T]AGAGN18CTCTTT [C/T]N | 27 | DNA synthesis and repair |
WM124 | NTTAG [A/T]N6TTAGN | 17 | Transport |
Identified using COG functional categories | |||
+WM2 | AANNAGGGTGGTAGGGCGNN | 24 | T-box, translation, ribosomal structure, and biogenesis (12) |
+WM317 | [A/T]TGTAA [A/G]GG [C/T]TT [A/T]N [A/T] | 54 | CcpA, carbohydrate transport and metabolism (6.5), energy production and conversion (3.0) |
WM130 | N4TTGAN14 [A/T]N4TGAAAN | 38 | Posttranslational modification, protein turnover, and chaperones (4.2) |
+WM1 | N7TTGAN19TATAATAN6 | 1141 | σA, transcription (3.3) |
+WM212 | TGGCA [C/T]N4GTTGCAT | 5 | σL, energy production and conversion (3.1) |
WM255 | NCTGAAN26TTCAGN | 3 | Cell motility and secretion (2.9) |
+WM22 | [A/T]AAN [A/C]GAACNN [A/T]NGTTCNNTTN | 29 | LexA, DNA replication, recombination, and repair (2.6) |
WM39 | [A/G]NNTGCTN30AGCAN | 21 | Secondary metabolites biosynthesis transport, and catabolism (2.5) |
WM228 | NGCAGAN13TCTGCN | 3 | Secondary metabolites biosynthesis transport, and catabolism (2.5) |
WM283 | AGCTGN13GAGGTT | 3 | Translation, ribosomal structure, and biogenesis (2.4) |
WM80 | NGTTTN29AAACN | 86 | Energy production and conversion (2.3) |
WM223 | NATTTN28AAATN | 69 | Transcription (2.3) |
WM16 | NCCGGC [C/T]N6GCCGGN [G/T]TTTT | 27 | Signal transduction mechanisms (2.3) |
WM17 | [A/G]NCGGCN8 [A/G]NGCCGN | 40 | Cell motility and secretion (2.3) |
WM23 | [A/T]CGAAN27TTCG [A/T] | 25 | Amino acid transport and metabolism (2.2) |
WM221 | NGCGGN29CGGCN | 6 | Amino acid transport and metabolism (2.2) |
WM119 | NAATAN9TATTN | 62 | Cell envelope biogenesis, outer membrane (2.1) |
+WM304 | AGTGTN15ACACT | 4 | Inorganic ion transport and metabolism (2.1) |
WM46 | NTATAN17AAAGGAG [A/G]N | 109 | DNA replication, recombinaion, and repair (2.1) |
WM75 | [G/T]N3CTACN9GN12CTACA | 5 | Secondary metabolites biosynthesis transport, and catabolism (2.0) |
WM31 | NTGTTN5AACAN | 58 | Carbohydrate transport and metabolism (2.0) |
Positions of binding sites are highly biased with respect to σ A sites. | |||
+WM46 | NTATAN17AAAGGAG [A/G]N | 109 | Repressor (17) |
WM21 | AANGCGN15GGGNTTTTTT | 128 | Activator (7.9) |
WM33 | NAAGC [A/T]GN12C [A/T]GCTTN | 96 | Activator (4.7) |
WM50 | NNGGTTTTTTTATTN | 152 | Activator (3.6) |
WM173 | NAAAGN [A/G]NGGAAN4 | 35 | Repressor (3.0) |
WM169 | NAAAGN3GTGAN | 40 | Repressor (2.9) |
WM13 | [A/G] [A/C] [A/G]CGG [G/T]... [G/T]N9GGG [G/T] [G/T]TT [A/T]T | 21 | Activator (2.8) |
WM180 | [A/T]AGAGN5AGAGN | 15 | Repressor (2.6) |
WM58 | NAAAGANAN15TGTTTTN | 42 | Activator (2.6) |
WM79 | NTTGT[A/T N4TTGTN | 67 | Activator (2.5) |
WM84 | AN3AACATN3GGAGGN | 19 | Repressor (2.4) |
WM7 | NAAAGN19 [G/T]CTTTN3 | 90 | Activator (2.3) |
+WM17 | [A/G]NGGGGN8 [A/C]NGCCGN | 40 | Activator (2.1) |
Absolute positions of binding sites are highly biased. | |||
+WM46 | NTATA-17-AAAGGAG [A/G]N | 109 | (61) |
+WM1 | N7TTGAN19TATAATAN6 | 1141 | σA(16) |
+WM169 | NAAAGN3GTGAN | 40 | (10) |
+WM21 | AANCCGN15CGGNTTTTTT | 128 | (6.3) |
+WM2 | AANNAGGGTGGTAGGGGGNN | 24 | T-box (4.8) |
+WM16 | NCGGGG [C/T]-6-GGCGGN [G/T]TTTT | 27 | (4.1) |
+WM13 | [A/G] [A/C] [A/G]CCC[G/T ... | 21 | (3.9) |
+WM58 | NAAAGANA-15-TGTTTTN | 42 | (3.4) |
+WM11 | NTGAAACNTTTN12CGTAT [A/T] | 16 | σw(3.1) |
+WM17 | [A/G]NCGGCN8 [A/C]NGCCGN | 40 | (3.0) |
WM25 | NNGTTT-17-GG [A/T]A [A/T] | 59 | (3.0) |
WM37 | NAAGC [A/T]-19-GCTTT | 25 | (3.0) |
WM14 | N3CGGCN11GCCGN3 | 197 | Tends to co-occur with T-box (3.0) |
WM143 | NCGTCN24TTATN | 25 | (2.8) |
WM185 | NAACC-15-GGTTNNTT | 15 | (2.7) |
+WM47 | A [A/T]AGAGN18CTCTTT [C/T]N | 27 | (2.6) |
+WM33 | NAAGG [A/T]GN12C [A/T]GCTTN | 96 | (2.1) |
WM28 | [A/G]AAAGC-21- [A/G]GCTT [C/T]TT | 30 | (2.0) |
Unusually high number of matches in a single promter. | |||
WM34 | NCACA [A/T]N [A/T]TGTGN | 17 | Three repeats overlap dnaA boxes TTATCCAGA [60], may inhibit chromosome replication, (7.8) |