Table 3.
Significant motifs returned by SLiMFinder in each dataset (where probability <0.05).
| Virulence protein group | Number of sequences | Motif pattern | Motif name | Information content | Occurrences | Unrelated proteins | Probability (Sig value) | References |
|---|---|---|---|---|---|---|---|---|
| (A) PREVIOUSLY DESCRIBED MOTIFS | ||||||||
| Adherence | 749 | ∧.K.{0,2}K | Signal peptide motif | 3 | 151 | 47 | 0.00E+00 | Juncker et al., 2003; Bagos et al., 2008 |
| ∧.{1,2}K.{1,2}L | Signal peptide motif | 3 | 102 | 35 | 1.15E–10 | Juncker et al., 2003; Bagos et al., 2008 | ||
| ∧.{1,2}K.{0,2}I | Signal peptide motif | 3 | 91 | 34 | 1.41E–08 | Juncker et al., 2003; Bagos et al., 2008 | ||
| ∧.K.[IL] | Signal peptide motif | 2.77 | 58 | 21 | 5.80E–07 | Juncker et al., 2003; Bagos et al., 2008 | ||
| ∧.K..S | Signal peptide motif | 3 | 24 | 12 | 0.002 | Juncker et al., 2003; Bagos et al., 2008 | ||
| KK$ | C-terminal KK | 3 | 23 | 11 | 0.034 | Bergmann et al., 2003; Itzek et al., 2010 | ||
| Capsule | 332 | ∧.{1,2}K.{0,1}I | Signal peptide motif | 3 | 55 | 18 | 6.96E–06 | Juncker et al., 2003; Bagos et al., 2008 |
| ∧.{1,2}K.{0,1}I..V | Signal peptide motif | 4 | 16 | 7 | 0.002 | Juncker et al., 2003; Bagos et al., 2008 | ||
| ∧.{1,2}K.{0,2}I | Signal peptide motif | 3 | 59 | 18 | 0.003 | Juncker et al., 2003; Bagos et al., 2008 | ||
| ∧.K.[ILV] | Signal peptide motif | 2.63 | 39 | 13 | 0.003 | Juncker et al., 2003; Bagos et al., 2008 | ||
| ∧.{1,2}K.{0,2}K | Signal peptide motif | 3 | 52 | 17 | 0.006 | Juncker et al., 2003; Bagos et al., 2008 | ||
| Chemotaxis | 192 | – | – | – | – | – | – | |
| Effector | 111 | – | – | – | – | – | – | |
| Endotoxin | 66 | – | – | – | – | – | – | |
| Enzyme | 647 | ∧.{1,2}KK | Signal peptide motif | 3 | 27 | 14 | 9.52E–05 | Juncker et al., 2003; Bagos et al., 2008 |
| ∧..K.{0,2}I | Signal peptide motif | 3 | 30 | 13 | 0.042 | Juncker et al., 2003; Bagos et al., 2008 | ||
| Exotoxin | 92 | – | – | – | – | – | – | |
| Lipoprotein | 463 | L.[AG]C[AGS] | Lipobox | 3.4 | 78 | 30 | 0.00E+00 | Braun and Rehn, 1969; Babu et al., 2006 |
| [FLV].L.[AG]C | Lipobox | 3.4 | 136 | 24 | 0.00E+00 | Braun and Rehn, 1969; Babu et al., 2006 | ||
| [ILV].[AGS]C | Lipobox | 2.27 | 370 | 53 | 0.00E+00 | Braun and Rehn, 1969; Babu et al., 2006 | ||
| [AGS]C[AGS] | Lipobox | 2.27 | 285 | 50 | 7.22E–15 | Braun and Rehn, 1969; Babu et al., 2006 | ||
| ∧.{1,2}K.{0,2}K | Signal peptide motif | 3 | 109 | 27 | 1.27E–09 | Juncker et al., 2003; Bagos et al., 2008 | ||
| L.{1,2}GC.{0,1}A | Lipobox | 4 | 41 | 15 | 1.65E–09 | Braun and Rehn, 1969; Babu et al., 2006 | ||
| A.{0,2}L..C.{0,2}S | Lipobox | 4 | 68 | 19 | 3.02E–09 | Braun and Rehn, 1969; Babu et al., 2006 | ||
| ∧.K..[ILV] | Signal peptide motif | 2.63 | 66 | 19 | 4.36E–09 | Juncker et al., 2003; Bagos et al., 2008 | ||
| ∧..K..[FLV] | Signal peptide motif | 2.63 | 65 | 17 | 1.07E–07 | Juncker et al., 2003; Bagos et al., 2008 | ||
| [ILV]..C.[AGS] | Lipobox | 2.27 | 217 | 36 | 4.11E–06 | Braun and Rehn, 1969; Babu et al., 2006 | ||
| KK$ | C-terminal KK | 3 | 22 | 9 | 0.016 | Bergmann et al., 2003; Itzek et al., 2010 | ||
| Motility | 86 | – | – | – | – | – | – | |
| Siderophore | 150 | ∧.[KR]I | Signal peptide motif | 2.77 | 12 | 7 | 0.024 | Juncker et al., 2003; Bagos et al., 2008 |
| Type III secretion | 571 | – | – | – | – | – | – | |
| Type IV secretion | 181 | ∧.K[KR] | Signal peptide motif | 2.77 | 29 | 9 | 0.003 | Juncker et al., 2003; Bagos et al., 2008 |
| ∧.K..[FIL] | Signal peptide motif | 2.63 | 27 | 10 | 0.025 | Juncker et al., 2003; Bagos et al., 2008 | ||
| (B) NOVEL MOTIFS | ||||||||
| Adherence | 749 | LP.G.Y | 4 | 37 | 12 | 0.012 | ||
| Capsule | 332 | G.S..M.L | 4 | 15 | 7 | 0.029 | ||
| Chemotaxis | 192 | E..Q.I[AG].I | 4.77 | 22 | 5 | 0.004 | ||
| E..Q.[IV]..I | 3.77 | 24 | 7 | 0.02 | ||||
| Effector | 111 | ∧..I.{0,1}N | 3 | 21 | 6 | 0.012 | ||
| [LV].PY | 2.77 | 46 | 11 | 0.042 | ||||
| ∧..I[ST] | 2.77 | 17 | 6 | 0.049 | ||||
| Endotoxin | 66 | – | – | – | – | – | ||
| Enzyme | 647 | A.I.P.VL | 5 | 14 | 7 | 0.019 | ||
| VSIL.S | 5 | 11 | 7 | 0.049 | ||||
| Exotoxin | 92 | – | – | – | – | – | ||
| Lipoprotein | 463 | ML..C | 3 | 14 | 7 | 0.017 | ||
| Motility | 86 | – | – | – | – | – | ||
| Siderophore | 150 | I.K..G | 3 | 28 | 17 | 0.044 | ||
| GYP..TP | 5 | 5 | 4 | 0.052 | ||||
| Type III secretion | 571 | – | – | – | – | – | ||
| Type IV secretion | 181 | G[AG].$ | 2.77 | 19 | 9 | 2.64E–04 | ||
Where very similar motifs are returned for a protein group, only a representative motif is shown.
Information content (Edwards et al., 2007),
“∧”
start of the protein, “$” end of the protein, “.” any amino acid, {} defines the range of a repeat in the motif sequence, [] defines which amino acids can occur at a given motif position.
Italic font is used when Probability (Sig-value) is higher than the 0.05 confidence level.