| Adam S Frost 1-310 |
| ID: | 1490116048 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 310 (287) | ||
| Sequences: | 368 (268.9) | ||
| Seq/Len: | 1.282 | ||
| Nf(neff/√len): | 15.9 |
HHblits Results: (2016_02)
Sequences per length for each position, BEFORE the coverage/gap filter was applied
Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 1.282).
Sequences per length for each position, AFTER the coverage/gap filter was applied
Residue pairs sorted by coevolution strength:
Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.
| i | j | Scaled score | Prob |
| 102_V | 111_Y | 4.182 | 1.00 |
| 2_K | 9_D | 3.046 | 1.00 |
| 4_R | 9_D | 2.886 | 1.00 |
| 26_L | 43_F | 2.456 | 1.00 |
| 26_L | 41_L | 2.318 | 0.99 |
| 89_L | 103_L | 2.311 | 0.99 |
| 79_K | 83_H | 2.139 | 0.98 |
| 56_C | 135_Q | 2.089 | 0.98 |
| 1_M | 5_I | 1.907 | 0.96 |
| 102_V | 113_V | 1.785 | 0.94 |
| 1_M | 9_D | 1.713 | 0.92 |
| 130_R | 148_I | 1.708 | 0.92 |
| 41_L | 54_V | 1.663 | 0.90 |
| 26_L | 130_R | 1.654 | 0.90 |
| 113_V | 129_R | 1.640 | 0.89 |
| 95_V | 237_S | 1.634 | 0.89 |
| 116_F | 138_V | 1.617 | 0.88 |
| 3_Q | 8_L | 1.562 | 0.86 |
| 112_L | 124_L | 1.544 | 0.85 |
| 41_L | 112_L | 1.528 | 0.84 |
| 54_V | 123_I | 1.524 | 0.84 |
| 102_V | 129_R | 1.472 | 0.81 |
| 89_L | 105_F | 1.467 | 0.81 |
| 100_I | 104_Q | 1.392 | 0.76 |
| 24_Y | 233_S | 1.391 | 0.76 |
| 144_K | 239_N | 1.387 | 0.76 |
| 128_N | 148_I | 1.370 | 0.74 |
| 41_L | 260_S | 1.370 | 0.74 |
| 1_M | 4_R | 1.369 | 0.74 |
| 242_V | 267_S | 1.363 | 0.74 |
| 3_Q | 138_V | 1.358 | 0.73 |
| 4_R | 8_L | 1.345 | 0.72 |
| 26_L | 29_I | 1.337 | 0.72 |
| 118_S | 138_V | 1.324 | 0.71 |
| 41_L | 52_V | 1.324 | 0.71 |
| 134_L | 235_L | 1.322 | 0.70 |
| 24_Y | 50_L | 1.314 | 0.70 |
| 13_L | 16_E | 1.314 | 0.70 |
| 54_V | 103_L | 1.313 | 0.70 |
| 75_G | 79_K | 1.312 | 0.70 |
| 67_R | 119_A | 1.298 | 0.68 |
| 6_S | 9_D | 1.289 | 0.68 |
| 42_K | 80_L | 1.283 | 0.67 |
| 26_L | 78_V | 1.278 | 0.67 |
| 24_Y | 51_N | 1.275 | 0.66 |
| 294_I | 297_K | 1.268 | 0.66 |
| 129_R | 143_N | 1.260 | 0.65 |
| 16_E | 110_F | 1.250 | 0.64 |
| 231_L | 269_Q | 1.245 | 0.64 |
| 29_I | 47_D | 1.244 | 0.64 |
| 15_R | 229_P | 1.242 | 0.63 |
| 79_K | 133_A | 1.239 | 0.63 |
| 92_L | 103_L | 1.236 | 0.63 |
| 271_E | 282_K | 1.233 | 0.63 |
| 2_K | 6_S | 1.224 | 0.62 |
| 27_S | 86_A | 1.224 | 0.62 |
| 28_N | 87_K | 1.223 | 0.62 |
| 28_N | 86_A | 1.217 | 0.61 |
| 260_S | 263_E | 1.205 | 0.60 |
| 26_L | 105_F | 1.204 | 0.60 |
| 90_T | 138_V | 1.202 | 0.60 |
| 116_F | 119_A | 1.199 | 0.59 |
| 2_K | 8_L | 1.190 | 0.59 |
| 67_R | 118_S | 1.183 | 0.58 |
| 2_K | 5_I | 1.171 | 0.57 |
| 103_L | 236_L | 1.170 | 0.57 |
| 267_S | 270_L | 1.170 | 0.57 |
| 17_L | 21_L | 1.169 | 0.57 |
| 190_A | 195_D | 1.156 | 0.55 |
| 221_H | 233_S | 1.156 | 0.55 |
| 10_L | 17_L | 1.155 | 0.55 |
| 101_L | 286_L | 1.155 | 0.55 |
| 21_L | 43_F | 1.144 | 0.54 |
| 36_S | 213_K | 1.141 | 0.54 |
| 296_E | 299_T | 1.137 | 0.53 |
| 101_L | 240_L | 1.135 | 0.53 |
| 102_V | 125_L | 1.135 | 0.53 |
| 188_V | 192_Y | 1.130 | 0.53 |
| 112_L | 234_D | 1.130 | 0.53 |
| 24_Y | 269_Q | 1.127 | 0.52 |
| 43_F | 52_V | 1.126 | 0.52 |
| 114_L | 138_V | 1.126 | 0.52 |
| 1_M | 222_K | 1.126 | 0.52 |
| 82_K | 88_R | 1.122 | 0.52 |
| 2_K | 10_L | 1.119 | 0.52 |
| 116_F | 232_S | 1.118 | 0.51 |
| 33_A | 70_P | 1.114 | 0.51 |
| 21_L | 181_V | 1.112 | 0.51 |
| 86_A | 261_L | 1.108 | 0.51 |
| 191_K | 211_K | 1.103 | 0.50 |
| 65_F | 110_F | 1.098 | 0.50 |
| 1_M | 8_L | 1.097 | 0.49 |
| 26_L | 52_V | 1.094 | 0.49 |
| 44_N | 54_V | 1.094 | 0.49 |
| 119_A | 138_V | 1.092 | 0.49 |
| 233_S | 276_L | 1.087 | 0.48 |
| 117_F | 148_I | 1.086 | 0.48 |
| 108_G | 114_L | 1.080 | 0.48 |
| 306_Y | 309_F | 1.074 | 0.47 |
| 213_K | 266_N | 1.072 | 0.47 |
| 54_V | 114_L | 1.071 | 0.47 |
| 109_H | 147_Q | 1.067 | 0.46 |
| 120_G | 126_D | 1.066 | 0.46 |
| 27_S | 133_A | 1.061 | 0.46 |
| 75_G | 83_H | 1.060 | 0.46 |
| 10_L | 223_L | 1.058 | 0.46 |
| 190_A | 197_T | 1.058 | 0.46 |
| 14_A | 23_G | 1.057 | 0.45 |
| 192_Y | 195_D | 1.046 | 0.44 |
| 224_L | 309_F | 1.043 | 0.44 |
| 53_V | 295_S | 1.043 | 0.44 |
| 69_I | 106_A | 1.041 | 0.44 |
| 117_F | 192_Y | 1.040 | 0.44 |
| 3_Q | 39_F | 1.040 | 0.44 |
| 134_L | 240_L | 1.039 | 0.44 |
| 178_S | 259_D | 1.038 | 0.44 |
| 111_Y | 129_R | 1.036 | 0.43 |
| 144_K | 147_Q | 1.031 | 0.43 |
| 138_V | 146_G | 1.030 | 0.43 |
| 31_N | 237_S | 1.030 | 0.43 |
| 56_C | 101_L | 1.028 | 0.43 |
| 52_V | 122_V | 1.026 | 0.42 |
| 31_N | 238_K | 1.023 | 0.42 |
| 121_N | 126_D | 1.023 | 0.42 |
| 1_M | 16_E | 1.022 | 0.42 |
| 50_L | 117_F | 1.020 | 0.42 |
| 27_S | 44_N | 1.019 | 0.42 |
| 103_L | 261_L | 1.019 | 0.42 |
| 138_V | 222_K | 1.013 | 0.41 |
| 1_M | 6_S | 1.012 | 0.41 |
| 6_S | 112_L | 1.012 | 0.41 |
| 243_F | 286_L | 1.011 | 0.41 |
| 53_V | 100_I | 1.010 | 0.41 |
| 21_L | 42_K | 1.009 | 0.41 |
| 39_F | 109_H | 1.008 | 0.41 |
| 36_S | 85_K | 1.007 | 0.41 |
| 5_I | 8_L | 1.007 | 0.41 |
| 190_A | 209_G | 1.005 | 0.40 |
| 244_N | 252_L | 1.004 | 0.40 |
| 188_V | 210_A | 1.003 | 0.40 |
| 195_D | 294_I | 1.001 | 0.40 |
| 5_I | 9_D | 1.001 | 0.40 |
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
- Text file of contact predictions (all 3L/2 predictions)
- Generate restraints for ROSETTA Structure Modeling
- Import to GREMLIN BETA - features includes ability to upload PDB and latest P(contact) calculation based on eLife 2015 fitting to PDB data.
GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
| PDB | M | Cov | P(%) | HHΔ | |
| 3doaA | 1 | 0.7613 | 100 | 0.568 | Contact Map |
| 1ee8A | 2 | 0.7 | 97 | 0.923 | Contact Map |
| 3twlA | 1 | 0.6677 | 41.7 | 0.963 | Contact Map |
| 4mb7A | 1 | 0.6968 | 37.5 | 0.964 | Contact Map |
| 4pd2A | 1 | 0.7065 | 32.5 | 0.966 | Contact Map |
| 1k82A | 4 | 0.5903 | 29.9 | 0.966 | Contact Map |
| 3u6pA | 1 | 0.6 | 23.5 | 0.968 | Contact Map |
| 1k3xA | 1 | 0.6419 | 14.8 | 0.971 | Contact Map |
| 3duwA | 2 | 0.6677 | 10.1 | 0.973 | Contact Map |
| 3w0fA | 1 | 0.6742 | 9.6 | 0.973 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)