| 1B65A |
| ID: | 1411598498 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 367 (355) | ||
| Sequences: | 595 (377.6) | ||
| Seq/Len: | 1.676 | ||
| Nf(neff/√len): | 20.0 |
HHblits Results: (2013_03)
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: 1.676).
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 |
| 21_I | 204_G | 3.684 | 1.00 |
| 137_T | 208_Q | 3.319 | 1.00 |
| 53_A | 96_V | 2.863 | 1.00 |
| 86_E | 259_K | 2.781 | 1.00 |
| 141_A | 346_L | 2.703 | 1.00 |
| 20_A | 189_T | 2.651 | 1.00 |
| 209_A | 331_A | 2.649 | 1.00 |
| 169_E | 330_N | 2.629 | 1.00 |
| 202_T | 250_D | 2.538 | 1.00 |
| 243_I | 328_V | 2.416 | 1.00 |
| 69_G | 259_K | 2.384 | 1.00 |
| 262_A | 286_A | 2.213 | 0.99 |
| 171_N | 336_E | 2.188 | 0.99 |
| 194_V | 200_S | 2.155 | 0.99 |
| 112_R | 152_E | 2.070 | 0.99 |
| 205_A | 247_L | 2.061 | 0.99 |
| 96_V | 106_A | 2.060 | 0.99 |
| 337_D | 349_Q | 2.054 | 0.99 |
| 179_I | 348_V | 2.018 | 0.99 |
| 261_L | 316_V | 2.000 | 0.98 |
| 167_V | 189_T | 1.962 | 0.98 |
| 96_V | 155_V | 1.943 | 0.98 |
| 251_L | 316_V | 1.876 | 0.97 |
| 245_V | 324_V | 1.875 | 0.97 |
| 33_T | 176_T | 1.848 | 0.97 |
| 247_L | 320_A | 1.825 | 0.97 |
| 79_M | 135_A | 1.807 | 0.97 |
| 339_G | 347_L | 1.805 | 0.96 |
| 24_V | 204_G | 1.761 | 0.96 |
| 180_T | 209_A | 1.760 | 0.96 |
| 20_A | 167_V | 1.759 | 0.96 |
| 32_Q | 154_D | 1.750 | 0.96 |
| 31_F | 172_C | 1.736 | 0.95 |
| 31_F | 187_T | 1.714 | 0.95 |
| 205_A | 324_V | 1.712 | 0.95 |
| 248_A | 287_F | 1.620 | 0.93 |
| 116_D | 156_R | 1.619 | 0.93 |
| 18_Y | 165_G | 1.611 | 0.92 |
| 135_A | 244_I | 1.592 | 0.92 |
| 181_Y | 211_H | 1.584 | 0.91 |
| 48_R | 338_M | 1.571 | 0.91 |
| 245_V | 284_F | 1.565 | 0.91 |
| 192_R | 241_G | 1.555 | 0.90 |
| 24_V | 202_T | 1.555 | 0.90 |
| 153_A | 157_K | 1.541 | 0.90 |
| 99_N | 145_I | 1.540 | 0.90 |
| 113_W | 159_L | 1.539 | 0.90 |
| 131_M | 138_Y | 1.532 | 0.90 |
| 330_N | 334_A | 1.526 | 0.89 |
| 57_H | 66_V | 1.485 | 0.88 |
| 223_P | 228_M | 1.484 | 0.88 |
| 151_T | 154_D | 1.478 | 0.87 |
| 56_P | 287_F | 1.466 | 0.87 |
| 195_E | 200_S | 1.461 | 0.86 |
| 176_T | 338_M | 1.440 | 0.85 |
| 34_I | 47_A | 1.412 | 0.84 |
| 88_G | 131_M | 1.410 | 0.84 |
| 84_W | 88_G | 1.404 | 0.83 |
| 80_T | 132_P | 1.396 | 0.83 |
| 18_Y | 164_S | 1.394 | 0.83 |
| 341_T | 344_D | 1.394 | 0.83 |
| 107_H | 132_P | 1.386 | 0.82 |
| 20_A | 165_G | 1.379 | 0.82 |
| 78_E | 131_M | 1.372 | 0.81 |
| 80_T | 107_H | 1.367 | 0.81 |
| 109_A | 152_E | 1.361 | 0.81 |
| 239_E | 277_G | 1.358 | 0.80 |
| 113_W | 117_R | 1.342 | 0.79 |
| 88_G | 138_Y | 1.328 | 0.78 |
| 156_R | 159_L | 1.325 | 0.78 |
| 104_G | 107_H | 1.317 | 0.77 |
| 105_M | 109_A | 1.300 | 0.76 |
| 35_I | 338_M | 1.298 | 0.76 |
| 337_D | 347_L | 1.296 | 0.76 |
| 35_I | 48_R | 1.292 | 0.76 |
| 260_R | 278_N | 1.283 | 0.75 |
| 5_R | 15_T | 1.283 | 0.75 |
| 152_E | 156_R | 1.279 | 0.75 |
| 201_F | 252_P | 1.278 | 0.74 |
| 258_L | 288_S | 1.272 | 0.74 |
| 264_R | 317_Y | 1.266 | 0.73 |
| 333_I | 353_H | 1.255 | 0.73 |
| 224_V | 323_S | 1.248 | 0.72 |
| 194_V | 319_A | 1.246 | 0.72 |
| 157_K | 161_N | 1.242 | 0.71 |
| 105_M | 108_H | 1.238 | 0.71 |
| 48_R | 176_T | 1.227 | 0.70 |
| 106_A | 278_N | 1.226 | 0.70 |
| 205_A | 323_S | 1.211 | 0.69 |
| 91_F | 133_V | 1.208 | 0.68 |
| 16_G | 19_N | 1.206 | 0.68 |
| 84_W | 138_Y | 1.205 | 0.68 |
| 66_V | 258_L | 1.187 | 0.66 |
| 269_I | 324_V | 1.179 | 0.66 |
| 253_L | 316_V | 1.178 | 0.66 |
| 98_T | 102_G | 1.178 | 0.66 |
| 113_W | 160_D | 1.175 | 0.65 |
| 360_L | 363_Y | 1.170 | 0.65 |
| 257_Q | 310_D | 1.170 | 0.65 |
| 178_M | 208_Q | 1.166 | 0.64 |
| 104_G | 132_P | 1.165 | 0.64 |
| 115_V | 146_N | 1.164 | 0.64 |
| 257_Q | 283_I | 1.155 | 0.63 |
| 217_L | 332_M | 1.155 | 0.63 |
| 112_R | 148_F | 1.152 | 0.63 |
| 194_V | 199_R | 1.151 | 0.63 |
| 216_W | 318_L | 1.149 | 0.63 |
| 3_R | 169_E | 1.148 | 0.63 |
| 109_A | 156_R | 1.145 | 0.62 |
| 101_H | 146_N | 1.144 | 0.62 |
| 55_L | 159_L | 1.143 | 0.62 |
| 76_N | 131_M | 1.142 | 0.62 |
| 91_F | 159_L | 1.139 | 0.62 |
| 171_N | 335_A | 1.138 | 0.62 |
| 78_E | 138_Y | 1.137 | 0.62 |
| 192_R | 252_P | 1.134 | 0.61 |
| 267_I | 321_V | 1.123 | 0.60 |
| 69_G | 258_L | 1.123 | 0.60 |
| 203_I | 251_L | 1.123 | 0.60 |
| 105_M | 152_E | 1.122 | 0.60 |
| 70_V | 82_T | 1.112 | 0.59 |
| 193_V | 202_T | 1.110 | 0.59 |
| 169_E | 189_T | 1.107 | 0.58 |
| 1_K | 353_H | 1.096 | 0.57 |
| 244_I | 285_I | 1.094 | 0.57 |
| 268_G | 321_V | 1.093 | 0.57 |
| 88_G | 256_H | 1.088 | 0.56 |
| 27_V | 205_A | 1.087 | 0.56 |
| 270_G | 282_D | 1.086 | 0.56 |
| 153_A | 285_I | 1.084 | 0.56 |
| 35_I | 176_T | 1.076 | 0.55 |
| 53_A | 106_A | 1.069 | 0.54 |
| 30_G | 158_A | 1.065 | 0.54 |
| 73_F | 266_S | 1.065 | 0.54 |
| 80_T | 348_V | 1.062 | 0.54 |
| 51_V | 273_G | 1.062 | 0.54 |
| 73_F | 276_G | 1.057 | 0.53 |
| 227_H | 359_V | 1.055 | 0.53 |
| 78_E | 88_G | 1.052 | 0.53 |
| 59_Q | 64_V | 1.050 | 0.52 |
| 54_I | 159_L | 1.048 | 0.52 |
| 249_T | 252_P | 1.046 | 0.52 |
| 33_T | 172_C | 1.046 | 0.52 |
| 169_E | 326_E | 1.041 | 0.52 |
| 1_K | 334_A | 1.039 | 0.51 |
| 182_G | 213_Q | 1.039 | 0.51 |
| 27_V | 287_F | 1.036 | 0.51 |
| 49_S | 95_V | 1.034 | 0.51 |
| 65_P | 130_I | 1.032 | 0.51 |
| 20_A | 169_E | 1.031 | 0.50 |
| 84_W | 92_L | 1.031 | 0.50 |
| 2_P | 7_L | 1.029 | 0.50 |
| 326_E | 330_N | 1.025 | 0.50 |
| 23_D | 191_S | 1.025 | 0.50 |
| 32_Q | 109_A | 1.023 | 0.50 |
| 115_V | 149_P | 1.022 | 0.49 |
| 137_T | 178_M | 1.020 | 0.49 |
| 282_D | 320_A | 1.018 | 0.49 |
| 109_A | 159_L | 1.018 | 0.49 |
| 76_N | 88_G | 1.017 | 0.49 |
| 267_I | 270_G | 1.016 | 0.49 |
| 88_G | 92_L | 1.016 | 0.49 |
| 102_G | 108_H | 1.016 | 0.49 |
| 28_G | 323_S | 1.014 | 0.49 |
| 141_A | 340_G | 1.011 | 0.48 |
| 269_I | 282_D | 1.009 | 0.48 |
| 4_A | 9_L | 1.008 | 0.48 |
| 225_G | 228_M | 1.008 | 0.48 |
| 178_M | 244_I | 1.008 | 0.48 |
| 250_D | 286_A | 1.002 | 0.47 |
| 108_H | 148_F | 1.001 | 0.47 |
| 187_T | 208_Q | 1.001 | 0.47 |
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 | |
| 1b65A | 6 | 0.9891 | 100 | 0.074 | Contact Map |
| 3n2wA | 4 | 0.9619 | 100 | 0.106 | Contact Map |
| 2drhA | 4 | 0.9591 | 100 | 0.12 | Contact Map |
| 4iheA | 2 | 0.8256 | 100 | 0.291 | Contact Map |
| 3axgA | 15 | 0.7956 | 100 | 0.358 | Contact Map |
| 1vraB | 1 | 0.327 | 85.8 | 0.963 | Contact Map |
| 2v4iB | 4 | 0.2943 | 57.2 | 0.971 | Contact Map |
| 3it4B | 2 | 0.3188 | 46.8 | 0.973 | Contact Map |
| 4pwwA | 1 | 0.1744 | 3.2 | 0.984 | Contact Map |
| 2qveA | 2 | 0.3215 | 3 | 0.985 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)