| T40 |
| ID: | 1446753498 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 349 (328) | ||
| Sequences: | 358 (216.7) | ||
| Seq/Len: | 1.091 | ||
| Nf(neff/√len): | 12.0 |
HHblits Results: (2015_06)
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: 1.091).
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 |
| 154_D | 181_Q | 2.211 | 0.98 |
| 238_K | 307_L | 1.903 | 0.95 |
| 222_S | 234_S | 1.802 | 0.92 |
| 183_V | 189_L | 1.668 | 0.88 |
| 119_T | 135_F | 1.616 | 0.85 |
| 14_R | 19_Y | 1.597 | 0.84 |
| 43_T | 156_S | 1.568 | 0.83 |
| 62_F | 310_A | 1.541 | 0.81 |
| 45_E | 96_F | 1.501 | 0.79 |
| 100_Y | 161_A | 1.494 | 0.79 |
| 18_I | 22_L | 1.490 | 0.78 |
| 12_M | 18_I | 1.477 | 0.78 |
| 83_H | 94_Y | 1.474 | 0.77 |
| 133_T | 212_A | 1.456 | 0.76 |
| 38_L | 182_A | 1.451 | 0.76 |
| 11_A | 23_S | 1.430 | 0.74 |
| 15_D | 18_I | 1.411 | 0.73 |
| 110_N | 118_S | 1.398 | 0.72 |
| 224_Q | 275_Y | 1.389 | 0.71 |
| 67_A | 161_A | 1.379 | 0.70 |
| 136_S | 163_N | 1.373 | 0.70 |
| 111_L | 183_V | 1.363 | 0.69 |
| 49_R | 322_L | 1.358 | 0.69 |
| 14_R | 331_S | 1.346 | 0.68 |
| 249_M | 269_T | 1.346 | 0.68 |
| 28_A | 286_I | 1.333 | 0.67 |
| 128_R | 153_D | 1.312 | 0.65 |
| 119_T | 128_R | 1.309 | 0.65 |
| 20_S | 23_S | 1.292 | 0.63 |
| 19_Y | 23_S | 1.290 | 0.63 |
| 182_A | 188_G | 1.284 | 0.62 |
| 247_V | 288_S | 1.276 | 0.62 |
| 14_R | 23_S | 1.272 | 0.61 |
| 19_Y | 310_A | 1.264 | 0.61 |
| 160_K | 290_G | 1.262 | 0.60 |
| 19_Y | 25_A | 1.262 | 0.60 |
| 88_G | 275_Y | 1.258 | 0.60 |
| 12_M | 23_S | 1.258 | 0.60 |
| 22_L | 27_N | 1.256 | 0.60 |
| 305_V | 327_S | 1.251 | 0.59 |
| 11_A | 14_R | 1.249 | 0.59 |
| 193_A | 208_I | 1.246 | 0.59 |
| 11_A | 19_Y | 1.246 | 0.59 |
| 334_D | 338_Q | 1.245 | 0.59 |
| 13_L | 23_S | 1.245 | 0.59 |
| 136_S | 317_T | 1.244 | 0.59 |
| 223_A | 299_R | 1.244 | 0.59 |
| 213_R | 337_E | 1.241 | 0.58 |
| 335_L | 338_Q | 1.237 | 0.58 |
| 146_F | 156_S | 1.235 | 0.58 |
| 47_I | 222_S | 1.232 | 0.58 |
| 33_R | 36_F | 1.230 | 0.57 |
| 308_T | 325_S | 1.230 | 0.57 |
| 11_A | 24_D | 1.228 | 0.57 |
| 171_L | 283_R | 1.223 | 0.57 |
| 56_L | 272_G | 1.219 | 0.56 |
| 10_L | 14_R | 1.218 | 0.56 |
| 297_E | 325_S | 1.210 | 0.56 |
| 149_E | 156_S | 1.210 | 0.56 |
| 89_E | 306_T | 1.208 | 0.55 |
| 13_L | 16_N | 1.204 | 0.55 |
| 233_T | 310_A | 1.203 | 0.55 |
| 265_K | 292_L | 1.202 | 0.55 |
| 332_D | 335_L | 1.194 | 0.54 |
| 10_L | 13_L | 1.191 | 0.54 |
| 284_A | 320_A | 1.189 | 0.54 |
| 25_A | 75_L | 1.188 | 0.53 |
| 119_T | 331_S | 1.184 | 0.53 |
| 237_K | 248_D | 1.183 | 0.53 |
| 129_T | 148_H | 1.177 | 0.52 |
| 21_S | 262_G | 1.171 | 0.52 |
| 114_E | 275_Y | 1.169 | 0.52 |
| 104_Q | 141_Q | 1.168 | 0.52 |
| 187_L | 225_L | 1.167 | 0.51 |
| 95_A | 110_N | 1.165 | 0.51 |
| 12_M | 19_Y | 1.165 | 0.51 |
| 157_A | 179_Y | 1.163 | 0.51 |
| 50_E | 154_D | 1.162 | 0.51 |
| 11_A | 18_I | 1.161 | 0.51 |
| 14_R | 17_A | 1.160 | 0.51 |
| 88_G | 114_E | 1.155 | 0.50 |
| 233_T | 243_V | 1.155 | 0.50 |
| 23_S | 26_F | 1.154 | 0.50 |
| 52_Q | 249_M | 1.152 | 0.50 |
| 42_G | 180_L | 1.151 | 0.50 |
| 262_G | 334_D | 1.151 | 0.50 |
| 56_L | 304_P | 1.151 | 0.50 |
| 94_Y | 272_G | 1.146 | 0.49 |
| 299_R | 306_T | 1.146 | 0.49 |
| 128_R | 151_L | 1.145 | 0.49 |
| 52_Q | 303_A | 1.145 | 0.49 |
| 23_S | 332_D | 1.144 | 0.49 |
| 213_R | 289_K | 1.143 | 0.49 |
| 153_D | 286_I | 1.139 | 0.49 |
| 27_N | 183_V | 1.138 | 0.49 |
| 11_A | 16_N | 1.137 | 0.49 |
| 15_D | 25_A | 1.134 | 0.48 |
| 43_T | 47_I | 1.134 | 0.48 |
| 10_L | 15_D | 1.133 | 0.48 |
| 53_R | 72_A | 1.132 | 0.48 |
| 11_A | 332_D | 1.132 | 0.48 |
| 182_A | 233_T | 1.124 | 0.47 |
| 13_L | 18_I | 1.124 | 0.47 |
| 15_D | 22_L | 1.121 | 0.47 |
| 100_Y | 128_R | 1.121 | 0.47 |
| 64_G | 83_H | 1.118 | 0.47 |
| 33_R | 183_V | 1.118 | 0.47 |
| 174_I | 194_V | 1.114 | 0.46 |
| 184_T | 189_L | 1.111 | 0.46 |
| 163_N | 189_L | 1.101 | 0.45 |
| 92_N | 233_T | 1.100 | 0.45 |
| 14_R | 18_I | 1.096 | 0.45 |
| 259_M | 330_A | 1.096 | 0.45 |
| 333_V | 337_E | 1.094 | 0.45 |
| 217_G | 241_D | 1.093 | 0.44 |
| 109_G | 242_R | 1.092 | 0.44 |
| 174_I | 222_S | 1.091 | 0.44 |
| 50_E | 290_G | 1.091 | 0.44 |
| 290_G | 314_D | 1.086 | 0.44 |
| 246_G | 292_L | 1.084 | 0.44 |
| 17_A | 23_S | 1.084 | 0.44 |
| 134_Q | 240_T | 1.083 | 0.44 |
| 40_N | 218_D | 1.081 | 0.43 |
| 18_I | 27_N | 1.080 | 0.43 |
| 16_N | 24_D | 1.080 | 0.43 |
| 51_V | 246_G | 1.077 | 0.43 |
| 80_Q | 328_I | 1.072 | 0.43 |
| 11_A | 15_D | 1.071 | 0.42 |
| 16_N | 23_S | 1.071 | 0.42 |
| 17_A | 22_L | 1.067 | 0.42 |
| 15_D | 20_S | 1.066 | 0.42 |
| 331_S | 337_E | 1.066 | 0.42 |
| 284_A | 321_K | 1.066 | 0.42 |
| 10_L | 24_D | 1.065 | 0.42 |
| 10_L | 18_I | 1.062 | 0.42 |
| 291_K | 312_D | 1.060 | 0.41 |
| 11_A | 20_S | 1.058 | 0.41 |
| 154_D | 283_R | 1.057 | 0.41 |
| 14_R | 336_Q | 1.055 | 0.41 |
| 82_S | 97_A | 1.055 | 0.41 |
| 193_A | 225_L | 1.051 | 0.41 |
| 247_V | 282_F | 1.051 | 0.41 |
| 245_A | 310_A | 1.048 | 0.40 |
| 10_L | 22_L | 1.045 | 0.40 |
| 284_A | 326_V | 1.045 | 0.40 |
| 173_G | 303_A | 1.045 | 0.40 |
| 15_D | 19_Y | 1.043 | 0.40 |
| 114_E | 143_M | 1.040 | 0.40 |
| 43_T | 218_D | 1.039 | 0.39 |
| 25_A | 76_A | 1.035 | 0.39 |
| 67_A | 149_E | 1.035 | 0.39 |
| 89_E | 317_T | 1.031 | 0.39 |
| 182_A | 312_D | 1.030 | 0.39 |
| 67_A | 205_D | 1.030 | 0.39 |
| 147_E | 307_L | 1.030 | 0.39 |
| 13_L | 21_S | 1.026 | 0.38 |
| 13_L | 19_Y | 1.025 | 0.38 |
| 254_A | 262_G | 1.024 | 0.38 |
| 43_T | 149_E | 1.023 | 0.38 |
| 163_N | 315_H | 1.023 | 0.38 |
| 75_L | 337_E | 1.022 | 0.38 |
| 255_P | 258_S | 1.022 | 0.38 |
| 92_N | 178_D | 1.022 | 0.38 |
| 83_H | 297_E | 1.020 | 0.38 |
| 144_A | 156_S | 1.019 | 0.38 |
| 17_A | 76_A | 1.017 | 0.37 |
| 129_T | 150_H | 1.016 | 0.37 |
| 12_M | 15_D | 1.014 | 0.37 |
| 126_G | 175_F | 1.013 | 0.37 |
| 244_Q | 307_L | 1.013 | 0.37 |
| 291_K | 314_D | 1.012 | 0.37 |
| 111_L | 117_L | 1.011 | 0.37 |
| 10_L | 23_S | 1.011 | 0.37 |
| 77_P | 108_Q | 1.010 | 0.37 |
| 53_R | 99_L | 1.007 | 0.37 |
| 53_R | 307_L | 1.007 | 0.37 |
| 65_L | 269_T | 1.006 | 0.37 |
| 200_L | 337_E | 1.005 | 0.36 |
| 78_L | 102_T | 1.003 | 0.36 |
| 15_D | 258_S | 1.001 | 0.36 |
| 16_N | 22_L | 1.000 | 0.36 |
| 10_L | 17_A | 1.000 | 0.36 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 4c69X | 1 | 0.7708 | 100 | 0.541 | Contact Map |
| 2x55A | 1 | 0.6934 | 43 | 0.966 | Contact Map |
| 4q35A | 1 | 0.7421 | 33.6 | 0.968 | Contact Map |
| 4rlcA | 1 | 0 | 10.1 | 0.975 | Contact Map |
| 1ormA | 1 | 0.3295 | 9.8 | 0.975 | Contact Map |
| 3qraA | 1 | 0.3524 | 9.7 | 0.975 | Contact Map |
| 2lhfA | 1 | 0.4642 | 8.4 | 0.976 | Contact Map |
| 2v4nA | 1 | 0.4556 | 8.3 | 0.976 | Contact Map |
| 4e1tA | 1 | 0.6218 | 6.6 | 0.977 | Contact Map |
| 4tp9F | 1 | 0.4585 | 5 | 0.978 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)