| SMARCD1 120-515 |
| ID: | 1493658554 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 396 (379) | ||
| Sequences: | 659 (370.8) | ||
| Seq/Len: | 1.739 | ||
| Nf(neff/√len): | 19.0 |
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: 1.739).
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 |
| 179_D | 245_L | 3.809 | 1.00 |
| 328_D | 331_G | 3.057 | 1.00 |
| 123_I | 153_V | 2.814 | 1.00 |
| 65_I | 273_I | 2.776 | 1.00 |
| 191_Q | 195_V | 2.730 | 1.00 |
| 200_L | 204_I | 2.531 | 1.00 |
| 177_K | 250_E | 2.113 | 0.99 |
| 203_Y | 221_D | 2.023 | 0.99 |
| 178_L | 186_L | 1.981 | 0.98 |
| 65_I | 114_F | 1.898 | 0.98 |
| 120_S | 140_H | 1.869 | 0.98 |
| 154_K | 157_G | 1.781 | 0.96 |
| 117_F | 275_V | 1.743 | 0.96 |
| 355_E | 358_R | 1.735 | 0.96 |
| 203_Y | 209_L | 1.716 | 0.95 |
| 35_E | 39_D | 1.680 | 0.95 |
| 118_F | 167_L | 1.656 | 0.94 |
| 192_T | 233_M | 1.625 | 0.93 |
| 209_L | 224_L | 1.620 | 0.93 |
| 74_A | 77_D | 1.596 | 0.92 |
| 220_C | 224_L | 1.576 | 0.92 |
| 14_L | 25_S | 1.561 | 0.91 |
| 92_V | 123_I | 1.468 | 0.87 |
| 153_V | 162_R | 1.466 | 0.87 |
| 201_W | 210_Q | 1.464 | 0.87 |
| 113_K | 149_D | 1.457 | 0.87 |
| 204_I | 278_D | 1.455 | 0.87 |
| 340_Q | 343_D | 1.444 | 0.86 |
| 33_A | 36_R | 1.429 | 0.85 |
| 93_E | 138_E | 1.427 | 0.85 |
| 209_L | 221_D | 1.420 | 0.85 |
| 115_S | 151_F | 1.417 | 0.85 |
| 88_W | 153_V | 1.411 | 0.85 |
| 141_R | 170_D | 1.401 | 0.84 |
| 92_V | 153_V | 1.397 | 0.84 |
| 193_R | 210_Q | 1.392 | 0.83 |
| 200_L | 238_I | 1.387 | 0.83 |
| 367_W | 371_A | 1.370 | 0.82 |
| 15_P | 22_V | 1.365 | 0.82 |
| 235_F | 238_I | 1.346 | 0.80 |
| 49_I | 200_L | 1.341 | 0.80 |
| 237_E | 240_Q | 1.340 | 0.80 |
| 271_Y | 275_V | 1.340 | 0.80 |
| 186_L | 327_R | 1.331 | 0.79 |
| 69_N | 87_S | 1.327 | 0.79 |
| 40_Q | 48_D | 1.308 | 0.78 |
| 258_I | 272_D | 1.307 | 0.78 |
| 235_F | 239_P | 1.303 | 0.77 |
| 29_M | 185_L | 1.296 | 0.77 |
| 11_D | 14_L | 1.296 | 0.77 |
| 167_L | 183_A | 1.290 | 0.76 |
| 352_G | 360_A | 1.290 | 0.76 |
| 93_E | 149_D | 1.288 | 0.76 |
| 314_Q | 318_Q | 1.285 | 0.76 |
| 336_W | 340_Q | 1.282 | 0.76 |
| 119_K | 193_R | 1.272 | 0.75 |
| 273_I | 279_D | 1.268 | 0.75 |
| 123_I | 133_D | 1.263 | 0.74 |
| 302_D | 305_I | 1.263 | 0.74 |
| 86_A | 110_Q | 1.249 | 0.73 |
| 63_L | 163_C | 1.248 | 0.73 |
| 125_L | 163_C | 1.243 | 0.73 |
| 174_P | 193_R | 1.242 | 0.72 |
| 296_Q | 300_T | 1.239 | 0.72 |
| 90_L | 165_V | 1.230 | 0.71 |
| 205_K | 228_F | 1.226 | 0.71 |
| 281_L | 285_M | 1.224 | 0.71 |
| 41_T | 119_K | 1.221 | 0.71 |
| 357_E | 363_Y | 1.214 | 0.70 |
| 201_W | 340_Q | 1.209 | 0.70 |
| 142_T | 147_E | 1.206 | 0.69 |
| 91_R | 113_K | 1.205 | 0.69 |
| 58_K | 278_D | 1.203 | 0.69 |
| 217_F | 222_K | 1.197 | 0.68 |
| 243_H | 322_M | 1.194 | 0.68 |
| 93_E | 96_L | 1.193 | 0.68 |
| 221_D | 224_L | 1.191 | 0.68 |
| 203_Y | 339_S | 1.187 | 0.68 |
| 178_L | 201_W | 1.186 | 0.67 |
| 86_A | 218_V | 1.183 | 0.67 |
| 165_V | 254_I | 1.179 | 0.67 |
| 379_K | 382_Q | 1.176 | 0.66 |
| 36_R | 46_R | 1.169 | 0.66 |
| 155_R | 173_P | 1.168 | 0.66 |
| 28_Y | 45_K | 1.165 | 0.65 |
| 38_L | 101_A | 1.163 | 0.65 |
| 342_R | 359_R | 1.159 | 0.65 |
| 287_S | 290_L | 1.157 | 0.65 |
| 312_I | 316_K | 1.155 | 0.64 |
| 327_R | 335_D | 1.155 | 0.64 |
| 201_W | 235_F | 1.153 | 0.64 |
| 94_G | 97_L | 1.147 | 0.64 |
| 71_F | 260_V | 1.143 | 0.63 |
| 31_L | 39_D | 1.141 | 0.63 |
| 31_L | 35_E | 1.141 | 0.63 |
| 87_S | 154_K | 1.140 | 0.63 |
| 88_W | 155_R | 1.138 | 0.63 |
| 182_L | 196_I | 1.136 | 0.63 |
| 28_Y | 309_I | 1.135 | 0.62 |
| 273_I | 276_E | 1.135 | 0.62 |
| 210_Q | 218_V | 1.134 | 0.62 |
| 316_K | 320_E | 1.129 | 0.62 |
| 36_R | 79_E | 1.126 | 0.62 |
| 220_C | 245_L | 1.119 | 0.61 |
| 218_V | 233_M | 1.116 | 0.61 |
| 235_F | 305_I | 1.111 | 0.60 |
| 90_L | 153_V | 1.110 | 0.60 |
| 235_F | 240_Q | 1.108 | 0.60 |
| 30_D | 87_S | 1.106 | 0.59 |
| 324_S | 363_Y | 1.105 | 0.59 |
| 62_K | 67_I | 1.104 | 0.59 |
| 3_N | 6_K | 1.104 | 0.59 |
| 374_R | 377_Y | 1.103 | 0.59 |
| 363_Y | 375_Y | 1.103 | 0.59 |
| 252_I | 258_I | 1.102 | 0.59 |
| 96_L | 117_F | 1.100 | 0.59 |
| 171_Y | 249_P | 1.097 | 0.59 |
| 34_F | 49_I | 1.096 | 0.58 |
| 20_E | 30_D | 1.091 | 0.58 |
| 350_V | 354_P | 1.090 | 0.58 |
| 88_W | 157_G | 1.088 | 0.58 |
| 199_A | 242_L | 1.087 | 0.58 |
| 201_W | 332_F | 1.085 | 0.57 |
| 362_F | 365_Q | 1.085 | 0.57 |
| 25_S | 151_F | 1.082 | 0.57 |
| 373_C | 377_Y | 1.082 | 0.57 |
| 204_I | 243_H | 1.081 | 0.57 |
| 183_A | 231_Q | 1.080 | 0.57 |
| 123_I | 141_R | 1.076 | 0.56 |
| 90_L | 163_C | 1.075 | 0.56 |
| 15_P | 24_E | 1.074 | 0.56 |
| 184_R | 188_I | 1.073 | 0.56 |
| 27_A | 34_F | 1.071 | 0.56 |
| 119_K | 133_D | 1.068 | 0.55 |
| 65_I | 228_F | 1.067 | 0.55 |
| 336_W | 343_D | 1.067 | 0.55 |
| 345_K | 374_R | 1.063 | 0.55 |
| 204_I | 252_I | 1.063 | 0.55 |
| 197_I | 208_K | 1.054 | 0.54 |
| 196_I | 201_W | 1.053 | 0.54 |
| 363_Y | 368_A | 1.053 | 0.54 |
| 48_D | 371_A | 1.053 | 0.54 |
| 225_Q | 231_Q | 1.050 | 0.54 |
| 44_R | 48_D | 1.043 | 0.53 |
| 14_L | 121_L | 1.042 | 0.53 |
| 227_I | 299_A | 1.042 | 0.53 |
| 187_G | 202_Q | 1.040 | 0.53 |
| 114_F | 150_G | 1.039 | 0.52 |
| 14_L | 37_K | 1.039 | 0.52 |
| 64_R | 272_D | 1.039 | 0.52 |
| 367_W | 375_Y | 1.038 | 0.52 |
| 58_K | 165_V | 1.034 | 0.52 |
| 18_I | 40_Q | 1.033 | 0.52 |
| 11_D | 15_P | 1.029 | 0.51 |
| 160_N | 260_V | 1.028 | 0.51 |
| 214_E | 217_F | 1.027 | 0.51 |
| 326_A | 331_G | 1.025 | 0.51 |
| 216_E | 318_Q | 1.023 | 0.51 |
| 22_V | 120_S | 1.020 | 0.50 |
| 11_D | 47_L | 1.019 | 0.50 |
| 12_K | 15_P | 1.018 | 0.50 |
| 254_I | 334_N | 1.018 | 0.50 |
| 113_K | 152_Q | 1.018 | 0.50 |
| 20_E | 38_L | 1.017 | 0.50 |
| 171_Y | 225_Q | 1.016 | 0.50 |
| 333_I | 340_Q | 1.015 | 0.50 |
| 234_K | 345_K | 1.014 | 0.50 |
| 74_A | 86_A | 1.014 | 0.50 |
| 239_P | 251_P | 1.014 | 0.50 |
| 339_S | 343_D | 1.013 | 0.50 |
| 69_N | 160_N | 1.012 | 0.49 |
| 54_K | 123_I | 1.011 | 0.49 |
| 201_W | 329_P | 1.010 | 0.49 |
| 111_K | 146_Q | 1.004 | 0.49 |
| 88_W | 94_G | 1.004 | 0.49 |
| 189_H | 227_I | 1.004 | 0.49 |
| 254_I | 273_I | 1.003 | 0.49 |
| 205_K | 325_F | 1.002 | 0.48 |
| 7_K | 76_S | 1.001 | 0.48 |
| 183_A | 201_W | 1.000 | 0.48 |
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 | |
| 1uhrA | 1 | 0.2348 | 99.9 | 0.781 | Contact Map |
| 1v31A | 1 | 0.2348 | 99.9 | 0.782 | Contact Map |
| 1v32A | 1 | 0.2399 | 99.8 | 0.825 | Contact Map |
| 4ognA | 1 | 0.2298 | 96 | 0.942 | Contact Map |
| 4n5tA | 1 | 0.2045 | 95.8 | 0.943 | Contact Map |
| 3feaA | 1 | 0.1869 | 95.6 | 0.944 | Contact Map |
| 1ycqA | 1 | 0.2121 | 94.9 | 0.946 | Contact Map |
| 4lwuA | 1 | 0.1919 | 94.5 | 0.947 | Contact Map |
| 3dacM | 2 | 0.2045 | 94.4 | 0.947 | Contact Map |
| 2z5sM | 3 | 0.2121 | 93.2 | 0.95 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)