| SMARCD1 120-515 |
| ID: | 1493655732 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 396 (381) | ||
| Sequences: | 463 (332.3) | ||
| Seq/Len: | 1.215 | ||
| Nf(neff/√len): | 17.0 |
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: 1.215).
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 | 3.523 | 1.00 |
| 65_I | 273_I | 3.267 | 1.00 |
| 328_D | 331_G | 3.005 | 1.00 |
| 123_I | 153_V | 2.803 | 1.00 |
| 191_Q | 195_V | 2.736 | 1.00 |
| 200_L | 204_I | 2.551 | 1.00 |
| 177_K | 250_E | 2.289 | 0.99 |
| 65_I | 114_F | 2.108 | 0.98 |
| 178_L | 186_L | 1.921 | 0.96 |
| 117_F | 275_V | 1.912 | 0.96 |
| 120_S | 140_H | 1.865 | 0.95 |
| 154_K | 157_G | 1.858 | 0.95 |
| 355_E | 358_R | 1.777 | 0.93 |
| 203_Y | 221_D | 1.751 | 0.92 |
| 192_T | 233_M | 1.737 | 0.92 |
| 92_V | 123_I | 1.695 | 0.90 |
| 35_E | 39_D | 1.688 | 0.90 |
| 203_Y | 209_L | 1.677 | 0.90 |
| 118_F | 167_L | 1.674 | 0.90 |
| 153_V | 162_R | 1.658 | 0.89 |
| 33_A | 36_R | 1.615 | 0.87 |
| 92_V | 153_V | 1.593 | 0.86 |
| 115_S | 151_F | 1.560 | 0.85 |
| 93_E | 138_E | 1.517 | 0.83 |
| 123_I | 133_D | 1.506 | 0.82 |
| 74_A | 77_D | 1.506 | 0.82 |
| 49_I | 200_L | 1.486 | 0.81 |
| 14_L | 25_S | 1.472 | 0.80 |
| 367_W | 371_A | 1.470 | 0.80 |
| 69_N | 87_S | 1.454 | 0.79 |
| 340_Q | 343_D | 1.452 | 0.79 |
| 220_C | 224_L | 1.448 | 0.78 |
| 209_L | 224_L | 1.422 | 0.77 |
| 218_V | 233_M | 1.421 | 0.77 |
| 15_P | 22_V | 1.421 | 0.77 |
| 165_V | 254_I | 1.420 | 0.76 |
| 141_R | 170_D | 1.417 | 0.76 |
| 209_L | 221_D | 1.416 | 0.76 |
| 302_D | 305_I | 1.413 | 0.76 |
| 113_K | 149_D | 1.379 | 0.73 |
| 174_P | 193_R | 1.379 | 0.73 |
| 64_R | 272_D | 1.373 | 0.73 |
| 88_W | 153_V | 1.367 | 0.73 |
| 181_R | 185_L | 1.357 | 0.72 |
| 119_K | 193_R | 1.345 | 0.71 |
| 86_A | 218_V | 1.335 | 0.70 |
| 90_L | 165_V | 1.332 | 0.70 |
| 352_G | 360_A | 1.324 | 0.69 |
| 28_Y | 45_K | 1.322 | 0.69 |
| 314_Q | 318_Q | 1.321 | 0.69 |
| 71_F | 260_V | 1.318 | 0.69 |
| 93_E | 149_D | 1.307 | 0.68 |
| 157_G | 297_E | 1.305 | 0.67 |
| 171_Y | 249_P | 1.305 | 0.67 |
| 125_L | 163_C | 1.302 | 0.67 |
| 142_T | 147_E | 1.291 | 0.66 |
| 167_L | 183_A | 1.286 | 0.66 |
| 11_D | 14_L | 1.283 | 0.66 |
| 357_E | 363_Y | 1.280 | 0.65 |
| 88_W | 155_R | 1.279 | 0.65 |
| 88_W | 157_G | 1.271 | 0.64 |
| 271_Y | 275_V | 1.271 | 0.64 |
| 58_K | 278_D | 1.250 | 0.63 |
| 36_R | 46_R | 1.241 | 0.62 |
| 155_R | 173_P | 1.239 | 0.62 |
| 65_I | 228_F | 1.239 | 0.62 |
| 342_R | 359_R | 1.237 | 0.61 |
| 173_P | 211_D | 1.236 | 0.61 |
| 63_L | 325_F | 1.235 | 0.61 |
| 193_R | 210_Q | 1.231 | 0.61 |
| 41_T | 119_K | 1.228 | 0.61 |
| 31_L | 35_E | 1.226 | 0.60 |
| 336_W | 340_Q | 1.223 | 0.60 |
| 86_A | 110_Q | 1.223 | 0.60 |
| 235_F | 305_I | 1.220 | 0.60 |
| 201_W | 332_F | 1.212 | 0.59 |
| 201_W | 340_Q | 1.211 | 0.59 |
| 91_R | 113_K | 1.208 | 0.59 |
| 40_Q | 48_D | 1.205 | 0.58 |
| 281_L | 285_M | 1.201 | 0.58 |
| 114_F | 150_G | 1.183 | 0.56 |
| 324_S | 363_Y | 1.182 | 0.56 |
| 208_K | 273_I | 1.169 | 0.55 |
| 327_R | 335_D | 1.166 | 0.55 |
| 27_A | 34_F | 1.161 | 0.54 |
| 319_R | 323_L | 1.153 | 0.53 |
| 58_K | 165_V | 1.153 | 0.53 |
| 312_I | 316_K | 1.153 | 0.53 |
| 379_K | 382_Q | 1.152 | 0.53 |
| 204_I | 278_D | 1.152 | 0.53 |
| 296_Q | 300_T | 1.150 | 0.53 |
| 350_V | 354_P | 1.148 | 0.53 |
| 96_L | 117_F | 1.144 | 0.52 |
| 38_L | 101_A | 1.140 | 0.52 |
| 160_N | 260_V | 1.139 | 0.52 |
| 93_E | 96_L | 1.139 | 0.52 |
| 243_H | 322_M | 1.138 | 0.52 |
| 67_I | 118_F | 1.136 | 0.52 |
| 18_I | 40_Q | 1.134 | 0.51 |
| 173_P | 205_K | 1.130 | 0.51 |
| 339_S | 343_D | 1.128 | 0.51 |
| 321_F | 344_L | 1.125 | 0.51 |
| 30_D | 87_S | 1.123 | 0.50 |
| 31_L | 39_D | 1.122 | 0.50 |
| 90_L | 163_C | 1.122 | 0.50 |
| 48_D | 371_A | 1.121 | 0.50 |
| 305_I | 319_R | 1.120 | 0.50 |
| 29_M | 185_L | 1.119 | 0.50 |
| 63_L | 163_C | 1.117 | 0.50 |
| 258_I | 272_D | 1.116 | 0.50 |
| 11_D | 47_L | 1.114 | 0.50 |
| 336_W | 343_D | 1.114 | 0.50 |
| 3_N | 6_K | 1.112 | 0.49 |
| 157_G | 165_V | 1.110 | 0.49 |
| 165_V | 224_L | 1.107 | 0.49 |
| 14_L | 37_K | 1.104 | 0.49 |
| 363_Y | 375_Y | 1.104 | 0.49 |
| 315_L | 318_Q | 1.104 | 0.49 |
| 28_Y | 309_I | 1.102 | 0.48 |
| 171_Y | 225_Q | 1.098 | 0.48 |
| 62_K | 67_I | 1.098 | 0.48 |
| 15_P | 24_E | 1.097 | 0.48 |
| 345_K | 374_R | 1.095 | 0.48 |
| 5_K | 8_K | 1.094 | 0.48 |
| 163_C | 254_I | 1.094 | 0.48 |
| 90_L | 153_V | 1.088 | 0.47 |
| 204_I | 252_I | 1.087 | 0.47 |
| 367_W | 375_Y | 1.087 | 0.47 |
| 67_I | 146_Q | 1.086 | 0.47 |
| 287_S | 290_L | 1.083 | 0.46 |
| 28_Y | 321_F | 1.082 | 0.46 |
| 158_D | 254_I | 1.077 | 0.46 |
| 306_H | 326_A | 1.075 | 0.46 |
| 242_L | 349_D | 1.074 | 0.46 |
| 234_K | 345_K | 1.073 | 0.46 |
| 362_F | 365_Q | 1.072 | 0.45 |
| 235_F | 238_I | 1.070 | 0.45 |
| 94_G | 97_L | 1.068 | 0.45 |
| 196_I | 238_I | 1.066 | 0.45 |
| 219_I | 232_R | 1.064 | 0.45 |
| 20_E | 30_D | 1.063 | 0.45 |
| 153_V | 187_G | 1.060 | 0.44 |
| 349_D | 353_N | 1.057 | 0.44 |
| 186_L | 194_P | 1.056 | 0.44 |
| 164_T | 258_I | 1.056 | 0.44 |
| 363_Y | 368_A | 1.056 | 0.44 |
| 160_N | 259_S | 1.054 | 0.44 |
| 12_K | 15_P | 1.054 | 0.44 |
| 113_K | 152_Q | 1.054 | 0.44 |
| 63_L | 224_L | 1.050 | 0.43 |
| 373_C | 377_Y | 1.048 | 0.43 |
| 374_R | 377_Y | 1.047 | 0.43 |
| 119_K | 133_D | 1.046 | 0.43 |
| 98_E | 260_V | 1.041 | 0.42 |
| 294_S | 298_I | 1.040 | 0.42 |
| 160_N | 261_D | 1.040 | 0.42 |
| 69_N | 160_N | 1.039 | 0.42 |
| 105_Y | 108_T | 1.039 | 0.42 |
| 150_G | 312_I | 1.037 | 0.42 |
| 316_K | 320_E | 1.036 | 0.42 |
| 25_S | 151_F | 1.035 | 0.42 |
| 221_D | 224_L | 1.034 | 0.42 |
| 199_A | 242_L | 1.033 | 0.42 |
| 11_D | 15_P | 1.031 | 0.41 |
| 90_L | 192_T | 1.031 | 0.41 |
| 326_A | 331_G | 1.030 | 0.41 |
| 42_I | 50_Q | 1.027 | 0.41 |
| 88_W | 150_G | 1.026 | 0.41 |
| 185_L | 254_I | 1.023 | 0.41 |
| 20_E | 38_L | 1.023 | 0.41 |
| 87_S | 154_K | 1.021 | 0.41 |
| 137_V | 199_A | 1.021 | 0.41 |
| 66_F | 95_R | 1.017 | 0.40 |
| 74_A | 86_A | 1.015 | 0.40 |
| 237_E | 303_N | 1.014 | 0.40 |
| 243_H | 309_I | 1.013 | 0.40 |
| 44_R | 48_D | 1.010 | 0.40 |
| 150_G | 187_G | 1.008 | 0.39 |
| 260_V | 276_E | 1.007 | 0.39 |
| 14_L | 108_T | 1.007 | 0.39 |
| 189_H | 250_E | 1.006 | 0.39 |
| 9_M | 15_P | 1.006 | 0.39 |
| 87_S | 157_G | 1.003 | 0.39 |
| 7_K | 76_S | 1.001 | 0.39 |
| 91_R | 333_I | 1.000 | 0.39 |
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 | 0.789 | Contact Map |
| 1v31A | 1 | 0.2348 | 99.9 | 0.79 | Contact Map |
| 1v32A | 1 | 0.2399 | 99.8 | 0.837 | Contact Map |
| 4ognA | 1 | 0.2298 | 95.7 | 0.945 | Contact Map |
| 4n5tA | 1 | 0.2045 | 95.3 | 0.947 | Contact Map |
| 3feaA | 1 | 0.1869 | 95.2 | 0.947 | Contact Map |
| 3dacM | 2 | 0.2045 | 94.1 | 0.95 | Contact Map |
| 1ycqA | 1 | 0.2121 | 93.6 | 0.951 | Contact Map |
| 4lwuA | 1 | 0.1919 | 93.3 | 0.951 | Contact Map |
| 2axiA | 1 | 0.2096 | 92 | 0.953 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)