| 3ncy |
| ID: | 1408344538 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 432 (417) | ||
| Sequences: | 11800 (7718.4) | ||
| Seq/Len: | 28.297 | ||
| Nf(neff/√len): | 378.0 |
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: 28.297).
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 |
| 304_I | 316_A | 3.907 | 1.00 |
| 296_A | 306_A | 3.702 | 1.00 |
| 128_V | 322_G | 3.580 | 1.00 |
| 160_G | 236_A | 3.335 | 1.00 |
| 41_I | 227_A | 3.089 | 1.00 |
| 213_R | 217_I | 3.017 | 1.00 |
| 307_R | 316_A | 2.742 | 1.00 |
| 65_Y | 298_D | 2.742 | 1.00 |
| 319_L | 323_V | 2.658 | 1.00 |
| 81_N | 295_A | 2.643 | 1.00 |
| 365_L | 369_G | 2.640 | 1.00 |
| 206_G | 297_D | 2.599 | 1.00 |
| 208_V | 214_N | 2.595 | 1.00 |
| 210_N | 213_R | 2.501 | 1.00 |
| 299_G | 303_P | 2.466 | 1.00 |
| 207_V | 290_Q | 2.397 | 1.00 |
| 53_K | 367_G | 2.387 | 1.00 |
| 264_T | 268_I | 2.364 | 1.00 |
| 293_K | 297_D | 2.357 | 1.00 |
| 50_V | 360_C | 2.348 | 1.00 |
| 357_L | 386_F | 2.297 | 1.00 |
| 69_R | 77_G | 2.182 | 1.00 |
| 360_C | 385_A | 2.159 | 1.00 |
| 121_V | 330_F | 2.098 | 1.00 |
| 304_I | 307_R | 2.071 | 1.00 |
| 245_A | 259_M | 2.031 | 1.00 |
| 7_T | 221_G | 2.004 | 1.00 |
| 305_F | 320_I | 1.998 | 1.00 |
| 136_K | 140_R | 1.990 | 1.00 |
| 85_W | 321_V | 1.982 | 1.00 |
| 69_R | 74_P | 1.981 | 1.00 |
| 120_C | 329_Q | 1.956 | 1.00 |
| 158_V | 162_F | 1.951 | 1.00 |
| 128_V | 318_L | 1.946 | 1.00 |
| 309_N | 315_V | 1.946 | 1.00 |
| 242_P | 245_A | 1.936 | 1.00 |
| 125_W | 326_T | 1.931 | 1.00 |
| 132_I | 319_L | 1.883 | 1.00 |
| 132_I | 315_V | 1.864 | 1.00 |
| 131_N | 282_G | 1.847 | 1.00 |
| 121_V | 326_T | 1.837 | 1.00 |
| 150_L | 154_V | 1.834 | 1.00 |
| 365_L | 368_H | 1.831 | 1.00 |
| 3_L | 221_G | 1.824 | 1.00 |
| 72_F | 361_A | 1.810 | 1.00 |
| 42_I | 46_A | 1.764 | 1.00 |
| 73_G | 76_L | 1.750 | 1.00 |
| 210_N | 217_I | 1.743 | 1.00 |
| 72_F | 365_L | 1.728 | 1.00 |
| 129_L | 133_V | 1.724 | 1.00 |
| 217_I | 221_G | 1.713 | 1.00 |
| 3_L | 214_N | 1.706 | 1.00 |
| 309_N | 313_T | 1.705 | 1.00 |
| 383_F | 387_V | 1.684 | 1.00 |
| 3_L | 7_T | 1.681 | 1.00 |
| 204_A | 286_L | 1.676 | 1.00 |
| 211_P | 216_P | 1.657 | 1.00 |
| 220_I | 224_L | 1.634 | 1.00 |
| 68_A | 80_T | 1.632 | 1.00 |
| 292_A | 301_F | 1.622 | 1.00 |
| 80_T | 358_Y | 1.603 | 1.00 |
| 36_G | 187_T | 1.601 | 1.00 |
| 117_T | 121_V | 1.593 | 1.00 |
| 48_S | 223_V | 1.562 | 1.00 |
| 42_I | 384_V | 1.548 | 1.00 |
| 96_V | 281_L | 1.538 | 1.00 |
| 292_A | 317_G | 1.508 | 1.00 |
| 316_A | 320_I | 1.504 | 1.00 |
| 6_V | 208_V | 1.502 | 1.00 |
| 53_K | 56_S | 1.499 | 1.00 |
| 288_A | 321_V | 1.485 | 1.00 |
| 255_D | 259_M | 1.459 | 1.00 |
| 72_F | 76_L | 1.457 | 1.00 |
| 68_A | 358_Y | 1.453 | 1.00 |
| 289_G | 318_L | 1.451 | 1.00 |
| 78_Y | 82_V | 1.450 | 1.00 |
| 147_V | 151_V | 1.449 | 1.00 |
| 121_V | 125_W | 1.438 | 1.00 |
| 92_N | 325_M | 1.436 | 1.00 |
| 124_L | 325_M | 1.435 | 1.00 |
| 210_N | 214_N | 1.424 | 1.00 |
| 407_T | 411_I | 1.422 | 1.00 |
| 127_F | 281_L | 1.416 | 1.00 |
| 40_T | 191_T | 1.412 | 1.00 |
| 224_L | 228_V | 1.393 | 0.99 |
| 380_L | 384_V | 1.390 | 0.99 |
| 357_L | 361_A | 1.384 | 0.99 |
| 61_P | 206_G | 1.383 | 0.99 |
| 255_D | 258_R | 1.380 | 0.99 |
| 262_G | 265_A | 1.376 | 0.99 |
| 10_V | 222_G | 1.374 | 0.99 |
| 214_N | 217_I | 1.364 | 0.99 |
| 55_S | 67_Y | 1.363 | 0.99 |
| 112_D | 115_V | 1.355 | 0.99 |
| 47_L | 360_C | 1.346 | 0.99 |
| 125_W | 322_G | 1.338 | 0.99 |
| 303_P | 306_A | 1.335 | 0.99 |
| 293_K | 308_V | 1.327 | 0.99 |
| 132_I | 313_T | 1.326 | 0.99 |
| 71_C | 362_A | 1.325 | 0.99 |
| 2_G | 5_P | 1.320 | 0.99 |
| 249_S | 255_D | 1.311 | 0.99 |
| 65_Y | 294_A | 1.303 | 0.99 |
| 48_S | 219_T | 1.302 | 0.99 |
| 62_G | 65_Y | 1.301 | 0.99 |
| 41_I | 195_F | 1.301 | 0.99 |
| 128_V | 319_L | 1.293 | 0.99 |
| 387_V | 391_W | 1.290 | 0.99 |
| 323_V | 327_I | 1.290 | 0.99 |
| 3_L | 217_I | 1.289 | 0.99 |
| 205_A | 215_V | 1.288 | 0.99 |
| 196_I | 352_T | 1.275 | 0.99 |
| 261_L | 265_A | 1.271 | 0.99 |
| 11_S | 225_I | 1.264 | 0.99 |
| 82_V | 301_F | 1.262 | 0.99 |
| 50_V | 382_T | 1.262 | 0.99 |
| 38_L | 231_V | 1.261 | 0.99 |
| 38_L | 42_I | 1.248 | 0.99 |
| 316_A | 319_L | 1.240 | 0.98 |
| 311_A | 315_V | 1.240 | 0.98 |
| 151_V | 155_G | 1.237 | 0.98 |
| 308_V | 312_G | 1.234 | 0.98 |
| 199_E | 203_V | 1.233 | 0.98 |
| 4_I | 8_L | 1.230 | 0.98 |
| 406_V | 410_V | 1.230 | 0.98 |
| 303_P | 307_R | 1.226 | 0.98 |
| 156_I | 257_A | 1.226 | 0.98 |
| 128_V | 132_I | 1.215 | 0.98 |
| 66_A | 70_R | 1.213 | 0.98 |
| 5_P | 143_A | 1.209 | 0.98 |
| 95_M | 98_I | 1.208 | 0.98 |
| 152_P | 272_C | 1.207 | 0.98 |
| 14_I | 226_A | 1.204 | 0.98 |
| 103_L | 119_T | 1.203 | 0.98 |
| 389_C | 392_A | 1.202 | 0.98 |
| 51_Y | 64_S | 1.201 | 0.98 |
| 35_Y | 184_I | 1.196 | 0.98 |
| 46_A | 384_V | 1.194 | 0.98 |
| 118_L | 122_A | 1.187 | 0.98 |
| 49_M | 220_I | 1.187 | 0.98 |
| 32_I | 184_I | 1.186 | 0.98 |
| 60_S | 66_A | 1.186 | 0.98 |
| 361_A | 365_L | 1.181 | 0.98 |
| 135_P | 286_L | 1.179 | 0.98 |
| 141_V | 145_A | 1.178 | 0.98 |
| 142_Q | 282_G | 1.175 | 0.98 |
| 309_N | 312_G | 1.173 | 0.98 |
| 133_V | 311_A | 1.172 | 0.98 |
| 99_G | 274_A | 1.166 | 0.97 |
| 367_G | 371_F | 1.160 | 0.97 |
| 58_D | 70_R | 1.153 | 0.97 |
| 124_L | 322_G | 1.144 | 0.97 |
| 307_R | 315_V | 1.134 | 0.97 |
| 242_P | 259_M | 1.131 | 0.97 |
| 96_V | 124_L | 1.130 | 0.97 |
| 45_L | 49_M | 1.124 | 0.97 |
| 285_T | 289_G | 1.123 | 0.97 |
| 155_G | 159_F | 1.120 | 0.96 |
| 132_I | 309_N | 1.118 | 0.96 |
| 154_V | 158_V | 1.112 | 0.96 |
| 404_S | 411_I | 1.109 | 0.96 |
| 115_V | 118_L | 1.108 | 0.96 |
| 382_T | 386_F | 1.106 | 0.96 |
| 7_T | 225_I | 1.098 | 0.96 |
| 52_A | 56_S | 1.097 | 0.96 |
| 65_Y | 81_N | 1.092 | 0.96 |
| 289_G | 317_G | 1.092 | 0.96 |
| 371_F | 375_R | 1.089 | 0.96 |
| 54_M | 363_L | 1.088 | 0.96 |
| 85_W | 292_A | 1.087 | 0.96 |
| 84_Y | 88_C | 1.085 | 0.96 |
| 46_A | 50_V | 1.085 | 0.96 |
| 160_G | 240_M | 1.083 | 0.96 |
| 35_Y | 38_L | 1.083 | 0.96 |
| 68_A | 362_A | 1.075 | 0.95 |
| 267_A | 271_F | 1.075 | 0.95 |
| 285_T | 322_G | 1.074 | 0.95 |
| 93_I | 96_V | 1.069 | 0.95 |
| 139_T | 282_G | 1.069 | 0.95 |
| 9_M | 204_A | 1.068 | 0.95 |
| 2_G | 209_K | 1.066 | 0.95 |
| 87_A | 352_T | 1.063 | 0.95 |
| 45_L | 220_I | 1.056 | 0.95 |
| 104_S | 107_F | 1.055 | 0.95 |
| 227_A | 231_V | 1.052 | 0.95 |
| 131_N | 318_L | 1.050 | 0.94 |
| 149_A | 276_G | 1.050 | 0.94 |
| 361_A | 386_F | 1.048 | 0.94 |
| 364_L | 383_F | 1.046 | 0.94 |
| 405_F | 409_M | 1.046 | 0.94 |
| 164_F | 239_G | 1.042 | 0.94 |
| 140_R | 144_V | 1.039 | 0.94 |
| 258_R | 266_G | 1.037 | 0.94 |
| 236_A | 239_G | 1.036 | 0.94 |
| 379_L | 383_F | 1.036 | 0.94 |
| 403_W | 406_V | 1.032 | 0.94 |
| 68_A | 76_L | 1.030 | 0.94 |
| 290_Q | 293_K | 1.027 | 0.94 |
| 130_L | 141_V | 1.027 | 0.94 |
| 157_A | 160_G | 1.018 | 0.93 |
| 34_I | 235_T | 1.016 | 0.93 |
| 62_G | 66_A | 1.015 | 0.93 |
| 363_L | 367_G | 1.013 | 0.93 |
| 232_L | 236_A | 1.010 | 0.93 |
| 216_P | 219_T | 1.009 | 0.93 |
| 207_V | 308_V | 1.002 | 0.92 |
| 3_L | 218_A | 1.002 | 0.92 |
| 385_A | 389_C | 1.001 | 0.92 |
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 | |
| 3l1lA | 1 | 0.9722 | 100 | 0.196 | Contact Map |
| 3giaA | 1 | 0.9606 | 100 | 0.324 | Contact Map |
| 4djkA | 2 | 0.9421 | 100 | 0.364 | Contact Map |
| 2jlnA | 1 | 0.919 | 99.6 | 0.796 | Contact Map |
| 3dh4A | 4 | 0.9468 | 98.9 | 0.861 | Contact Map |
| 2xq2A | 1 | 0.9514 | 98.8 | 0.863 | Contact Map |
| 2a65A | 1 | 0.9421 | 94.7 | 0.927 | Contact Map |
| 2wswA | 1 | 0.8148 | 91.3 | 0.935 | Contact Map |
| 4m48A | 1 | 0.9537 | 90.2 | 0.937 | Contact Map |
| 4c7rA | 3 | 0.9028 | 89.5 | 0.938 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)