| 3tt1 |
| ID: | 1498662164 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 498 (446) | ||
| Sequences: | 3640 (2218.9) | ||
| Seq/Len: | 8.161 | ||
| Nf(neff/√len): | 105.1 |
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: 8.161).
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 |
| 216_D | 219_N | 3.691 | 1.00 |
| 219_N | 223_T | 3.550 | 1.00 |
| 161_I | 378_F | 3.400 | 1.00 |
| 171_V | 374_A | 3.313 | 1.00 |
| 225_D | 228_K | 2.899 | 1.00 |
| 314_G | 339_L | 2.873 | 1.00 |
| 65_G | 72_T | 2.783 | 1.00 |
| 55_M | 253_I | 2.739 | 1.00 |
| 115_A | 337_F | 2.633 | 1.00 |
| 331_L | 334_L | 2.608 | 1.00 |
| 67_A | 75_A | 2.541 | 1.00 |
| 160_Y | 381_A | 2.486 | 1.00 |
| 1_R | 258_S | 2.428 | 1.00 |
| 218_L | 286_G | 2.325 | 1.00 |
| 66_G | 262_K | 2.284 | 1.00 |
| 170_N | 347_S | 2.270 | 1.00 |
| 203_R | 206_L | 2.263 | 1.00 |
| 26_R | 241_Q | 2.224 | 1.00 |
| 222_W | 286_G | 2.184 | 1.00 |
| 117_K | 138_F | 2.159 | 1.00 |
| 61_M | 72_T | 2.143 | 1.00 |
| 262_K | 429_R | 2.121 | 1.00 |
| 23_N | 277_N | 2.055 | 1.00 |
| 111_T | 340_F | 2.051 | 1.00 |
| 205_F | 218_L | 2.049 | 1.00 |
| 158_F | 165_I | 2.009 | 1.00 |
| 52_I | 274_A | 1.992 | 1.00 |
| 17_N | 247_S | 1.967 | 1.00 |
| 215_A | 218_L | 1.959 | 1.00 |
| 352_Q | 366_R | 1.940 | 1.00 |
| 228_K | 231_D | 1.926 | 1.00 |
| 194_F | 280_A | 1.917 | 1.00 |
| 442_V | 446_I | 1.899 | 1.00 |
| 15_A | 276_L | 1.849 | 1.00 |
| 419_G | 422_K | 1.844 | 1.00 |
| 108_E | 343_G | 1.838 | 1.00 |
| 136_K | 140_Y | 1.837 | 1.00 |
| 412_I | 417_I | 1.827 | 1.00 |
| 51_G | 246_L | 1.788 | 1.00 |
| 8_L | 12_L | 1.747 | 1.00 |
| 64_Y | 426_E | 1.720 | 1.00 |
| 15_A | 19_V | 1.715 | 1.00 |
| 201_V | 287_S | 1.704 | 1.00 |
| 68_Q | 360_D | 1.702 | 1.00 |
| 384_V | 390_S | 1.700 | 1.00 |
| 113_G | 117_K | 1.684 | 1.00 |
| 180_K | 184_R | 1.679 | 1.00 |
| 115_A | 340_F | 1.679 | 1.00 |
| 255_T | 353_P | 1.678 | 1.00 |
| 215_A | 219_N | 1.675 | 1.00 |
| 198_V | 202_I | 1.669 | 1.00 |
| 112_L | 340_F | 1.664 | 1.00 |
| 136_K | 316_I | 1.650 | 1.00 |
| 172_S | 176_R | 1.650 | 1.00 |
| 156_S | 161_I | 1.650 | 1.00 |
| 382_H | 386_F | 1.650 | 1.00 |
| 1_R | 360_D | 1.645 | 1.00 |
| 3_H | 66_G | 1.632 | 1.00 |
| 300_A | 307_K | 1.629 | 1.00 |
| 56_W | 270_G | 1.612 | 1.00 |
| 395_D | 399_G | 1.607 | 1.00 |
| 441_Y | 445_Y | 1.600 | 1.00 |
| 176_R | 184_R | 1.587 | 1.00 |
| 17_N | 349_A | 1.582 | 1.00 |
| 161_I | 168_F | 1.567 | 1.00 |
| 380_S | 383_L | 1.564 | 1.00 |
| 157_L | 385_M | 1.562 | 1.00 |
| 198_V | 283_I | 1.555 | 1.00 |
| 337_F | 341_F | 1.536 | 1.00 |
| 67_A | 71_G | 1.526 | 1.00 |
| 188_I | 192_T | 1.517 | 1.00 |
| 195_I | 199_F | 1.517 | 1.00 |
| 168_F | 172_S | 1.508 | 1.00 |
| 418_F | 426_E | 1.497 | 1.00 |
| 277_N | 281_E | 1.491 | 1.00 |
| 38_A | 226_F | 1.491 | 1.00 |
| 428_N | 435_V | 1.485 | 0.99 |
| 221_L | 286_G | 1.480 | 0.99 |
| 356_A | 360_D | 1.473 | 0.99 |
| 116_I | 159_A | 1.462 | 0.99 |
| 56_W | 266_I | 1.461 | 0.99 |
| 156_S | 385_M | 1.456 | 0.99 |
| 256_Y | 349_A | 1.449 | 0.99 |
| 113_G | 155_P | 1.447 | 0.99 |
| 102_I | 380_S | 1.439 | 0.99 |
| 74_P | 87_K | 1.434 | 0.99 |
| 42_P | 229_L | 1.429 | 0.99 |
| 291_P | 321_I | 1.405 | 0.99 |
| 101_A | 347_S | 1.400 | 0.99 |
| 100_V | 250_F | 1.398 | 0.99 |
| 137_E | 141_S | 1.397 | 0.99 |
| 40_M | 282_V | 1.385 | 0.99 |
| 222_W | 282_V | 1.372 | 0.99 |
| 249_G | 407_G | 1.372 | 0.99 |
| 365_S | 368_H | 1.372 | 0.99 |
| 189_A | 341_F | 1.370 | 0.99 |
| 105_V | 160_Y | 1.367 | 0.99 |
| 47_F | 242_I | 1.367 | 0.99 |
| 391_L | 395_D | 1.360 | 0.99 |
| 168_F | 378_F | 1.345 | 0.99 |
| 408_L | 452_A | 1.339 | 0.99 |
| 440_Y | 444_R | 1.334 | 0.99 |
| 85_F | 88_I | 1.328 | 0.99 |
| 118_F | 336_F | 1.326 | 0.99 |
| 204_V | 291_P | 1.326 | 0.99 |
| 375_A | 379_F | 1.323 | 0.99 |
| 9_G | 183_E | 1.315 | 0.98 |
| 108_E | 166_T | 1.291 | 0.98 |
| 113_G | 142_Y | 1.289 | 0.98 |
| 355_I | 370_V | 1.279 | 0.98 |
| 5_A | 8_L | 1.278 | 0.98 |
| 418_F | 422_K | 1.277 | 0.98 |
| 415_F | 444_R | 1.275 | 0.98 |
| 161_I | 382_H | 1.275 | 0.98 |
| 207_L | 214_A | 1.275 | 0.98 |
| 199_F | 202_I | 1.273 | 0.98 |
| 69_G | 251_G | 1.271 | 0.98 |
| 199_F | 203_R | 1.270 | 0.98 |
| 201_V | 283_I | 1.266 | 0.98 |
| 247_S | 252_A | 1.263 | 0.98 |
| 384_V | 394_M | 1.261 | 0.98 |
| 405_F | 455_L | 1.260 | 0.98 |
| 221_L | 285_G | 1.260 | 0.98 |
| 159_A | 165_I | 1.259 | 0.98 |
| 359_E | 369_A | 1.259 | 0.98 |
| 208_E | 299_V | 1.250 | 0.98 |
| 221_L | 282_V | 1.250 | 0.98 |
| 16_G | 345_T | 1.250 | 0.98 |
| 47_F | 278_E | 1.244 | 0.98 |
| 108_E | 347_S | 1.244 | 0.98 |
| 175_I | 371_L | 1.242 | 0.98 |
| 157_L | 382_H | 1.241 | 0.98 |
| 203_R | 335_W | 1.241 | 0.98 |
| 56_W | 60_A | 1.241 | 0.98 |
| 242_I | 278_E | 1.235 | 0.97 |
| 388_N | 391_L | 1.231 | 0.97 |
| 71_G | 361_E | 1.228 | 0.97 |
| 96_I | 402_G | 1.219 | 0.97 |
| 68_Q | 71_G | 1.214 | 0.97 |
| 49_L | 53_P | 1.213 | 0.97 |
| 173_I | 344_L | 1.199 | 0.97 |
| 208_E | 212_G | 1.198 | 0.97 |
| 205_F | 214_A | 1.188 | 0.97 |
| 32_A | 295_A | 1.184 | 0.97 |
| 46_A | 239_V | 1.179 | 0.96 |
| 24_F | 339_L | 1.178 | 0.96 |
| 30_Q | 237_A | 1.175 | 0.96 |
| 379_F | 383_L | 1.174 | 0.96 |
| 371_L | 375_A | 1.167 | 0.96 |
| 5_A | 9_G | 1.165 | 0.96 |
| 208_E | 296_F | 1.163 | 0.96 |
| 208_E | 214_A | 1.163 | 0.96 |
| 393_E | 397_W | 1.161 | 0.96 |
| 426_E | 429_R | 1.161 | 0.96 |
| 63_R | 426_E | 1.157 | 0.96 |
| 275_T | 279_A | 1.153 | 0.96 |
| 351_M | 373_T | 1.151 | 0.96 |
| 26_R | 30_Q | 1.150 | 0.96 |
| 197_A | 287_S | 1.148 | 0.96 |
| 4_W | 13_A | 1.146 | 0.96 |
| 202_I | 206_L | 1.145 | 0.96 |
| 271_L | 275_T | 1.143 | 0.96 |
| 102_I | 347_S | 1.143 | 0.96 |
| 113_G | 159_A | 1.139 | 0.95 |
| 441_Y | 446_I | 1.139 | 0.95 |
| 99_V | 398_A | 1.137 | 0.95 |
| 364_L | 372_W | 1.133 | 0.95 |
| 294_V | 299_V | 1.133 | 0.95 |
| 101_A | 377_V | 1.129 | 0.95 |
| 278_E | 282_V | 1.129 | 0.95 |
| 242_I | 277_N | 1.128 | 0.95 |
| 389_K | 392_D | 1.126 | 0.95 |
| 314_G | 317_T | 1.123 | 0.95 |
| 167_M | 377_V | 1.123 | 0.95 |
| 421_D | 444_R | 1.121 | 0.95 |
| 198_V | 201_V | 1.120 | 0.95 |
| 44_I | 48_L | 1.120 | 0.95 |
| 176_R | 180_K | 1.119 | 0.95 |
| 278_E | 281_E | 1.117 | 0.95 |
| 408_L | 412_I | 1.114 | 0.95 |
| 250_F | 403_V | 1.110 | 0.95 |
| 191_P | 195_I | 1.109 | 0.94 |
| 11_I | 15_A | 1.108 | 0.94 |
| 438_I | 441_Y | 1.104 | 0.94 |
| 32_A | 294_V | 1.099 | 0.94 |
| 59_W | 273_A | 1.094 | 0.94 |
| 59_W | 257_A | 1.093 | 0.94 |
| 86_A | 413_I | 1.092 | 0.94 |
| 387_L | 391_L | 1.086 | 0.94 |
| 416_W | 444_R | 1.086 | 0.94 |
| 424_W | 440_Y | 1.082 | 0.93 |
| 295_A | 301_N | 1.077 | 0.93 |
| 23_N | 43_Y | 1.077 | 0.93 |
| 59_W | 253_I | 1.071 | 0.93 |
| 111_T | 339_L | 1.069 | 0.93 |
| 102_I | 394_M | 1.068 | 0.93 |
| 26_R | 391_L | 1.067 | 0.93 |
| 368_H | 372_W | 1.064 | 0.93 |
| 6_T | 9_G | 1.060 | 0.93 |
| 69_G | 72_T | 1.058 | 0.92 |
| 348_I | 352_Q | 1.057 | 0.92 |
| 60_A | 427_I | 1.055 | 0.92 |
| 102_I | 384_V | 1.055 | 0.92 |
| 422_K | 425_E | 1.054 | 0.92 |
| 30_Q | 241_Q | 1.042 | 0.92 |
| 10_L | 14_M | 1.041 | 0.92 |
| 208_E | 217_G | 1.041 | 0.92 |
| 322_F | 336_F | 1.038 | 0.92 |
| 241_Q | 245_T | 1.038 | 0.92 |
| 57_I | 439_Y | 1.036 | 0.91 |
| 92_F | 406_F | 1.035 | 0.91 |
| 69_G | 254_I | 1.031 | 0.91 |
| 34_N | 237_A | 1.031 | 0.91 |
| 421_D | 445_Y | 1.026 | 0.91 |
| 61_M | 76_I | 1.025 | 0.91 |
| 94_L | 357_F | 1.025 | 0.91 |
| 203_R | 207_L | 1.024 | 0.91 |
| 98_L | 376_I | 1.018 | 0.90 |
| 101_A | 351_M | 1.013 | 0.90 |
| 100_V | 350_I | 1.012 | 0.90 |
| 13_A | 256_Y | 1.011 | 0.90 |
| 383_L | 390_S | 1.011 | 0.90 |
| 94_L | 353_P | 1.009 | 0.90 |
| 32_A | 220_F | 1.004 | 0.90 |
| 84_R | 87_K | 1.004 | 0.90 |
| 100_V | 398_A | 1.004 | 0.90 |
| 4_W | 10_L | 1.000 | 0.89 |
| 105_V | 166_T | 1.000 | 0.89 |
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 | |
| 4xp4A | 1 | 0 | 100 | 0.119 | Contact Map |
| 2a65A | 1 | 0.9578 | 100 | 0.144 | Contact Map |
| 4us3A | 1 | 0.8514 | 100 | 0.18 | Contact Map |
| 3giaA | 1 | 0.8052 | 97.8 | 0.936 | Contact Map |
| 3l1lA | 1 | 0.7751 | 95.3 | 0.953 | Contact Map |
| 4djkA | 2 | 0.8052 | 93.2 | 0.957 | Contact Map |
| 2jlnA | 1 | 0.8032 | 88.1 | 0.962 | Contact Map |
| 2wswA | 1 | 0.7249 | 59.9 | 0.971 | Contact Map |
| 4wgvA | 2 | 0.7309 | 36.8 | 0.974 | Contact Map |
| 2c4wA | 1 | 0.0984 | 6.6 | 0.982 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)