| nd4 |
| ID: | 1401285277 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 459 (405) | ||
| Sequences: | 8653 (4677.4) | ||
| Seq/Len: | 21.365 | ||
| Nf(neff/√len): | 232.4 |
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: 21.365).
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 |
| 59_D | 245_R | 5.159 | 1.00 |
| 108_M | 121_F | 3.826 | 1.00 |
| 325_L | 362_A | 3.751 | 1.00 |
| 286_I | 330_A | 3.672 | 1.00 |
| 148_Y | 218_K | 3.260 | 1.00 |
| 315_L | 377_G | 3.246 | 1.00 |
| 134_T | 146_G | 3.167 | 1.00 |
| 66_L | 111_T | 3.117 | 1.00 |
| 318_A | 373_I | 3.045 | 1.00 |
| 281_D | 340_R | 2.938 | 1.00 |
| 173_S | 178_L | 2.674 | 1.00 |
| 269_M | 399_N | 2.651 | 1.00 |
| 69_T | 110_F | 2.620 | 1.00 |
| 277_L | 405_L | 2.541 | 1.00 |
| 175_N | 178_L | 2.504 | 1.00 |
| 220_H | 236_L | 2.446 | 1.00 |
| 273_S | 292_S | 2.377 | 1.00 |
| 360_L | 411_F | 2.353 | 1.00 |
| 62_T | 241_Y | 2.237 | 1.00 |
| 105_S | 124_T | 2.191 | 1.00 |
| 209_L | 298_V | 2.187 | 1.00 |
| 314_I | 377_G | 2.180 | 1.00 |
| 352_L | 355_M | 2.168 | 1.00 |
| 265_S | 302_L | 2.163 | 1.00 |
| 115_L | 246_L | 2.163 | 1.00 |
| 285_L | 342_M | 2.143 | 1.00 |
| 339_S | 344_L | 2.111 | 1.00 |
| 299_T | 396_T | 2.107 | 1.00 |
| 112_A | 117_M | 2.046 | 1.00 |
| 303_I | 308_S | 2.039 | 1.00 |
| 163_A | 198_A | 2.035 | 1.00 |
| 220_H | 228_S | 2.020 | 1.00 |
| 311_G | 384_T | 2.010 | 1.00 |
| 163_A | 202_A | 1.999 | 1.00 |
| 68_L | 320_G | 1.987 | 1.00 |
| 280_T | 343_I | 1.971 | 1.00 |
| 300_A | 381_V | 1.970 | 1.00 |
| 289_S | 406_Y | 1.933 | 1.00 |
| 363_S | 407_S | 1.850 | 1.00 |
| 336_R | 433_E | 1.814 | 1.00 |
| 382_L | 396_T | 1.795 | 1.00 |
| 115_L | 179_L | 1.791 | 1.00 |
| 208_P | 216_L | 1.780 | 1.00 |
| 57_S | 113_T | 1.757 | 1.00 |
| 59_D | 62_T | 1.731 | 1.00 |
| 145_A | 222_E | 1.720 | 1.00 |
| 64_P | 313_V | 1.672 | 1.00 |
| 270_I | 399_N | 1.665 | 1.00 |
| 80_S | 95_Y | 1.646 | 1.00 |
| 333_N | 348_L | 1.626 | 1.00 |
| 244_M | 301_I | 1.624 | 1.00 |
| 66_L | 107_I | 1.590 | 1.00 |
| 118_F | 242_G | 1.579 | 1.00 |
| 303_I | 385_T | 1.577 | 1.00 |
| 114_E | 174_L | 1.544 | 1.00 |
| 173_S | 179_L | 1.535 | 1.00 |
| 364_L | 369_L | 1.525 | 1.00 |
| 441_L | 445_L | 1.506 | 1.00 |
| 204_M | 209_L | 1.502 | 1.00 |
| 64_P | 317_I | 1.499 | 1.00 |
| 357_F | 361_L | 1.493 | 1.00 |
| 282_L | 410_M | 1.488 | 1.00 |
| 139_Q | 222_E | 1.482 | 1.00 |
| 280_T | 341_I | 1.446 | 1.00 |
| 342_M | 414_T | 1.445 | 1.00 |
| 73_L | 103_Q | 1.444 | 1.00 |
| 132_I | 227_G | 1.424 | 1.00 |
| 152_Y | 214_L | 1.419 | 1.00 |
| 279_Q | 284_S | 1.417 | 1.00 |
| 341_I | 344_L | 1.407 | 0.99 |
| 101_S | 105_S | 1.407 | 0.99 |
| 217_P | 288_Y | 1.406 | 0.99 |
| 334_Y | 340_R | 1.396 | 0.99 |
| 301_I | 312_A | 1.392 | 0.99 |
| 359_W | 363_S | 1.385 | 0.99 |
| 141_E | 222_E | 1.385 | 0.99 |
| 438_F | 442_S | 1.381 | 0.99 |
| 156_G | 205_V | 1.356 | 0.99 |
| 300_A | 311_G | 1.350 | 0.99 |
| 273_S | 399_N | 1.342 | 0.99 |
| 130_L | 146_G | 1.334 | 0.99 |
| 200_T | 204_M | 1.333 | 0.99 |
| 261_F | 302_L | 1.330 | 0.99 |
| 349_Q | 356_A | 1.329 | 0.99 |
| 300_A | 308_S | 1.324 | 0.99 |
| 165_I | 169_N | 1.323 | 0.99 |
| 439_M | 443_P | 1.319 | 0.99 |
| 142_R | 222_E | 1.319 | 0.99 |
| 243_M | 301_I | 1.317 | 0.99 |
| 366_N | 407_S | 1.314 | 0.99 |
| 385_T | 393_L | 1.307 | 0.99 |
| 70_T | 107_I | 1.295 | 0.99 |
| 144_N | 148_Y | 1.290 | 0.99 |
| 168_H | 174_L | 1.287 | 0.99 |
| 228_S | 231_L | 1.283 | 0.99 |
| 77_I | 99_L | 1.277 | 0.99 |
| 243_M | 298_V | 1.270 | 0.99 |
| 409_Y | 413_T | 1.269 | 0.99 |
| 356_A | 416_W | 1.266 | 0.99 |
| 160_L | 202_A | 1.253 | 0.99 |
| 52_C | 116_I | 1.251 | 0.99 |
| 394_L | 398_L | 1.248 | 0.99 |
| 292_S | 403_T | 1.246 | 0.98 |
| 139_Q | 142_R | 1.244 | 0.98 |
| 293_H | 406_Y | 1.240 | 0.98 |
| 266_L | 392_T | 1.236 | 0.98 |
| 407_S | 410_M | 1.233 | 0.98 |
| 200_T | 261_F | 1.232 | 0.98 |
| 299_T | 385_T | 1.229 | 0.98 |
| 210_Y | 267_W | 1.228 | 0.98 |
| 114_E | 175_N | 1.228 | 0.98 |
| 197_L | 201_M | 1.224 | 0.98 |
| 274_S | 402_V | 1.222 | 0.98 |
| 271_M | 275_I | 1.221 | 0.98 |
| 203_F | 242_G | 1.221 | 0.98 |
| 218_K | 284_S | 1.217 | 0.98 |
| 450_N | 453_I | 1.211 | 0.98 |
| 269_M | 299_T | 1.210 | 0.98 |
| 94_L | 101_S | 1.201 | 0.98 |
| 209_L | 264_L | 1.196 | 0.98 |
| 311_G | 380_S | 1.196 | 0.98 |
| 273_S | 402_V | 1.193 | 0.98 |
| 322_T | 365_A | 1.192 | 0.98 |
| 442_S | 446_L | 1.189 | 0.98 |
| 227_G | 230_V | 1.186 | 0.98 |
| 116_I | 174_L | 1.184 | 0.98 |
| 318_A | 377_G | 1.182 | 0.98 |
| 58_S | 111_T | 1.177 | 0.98 |
| 269_M | 295_A | 1.174 | 0.98 |
| 337_T | 345_S | 1.173 | 0.98 |
| 321_L | 443_P | 1.172 | 0.98 |
| 265_S | 295_A | 1.167 | 0.97 |
| 229_M | 328_C | 1.167 | 0.97 |
| 361_L | 441_L | 1.165 | 0.97 |
| 356_A | 411_F | 1.164 | 0.97 |
| 119_Y | 161_L | 1.160 | 0.97 |
| 204_M | 264_L | 1.156 | 0.97 |
| 305_T | 384_T | 1.148 | 0.97 |
| 290_S | 319_H | 1.148 | 0.97 |
| 232_A | 323_S | 1.147 | 0.97 |
| 133_I | 219_A | 1.134 | 0.97 |
| 272_T | 292_S | 1.127 | 0.97 |
| 363_S | 411_F | 1.124 | 0.97 |
| 308_S | 384_T | 1.120 | 0.96 |
| 297_V | 312_A | 1.119 | 0.96 |
| 272_T | 275_I | 1.114 | 0.96 |
| 378_E | 400_M | 1.113 | 0.96 |
| 224_P | 283_K | 1.113 | 0.96 |
| 240_G | 297_V | 1.106 | 0.96 |
| 77_I | 96_L | 1.100 | 0.96 |
| 228_S | 283_K | 1.097 | 0.96 |
| 216_L | 220_H | 1.097 | 0.96 |
| 262_L | 302_L | 1.094 | 0.96 |
| 94_L | 97_S | 1.093 | 0.96 |
| 79_A | 328_C | 1.092 | 0.96 |
| 205_V | 212_L | 1.090 | 0.96 |
| 166_Y | 195_M | 1.089 | 0.96 |
| 300_A | 312_A | 1.086 | 0.96 |
| 225_I | 283_K | 1.085 | 0.96 |
| 57_S | 60_P | 1.083 | 0.96 |
| 220_H | 290_S | 1.074 | 0.95 |
| 98_M | 131_A | 1.073 | 0.95 |
| 176_I | 180_T | 1.072 | 0.95 |
| 322_T | 374_N | 1.070 | 0.95 |
| 72_L | 233_A | 1.068 | 0.95 |
| 178_L | 181_L | 1.066 | 0.95 |
| 262_L | 299_T | 1.063 | 0.95 |
| 71_W | 75_L | 1.056 | 0.95 |
| 125_T | 235_L | 1.054 | 0.95 |
| 207_M | 240_G | 1.050 | 0.94 |
| 236_L | 240_G | 1.049 | 0.94 |
| 265_S | 298_V | 1.045 | 0.94 |
| 191_A | 195_M | 1.045 | 0.94 |
| 236_L | 241_Y | 1.043 | 0.94 |
| 362_A | 441_L | 1.042 | 0.94 |
| 193_N | 257_M | 1.036 | 0.94 |
| 217_P | 279_Q | 1.033 | 0.94 |
| 102_L | 106_L | 1.031 | 0.94 |
| 265_S | 299_T | 1.029 | 0.94 |
| 319_H | 323_S | 1.017 | 0.93 |
| 328_C | 436_L | 1.017 | 0.93 |
| 156_G | 202_A | 1.016 | 0.93 |
| 236_L | 290_S | 1.014 | 0.93 |
| 76_T | 328_C | 1.012 | 0.93 |
| 129_T | 132_I | 1.012 | 0.93 |
| 109_T | 238_L | 1.010 | 0.93 |
| 217_P | 291_I | 1.008 | 0.93 |
| 326_L | 362_A | 1.007 | 0.93 |
| 62_T | 66_L | 1.006 | 0.93 |
| 430_F | 433_E | 1.002 | 0.92 |
| 259_Y | 263_V | 1.002 | 0.92 |
| 305_T | 308_S | 1.001 | 0.92 |
| 403_T | 406_Y | 1.000 | 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 | |
| 3rkoM | 2 | 0.9847 | 100 | 0.255 | Contact Map |
| 4he8M | 2 | 0.9542 | 100 | 0.264 | Contact Map |
| 3rkoN | 2 | 0.9608 | 100 | 0.29 | Contact Map |
| 4he8L | 2 | 0.9782 | 100 | 0.305 | Contact Map |
| 3rkoL | 2 | 0.9717 | 100 | 0.306 | Contact Map |
| 4he8N | 2 | 0.9129 | 100 | 0.32 | Contact Map |
| 4he8K | 2 | 0.2026 | 29.4 | 0.968 | Contact Map |
| 3rkoK | 2 | 0.2113 | 18.4 | 0.971 | Contact Map |
| 2yevB | 2 | 0.1895 | 3.3 | 0.98 | Contact Map |
| 3bz1y | 1 | 0.061 | 1.9 | 0.982 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)