| T0858 |
| ID: | 1451377329 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 494 (433) | ||
| Sequences: | 1295 (959.7) | ||
| Seq/Len: | 2.991 | ||
| Nf(neff/√len): | 46.1 |
HHblits Results: (2015_06)
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: 2.991).
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_C | 246_L | 5.374 | 1.00 |
| 428_A | 448_N | 3.877 | 1.00 |
| 262_G | 305_Y | 3.862 | 1.00 |
| 79_M | 365_I | 3.363 | 1.00 |
| 262_G | 266_K | 3.119 | 1.00 |
| 214_F | 231_V | 3.064 | 1.00 |
| 220_A | 223_A | 3.011 | 1.00 |
| 152_E | 224_E | 2.983 | 1.00 |
| 215_V | 268_A | 2.826 | 1.00 |
| 75_Q | 447_E | 2.765 | 1.00 |
| 143_I | 209_D | 2.719 | 1.00 |
| 325_H | 368_W | 2.690 | 1.00 |
| 478_Y | 488_Y | 2.679 | 1.00 |
| 212_T | 264_Q | 2.663 | 1.00 |
| 265_M | 270_L | 2.614 | 1.00 |
| 457_L | 488_Y | 2.563 | 1.00 |
| 365_I | 424_V | 2.443 | 1.00 |
| 219_Q | 268_A | 2.409 | 1.00 |
| 102_R | 162_E | 2.320 | 1.00 |
| 119_S | 426_P | 2.318 | 1.00 |
| 108_E | 410_R | 2.306 | 1.00 |
| 322_L | 367_N | 2.289 | 1.00 |
| 125_I | 214_F | 2.276 | 1.00 |
| 448_N | 452_T | 2.257 | 1.00 |
| 78_T | 429_V | 2.239 | 1.00 |
| 208_Q | 260_A | 2.234 | 1.00 |
| 222_K | 227_D | 2.229 | 1.00 |
| 86_I | 121_I | 2.178 | 1.00 |
| 266_K | 304_Q | 2.147 | 1.00 |
| 76_Y | 430_R | 2.141 | 1.00 |
| 175_A | 232_T | 2.128 | 1.00 |
| 334_L | 371_G | 2.106 | 1.00 |
| 208_Q | 264_Q | 2.075 | 1.00 |
| 428_A | 450_D | 2.074 | 1.00 |
| 428_A | 452_T | 2.053 | 1.00 |
| 313_N | 338_T | 2.051 | 1.00 |
| 74_E | 432_A | 2.016 | 1.00 |
| 216_K | 220_A | 1.990 | 1.00 |
| 101_D | 104_A | 1.982 | 1.00 |
| 258_K | 299_D | 1.934 | 0.99 |
| 457_L | 467_I | 1.933 | 0.99 |
| 143_I | 212_T | 1.928 | 0.99 |
| 173_I | 373_I | 1.916 | 0.99 |
| 72_P | 431_I | 1.901 | 0.99 |
| 107_T | 111_S | 1.897 | 0.99 |
| 107_T | 166_I | 1.887 | 0.99 |
| 125_I | 174_A | 1.880 | 0.99 |
| 116_F | 418_A | 1.848 | 0.99 |
| 441_I | 457_L | 1.836 | 0.99 |
| 264_Q | 268_A | 1.833 | 0.99 |
| 103_H | 162_E | 1.825 | 0.99 |
| 208_Q | 212_T | 1.824 | 0.99 |
| 215_V | 264_Q | 1.781 | 0.99 |
| 80_D | 332_E | 1.759 | 0.99 |
| 75_Q | 429_V | 1.734 | 0.99 |
| 480_V | 486_T | 1.703 | 0.98 |
| 464_S | 479_D | 1.675 | 0.98 |
| 231_V | 274_I | 1.647 | 0.98 |
| 176_P | 234_Q | 1.643 | 0.98 |
| 157_L | 226_I | 1.588 | 0.97 |
| 172_V | 226_I | 1.577 | 0.97 |
| 94_L | 378_M | 1.575 | 0.97 |
| 212_T | 215_V | 1.547 | 0.97 |
| 71_N | 74_E | 1.541 | 0.96 |
| 255_D | 259_T | 1.538 | 0.96 |
| 238_L | 277_F | 1.523 | 0.96 |
| 218_I | 228_I | 1.503 | 0.96 |
| 431_I | 447_E | 1.503 | 0.96 |
| 445_A | 455_F | 1.497 | 0.96 |
| 323_N | 326_Q | 1.491 | 0.95 |
| 276_A | 296_I | 1.487 | 0.95 |
| 106_L | 163_I | 1.485 | 0.95 |
| 148_L | 220_A | 1.474 | 0.95 |
| 425_K | 428_A | 1.473 | 0.95 |
| 130_F | 379_L | 1.459 | 0.95 |
| 462_E | 483_K | 1.454 | 0.95 |
| 248_M | 253_Q | 1.449 | 0.94 |
| 181_K | 189_T | 1.440 | 0.94 |
| 161_K | 224_E | 1.430 | 0.94 |
| 431_I | 453_Y | 1.429 | 0.94 |
| 425_K | 448_N | 1.426 | 0.94 |
| 258_K | 301_A | 1.419 | 0.94 |
| 276_A | 306_L | 1.417 | 0.94 |
| 310_A | 336_T | 1.404 | 0.93 |
| 79_M | 82_F | 1.390 | 0.93 |
| 311_Y | 333_L | 1.389 | 0.93 |
| 103_H | 107_T | 1.385 | 0.93 |
| 148_L | 224_E | 1.384 | 0.92 |
| 82_F | 365_I | 1.379 | 0.92 |
| 469_V | 476_F | 1.379 | 0.92 |
| 212_T | 268_A | 1.376 | 0.92 |
| 418_A | 422_S | 1.357 | 0.91 |
| 98_K | 101_D | 1.357 | 0.91 |
| 215_V | 219_Q | 1.345 | 0.91 |
| 275_Y | 310_A | 1.344 | 0.91 |
| 298_E | 328_Y | 1.341 | 0.91 |
| 219_Q | 270_L | 1.339 | 0.91 |
| 454_A | 489_R | 1.337 | 0.91 |
| 332_E | 370_K | 1.324 | 0.90 |
| 174_A | 217_W | 1.320 | 0.90 |
| 210_Y | 214_F | 1.318 | 0.90 |
| 177_W | 184_K | 1.313 | 0.90 |
| 257_V | 306_L | 1.299 | 0.89 |
| 172_V | 228_I | 1.298 | 0.89 |
| 455_F | 490_W | 1.297 | 0.89 |
| 111_S | 117_G | 1.296 | 0.89 |
| 376_N | 379_L | 1.294 | 0.89 |
| 257_V | 262_G | 1.273 | 0.88 |
| 123_I | 228_I | 1.269 | 0.87 |
| 273_K | 307_A | 1.262 | 0.87 |
| 176_P | 214_F | 1.258 | 0.87 |
| 98_K | 406_K | 1.253 | 0.87 |
| 322_L | 326_Q | 1.252 | 0.86 |
| 374_V | 417_I | 1.251 | 0.86 |
| 480_V | 484_S | 1.248 | 0.86 |
| 104_A | 108_E | 1.247 | 0.86 |
| 138_C | 143_I | 1.238 | 0.86 |
| 174_A | 228_I | 1.233 | 0.85 |
| 82_F | 421_S | 1.232 | 0.85 |
| 237_P | 314_Y | 1.231 | 0.85 |
| 364_T | 369_C | 1.221 | 0.85 |
| 217_W | 221_F | 1.219 | 0.84 |
| 307_A | 332_E | 1.215 | 0.84 |
| 423_V | 487_S | 1.214 | 0.84 |
| 69_T | 470_S | 1.214 | 0.84 |
| 464_S | 482_G | 1.208 | 0.84 |
| 262_G | 302_A | 1.204 | 0.83 |
| 358_E | 458_I | 1.202 | 0.83 |
| 219_Q | 269_G | 1.190 | 0.82 |
| 216_K | 219_Q | 1.183 | 0.82 |
| 476_F | 488_Y | 1.181 | 0.82 |
| 265_M | 272_T | 1.173 | 0.81 |
| 203_N | 206_Y | 1.170 | 0.81 |
| 94_L | 105_F | 1.170 | 0.81 |
| 455_F | 469_V | 1.161 | 0.80 |
| 123_I | 217_W | 1.153 | 0.80 |
| 137_C | 151_E | 1.151 | 0.79 |
| 116_F | 422_S | 1.146 | 0.79 |
| 89_S | 379_L | 1.144 | 0.79 |
| 232_T | 278_D | 1.141 | 0.79 |
| 335_F | 338_T | 1.140 | 0.79 |
| 429_V | 432_A | 1.136 | 0.78 |
| 151_E | 221_F | 1.136 | 0.78 |
| 264_Q | 267_A | 1.134 | 0.78 |
| 433_T | 443_C | 1.130 | 0.78 |
| 94_L | 102_R | 1.129 | 0.78 |
| 86_I | 160_L | 1.127 | 0.77 |
| 441_I | 480_V | 1.126 | 0.77 |
| 262_G | 304_Q | 1.123 | 0.77 |
| 107_T | 114_D | 1.122 | 0.77 |
| 162_E | 165_A | 1.120 | 0.77 |
| 88_G | 124_S | 1.116 | 0.76 |
| 124_S | 128_S | 1.114 | 0.76 |
| 171_K | 426_P | 1.113 | 0.76 |
| 86_I | 163_I | 1.109 | 0.76 |
| 257_V | 305_Y | 1.108 | 0.76 |
| 378_M | 400_I | 1.107 | 0.76 |
| 120_Y | 371_G | 1.104 | 0.75 |
| 136_T | 189_T | 1.104 | 0.75 |
| 118_F | 374_V | 1.102 | 0.75 |
| 297_Y | 309_A | 1.102 | 0.75 |
| 178_T | 184_K | 1.101 | 0.75 |
| 281_Y | 321_L | 1.099 | 0.75 |
| 84_A | 397_A | 1.099 | 0.75 |
| 378_M | 408_I | 1.095 | 0.74 |
| 110_F | 163_I | 1.094 | 0.74 |
| 178_T | 181_K | 1.093 | 0.74 |
| 197_W | 200_G | 1.091 | 0.74 |
| 67_T | 468_T | 1.088 | 0.74 |
| 399_D | 411_N | 1.087 | 0.74 |
| 254_R | 258_K | 1.086 | 0.74 |
| 164_L | 226_I | 1.084 | 0.73 |
| 250_W | 295_K | 1.081 | 0.73 |
| 125_I | 217_W | 1.079 | 0.73 |
| 127_C | 244_A | 1.075 | 0.73 |
| 76_Y | 431_I | 1.075 | 0.73 |
| 80_D | 171_K | 1.066 | 0.72 |
| 339_S | 395_Y | 1.064 | 0.71 |
| 149_Q | 152_E | 1.063 | 0.71 |
| 311_Y | 369_C | 1.060 | 0.71 |
| 109_T | 118_F | 1.053 | 0.70 |
| 117_G | 425_K | 1.051 | 0.70 |
| 116_F | 423_V | 1.050 | 0.70 |
| 296_I | 306_L | 1.050 | 0.70 |
| 148_L | 152_E | 1.049 | 0.70 |
| 307_A | 331_K | 1.044 | 0.69 |
| 125_I | 231_V | 1.044 | 0.69 |
| 254_R | 299_D | 1.038 | 0.69 |
| 124_S | 244_A | 1.037 | 0.69 |
| 76_Y | 432_A | 1.037 | 0.69 |
| 130_F | 376_N | 1.036 | 0.69 |
| 420_L | 424_V | 1.035 | 0.68 |
| 355_E | 483_K | 1.027 | 0.68 |
| 362_L | 420_L | 1.026 | 0.67 |
| 121_I | 170_I | 1.026 | 0.67 |
| 294_G | 327_A | 1.026 | 0.67 |
| 110_F | 121_I | 1.021 | 0.67 |
| 256_F | 263_P | 1.014 | 0.66 |
| 260_A | 263_P | 1.013 | 0.66 |
| 364_T | 372_V | 1.013 | 0.66 |
| 401_N | 407_T | 1.012 | 0.66 |
| 308_G | 379_L | 1.010 | 0.66 |
| 95_L | 155_Y | 1.009 | 0.66 |
| 94_L | 162_E | 1.006 | 0.65 |
| 424_V | 456_V | 1.003 | 0.65 |
| 265_M | 271_S | 1.000 | 0.65 |
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 | |
| 2nt0A | 4 | 0.9676 | 100 | 0.136 | Contact Map |
| 2wnwA | 2 | 0.8846 | 100 | 0.283 | Contact Map |
| 3clwA | 6 | 0.8259 | 100 | 0.321 | Contact Map |
| 4ccdA | 1 | 0.7571 | 100 | 0.327 | Contact Map |
| 4qawA | 8 | 0.7267 | 100 | 0.398 | Contact Map |
| 4uqdA | 1 | 0 | 100 | 0.42 | Contact Map |
| 4fmvA | 1 | 0.7206 | 100 | 0.425 | Contact Map |
| 2y24A | 1 | 0.7166 | 100 | 0.432 | Contact Map |
| 4m29A | 1 | 0.7368 | 100 | 0.744 | Contact Map |
| 1w91A | 8 | 0.7611 | 100 | 0.763 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)