| 11 |
| ID: | 1472484125 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 333 (311) | ||
| Sequences: | 3575 (2156) | ||
| Seq/Len: | 11.495 | ||
| Nf(neff/√len): | 122.3 |
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: 11.495).
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 |
| 242_T | 275_Y | 3.526 | 1.00 |
| 113_D | 188_V | 3.394 | 1.00 |
| 269_V | 324_L | 3.354 | 1.00 |
| 189_I | 248_T | 3.305 | 1.00 |
| 116_L | 186_V | 3.298 | 1.00 |
| 32_I | 37_V | 3.090 | 1.00 |
| 238_F | 271_K | 2.974 | 1.00 |
| 307_F | 320_F | 2.899 | 1.00 |
| 248_T | 253_I | 2.811 | 1.00 |
| 191_L | 240_Q | 2.778 | 1.00 |
| 31_K | 162_G | 2.601 | 1.00 |
| 126_V | 142_V | 2.560 | 1.00 |
| 33_S | 36_E | 2.417 | 1.00 |
| 280_V | 327_E | 2.401 | 1.00 |
| 198_L | 261_S | 2.353 | 1.00 |
| 106_K | 110_N | 2.353 | 1.00 |
| 257_T | 265_N | 2.344 | 1.00 |
| 254_V | 323_I | 2.335 | 1.00 |
| 139_K | 167_E | 2.334 | 1.00 |
| 37_V | 91_L | 2.323 | 1.00 |
| 174_L | 239_E | 2.322 | 1.00 |
| 25_A | 91_L | 2.312 | 1.00 |
| 38_Y | 70_L | 2.301 | 1.00 |
| 158_F | 166_I | 2.244 | 1.00 |
| 242_T | 276_Q | 2.207 | 1.00 |
| 187_K | 249_K | 2.186 | 1.00 |
| 266_E | 309_R | 2.161 | 1.00 |
| 102_V | 128_H | 2.160 | 1.00 |
| 120_T | 154_A | 2.126 | 1.00 |
| 133_T | 138_S | 2.119 | 1.00 |
| 38_Y | 48_K | 2.107 | 1.00 |
| 238_F | 268_V | 2.095 | 1.00 |
| 136_H | 165_N | 2.095 | 1.00 |
| 141_F | 186_V | 2.069 | 1.00 |
| 118_V | 244_A | 2.014 | 1.00 |
| 107_A | 113_D | 2.008 | 1.00 |
| 40_N | 90_K | 1.932 | 1.00 |
| 280_V | 325_T | 1.928 | 1.00 |
| 127_A | 158_F | 1.926 | 1.00 |
| 27_I | 37_V | 1.879 | 1.00 |
| 234_V | 268_V | 1.859 | 1.00 |
| 110_N | 113_D | 1.848 | 1.00 |
| 24_Y | 71_I | 1.829 | 1.00 |
| 29_T | 68_N | 1.829 | 1.00 |
| 241_L | 272_A | 1.825 | 1.00 |
| 69_V | 99_S | 1.789 | 1.00 |
| 198_L | 259_S | 1.777 | 1.00 |
| 245_M | 272_A | 1.768 | 1.00 |
| 245_M | 279_G | 1.756 | 1.00 |
| 114_D | 139_K | 1.735 | 1.00 |
| 245_M | 253_I | 1.729 | 1.00 |
| 130_S | 163_C | 1.717 | 1.00 |
| 105_V | 129_M | 1.686 | 1.00 |
| 127_A | 161_M | 1.668 | 1.00 |
| 270_E | 274_E | 1.667 | 1.00 |
| 49_V | 73_P | 1.661 | 1.00 |
| 44_K | 85_L | 1.658 | 1.00 |
| 151_D | 154_A | 1.656 | 1.00 |
| 126_V | 140_I | 1.654 | 1.00 |
| 97_S | 316_N | 1.649 | 1.00 |
| 66_C | 96_K | 1.648 | 1.00 |
| 282_M | 325_T | 1.646 | 1.00 |
| 104_S | 321_L | 1.606 | 1.00 |
| 271_K | 275_Y | 1.600 | 1.00 |
| 101_A | 321_L | 1.580 | 1.00 |
| 128_H | 132_L | 1.569 | 1.00 |
| 102_V | 129_M | 1.561 | 1.00 |
| 151_D | 168_I | 1.553 | 1.00 |
| 281_K | 322_S | 1.532 | 1.00 |
| 84_D | 88_D | 1.531 | 1.00 |
| 196_S | 233_L | 1.504 | 1.00 |
| 144_G | 151_D | 1.500 | 1.00 |
| 310_L | 316_N | 1.493 | 1.00 |
| 282_M | 323_I | 1.453 | 1.00 |
| 238_F | 272_A | 1.421 | 1.00 |
| 66_C | 69_V | 1.419 | 1.00 |
| 127_A | 157_L | 1.405 | 0.99 |
| 151_D | 170_H | 1.390 | 0.99 |
| 92_I | 127_A | 1.384 | 0.99 |
| 51_S | 69_V | 1.375 | 0.99 |
| 262_K | 267_D | 1.367 | 0.99 |
| 163_C | 166_I | 1.365 | 0.99 |
| 114_D | 185_N | 1.363 | 0.99 |
| 63_D | 96_K | 1.361 | 0.99 |
| 241_L | 253_I | 1.350 | 0.99 |
| 231_E | 263_E | 1.350 | 0.99 |
| 307_F | 322_S | 1.339 | 0.99 |
| 85_L | 90_K | 1.334 | 0.99 |
| 103_H | 132_L | 1.328 | 0.99 |
| 96_K | 316_N | 1.321 | 0.99 |
| 29_T | 131_I | 1.316 | 0.99 |
| 133_T | 140_I | 1.302 | 0.99 |
| 129_M | 190_L | 1.300 | 0.99 |
| 272_A | 276_Q | 1.298 | 0.99 |
| 115_V | 133_T | 1.295 | 0.99 |
| 105_V | 109_I | 1.286 | 0.99 |
| 49_V | 71_I | 1.277 | 0.99 |
| 32_I | 90_K | 1.262 | 0.99 |
| 155_R | 159_T | 1.252 | 0.99 |
| 114_D | 186_V | 1.247 | 0.99 |
| 238_F | 242_T | 1.247 | 0.99 |
| 105_V | 188_V | 1.238 | 0.98 |
| 116_L | 143_C | 1.230 | 0.98 |
| 230_L | 234_V | 1.227 | 0.98 |
| 51_S | 96_K | 1.223 | 0.98 |
| 85_L | 91_L | 1.220 | 0.98 |
| 34_L | 50_K | 1.213 | 0.98 |
| 243_H | 246_K | 1.205 | 0.98 |
| 114_D | 141_F | 1.201 | 0.98 |
| 238_F | 275_Y | 1.196 | 0.98 |
| 101_A | 128_H | 1.182 | 0.98 |
| 67_F | 103_H | 1.181 | 0.98 |
| 42_R | 48_K | 1.178 | 0.98 |
| 24_Y | 96_K | 1.170 | 0.97 |
| 105_V | 254_V | 1.164 | 0.97 |
| 248_T | 326_R | 1.157 | 0.97 |
| 98_R | 319_C | 1.130 | 0.97 |
| 263_E | 267_D | 1.130 | 0.97 |
| 68_N | 103_H | 1.128 | 0.97 |
| 37_V | 85_L | 1.128 | 0.97 |
| 38_Y | 42_R | 1.123 | 0.97 |
| 34_L | 70_L | 1.105 | 0.96 |
| 267_D | 270_E | 1.099 | 0.96 |
| 173_F | 240_Q | 1.092 | 0.96 |
| 115_V | 138_S | 1.079 | 0.95 |
| 44_K | 84_D | 1.077 | 0.95 |
| 69_V | 96_K | 1.076 | 0.95 |
| 39_N | 43_R | 1.069 | 0.95 |
| 134_S | 137_T | 1.058 | 0.95 |
| 152_F | 155_R | 1.058 | 0.95 |
| 27_I | 70_L | 1.056 | 0.95 |
| 153_N | 156_K | 1.048 | 0.94 |
| 25_A | 72_F | 1.035 | 0.94 |
| 21_L | 210_E | 1.032 | 0.94 |
| 272_A | 279_G | 1.029 | 0.94 |
| 141_F | 169_L | 1.026 | 0.94 |
| 104_S | 323_I | 1.019 | 0.93 |
| 118_V | 173_F | 1.009 | 0.93 |
| 100_L | 308_F | 1.009 | 0.93 |
| 106_K | 109_I | 1.006 | 0.93 |
| 28_N | 31_K | 1.003 | 0.93 |
| 106_K | 188_V | 1.002 | 0.92 |
| 133_T | 137_T | 1.000 | 0.92 |
| 48_K | 70_L | 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 | |
| 2b9eA | 1 | 0.8018 | 100 | 0.343 | Contact Map |
| 2frxA | 4 | 0.8589 | 100 | 0.368 | Contact Map |
| 1ixkA | 1 | 0.8498 | 100 | 0.398 | Contact Map |
| 2yxlA | 1 | 0.8468 | 100 | 0.405 | Contact Map |
| 3m6wA | 1 | 0.8769 | 100 | 0.409 | Contact Map |
| 3m4xA | 1 | 0.8589 | 100 | 0.416 | Contact Map |
| 1sqgA | 1 | 0.8258 | 100 | 0.438 | Contact Map |
| 3ajdA | 1 | 0.7568 | 100 | 0.446 | Contact Map |
| 4fzvA | 1 | 0.9099 | 100 | 0.52 | Contact Map |
| 3axsA | 1 | 0.6757 | 99.7 | 0.781 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)