| zero iteration |
| ID: | 1382234293 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 398 (397) | ||
| Sequences: | 873 (821.2) | ||
| Seq/Len: | 2.199 | ||
| Nf(neff/√len): | 41.2 |
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: 2.199).
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 |
| 139_D | 143_G | 4.791 | 1.00 |
| 31_V | 45_V | 3.651 | 1.00 |
| 25_R | 203_G | 3.241 | 1.00 |
| 353_E | 372_G | 3.151 | 1.00 |
| 204_E | 220_I | 2.974 | 1.00 |
| 108_D | 167_T | 2.957 | 1.00 |
| 197_E | 227_R | 2.893 | 1.00 |
| 243_D | 246_E | 2.849 | 1.00 |
| 223_A | 241_D | 2.820 | 1.00 |
| 198_D | 204_E | 2.711 | 1.00 |
| 108_D | 168_A | 2.646 | 1.00 |
| 224_G | 242_T | 2.641 | 1.00 |
| 168_A | 180_Y | 2.569 | 1.00 |
| 235_L | 247_R | 2.426 | 1.00 |
| 29_D | 206_L | 2.402 | 1.00 |
| 198_D | 239_L | 2.381 | 1.00 |
| 196_E | 218_M | 2.366 | 1.00 |
| 27_V | 45_V | 2.335 | 1.00 |
| 19_Q | 107_Q | 2.312 | 1.00 |
| 167_T | 171_Y | 2.298 | 1.00 |
| 204_E | 222_T | 2.211 | 1.00 |
| 138_E | 177_R | 2.138 | 1.00 |
| 238_V | 262_E | 2.098 | 0.99 |
| 7_E | 10_T | 2.083 | 0.99 |
| 224_G | 247_R | 2.043 | 0.99 |
| 225_G | 241_D | 2.035 | 0.99 |
| 194_V | 232_I | 2.027 | 0.99 |
| 195_M | 221_E | 2.009 | 0.99 |
| 165_E | 169_D | 2.002 | 0.99 |
| 104_I | 107_Q | 1.991 | 0.99 |
| 228_F | 242_T | 1.984 | 0.99 |
| 235_L | 248_E | 1.968 | 0.99 |
| 197_E | 239_L | 1.959 | 0.99 |
| 318_E | 344_V | 1.930 | 0.99 |
| 15_T | 155_R | 1.914 | 0.99 |
| 210_L | 284_L | 1.887 | 0.99 |
| 232_I | 295_L | 1.809 | 0.98 |
| 207_I | 287_M | 1.799 | 0.98 |
| 273_E | 292_D | 1.787 | 0.98 |
| 13_Y | 19_Q | 1.780 | 0.98 |
| 173_L | 178_F | 1.780 | 0.98 |
| 237_G | 245_L | 1.770 | 0.98 |
| 268_A | 286_R | 1.755 | 0.98 |
| 239_L | 242_T | 1.754 | 0.97 |
| 277_H | 297_L | 1.746 | 0.97 |
| 13_Y | 16_V | 1.744 | 0.97 |
| 242_T | 250_Q | 1.702 | 0.97 |
| 232_I | 291_I | 1.670 | 0.96 |
| 144_I | 152_I | 1.658 | 0.96 |
| 28_Q | 50_E | 1.648 | 0.96 |
| 108_D | 180_Y | 1.614 | 0.95 |
| 252_K | 257_N | 1.613 | 0.95 |
| 374_G | 377_I | 1.581 | 0.95 |
| 135_V | 180_Y | 1.553 | 0.94 |
| 341_G | 345_E | 1.534 | 0.93 |
| 21_R | 261_A | 1.528 | 0.93 |
| 151_D | 154_E | 1.510 | 0.93 |
| 337_D | 381_V | 1.502 | 0.92 |
| 27_V | 49_T | 1.498 | 0.92 |
| 12_Q | 15_T | 1.475 | 0.92 |
| 221_E | 227_R | 1.465 | 0.91 |
| 270_E | 273_E | 1.463 | 0.91 |
| 286_R | 290_L | 1.462 | 0.91 |
| 112_V | 178_F | 1.456 | 0.91 |
| 76_D | 79_E | 1.441 | 0.90 |
| 111_G | 164_V | 1.440 | 0.90 |
| 346_D | 349_Q | 1.439 | 0.90 |
| 199_H | 282_Q | 1.418 | 0.89 |
| 101_D | 104_I | 1.415 | 0.89 |
| 26_I | 206_L | 1.413 | 0.89 |
| 145_E | 148_I | 1.404 | 0.89 |
| 47_V | 202_R | 1.394 | 0.88 |
| 108_D | 164_V | 1.387 | 0.88 |
| 252_K | 296_S | 1.377 | 0.87 |
| 233_S | 257_N | 1.359 | 0.86 |
| 26_I | 200_V | 1.355 | 0.86 |
| 208_E | 212_S | 1.351 | 0.86 |
| 235_L | 239_L | 1.349 | 0.86 |
| 48_D | 202_R | 1.346 | 0.86 |
| 28_Q | 49_T | 1.343 | 0.86 |
| 233_S | 251_L | 1.332 | 0.85 |
| 204_E | 239_L | 1.327 | 0.85 |
| 17_V | 20_S | 1.323 | 0.84 |
| 228_F | 247_R | 1.299 | 0.83 |
| 223_A | 226_E | 1.282 | 0.82 |
| 48_D | 51_A | 1.282 | 0.82 |
| 221_E | 226_E | 1.279 | 0.82 |
| 269_M | 272_C | 1.276 | 0.81 |
| 234_L | 294_V | 1.266 | 0.81 |
| 26_I | 202_R | 1.262 | 0.80 |
| 239_L | 247_R | 1.246 | 0.79 |
| 364_Y | 367_A | 1.242 | 0.79 |
| 270_E | 274_S | 1.240 | 0.79 |
| 20_S | 52_G | 1.231 | 0.78 |
| 45_V | 49_T | 1.231 | 0.78 |
| 139_D | 142_T | 1.226 | 0.78 |
| 30_T | 206_L | 1.226 | 0.78 |
| 84_A | 113_V | 1.225 | 0.78 |
| 21_R | 57_V | 1.213 | 0.77 |
| 279_S | 286_R | 1.196 | 0.75 |
| 77_I | 135_V | 1.192 | 0.75 |
| 153_T | 178_F | 1.192 | 0.75 |
| 246_E | 250_Q | 1.186 | 0.74 |
| 234_L | 259_L | 1.185 | 0.74 |
| 387_I | 394_R | 1.184 | 0.74 |
| 198_D | 220_I | 1.183 | 0.74 |
| 261_A | 279_S | 1.171 | 0.73 |
| 271_N | 279_S | 1.171 | 0.73 |
| 108_D | 112_V | 1.171 | 0.73 |
| 199_H | 236_D | 1.165 | 0.72 |
| 338_L | 344_V | 1.164 | 0.72 |
| 19_Q | 104_I | 1.159 | 0.72 |
| 224_G | 241_D | 1.151 | 0.71 |
| 58_E | 104_I | 1.143 | 0.70 |
| 248_E | 276_H | 1.143 | 0.70 |
| 363_G | 367_A | 1.141 | 0.70 |
| 47_V | 83_Q | 1.140 | 0.70 |
| 112_V | 251_L | 1.140 | 0.70 |
| 267_L | 271_N | 1.131 | 0.69 |
| 20_S | 24_I | 1.131 | 0.69 |
| 228_F | 250_Q | 1.129 | 0.69 |
| 196_E | 207_I | 1.126 | 0.69 |
| 119_V | 142_T | 1.126 | 0.69 |
| 268_A | 271_N | 1.125 | 0.69 |
| 16_V | 59_L | 1.120 | 0.68 |
| 290_L | 379_R | 1.119 | 0.68 |
| 194_V | 216_F | 1.118 | 0.68 |
| 162_T | 291_I | 1.118 | 0.68 |
| 198_D | 259_L | 1.113 | 0.67 |
| 46_E | 233_S | 1.110 | 0.67 |
| 201_E | 204_E | 1.110 | 0.67 |
| 242_T | 247_R | 1.109 | 0.67 |
| 19_Q | 61_V | 1.108 | 0.67 |
| 234_L | 291_I | 1.103 | 0.66 |
| 108_D | 171_Y | 1.097 | 0.66 |
| 265_L | 269_M | 1.096 | 0.66 |
| 293_D | 297_L | 1.088 | 0.65 |
| 211_L | 291_I | 1.087 | 0.65 |
| 51_A | 200_V | 1.086 | 0.65 |
| 236_D | 282_Q | 1.085 | 0.64 |
| 262_E | 267_L | 1.084 | 0.64 |
| 26_I | 107_Q | 1.080 | 0.64 |
| 365_S | 368_A | 1.079 | 0.64 |
| 225_G | 242_T | 1.078 | 0.64 |
| 109_I | 113_V | 1.074 | 0.63 |
| 19_Q | 390_T | 1.071 | 0.63 |
| 388_E | 393_A | 1.065 | 0.62 |
| 272_C | 296_S | 1.061 | 0.62 |
| 164_V | 198_D | 1.060 | 0.62 |
| 7_E | 11_Q | 1.059 | 0.62 |
| 278_D | 290_L | 1.057 | 0.61 |
| 55_L | 260_N | 1.053 | 0.61 |
| 205_Q | 209_S | 1.049 | 0.61 |
| 158_H | 161_E | 1.048 | 0.61 |
| 290_L | 392_S | 1.039 | 0.60 |
| 26_I | 203_G | 1.037 | 0.59 |
| 197_E | 221_E | 1.036 | 0.59 |
| 29_D | 107_Q | 1.035 | 0.59 |
| 17_V | 21_R | 1.033 | 0.59 |
| 347_D | 351_I | 1.032 | 0.59 |
| 196_E | 220_I | 1.031 | 0.59 |
| 228_F | 241_D | 1.027 | 0.58 |
| 194_V | 250_Q | 1.025 | 0.58 |
| 267_L | 277_H | 1.024 | 0.58 |
| 81_K | 154_E | 1.023 | 0.58 |
| 194_V | 291_I | 1.020 | 0.57 |
| 368_A | 371_T | 1.020 | 0.57 |
| 150_P | 165_E | 1.018 | 0.57 |
| 13_Y | 17_V | 1.009 | 0.56 |
| 383_E | 387_I | 1.007 | 0.56 |
| 216_F | 273_E | 1.000 | 0.55 |
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 | |
| 3r0jA | 2 | 0.5101 | 100 | 0.708 | Contact Map |
| 2gwrA | 1 | 0.5126 | 100 | 0.71 | Contact Map |
| 1ys7A | 2 | 0.5176 | 100 | 0.716 | Contact Map |
| 2oqrA | 1 | 0.5151 | 100 | 0.717 | Contact Map |
| 1kgsA | 1 | 0.4975 | 99.9 | 0.718 | Contact Map |
| 4b09A | 12 | 0.4774 | 99.9 | 0.721 | Contact Map |
| 1p2fA | 1 | 0.495 | 99.9 | 0.729 | Contact Map |
| 2hqrA | 2 | 0.4899 | 99.9 | 0.738 | Contact Map |
| 3q9sA | 1 | 0.4799 | 99.9 | 0.739 | Contact Map |
| 4i5sA | 2 | 0.4623 | 99.9 | 0.75 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)