| 1VJ7 full sequence |
| ID: | 1421415090 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 393 (373) | ||
| Sequences: | 1742 (1011.7) | ||
| Seq/Len: | 4.670 | ||
| Nf(neff/√len): | 52.4 |
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: 4.670).
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 |
| 91_E | 96_K | 4.005 | 1.00 |
| 150_R | 186_E | 3.210 | 1.00 |
| 66_L | 139_L | 3.109 | 1.00 |
| 80_V | 87_L | 3.042 | 1.00 |
| 274_T | 277_D | 3.003 | 1.00 |
| 30_K | 93_D | 2.960 | 1.00 |
| 228_Y | 231_E | 2.707 | 1.00 |
| 225_I | 285_I | 2.605 | 1.00 |
| 69_V | 97_D | 2.436 | 1.00 |
| 27_F | 72_A | 2.283 | 1.00 |
| 273_E | 329_K | 2.280 | 1.00 |
| 235_F | 273_E | 2.242 | 1.00 |
| 237_D | 329_K | 2.242 | 1.00 |
| 271_V | 329_K | 2.229 | 1.00 |
| 157_K | 160_Q | 2.186 | 1.00 |
| 28_V | 71_V | 2.150 | 1.00 |
| 152_L | 194_Y | 2.074 | 1.00 |
| 80_V | 90_I | 1.993 | 1.00 |
| 239_Y | 332_H | 1.991 | 1.00 |
| 196_N | 199_E | 1.980 | 1.00 |
| 220_D | 319_K | 1.932 | 1.00 |
| 217_L | 317_G | 1.889 | 1.00 |
| 165_R | 169_E | 1.880 | 1.00 |
| 257_K | 262_I | 1.859 | 1.00 |
| 66_L | 70_T | 1.853 | 1.00 |
| 206_M | 259_F | 1.836 | 1.00 |
| 152_L | 163_I | 1.763 | 1.00 |
| 27_F | 69_V | 1.748 | 1.00 |
| 58_A | 71_V | 1.728 | 1.00 |
| 203_I | 245_I | 1.726 | 1.00 |
| 160_Q | 194_Y | 1.702 | 0.99 |
| 87_L | 103_D | 1.694 | 0.99 |
| 218_V | 240_G | 1.691 | 0.99 |
| 34_Y | 85_I | 1.676 | 0.99 |
| 61_L | 70_T | 1.623 | 0.99 |
| 226_K | 230_T | 1.621 | 0.99 |
| 276_S | 280_A | 1.606 | 0.99 |
| 45_K | 155_L | 1.594 | 0.99 |
| 157_K | 161_E | 1.588 | 0.99 |
| 272_M | 281_M | 1.588 | 0.99 |
| 204_S | 245_I | 1.573 | 0.99 |
| 168_M | 246_Y | 1.560 | 0.99 |
| 342_H | 345_Y | 1.550 | 0.99 |
| 37_A | 40_F | 1.543 | 0.99 |
| 207_M | 245_I | 1.537 | 0.99 |
| 366_K | 369_V | 1.533 | 0.99 |
| 60_I | 150_R | 1.514 | 0.98 |
| 89_N | 92_F | 1.505 | 0.98 |
| 148_N | 151_T | 1.474 | 0.98 |
| 286_H | 313_T | 1.447 | 0.98 |
| 332_H | 336_E | 1.446 | 0.98 |
| 16_A | 28_V | 1.446 | 0.98 |
| 228_Y | 288_L | 1.441 | 0.98 |
| 100_D | 133_K | 1.440 | 0.98 |
| 61_L | 74_G | 1.431 | 0.97 |
| 221_I | 322_I | 1.430 | 0.97 |
| 210_K | 213_E | 1.407 | 0.97 |
| 29_K | 33_D | 1.393 | 0.97 |
| 243_K | 251_K | 1.389 | 0.97 |
| 149_M | 187_L | 1.383 | 0.97 |
| 185_W | 244_H | 1.375 | 0.97 |
| 19_Y | 65_H | 1.366 | 0.96 |
| 82_D | 148_N | 1.346 | 0.96 |
| 202_K | 206_M | 1.343 | 0.96 |
| 295_R | 314_T | 1.342 | 0.96 |
| 199_E | 202_K | 1.335 | 0.96 |
| 215_E | 219_D | 1.329 | 0.96 |
| 217_L | 318_P | 1.318 | 0.95 |
| 226_K | 237_D | 1.312 | 0.95 |
| 44_R | 151_T | 1.308 | 0.95 |
| 35_A | 51_I | 1.308 | 0.95 |
| 78_D | 82_D | 1.307 | 0.95 |
| 101_I | 140_V | 1.304 | 0.95 |
| 87_L | 100_D | 1.303 | 0.95 |
| 185_W | 211_R | 1.299 | 0.95 |
| 172_A | 191_A | 1.289 | 0.95 |
| 203_I | 259_F | 1.286 | 0.94 |
| 185_W | 242_P | 1.285 | 0.94 |
| 60_I | 186_E | 1.284 | 0.94 |
| 38_A | 89_N | 1.277 | 0.94 |
| 229_T | 281_M | 1.276 | 0.94 |
| 246_Y | 250_R | 1.271 | 0.94 |
| 211_R | 242_P | 1.271 | 0.94 |
| 27_F | 30_K | 1.270 | 0.94 |
| 44_R | 50_Y | 1.268 | 0.94 |
| 61_L | 71_V | 1.241 | 0.93 |
| 34_Y | 93_D | 1.240 | 0.93 |
| 277_D | 280_A | 1.239 | 0.93 |
| 152_L | 164_S | 1.238 | 0.93 |
| 82_D | 151_T | 1.236 | 0.93 |
| 44_R | 148_N | 1.231 | 0.93 |
| 15_L | 63_D | 1.229 | 0.92 |
| 309_Q | 334_V | 1.228 | 0.92 |
| 87_L | 99_R | 1.218 | 0.92 |
| 44_R | 82_D | 1.217 | 0.92 |
| 371_L | 375_S | 1.213 | 0.92 |
| 33_D | 36_T | 1.204 | 0.91 |
| 104_G | 137_V | 1.202 | 0.91 |
| 227_S | 231_E | 1.202 | 0.91 |
| 273_E | 277_D | 1.201 | 0.91 |
| 192_F | 199_E | 1.200 | 0.91 |
| 225_I | 324_I | 1.197 | 0.91 |
| 87_L | 91_E | 1.191 | 0.91 |
| 251_K | 323_E | 1.182 | 0.90 |
| 342_H | 346_K | 1.182 | 0.90 |
| 81_E | 148_N | 1.176 | 0.90 |
| 147_H | 151_T | 1.175 | 0.90 |
| 223_T | 227_S | 1.174 | 0.90 |
| 85_I | 89_N | 1.172 | 0.90 |
| 249_Y | 253_R | 1.164 | 0.90 |
| 272_M | 277_D | 1.162 | 0.89 |
| 53_H | 147_H | 1.153 | 0.89 |
| 285_I | 315_V | 1.149 | 0.89 |
| 251_K | 269_R | 1.148 | 0.89 |
| 224_K | 289_W | 1.147 | 0.89 |
| 80_V | 103_D | 1.146 | 0.89 |
| 145_R | 167_T | 1.144 | 0.88 |
| 125_R | 318_P | 1.144 | 0.88 |
| 13_V | 25_A | 1.142 | 0.88 |
| 57_V | 144_D | 1.140 | 0.88 |
| 39_H | 148_N | 1.139 | 0.88 |
| 82_D | 107_K | 1.132 | 0.88 |
| 26_A | 30_K | 1.132 | 0.88 |
| 71_V | 74_G | 1.131 | 0.88 |
| 81_E | 106_T | 1.127 | 0.87 |
| 88_D | 91_E | 1.127 | 0.87 |
| 243_K | 342_H | 1.123 | 0.87 |
| 68_A | 72_A | 1.120 | 0.87 |
| 294_G | 332_H | 1.120 | 0.87 |
| 281_M | 284_Y | 1.120 | 0.87 |
| 73_C | 101_I | 1.116 | 0.87 |
| 127_M | 130_A | 1.116 | 0.87 |
| 69_V | 72_A | 1.113 | 0.87 |
| 78_D | 148_N | 1.109 | 0.86 |
| 219_D | 222_V | 1.107 | 0.86 |
| 222_V | 226_K | 1.101 | 0.86 |
| 251_K | 264_D | 1.100 | 0.86 |
| 149_M | 167_T | 1.098 | 0.86 |
| 53_H | 77_H | 1.095 | 0.85 |
| 329_K | 333_Q | 1.089 | 0.85 |
| 39_H | 42_Q | 1.086 | 0.85 |
| 39_H | 78_D | 1.086 | 0.85 |
| 144_D | 148_N | 1.079 | 0.84 |
| 243_K | 267_A | 1.078 | 0.84 |
| 323_E | 342_H | 1.074 | 0.84 |
| 48_E | 53_H | 1.074 | 0.84 |
| 269_R | 325_Q | 1.069 | 0.83 |
| 78_D | 81_E | 1.069 | 0.83 |
| 69_V | 98_V | 1.068 | 0.83 |
| 149_M | 152_L | 1.067 | 0.83 |
| 153_K | 193_R | 1.064 | 0.83 |
| 267_A | 342_H | 1.062 | 0.83 |
| 269_R | 345_Y | 1.061 | 0.83 |
| 31_A | 35_A | 1.056 | 0.82 |
| 78_D | 83_T | 1.056 | 0.82 |
| 155_L | 163_I | 1.053 | 0.82 |
| 243_K | 325_Q | 1.045 | 0.81 |
| 50_Y | 148_N | 1.045 | 0.81 |
| 252_M | 259_F | 1.044 | 0.81 |
| 146_L | 183_I | 1.043 | 0.81 |
| 10_E | 14_A | 1.042 | 0.81 |
| 251_K | 267_A | 1.039 | 0.81 |
| 269_R | 323_E | 1.037 | 0.81 |
| 91_E | 99_R | 1.035 | 0.81 |
| 16_A | 21_N | 1.035 | 0.81 |
| 201_Y | 204_S | 1.030 | 0.80 |
| 251_K | 342_H | 1.025 | 0.80 |
| 282_V | 286_H | 1.024 | 0.80 |
| 323_E | 340_A | 1.024 | 0.80 |
| 243_K | 323_E | 1.022 | 0.79 |
| 269_R | 342_H | 1.020 | 0.79 |
| 193_R | 204_S | 1.017 | 0.79 |
| 155_L | 159_K | 1.015 | 0.79 |
| 73_C | 140_V | 1.014 | 0.79 |
| 44_R | 144_D | 1.014 | 0.79 |
| 81_E | 151_T | 1.013 | 0.79 |
| 53_H | 82_D | 1.010 | 0.78 |
| 285_I | 324_I | 1.009 | 0.78 |
| 229_T | 236_G | 1.006 | 0.78 |
| 53_H | 148_N | 1.005 | 0.78 |
| 243_K | 269_R | 1.005 | 0.78 |
| 44_R | 47_G | 1.005 | 0.78 |
| 267_A | 345_Y | 1.000 | 0.77 |
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 | |
| 1vj7A | 2 | 0.8524 | 100 | 0.151 | Contact Map |
| 3l9dA | 2 | 0.4656 | 100 | 0.664 | Contact Map |
| 2be3A | 2 | 0.4784 | 100 | 0.729 | Contact Map |
| 3nqwA | 2 | 0.4427 | 100 | 0.735 | Contact Map |
| 3nr1A | 2 | 0.4351 | 100 | 0.741 | Contact Map |
| 3djbA | 2 | 0.458 | 87.4 | 0.967 | Contact Map |
| 2pq7A | 1 | 0.4173 | 81.5 | 0.969 | Contact Map |
| 3b57A | 1 | 0.4377 | 78.5 | 0.97 | Contact Map |
| 4mlmA | 2 | 0.3995 | 74.2 | 0.971 | Contact Map |
| 2pjqA | 4 | 0.4784 | 72.8 | 0.971 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)