| alex |
| ID: | 1452273470 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 347 (332) | ||
| Sequences: | 15816 (9588.6) | ||
| Seq/Len: | 47.639 | ||
| Nf(neff/√len): | 526.2 |
Jackhmmer Results: (2015_08)
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: 47.639).
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 |
| 164_V | 267_I | 2.935 | 1.00 |
| 272_M | 310_E | 2.750 | 1.00 |
| 197_A | 262_E | 2.663 | 1.00 |
| 186_S | 266_G | 2.646 | 1.00 |
| 109_R | 136_R | 2.622 | 1.00 |
| 20_A | 168_G | 2.607 | 1.00 |
| 205_N | 255_E | 2.546 | 1.00 |
| 233_E | 250_T | 2.406 | 1.00 |
| 320_D | 323_T | 2.294 | 1.00 |
| 261_Q | 265_T | 2.169 | 1.00 |
| 112_V | 130_A | 2.164 | 1.00 |
| 217_R | 221_E | 2.043 | 1.00 |
| 252_N | 255_E | 2.031 | 1.00 |
| 305_R | 309_E | 2.004 | 1.00 |
| 308_M | 314_P | 1.994 | 1.00 |
| 90_M | 94_F | 1.978 | 1.00 |
| 19_T | 169_G | 1.975 | 1.00 |
| 255_E | 258_E | 1.969 | 1.00 |
| 306_L | 309_E | 1.966 | 1.00 |
| 299_L | 322_L | 1.897 | 1.00 |
| 160_G | 177_S | 1.889 | 1.00 |
| 201_Y | 259_A | 1.883 | 1.00 |
| 93_H | 96_K | 1.859 | 1.00 |
| 223_G | 226_Y | 1.858 | 1.00 |
| 297_G | 300_L | 1.858 | 1.00 |
| 175_V | 274_A | 1.852 | 1.00 |
| 72_A | 192_D | 1.846 | 1.00 |
| 304_D | 317_V | 1.836 | 1.00 |
| 124_R | 128_E | 1.827 | 1.00 |
| 223_G | 227_P | 1.826 | 1.00 |
| 194_F | 260_L | 1.819 | 1.00 |
| 22_T | 37_S | 1.787 | 1.00 |
| 198_I | 251_L | 1.782 | 1.00 |
| 25_Y | 330_G | 1.750 | 1.00 |
| 235_E | 250_T | 1.748 | 1.00 |
| 268_V | 310_E | 1.745 | 1.00 |
| 113_C | 329_G | 1.716 | 1.00 |
| 197_A | 263_P | 1.712 | 1.00 |
| 268_V | 306_L | 1.684 | 1.00 |
| 264_L | 302_N | 1.663 | 1.00 |
| 194_F | 263_P | 1.662 | 1.00 |
| 13_L | 24_I | 1.654 | 1.00 |
| 175_V | 278_C | 1.634 | 1.00 |
| 323_T | 327_R | 1.632 | 1.00 |
| 166_I | 171_T | 1.620 | 1.00 |
| 57_H | 61_Q | 1.616 | 1.00 |
| 253_S | 257_L | 1.606 | 1.00 |
| 28_G | 33_L | 1.602 | 1.00 |
| 127_R | 131_Q | 1.583 | 1.00 |
| 260_L | 264_L | 1.575 | 1.00 |
| 87_T | 91_L | 1.569 | 1.00 |
| 261_Q | 306_L | 1.563 | 1.00 |
| 235_E | 248_G | 1.562 | 1.00 |
| 25_Y | 326_A | 1.555 | 1.00 |
| 141_I | 332_A | 1.553 | 1.00 |
| 268_V | 272_M | 1.544 | 1.00 |
| 201_Y | 205_N | 1.533 | 1.00 |
| 256_I | 300_L | 1.531 | 1.00 |
| 159_T | 288_E | 1.521 | 1.00 |
| 162_M | 175_V | 1.519 | 1.00 |
| 191_G | 297_G | 1.518 | 1.00 |
| 197_A | 200_N | 1.502 | 1.00 |
| 273_V | 277_Q | 1.492 | 1.00 |
| 128_E | 131_Q | 1.475 | 1.00 |
| 264_L | 306_L | 1.456 | 1.00 |
| 82_A | 85_F | 1.455 | 1.00 |
| 27_K | 30_G | 1.447 | 1.00 |
| 304_D | 308_M | 1.442 | 1.00 |
| 10_S | 109_R | 1.439 | 1.00 |
| 260_L | 300_L | 1.419 | 1.00 |
| 234_I | 238_G | 1.415 | 1.00 |
| 306_L | 310_E | 1.411 | 1.00 |
| 119_T | 122_E | 1.408 | 1.00 |
| 281_E | 284_S | 1.395 | 0.99 |
| 171_T | 267_I | 1.382 | 0.99 |
| 90_M | 98_V | 1.382 | 0.99 |
| 166_I | 194_F | 1.376 | 0.99 |
| 260_L | 263_P | 1.361 | 0.99 |
| 320_D | 327_R | 1.357 | 0.99 |
| 80_V | 85_F | 1.353 | 0.99 |
| 115_P | 118_A | 1.346 | 0.99 |
| 291_M | 311_T | 1.342 | 0.99 |
| 91_L | 98_V | 1.333 | 0.99 |
| 199_I | 219_K | 1.333 | 0.99 |
| 142_E | 145_M | 1.327 | 0.99 |
| 92_Q | 96_K | 1.326 | 0.99 |
| 14_S | 329_G | 1.322 | 0.99 |
| 42_R | 52_V | 1.308 | 0.99 |
| 81_I | 85_F | 1.306 | 0.99 |
| 201_Y | 255_E | 1.299 | 0.99 |
| 97_Q | 100_S | 1.293 | 0.99 |
| 173_V | 274_A | 1.284 | 0.99 |
| 293_L | 307_L | 1.280 | 0.99 |
| 23_L | 34_N | 1.278 | 0.99 |
| 194_F | 264_L | 1.278 | 0.99 |
| 131_Q | 136_R | 1.272 | 0.99 |
| 77_K | 81_I | 1.270 | 0.99 |
| 196_E | 200_N | 1.261 | 0.99 |
| 202_V | 249_F | 1.260 | 0.99 |
| 91_L | 95_I | 1.257 | 0.99 |
| 272_M | 276_E | 1.257 | 0.99 |
| 194_F | 297_G | 1.255 | 0.99 |
| 93_H | 97_Q | 1.255 | 0.99 |
| 258_E | 261_Q | 1.253 | 0.99 |
| 257_L | 305_R | 1.244 | 0.98 |
| 147_A | 325_V | 1.242 | 0.98 |
| 269_S | 273_V | 1.235 | 0.98 |
| 70_I | 73_I | 1.234 | 0.98 |
| 271_V | 307_L | 1.229 | 0.98 |
| 12_D | 333_L | 1.226 | 0.98 |
| 23_L | 326_A | 1.224 | 0.98 |
| 205_N | 208_S | 1.212 | 0.98 |
| 293_L | 298_A | 1.210 | 0.98 |
| 221_E | 224_S | 1.209 | 0.98 |
| 162_M | 173_V | 1.202 | 0.98 |
| 109_R | 138_V | 1.196 | 0.98 |
| 261_Q | 302_N | 1.193 | 0.98 |
| 88_E | 92_Q | 1.192 | 0.98 |
| 269_S | 272_M | 1.192 | 0.98 |
| 83_D | 86_V | 1.187 | 0.98 |
| 141_I | 146_A | 1.183 | 0.98 |
| 88_E | 132_G | 1.181 | 0.98 |
| 202_V | 222_I | 1.177 | 0.98 |
| 164_V | 171_T | 1.176 | 0.98 |
| 12_D | 109_R | 1.175 | 0.98 |
| 27_K | 33_L | 1.170 | 0.97 |
| 165_D | 172_E | 1.167 | 0.97 |
| 205_N | 209_L | 1.165 | 0.97 |
| 237_R | 248_G | 1.164 | 0.97 |
| 22_T | 98_V | 1.163 | 0.97 |
| 80_V | 86_V | 1.162 | 0.97 |
| 109_R | 137_E | 1.162 | 0.97 |
| 302_N | 305_R | 1.161 | 0.97 |
| 265_T | 269_S | 1.159 | 0.97 |
| 143_E | 172_E | 1.159 | 0.97 |
| 24_I | 98_V | 1.157 | 0.97 |
| 36_P | 40_A | 1.156 | 0.97 |
| 211_G | 214_T | 1.147 | 0.97 |
| 305_R | 308_M | 1.145 | 0.97 |
| 66_T | 69_N | 1.141 | 0.97 |
| 222_I | 226_Y | 1.139 | 0.97 |
| 14_S | 326_A | 1.137 | 0.97 |
| 89_K | 93_H | 1.131 | 0.97 |
| 127_R | 140_L | 1.129 | 0.97 |
| 35_E | 41_I | 1.122 | 0.97 |
| 21_N | 322_L | 1.120 | 0.96 |
| 28_G | 31_I | 1.120 | 0.96 |
| 159_T | 287_S | 1.116 | 0.96 |
| 274_A | 278_C | 1.116 | 0.96 |
| 123_R | 142_E | 1.114 | 0.96 |
| 175_V | 286_I | 1.111 | 0.96 |
| 90_M | 95_I | 1.108 | 0.96 |
| 173_V | 270_A | 1.107 | 0.96 |
| 29_Q | 32_V | 1.107 | 0.96 |
| 302_N | 306_L | 1.098 | 0.96 |
| 197_A | 260_L | 1.097 | 0.96 |
| 80_V | 83_D | 1.095 | 0.96 |
| 185_S | 273_V | 1.095 | 0.96 |
| 77_K | 80_V | 1.095 | 0.96 |
| 94_F | 98_V | 1.094 | 0.96 |
| 169_G | 172_E | 1.087 | 0.96 |
| 114_V | 140_L | 1.080 | 0.95 |
| 81_I | 86_V | 1.080 | 0.95 |
| 195_D | 223_G | 1.079 | 0.95 |
| 89_K | 92_Q | 1.077 | 0.95 |
| 159_T | 289_R | 1.076 | 0.95 |
| 265_T | 306_L | 1.071 | 0.95 |
| 219_K | 223_G | 1.070 | 0.95 |
| 162_M | 271_V | 1.069 | 0.95 |
| 273_V | 276_E | 1.064 | 0.95 |
| 116_V | 144_P | 1.054 | 0.95 |
| 307_L | 315_V | 1.053 | 0.95 |
| 17_L | 126_I | 1.053 | 0.95 |
| 41_I | 93_H | 1.049 | 0.94 |
| 194_F | 300_L | 1.044 | 0.94 |
| 166_I | 303_L | 1.043 | 0.94 |
| 82_A | 86_V | 1.041 | 0.94 |
| 27_K | 334_E | 1.039 | 0.94 |
| 90_M | 93_H | 1.039 | 0.94 |
| 79_G | 83_D | 1.038 | 0.94 |
| 257_L | 261_Q | 1.034 | 0.94 |
| 91_L | 94_F | 1.029 | 0.94 |
| 165_D | 169_G | 1.025 | 0.93 |
| 62_M | 66_T | 1.022 | 0.93 |
| 94_F | 97_Q | 1.021 | 0.93 |
| 222_I | 225_A | 1.020 | 0.93 |
| 93_H | 98_V | 1.019 | 0.93 |
| 164_V | 271_V | 1.015 | 0.93 |
| 29_Q | 33_L | 1.015 | 0.93 |
| 92_Q | 132_G | 1.015 | 0.93 |
| 27_K | 32_V | 1.013 | 0.93 |
| 294_T | 324_C | 1.012 | 0.93 |
| 166_I | 297_G | 1.010 | 0.93 |
| 151_A | 292_V | 1.008 | 0.93 |
| 160_G | 280_P | 1.004 | 0.93 |
| 147_A | 294_T | 1.001 | 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 | |
| 4jneA | 2 | 0.951 | 100 | 0.247 | Contact Map |
| 2v7yA | 1 | 0.9481 | 100 | 0.257 | Contact Map |
| 4fl9A | 1 | 0.9222 | 100 | 0.259 | Contact Map |
| 3d2fA | 2 | 0.9452 | 100 | 0.273 | Contact Map |
| 4rtfD | 1 | 0.9107 | 100 | 0.283 | Contact Map |
| 3i33A | 1 | 0.9164 | 100 | 0.289 | Contact Map |
| 1jceA | 1 | 0.9481 | 100 | 0.299 | Contact Map |
| 4kboA | 1 | 0.9164 | 100 | 0.3 | Contact Map |
| 4j8fA | 1 | 0.9568 | 100 | 0.308 | Contact Map |
| 4czgA | 1 | 0.9164 | 100 | 0.315 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)