| Prasanth Kumar |
| ID: | 1499887159 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 364 (300) | ||
| Sequences: | 4289 (2784) | ||
| Seq/Len: | 14.297 | ||
| Nf(neff/√len): | 160.7 |
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: 14.297).
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 |
| 67_S | 103_T | 5.576 | 1.00 |
| 94_N | 177_W | 3.962 | 1.00 |
| 237_L | 241_Q | 3.548 | 1.00 |
| 152_W | 157_K | 3.161 | 1.00 |
| 94_N | 143_S | 3.089 | 1.00 |
| 146_I | 176_S | 2.969 | 1.00 |
| 84_L | 89_N | 2.866 | 1.00 |
| 119_F | 122_G | 2.370 | 1.00 |
| 126_C | 203_C | 2.335 | 1.00 |
| 240_L | 244_L | 2.146 | 1.00 |
| 236_M | 240_L | 2.063 | 1.00 |
| 68_V | 100_L | 2.038 | 1.00 |
| 281_W | 311_A | 2.035 | 1.00 |
| 232_L | 278_C | 2.027 | 1.00 |
| 99_D | 140_G | 1.980 | 1.00 |
| 152_W | 156_C | 1.914 | 1.00 |
| 96_A | 99_D | 1.904 | 1.00 |
| 171_V | 175_F | 1.902 | 1.00 |
| 75_L | 100_L | 1.892 | 1.00 |
| 99_D | 318_N | 1.878 | 1.00 |
| 276_A | 321_I | 1.872 | 1.00 |
| 124_P | 128_L | 1.870 | 1.00 |
| 146_I | 172_G | 1.849 | 1.00 |
| 150_E | 154_V | 1.797 | 1.00 |
| 131_Y | 135_L | 1.790 | 1.00 |
| 70_T | 316_I | 1.783 | 1.00 |
| 244_L | 248_A | 1.760 | 1.00 |
| 234_I | 238_C | 1.738 | 1.00 |
| 90_W | 173_I | 1.732 | 1.00 |
| 75_L | 93_V | 1.711 | 1.00 |
| 313_S | 317_Y | 1.684 | 1.00 |
| 98_A | 139_T | 1.643 | 1.00 |
| 101_A | 136_C | 1.610 | 1.00 |
| 123_H | 127_V | 1.609 | 1.00 |
| 269_M | 325_M | 1.609 | 1.00 |
| 165_D | 168_L | 1.551 | 1.00 |
| 157_K | 160_G | 1.525 | 1.00 |
| 72_G | 100_L | 1.513 | 1.00 |
| 68_V | 103_T | 1.504 | 1.00 |
| 152_W | 241_Q | 1.502 | 1.00 |
| 131_Y | 188_I | 1.481 | 1.00 |
| 94_N | 173_I | 1.470 | 1.00 |
| 86_H | 89_N | 1.466 | 1.00 |
| 74_V | 319_P | 1.464 | 1.00 |
| 185_A | 189_F | 1.455 | 1.00 |
| 145_A | 238_C | 1.429 | 1.00 |
| 98_A | 177_W | 1.424 | 1.00 |
| 142_W | 179_W | 1.397 | 0.99 |
| 172_G | 176_S | 1.393 | 0.99 |
| 91_I | 147_I | 1.390 | 0.99 |
| 177_W | 319_P | 1.390 | 0.99 |
| 167_K | 171_V | 1.379 | 0.99 |
| 244_L | 247_R | 1.369 | 0.99 |
| 143_S | 177_W | 1.357 | 0.99 |
| 126_C | 319_P | 1.354 | 0.99 |
| 241_Q | 244_L | 1.350 | 0.99 |
| 70_T | 318_N | 1.345 | 0.99 |
| 143_S | 173_I | 1.343 | 0.99 |
| 263_E | 267_T | 1.340 | 0.99 |
| 144_L | 235_I | 1.329 | 0.99 |
| 149_W | 238_C | 1.318 | 0.99 |
| 98_A | 140_G | 1.301 | 0.99 |
| 75_L | 97_V | 1.299 | 0.99 |
| 85_R | 89_N | 1.296 | 0.99 |
| 51_W | 55_L | 1.290 | 0.99 |
| 72_G | 76_A | 1.284 | 0.99 |
| 148_S | 238_C | 1.270 | 0.99 |
| 91_I | 169_A | 1.267 | 0.99 |
| 232_L | 236_M | 1.265 | 0.99 |
| 78_T | 93_V | 1.264 | 0.99 |
| 154_V | 158_P | 1.257 | 0.99 |
| 74_V | 96_A | 1.248 | 0.99 |
| 303_M | 307_P | 1.234 | 0.98 |
| 91_I | 150_E | 1.232 | 0.98 |
| 243_W | 247_R | 1.223 | 0.98 |
| 286_F | 290_F | 1.220 | 0.98 |
| 155_V | 159_F | 1.215 | 0.98 |
| 152_W | 238_C | 1.215 | 0.98 |
| 272_V | 325_M | 1.214 | 0.98 |
| 108_T | 111_I | 1.208 | 0.98 |
| 122_G | 125_M | 1.201 | 0.98 |
| 329_F | 333_I | 1.199 | 0.98 |
| 222_V | 226_T | 1.197 | 0.98 |
| 103_T | 326_N | 1.189 | 0.98 |
| 167_K | 170_I | 1.173 | 0.98 |
| 95_L | 322_Y | 1.167 | 0.97 |
| 239_Y | 319_P | 1.165 | 0.97 |
| 100_L | 103_T | 1.163 | 0.97 |
| 183_W | 222_V | 1.161 | 0.97 |
| 228_C | 277_Y | 1.161 | 0.97 |
| 145_A | 234_I | 1.158 | 0.97 |
| 221_I | 225_V | 1.148 | 0.97 |
| 70_T | 96_A | 1.145 | 0.97 |
| 96_A | 322_Y | 1.137 | 0.97 |
| 99_D | 314_A | 1.137 | 0.97 |
| 155_V | 158_P | 1.136 | 0.97 |
| 112_V | 121_L | 1.133 | 0.97 |
| 74_V | 322_Y | 1.130 | 0.97 |
| 91_I | 143_S | 1.125 | 0.97 |
| 74_V | 323_V | 1.122 | 0.97 |
| 148_S | 235_I | 1.120 | 0.96 |
| 170_I | 174_A | 1.119 | 0.96 |
| 174_A | 178_I | 1.109 | 0.96 |
| 135_L | 181_A | 1.102 | 0.96 |
| 284_Y | 311_A | 1.101 | 0.96 |
| 67_S | 316_I | 1.100 | 0.96 |
| 243_W | 246_I | 1.095 | 0.96 |
| 46_H | 49_P | 1.088 | 0.96 |
| 186_P | 219_Y | 1.082 | 0.96 |
| 81_F | 332_C | 1.082 | 0.96 |
| 185_A | 188_I | 1.075 | 0.95 |
| 228_C | 282_G | 1.075 | 0.95 |
| 306_L | 310_F | 1.071 | 0.95 |
| 103_T | 147_I | 1.066 | 0.95 |
| 139_T | 143_S | 1.062 | 0.95 |
| 237_L | 240_L | 1.060 | 0.95 |
| 139_T | 180_S | 1.054 | 0.95 |
| 74_V | 281_W | 1.053 | 0.95 |
| 119_F | 126_C | 1.046 | 0.94 |
| 51_W | 54_H | 1.045 | 0.94 |
| 321_I | 325_M | 1.039 | 0.94 |
| 241_Q | 245_A | 1.035 | 0.94 |
| 149_W | 153_L | 1.034 | 0.94 |
| 142_W | 180_S | 1.033 | 0.94 |
| 77_A | 329_F | 1.033 | 0.94 |
| 171_V | 174_A | 1.032 | 0.94 |
| 49_P | 52_V | 1.031 | 0.94 |
| 249_V | 253_Q | 1.027 | 0.94 |
| 235_I | 238_C | 1.027 | 0.94 |
| 140_G | 318_N | 1.023 | 0.93 |
| 173_I | 180_S | 1.017 | 0.93 |
| 138_I | 223_L | 1.017 | 0.93 |
| 145_A | 235_I | 1.017 | 0.93 |
| 271_V | 275_F | 1.015 | 0.93 |
| 191_W | 246_I | 1.013 | 0.93 |
| 239_Y | 274_I | 1.007 | 0.93 |
| 74_V | 329_F | 1.004 | 0.93 |
| 46_H | 50_R | 1.004 | 0.93 |
| 242_V | 270_V | 1.002 | 0.92 |
| 74_V | 78_T | 1.002 | 0.92 |
| 151_R | 314_A | 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 | |
| 1u19A | 2 | 0.9478 | 100 | 0.335 | Contact Map |
| 4pxzA | 1 | 0.7637 | 100 | 0.349 | Contact Map |
| 4iarA | 1 | 0.772 | 100 | 0.351 | Contact Map |
| 4zwjA | 4 | 0 | 100 | 0.355 | Contact Map |
| 2rh1A | 1 | 0.7885 | 100 | 0.362 | Contact Map |
| 3uonA | 1 | 0.7747 | 100 | 0.364 | Contact Map |
| 3pblA | 2 | 0.7473 | 100 | 0.365 | Contact Map |
| 4s0vA | 1 | 0.7775 | 100 | 0.375 | Contact Map |
| 3vw7A | 1 | 0.7775 | 100 | 0.375 | Contact Map |
| 3oduA | 2 | 0.8269 | 100 | 0.376 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)