| VIPR-VIP |
| ID: | 1489432764 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 376 (370) | ||
| Sequences: | 769 (451.9) | ||
| Seq/Len: | 2.078 | ||
| Nf(neff/√len): | 23.5 |
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: 2.078).
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 |
| 352_C | 355_N | 2.741 | 1.00 |
| 31_D | 35_C | 2.629 | 1.00 |
| 352_C | 357_E | 2.563 | 1.00 |
| 277_C | 280_R | 2.503 | 1.00 |
| 351_Y | 357_E | 2.397 | 1.00 |
| 39_T | 45_V | 2.192 | 1.00 |
| 353_F | 357_E | 2.025 | 0.99 |
| 72_G | 81_Y | 1.909 | 0.99 |
| 31_D | 36_W | 1.897 | 0.99 |
| 344_G | 352_C | 1.887 | 0.98 |
| 351_Y | 355_N | 1.880 | 0.98 |
| 355_N | 358_V | 1.824 | 0.98 |
| 112_G | 120_L | 1.786 | 0.98 |
| 124_T | 142_M | 1.756 | 0.97 |
| 31_D | 50_P | 1.726 | 0.97 |
| 71_E | 79_G | 1.724 | 0.97 |
| 34_T | 47_L | 1.693 | 0.96 |
| 344_G | 355_N | 1.647 | 0.96 |
| 344_G | 347_V | 1.644 | 0.95 |
| 354_L | 357_E | 1.538 | 0.93 |
| 352_C | 358_V | 1.535 | 0.93 |
| 348_A | 357_E | 1.515 | 0.92 |
| 361_E | 364_R | 1.510 | 0.92 |
| 116_S | 123_A | 1.504 | 0.92 |
| 309_L | 314_G | 1.495 | 0.91 |
| 28_N | 38_A | 1.474 | 0.91 |
| 307_L | 311_P | 1.473 | 0.91 |
| 361_E | 366_W | 1.472 | 0.91 |
| 116_S | 120_L | 1.469 | 0.91 |
| 260_I | 264_I | 1.460 | 0.90 |
| 85_C | 90_K | 1.455 | 0.90 |
| 31_D | 49_C | 1.452 | 0.90 |
| 347_V | 355_N | 1.430 | 0.89 |
| 275_F | 302_L | 1.429 | 0.89 |
| 35_C | 50_P | 1.428 | 0.89 |
| 348_A | 352_C | 1.426 | 0.89 |
| 195_W | 199_E | 1.419 | 0.88 |
| 147_S | 192_N | 1.419 | 0.88 |
| 72_G | 85_C | 1.397 | 0.87 |
| 199_E | 203_L | 1.387 | 0.87 |
| 347_V | 357_E | 1.386 | 0.87 |
| 344_G | 357_E | 1.384 | 0.87 |
| 13_L | 26_I | 1.360 | 0.85 |
| 137_R | 141_H | 1.357 | 0.85 |
| 112_G | 126_I | 1.354 | 0.85 |
| 302_L | 305_S | 1.342 | 0.84 |
| 258_W | 262_A | 1.335 | 0.84 |
| 113_H | 123_A | 1.333 | 0.84 |
| 112_G | 116_S | 1.326 | 0.83 |
| 68_C | 85_C | 1.318 | 0.83 |
| 30_W | 35_C | 1.313 | 0.83 |
| 204_H | 277_C | 1.311 | 0.82 |
| 8_D | 12_R | 1.309 | 0.82 |
| 344_G | 348_A | 1.293 | 0.81 |
| 229_P | 236_W | 1.291 | 0.81 |
| 153_T | 157_I | 1.287 | 0.81 |
| 305_S | 336_E | 1.283 | 0.80 |
| 187_Y | 199_E | 1.283 | 0.80 |
| 71_E | 81_Y | 1.281 | 0.80 |
| 179_K | 245_D | 1.274 | 0.80 |
| 19_V | 23_L | 1.271 | 0.80 |
| 187_Y | 195_W | 1.269 | 0.79 |
| 200_G | 203_L | 1.253 | 0.78 |
| 282_L | 286_L | 1.252 | 0.78 |
| 72_G | 80_P | 1.250 | 0.78 |
| 35_C | 49_C | 1.246 | 0.78 |
| 72_G | 79_G | 1.243 | 0.77 |
| 30_W | 33_L | 1.229 | 0.76 |
| 21_K | 26_I | 1.227 | 0.76 |
| 11_T | 26_I | 1.223 | 0.76 |
| 116_S | 130_F | 1.221 | 0.76 |
| 204_H | 209_V | 1.220 | 0.76 |
| 11_T | 28_N | 1.218 | 0.75 |
| 133_L | 141_H | 1.216 | 0.75 |
| 136_T | 147_S | 1.216 | 0.75 |
| 192_N | 195_W | 1.213 | 0.75 |
| 13_L | 28_N | 1.211 | 0.75 |
| 116_S | 126_I | 1.209 | 0.75 |
| 286_L | 297_S | 1.206 | 0.74 |
| 353_F | 358_V | 1.201 | 0.74 |
| 178_C | 199_E | 1.199 | 0.74 |
| 19_V | 25_S | 1.198 | 0.74 |
| 134_H | 138_N | 1.191 | 0.73 |
| 141_H | 144_L | 1.179 | 0.72 |
| 240_R | 246_T | 1.178 | 0.72 |
| 17_M | 25_S | 1.174 | 0.72 |
| 15_K | 19_V | 1.173 | 0.71 |
| 9_N | 19_V | 1.166 | 0.71 |
| 9_N | 17_M | 1.166 | 0.71 |
| 36_W | 49_C | 1.166 | 0.71 |
| 36_W | 50_P | 1.164 | 0.71 |
| 18_A | 22_Y | 1.160 | 0.70 |
| 116_S | 127_L | 1.159 | 0.70 |
| 194_F | 224_I | 1.159 | 0.70 |
| 12_R | 19_V | 1.150 | 0.69 |
| 119_A | 161_I | 1.149 | 0.69 |
| 195_W | 203_L | 1.149 | 0.69 |
| 359_Q | 364_R | 1.149 | 0.69 |
| 12_R | 15_K | 1.148 | 0.69 |
| 135_C | 148_F | 1.148 | 0.69 |
| 348_A | 351_Y | 1.144 | 0.69 |
| 196_L | 275_F | 1.141 | 0.68 |
| 345_F | 349_I | 1.140 | 0.68 |
| 249_W | 263_P | 1.137 | 0.68 |
| 20_K | 23_L | 1.135 | 0.68 |
| 195_W | 226_W | 1.133 | 0.68 |
| 16_Q | 23_L | 1.133 | 0.68 |
| 216_K | 318_I | 1.132 | 0.68 |
| 9_N | 14_R | 1.130 | 0.67 |
| 204_H | 280_R | 1.127 | 0.67 |
| 9_N | 12_R | 1.125 | 0.67 |
| 16_Q | 19_V | 1.125 | 0.67 |
| 351_Y | 354_L | 1.124 | 0.67 |
| 274_L | 278_I | 1.119 | 0.66 |
| 200_G | 221_Y | 1.117 | 0.66 |
| 20_K | 25_S | 1.116 | 0.66 |
| 7_T | 10_Y | 1.115 | 0.66 |
| 344_G | 358_V | 1.113 | 0.66 |
| 178_C | 195_W | 1.112 | 0.66 |
| 86_G | 90_K | 1.112 | 0.66 |
| 119_A | 345_F | 1.111 | 0.65 |
| 8_D | 15_K | 1.111 | 0.65 |
| 24_N | 27_L | 1.103 | 0.65 |
| 17_M | 24_N | 1.103 | 0.65 |
| 8_D | 17_M | 1.102 | 0.65 |
| 344_G | 351_Y | 1.100 | 0.64 |
| 196_L | 207_L | 1.100 | 0.64 |
| 19_V | 24_N | 1.099 | 0.64 |
| 201_L | 274_L | 1.097 | 0.64 |
| 14_R | 26_I | 1.097 | 0.64 |
| 9_N | 15_K | 1.094 | 0.64 |
| 133_L | 137_R | 1.091 | 0.63 |
| 197_L | 231_I | 1.088 | 0.63 |
| 12_R | 17_M | 1.083 | 0.63 |
| 271_N | 285_K | 1.082 | 0.62 |
| 352_C | 356_G | 1.079 | 0.62 |
| 185_F | 313_F | 1.078 | 0.62 |
| 113_H | 120_L | 1.075 | 0.62 |
| 313_F | 337_L | 1.074 | 0.62 |
| 81_Y | 85_C | 1.073 | 0.61 |
| 350_L | 355_N | 1.073 | 0.61 |
| 311_P | 343_Q | 1.067 | 0.61 |
| 9_N | 16_Q | 1.065 | 0.61 |
| 12_R | 16_Q | 1.064 | 0.61 |
| 359_Q | 366_W | 1.064 | 0.61 |
| 238_I | 242_Y | 1.063 | 0.60 |
| 196_L | 305_S | 1.062 | 0.60 |
| 202_Y | 225_G | 1.061 | 0.60 |
| 22_Y | 26_I | 1.060 | 0.60 |
| 15_K | 20_K | 1.059 | 0.60 |
| 20_K | 24_N | 1.059 | 0.60 |
| 29_M | 38_A | 1.058 | 0.60 |
| 14_R | 23_L | 1.058 | 0.60 |
| 15_K | 25_S | 1.050 | 0.59 |
| 16_Q | 21_K | 1.049 | 0.59 |
| 120_L | 123_A | 1.048 | 0.59 |
| 8_D | 14_R | 1.045 | 0.58 |
| 278_I | 286_L | 1.043 | 0.58 |
| 239_I | 259_I | 1.043 | 0.58 |
| 112_G | 119_A | 1.043 | 0.58 |
| 343_Q | 355_N | 1.041 | 0.58 |
| 123_A | 126_I | 1.039 | 0.58 |
| 278_I | 285_K | 1.039 | 0.58 |
| 23_L | 26_I | 1.038 | 0.58 |
| 17_M | 22_Y | 1.037 | 0.58 |
| 347_V | 352_C | 1.037 | 0.58 |
| 349_I | 354_L | 1.033 | 0.57 |
| 8_D | 13_L | 1.033 | 0.57 |
| 109_Y | 130_F | 1.032 | 0.57 |
| 257_W | 261_K | 1.032 | 0.57 |
| 21_K | 25_S | 1.029 | 0.57 |
| 87_L | 90_K | 1.029 | 0.57 |
| 71_E | 82_P | 1.028 | 0.57 |
| 309_L | 343_Q | 1.027 | 0.56 |
| 138_N | 151_R | 1.024 | 0.56 |
| 15_K | 18_A | 1.021 | 0.56 |
| 278_I | 282_L | 1.016 | 0.55 |
| 358_V | 361_E | 1.015 | 0.55 |
| 332_K | 337_L | 1.012 | 0.55 |
| 348_A | 355_N | 1.011 | 0.55 |
| 351_Y | 358_V | 1.010 | 0.55 |
| 109_Y | 113_H | 1.006 | 0.54 |
| 315_V | 323_F | 1.004 | 0.54 |
| 199_E | 226_W | 1.002 | 0.54 |
| 18_A | 21_K | 1.002 | 0.54 |
| 16_Q | 26_I | 1.001 | 0.54 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 4k5yA | 3 | 0.6649 | 100 | 0.532 | Contact Map |
| 4l6rA | 1 | 0.9362 | 100 | 0.626 | Contact Map |
| 4jkvA | 2 | 0.9069 | 99.9 | 0.791 | Contact Map |
| 4qinA | 1 | 0.7979 | 99.9 | 0.8 | Contact Map |
| 3n94A | 1 | 0.2394 | 99.7 | 0.848 | Contact Map |
| 2jodA | 1 | 0.2473 | 99.7 | 0.852 | Contact Map |
| 4hj0A | 2 | 0.2234 | 99.7 | 0.855 | Contact Map |
| 2x57A | 3 | 0.234 | 99.7 | 0.855 | Contact Map |
| 2xdgA | 2 | 0.2181 | 99.7 | 0.857 | Contact Map |
| 2qkhA | 1 | 0.2101 | 99.7 | 0.858 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)