| rhod |
| ID: | 1431262161 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 328 (285) | ||
| Sequences: | 25227 (13089.4) | ||
| Seq/Len: | 88.516 | ||
| Nf(neff/√len): | 775.3 |
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: 88.516).
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 |
| 51_G | 87_V | 4.598 | 1.00 |
| 78_N | 161_W | 4.096 | 1.00 |
| 221_F | 225_Q | 3.150 | 1.00 |
| 130_V | 160_T | 2.602 | 1.00 |
| 151_N | 155_M | 2.597 | 1.00 |
| 141_K | 144_S | 2.497 | 1.00 |
| 78_N | 127_S | 2.349 | 1.00 |
| 110_C | 187_C | 2.213 | 1.00 |
| 108_T | 112_L | 2.199 | 1.00 |
| 107_P | 111_N | 2.189 | 1.00 |
| 130_V | 156_G | 2.165 | 1.00 |
| 136_Y | 141_K | 2.047 | 1.00 |
| 62_T | 77_L | 2.039 | 1.00 |
| 225_Q | 228_F | 2.038 | 1.00 |
| 82_A | 123_I | 2.028 | 1.00 |
| 68_L | 73_N | 2.025 | 1.00 |
| 224_G | 228_F | 2.013 | 1.00 |
| 93_T | 97_T | 2.006 | 1.00 |
| 136_Y | 140_C | 1.997 | 1.00 |
| 85_F | 120_G | 1.977 | 1.00 |
| 119_L | 165_L | 1.947 | 1.00 |
| 115_F | 119_L | 1.879 | 1.00 |
| 59_L | 77_L | 1.852 | 1.00 |
| 65_H | 316_C | 1.801 | 1.00 |
| 270_G | 274_Y | 1.766 | 1.00 |
| 78_N | 157_V | 1.722 | 1.00 |
| 51_G | 300_V | 1.716 | 1.00 |
| 48_I | 88_F | 1.693 | 1.00 |
| 63_V | 77_L | 1.691 | 1.00 |
| 74_Y | 157_V | 1.661 | 1.00 |
| 218_V | 222_C | 1.641 | 1.00 |
| 136_Y | 225_Q | 1.640 | 1.00 |
| 77_L | 81_V | 1.605 | 1.00 |
| 265_W | 295_A | 1.601 | 1.00 |
| 56_F | 60_Y | 1.598 | 1.00 |
| 91_F | 94_T | 1.581 | 1.00 |
| 149_G | 152_H | 1.577 | 1.00 |
| 169_A | 173_V | 1.541 | 1.00 |
| 111_N | 176_S | 1.511 | 1.00 |
| 225_Q | 229_T | 1.509 | 1.00 |
| 123_I | 164_A | 1.507 | 1.00 |
| 82_A | 124_A | 1.498 | 1.00 |
| 155_M | 159_F | 1.491 | 1.00 |
| 154_I | 158_A | 1.490 | 1.00 |
| 103_F | 106_G | 1.470 | 1.00 |
| 223_Y | 226_L | 1.460 | 1.00 |
| 248_K | 252_R | 1.457 | 1.00 |
| 134_E | 138_V | 1.445 | 1.00 |
| 144_S | 147_R | 1.441 | 1.00 |
| 122_E | 211_H | 1.438 | 1.00 |
| 106_G | 109_G | 1.431 | 1.00 |
| 302_N | 306_Y | 1.427 | 1.00 |
| 125_L | 129_V | 1.389 | 0.99 |
| 284_G | 287_F | 1.376 | 0.99 |
| 126_W | 160_T | 1.367 | 0.99 |
| 129_V | 218_V | 1.356 | 0.99 |
| 228_F | 232_E | 1.352 | 0.99 |
| 316_C | 319_T | 1.341 | 0.99 |
| 138_V | 142_P | 1.333 | 0.99 |
| 127_S | 157_V | 1.328 | 0.99 |
| 278_H | 281_S | 1.327 | 0.99 |
| 136_Y | 222_C | 1.327 | 0.99 |
| 140_C | 229_T | 1.311 | 0.99 |
| 281_S | 285_P | 1.307 | 0.99 |
| 50_L | 300_V | 1.299 | 0.99 |
| 282_D | 285_P | 1.292 | 0.99 |
| 156_G | 160_T | 1.284 | 0.99 |
| 81_V | 85_F | 1.284 | 0.99 |
| 260_A | 305_I | 1.272 | 0.99 |
| 56_F | 84_L | 1.271 | 0.99 |
| 108_T | 111_N | 1.270 | 0.99 |
| 75_I | 153_A | 1.267 | 0.99 |
| 79_L | 83_D | 1.262 | 0.99 |
| 57_L | 61_V | 1.250 | 0.99 |
| 115_F | 165_L | 1.236 | 0.98 |
| 262_L | 266_L | 1.234 | 0.98 |
| 128_L | 219_I | 1.234 | 0.98 |
| 58_T | 307_I | 1.233 | 0.98 |
| 115_F | 172_L | 1.231 | 0.98 |
| 70_T | 73_N | 1.228 | 0.98 |
| 253_M | 309_M | 1.214 | 0.98 |
| 60_Y | 64_Q | 1.208 | 0.98 |
| 125_L | 215_P | 1.197 | 0.98 |
| 38_S | 42_A | 1.193 | 0.98 |
| 54_I | 300_V | 1.176 | 0.98 |
| 83_D | 302_N | 1.173 | 0.98 |
| 127_S | 161_W | 1.171 | 0.98 |
| 52_F | 84_L | 1.170 | 0.97 |
| 65_H | 319_T | 1.170 | 0.97 |
| 256_I | 309_M | 1.167 | 0.97 |
| 93_T | 109_G | 1.163 | 0.97 |
| 122_E | 164_A | 1.159 | 0.97 |
| 129_V | 222_C | 1.153 | 0.97 |
| 297_T | 301_Y | 1.150 | 0.97 |
| 230_V | 250_V | 1.148 | 0.97 |
| 255_I | 259_I | 1.147 | 0.97 |
| 241_A | 244_Q | 1.145 | 0.97 |
| 285_P | 288_M | 1.144 | 0.97 |
| 202_S | 206_Y | 1.136 | 0.97 |
| 75_I | 131_L | 1.134 | 0.97 |
| 243_T | 247_E | 1.132 | 0.97 |
| 133_I | 222_C | 1.132 | 0.97 |
| 233_A | 237_Q | 1.131 | 0.97 |
| 54_I | 304_V | 1.126 | 0.97 |
| 92_T | 95_L | 1.120 | 0.96 |
| 220_F | 224_G | 1.119 | 0.96 |
| 61_V | 313_F | 1.118 | 0.96 |
| 62_T | 69_R | 1.116 | 0.96 |
| 125_L | 261_F | 1.115 | 0.96 |
| 227_V | 231_K | 1.114 | 0.96 |
| 59_L | 80_A | 1.111 | 0.96 |
| 208_F | 213_I | 1.108 | 0.96 |
| 126_W | 163_M | 1.107 | 0.96 |
| 275_I | 278_H | 1.106 | 0.96 |
| 150_E | 154_I | 1.105 | 0.96 |
| 152_H | 155_M | 1.102 | 0.96 |
| 74_Y | 154_I | 1.102 | 0.96 |
| 164_A | 168_A | 1.098 | 0.96 |
| 94_T | 98_S | 1.092 | 0.96 |
| 183_M | 190_D | 1.088 | 0.96 |
| 129_V | 215_P | 1.086 | 0.96 |
| 141_K | 147_R | 1.086 | 0.96 |
| 272_A | 276_F | 1.080 | 0.95 |
| 119_L | 168_A | 1.075 | 0.95 |
| 126_W | 215_P | 1.073 | 0.95 |
| 274_Y | 277_T | 1.073 | 0.95 |
| 89_G | 92_T | 1.072 | 0.95 |
| 273_F | 276_F | 1.069 | 0.95 |
| 269_A | 272_A | 1.067 | 0.95 |
| 151_N | 154_I | 1.067 | 0.95 |
| 155_M | 158_A | 1.067 | 0.95 |
| 58_T | 62_T | 1.065 | 0.95 |
| 139_V | 143_M | 1.062 | 0.95 |
| 89_G | 120_G | 1.061 | 0.95 |
| 129_V | 219_I | 1.061 | 0.95 |
| 219_I | 223_Y | 1.058 | 0.95 |
| 84_L | 88_F | 1.057 | 0.95 |
| 204_V | 207_M | 1.055 | 0.95 |
| 93_T | 96_Y | 1.055 | 0.95 |
| 175_W | 178_Y | 1.051 | 0.94 |
| 53_P | 56_F | 1.049 | 0.94 |
| 126_W | 164_A | 1.047 | 0.94 |
| 47_L | 300_V | 1.046 | 0.94 |
| 171_P | 174_G | 1.045 | 0.94 |
| 199_N | 203_F | 1.045 | 0.94 |
| 315_N | 318_V | 1.039 | 0.94 |
| 123_I | 127_S | 1.035 | 0.94 |
| 66_K | 69_R | 1.034 | 0.94 |
| 87_V | 91_F | 1.031 | 0.94 |
| 216_L | 262_L | 1.029 | 0.94 |
| 137_V | 141_K | 1.028 | 0.94 |
| 74_Y | 78_N | 1.026 | 0.94 |
| 52_F | 87_V | 1.021 | 0.93 |
| 227_V | 230_V | 1.004 | 0.93 |
| 58_T | 313_F | 1.003 | 0.93 |
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 | 1 | 100 | 0.247 | Contact Map |
| 2rh1A | 1 | 0.878 | 100 | 0.278 | Contact Map |
| 4pxzA | 1 | 0.8476 | 100 | 0.287 | Contact Map |
| 2z73A | 2 | 0.9604 | 100 | 0.288 | Contact Map |
| 3uonA | 1 | 0.8598 | 100 | 0.295 | Contact Map |
| 3pblA | 2 | 0.8293 | 100 | 0.298 | Contact Map |
| 3vw7A | 1 | 0.8628 | 100 | 0.305 | Contact Map |
| 4iarA | 1 | 0.8567 | 100 | 0.308 | Contact Map |
| 4u15A | 2 | 0.8598 | 100 | 0.311 | Contact Map |
| 4dklA | 1 | 0.872 | 100 | 0.312 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)