| cytb |
| ID: | 1499246244 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 363 (363) | ||
| Sequences: | 1039 (242.9) | ||
| Seq/Len: | 2.862 | ||
| Nf(neff/√len): | 12.7 |
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: 2.862).
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 |
| 336_I | 349_N | 3.357 | 1.00 |
| 100_M | 302_F | 3.144 | 1.00 |
| 119_F | 297_L | 3.064 | 1.00 |
| 121_T | 187_H | 2.951 | 1.00 |
| 43_V | 47_L | 2.795 | 1.00 |
| 332_N | 352_N | 2.677 | 1.00 |
| 127_I | 179_T | 2.476 | 1.00 |
| 25_L | 222_Y | 2.466 | 1.00 |
| 301_M | 305_C | 2.197 | 1.00 |
| 92_I | 121_T | 2.162 | 1.00 |
| 336_I | 348_S | 2.158 | 1.00 |
| 119_F | 293_L | 2.108 | 1.00 |
| 119_F | 123_A | 2.057 | 1.00 |
| 310_T | 316_T | 2.053 | 1.00 |
| 107_F | 311_V | 2.047 | 1.00 |
| 13_N | 18_D | 2.024 | 1.00 |
| 148_M | 158_I | 1.954 | 0.99 |
| 116_M | 300_M | 1.948 | 0.99 |
| 3_T | 18_D | 1.913 | 0.99 |
| 281_T | 349_N | 1.884 | 0.99 |
| 43_V | 188_S | 1.836 | 0.99 |
| 160_K | 200_T | 1.802 | 0.99 |
| 52_H | 66_H | 1.787 | 0.99 |
| 55_A | 174_S | 1.762 | 0.99 |
| 23_I | 214_D | 1.714 | 0.98 |
| 87_L | 233_N | 1.705 | 0.98 |
| 123_A | 293_L | 1.703 | 0.98 |
| 267_K | 338_K | 1.696 | 0.98 |
| 37_M | 230_Y | 1.666 | 0.98 |
| 329_N | 355_L | 1.650 | 0.98 |
| 264_I | 267_K | 1.646 | 0.98 |
| 179_T | 186_Y | 1.641 | 0.98 |
| 15_T | 21_A | 1.639 | 0.98 |
| 332_N | 348_S | 1.627 | 0.97 |
| 156_S | 160_K | 1.622 | 0.97 |
| 12_I | 17_I | 1.605 | 0.97 |
| 115_V | 300_M | 1.497 | 0.95 |
| 79_I | 167_R | 1.472 | 0.95 |
| 120_M | 190_I | 1.467 | 0.94 |
| 174_S | 312_N | 1.462 | 0.94 |
| 50_A | 177_Y | 1.461 | 0.94 |
| 293_L | 297_L | 1.440 | 0.94 |
| 298_I | 301_M | 1.435 | 0.94 |
| 25_L | 220_P | 1.435 | 0.94 |
| 339_S | 352_N | 1.424 | 0.93 |
| 292_L | 341_I | 1.417 | 0.93 |
| 112_I | 300_M | 1.415 | 0.93 |
| 302_F | 326_Y | 1.415 | 0.93 |
| 179_T | 292_L | 1.412 | 0.93 |
| 294_A | 301_M | 1.402 | 0.93 |
| 79_I | 246_Y | 1.401 | 0.93 |
| 118_M | 127_I | 1.392 | 0.92 |
| 50_A | 178_S | 1.390 | 0.92 |
| 12_I | 15_T | 1.349 | 0.91 |
| 11_I | 196_F | 1.346 | 0.90 |
| 179_T | 183_T | 1.339 | 0.90 |
| 50_A | 259_Y | 1.339 | 0.90 |
| 148_M | 162_N | 1.330 | 0.90 |
| 204_N | 320_Q | 1.326 | 0.90 |
| 133_W | 161_M | 1.324 | 0.89 |
| 151_I | 158_I | 1.323 | 0.89 |
| 118_M | 123_A | 1.319 | 0.89 |
| 167_R | 246_Y | 1.317 | 0.89 |
| 68_C | 252_Y | 1.308 | 0.89 |
| 28_L | 102_Y | 1.307 | 0.89 |
| 85_A | 296_I | 1.306 | 0.89 |
| 316_T | 352_N | 1.306 | 0.89 |
| 119_F | 296_I | 1.305 | 0.88 |
| 6_K | 109_Q | 1.304 | 0.88 |
| 55_A | 178_S | 1.301 | 0.88 |
| 118_M | 183_T | 1.300 | 0.88 |
| 330_T | 358_Y | 1.294 | 0.88 |
| 59_M | 170_R | 1.287 | 0.88 |
| 246_Y | 252_Y | 1.273 | 0.87 |
| 36_G | 52_H | 1.272 | 0.87 |
| 230_Y | 252_Y | 1.265 | 0.86 |
| 124_T | 183_T | 1.260 | 0.86 |
| 118_M | 148_M | 1.249 | 0.85 |
| 13_N | 45_T | 1.236 | 0.85 |
| 3_T | 13_N | 1.236 | 0.85 |
| 36_G | 195_F | 1.233 | 0.84 |
| 54_T | 240_L | 1.222 | 0.84 |
| 133_W | 173_N | 1.221 | 0.84 |
| 326_Y | 329_N | 1.212 | 0.83 |
| 31_M | 34_I | 1.205 | 0.82 |
| 19_L | 203_S | 1.202 | 0.82 |
| 123_A | 148_M | 1.201 | 0.82 |
| 347_L | 350_Q | 1.198 | 0.82 |
| 250_N | 265_Y | 1.190 | 0.81 |
| 336_I | 339_S | 1.189 | 0.81 |
| 204_N | 211_S | 1.187 | 0.81 |
| 68_C | 246_Y | 1.186 | 0.81 |
| 66_H | 71_V | 1.186 | 0.81 |
| 186_Y | 189_I | 1.184 | 0.81 |
| 66_H | 70_D | 1.177 | 0.80 |
| 138_F | 299_W | 1.175 | 0.80 |
| 196_F | 260_F | 1.169 | 0.80 |
| 116_M | 297_L | 1.169 | 0.80 |
| 50_A | 201_R | 1.165 | 0.79 |
| 14_S | 195_F | 1.161 | 0.79 |
| 302_F | 305_C | 1.157 | 0.79 |
| 237_S | 241_S | 1.156 | 0.79 |
| 166_I | 173_N | 1.154 | 0.79 |
| 55_A | 252_Y | 1.148 | 0.78 |
| 79_I | 241_S | 1.148 | 0.78 |
| 21_A | 195_F | 1.147 | 0.78 |
| 219_H | 223_S | 1.147 | 0.78 |
| 119_F | 193_T | 1.146 | 0.78 |
| 123_A | 183_T | 1.137 | 0.77 |
| 343_S | 347_L | 1.130 | 0.76 |
| 96_I | 118_M | 1.123 | 0.76 |
| 209_L | 290_L | 1.122 | 0.76 |
| 153_Y | 157_N | 1.117 | 0.75 |
| 6_K | 18_D | 1.109 | 0.75 |
| 310_T | 353_N | 1.107 | 0.74 |
| 3_T | 28_L | 1.105 | 0.74 |
| 110_T | 153_Y | 1.094 | 0.73 |
| 112_I | 117_L | 1.090 | 0.73 |
| 53_Y | 93_Y | 1.089 | 0.73 |
| 316_T | 339_S | 1.089 | 0.73 |
| 60_A | 63_S | 1.088 | 0.73 |
| 90_T | 242_K | 1.087 | 0.72 |
| 53_Y | 345_T | 1.087 | 0.72 |
| 80_M | 94_I | 1.085 | 0.72 |
| 3_T | 6_K | 1.084 | 0.72 |
| 248_V | 321_F | 1.083 | 0.72 |
| 167_R | 305_C | 1.082 | 0.72 |
| 54_T | 170_R | 1.080 | 0.72 |
| 121_T | 127_I | 1.074 | 0.71 |
| 190_I | 318_L | 1.065 | 0.70 |
| 107_F | 201_R | 1.064 | 0.70 |
| 87_L | 90_T | 1.062 | 0.70 |
| 69_R | 214_D | 1.061 | 0.70 |
| 12_I | 189_I | 1.061 | 0.70 |
| 57_I | 247_S | 1.057 | 0.69 |
| 304_I | 331_I | 1.056 | 0.69 |
| 274_M | 292_L | 1.054 | 0.69 |
| 109_Q | 112_I | 1.054 | 0.69 |
| 86_S | 270_W | 1.053 | 0.69 |
| 103_G | 311_V | 1.052 | 0.69 |
| 28_L | 320_Q | 1.052 | 0.69 |
| 92_I | 96_I | 1.048 | 0.69 |
| 8_L | 193_T | 1.048 | 0.69 |
| 113_T | 193_T | 1.047 | 0.68 |
| 99_G | 304_I | 1.045 | 0.68 |
| 339_S | 349_N | 1.044 | 0.68 |
| 109_Q | 127_I | 1.043 | 0.68 |
| 214_D | 291_A | 1.035 | 0.67 |
| 265_Y | 274_M | 1.035 | 0.67 |
| 254_Y | 274_M | 1.032 | 0.67 |
| 105_Y | 221_Y | 1.031 | 0.67 |
| 37_M | 92_I | 1.028 | 0.66 |
| 322_L | 325_S | 1.028 | 0.66 |
| 277_S | 349_N | 1.024 | 0.66 |
| 2_F | 154_I | 1.018 | 0.65 |
| 51_M | 60_A | 1.018 | 0.65 |
| 252_Y | 264_I | 1.018 | 0.65 |
| 16_I | 222_Y | 1.017 | 0.65 |
| 115_V | 127_I | 1.016 | 0.65 |
| 177_Y | 259_Y | 1.016 | 0.65 |
| 118_M | 355_L | 1.015 | 0.65 |
| 252_Y | 267_K | 1.015 | 0.65 |
| 40_T | 97_G | 1.013 | 0.65 |
| 92_I | 118_M | 1.012 | 0.65 |
| 54_T | 174_S | 1.009 | 0.64 |
| 212_D | 215_K | 1.006 | 0.64 |
| 19_L | 265_Y | 1.005 | 0.64 |
| 63_S | 173_N | 1.005 | 0.64 |
| 87_L | 195_F | 1.002 | 0.63 |
| 52_H | 134_G | 1.002 | 0.63 |
| 21_A | 57_I | 1.002 | 0.63 |
| 166_I | 222_Y | 1.000 | 0.63 |
| 96_I | 113_T | 1.000 | 0.63 |
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 | |
| 1pp9C | 2 | 0.9807 | 100 | 0.191 | Contact Map |
| 3cx5C | 2 | 1 | 100 | 0.201 | Contact Map |
| 2qjyA | 6 | 0.9972 | 100 | 0.23 | Contact Map |
| 4ogqA | 1 | 0.5647 | 100 | 0.541 | Contact Map |
| 4ogqB | 1 | 0.4022 | 100 | 0.769 | Contact Map |
| 4gx0A | 4 | 0.2149 | 18.3 | 0.985 | Contact Map |
| 4un4B | 1 | 0.1543 | 5.6 | 0.988 | Contact Map |
| 2qtsA | 6 | 0.157 | 4.2 | 0.989 | Contact Map |
| 2bezF | 1 | 0.0551 | 3.2 | 0.99 | Contact Map |
| 3d1bA | 3 | 0.1129 | 2.4 | 0.99 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)