| ompa |
| ID: | 1415238945 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 353 (336) | ||
| Sequences: | 348 (225.5) | ||
| Seq/Len: | 1.036 | ||
| Nf(neff/√len): | 12.3 |
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: 1.036).
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 |
| 234_N | 275_L | 3.340 | 1.00 |
| 277_E | 281_L | 3.265 | 1.00 |
| 316_N | 321_G | 2.484 | 0.99 |
| 234_N | 282_A | 2.410 | 0.99 |
| 232_D | 235_K | 2.334 | 0.99 |
| 316_N | 322_R | 2.280 | 0.98 |
| 266_H | 311_Q | 2.189 | 0.98 |
| 281_L | 285_N | 2.169 | 0.98 |
| 158_L | 164_L | 2.149 | 0.98 |
| 246_I | 290_A | 2.119 | 0.97 |
| 318_T | 321_G | 2.012 | 0.96 |
| 205_A | 208_E | 1.860 | 0.93 |
| 234_N | 286_S | 1.850 | 0.93 |
| 275_L | 309_W | 1.850 | 0.93 |
| 211_P | 214_P | 1.837 | 0.92 |
| 232_D | 239_K | 1.768 | 0.90 |
| 297_V | 301_R | 1.721 | 0.89 |
| 208_E | 211_P | 1.672 | 0.87 |
| 233_T | 270_T | 1.671 | 0.87 |
| 318_T | 325_N | 1.657 | 0.86 |
| 208_E | 214_P | 1.623 | 0.85 |
| 285_N | 289_S | 1.620 | 0.84 |
| 250_A | 291_L | 1.587 | 0.83 |
| 229_V | 287_V | 1.572 | 0.82 |
| 78_E | 169_R | 1.564 | 0.82 |
| 211_P | 253_L | 1.553 | 0.81 |
| 314_A | 321_G | 1.544 | 0.80 |
| 205_A | 211_P | 1.537 | 0.80 |
| 238_I | 242_Y | 1.530 | 0.80 |
| 233_T | 268_D | 1.461 | 0.75 |
| 247_A | 251_E | 1.457 | 0.75 |
| 207_V | 211_P | 1.455 | 0.75 |
| 245_E | 248_K | 1.455 | 0.75 |
| 124_L | 167_E | 1.448 | 0.74 |
| 277_E | 310_D | 1.438 | 0.73 |
| 200_P | 204_V | 1.437 | 0.73 |
| 313_I | 322_R | 1.433 | 0.73 |
| 264_E | 307_F | 1.426 | 0.72 |
| 238_I | 290_A | 1.408 | 0.71 |
| 269_N | 309_W | 1.394 | 0.70 |
| 76_E | 165_R | 1.376 | 0.69 |
| 124_L | 151_G | 1.359 | 0.67 |
| 235_K | 239_K | 1.357 | 0.67 |
| 28_P | 189_V | 1.357 | 0.67 |
| 203_E | 207_V | 1.342 | 0.66 |
| 168_A | 181_Y | 1.338 | 0.65 |
| 124_L | 165_R | 1.338 | 0.65 |
| 123_V | 152_V | 1.330 | 0.65 |
| 281_L | 304_T | 1.319 | 0.64 |
| 261_A | 302_L | 1.312 | 0.63 |
| 314_A | 318_T | 1.312 | 0.63 |
| 238_I | 246_I | 1.309 | 0.63 |
| 289_S | 293_N | 1.301 | 0.62 |
| 162_L | 189_V | 1.298 | 0.62 |
| 124_L | 169_R | 1.298 | 0.62 |
| 277_E | 306_G | 1.295 | 0.62 |
| 234_N | 249_V | 1.286 | 0.61 |
| 163_S | 167_E | 1.284 | 0.61 |
| 151_G | 307_F | 1.278 | 0.60 |
| 242_Y | 249_V | 1.268 | 0.59 |
| 40_H | 54_E | 1.260 | 0.59 |
| 312_P | 316_N | 1.259 | 0.58 |
| 66_G | 76_E | 1.257 | 0.58 |
| 133_E | 297_V | 1.255 | 0.58 |
| 78_E | 124_L | 1.244 | 0.57 |
| 119_I | 156_W | 1.240 | 0.57 |
| 253_L | 261_A | 1.236 | 0.56 |
| 235_K | 278_R | 1.234 | 0.56 |
| 232_D | 267_T | 1.229 | 0.56 |
| 229_V | 292_V | 1.219 | 0.55 |
| 269_N | 314_A | 1.217 | 0.55 |
| 128_G | 169_R | 1.216 | 0.55 |
| 177_K | 320_E | 1.210 | 0.54 |
| 7_A | 18_A | 1.206 | 0.54 |
| 96_K | 145_G | 1.202 | 0.53 |
| 159_N | 185_A | 1.202 | 0.53 |
| 204_V | 207_V | 1.194 | 0.52 |
| 166_T | 192_G | 1.191 | 0.52 |
| 11_M | 15_A | 1.185 | 0.52 |
| 245_E | 295_Y | 1.185 | 0.52 |
| 242_Y | 330_A | 1.184 | 0.52 |
| 203_E | 208_E | 1.177 | 0.51 |
| 57_D | 106_V | 1.173 | 0.50 |
| 164_L | 169_R | 1.169 | 0.50 |
| 63_A | 79_Y | 1.167 | 0.50 |
| 59_L | 69_L | 1.165 | 0.50 |
| 122_Y | 181_Y | 1.162 | 0.49 |
| 6_I | 17_L | 1.162 | 0.49 |
| 266_H | 310_D | 1.159 | 0.49 |
| 5_R | 9_A | 1.158 | 0.49 |
| 6_I | 14_A | 1.149 | 0.48 |
| 124_L | 149_N | 1.147 | 0.48 |
| 242_Y | 245_E | 1.147 | 0.48 |
| 128_G | 313_I | 1.147 | 0.48 |
| 278_R | 282_A | 1.145 | 0.48 |
| 13_V | 18_A | 1.144 | 0.48 |
| 265_G | 287_V | 1.139 | 0.47 |
| 155_F | 169_R | 1.136 | 0.47 |
| 238_I | 330_A | 1.129 | 0.46 |
| 31_L | 70_T | 1.128 | 0.46 |
| 124_L | 155_F | 1.125 | 0.46 |
| 234_N | 309_W | 1.123 | 0.46 |
| 69_L | 75_F | 1.119 | 0.45 |
| 188_N | 291_L | 1.114 | 0.45 |
| 274_K | 298_D | 1.109 | 0.45 |
| 76_E | 84_G | 1.109 | 0.45 |
| 257_P | 301_R | 1.108 | 0.44 |
| 127_A | 286_S | 1.105 | 0.44 |
| 259_A | 301_R | 1.103 | 0.44 |
| 211_P | 217_Q | 1.096 | 0.43 |
| 270_T | 313_I | 1.088 | 0.43 |
| 315_D | 321_G | 1.081 | 0.42 |
| 322_R | 327_R | 1.080 | 0.42 |
| 121_P | 124_L | 1.080 | 0.42 |
| 33_Y | 73_L | 1.080 | 0.42 |
| 155_F | 165_R | 1.078 | 0.42 |
| 192_G | 304_T | 1.077 | 0.42 |
| 162_L | 300_S | 1.073 | 0.41 |
| 237_N | 250_A | 1.071 | 0.41 |
| 165_R | 176_E | 1.070 | 0.41 |
| 208_E | 212_V | 1.070 | 0.41 |
| 278_R | 291_L | 1.070 | 0.41 |
| 207_V | 214_P | 1.069 | 0.41 |
| 227_L | 315_D | 1.067 | 0.41 |
| 73_L | 247_A | 1.067 | 0.41 |
| 31_L | 39_Q | 1.067 | 0.41 |
| 12_L | 15_A | 1.065 | 0.40 |
| 7_A | 229_V | 1.062 | 0.40 |
| 67_I | 76_E | 1.061 | 0.40 |
| 5_R | 12_L | 1.059 | 0.40 |
| 260_T | 303_S | 1.058 | 0.40 |
| 124_L | 128_G | 1.055 | 0.40 |
| 78_E | 149_N | 1.054 | 0.40 |
| 37_D | 40_H | 1.051 | 0.39 |
| 8_L | 19_A | 1.050 | 0.39 |
| 314_A | 325_N | 1.047 | 0.39 |
| 284_A | 306_G | 1.047 | 0.39 |
| 78_E | 121_P | 1.046 | 0.39 |
| 201_V | 207_V | 1.040 | 0.38 |
| 6_I | 11_M | 1.038 | 0.38 |
| 122_Y | 153_G | 1.035 | 0.38 |
| 317_K | 320_E | 1.034 | 0.38 |
| 4_S | 8_L | 1.033 | 0.38 |
| 101_N | 325_N | 1.030 | 0.37 |
| 315_D | 322_R | 1.024 | 0.37 |
| 234_N | 281_L | 1.023 | 0.37 |
| 205_A | 214_P | 1.020 | 0.37 |
| 321_G | 325_N | 1.020 | 0.37 |
| 34_T | 40_H | 1.018 | 0.36 |
| 233_T | 313_I | 1.016 | 0.36 |
| 253_L | 322_R | 1.015 | 0.36 |
| 121_P | 169_R | 1.014 | 0.36 |
| 205_A | 215_Q | 1.012 | 0.36 |
| 70_T | 289_S | 1.011 | 0.36 |
| 35_F | 176_E | 1.011 | 0.36 |
| 153_G | 165_R | 1.011 | 0.36 |
| 131_K | 185_A | 1.005 | 0.35 |
| 30_L | 169_R | 1.005 | 0.35 |
| 5_R | 16_P | 1.005 | 0.35 |
| 312_P | 328_V | 1.005 | 0.35 |
| 30_L | 191_L | 1.004 | 0.35 |
| 92_G | 125_L | 1.001 | 0.35 |
| 74_G | 256_Y | 1.000 | 0.35 |
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 | |
| 3nb3A | 3 | 0.3768 | 100 | 0.445 | Contact Map |
| 1r1mA | 1 | 0.3399 | 100 | 0.68 | Contact Map |
| 4erhA | 2 | 0.3371 | 100 | 0.684 | Contact Map |
| 2kgwA | 1 | 0.3654 | 100 | 0.693 | Contact Map |
| 4b5cA | 3 | 0.3428 | 100 | 0.697 | Contact Map |
| 3td3A | 8 | 0.3456 | 100 | 0.7 | Contact Map |
| 4pwtA | 3 | 0.3683 | 100 | 0.705 | Contact Map |
| 2hqsH | 4 | 0.3059 | 100 | 0.708 | Contact Map |
| 2aizP | 1 | 0.3796 | 100 | 0.71 | Contact Map |
| 3ldtA | 1 | 0.4079 | 100 | 0.71 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)