| TREK1 Truncated Nterm |
| ID: | 1428080999 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 411 (274) | ||
| Sequences: | 532 (328.9) | ||
| Seq/Len: | 1.942 | ||
| Nf(neff/√len): | 19.9 |
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: 1.942).
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 |
| 135_F | 159_C | 3.001 | 1.00 |
| 156_K | 240_D | 2.487 | 1.00 |
| 243_Y | 256_D | 2.058 | 0.99 |
| 222_F | 226_P | 1.944 | 0.99 |
| 248_T | 254_F | 1.864 | 0.98 |
| 248_T | 278_I | 1.760 | 0.97 |
| 129_L | 252_I | 1.748 | 0.97 |
| 226_P | 277_W | 1.710 | 0.96 |
| 64_V | 158_F | 1.681 | 0.96 |
| 253_G | 256_D | 1.613 | 0.94 |
| 146_G | 256_D | 1.598 | 0.94 |
| 163_A | 247_I | 1.569 | 0.93 |
| 277_W | 284_Y | 1.516 | 0.91 |
| 138_T | 143_I | 1.490 | 0.90 |
| 57_Y | 61_G | 1.464 | 0.89 |
| 65_F | 69_E | 1.463 | 0.89 |
| 58_L | 140_I | 1.439 | 0.88 |
| 230_F | 249_L | 1.424 | 0.87 |
| 170_F | 238_A | 1.422 | 0.87 |
| 303_T | 306_E | 1.391 | 0.86 |
| 302_K | 305_E | 1.384 | 0.85 |
| 230_F | 234_E | 1.365 | 0.84 |
| 145_F | 168_P | 1.352 | 0.83 |
| 173_L | 180_Q | 1.345 | 0.83 |
| 84_K | 88_I | 1.342 | 0.83 |
| 178_G | 182_G | 1.342 | 0.83 |
| 139_V | 254_F | 1.339 | 0.83 |
| 154_G | 158_F | 1.326 | 0.82 |
| 174_L | 249_L | 1.322 | 0.82 |
| 139_V | 143_I | 1.314 | 0.81 |
| 75_S | 84_K | 1.307 | 0.80 |
| 61_G | 65_F | 1.303 | 0.80 |
| 238_A | 277_W | 1.300 | 0.80 |
| 157_I | 278_I | 1.296 | 0.80 |
| 152_T | 155_G | 1.294 | 0.80 |
| 159_C | 284_Y | 1.289 | 0.79 |
| 87_F | 91_H | 1.289 | 0.79 |
| 143_I | 243_Y | 1.285 | 0.79 |
| 247_I | 251_T | 1.284 | 0.79 |
| 61_G | 69_E | 1.281 | 0.79 |
| 62_A | 133_F | 1.273 | 0.78 |
| 132_S | 137_G | 1.273 | 0.78 |
| 243_Y | 255_G | 1.270 | 0.78 |
| 226_P | 260_G | 1.264 | 0.77 |
| 176_G | 180_Q | 1.256 | 0.77 |
| 68_L | 158_F | 1.245 | 0.76 |
| 100_D | 104_Q | 1.240 | 0.75 |
| 236_W | 253_G | 1.239 | 0.75 |
| 254_F | 258_V | 1.233 | 0.75 |
| 283_A | 286_A | 1.231 | 0.75 |
| 301_K | 304_K | 1.218 | 0.74 |
| 135_F | 150_P | 1.209 | 0.73 |
| 298_V | 301_K | 1.209 | 0.73 |
| 163_A | 230_F | 1.209 | 0.73 |
| 156_K | 245_V | 1.205 | 0.72 |
| 301_K | 305_E | 1.196 | 0.72 |
| 251_T | 255_G | 1.193 | 0.71 |
| 237_S | 240_D | 1.193 | 0.71 |
| 226_P | 284_Y | 1.192 | 0.71 |
| 312_A | 315_A | 1.192 | 0.71 |
| 254_F | 289_L | 1.190 | 0.71 |
| 227_A | 246_V | 1.188 | 0.71 |
| 138_T | 142_T | 1.184 | 0.71 |
| 135_F | 164_L | 1.181 | 0.70 |
| 243_Y | 251_T | 1.180 | 0.70 |
| 139_V | 252_I | 1.179 | 0.70 |
| 243_Y | 253_G | 1.178 | 0.70 |
| 277_W | 285_F | 1.172 | 0.69 |
| 168_P | 282_L | 1.171 | 0.69 |
| 300_S | 306_E | 1.165 | 0.69 |
| 277_W | 286_A | 1.158 | 0.68 |
| 264_I | 267_L | 1.158 | 0.68 |
| 57_Y | 62_A | 1.157 | 0.68 |
| 248_T | 253_G | 1.155 | 0.68 |
| 223_V | 285_F | 1.154 | 0.68 |
| 68_L | 154_G | 1.144 | 0.67 |
| 45_K | 49_T | 1.140 | 0.66 |
| 254_F | 257_Y | 1.135 | 0.66 |
| 178_G | 248_T | 1.130 | 0.65 |
| 300_S | 304_K | 1.124 | 0.65 |
| 73_E | 134_F | 1.123 | 0.65 |
| 134_F | 137_G | 1.123 | 0.65 |
| 302_K | 306_E | 1.121 | 0.64 |
| 159_C | 247_I | 1.120 | 0.64 |
| 298_V | 305_E | 1.118 | 0.64 |
| 307_V | 310_F | 1.114 | 0.64 |
| 223_V | 250_T | 1.112 | 0.63 |
| 148_I | 243_Y | 1.110 | 0.63 |
| 69_E | 127_W | 1.108 | 0.63 |
| 303_T | 307_V | 1.108 | 0.63 |
| 140_I | 169_L | 1.105 | 0.63 |
| 236_W | 247_I | 1.105 | 0.63 |
| 42_M | 49_T | 1.104 | 0.63 |
| 310_F | 315_A | 1.101 | 0.62 |
| 131_S | 134_F | 1.101 | 0.62 |
| 109_A | 113_G | 1.098 | 0.62 |
| 111_N | 165_L | 1.098 | 0.62 |
| 48_S | 51_F | 1.095 | 0.62 |
| 236_W | 251_T | 1.093 | 0.62 |
| 138_T | 141_T | 1.093 | 0.62 |
| 300_S | 305_E | 1.090 | 0.61 |
| 46_T | 49_T | 1.089 | 0.61 |
| 163_A | 168_P | 1.082 | 0.60 |
| 82_I | 263_D | 1.081 | 0.60 |
| 42_M | 47_V | 1.080 | 0.60 |
| 244_F | 259_A | 1.079 | 0.60 |
| 298_V | 302_K | 1.078 | 0.60 |
| 311_R | 315_A | 1.078 | 0.60 |
| 299_I | 304_K | 1.076 | 0.60 |
| 74_I | 102_L | 1.074 | 0.60 |
| 90_Q | 97_T | 1.074 | 0.60 |
| 160_I | 202_S | 1.073 | 0.59 |
| 278_I | 281_G | 1.067 | 0.59 |
| 43_K | 46_T | 1.065 | 0.59 |
| 306_E | 309_E | 1.063 | 0.58 |
| 239_L | 260_G | 1.057 | 0.58 |
| 300_S | 303_T | 1.056 | 0.58 |
| 64_V | 157_I | 1.055 | 0.57 |
| 240_D | 257_Y | 1.053 | 0.57 |
| 149_S | 162_Y | 1.047 | 0.57 |
| 306_E | 310_F | 1.046 | 0.56 |
| 308_G | 311_R | 1.045 | 0.56 |
| 158_F | 287_A | 1.040 | 0.56 |
| 220_V | 241_A | 1.039 | 0.56 |
| 239_L | 249_L | 1.036 | 0.55 |
| 234_E | 253_G | 1.034 | 0.55 |
| 277_W | 288_V | 1.034 | 0.55 |
| 234_E | 256_D | 1.033 | 0.55 |
| 296_L | 303_T | 1.029 | 0.55 |
| 173_L | 239_L | 1.027 | 0.54 |
| 53_V | 132_S | 1.027 | 0.54 |
| 146_G | 243_Y | 1.026 | 0.54 |
| 129_L | 174_L | 1.024 | 0.54 |
| 66_K | 156_K | 1.023 | 0.54 |
| 129_L | 139_V | 1.022 | 0.54 |
| 299_I | 303_T | 1.019 | 0.54 |
| 234_E | 247_I | 1.019 | 0.54 |
| 159_C | 223_V | 1.018 | 0.53 |
| 220_V | 240_D | 1.017 | 0.53 |
| 288_V | 292_I | 1.016 | 0.53 |
| 132_S | 242_I | 1.015 | 0.53 |
| 251_T | 256_D | 1.013 | 0.53 |
| 247_I | 256_D | 1.013 | 0.53 |
| 298_V | 304_K | 1.013 | 0.53 |
| 298_V | 303_T | 1.012 | 0.53 |
| 310_F | 313_H | 1.011 | 0.53 |
| 165_L | 213_I | 1.010 | 0.53 |
| 143_I | 152_T | 1.005 | 0.52 |
| 81_V | 86_T | 1.003 | 0.52 |
| 148_I | 241_A | 1.003 | 0.52 |
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 | |
| 4twkA | 2 | 0.6399 | 100 | 0.525 | Contact Map |
| 4bw5A | 4 | 0.6253 | 100 | 0.539 | Contact Map |
| 4wfeA | 2 | 0.618 | 100 | 0.552 | Contact Map |
| 3ukmA | 4 | 0.6058 | 100 | 0.605 | Contact Map |
| 3effK | 4 | 0.3212 | 99.7 | 0.868 | Contact Map |
| 3pjsK | 4 | 0.3212 | 99.7 | 0.869 | Contact Map |
| 2k1eA | 4 | 0.2506 | 99.7 | 0.871 | Contact Map |
| 3vouA | 2 | 0.3285 | 99.7 | 0.874 | Contact Map |
| 4h33A | 1 | 0.219 | 99.6 | 0.877 | Contact Map |
| 4gx0A | 4 | 0.455 | 99.6 | 0.879 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)