| Actl6b |
| ID: | 1485663702 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 426 (419) | ||
| Sequences: | 1304 (822.8) | ||
| Seq/Len: | 3.112 | ||
| Nf(neff/√len): | 40.2 |
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: 3.112).
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 |
| 156_A | 164_G | 3.300 | 1.00 |
| 351_N | 354_L | 3.239 | 1.00 |
| 199_I | 301_I | 2.866 | 1.00 |
| 18_I | 100_L | 2.695 | 1.00 |
| 345_V | 365_L | 2.448 | 1.00 |
| 413_Y | 417_G | 2.418 | 1.00 |
| 352_T | 357_F | 2.395 | 1.00 |
| 360_R | 364_E | 2.309 | 1.00 |
| 169_S | 351_N | 2.286 | 1.00 |
| 171_A | 197_D | 2.277 | 1.00 |
| 134_T | 146_F | 2.198 | 1.00 |
| 117_V | 137_M | 2.162 | 1.00 |
| 30_E | 34_K | 2.156 | 1.00 |
| 97_R | 140_Q | 2.144 | 1.00 |
| 121_E | 130_R | 2.142 | 1.00 |
| 17_D | 24_R | 2.100 | 1.00 |
| 101_D | 141_Y | 2.076 | 1.00 |
| 15_V | 19_G | 2.059 | 1.00 |
| 392_I | 396_I | 1.925 | 1.00 |
| 92_D | 95_C | 1.913 | 0.99 |
| 28_A | 398_A | 1.875 | 0.99 |
| 29_G | 395_S | 1.863 | 0.99 |
| 169_S | 352_T | 1.850 | 0.99 |
| 68_D | 71_A | 1.807 | 0.99 |
| 391_W | 395_S | 1.798 | 0.99 |
| 260_Q | 264_L | 1.786 | 0.99 |
| 137_M | 146_F | 1.755 | 0.99 |
| 169_S | 357_F | 1.743 | 0.99 |
| 330_I | 342_Y | 1.718 | 0.99 |
| 167_L | 176_A | 1.702 | 0.98 |
| 391_W | 394_G | 1.701 | 0.98 |
| 101_D | 105_S | 1.696 | 0.98 |
| 196_G | 200_S | 1.690 | 0.98 |
| 16_F | 23_V | 1.646 | 0.98 |
| 167_L | 345_V | 1.631 | 0.98 |
| 408_I | 421_V | 1.626 | 0.98 |
| 63_K | 66_H | 1.625 | 0.98 |
| 43_L | 95_C | 1.616 | 0.98 |
| 19_G | 170_G | 1.612 | 0.98 |
| 15_V | 28_A | 1.607 | 0.98 |
| 25_A | 35_A | 1.594 | 0.97 |
| 326_V | 361_L | 1.587 | 0.97 |
| 19_G | 24_R | 1.582 | 0.97 |
| 19_G | 26_G | 1.581 | 0.97 |
| 149_C | 154_L | 1.570 | 0.97 |
| 422_E | 425_C | 1.561 | 0.97 |
| 100_L | 133_L | 1.556 | 0.97 |
| 17_D | 21_F | 1.552 | 0.97 |
| 408_I | 420_C | 1.546 | 0.97 |
| 135_E | 139_E | 1.545 | 0.97 |
| 414_E | 417_G | 1.524 | 0.96 |
| 395_S | 403_F | 1.520 | 0.96 |
| 190_V | 332_M | 1.511 | 0.96 |
| 410_K | 414_E | 1.494 | 0.96 |
| 260_Q | 266_V | 1.482 | 0.96 |
| 167_L | 174_T | 1.478 | 0.96 |
| 199_I | 203_C | 1.478 | 0.96 |
| 324_H | 328_T | 1.473 | 0.95 |
| 21_F | 24_R | 1.457 | 0.95 |
| 15_V | 398_A | 1.448 | 0.95 |
| 169_S | 174_T | 1.448 | 0.95 |
| 347_V | 357_F | 1.414 | 0.94 |
| 26_G | 29_G | 1.413 | 0.94 |
| 421_V | 425_C | 1.407 | 0.94 |
| 306_F | 360_R | 1.402 | 0.94 |
| 13_A | 28_A | 1.395 | 0.93 |
| 320_L | 325_V | 1.374 | 0.93 |
| 303_E | 306_F | 1.365 | 0.92 |
| 356_G | 364_E | 1.362 | 0.92 |
| 323_G | 364_E | 1.346 | 0.92 |
| 90_I | 93_W | 1.345 | 0.92 |
| 201_M | 232_P | 1.339 | 0.91 |
| 125_N | 129_K | 1.320 | 0.91 |
| 410_K | 415_E | 1.307 | 0.90 |
| 396_I | 400_L | 1.301 | 0.90 |
| 305_L | 321_G | 1.296 | 0.89 |
| 117_V | 143_I | 1.294 | 0.89 |
| 178_P | 188_G | 1.294 | 0.89 |
| 52_L | 55_E | 1.291 | 0.89 |
| 414_E | 418_K | 1.291 | 0.89 |
| 222_A | 227_R | 1.280 | 0.89 |
| 108_V | 112_P | 1.271 | 0.88 |
| 335_I | 338_R | 1.270 | 0.88 |
| 167_L | 326_V | 1.264 | 0.88 |
| 155_T | 402_T | 1.258 | 0.88 |
| 420_C | 425_C | 1.256 | 0.87 |
| 23_V | 39_T | 1.256 | 0.87 |
| 380_S | 389_S | 1.252 | 0.87 |
| 188_G | 329_S | 1.231 | 0.86 |
| 173_H | 195_A | 1.228 | 0.86 |
| 42_G | 79_A | 1.228 | 0.86 |
| 224_E | 227_R | 1.221 | 0.85 |
| 126_T | 129_K | 1.214 | 0.85 |
| 136_L | 202_Q | 1.210 | 0.85 |
| 154_L | 394_G | 1.206 | 0.84 |
| 357_F | 361_L | 1.203 | 0.84 |
| 143_I | 146_F | 1.199 | 0.84 |
| 347_V | 352_T | 1.197 | 0.84 |
| 56_G | 62_G | 1.197 | 0.84 |
| 190_V | 409_S | 1.196 | 0.84 |
| 237_K | 241_P | 1.194 | 0.84 |
| 11_V | 22_S | 1.193 | 0.84 |
| 118_L | 154_L | 1.193 | 0.84 |
| 296_A | 300_R | 1.192 | 0.83 |
| 261_A | 265_Q | 1.188 | 0.83 |
| 119_M | 295_G | 1.183 | 0.83 |
| 100_L | 119_M | 1.183 | 0.83 |
| 16_F | 20_S | 1.182 | 0.83 |
| 395_S | 400_L | 1.177 | 0.82 |
| 52_L | 56_G | 1.177 | 0.82 |
| 379_A | 386_R | 1.177 | 0.82 |
| 9_D | 12_G | 1.174 | 0.82 |
| 26_G | 33_P | 1.173 | 0.82 |
| 377_L | 380_S | 1.168 | 0.82 |
| 100_L | 120_S | 1.165 | 0.81 |
| 302_P | 354_L | 1.163 | 0.81 |
| 13_A | 41_V | 1.159 | 0.81 |
| 137_M | 143_I | 1.158 | 0.81 |
| 88_G | 172_T | 1.157 | 0.81 |
| 395_S | 399_S | 1.150 | 0.80 |
| 421_V | 424_K | 1.144 | 0.80 |
| 14_L | 22_S | 1.141 | 0.80 |
| 412_E | 415_E | 1.137 | 0.79 |
| 19_G | 350_G | 1.136 | 0.79 |
| 205_E | 365_L | 1.136 | 0.79 |
| 88_G | 93_W | 1.135 | 0.79 |
| 322_V | 326_V | 1.135 | 0.79 |
| 134_T | 177_I | 1.134 | 0.79 |
| 18_I | 21_F | 1.134 | 0.79 |
| 121_E | 125_N | 1.133 | 0.79 |
| 163_T | 330_I | 1.125 | 0.78 |
| 116_P | 144_P | 1.122 | 0.78 |
| 253_N | 262_S | 1.118 | 0.78 |
| 297_E | 308_P | 1.115 | 0.77 |
| 32_C | 35_A | 1.114 | 0.77 |
| 342_Y | 369_T | 1.111 | 0.77 |
| 138_F | 141_Y | 1.109 | 0.77 |
| 92_D | 296_A | 1.109 | 0.77 |
| 357_F | 363_R | 1.106 | 0.77 |
| 147_F | 153_V | 1.104 | 0.76 |
| 17_D | 26_G | 1.099 | 0.76 |
| 323_G | 326_V | 1.098 | 0.76 |
| 145_A | 407_W | 1.084 | 0.75 |
| 303_E | 308_P | 1.084 | 0.75 |
| 157_F | 390_P | 1.084 | 0.75 |
| 185_L | 188_G | 1.083 | 0.74 |
| 153_V | 184_V | 1.079 | 0.74 |
| 258_D | 262_S | 1.076 | 0.74 |
| 265_Q | 268_D | 1.075 | 0.74 |
| 320_L | 328_T | 1.073 | 0.73 |
| 282_V | 355_Q | 1.073 | 0.73 |
| 411_Q | 415_E | 1.071 | 0.73 |
| 17_D | 121_E | 1.071 | 0.73 |
| 210_M | 297_E | 1.070 | 0.73 |
| 96_F | 100_L | 1.063 | 0.72 |
| 393_G | 396_I | 1.059 | 0.72 |
| 184_V | 187_Q | 1.056 | 0.72 |
| 101_D | 112_P | 1.056 | 0.72 |
| 188_G | 332_M | 1.054 | 0.72 |
| 72_L | 79_A | 1.054 | 0.72 |
| 25_A | 31_D | 1.050 | 0.71 |
| 167_L | 322_V | 1.050 | 0.71 |
| 288_N | 415_E | 1.046 | 0.71 |
| 38_P | 152_A | 1.044 | 0.71 |
| 301_I | 354_L | 1.042 | 0.70 |
| 165_L | 326_V | 1.042 | 0.70 |
| 184_V | 189_I | 1.040 | 0.70 |
| 326_V | 376_K | 1.038 | 0.70 |
| 20_S | 91_E | 1.032 | 0.69 |
| 71_A | 238_E | 1.032 | 0.69 |
| 410_K | 417_G | 1.030 | 0.69 |
| 13_A | 144_P | 1.029 | 0.69 |
| 305_L | 351_N | 1.029 | 0.69 |
| 131_E | 174_T | 1.028 | 0.69 |
| 25_A | 37_F | 1.027 | 0.69 |
| 404_Q | 407_W | 1.027 | 0.69 |
| 135_E | 414_E | 1.027 | 0.69 |
| 22_S | 32_C | 1.025 | 0.69 |
| 201_M | 326_V | 1.023 | 0.68 |
| 416_G | 420_C | 1.022 | 0.68 |
| 189_I | 396_I | 1.022 | 0.68 |
| 233_N | 236_K | 1.022 | 0.68 |
| 176_A | 223_K | 1.021 | 0.68 |
| 17_D | 350_G | 1.021 | 0.68 |
| 119_M | 133_L | 1.020 | 0.68 |
| 121_E | 150_K | 1.019 | 0.68 |
| 333_C | 341_L | 1.016 | 0.68 |
| 29_G | 33_P | 1.016 | 0.68 |
| 286_M | 289_G | 1.015 | 0.67 |
| 127_R | 134_T | 1.010 | 0.67 |
| 242_Q | 246_S | 1.009 | 0.67 |
| 220_I | 223_K | 1.008 | 0.67 |
| 46_A | 49_G | 1.005 | 0.66 |
| 412_E | 420_C | 1.004 | 0.66 |
| 298_R | 303_E | 1.003 | 0.66 |
| 138_F | 144_P | 1.002 | 0.66 |
| 170_G | 350_G | 1.000 | 0.66 |
| 353_L | 387_K | 1.000 | 0.66 |
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 | |
| 4am6A | 2 | 0.9202 | 100 | 0.223 | Contact Map |
| 4fo0A | 1 | 0.9155 | 100 | 0.255 | Contact Map |
| 3qb0A | 4 | 0.9343 | 100 | 0.265 | Contact Map |
| 4i6mB | 1 | 0.8052 | 100 | 0.305 | Contact Map |
| 4pl7A | 2 | 0.8122 | 100 | 0.32 | Contact Map |
| 4i6mA | 1 | 0.8545 | 100 | 0.322 | Contact Map |
| 3dwlA | 2 | 0.8075 | 100 | 0.333 | Contact Map |
| 5afuJ | 1 | 0.8239 | 100 | 0.342 | Contact Map |
| 1k8kA | 1 | 0.8685 | 100 | 0.345 | Contact Map |
| 4cj7A | 2 | 0.8615 | 100 | 0.353 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)