| wspC |
| ID: | 1434485875 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 422 (417) | ||
| Sequences: | 645 (546.1) | ||
| Seq/Len: | 1.547 | ||
| Nf(neff/√len): | 26.7 |
Jackhmmer Results: (2015_01_07)
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: 1.547).
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 |
| 144_G | 172_L | 3.395 | 1.00 |
| 335_Q | 338_E | 3.140 | 1.00 |
| 99_L | 131_L | 3.114 | 1.00 |
| 32_R | 54_E | 3.094 | 1.00 |
| 32_R | 44_Y | 2.569 | 1.00 |
| 44_Y | 54_E | 2.301 | 0.99 |
| 187_L | 207_L | 2.121 | 0.99 |
| 369_Q | 372_E | 2.107 | 0.99 |
| 403_D | 406_G | 2.054 | 0.99 |
| 101_L | 207_L | 2.049 | 0.98 |
| 117_L | 176_V | 2.049 | 0.98 |
| 76_F | 111_S | 1.966 | 0.98 |
| 44_Y | 58_L | 1.963 | 0.98 |
| 75_S | 234_F | 1.934 | 0.98 |
| 158_F | 162_H | 1.932 | 0.98 |
| 224_K | 248_M | 1.893 | 0.97 |
| 202_V | 227_L | 1.850 | 0.97 |
| 138_I | 184_C | 1.831 | 0.96 |
| 207_L | 211_F | 1.785 | 0.96 |
| 65_P | 134_S | 1.760 | 0.95 |
| 102_P | 223_L | 1.736 | 0.95 |
| 314_G | 317_L | 1.708 | 0.94 |
| 87_L | 96_L | 1.656 | 0.93 |
| 155_E | 158_F | 1.653 | 0.93 |
| 98_I | 112_I | 1.640 | 0.92 |
| 67_T | 105_T | 1.609 | 0.91 |
| 8_L | 55_V | 1.600 | 0.91 |
| 135_A | 138_I | 1.579 | 0.90 |
| 134_S | 137_V | 1.542 | 0.89 |
| 307_S | 311_P | 1.542 | 0.89 |
| 100_S | 203_F | 1.534 | 0.88 |
| 112_I | 203_F | 1.499 | 0.87 |
| 126_F | 179_K | 1.498 | 0.87 |
| 297_P | 305_L | 1.478 | 0.86 |
| 305_L | 311_P | 1.476 | 0.86 |
| 313_S | 317_L | 1.457 | 0.85 |
| 365_D | 377_Y | 1.451 | 0.84 |
| 314_G | 318_A | 1.433 | 0.83 |
| 294_S | 297_P | 1.431 | 0.83 |
| 336_H | 363_L | 1.425 | 0.83 |
| 321_V | 326_E | 1.421 | 0.83 |
| 327_I | 356_V | 1.419 | 0.82 |
| 166_V | 171_Q | 1.417 | 0.82 |
| 290_S | 293_P | 1.416 | 0.82 |
| 293_P | 297_P | 1.406 | 0.82 |
| 313_S | 316_P | 1.401 | 0.81 |
| 330_L | 335_Q | 1.385 | 0.80 |
| 284_A | 288_R | 1.380 | 0.80 |
| 13_I | 133_V | 1.372 | 0.79 |
| 331_A | 334_G | 1.367 | 0.79 |
| 118_D | 161_R | 1.365 | 0.79 |
| 149_N | 152_R | 1.356 | 0.78 |
| 249_Q | 260_R | 1.352 | 0.78 |
| 68_W | 152_R | 1.349 | 0.78 |
| 319_S | 322_G | 1.347 | 0.78 |
| 144_G | 223_L | 1.330 | 0.76 |
| 340_R | 360_L | 1.327 | 0.76 |
| 292_R | 306_S | 1.319 | 0.76 |
| 320_P | 323_E | 1.310 | 0.75 |
| 151_F | 159_R | 1.306 | 0.74 |
| 199_Y | 223_L | 1.294 | 0.74 |
| 190_P | 361_G | 1.294 | 0.74 |
| 174_E | 177_R | 1.284 | 0.73 |
| 361_G | 377_Y | 1.283 | 0.73 |
| 305_L | 308_L | 1.272 | 0.72 |
| 306_S | 309_V | 1.270 | 0.72 |
| 321_V | 328_A | 1.270 | 0.72 |
| 295_P | 309_V | 1.255 | 0.70 |
| 304_R | 307_S | 1.252 | 0.70 |
| 273_A | 281_V | 1.251 | 0.70 |
| 294_S | 302_R | 1.249 | 0.70 |
| 301_P | 306_S | 1.247 | 0.70 |
| 40_D | 43_E | 1.247 | 0.70 |
| 166_V | 169_G | 1.242 | 0.69 |
| 301_P | 305_L | 1.239 | 0.69 |
| 303_Q | 311_P | 1.233 | 0.68 |
| 294_S | 309_V | 1.233 | 0.68 |
| 299_A | 302_R | 1.233 | 0.68 |
| 300_K | 307_S | 1.232 | 0.68 |
| 105_T | 137_V | 1.223 | 0.67 |
| 302_R | 307_S | 1.221 | 0.67 |
| 68_W | 149_N | 1.220 | 0.67 |
| 109_P | 130_A | 1.219 | 0.67 |
| 304_R | 311_P | 1.219 | 0.67 |
| 32_R | 58_L | 1.218 | 0.67 |
| 313_S | 318_A | 1.215 | 0.67 |
| 358_Y | 381_L | 1.214 | 0.67 |
| 113_V | 128_V | 1.213 | 0.66 |
| 116_L | 126_F | 1.212 | 0.66 |
| 76_F | 79_L | 1.211 | 0.66 |
| 290_S | 304_R | 1.209 | 0.66 |
| 319_S | 326_E | 1.206 | 0.66 |
| 188_L | 215_T | 1.206 | 0.66 |
| 146_Y | 240_A | 1.196 | 0.65 |
| 164_S | 173_A | 1.196 | 0.65 |
| 72_Y | 200_D | 1.195 | 0.65 |
| 290_S | 303_Q | 1.192 | 0.64 |
| 104_S | 228_R | 1.192 | 0.64 |
| 301_P | 311_P | 1.185 | 0.64 |
| 229_P | 262_T | 1.183 | 0.64 |
| 358_Y | 362_L | 1.182 | 0.64 |
| 315_Q | 318_A | 1.176 | 0.63 |
| 101_L | 187_L | 1.173 | 0.63 |
| 272_K | 277_G | 1.173 | 0.63 |
| 319_S | 323_E | 1.170 | 0.62 |
| 302_R | 310_P | 1.170 | 0.62 |
| 114_M | 158_F | 1.168 | 0.62 |
| 66_E | 152_R | 1.165 | 0.62 |
| 308_L | 311_P | 1.164 | 0.62 |
| 107_E | 150_S | 1.160 | 0.61 |
| 360_L | 364_S | 1.154 | 0.61 |
| 70_F | 111_S | 1.151 | 0.60 |
| 283_A | 290_S | 1.150 | 0.60 |
| 302_R | 309_V | 1.149 | 0.60 |
| 44_Y | 236_G | 1.148 | 0.60 |
| 322_G | 329_R | 1.146 | 0.60 |
| 300_K | 303_Q | 1.145 | 0.60 |
| 17_A | 21_G | 1.139 | 0.59 |
| 300_K | 306_S | 1.138 | 0.59 |
| 290_S | 302_R | 1.137 | 0.59 |
| 112_I | 234_F | 1.130 | 0.58 |
| 317_L | 321_V | 1.130 | 0.58 |
| 105_T | 140_R | 1.127 | 0.58 |
| 395_A | 411_Q | 1.126 | 0.58 |
| 298_P | 301_P | 1.125 | 0.58 |
| 290_S | 297_P | 1.124 | 0.58 |
| 99_L | 199_Y | 1.123 | 0.58 |
| 65_P | 99_L | 1.123 | 0.58 |
| 212_D | 215_T | 1.118 | 0.57 |
| 314_G | 321_V | 1.110 | 0.56 |
| 297_P | 304_R | 1.110 | 0.56 |
| 285_A | 289_A | 1.102 | 0.56 |
| 346_Q | 355_T | 1.099 | 0.55 |
| 288_R | 307_S | 1.097 | 0.55 |
| 32_R | 236_G | 1.095 | 0.55 |
| 84_F | 226_L | 1.095 | 0.55 |
| 391_L | 410_L | 1.094 | 0.55 |
| 102_P | 207_L | 1.092 | 0.54 |
| 172_L | 202_V | 1.091 | 0.54 |
| 109_P | 203_F | 1.087 | 0.54 |
| 391_L | 413_R | 1.087 | 0.54 |
| 9_L | 161_R | 1.087 | 0.54 |
| 289_A | 303_Q | 1.083 | 0.54 |
| 324_F | 356_V | 1.074 | 0.53 |
| 111_S | 209_I | 1.073 | 0.52 |
| 118_D | 158_F | 1.073 | 0.52 |
| 289_A | 295_P | 1.071 | 0.52 |
| 292_R | 301_P | 1.068 | 0.52 |
| 268_G | 273_A | 1.064 | 0.52 |
| 117_L | 179_K | 1.064 | 0.52 |
| 80_A | 83_A | 1.064 | 0.52 |
| 303_Q | 309_V | 1.064 | 0.52 |
| 290_S | 295_P | 1.062 | 0.51 |
| 69_F | 110_Y | 1.062 | 0.51 |
| 306_S | 311_P | 1.062 | 0.51 |
| 209_I | 236_G | 1.062 | 0.51 |
| 374_Q | 396_A | 1.061 | 0.51 |
| 72_Y | 75_S | 1.059 | 0.51 |
| 203_F | 234_F | 1.057 | 0.51 |
| 312_A | 316_P | 1.057 | 0.51 |
| 98_I | 121_L | 1.056 | 0.51 |
| 297_P | 303_Q | 1.053 | 0.50 |
| 95_A | 220_V | 1.053 | 0.50 |
| 340_R | 344_E | 1.052 | 0.50 |
| 300_K | 309_V | 1.051 | 0.50 |
| 403_D | 413_R | 1.049 | 0.50 |
| 323_E | 328_A | 1.048 | 0.50 |
| 275_S | 280_P | 1.046 | 0.50 |
| 270_R | 275_S | 1.045 | 0.50 |
| 21_G | 28_A | 1.042 | 0.49 |
| 304_R | 312_A | 1.037 | 0.49 |
| 292_R | 300_K | 1.035 | 0.49 |
| 395_A | 399_A | 1.032 | 0.48 |
| 72_Y | 409_R | 1.031 | 0.48 |
| 296_P | 310_P | 1.031 | 0.48 |
| 42_D | 46_M | 1.030 | 0.48 |
| 300_K | 304_R | 1.029 | 0.48 |
| 364_S | 367_A | 1.029 | 0.48 |
| 297_P | 307_S | 1.028 | 0.48 |
| 353_S | 376_F | 1.027 | 0.48 |
| 291_I | 304_R | 1.026 | 0.48 |
| 388_A | 392_A | 1.026 | 0.48 |
| 363_L | 381_L | 1.024 | 0.47 |
| 46_M | 157_G | 1.022 | 0.47 |
| 318_A | 321_V | 1.019 | 0.47 |
| 302_R | 311_P | 1.017 | 0.47 |
| 303_Q | 312_A | 1.014 | 0.46 |
| 297_P | 311_P | 1.011 | 0.46 |
| 292_R | 296_P | 1.010 | 0.46 |
| 281_V | 307_S | 1.008 | 0.46 |
| 99_L | 185_G | 1.005 | 0.45 |
| 398_L | 406_G | 1.005 | 0.45 |
| 47_R | 51_S | 1.004 | 0.45 |
| 211_F | 215_T | 1.002 | 0.45 |
| 272_K | 275_S | 1.001 | 0.45 |
| 68_W | 151_F | 1.000 | 0.45 |
| 6_E | 22_S | 1.000 | 0.45 |
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 | |
| 1af7A | 1 | 0.5972 | 100 | 0.547 | Contact Map |
| 4gqbA | 1 | 0.8152 | 99.9 | 0.817 | Contact Map |
| 3i53A | 2 | 0.5924 | 99.8 | 0.84 | Contact Map |
| 4qnuA | 8 | 0.6896 | 99.8 | 0.846 | Contact Map |
| 3gwzA | 4 | 0.6043 | 99.8 | 0.848 | Contact Map |
| 1tw3A | 2 | 0.6114 | 99.7 | 0.856 | Contact Map |
| 1qzzA | 1 | 0.5877 | 99.7 | 0.859 | Contact Map |
| 2ip2A | 2 | 0.5995 | 99.7 | 0.866 | Contact Map |
| 2vsyA | 2 | 0.2488 | 99.5 | 0.878 | Contact Map |
| 3lstA | 2 | 0.59 | 99.5 | 0.878 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)