| SrcFL |
| ID: | 1394755011 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 452 (445) | ||
| Sequences: | 927 (556.4) | ||
| Seq/Len: | 2.083 | ||
| Nf(neff/√len): | 26.4 |
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: 2.083).
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 |
| 286_A | 371_L | 2.971 | 1.00 |
| 383_P | 400_M | 2.622 | 1.00 |
| 419_R | 424_E | 2.599 | 1.00 |
| 203_G | 213_I | 2.562 | 1.00 |
| 293_M | 306_L | 2.555 | 1.00 |
| 188_L | 213_I | 2.384 | 1.00 |
| 328_R | 335_Y | 2.290 | 1.00 |
| 230_A | 233_M | 2.229 | 1.00 |
| 13_S | 20_S | 2.099 | 0.99 |
| 148_Y | 154_D | 2.040 | 0.99 |
| 51_I | 56_V | 1.976 | 0.99 |
| 25_E | 42_S | 1.968 | 0.99 |
| 202_M | 210_R | 1.842 | 0.98 |
| 200_V | 212_A | 1.808 | 0.98 |
| 421_E | 424_E | 1.805 | 0.98 |
| 292_G | 321_V | 1.773 | 0.97 |
| 297_E | 365_W | 1.698 | 0.96 |
| 68_Y | 95_E | 1.686 | 0.96 |
| 293_M | 428_F | 1.666 | 0.96 |
| 237_R | 243_Q | 1.665 | 0.96 |
| 193_G | 200_V | 1.642 | 0.95 |
| 306_L | 428_F | 1.635 | 0.95 |
| 305_D | 323_D | 1.633 | 0.95 |
| 89_G | 94_R | 1.625 | 0.95 |
| 416_Q | 434_F | 1.618 | 0.95 |
| 406_C | 414_M | 1.602 | 0.95 |
| 29_I | 40_A | 1.580 | 0.94 |
| 155_G | 160_L | 1.576 | 0.94 |
| 393_Q | 398_Y | 1.544 | 0.93 |
| 212_A | 229_E | 1.537 | 0.93 |
| 311_I | 319_C | 1.533 | 0.93 |
| 190_V | 202_M | 1.514 | 0.92 |
| 285_M | 313_V | 1.510 | 0.92 |
| 307_R | 344_P | 1.471 | 0.91 |
| 348_T | 352_A | 1.468 | 0.91 |
| 67_W | 74_R | 1.465 | 0.90 |
| 399_R | 418_W | 1.458 | 0.90 |
| 305_D | 324_F | 1.442 | 0.89 |
| 233_M | 242_V | 1.442 | 0.89 |
| 304_R | 324_F | 1.429 | 0.89 |
| 284_D | 288_Q | 1.406 | 0.88 |
| 27_L | 42_S | 1.403 | 0.88 |
| 378_G | 381_P | 1.399 | 0.87 |
| 246_A | 372_T | 1.399 | 0.87 |
| 211_V | 214_K | 1.386 | 0.87 |
| 326_L | 358_F | 1.382 | 0.87 |
| 37_W | 40_A | 1.374 | 0.86 |
| 344_P | 358_F | 1.347 | 0.85 |
| 383_P | 398_Y | 1.341 | 0.84 |
| 309_A | 344_P | 1.330 | 0.84 |
| 52_P | 55_Y | 1.327 | 0.83 |
| 18_D | 51_I | 1.323 | 0.83 |
| 304_R | 325_G | 1.311 | 0.82 |
| 398_Y | 401_P | 1.309 | 0.82 |
| 193_G | 325_G | 1.308 | 0.82 |
| 289_I | 370_L | 1.300 | 0.82 |
| 425_R | 428_F | 1.287 | 0.81 |
| 305_D | 310_N | 1.284 | 0.81 |
| 21_F | 27_L | 1.278 | 0.80 |
| 369_I | 382_Y | 1.277 | 0.80 |
| 198_G | 305_D | 1.277 | 0.80 |
| 308_A | 347_W | 1.273 | 0.80 |
| 230_A | 238_H | 1.270 | 0.80 |
| 238_H | 258_E | 1.265 | 0.79 |
| 142_L | 311_I | 1.260 | 0.79 |
| 304_R | 328_R | 1.259 | 0.79 |
| 141_S | 144_Q | 1.252 | 0.78 |
| 359_T | 362_S | 1.252 | 0.78 |
| 236_L | 301_Y | 1.251 | 0.78 |
| 5_F | 14_R | 1.244 | 0.78 |
| 296_V | 307_R | 1.240 | 0.77 |
| 91_F | 146_V | 1.240 | 0.77 |
| 74_R | 94_R | 1.236 | 0.77 |
| 343_F | 348_T | 1.230 | 0.76 |
| 312_L | 320_K | 1.229 | 0.76 |
| 5_F | 15_T | 1.228 | 0.76 |
| 94_R | 106_S | 1.223 | 0.76 |
| 74_R | 78_E | 1.223 | 0.76 |
| 240_K | 246_A | 1.221 | 0.76 |
| 106_S | 120_H | 1.219 | 0.76 |
| 101_G | 342_K | 1.213 | 0.75 |
| 15_T | 21_F | 1.212 | 0.75 |
| 12_E | 22_K | 1.203 | 0.74 |
| 25_E | 213_I | 1.203 | 0.74 |
| 94_R | 120_H | 1.203 | 0.74 |
| 19_L | 40_A | 1.199 | 0.74 |
| 277_L | 282_L | 1.189 | 0.73 |
| 400_M | 418_W | 1.189 | 0.73 |
| 142_L | 149_Y | 1.187 | 0.73 |
| 193_G | 198_G | 1.186 | 0.73 |
| 216_L | 227_L | 1.186 | 0.73 |
| 297_E | 428_F | 1.185 | 0.73 |
| 67_W | 93_V | 1.183 | 0.72 |
| 411_H | 414_M | 1.177 | 0.72 |
| 195_G | 200_V | 1.175 | 0.72 |
| 406_C | 418_W | 1.175 | 0.72 |
| 139_F | 149_Y | 1.175 | 0.72 |
| 403_P | 418_W | 1.172 | 0.71 |
| 37_W | 41_H | 1.170 | 0.71 |
| 96_S | 104_C | 1.170 | 0.71 |
| 40_A | 51_I | 1.164 | 0.71 |
| 254_Y | 327_A | 1.161 | 0.70 |
| 308_A | 346_K | 1.159 | 0.70 |
| 51_I | 54_N | 1.159 | 0.70 |
| 310_N | 323_D | 1.155 | 0.70 |
| 10_D | 22_K | 1.152 | 0.70 |
| 359_T | 365_W | 1.151 | 0.69 |
| 169_P | 173_G | 1.151 | 0.69 |
| 286_A | 374_L | 1.150 | 0.69 |
| 414_M | 417_C | 1.145 | 0.69 |
| 15_T | 50_Y | 1.136 | 0.68 |
| 42_S | 45_T | 1.134 | 0.68 |
| 292_G | 305_D | 1.133 | 0.68 |
| 186_L | 230_A | 1.132 | 0.68 |
| 31_N | 39_L | 1.129 | 0.67 |
| 428_F | 431_L | 1.125 | 0.67 |
| 41_H | 48_T | 1.124 | 0.67 |
| 13_S | 21_F | 1.119 | 0.66 |
| 198_G | 215_T | 1.118 | 0.66 |
| 307_R | 346_K | 1.117 | 0.66 |
| 241_L | 378_G | 1.117 | 0.66 |
| 23_K | 29_I | 1.113 | 0.66 |
| 413_L | 431_L | 1.111 | 0.66 |
| 283_V | 410_L | 1.111 | 0.66 |
| 305_D | 321_V | 1.108 | 0.65 |
| 385_M | 400_M | 1.107 | 0.65 |
| 304_R | 323_D | 1.105 | 0.65 |
| 289_I | 311_I | 1.102 | 0.65 |
| 214_K | 230_A | 1.102 | 0.65 |
| 215_T | 226_F | 1.100 | 0.64 |
| 189_E | 202_M | 1.098 | 0.64 |
| 264_S | 311_I | 1.098 | 0.64 |
| 297_E | 308_A | 1.097 | 0.64 |
| 402_C | 414_M | 1.097 | 0.64 |
| 18_D | 56_V | 1.096 | 0.64 |
| 305_D | 312_L | 1.091 | 0.63 |
| 403_P | 428_F | 1.091 | 0.63 |
| 11_Y | 15_T | 1.091 | 0.63 |
| 197_F | 200_V | 1.090 | 0.63 |
| 226_F | 244_L | 1.090 | 0.63 |
| 247_V | 256_V | 1.084 | 0.63 |
| 406_C | 411_H | 1.084 | 0.63 |
| 11_Y | 206_N | 1.084 | 0.63 |
| 393_Q | 396_R | 1.083 | 0.63 |
| 266_L | 346_K | 1.082 | 0.63 |
| 192_L | 259_Y | 1.082 | 0.63 |
| 422_P | 425_R | 1.081 | 0.62 |
| 302_V | 436_E | 1.081 | 0.62 |
| 397_G | 414_M | 1.078 | 0.62 |
| 179_W | 199_E | 1.075 | 0.62 |
| 368_G | 373_E | 1.074 | 0.62 |
| 15_T | 36_D | 1.073 | 0.62 |
| 40_A | 55_Y | 1.072 | 0.61 |
| 9_Y | 13_S | 1.071 | 0.61 |
| 177_D | 180_E | 1.070 | 0.61 |
| 229_E | 238_H | 1.070 | 0.61 |
| 226_F | 238_H | 1.070 | 0.61 |
| 21_F | 38_W | 1.066 | 0.61 |
| 67_W | 91_F | 1.066 | 0.61 |
| 17_T | 20_S | 1.065 | 0.61 |
| 191_K | 194_Q | 1.064 | 0.61 |
| 305_D | 326_L | 1.062 | 0.60 |
| 89_G | 96_S | 1.061 | 0.60 |
| 81_L | 89_G | 1.060 | 0.60 |
| 296_V | 309_A | 1.060 | 0.60 |
| 418_W | 426_P | 1.060 | 0.60 |
| 412_D | 416_Q | 1.057 | 0.60 |
| 28_Q | 36_D | 1.056 | 0.60 |
| 346_K | 390_V | 1.055 | 0.60 |
| 312_L | 323_D | 1.054 | 0.60 |
| 37_W | 50_Y | 1.053 | 0.59 |
| 230_A | 247_V | 1.052 | 0.59 |
| 11_Y | 55_Y | 1.051 | 0.59 |
| 131_F | 426_P | 1.050 | 0.59 |
| 92_L | 96_S | 1.048 | 0.59 |
| 126_L | 130_G | 1.048 | 0.59 |
| 21_F | 29_I | 1.046 | 0.59 |
| 241_L | 257_T | 1.046 | 0.59 |
| 414_M | 428_F | 1.046 | 0.59 |
| 340_G | 355_Y | 1.042 | 0.58 |
| 352_A | 428_F | 1.041 | 0.58 |
| 247_V | 255_I | 1.041 | 0.58 |
| 229_E | 233_M | 1.038 | 0.58 |
| 304_R | 358_F | 1.038 | 0.58 |
| 312_L | 325_G | 1.037 | 0.58 |
| 257_T | 370_L | 1.036 | 0.58 |
| 6_V | 30_V | 1.036 | 0.58 |
| 193_G | 323_D | 1.035 | 0.57 |
| 217_K | 241_L | 1.035 | 0.57 |
| 297_E | 360_I | 1.034 | 0.57 |
| 310_N | 324_F | 1.034 | 0.57 |
| 345_I | 383_P | 1.028 | 0.57 |
| 349_A | 369_I | 1.027 | 0.57 |
| 19_L | 24_G | 1.025 | 0.56 |
| 200_V | 307_R | 1.023 | 0.56 |
| 363_D | 368_G | 1.023 | 0.56 |
| 375_T | 410_L | 1.022 | 0.56 |
| 193_G | 212_A | 1.021 | 0.56 |
| 81_L | 94_R | 1.020 | 0.56 |
| 311_I | 366_S | 1.020 | 0.56 |
| 282_L | 293_M | 1.019 | 0.56 |
| 9_Y | 27_L | 1.018 | 0.56 |
| 352_A | 362_S | 1.017 | 0.55 |
| 200_V | 229_E | 1.016 | 0.55 |
| 95_E | 101_G | 1.016 | 0.55 |
| 372_T | 375_T | 1.013 | 0.55 |
| 17_T | 22_K | 1.012 | 0.55 |
| 319_C | 432_Q | 1.012 | 0.55 |
| 216_L | 226_F | 1.011 | 0.55 |
| 200_V | 305_D | 1.011 | 0.55 |
| 20_S | 31_N | 1.010 | 0.55 |
| 93_V | 243_Q | 1.010 | 0.55 |
| 394_V | 397_G | 1.008 | 0.54 |
| 229_E | 304_R | 1.008 | 0.54 |
| 21_F | 35_G | 1.008 | 0.54 |
| 361_K | 364_V | 1.006 | 0.54 |
| 92_L | 105_L | 1.006 | 0.54 |
| 411_H | 418_W | 1.005 | 0.54 |
| 238_H | 244_L | 1.004 | 0.54 |
| 118_V | 149_Y | 1.004 | 0.54 |
| 307_R | 310_N | 1.000 | 0.54 |
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 | |
| 1fmkA | 1 | 0.9668 | 100 | 0.201 | Contact Map |
| 2h8hA | 1 | 0.9823 | 100 | 0.209 | Contact Map |
| 1qcfA | 1 | 0.9889 | 100 | 0.226 | Contact Map |
| 1opkA | 1 | 0.9757 | 100 | 0.268 | Contact Map |
| 1k9aA | 6 | 0.9447 | 100 | 0.276 | Contact Map |
| 2ozoA | 1 | 0.9292 | 100 | 0.376 | Contact Map |
| 4fl3A | 1 | 0.9181 | 100 | 0.379 | Contact Map |
| 3cblA | 1 | 0.7765 | 100 | 0.409 | Contact Map |
| 1u59A | 1 | 0.6018 | 100 | 0.575 | Contact Map |
| 4fyoA | 1 | 0.573 | 100 | 0.577 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)