| 1pp9-B |
| ID: | 1408346494 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 423 (402) | ||
| Sequences: | 7223 (5629.6) | ||
| Seq/Len: | 17.968 | ||
| Nf(neff/√len): | 280.8 |
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: 17.968).
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 |
| 338_N | 342_Q | 4.624 | 1.00 |
| 278_S | 340_D | 4.073 | 1.00 |
| 172_P | 176_H | 4.056 | 1.00 |
| 327_Q | 330_T | 3.984 | 1.00 |
| 330_T | 334_G | 3.599 | 1.00 |
| 118_R | 122_A | 3.407 | 1.00 |
| 393_D | 396_N | 3.390 | 1.00 |
| 173_V | 177_D | 3.256 | 1.00 |
| 349_K | 387_D | 3.030 | 1.00 |
| 282_A | 286_G | 3.003 | 1.00 |
| 21_S | 195_V | 2.951 | 1.00 |
| 196_S | 199_V | 2.860 | 1.00 |
| 338_N | 391_D | 2.841 | 1.00 |
| 390_A | 393_D | 2.826 | 1.00 |
| 65_S | 68_K | 2.744 | 1.00 |
| 147_L | 242_V | 2.668 | 1.00 |
| 316_S | 319_D | 2.643 | 1.00 |
| 252_E | 400_K | 2.536 | 1.00 |
| 329_K | 333_Q | 2.495 | 1.00 |
| 62_K | 113_A | 2.416 | 1.00 |
| 46_N | 174_E | 2.380 | 1.00 |
| 101_D | 203_V | 2.378 | 1.00 |
| 260_Q | 295_A | 2.339 | 1.00 |
| 262_V | 336_L | 2.313 | 1.00 |
| 129_R | 168_G | 2.306 | 1.00 |
| 33_L | 190_L | 2.200 | 1.00 |
| 35_I | 188_M | 2.193 | 1.00 |
| 308_F | 324_A | 2.150 | 1.00 |
| 50_S | 178_Y | 2.139 | 1.00 |
| 171_T | 174_E | 2.136 | 1.00 |
| 14_P | 205_E | 2.134 | 1.00 |
| 109_N | 113_A | 2.128 | 1.00 |
| 337_S | 340_D | 2.114 | 1.00 |
| 95_C | 103_L | 2.109 | 1.00 |
| 83_T | 90_A | 2.068 | 1.00 |
| 282_A | 287_V | 2.054 | 1.00 |
| 12_R | 18_V | 2.054 | 1.00 |
| 391_D | 395_I | 2.030 | 1.00 |
| 63_G | 105_E | 2.010 | 1.00 |
| 335_N | 395_I | 2.005 | 1.00 |
| 252_E | 396_N | 2.001 | 1.00 |
| 122_A | 125_Q | 1.999 | 1.00 |
| 255_A | 397_A | 1.998 | 1.00 |
| 177_D | 181_N | 1.997 | 1.00 |
| 192_G | 200_L | 1.897 | 1.00 |
| 64_A | 109_N | 1.877 | 1.00 |
| 201_K | 205_E | 1.875 | 1.00 |
| 284_A | 291_F | 1.846 | 1.00 |
| 396_N | 400_K | 1.834 | 1.00 |
| 282_A | 327_Q | 1.792 | 1.00 |
| 258_V | 389_V | 1.792 | 1.00 |
| 89_M | 183_F | 1.782 | 1.00 |
| 259_L | 398_A | 1.756 | 1.00 |
| 287_V | 323_A | 1.755 | 1.00 |
| 146_N | 149_A | 1.753 | 1.00 |
| 323_A | 326_N | 1.751 | 1.00 |
| 384_Q | 387_D | 1.728 | 1.00 |
| 322_K | 326_N | 1.723 | 1.00 |
| 318_G | 322_K | 1.720 | 1.00 |
| 163_P | 166_R | 1.719 | 1.00 |
| 22_L | 362_F | 1.671 | 1.00 |
| 329_K | 332_A | 1.665 | 1.00 |
| 63_G | 109_N | 1.646 | 1.00 |
| 202_Q | 205_E | 1.632 | 1.00 |
| 17_L | 190_L | 1.628 | 1.00 |
| 101_D | 206_Q | 1.615 | 1.00 |
| 61_T | 109_N | 1.601 | 1.00 |
| 73_I | 78_G | 1.584 | 1.00 |
| 11_T | 201_K | 1.580 | 1.00 |
| 392_A | 395_I | 1.580 | 1.00 |
| 52_L | 121_V | 1.576 | 1.00 |
| 164_D | 168_G | 1.561 | 1.00 |
| 21_S | 197_H | 1.552 | 1.00 |
| 64_A | 72_G | 1.549 | 1.00 |
| 199_V | 202_Q | 1.548 | 1.00 |
| 17_L | 188_M | 1.532 | 1.00 |
| 49_T | 170_V | 1.514 | 1.00 |
| 342_Q | 346_N | 1.496 | 1.00 |
| 332_A | 399_K | 1.495 | 1.00 |
| 20_A | 189_A | 1.494 | 1.00 |
| 18_V | 189_A | 1.479 | 1.00 |
| 45_N | 174_E | 1.479 | 1.00 |
| 9_E | 198_P | 1.475 | 1.00 |
| 202_Q | 206_Q | 1.468 | 1.00 |
| 40_R | 302_D | 1.467 | 1.00 |
| 117_R | 120_E | 1.466 | 1.00 |
| 395_I | 399_K | 1.462 | 1.00 |
| 53_L | 116_F | 1.459 | 1.00 |
| 129_R | 164_D | 1.457 | 1.00 |
| 287_V | 319_D | 1.456 | 1.00 |
| 296_F | 307_G | 1.456 | 1.00 |
| 278_S | 327_Q | 1.454 | 1.00 |
| 133_A | 164_D | 1.448 | 1.00 |
| 72_G | 102_I | 1.443 | 1.00 |
| 93_V | 103_L | 1.435 | 1.00 |
| 11_T | 19_I | 1.405 | 0.99 |
| 255_A | 389_V | 1.399 | 0.99 |
| 10_F | 18_V | 1.391 | 0.99 |
| 256_F | 397_A | 1.389 | 0.99 |
| 319_D | 322_K | 1.384 | 0.99 |
| 43_N | 46_N | 1.381 | 0.99 |
| 76_V | 102_I | 1.373 | 0.99 |
| 121_V | 172_P | 1.366 | 0.99 |
| 341_V | 391_D | 1.364 | 0.99 |
| 342_Q | 345_K | 1.354 | 0.99 |
| 62_K | 115_E | 1.334 | 0.99 |
| 125_Q | 129_R | 1.325 | 0.99 |
| 392_A | 396_N | 1.323 | 0.99 |
| 310_T | 324_A | 1.319 | 0.99 |
| 10_F | 370_A | 1.316 | 0.99 |
| 121_V | 175_L | 1.310 | 0.99 |
| 34_F | 367_G | 1.307 | 0.99 |
| 345_K | 386_I | 1.299 | 0.99 |
| 151_A | 305_L | 1.299 | 0.99 |
| 87_E | 156_L | 1.294 | 0.99 |
| 33_L | 188_M | 1.292 | 0.99 |
| 31_I | 192_G | 1.286 | 0.99 |
| 51_H | 54_R | 1.279 | 0.99 |
| 341_V | 345_K | 1.266 | 0.99 |
| 23_E | 196_S | 1.265 | 0.99 |
| 251_A | 393_D | 1.259 | 0.99 |
| 176_H | 180_Q | 1.254 | 0.99 |
| 36_K | 187_R | 1.251 | 0.99 |
| 203_V | 207_F | 1.249 | 0.99 |
| 112_T | 209_N | 1.242 | 0.98 |
| 51_H | 55_L | 1.238 | 0.98 |
| 203_V | 206_Q | 1.235 | 0.98 |
| 326_N | 330_T | 1.233 | 0.98 |
| 193_L | 363_L | 1.222 | 0.98 |
| 331_I | 336_L | 1.213 | 0.98 |
| 385_Q | 388_A | 1.210 | 0.98 |
| 199_V | 203_V | 1.202 | 0.98 |
| 255_A | 393_D | 1.199 | 0.98 |
| 283_V | 290_P | 1.197 | 0.98 |
| 54_R | 84_S | 1.191 | 0.98 |
| 237_V | 317_A | 1.188 | 0.98 |
| 173_V | 176_H | 1.183 | 0.98 |
| 51_H | 131_D | 1.175 | 0.98 |
| 381_T | 384_Q | 1.175 | 0.98 |
| 101_D | 207_F | 1.173 | 0.98 |
| 260_Q | 306_F | 1.172 | 0.98 |
| 59_L | 124_L | 1.171 | 0.98 |
| 107_L | 110_V | 1.159 | 0.97 |
| 245_S | 297_N | 1.155 | 0.97 |
| 101_D | 199_V | 1.151 | 0.97 |
| 310_T | 320_V | 1.144 | 0.97 |
| 174_E | 177_D | 1.142 | 0.97 |
| 259_L | 394_V | 1.141 | 0.97 |
| 384_Q | 388_A | 1.140 | 0.97 |
| 52_L | 128_L | 1.140 | 0.97 |
| 282_A | 323_A | 1.135 | 0.97 |
| 102_I | 105_E | 1.128 | 0.97 |
| 177_D | 180_Q | 1.127 | 0.97 |
| 290_P | 293_V | 1.122 | 0.97 |
| 53_L | 175_L | 1.119 | 0.96 |
| 11_T | 21_S | 1.116 | 0.96 |
| 254_N | 389_V | 1.114 | 0.96 |
| 381_T | 385_Q | 1.112 | 0.96 |
| 195_V | 200_L | 1.110 | 0.96 |
| 55_L | 124_L | 1.107 | 0.96 |
| 23_E | 197_H | 1.106 | 0.96 |
| 241_L | 325_Y | 1.102 | 0.96 |
| 114_P | 179_V | 1.101 | 0.96 |
| 129_R | 167_I | 1.100 | 0.96 |
| 68_K | 72_G | 1.097 | 0.96 |
| 132_K | 167_I | 1.097 | 0.96 |
| 55_L | 84_S | 1.091 | 0.96 |
| 258_V | 341_V | 1.086 | 0.96 |
| 17_L | 185_S | 1.085 | 0.96 |
| 37_A | 178_Y | 1.085 | 0.96 |
| 375_S | 381_T | 1.083 | 0.96 |
| 377_T | 381_T | 1.081 | 0.95 |
| 398_A | 402_V | 1.067 | 0.95 |
| 42_E | 48_G | 1.066 | 0.95 |
| 56_A | 175_L | 1.066 | 0.95 |
| 241_L | 408_M | 1.062 | 0.95 |
| 200_L | 204_A | 1.061 | 0.95 |
| 118_R | 172_P | 1.059 | 0.95 |
| 54_R | 58_S | 1.057 | 0.95 |
| 190_L | 204_A | 1.056 | 0.95 |
| 125_Q | 167_I | 1.051 | 0.94 |
| 13_L | 19_I | 1.045 | 0.94 |
| 63_G | 113_A | 1.044 | 0.94 |
| 108_L | 208_L | 1.042 | 0.94 |
| 73_I | 80_L | 1.041 | 0.94 |
| 86_R | 148_H | 1.037 | 0.94 |
| 69_I | 106_F | 1.037 | 0.94 |
| 275_A | 280_Y | 1.032 | 0.94 |
| 35_I | 111_T | 1.031 | 0.94 |
| 252_E | 401_F | 1.030 | 0.94 |
| 396_N | 399_K | 1.029 | 0.94 |
| 9_E | 197_H | 1.025 | 0.93 |
| 290_P | 310_T | 1.023 | 0.93 |
| 99_D | 102_I | 1.022 | 0.93 |
| 18_V | 370_A | 1.022 | 0.93 |
| 339_P | 343_A | 1.019 | 0.93 |
| 108_L | 112_T | 1.010 | 0.93 |
| 312_S | 320_V | 1.008 | 0.93 |
| 198_P | 201_K | 1.008 | 0.93 |
| 128_L | 131_D | 1.006 | 0.93 |
| 262_V | 344_A | 1.005 | 0.93 |
| 29_S | 194_G | 1.001 | 0.92 |
| 55_L | 131_D | 1.000 | 0.92 |
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 | |
| 1pp9B | 2 | 1 | 100 | 0.18 | Contact Map |
| 1hr6A | 4 | 0.9953 | 100 | 0.199 | Contact Map |
| 3eoqA | 2 | 0.9456 | 100 | 0.202 | Contact Map |
| 3hdiA | 2 | 0.9622 | 100 | 0.21 | Contact Map |
| 1pp9A | 2 | 0.9953 | 100 | 0.214 | Contact Map |
| 1hr6B | 4 | 0.9976 | 100 | 0.221 | Contact Map |
| 3amiA | 2 | 0.9574 | 100 | 0.238 | Contact Map |
| 4nnzA | 2 | 0.8983 | 100 | 0.26 | Contact Map |
| 3gwbA | 2 | 0.9574 | 100 | 0.267 | Contact Map |
| 3amjB | 2 | 0.9456 | 100 | 0.279 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)