| CARR |
| ID: | 1384449696 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 484 (425) | ||
| Sequences: | 1653 (1412.8) | ||
| Seq/Len: | 3.889 | ||
| Nf(neff/√len): | 68.5 |
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: 3.889).
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 |
| 282_D | 306_E | 4.048 | 1.00 |
| 284_R | 306_E | 3.759 | 1.00 |
| 263_S | 279_T | 3.714 | 1.00 |
| 81_T | 122_I | 3.461 | 1.00 |
| 175_L | 216_A | 3.397 | 1.00 |
| 219_E | 222_E | 3.314 | 1.00 |
| 300_L | 312_V | 3.287 | 1.00 |
| 300_L | 326_M | 3.010 | 1.00 |
| 130_V | 206_I | 2.988 | 1.00 |
| 207_V | 228_I | 2.976 | 1.00 |
| 204_K | 208_K | 2.826 | 1.00 |
| 346_D | 360_R | 2.820 | 1.00 |
| 281_F | 285_E | 2.805 | 1.00 |
| 26_K | 53_T | 2.757 | 1.00 |
| 29_L | 49_S | 2.730 | 1.00 |
| 165_D | 169_G | 2.691 | 1.00 |
| 142_S | 166_Q | 2.652 | 1.00 |
| 278_I | 295_P | 2.644 | 1.00 |
| 57_M | 61_T | 2.596 | 1.00 |
| 308_D | 311_E | 2.548 | 1.00 |
| 257_D | 263_S | 2.336 | 1.00 |
| 165_D | 223_G | 2.328 | 1.00 |
| 215_W | 227_T | 2.327 | 1.00 |
| 256_V | 286_A | 2.295 | 1.00 |
| 164_S | 225_T | 2.265 | 1.00 |
| 130_V | 207_V | 2.256 | 1.00 |
| 290_Y | 298_I | 2.185 | 1.00 |
| 171_P | 174_D | 2.184 | 1.00 |
| 408_E | 411_H | 2.155 | 1.00 |
| 252_K | 278_I | 2.098 | 1.00 |
| 252_K | 276_D | 2.089 | 1.00 |
| 286_A | 312_V | 2.083 | 1.00 |
| 299_I | 361_V | 2.068 | 1.00 |
| 286_A | 290_Y | 2.041 | 1.00 |
| 282_D | 285_E | 2.030 | 1.00 |
| 298_I | 324_I | 2.025 | 1.00 |
| 24_S | 28_Y | 2.025 | 1.00 |
| 290_Y | 316_V | 2.002 | 1.00 |
| 170_I | 174_D | 1.998 | 1.00 |
| 203_A | 214_I | 1.954 | 1.00 |
| 270_L | 361_V | 1.951 | 1.00 |
| 91_L | 109_I | 1.932 | 1.00 |
| 263_S | 281_F | 1.895 | 1.00 |
| 280_A | 289_K | 1.871 | 1.00 |
| 30_E | 353_S | 1.855 | 1.00 |
| 218_S | 224_S | 1.851 | 1.00 |
| 216_A | 226_F | 1.832 | 1.00 |
| 135_L | 150_I | 1.828 | 1.00 |
| 28_Y | 265_I | 1.826 | 1.00 |
| 161_L | 228_I | 1.820 | 1.00 |
| 126_K | 206_I | 1.804 | 0.99 |
| 300_L | 313_A | 1.801 | 0.99 |
| 208_K | 213_F | 1.794 | 0.99 |
| 313_A | 344_A | 1.791 | 0.99 |
| 339_G | 344_A | 1.708 | 0.99 |
| 255_I | 266_I | 1.708 | 0.99 |
| 214_I | 228_I | 1.688 | 0.99 |
| 307_L | 315_E | 1.685 | 0.99 |
| 287_L | 312_V | 1.680 | 0.99 |
| 207_V | 214_I | 1.665 | 0.99 |
| 298_I | 316_V | 1.650 | 0.99 |
| 218_S | 221_G | 1.649 | 0.99 |
| 130_V | 203_A | 1.636 | 0.99 |
| 317_R | 345_D | 1.607 | 0.99 |
| 307_L | 311_E | 1.595 | 0.98 |
| 284_R | 288_S | 1.583 | 0.98 |
| 112_D | 151_T | 1.582 | 0.98 |
| 326_M | 344_A | 1.579 | 0.98 |
| 165_D | 224_S | 1.573 | 0.98 |
| 76_L | 210_H | 1.570 | 0.98 |
| 146_G | 166_Q | 1.548 | 0.98 |
| 290_Y | 295_P | 1.547 | 0.98 |
| 175_L | 218_S | 1.541 | 0.98 |
| 313_A | 324_I | 1.526 | 0.98 |
| 122_I | 210_H | 1.522 | 0.98 |
| 24_S | 52_E | 1.519 | 0.98 |
| 302_L | 339_G | 1.513 | 0.98 |
| 35_G | 42_A | 1.507 | 0.98 |
| 142_S | 146_G | 1.502 | 0.97 |
| 178_I | 216_A | 1.490 | 0.97 |
| 255_I | 277_T | 1.488 | 0.97 |
| 267_K | 279_T | 1.482 | 0.97 |
| 8_R | 67_S | 1.472 | 0.97 |
| 172_K | 219_E | 1.460 | 0.97 |
| 253_I | 297_L | 1.459 | 0.97 |
| 141_Y | 184_R | 1.457 | 0.97 |
| 109_I | 139_I | 1.455 | 0.97 |
| 151_T | 164_S | 1.447 | 0.97 |
| 339_G | 347_Y | 1.441 | 0.96 |
| 287_L | 307_L | 1.436 | 0.96 |
| 174_D | 177_L | 1.431 | 0.96 |
| 151_T | 162_S | 1.431 | 0.96 |
| 68_R | 196_T | 1.424 | 0.96 |
| 404_G | 407_V | 1.422 | 0.96 |
| 304_L | 307_L | 1.412 | 0.96 |
| 169_G | 224_S | 1.406 | 0.96 |
| 317_R | 324_I | 1.394 | 0.96 |
| 87_M | 152_M | 1.392 | 0.95 |
| 82_N | 117_S | 1.391 | 0.95 |
| 291_E | 319_N | 1.388 | 0.95 |
| 171_P | 220_E | 1.365 | 0.95 |
| 19_R | 61_T | 1.345 | 0.94 |
| 30_E | 50_L | 1.336 | 0.94 |
| 105_K | 139_I | 1.336 | 0.94 |
| 298_I | 322_V | 1.334 | 0.94 |
| 396_D | 400_A | 1.329 | 0.94 |
| 130_V | 228_I | 1.328 | 0.94 |
| 316_V | 324_I | 1.321 | 0.94 |
| 303_M | 330_K | 1.309 | 0.93 |
| 122_I | 127_M | 1.307 | 0.93 |
| 55_R | 128_T | 1.306 | 0.93 |
| 203_A | 207_V | 1.306 | 0.93 |
| 184_R | 195_G | 1.282 | 0.92 |
| 149_T | 164_S | 1.281 | 0.92 |
| 172_K | 175_L | 1.274 | 0.92 |
| 218_S | 222_E | 1.255 | 0.91 |
| 44_S | 264_D | 1.254 | 0.91 |
| 317_R | 322_V | 1.249 | 0.91 |
| 24_S | 29_L | 1.246 | 0.91 |
| 19_R | 57_M | 1.239 | 0.90 |
| 126_K | 129_Q | 1.237 | 0.90 |
| 256_V | 280_A | 1.236 | 0.90 |
| 55_R | 132_D | 1.234 | 0.90 |
| 278_I | 289_K | 1.229 | 0.90 |
| 260_K | 263_S | 1.217 | 0.89 |
| 135_L | 139_I | 1.217 | 0.89 |
| 217_N | 225_T | 1.208 | 0.89 |
| 80_L | 121_E | 1.206 | 0.89 |
| 95_D | 99_S | 1.201 | 0.88 |
| 62_D | 126_K | 1.192 | 0.88 |
| 79_E | 124_T | 1.191 | 0.88 |
| 98_Q | 148_V | 1.189 | 0.88 |
| 311_E | 315_E | 1.189 | 0.88 |
| 269_N | 354_N | 1.184 | 0.87 |
| 312_V | 326_M | 1.182 | 0.87 |
| 50_L | 54_N | 1.177 | 0.87 |
| 278_I | 293_E | 1.173 | 0.87 |
| 255_I | 263_S | 1.168 | 0.86 |
| 61_T | 196_T | 1.165 | 0.86 |
| 134_I | 163_I | 1.160 | 0.86 |
| 273_E | 358_L | 1.160 | 0.86 |
| 256_V | 312_V | 1.156 | 0.86 |
| 302_L | 344_A | 1.147 | 0.85 |
| 143_P | 146_G | 1.140 | 0.85 |
| 80_L | 119_W | 1.139 | 0.85 |
| 287_L | 315_E | 1.137 | 0.84 |
| 302_L | 326_M | 1.137 | 0.84 |
| 313_A | 328_S | 1.133 | 0.84 |
| 280_A | 286_A | 1.133 | 0.84 |
| 5_R | 9_L | 1.129 | 0.84 |
| 346_D | 364_H | 1.127 | 0.84 |
| 300_L | 304_L | 1.119 | 0.83 |
| 78_V | 121_E | 1.119 | 0.83 |
| 108_E | 147_K | 1.113 | 0.83 |
| 312_V | 316_V | 1.102 | 0.82 |
| 177_L | 180_D | 1.101 | 0.82 |
| 37_L | 42_A | 1.095 | 0.81 |
| 198_L | 202_I | 1.092 | 0.81 |
| 112_D | 149_T | 1.083 | 0.80 |
| 129_Q | 202_I | 1.082 | 0.80 |
| 12_S | 67_S | 1.081 | 0.80 |
| 106_V | 144_D | 1.080 | 0.80 |
| 8_R | 70_D | 1.079 | 0.80 |
| 24_S | 265_I | 1.073 | 0.79 |
| 290_Y | 322_V | 1.072 | 0.79 |
| 340_L | 346_D | 1.070 | 0.79 |
| 62_D | 129_Q | 1.066 | 0.79 |
| 11_V | 129_Q | 1.066 | 0.79 |
| 287_L | 290_Y | 1.064 | 0.79 |
| 189_R | 194_G | 1.058 | 0.78 |
| 82_N | 118_V | 1.057 | 0.78 |
| 288_S | 291_E | 1.055 | 0.78 |
| 141_Y | 193_Q | 1.048 | 0.77 |
| 31_A | 265_I | 1.045 | 0.77 |
| 91_L | 150_I | 1.045 | 0.77 |
| 160_I | 229_V | 1.043 | 0.77 |
| 283_G | 307_L | 1.042 | 0.77 |
| 8_R | 12_S | 1.039 | 0.76 |
| 283_G | 312_V | 1.038 | 0.76 |
| 35_G | 38_T | 1.034 | 0.76 |
| 152_M | 161_L | 1.031 | 0.76 |
| 134_I | 228_I | 1.031 | 0.76 |
| 121_E | 233_E | 1.031 | 0.76 |
| 287_L | 324_I | 1.024 | 0.75 |
| 68_R | 184_R | 1.022 | 0.75 |
| 306_E | 312_V | 1.020 | 0.74 |
| 411_H | 419_H | 1.016 | 0.74 |
| 52_E | 261_P | 1.016 | 0.74 |
| 169_G | 223_G | 1.015 | 0.74 |
| 286_A | 295_P | 1.013 | 0.74 |
| 398_F | 402_K | 1.010 | 0.73 |
| 160_I | 227_T | 1.009 | 0.73 |
| 416_L | 420_L | 1.008 | 0.73 |
| 33_D | 46_I | 1.004 | 0.73 |
| 326_M | 339_G | 1.002 | 0.73 |
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 | |
| 4i5sA | 2 | 0.4607 | 100 | 0.669 | Contact Map |
| 2c2aA | 1 | 0.4566 | 100 | 0.677 | Contact Map |
| 2e0aA | 2 | 0.5021 | 100 | 0.695 | Contact Map |
| 4mpcA | 1 | 0.5041 | 100 | 0.701 | Contact Map |
| 1y8oA | 1 | 0.5331 | 100 | 0.701 | Contact Map |
| 4ew8A | 2 | 0.4628 | 100 | 0.705 | Contact Map |
| 4e01A | 1 | 0.4587 | 100 | 0.707 | Contact Map |
| 3jz3A | 2 | 0.3347 | 100 | 0.708 | Contact Map |
| 3a0rA | 1 | 0.4463 | 100 | 0.71 | Contact Map |
| 4gczA | 2 | 0.469 | 100 | 0.712 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)