| 1C0PA |
| ID: | 1411601396 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 363 (326) | ||
| Sequences: | 8540 (6170.2) | ||
| Seq/Len: | 26.196 | ||
| Nf(neff/√len): | 341.7 |
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: 26.196).
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 |
| 152_L | 157_A | 5.812 | 1.00 |
| 7_K | 33_H | 4.282 | 1.00 |
| 37_R | 163_T | 3.932 | 1.00 |
| 8_R | 175_D | 3.763 | 1.00 |
| 118_R | 124_E | 3.612 | 1.00 |
| 75_S | 348_E | 3.457 | 1.00 |
| 10_V | 35_L | 3.423 | 1.00 |
| 121_P | 124_E | 3.278 | 1.00 |
| 10_V | 174_A | 3.238 | 1.00 |
| 8_R | 31_S | 3.018 | 1.00 |
| 26_A | 155_L | 2.894 | 1.00 |
| 33_H | 160_E | 2.866 | 1.00 |
| 9_V | 25_L | 2.777 | 1.00 |
| 21_S | 178_V | 2.715 | 1.00 |
| 81_V | 92_L | 2.648 | 1.00 |
| 31_S | 158_T | 2.594 | 1.00 |
| 335_F | 346_A | 2.481 | 1.00 |
| 9_V | 30_Y | 2.415 | 1.00 |
| 26_A | 157_A | 2.401 | 1.00 |
| 332_A | 346_A | 2.384 | 1.00 |
| 201_G | 287_R | 2.306 | 1.00 |
| 14_S | 40_P | 2.235 | 1.00 |
| 27_R | 86_T | 2.190 | 1.00 |
| 120_L | 124_E | 2.185 | 1.00 |
| 24_I | 348_E | 2.168 | 1.00 |
| 178_V | 354_V | 2.162 | 1.00 |
| 330_V | 350_V | 2.105 | 1.00 |
| 19_L | 149_A | 2.083 | 1.00 |
| 26_A | 152_L | 2.082 | 1.00 |
| 19_L | 145_C | 2.035 | 1.00 |
| 207_K | 278_E | 2.024 | 1.00 |
| 185_A | 333_Y | 2.000 | 1.00 |
| 24_I | 347_A | 1.997 | 1.00 |
| 179_N | 185_A | 1.971 | 1.00 |
| 30_Y | 355_D | 1.939 | 1.00 |
| 80_W | 144_Y | 1.930 | 1.00 |
| 347_A | 351_A | 1.922 | 1.00 |
| 23_L | 151_E | 1.899 | 1.00 |
| 255_Q | 259_K | 1.886 | 1.00 |
| 332_A | 350_V | 1.868 | 1.00 |
| 125_C | 131_G | 1.852 | 1.00 |
| 40_P | 149_A | 1.843 | 1.00 |
| 27_R | 155_L | 1.823 | 1.00 |
| 330_V | 354_V | 1.808 | 1.00 |
| 14_S | 34_I | 1.803 | 1.00 |
| 17_I | 335_F | 1.791 | 1.00 |
| 176_L | 330_V | 1.780 | 1.00 |
| 17_I | 332_A | 1.760 | 1.00 |
| 28_K | 351_A | 1.742 | 1.00 |
| 149_A | 159_F | 1.724 | 1.00 |
| 23_L | 27_R | 1.721 | 1.00 |
| 35_L | 174_A | 1.713 | 1.00 |
| 10_V | 33_H | 1.705 | 1.00 |
| 179_N | 331_H | 1.689 | 1.00 |
| 20_S | 24_I | 1.683 | 1.00 |
| 19_L | 152_L | 1.679 | 1.00 |
| 14_S | 36_A | 1.670 | 1.00 |
| 79_K | 348_E | 1.664 | 1.00 |
| 179_N | 329_L | 1.634 | 1.00 |
| 75_S | 78_K | 1.602 | 1.00 |
| 7_K | 158_T | 1.601 | 1.00 |
| 349_D | 352_Q | 1.595 | 1.00 |
| 8_R | 30_Y | 1.573 | 1.00 |
| 8_R | 33_H | 1.567 | 1.00 |
| 151_E | 154_K | 1.560 | 1.00 |
| 21_S | 332_A | 1.556 | 1.00 |
| 122_S | 126_P | 1.544 | 1.00 |
| 39_L | 161_R | 1.543 | 1.00 |
| 28_K | 355_D | 1.529 | 1.00 |
| 208_S | 278_E | 1.522 | 1.00 |
| 167_L | 177_V | 1.516 | 1.00 |
| 35_L | 164_V | 1.511 | 1.00 |
| 16_V | 343_S | 1.501 | 1.00 |
| 7_K | 10_V | 1.496 | 1.00 |
| 19_L | 34_I | 1.491 | 1.00 |
| 34_I | 159_F | 1.478 | 1.00 |
| 150_R | 154_K | 1.474 | 1.00 |
| 12_L | 177_V | 1.469 | 1.00 |
| 24_I | 28_K | 1.467 | 1.00 |
| 150_R | 153_Q | 1.464 | 1.00 |
| 24_I | 27_R | 1.456 | 1.00 |
| 174_A | 177_V | 1.442 | 1.00 |
| 149_A | 153_Q | 1.440 | 1.00 |
| 116_N | 135_D | 1.437 | 1.00 |
| 11_V | 21_S | 1.428 | 1.00 |
| 79_K | 82_E | 1.420 | 1.00 |
| 35_L | 160_E | 1.418 | 1.00 |
| 11_V | 22_A | 1.412 | 1.00 |
| 176_L | 354_V | 1.402 | 0.99 |
| 332_A | 335_F | 1.392 | 0.99 |
| 330_V | 353_L | 1.369 | 0.99 |
| 33_H | 158_T | 1.361 | 0.99 |
| 40_P | 161_R | 1.356 | 0.99 |
| 251_P | 255_Q | 1.350 | 0.99 |
| 21_S | 180_A | 1.343 | 0.99 |
| 152_L | 156_G | 1.341 | 0.99 |
| 82_E | 86_T | 1.329 | 0.99 |
| 151_E | 155_L | 1.320 | 0.99 |
| 259_K | 263_R | 1.310 | 0.99 |
| 258_L | 262_L | 1.302 | 0.99 |
| 22_A | 32_V | 1.291 | 0.99 |
| 140_H | 143_K | 1.288 | 0.99 |
| 6_Q | 175_D | 1.282 | 0.99 |
| 28_K | 352_Q | 1.279 | 0.99 |
| 254_V | 282_H | 1.274 | 0.99 |
| 12_L | 181_T | 1.248 | 0.99 |
| 76_T | 80_W | 1.246 | 0.98 |
| 22_A | 157_A | 1.242 | 0.98 |
| 21_S | 347_A | 1.241 | 0.98 |
| 41_E | 145_C | 1.237 | 0.98 |
| 38_D | 42_D | 1.237 | 0.98 |
| 181_T | 185_A | 1.230 | 0.98 |
| 9_V | 176_L | 1.225 | 0.98 |
| 22_A | 34_I | 1.223 | 0.98 |
| 139_V | 144_Y | 1.219 | 0.98 |
| 6_Q | 173_G | 1.217 | 0.98 |
| 250_N | 253_T | 1.191 | 0.98 |
| 25_L | 351_A | 1.186 | 0.98 |
| 11_V | 32_V | 1.185 | 0.98 |
| 32_V | 157_A | 1.175 | 0.98 |
| 164_V | 167_L | 1.155 | 0.97 |
| 94_G | 133_T | 1.153 | 0.97 |
| 23_L | 155_L | 1.147 | 0.97 |
| 299_E | 327_V | 1.136 | 0.97 |
| 297_E | 346_A | 1.135 | 0.97 |
| 12_L | 164_V | 1.135 | 0.97 |
| 233_E | 280_L | 1.131 | 0.97 |
| 40_P | 159_F | 1.123 | 0.97 |
| 180_A | 332_A | 1.116 | 0.96 |
| 34_I | 157_A | 1.113 | 0.96 |
| 269_S | 276_G | 1.113 | 0.96 |
| 78_K | 82_E | 1.106 | 0.96 |
| 7_K | 31_S | 1.105 | 0.96 |
| 80_W | 343_S | 1.104 | 0.96 |
| 300_R | 325_K | 1.092 | 0.96 |
| 75_S | 79_K | 1.090 | 0.96 |
| 20_S | 148_L | 1.086 | 0.96 |
| 236_C | 261_C | 1.081 | 0.95 |
| 179_N | 189_A | 1.076 | 0.95 |
| 20_S | 347_A | 1.071 | 0.95 |
| 7_K | 175_D | 1.069 | 0.95 |
| 108_H | 111_K | 1.066 | 0.95 |
| 348_E | 352_Q | 1.065 | 0.95 |
| 195_A | 291_R | 1.053 | 0.95 |
| 84_V | 88_H | 1.048 | 0.94 |
| 19_L | 159_F | 1.028 | 0.94 |
| 89_A | 143_K | 1.019 | 0.93 |
| 90_M | 137_L | 1.017 | 0.93 |
| 169_Q | 328_T | 1.014 | 0.93 |
| 142_P | 146_Q | 1.001 | 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 | |
| 1c0pA | 1 | 1 | 100 | 0.252 | Contact Map |
| 3wgtA | 2 | 0.8705 | 100 | 0.408 | Contact Map |
| 1y56B | 1 | 0.8898 | 100 | 0.423 | Contact Map |
| 3ps9A | 1 | 0.9642 | 100 | 0.43 | Contact Map |
| 3axbA | 1 | 0.8815 | 100 | 0.43 | Contact Map |
| 4h1bA | 1 | 0.8898 | 100 | 0.432 | Contact Map |
| 1ryiA | 4 | 0.8926 | 100 | 0.432 | Contact Map |
| 2uzzA | 4 | 0.8843 | 100 | 0.436 | Contact Map |
| 3pvcA | 1 | 0.9642 | 100 | 0.438 | Contact Map |
| 2gf3A | 2 | 0.8953 | 100 | 0.442 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)