| CK1e |
| ID: | 1402261249 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 416 (388) | ||
| Sequences: | 9615 (8134.2) | ||
| Seq/Len: | 24.781 | ||
| Nf(neff/√len): | 413.0 |
Jackhmmer Results: (2014_04_16)
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: 24.781).
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 |
| 102_L | 245_P | 4.440 | 1.00 |
| 26_G | 37_I | 3.802 | 1.00 |
| 26_G | 35_V | 3.572 | 1.00 |
| 129_V | 202_V | 3.531 | 1.00 |
| 135_L | 148_I | 3.490 | 1.00 |
| 196_L | 255_C | 3.309 | 1.00 |
| 109_A | 203_L | 3.238 | 1.00 |
| 83_E | 146_Y | 3.155 | 1.00 |
| 13_R | 25_L | 3.124 | 1.00 |
| 115_R | 147_I | 2.879 | 1.00 |
| 60_Q | 67_S | 2.832 | 1.00 |
| 257_S | 262_D | 2.770 | 1.00 |
| 259_R | 262_D | 2.729 | 1.00 |
| 25_L | 34_E | 2.692 | 1.00 |
| 130_K | 176_T | 2.655 | 1.00 |
| 28_N | 31_S | 2.552 | 1.00 |
| 10_R | 27_A | 2.509 | 1.00 |
| 10_R | 29_I | 2.452 | 1.00 |
| 250_T | 272_L | 2.314 | 1.00 |
| 117_E | 121_S | 2.271 | 1.00 |
| 105_V | 207_N | 2.240 | 1.00 |
| 69_K | 83_E | 2.176 | 1.00 |
| 116_I | 199_L | 2.138 | 1.00 |
| 25_L | 84_L | 2.133 | 1.00 |
| 117_E | 267_S | 2.130 | 1.00 |
| 254_F | 264_P | 2.110 | 1.00 |
| 207_N | 248_F | 2.099 | 1.00 |
| 62_G | 118_Y | 2.039 | 1.00 |
| 68_I | 80_M | 2.015 | 1.00 |
| 66_P | 85_L | 1.997 | 1.00 |
| 265_D | 268_Y | 1.927 | 1.00 |
| 101_S | 104_T | 1.926 | 1.00 |
| 14_K | 17_S | 1.911 | 1.00 |
| 23_I | 36_A | 1.909 | 1.00 |
| 90_E | 132_D | 1.873 | 1.00 |
| 88_S | 91_D | 1.858 | 1.00 |
| 175_G | 180_A | 1.854 | 1.00 |
| 116_I | 129_V | 1.837 | 1.00 |
| 113_I | 269_L | 1.821 | 1.00 |
| 12_G | 27_A | 1.819 | 1.00 |
| 8_K | 28_N | 1.814 | 1.00 |
| 108_L | 145_V | 1.813 | 1.00 |
| 137_G | 144_L | 1.799 | 1.00 |
| 255_C | 269_L | 1.780 | 1.00 |
| 37_I | 81_V | 1.749 | 1.00 |
| 131_P | 179_Y | 1.746 | 1.00 |
| 109_A | 199_L | 1.730 | 1.00 |
| 179_Y | 205_Y | 1.714 | 1.00 |
| 251_Y | 255_C | 1.700 | 1.00 |
| 42_V | 73_A | 1.688 | 1.00 |
| 27_A | 34_E | 1.653 | 1.00 |
| 127_R | 190_Q | 1.644 | 1.00 |
| 254_F | 268_Y | 1.630 | 1.00 |
| 35_V | 81_V | 1.625 | 1.00 |
| 113_I | 199_L | 1.613 | 1.00 |
| 117_E | 270_R | 1.608 | 1.00 |
| 250_T | 254_F | 1.607 | 1.00 |
| 251_Y | 269_L | 1.591 | 1.00 |
| 137_G | 142_G | 1.591 | 1.00 |
| 14_K | 22_D | 1.579 | 1.00 |
| 111_Q | 145_V | 1.568 | 1.00 |
| 193_R | 265_D | 1.563 | 1.00 |
| 152_L | 174_T | 1.496 | 1.00 |
| 66_P | 82_M | 1.478 | 1.00 |
| 27_A | 32_G | 1.477 | 1.00 |
| 201_Y | 211_L | 1.470 | 1.00 |
| 9_Y | 70_W | 1.459 | 1.00 |
| 181_S | 194_D | 1.455 | 1.00 |
| 134_F | 145_V | 1.438 | 1.00 |
| 251_Y | 264_P | 1.423 | 1.00 |
| 14_K | 24_Y | 1.405 | 0.99 |
| 196_L | 266_Y | 1.402 | 0.99 |
| 112_M | 134_F | 1.400 | 0.99 |
| 130_K | 149_D | 1.400 | 0.99 |
| 203_L | 251_Y | 1.393 | 0.99 |
| 190_Q | 194_D | 1.389 | 0.99 |
| 68_I | 71_C | 1.366 | 0.99 |
| 231_K | 258_L | 1.357 | 0.99 |
| 24_Y | 39_L | 1.355 | 0.99 |
| 111_Q | 144_L | 1.351 | 0.99 |
| 39_L | 77_Y | 1.340 | 0.99 |
| 33_E | 69_K | 1.336 | 0.99 |
| 197_E | 201_Y | 1.318 | 0.99 |
| 183_N | 260_F | 1.299 | 0.99 |
| 205_Y | 211_L | 1.278 | 0.99 |
| 128_D | 133_N | 1.267 | 0.99 |
| 266_Y | 269_L | 1.247 | 0.99 |
| 113_I | 266_Y | 1.247 | 0.99 |
| 112_M | 145_V | 1.235 | 0.98 |
| 64_G | 114_S | 1.228 | 0.98 |
| 196_L | 269_L | 1.226 | 0.98 |
| 134_F | 202_V | 1.223 | 0.98 |
| 97_S | 104_T | 1.222 | 0.98 |
| 120_H | 266_Y | 1.218 | 0.98 |
| 128_D | 149_D | 1.215 | 0.98 |
| 92_L | 100_F | 1.190 | 0.98 |
| 127_R | 174_T | 1.182 | 0.98 |
| 130_K | 175_G | 1.178 | 0.98 |
| 119_I | 147_I | 1.175 | 0.98 |
| 254_F | 272_L | 1.168 | 0.97 |
| 323_S | 326_R | 1.168 | 0.97 |
| 124_F | 153_A | 1.166 | 0.97 |
| 178_R | 197_E | 1.159 | 0.97 |
| 266_Y | 270_R | 1.153 | 0.97 |
| 128_D | 151_G | 1.141 | 0.97 |
| 220_T | 223_Q | 1.140 | 0.97 |
| 254_F | 257_S | 1.136 | 0.97 |
| 184_T | 198_S | 1.135 | 0.97 |
| 130_K | 133_N | 1.120 | 0.96 |
| 252_L | 256_R | 1.119 | 0.96 |
| 35_V | 69_K | 1.117 | 0.96 |
| 116_I | 266_Y | 1.111 | 0.96 |
| 112_M | 202_V | 1.104 | 0.96 |
| 268_Y | 271_Q | 1.103 | 0.96 |
| 113_I | 270_R | 1.100 | 0.96 |
| 369_R | 372_R | 1.096 | 0.96 |
| 201_Y | 212_P | 1.095 | 0.96 |
| 118_Y | 121_S | 1.091 | 0.96 |
| 184_T | 194_D | 1.089 | 0.96 |
| 131_P | 202_V | 1.087 | 0.96 |
| 359_A | 362_T | 1.073 | 0.95 |
| 133_N | 149_D | 1.073 | 0.95 |
| 372_R | 375_K | 1.071 | 0.95 |
| 11_L | 26_G | 1.068 | 0.95 |
| 58_M | 155_K | 1.066 | 0.95 |
| 329_P | 332_P | 1.065 | 0.95 |
| 264_P | 272_L | 1.063 | 0.95 |
| 207_N | 244_Y | 1.056 | 0.95 |
| 197_E | 256_R | 1.055 | 0.95 |
| 129_V | 147_I | 1.048 | 0.94 |
| 86_G | 143_N | 1.048 | 0.94 |
| 110_D | 114_S | 1.047 | 0.94 |
| 377_S | 381_H | 1.047 | 0.94 |
| 34_E | 84_L | 1.045 | 0.94 |
| 131_P | 205_Y | 1.044 | 0.94 |
| 55_F | 153_A | 1.044 | 0.94 |
| 329_P | 333_P | 1.043 | 0.94 |
| 65_I | 119_I | 1.037 | 0.94 |
| 264_P | 269_L | 1.035 | 0.94 |
| 322_G | 326_R | 1.032 | 0.94 |
| 382_R | 385_P | 1.026 | 0.94 |
| 128_D | 176_T | 1.025 | 0.93 |
| 174_T | 190_Q | 1.022 | 0.93 |
| 119_I | 124_F | 1.022 | 0.93 |
| 264_P | 268_Y | 1.021 | 0.93 |
| 20_F | 152_L | 1.017 | 0.93 |
| 313_R | 316_R | 1.017 | 0.93 |
| 123_N | 192_R | 1.015 | 0.93 |
| 199_L | 255_C | 1.014 | 0.93 |
| 12_G | 25_L | 1.013 | 0.93 |
| 85_L | 146_Y | 1.012 | 0.93 |
| 36_A | 84_L | 1.009 | 0.93 |
| 55_F | 124_F | 1.008 | 0.93 |
| 331_G | 334_T | 1.004 | 0.93 |
| 376_V | 379_R | 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 | |
| 2izrA | 1 | 0.7019 | 100 | 0.289 | Contact Map |
| 1csnA | 1 | 0.6995 | 100 | 0.301 | Contact Map |
| 4lgdA | 4 | 0.8341 | 100 | 0.302 | Contact Map |
| 1tkiA | 2 | 0.7644 | 100 | 0.305 | Contact Map |
| 4btkA | 1 | 0.6755 | 100 | 0.308 | Contact Map |
| 4hgtA | 2 | 0.6971 | 100 | 0.308 | Contact Map |
| 2yabA | 2 | 0.6899 | 100 | 0.309 | Contact Map |
| 4kb8A | 4 | 0.6995 | 100 | 0.31 | Contact Map |
| 2bdwA | 2 | 0.738 | 100 | 0.311 | Contact Map |
| 3c0iA | 1 | 0.6899 | 100 | 0.312 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)