| all optimizd 2 |
| ID: | 1387857033 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 309 (309) | ||
| Sequences: | 9983 (7838) | ||
| Seq/Len: | 32.307 | ||
| Nf(neff/√len): | 445.9 |
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: 32.307).
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 |
| 153_K | 212_T | 3.330 | 1.00 |
| 191_K | 195_E | 3.067 | 1.00 |
| 221_H | 234_D | 2.973 | 1.00 |
| 154_D | 158_G | 2.897 | 1.00 |
| 261_R | 280_D | 2.816 | 1.00 |
| 24_T | 43_V | 2.699 | 1.00 |
| 224_I | 252_A | 2.673 | 1.00 |
| 131_T | 155_T | 2.651 | 1.00 |
| 190_C | 201_I | 2.560 | 1.00 |
| 230_R | 237_E | 2.510 | 1.00 |
| 119_V | 193_I | 2.437 | 1.00 |
| 119_V | 194_I | 2.421 | 1.00 |
| 164_L | 205_S | 2.412 | 1.00 |
| 21_Q | 48_K | 2.363 | 1.00 |
| 249_I | 253_K | 2.355 | 1.00 |
| 168_F | 201_I | 2.327 | 1.00 |
| 111_Y | 116_M | 2.307 | 1.00 |
| 250_Y | 264_L | 2.292 | 1.00 |
| 203_V | 213_F | 2.264 | 1.00 |
| 75_Q | 111_Y | 2.235 | 1.00 |
| 147_E | 216_K | 2.138 | 1.00 |
| 111_Y | 197_H | 2.109 | 1.00 |
| 206_E | 209_K | 2.062 | 1.00 |
| 277_R | 280_D | 2.058 | 1.00 |
| 136_E | 155_T | 2.051 | 1.00 |
| 223_E | 232_L | 2.026 | 1.00 |
| 151_Y | 212_T | 2.024 | 1.00 |
| 194_I | 199_G | 2.016 | 1.00 |
| 202_D | 214_I | 1.993 | 1.00 |
| 194_I | 215_I | 1.992 | 1.00 |
| 166_Q | 169_D | 1.930 | 1.00 |
| 205_S | 211_T | 1.907 | 1.00 |
| 204_K | 214_I | 1.901 | 1.00 |
| 138_A | 153_K | 1.881 | 1.00 |
| 140_T | 151_Y | 1.879 | 1.00 |
| 131_T | 135_D | 1.859 | 1.00 |
| 160_A | 163_H | 1.856 | 1.00 |
| 151_Y | 214_I | 1.855 | 1.00 |
| 140_T | 153_K | 1.848 | 1.00 |
| 74_V | 108_V | 1.846 | 1.00 |
| 100_T | 138_A | 1.840 | 1.00 |
| 300_Q | 308_K | 1.833 | 1.00 |
| 225_D | 228_A | 1.824 | 1.00 |
| 229_H | 246_E | 1.812 | 1.00 |
| 254_T | 257_K | 1.811 | 1.00 |
| 204_K | 212_T | 1.807 | 1.00 |
| 74_V | 110_S | 1.754 | 1.00 |
| 98_N | 136_E | 1.733 | 1.00 |
| 159_I | 167_V | 1.724 | 1.00 |
| 149_I | 216_K | 1.722 | 1.00 |
| 28_V | 41_A | 1.721 | 1.00 |
| 135_D | 155_T | 1.707 | 1.00 |
| 102_N | 140_T | 1.695 | 1.00 |
| 164_L | 203_V | 1.688 | 1.00 |
| 4_D | 8_N | 1.687 | 1.00 |
| 144_N | 149_I | 1.687 | 1.00 |
| 193_I | 197_H | 1.673 | 1.00 |
| 255_P | 259_F | 1.671 | 1.00 |
| 282_H | 285_R | 1.670 | 1.00 |
| 28_V | 44_L | 1.646 | 1.00 |
| 199_G | 217_L | 1.640 | 1.00 |
| 21_Q | 51_N | 1.635 | 1.00 |
| 138_A | 155_T | 1.629 | 1.00 |
| 167_V | 203_V | 1.598 | 1.00 |
| 73_E | 113_M | 1.597 | 1.00 |
| 142_D | 149_I | 1.590 | 1.00 |
| 163_H | 172_Y | 1.586 | 1.00 |
| 243_K | 246_E | 1.584 | 1.00 |
| 293_S | 296_A | 1.570 | 1.00 |
| 163_H | 174_V | 1.556 | 1.00 |
| 142_D | 151_Y | 1.528 | 1.00 |
| 125_D | 129_R | 1.525 | 1.00 |
| 294_E | 297_H | 1.503 | 1.00 |
| 200_S | 216_K | 1.501 | 1.00 |
| 20_L | 43_V | 1.483 | 1.00 |
| 232_L | 237_E | 1.469 | 1.00 |
| 32_E | 35_E | 1.467 | 1.00 |
| 83_K | 117_D | 1.446 | 1.00 |
| 100_T | 136_E | 1.440 | 1.00 |
| 224_I | 245_Y | 1.439 | 1.00 |
| 92_A | 128_S | 1.438 | 1.00 |
| 120_L | 150_L | 1.425 | 1.00 |
| 250_Y | 267_E | 1.410 | 1.00 |
| 224_I | 231_V | 1.397 | 0.99 |
| 51_N | 55_N | 1.396 | 0.99 |
| 149_I | 214_I | 1.389 | 0.99 |
| 175_D | 178_R | 1.388 | 0.99 |
| 231_V | 238_V | 1.386 | 0.99 |
| 88_Y | 121_T | 1.354 | 0.99 |
| 119_V | 215_I | 1.352 | 0.99 |
| 161_P | 164_L | 1.351 | 0.99 |
| 257_K | 263_Q | 1.350 | 0.99 |
| 154_D | 210_G | 1.346 | 0.99 |
| 122_N | 190_C | 1.335 | 0.99 |
| 8_N | 170_R | 1.334 | 0.99 |
| 25_E | 44_L | 1.322 | 0.99 |
| 33_P | 36_I | 1.316 | 0.99 |
| 226_N | 249_I | 1.306 | 0.99 |
| 116_M | 197_H | 1.305 | 0.99 |
| 205_S | 209_K | 1.300 | 0.99 |
| 20_L | 47_S | 1.296 | 0.99 |
| 130_Y | 173_K | 1.295 | 0.99 |
| 21_Q | 47_S | 1.290 | 0.99 |
| 250_Y | 259_F | 1.286 | 0.99 |
| 76_P | 79_A | 1.284 | 0.99 |
| 83_K | 113_M | 1.283 | 0.99 |
| 102_N | 138_A | 1.282 | 0.99 |
| 232_L | 235_N | 1.270 | 0.99 |
| 302_V | 308_K | 1.262 | 0.99 |
| 150_L | 215_I | 1.261 | 0.99 |
| 229_H | 305_V | 1.259 | 0.99 |
| 72_K | 110_S | 1.240 | 0.98 |
| 244_E | 289_K | 1.238 | 0.98 |
| 159_I | 211_T | 1.237 | 0.98 |
| 224_I | 249_I | 1.234 | 0.98 |
| 163_H | 166_Q | 1.221 | 0.98 |
| 259_F | 263_Q | 1.221 | 0.98 |
| 219_F | 252_A | 1.218 | 0.98 |
| 195_E | 200_S | 1.212 | 0.98 |
| 203_V | 211_T | 1.206 | 0.98 |
| 293_S | 297_H | 1.201 | 0.98 |
| 24_T | 47_S | 1.192 | 0.98 |
| 24_T | 44_L | 1.190 | 0.98 |
| 241_T | 289_K | 1.189 | 0.98 |
| 87_K | 117_D | 1.179 | 0.98 |
| 219_F | 309_F | 1.176 | 0.98 |
| 12_E | 118_Q | 1.175 | 0.98 |
| 227_D | 257_K | 1.173 | 0.98 |
| 147_E | 200_S | 1.172 | 0.98 |
| 5_F | 9_V | 1.167 | 0.97 |
| 115_R | 118_Q | 1.157 | 0.97 |
| 205_S | 208_G | 1.139 | 0.97 |
| 24_T | 40_L | 1.138 | 0.97 |
| 173_K | 182_G | 1.138 | 0.97 |
| 119_V | 190_C | 1.134 | 0.97 |
| 221_H | 233_A | 1.130 | 0.97 |
| 78_A | 82_D | 1.128 | 0.97 |
| 202_D | 216_K | 1.120 | 0.96 |
| 250_Y | 254_T | 1.120 | 0.96 |
| 194_I | 201_I | 1.118 | 0.96 |
| 251_L | 259_F | 1.115 | 0.96 |
| 222_L | 231_V | 1.110 | 0.96 |
| 76_P | 106_K | 1.099 | 0.96 |
| 166_Q | 172_Y | 1.089 | 0.96 |
| 154_D | 211_T | 1.086 | 0.96 |
| 70_V | 112_D | 1.076 | 0.95 |
| 223_E | 235_N | 1.074 | 0.95 |
| 80_L | 111_Y | 1.063 | 0.95 |
| 278_T | 282_H | 1.063 | 0.95 |
| 77_I | 150_L | 1.063 | 0.95 |
| 81_L | 141_C | 1.055 | 0.95 |
| 281_T | 284_K | 1.054 | 0.95 |
| 231_V | 248_L | 1.052 | 0.95 |
| 84_M | 124_I | 1.047 | 0.94 |
| 260_D | 263_Q | 1.043 | 0.94 |
| 92_A | 137_I | 1.040 | 0.94 |
| 85_K | 139_I | 1.036 | 0.94 |
| 27_I | 40_L | 1.035 | 0.94 |
| 222_L | 233_A | 1.035 | 0.94 |
| 168_F | 213_F | 1.034 | 0.94 |
| 21_Q | 44_L | 1.021 | 0.93 |
| 229_H | 245_Y | 1.020 | 0.93 |
| 168_F | 203_V | 1.018 | 0.93 |
| 277_R | 281_T | 1.013 | 0.93 |
| 284_K | 288_E | 1.011 | 0.93 |
| 185_L | 189_I | 1.011 | 0.93 |
| 240_L | 286_L | 1.008 | 0.93 |
| 81_L | 120_L | 1.003 | 0.93 |
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 | 0.6861 | 100 | 0.506 | Contact Map |
| 2c2aA | 1 | 0.6926 | 100 | 0.508 | Contact Map |
| 2e0aA | 2 | 0.7605 | 100 | 0.535 | Contact Map |
| 3jz3A | 2 | 0.5178 | 100 | 0.538 | Contact Map |
| 1y8oA | 1 | 0.8091 | 100 | 0.54 | Contact Map |
| 4e01A | 1 | 0.699 | 100 | 0.541 | Contact Map |
| 4ew8A | 2 | 0.7023 | 100 | 0.544 | Contact Map |
| 4mpcA | 1 | 0.7702 | 100 | 0.545 | Contact Map |
| 4gczA | 2 | 0.712 | 100 | 0.55 | Contact Map |
| 3d36A | 2 | 0.6796 | 100 | 0.55 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)