| 3499 |
| ID: | 1450343176 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 400 (299) | ||
| Sequences: | 4404 (3290.4) | ||
| Seq/Len: | 14.729 | ||
| Nf(neff/√len): | 190.3 |
HHblits Results: (2015_06)
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: 14.729).
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 |
| 45_V | 84_L | 4.709 | 1.00 |
| 46_S | 81_R | 4.134 | 1.00 |
| 44_T | 81_R | 3.599 | 1.00 |
| 98_A | 115_F | 3.421 | 1.00 |
| 72_D | 83_K | 3.149 | 1.00 |
| 71_T | 85_A | 3.077 | 1.00 |
| 46_S | 131_H | 2.792 | 1.00 |
| 42_T | 83_K | 2.786 | 1.00 |
| 74_S | 83_K | 2.755 | 1.00 |
| 84_L | 113_V | 2.753 | 1.00 |
| 127_S | 130_A | 2.659 | 1.00 |
| 59_K | 66_Q | 2.597 | 1.00 |
| 133_A | 136_Q | 2.589 | 1.00 |
| 100_V | 115_F | 2.580 | 1.00 |
| 278_K | 282_D | 2.578 | 1.00 |
| 44_T | 83_K | 2.483 | 1.00 |
| 76_S | 81_R | 2.458 | 1.00 |
| 44_T | 131_H | 2.381 | 1.00 |
| 62_Y | 67_V | 2.334 | 1.00 |
| 93_F | 125_P | 2.275 | 1.00 |
| 43_V | 84_L | 2.264 | 1.00 |
| 74_S | 81_R | 2.213 | 1.00 |
| 54_M | 82_L | 2.144 | 1.00 |
| 256_Y | 260_A | 2.143 | 1.00 |
| 56_K | 72_D | 2.067 | 1.00 |
| 283_Y | 286_V | 2.003 | 1.00 |
| 66_Q | 69_K | 1.933 | 1.00 |
| 56_K | 73_I | 1.884 | 1.00 |
| 94_I | 98_A | 1.870 | 1.00 |
| 96_S | 124_K | 1.847 | 1.00 |
| 43_V | 128_P | 1.771 | 1.00 |
| 47_S | 82_L | 1.767 | 1.00 |
| 211_N | 215_D | 1.747 | 1.00 |
| 237_Q | 240_N | 1.735 | 1.00 |
| 42_T | 71_T | 1.730 | 1.00 |
| 232_K | 236_D | 1.694 | 1.00 |
| 97_N | 118_P | 1.687 | 1.00 |
| 57_G | 69_K | 1.659 | 1.00 |
| 61_K | 112_S | 1.653 | 1.00 |
| 279_V | 282_D | 1.636 | 1.00 |
| 280_T | 287_F | 1.633 | 1.00 |
| 288_G | 292_K | 1.621 | 1.00 |
| 99_T | 116_I | 1.606 | 1.00 |
| 257_E | 261_P | 1.592 | 1.00 |
| 48_P | 134_A | 1.578 | 1.00 |
| 101_R | 116_I | 1.575 | 1.00 |
| 96_S | 130_A | 1.544 | 1.00 |
| 181_L | 185_L | 1.530 | 1.00 |
| 205_K | 208_V | 1.496 | 1.00 |
| 274_R | 278_K | 1.487 | 1.00 |
| 148_L | 151_L | 1.481 | 1.00 |
| 47_S | 102_I | 1.480 | 1.00 |
| 40_T | 85_A | 1.480 | 1.00 |
| 43_V | 86_I | 1.476 | 1.00 |
| 97_N | 119_K | 1.453 | 1.00 |
| 54_M | 58_A | 1.445 | 1.00 |
| 126_L | 130_A | 1.430 | 1.00 |
| 73_I | 82_L | 1.426 | 1.00 |
| 195_K | 198_A | 1.425 | 1.00 |
| 100_V | 132_V | 1.416 | 1.00 |
| 168_S | 172_R | 1.405 | 0.99 |
| 71_T | 83_K | 1.397 | 0.99 |
| 207_A | 211_N | 1.385 | 0.99 |
| 67_V | 86_I | 1.383 | 0.99 |
| 190_R | 194_P | 1.366 | 0.99 |
| 180_A | 184_G | 1.363 | 0.99 |
| 148_L | 152_L | 1.350 | 0.99 |
| 96_S | 125_P | 1.347 | 0.99 |
| 149_I | 153_H | 1.334 | 0.99 |
| 275_A | 279_V | 1.333 | 0.99 |
| 95_P | 98_A | 1.308 | 0.99 |
| 67_V | 115_F | 1.300 | 0.99 |
| 169_E | 172_R | 1.267 | 0.99 |
| 45_V | 113_V | 1.266 | 0.99 |
| 46_S | 133_A | 1.261 | 0.99 |
| 193_N | 196_L | 1.252 | 0.99 |
| 165_S | 169_E | 1.239 | 0.98 |
| 272_R | 275_A | 1.234 | 0.98 |
| 229_T | 232_K | 1.223 | 0.98 |
| 70_V | 113_V | 1.220 | 0.98 |
| 119_K | 123_P | 1.217 | 0.98 |
| 42_T | 85_A | 1.216 | 0.98 |
| 216_A | 219_D | 1.209 | 0.98 |
| 281_S | 284_S | 1.201 | 0.98 |
| 23_V | 27_V | 1.200 | 0.98 |
| 156_D | 159_E | 1.194 | 0.98 |
| 105_N | 112_S | 1.193 | 0.98 |
| 46_S | 79_Q | 1.174 | 0.98 |
| 58_A | 70_V | 1.173 | 0.98 |
| 189_T | 193_N | 1.170 | 0.97 |
| 39_S | 88_S | 1.169 | 0.97 |
| 58_A | 111_K | 1.167 | 0.97 |
| 183_S | 187_T | 1.162 | 0.97 |
| 201_E | 205_K | 1.155 | 0.97 |
| 174_H | 177_D | 1.150 | 0.97 |
| 159_E | 162_A | 1.150 | 0.97 |
| 268_D | 272_R | 1.147 | 0.97 |
| 249_I | 253_N | 1.146 | 0.97 |
| 294_I | 298_V | 1.145 | 0.97 |
| 62_Y | 90_E | 1.143 | 0.97 |
| 289_C | 292_K | 1.138 | 0.97 |
| 67_V | 94_I | 1.126 | 0.97 |
| 30_Y | 34_T | 1.123 | 0.97 |
| 58_A | 110_A | 1.121 | 0.97 |
| 279_V | 283_Y | 1.120 | 0.96 |
| 14_A | 17_L | 1.117 | 0.96 |
| 289_C | 293_G | 1.115 | 0.96 |
| 21_L | 24_G | 1.113 | 0.96 |
| 22_M | 26_A | 1.108 | 0.96 |
| 273_L | 276_P | 1.106 | 0.96 |
| 41_D | 86_I | 1.103 | 0.96 |
| 69_K | 85_A | 1.101 | 0.96 |
| 21_L | 27_V | 1.101 | 0.96 |
| 254_N | 257_E | 1.101 | 0.96 |
| 26_A | 29_T | 1.099 | 0.96 |
| 106_T | 110_A | 1.098 | 0.96 |
| 197_P | 201_E | 1.096 | 0.96 |
| 20_G | 23_V | 1.094 | 0.96 |
| 41_D | 88_S | 1.092 | 0.96 |
| 22_M | 27_V | 1.088 | 0.96 |
| 238_K | 242_N | 1.072 | 0.95 |
| 222_T | 226_N | 1.072 | 0.95 |
| 16_A | 19_A | 1.069 | 0.95 |
| 198_A | 201_E | 1.068 | 0.95 |
| 176_D | 180_A | 1.046 | 0.94 |
| 191_Q | 194_P | 1.040 | 0.94 |
| 109_G | 112_S | 1.034 | 0.94 |
| 296_R | 299_K | 1.025 | 0.93 |
| 41_D | 128_P | 1.024 | 0.93 |
| 304_L | 312_L | 1.020 | 0.93 |
| 271_N | 275_A | 1.018 | 0.93 |
| 132_V | 136_Q | 1.014 | 0.93 |
| 103_A | 114_E | 1.014 | 0.93 |
| 231_N | 235_V | 1.009 | 0.93 |
| 53_V | 106_T | 1.007 | 0.93 |
| 221_N | 225_D | 1.003 | 0.93 |
| 215_D | 218_G | 1.003 | 0.93 |
| 185_L | 189_T | 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 | |
| 3tulA | 4 | 0.345 | 70.8 | 0.954 | Contact Map |
| 4linA | 12 | 0.6875 | 39.2 | 0.962 | Contact Map |
| 3g67A | 2 | 0.4325 | 38.6 | 0.962 | Contact Map |
| 4i3mA | 1 | 0.3675 | 35.9 | 0.963 | Contact Map |
| 2ieqA | 3 | 0.225 | 24.3 | 0.966 | Contact Map |
| 2p22A | 1 | 0.3975 | 22.5 | 0.966 | Contact Map |
| 3favA | 2 | 0.225 | 21.5 | 0.967 | Contact Map |
| 1zvaA | 1 | 0.1875 | 19.7 | 0.967 | Contact Map |
| 4f7gB | 1 | 0.365 | 18.7 | 0.968 | Contact Map |
| 3ogiB | 2 | 0.2225 | 17.9 | 0.968 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)