| 4Q2EAPDBIDCHAINSEQUENCE |
| ID: | 1465599487 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 290 (264) | ||
| Sequences: | 2996 (2021.6) | ||
| Seq/Len: | 11.348 | ||
| Nf(neff/√len): | 124.4 |
HHblits Results: (2016_02)
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: 11.348).
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 |
| 30_T | 258_L | 5.874 | 1.00 |
| 166_F | 198_G | 4.637 | 1.00 |
| 170_T | 194_G | 4.103 | 1.00 |
| 177_T | 190_E | 3.949 | 1.00 |
| 192_V | 236_T | 3.511 | 1.00 |
| 242_E | 254_S | 3.032 | 1.00 |
| 261_H | 267_R | 2.684 | 1.00 |
| 176_R | 190_E | 2.604 | 1.00 |
| 172_L | 188_S | 2.558 | 1.00 |
| 162_V | 202_Y | 2.454 | 1.00 |
| 59_A | 264_M | 2.435 | 1.00 |
| 163_F | 236_T | 2.410 | 1.00 |
| 170_T | 174_F | 2.388 | 1.00 |
| 157_L | 161_W | 2.301 | 1.00 |
| 31_A | 36_P | 2.281 | 1.00 |
| 63_L | 130_A | 2.266 | 1.00 |
| 66_L | 251_V | 2.265 | 1.00 |
| 169_F | 173_K | 2.189 | 1.00 |
| 66_L | 254_S | 2.171 | 1.00 |
| 24_L | 169_F | 1.973 | 1.00 |
| 156_V | 275_A | 1.965 | 1.00 |
| 31_A | 35_A | 1.873 | 1.00 |
| 203_T | 228_A | 1.843 | 1.00 |
| 179_I | 240_I | 1.842 | 1.00 |
| 163_F | 235_D | 1.831 | 1.00 |
| 58_L | 264_M | 1.809 | 1.00 |
| 28_V | 169_F | 1.809 | 1.00 |
| 178_R | 186_R | 1.808 | 1.00 |
| 170_T | 198_G | 1.803 | 1.00 |
| 59_A | 265_L | 1.708 | 1.00 |
| 179_I | 189_L | 1.706 | 1.00 |
| 54_A | 58_L | 1.701 | 1.00 |
| 163_F | 232_A | 1.696 | 1.00 |
| 64_I | 77_Y | 1.688 | 1.00 |
| 227_F | 281_V | 1.683 | 1.00 |
| 24_L | 28_V | 1.657 | 1.00 |
| 158_T | 202_Y | 1.650 | 1.00 |
| 177_T | 189_L | 1.646 | 1.00 |
| 223_T | 281_V | 1.592 | 1.00 |
| 29_I | 33_V | 1.574 | 1.00 |
| 61_Y | 255_G | 1.526 | 1.00 |
| 66_L | 249_Y | 1.520 | 1.00 |
| 32_S | 36_P | 1.510 | 1.00 |
| 25_K | 29_I | 1.501 | 1.00 |
| 161_W | 261_H | 1.500 | 1.00 |
| 167_A | 195_G | 1.496 | 1.00 |
| 200_V | 225_L | 1.478 | 1.00 |
| 179_I | 192_V | 1.476 | 1.00 |
| 234_M | 277_V | 1.472 | 1.00 |
| 60_G | 64_I | 1.468 | 1.00 |
| 50_G | 54_A | 1.463 | 1.00 |
| 61_Y | 65_T | 1.442 | 1.00 |
| 189_L | 193_I | 1.440 | 1.00 |
| 34_V | 268_I | 1.421 | 1.00 |
| 64_I | 130_A | 1.415 | 1.00 |
| 170_T | 173_K | 1.405 | 0.99 |
| 196_F | 232_A | 1.386 | 0.99 |
| 161_W | 267_R | 1.381 | 0.99 |
| 159_S | 199_V | 1.373 | 0.99 |
| 140_F | 279_Y | 1.352 | 0.99 |
| 137_F | 140_F | 1.346 | 0.99 |
| 160_T | 274_V | 1.330 | 0.99 |
| 193_I | 197_L | 1.329 | 0.99 |
| 268_I | 271_L | 1.289 | 0.99 |
| 162_V | 198_G | 1.287 | 0.99 |
| 166_F | 194_G | 1.283 | 0.99 |
| 163_F | 195_G | 1.282 | 0.99 |
| 178_R | 188_S | 1.280 | 0.99 |
| 160_T | 270_G | 1.276 | 0.99 |
| 140_F | 280_I | 1.274 | 0.99 |
| 178_R | 181_P | 1.270 | 0.99 |
| 160_T | 271_L | 1.260 | 0.99 |
| 170_T | 188_S | 1.231 | 0.98 |
| 59_A | 268_I | 1.229 | 0.98 |
| 166_F | 170_T | 1.229 | 0.98 |
| 156_V | 278_S | 1.220 | 0.98 |
| 133_Y | 242_E | 1.219 | 0.98 |
| 224_F | 228_A | 1.201 | 0.98 |
| 196_F | 229_A | 1.200 | 0.98 |
| 234_M | 274_V | 1.195 | 0.98 |
| 180_S | 183_Y | 1.194 | 0.98 |
| 63_L | 67_E | 1.193 | 0.98 |
| 55_I | 264_M | 1.174 | 0.98 |
| 172_L | 186_R | 1.166 | 0.97 |
| 36_P | 40_L | 1.157 | 0.97 |
| 160_T | 235_D | 1.155 | 0.97 |
| 159_S | 203_T | 1.154 | 0.97 |
| 235_D | 270_G | 1.149 | 0.97 |
| 160_T | 254_S | 1.141 | 0.97 |
| 36_P | 161_W | 1.133 | 0.97 |
| 25_K | 28_V | 1.127 | 0.97 |
| 195_G | 232_A | 1.124 | 0.97 |
| 200_V | 229_A | 1.122 | 0.97 |
| 56_L | 138_L | 1.105 | 0.96 |
| 34_V | 37_F | 1.105 | 0.96 |
| 41_C | 51_L | 1.092 | 0.96 |
| 231_V | 278_S | 1.091 | 0.96 |
| 143_P | 279_Y | 1.082 | 0.96 |
| 222_R | 226_P | 1.082 | 0.96 |
| 39_V | 43_V | 1.080 | 0.95 |
| 205_L | 208_L | 1.078 | 0.95 |
| 242_E | 265_L | 1.075 | 0.95 |
| 175_G | 190_E | 1.073 | 0.95 |
| 27_R | 30_T | 1.069 | 0.95 |
| 30_T | 33_V | 1.066 | 0.95 |
| 155_L | 228_A | 1.066 | 0.95 |
| 60_G | 130_A | 1.064 | 0.95 |
| 241_F | 245_L | 1.063 | 0.95 |
| 155_L | 278_S | 1.063 | 0.95 |
| 170_T | 197_L | 1.062 | 0.95 |
| 255_G | 258_L | 1.043 | 0.94 |
| 201_I | 205_L | 1.038 | 0.94 |
| 26_T | 30_T | 1.034 | 0.94 |
| 189_L | 192_V | 1.032 | 0.94 |
| 42_F | 153_A | 1.032 | 0.94 |
| 140_F | 275_A | 1.030 | 0.94 |
| 174_F | 190_E | 1.028 | 0.94 |
| 145_Y | 150_A | 1.020 | 0.93 |
| 192_V | 233_I | 1.020 | 0.93 |
| 24_L | 168_Y | 1.017 | 0.93 |
| 163_F | 199_V | 1.017 | 0.93 |
| 211_N | 217_N | 1.005 | 0.93 |
| 199_V | 202_Y | 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 | |
| 4q2eA | 2 | 0.9103 | 100 | 0.102 | Contact Map |
| 2kogA | 1 | 0.1621 | 3.3 | 0.97 | Contact Map |
| 4ev6A | 5 | 0.2897 | 2.3 | 0.972 | Contact Map |
| 4c48C | 1 | 0.1586 | 2.2 | 0.972 | Contact Map |
| 4i0uA | 10 | 0.2828 | 1.5 | 0.975 | Contact Map |
| 1skhA | 1 | 0.1034 | 1.5 | 0.975 | Contact Map |
| 3hd7A | 2 | 0.1621 | 1.5 | 0.975 | Contact Map |
| 3fymA | 1 | 0.0379 | 1.3 | 0.975 | Contact Map |
| 4y7lA | 2 | 0 | 1.3 | 0.975 | Contact Map |
| 3pt3A | 2 | 0.1138 | 1.3 | 0.976 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)