| T122 |
| ID: | 1494863317 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 321 (281) | ||
| Sequences: | 4478 (2926.9) | ||
| Seq/Len: | 15.936 | ||
| Nf(neff/√len): | 174.6 |
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: 15.936).
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 |
| 108_H | 111_E | 4.552 | 1.00 |
| 256_R | 293_Q | 4.492 | 1.00 |
| 258_K | 291_V | 3.688 | 1.00 |
| 48_I | 119_I | 3.683 | 1.00 |
| 56_I | 63_K | 3.352 | 1.00 |
| 42_F | 92_F | 2.960 | 1.00 |
| 200_N | 203_G | 2.884 | 1.00 |
| 281_E | 292_F | 2.799 | 1.00 |
| 54_A | 103_A | 2.681 | 1.00 |
| 252_S | 297_Q | 2.615 | 1.00 |
| 225_I | 243_D | 2.552 | 1.00 |
| 56_I | 60_Q | 2.525 | 1.00 |
| 60_Q | 63_K | 2.360 | 1.00 |
| 76_Q | 96_H | 2.340 | 1.00 |
| 255_M | 279_Q | 2.308 | 1.00 |
| 238_T | 313_H | 2.259 | 1.00 |
| 105_C | 108_H | 2.255 | 1.00 |
| 255_M | 294_V | 2.193 | 1.00 |
| 254_E | 295_R | 2.159 | 1.00 |
| 161_H | 195_W | 2.133 | 1.00 |
| 179_I | 183_T | 2.115 | 1.00 |
| 52_C | 101_C | 2.082 | 1.00 |
| 234_T | 237_K | 2.010 | 1.00 |
| 295_R | 304_W | 2.001 | 1.00 |
| 68_K | 102_T | 1.997 | 1.00 |
| 265_W | 293_Q | 1.961 | 1.00 |
| 228_A | 238_T | 1.902 | 1.00 |
| 244_S | 253_C | 1.881 | 1.00 |
| 253_C | 296_C | 1.871 | 1.00 |
| 226_S | 240_I | 1.868 | 1.00 |
| 100_Y | 116_G | 1.863 | 1.00 |
| 98_S | 116_G | 1.855 | 1.00 |
| 199_A | 204_M | 1.783 | 1.00 |
| 289_K | 314_K | 1.768 | 1.00 |
| 67_Y | 87_L | 1.727 | 1.00 |
| 292_F | 313_H | 1.714 | 1.00 |
| 98_S | 118_D | 1.712 | 1.00 |
| 259_A | 285_E | 1.712 | 1.00 |
| 256_R | 295_R | 1.698 | 1.00 |
| 284_L | 290_Y | 1.682 | 1.00 |
| 49_S | 88_W | 1.678 | 1.00 |
| 139_S | 142_M | 1.673 | 1.00 |
| 245_Q | 253_C | 1.661 | 1.00 |
| 56_I | 105_C | 1.652 | 1.00 |
| 100_Y | 114_I | 1.644 | 1.00 |
| 50_I | 99_M | 1.641 | 1.00 |
| 50_I | 119_I | 1.634 | 1.00 |
| 183_T | 194_V | 1.623 | 1.00 |
| 104_E | 112_T | 1.619 | 1.00 |
| 221_S | 302_R | 1.616 | 1.00 |
| 157_K | 199_A | 1.615 | 1.00 |
| 254_E | 297_Q | 1.575 | 1.00 |
| 65_H | 103_A | 1.550 | 1.00 |
| 297_Q | 301_K | 1.540 | 1.00 |
| 284_L | 315_T | 1.505 | 1.00 |
| 245_Q | 250_K | 1.492 | 1.00 |
| 239_I | 280_S | 1.471 | 1.00 |
| 49_S | 86_R | 1.470 | 1.00 |
| 305_Q | 308_S | 1.456 | 1.00 |
| 47_N | 90_K | 1.450 | 1.00 |
| 238_T | 292_F | 1.445 | 1.00 |
| 158_Y | 198_A | 1.429 | 1.00 |
| 125_P | 203_G | 1.417 | 1.00 |
| 240_I | 292_F | 1.414 | 1.00 |
| 50_I | 117_K | 1.410 | 1.00 |
| 137_E | 142_M | 1.397 | 0.99 |
| 186_L | 192_Y | 1.391 | 0.99 |
| 188_G | 192_Y | 1.385 | 0.99 |
| 288_I | 315_T | 1.382 | 0.99 |
| 163_K | 193_L | 1.363 | 0.99 |
| 47_N | 88_W | 1.361 | 0.99 |
| 51_Y | 84_T | 1.354 | 0.99 |
| 60_Q | 105_C | 1.343 | 0.99 |
| 44_M | 123_Y | 1.341 | 0.99 |
| 258_K | 265_W | 1.327 | 0.99 |
| 190_K | 194_V | 1.320 | 0.99 |
| 170_E | 195_W | 1.317 | 0.99 |
| 42_F | 48_I | 1.312 | 0.99 |
| 281_E | 284_L | 1.310 | 0.99 |
| 68_K | 100_Y | 1.307 | 0.99 |
| 287_N | 317_E | 1.302 | 0.99 |
| 197_Q | 204_M | 1.296 | 0.99 |
| 295_R | 302_R | 1.277 | 0.99 |
| 198_A | 205_E | 1.255 | 0.99 |
| 101_C | 119_I | 1.252 | 0.99 |
| 159_V | 199_A | 1.250 | 0.99 |
| 122_G | 202_L | 1.236 | 0.98 |
| 42_F | 121_S | 1.234 | 0.98 |
| 105_C | 111_E | 1.231 | 0.98 |
| 89_Y | 96_H | 1.227 | 0.98 |
| 96_H | 99_M | 1.215 | 0.98 |
| 149_G | 152_T | 1.200 | 0.98 |
| 249_E | 298_E | 1.198 | 0.98 |
| 133_C | 146_W | 1.193 | 0.98 |
| 191_K | 213_H | 1.190 | 0.98 |
| 47_N | 91_N | 1.190 | 0.98 |
| 43_K | 46_M | 1.158 | 0.97 |
| 102_T | 114_I | 1.152 | 0.97 |
| 240_I | 255_M | 1.147 | 0.97 |
| 250_K | 296_C | 1.144 | 0.97 |
| 96_H | 121_S | 1.140 | 0.97 |
| 76_Q | 89_Y | 1.140 | 0.97 |
| 226_S | 294_V | 1.136 | 0.97 |
| 291_V | 310_L | 1.135 | 0.97 |
| 152_T | 155_D | 1.122 | 0.97 |
| 56_I | 111_E | 1.117 | 0.96 |
| 295_R | 301_K | 1.116 | 0.96 |
| 69_N | 96_H | 1.111 | 0.96 |
| 149_G | 153_Y | 1.108 | 0.96 |
| 173_Y | 179_I | 1.103 | 0.96 |
| 296_C | 300_G | 1.102 | 0.96 |
| 125_P | 200_N | 1.100 | 0.96 |
| 224_V | 243_D | 1.099 | 0.96 |
| 133_C | 196_V | 1.097 | 0.96 |
| 137_E | 141_N | 1.088 | 0.96 |
| 54_A | 65_H | 1.081 | 0.95 |
| 42_F | 46_M | 1.074 | 0.95 |
| 51_Y | 86_R | 1.068 | 0.95 |
| 239_I | 278_Q | 1.058 | 0.95 |
| 133_C | 136_Y | 1.055 | 0.95 |
| 317_E | 320_G | 1.038 | 0.94 |
| 228_A | 311_F | 1.034 | 0.94 |
| 85_A | 101_C | 1.033 | 0.94 |
| 146_W | 149_G | 1.017 | 0.93 |
| 53_Q | 84_T | 1.012 | 0.93 |
| 183_T | 190_K | 1.011 | 0.93 |
| 144_C | 160_V | 1.009 | 0.93 |
| 92_F | 119_I | 1.009 | 0.93 |
| 219_I | 303_Y | 1.008 | 0.93 |
| 287_N | 320_G | 1.008 | 0.93 |
| 192_Y | 196_V | 1.002 | 0.92 |
| 223_A | 296_C | 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 | |
| 2d9qB | 1 | 0.8692 | 100 | 0.402 | Contact Map |
| 1i1rA | 1 | 0.8941 | 100 | 0.413 | Contact Map |
| 3l5hA | 1 | 0.8816 | 100 | 0.431 | Contact Map |
| 1n26A | 1 | 0.8816 | 100 | 0.455 | Contact Map |
| 2q7nA | 2 | 0.9377 | 100 | 0.481 | Contact Map |
| 4yh7A | 1 | 0 | 100 | 0.522 | Contact Map |
| 3e0gA | 1 | 0.9283 | 100 | 0.526 | Contact Map |
| 4pbxA | 1 | 0.9377 | 100 | 0.527 | Contact Map |
| 2v5yA | 1 | 0.9564 | 100 | 0.532 | Contact Map |
| 4oe8A | 1 | 0.8006 | 100 | 0.557 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)