| 20170920B_a4 |
| ID: | 1505936639 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 301 (296) | ||
| Sequences: | 3882 (2932.3) | ||
| Seq/Len: | 13.115 | ||
| Nf(neff/√len): | 170.4 |
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: 13.115).
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 |
| 133_C | 147_C | 3.849 | 1.00 |
| 49_D | 52_N | 3.470 | 1.00 |
| 15_K | 77_Y | 3.298 | 1.00 |
| 66_H | 120_R | 2.538 | 1.00 |
| 90_I | 113_A | 2.399 | 1.00 |
| 146_N | 210_V | 2.287 | 1.00 |
| 12_L | 16_L | 2.255 | 1.00 |
| 98_Y | 152_G | 2.254 | 1.00 |
| 95_I | 163_L | 2.164 | 1.00 |
| 252_S | 255_L | 2.049 | 1.00 |
| 67_D | 70_L | 2.031 | 1.00 |
| 131_S | 149_M | 1.904 | 1.00 |
| 146_N | 208_A | 1.880 | 1.00 |
| 66_H | 118_D | 1.876 | 1.00 |
| 144_Q | 210_V | 1.857 | 1.00 |
| 140_F | 143_D | 1.854 | 1.00 |
| 74_P | 117_H | 1.836 | 1.00 |
| 191_N | 204_D | 1.792 | 1.00 |
| 153_S | 156_Y | 1.728 | 1.00 |
| 141_P | 145_Q | 1.718 | 1.00 |
| 162_D | 203_P | 1.716 | 1.00 |
| 158_K | 203_P | 1.706 | 1.00 |
| 64_E | 120_R | 1.698 | 1.00 |
| 162_D | 190_Y | 1.691 | 1.00 |
| 157_D | 160_K | 1.679 | 1.00 |
| 35_L | 164_V | 1.677 | 1.00 |
| 182_V | 212_R | 1.671 | 1.00 |
| 143_D | 147_C | 1.662 | 1.00 |
| 248_T | 252_S | 1.617 | 1.00 |
| 8_A | 78_E | 1.570 | 1.00 |
| 252_S | 256_S | 1.559 | 1.00 |
| 116_F | 120_R | 1.545 | 1.00 |
| 236_V | 250_C | 1.543 | 1.00 |
| 17_F | 85_I | 1.531 | 1.00 |
| 63_Q | 95_I | 1.530 | 1.00 |
| 115_L | 121_V | 1.527 | 1.00 |
| 8_A | 11_R | 1.525 | 1.00 |
| 17_F | 20_Y | 1.514 | 1.00 |
| 195_Y | 198_C | 1.505 | 1.00 |
| 20_Y | 26_P | 1.493 | 1.00 |
| 73_D | 76_D | 1.490 | 1.00 |
| 144_Q | 212_R | 1.478 | 1.00 |
| 184_V | 212_R | 1.472 | 1.00 |
| 215_P | 219_T | 1.451 | 1.00 |
| 182_V | 214_L | 1.443 | 1.00 |
| 175_F | 181_W | 1.443 | 1.00 |
| 254_L | 257_L | 1.439 | 1.00 |
| 276_P | 279_G | 1.418 | 1.00 |
| 178_S | 181_W | 1.416 | 1.00 |
| 16_L | 20_Y | 1.406 | 0.99 |
| 148_T | 208_A | 1.397 | 0.99 |
| 65_W | 93_P | 1.383 | 0.99 |
| 172_Q | 175_F | 1.376 | 0.99 |
| 11_R | 15_K | 1.364 | 0.99 |
| 143_D | 213_R | 1.355 | 0.99 |
| 115_L | 119_G | 1.349 | 0.99 |
| 277_L | 281_Y | 1.338 | 0.99 |
| 48_V | 55_M | 1.331 | 0.99 |
| 40_L | 59_V | 1.331 | 0.99 |
| 67_D | 90_I | 1.322 | 0.99 |
| 245_E | 248_T | 1.318 | 0.99 |
| 290_T | 295_I | 1.298 | 0.99 |
| 65_W | 91_W | 1.296 | 0.99 |
| 48_V | 135_I | 1.292 | 0.99 |
| 85_I | 115_L | 1.289 | 0.99 |
| 281_Y | 286_M | 1.280 | 0.99 |
| 91_W | 94_D | 1.279 | 0.99 |
| 194_K | 201_I | 1.267 | 0.99 |
| 35_L | 162_D | 1.245 | 0.98 |
| 72_W | 77_Y | 1.245 | 0.98 |
| 175_F | 178_S | 1.238 | 0.98 |
| 251_I | 255_L | 1.226 | 0.98 |
| 75_A | 81_T | 1.224 | 0.98 |
| 218_Y | 222_L | 1.223 | 0.98 |
| 135_I | 140_F | 1.219 | 0.98 |
| 65_W | 70_L | 1.211 | 0.98 |
| 191_N | 206_T | 1.209 | 0.98 |
| 67_D | 91_W | 1.208 | 0.98 |
| 57_T | 131_S | 1.207 | 0.98 |
| 140_F | 145_Q | 1.206 | 0.98 |
| 133_C | 143_D | 1.183 | 0.98 |
| 49_D | 53_Q | 1.183 | 0.98 |
| 21_N | 26_P | 1.157 | 0.97 |
| 267_I | 270_S | 1.150 | 0.97 |
| 29_N | 32_D | 1.143 | 0.97 |
| 142_F | 145_Q | 1.142 | 0.97 |
| 94_D | 153_S | 1.137 | 0.97 |
| 213_R | 218_Y | 1.133 | 0.97 |
| 234_V | 238_Y | 1.123 | 0.97 |
| 70_L | 90_I | 1.117 | 0.96 |
| 237_F | 244_G | 1.113 | 0.96 |
| 135_I | 145_Q | 1.111 | 0.96 |
| 56_T | 130_K | 1.110 | 0.96 |
| 13_L | 21_N | 1.108 | 0.96 |
| 90_I | 121_V | 1.108 | 0.96 |
| 70_L | 91_W | 1.104 | 0.96 |
| 21_N | 24_S | 1.097 | 0.96 |
| 67_D | 93_P | 1.088 | 0.96 |
| 269_P | 272_S | 1.076 | 0.95 |
| 65_W | 72_W | 1.074 | 0.95 |
| 158_K | 201_I | 1.073 | 0.95 |
| 153_S | 161_I | 1.072 | 0.95 |
| 282_L | 288_F | 1.067 | 0.95 |
| 253_V | 257_L | 1.067 | 0.95 |
| 47_D | 52_N | 1.063 | 0.95 |
| 10_E | 14_K | 1.060 | 0.95 |
| 67_D | 121_V | 1.054 | 0.95 |
| 195_Y | 204_D | 1.048 | 0.94 |
| 39_G | 62_K | 1.048 | 0.94 |
| 66_H | 71_R | 1.046 | 0.94 |
| 113_A | 121_V | 1.043 | 0.94 |
| 70_L | 121_V | 1.042 | 0.94 |
| 251_I | 254_L | 1.041 | 0.94 |
| 32_D | 68_Y | 1.037 | 0.94 |
| 140_F | 218_Y | 1.036 | 0.94 |
| 230_S | 285_T | 1.036 | 0.94 |
| 59_V | 127_A | 1.035 | 0.94 |
| 297_V | 301_N | 1.035 | 0.94 |
| 93_P | 99_N | 1.033 | 0.94 |
| 103_G | 106_A | 1.032 | 0.94 |
| 37_R | 164_V | 1.031 | 0.94 |
| 213_R | 225_P | 1.031 | 0.94 |
| 248_T | 255_L | 1.029 | 0.94 |
| 59_V | 129_Y | 1.027 | 0.94 |
| 292_S | 299_V | 1.026 | 0.94 |
| 262_L | 266_E | 1.026 | 0.94 |
| 141_P | 147_C | 1.025 | 0.93 |
| 150_K | 206_T | 1.020 | 0.93 |
| 227_L | 232_L | 1.016 | 0.93 |
| 9_E | 13_L | 1.012 | 0.93 |
| 67_D | 72_W | 1.007 | 0.93 |
| 259_V | 263_L | 1.006 | 0.93 |
| 14_K | 19_G | 1.002 | 0.92 |
| 281_Y | 288_F | 1.001 | 0.92 |
| 197_C | 200_E | 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 | |
| 4aq5E | 1 | 0.9801 | 100 | 0.033 | Contact Map |
| 2bg9A | 2 | 0.9834 | 100 | 0.034 | Contact Map |
| 4aq5A | 2 | 0.9834 | 100 | 0.037 | Contact Map |
| 4aq5C | 1 | 0.9701 | 100 | 0.043 | Contact Map |
| 2bg9B | 1 | 0.9734 | 100 | 0.045 | Contact Map |
| 4aq5B | 1 | 0.9734 | 100 | 0.047 | Contact Map |
| 2bg9E | 1 | 0.9801 | 100 | 0.053 | Contact Map |
| 2bg9C | 1 | 0.9734 | 100 | 0.061 | Contact Map |
| 4pirA | 5 | 0.9668 | 100 | 0.063 | Contact Map |
| 4tnwA | 10 | 0.9668 | 100 | 0.092 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)