| 5_blade 4NOV_A |
| ID: | 1483622664 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 306 (293) | ||
| Sequences: | 5786 (3303.2) | ||
| Seq/Len: | 19.747 | ||
| Nf(neff/√len): | 193.0 |
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: 19.747).
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 |
| 144_Q | 158_L | 6.920 | 1.00 |
| 55_D | 58_N | 5.436 | 1.00 |
| 26_T | 52_S | 5.265 | 1.00 |
| 205_L | 228_D | 5.089 | 1.00 |
| 260_H | 284_E | 4.237 | 1.00 |
| 141_D | 201_K | 3.898 | 1.00 |
| 288_N | 292_T | 3.855 | 1.00 |
| 205_L | 226_T | 3.837 | 1.00 |
| 26_T | 54_K | 3.820 | 1.00 |
| 89_K | 109_I | 3.774 | 1.00 |
| 89_K | 111_D | 3.691 | 1.00 |
| 30_Y | 117_F | 3.654 | 1.00 |
| 158_L | 167_D | 3.272 | 1.00 |
| 139_I | 145_A | 3.130 | 1.00 |
| 148_Y | 156_Y | 2.945 | 1.00 |
| 160_N | 165_T | 2.695 | 1.00 |
| 85_E | 88_G | 2.655 | 1.00 |
| 157_V | 166_Y | 2.373 | 1.00 |
| 156_Y | 231_T | 2.331 | 1.00 |
| 162_N | 165_T | 2.318 | 1.00 |
| 230_P | 234_W | 2.253 | 1.00 |
| 256_D | 261_S | 2.197 | 1.00 |
| 257_F | 260_H | 2.155 | 1.00 |
| 23_Y | 90_F | 2.125 | 1.00 |
| 30_Y | 83_A | 2.077 | 1.00 |
| 65_I | 92_L | 2.042 | 1.00 |
| 27_L | 53_T | 2.014 | 1.00 |
| 110_S | 116_P | 2.005 | 1.00 |
| 52_S | 62_H | 1.983 | 1.00 |
| 83_A | 92_L | 1.981 | 1.00 |
| 160_N | 167_D | 1.977 | 1.00 |
| 254_I | 285_F | 1.958 | 1.00 |
| 202_R | 287_Y | 1.943 | 1.00 |
| 148_Y | 230_P | 1.932 | 1.00 |
| 138_F | 206_Y | 1.868 | 1.00 |
| 148_Y | 234_W | 1.790 | 1.00 |
| 30_Y | 113_P | 1.721 | 1.00 |
| 48_W | 92_L | 1.680 | 1.00 |
| 226_T | 235_K | 1.670 | 1.00 |
| 200_Y | 254_I | 1.668 | 1.00 |
| 199_F | 234_W | 1.657 | 1.00 |
| 261_S | 287_Y | 1.656 | 1.00 |
| 23_Y | 85_E | 1.626 | 1.00 |
| 265_Y | 283_A | 1.623 | 1.00 |
| 52_S | 60_T | 1.618 | 1.00 |
| 228_D | 235_K | 1.614 | 1.00 |
| 226_T | 292_T | 1.595 | 1.00 |
| 160_N | 164_I | 1.584 | 1.00 |
| 171_G | 231_T | 1.583 | 1.00 |
| 156_Y | 234_W | 1.575 | 1.00 |
| 267_T | 281_C | 1.564 | 1.00 |
| 227_S | 234_W | 1.563 | 1.00 |
| 149_F | 157_V | 1.556 | 1.00 |
| 209_V | 224_Y | 1.550 | 1.00 |
| 148_Y | 199_F | 1.547 | 1.00 |
| 264_F | 282_V | 1.530 | 1.00 |
| 201_K | 206_Y | 1.519 | 1.00 |
| 15_T | 51_F | 1.501 | 1.00 |
| 109_I | 118_K | 1.487 | 1.00 |
| 53_T | 59_W | 1.475 | 1.00 |
| 52_S | 114_T | 1.452 | 1.00 |
| 286_T | 294_N | 1.434 | 1.00 |
| 22_V | 25_D | 1.412 | 1.00 |
| 200_Y | 287_Y | 1.406 | 0.99 |
| 93_Y | 137_V | 1.396 | 0.99 |
| 135_P | 147_L | 1.392 | 0.99 |
| 85_E | 90_F | 1.376 | 0.99 |
| 222_L | 263_L | 1.370 | 0.99 |
| 91_Y | 107_V | 1.369 | 0.99 |
| 15_T | 31_T | 1.360 | 0.99 |
| 227_S | 233_P | 1.355 | 0.99 |
| 252_P | 263_L | 1.337 | 0.99 |
| 288_N | 294_N | 1.328 | 0.99 |
| 29_L | 280_V | 1.319 | 0.99 |
| 209_V | 222_L | 1.304 | 0.99 |
| 262_Y | 284_E | 1.303 | 0.99 |
| 93_Y | 107_V | 1.286 | 0.99 |
| 226_T | 237_G | 1.286 | 0.99 |
| 48_W | 78_A | 1.280 | 0.99 |
| 209_V | 254_I | 1.265 | 0.99 |
| 146_Y | 231_T | 1.261 | 0.99 |
| 49_R | 61_D | 1.256 | 0.99 |
| 140_D | 201_K | 1.254 | 0.99 |
| 56_M | 282_V | 1.239 | 0.98 |
| 200_Y | 209_V | 1.235 | 0.98 |
| 229_S | 233_P | 1.223 | 0.98 |
| 204_D | 228_D | 1.220 | 0.98 |
| 160_N | 163_M | 1.211 | 0.98 |
| 201_K | 204_D | 1.199 | 0.98 |
| 256_D | 259_G | 1.191 | 0.98 |
| 82_Q | 136_T | 1.190 | 0.98 |
| 73_W | 106_A | 1.190 | 0.98 |
| 246_G | 281_C | 1.188 | 0.98 |
| 94_C | 119_D | 1.184 | 0.98 |
| 110_S | 115_G | 1.179 | 0.98 |
| 53_T | 56_M | 1.173 | 0.98 |
| 229_S | 234_W | 1.157 | 0.97 |
| 161_E | 164_I | 1.148 | 0.97 |
| 21_M | 90_F | 1.143 | 0.97 |
| 20_P | 264_F | 1.142 | 0.97 |
| 25_D | 54_K | 1.136 | 0.97 |
| 28_Y | 52_S | 1.134 | 0.97 |
| 156_Y | 230_P | 1.128 | 0.97 |
| 106_A | 119_D | 1.122 | 0.97 |
| 140_D | 206_Y | 1.122 | 0.97 |
| 142_D | 201_K | 1.120 | 0.96 |
| 147_L | 157_V | 1.116 | 0.96 |
| 212_A | 223_A | 1.105 | 0.96 |
| 202_R | 261_S | 1.103 | 0.96 |
| 148_Y | 208_M | 1.103 | 0.96 |
| 31_T | 51_F | 1.093 | 0.96 |
| 261_S | 285_F | 1.086 | 0.96 |
| 155_R | 172_I | 1.085 | 0.96 |
| 30_Y | 50_C | 1.083 | 0.96 |
| 262_Y | 282_V | 1.078 | 0.95 |
| 194_G | 210_Y | 1.055 | 0.95 |
| 33_H | 47_D | 1.043 | 0.94 |
| 53_T | 57_V | 1.043 | 0.94 |
| 255_A | 264_F | 1.043 | 0.94 |
| 71_I | 78_A | 1.038 | 0.94 |
| 205_L | 227_S | 1.035 | 0.94 |
| 22_V | 257_F | 1.027 | 0.94 |
| 202_R | 256_D | 1.019 | 0.93 |
| 248_F | 268_G | 1.018 | 0.93 |
| 157_V | 168_K | 1.016 | 0.93 |
| 112_S | 116_P | 1.016 | 0.93 |
| 138_F | 230_P | 1.011 | 0.93 |
| 50_C | 83_A | 1.007 | 0.93 |
| 97_H | 103_M | 1.005 | 0.93 |
| 146_Y | 158_L | 1.004 | 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 | |
| 4novA | 1 | 0.9935 | 100 | 0.197 | Contact Map |
| 3c7fA | 1 | 0.9346 | 100 | 0.238 | Contact Map |
| 3qeeA | 2 | 0.9314 | 100 | 0.241 | Contact Map |
| 3c2uA | 4 | 0.902 | 100 | 0.256 | Contact Map |
| 1yrzA | 2 | 0.902 | 100 | 0.256 | Contact Map |
| 1yifA | 4 | 0.8987 | 100 | 0.259 | Contact Map |
| 4kc7A | 3 | 0.8954 | 100 | 0.26 | Contact Map |
| 4mlgA | 12 | 0.9444 | 100 | 0.26 | Contact Map |
| 4qqsA | 2 | 0.9444 | 100 | 0.261 | Contact Map |
| 2exhA | 4 | 0.8987 | 100 | 0.263 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)