| my_study_4v8h |
| ID: | 1503004511 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 256 (229) | ||
| Sequences: | 2543 (1240.3) | ||
| Seq/Len: | 11.105 | ||
| Nf(neff/√len): | 82.0 |
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: 11.105).
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 |
| 66_G | 160_D | 3.237 | 1.00 |
| 163_F | 218_A | 2.893 | 1.00 |
| 50_E | 53_R | 2.874 | 1.00 |
| 221_L | 225_A | 2.823 | 1.00 |
| 82_R | 86_E | 2.809 | 1.00 |
| 61_L | 161_A | 2.694 | 1.00 |
| 57_F | 185_I | 2.647 | 1.00 |
| 119_E | 153_R | 2.604 | 1.00 |
| 187_L | 203_G | 2.556 | 1.00 |
| 114_R | 141_E | 2.551 | 1.00 |
| 122_F | 139_K | 2.479 | 1.00 |
| 84_E | 87_R | 2.442 | 1.00 |
| 62_A | 68_I | 2.400 | 1.00 |
| 32_I | 190_T | 2.367 | 1.00 |
| 58_I | 218_A | 2.348 | 1.00 |
| 120_A | 124_S | 2.334 | 1.00 |
| 162_I | 177_A | 2.252 | 1.00 |
| 122_F | 142_L | 2.063 | 1.00 |
| 61_L | 66_G | 2.063 | 1.00 |
| 59_E | 224_Q | 2.058 | 1.00 |
| 93_V | 101_M | 2.058 | 1.00 |
| 15_V | 203_G | 2.020 | 1.00 |
| 187_L | 214_I | 2.010 | 1.00 |
| 15_V | 210_S | 2.005 | 1.00 |
| 42_I | 190_T | 1.956 | 1.00 |
| 178_R | 196_L | 1.940 | 1.00 |
| 146_Q | 150_S | 1.938 | 1.00 |
| 164_V | 184_V | 1.935 | 1.00 |
| 84_E | 216_S | 1.924 | 1.00 |
| 77_A | 211_I | 1.875 | 1.00 |
| 43_D | 46_K | 1.833 | 1.00 |
| 57_F | 161_A | 1.823 | 1.00 |
| 136_V | 140_H | 1.800 | 1.00 |
| 10_L | 15_V | 1.783 | 1.00 |
| 58_I | 185_I | 1.754 | 1.00 |
| 189_D | 206_D | 1.727 | 1.00 |
| 24_W | 40_H | 1.726 | 1.00 |
| 122_F | 127_I | 1.712 | 1.00 |
| 19_H | 189_D | 1.695 | 1.00 |
| 119_E | 142_L | 1.614 | 1.00 |
| 88_A | 222_I | 1.610 | 1.00 |
| 119_E | 146_Q | 1.595 | 1.00 |
| 27_K | 195_D | 1.592 | 1.00 |
| 203_G | 214_I | 1.575 | 1.00 |
| 127_I | 135_Q | 1.574 | 1.00 |
| 171_A | 175_R | 1.543 | 1.00 |
| 178_R | 198_D | 1.520 | 1.00 |
| 87_R | 223_I | 1.502 | 1.00 |
| 161_A | 185_I | 1.500 | 1.00 |
| 57_F | 61_L | 1.482 | 1.00 |
| 19_H | 206_D | 1.477 | 1.00 |
| 55_F | 217_R | 1.475 | 1.00 |
| 117_E | 121_L | 1.473 | 1.00 |
| 175_R | 179_K | 1.470 | 1.00 |
| 116_E | 153_R | 1.442 | 1.00 |
| 188_A | 200_I | 1.439 | 1.00 |
| 216_S | 220_D | 1.401 | 0.99 |
| 203_G | 210_S | 1.386 | 0.99 |
| 116_E | 154_L | 1.374 | 0.99 |
| 55_F | 221_L | 1.365 | 0.99 |
| 87_R | 220_D | 1.337 | 0.99 |
| 51_L | 217_R | 1.336 | 0.99 |
| 62_A | 222_I | 1.329 | 0.99 |
| 25_N | 193_D | 1.310 | 0.99 |
| 125_P | 128_E | 1.301 | 0.99 |
| 165_V | 187_L | 1.296 | 0.99 |
| 67_T | 160_D | 1.293 | 0.99 |
| 60_D | 63_M | 1.275 | 0.99 |
| 31_Y | 50_E | 1.269 | 0.99 |
| 84_E | 219_V | 1.267 | 0.99 |
| 98_L | 101_M | 1.266 | 0.99 |
| 56_R | 59_E | 1.252 | 0.99 |
| 142_L | 146_Q | 1.236 | 0.98 |
| 78_Q | 95_Q | 1.231 | 0.98 |
| 87_R | 219_V | 1.221 | 0.98 |
| 139_K | 143_E | 1.214 | 0.98 |
| 67_T | 91_P | 1.207 | 0.98 |
| 55_F | 218_A | 1.176 | 0.98 |
| 186_A | 197_V | 1.176 | 0.98 |
| 102_L | 180_L | 1.171 | 0.98 |
| 121_L | 125_P | 1.170 | 0.97 |
| 106_K | 110_Q | 1.161 | 0.97 |
| 83_M | 212_Q | 1.148 | 0.97 |
| 163_F | 215_L | 1.143 | 0.97 |
| 130_R | 138_L | 1.143 | 0.97 |
| 116_E | 156_K | 1.131 | 0.97 |
| 98_L | 149_L | 1.126 | 0.97 |
| 118_L | 142_L | 1.122 | 0.97 |
| 14_G | 17_F | 1.116 | 0.96 |
| 111_R | 114_R | 1.115 | 0.96 |
| 74_K | 170_E | 1.113 | 0.96 |
| 53_R | 56_R | 1.111 | 0.96 |
| 21_R | 35_E | 1.103 | 0.96 |
| 63_M | 228_G | 1.095 | 0.96 |
| 61_L | 185_I | 1.089 | 0.96 |
| 178_R | 184_V | 1.084 | 0.96 |
| 127_I | 138_L | 1.080 | 0.95 |
| 214_I | 218_A | 1.079 | 0.95 |
| 201_I | 218_A | 1.074 | 0.95 |
| 74_K | 166_D | 1.070 | 0.95 |
| 9_E | 217_R | 1.069 | 0.95 |
| 62_A | 225_A | 1.068 | 0.95 |
| 133_K | 137_R | 1.067 | 0.95 |
| 122_F | 125_P | 1.059 | 0.95 |
| 128_E | 135_Q | 1.058 | 0.95 |
| 113_H | 117_E | 1.055 | 0.95 |
| 188_A | 197_V | 1.049 | 0.94 |
| 59_E | 228_G | 1.047 | 0.94 |
| 158_L | 182_I | 1.047 | 0.94 |
| 70_F | 85_A | 1.045 | 0.94 |
| 165_V | 170_E | 1.044 | 0.94 |
| 50_E | 202_P | 1.041 | 0.94 |
| 95_Q | 148_Y | 1.038 | 0.94 |
| 197_V | 200_I | 1.035 | 0.94 |
| 144_R | 148_Y | 1.026 | 0.94 |
| 27_K | 193_D | 1.019 | 0.93 |
| 139_K | 142_L | 1.010 | 0.93 |
| 70_F | 90_M | 1.009 | 0.93 |
| 96_R | 99_G | 1.007 | 0.93 |
| 174_V | 197_V | 1.002 | 0.92 |
| 58_I | 161_A | 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 | |
| 4rb5B | 1 | 0.9023 | 100 | 0.109 | Contact Map |
| 3bbnB | 1 | 0.9023 | 100 | 0.168 | Contact Map |
| 5aj3B | 1 | 0 | 100 | 0.304 | Contact Map |
| 4bpeB | 1 | 0.7383 | 100 | 0.338 | Contact Map |
| 4toiA | 1 | 0.9766 | 100 | 0.339 | Contact Map |
| 3j7aC | 1 | 0.7266 | 100 | 0.339 | Contact Map |
| 4ujpB | 1 | 0.7227 | 100 | 0.341 | Contact Map |
| 3zeyC | 1 | 0.7383 | 100 | 0.342 | Contact Map |
| 3j60A | 1 | 0.7188 | 100 | 0.348 | Contact Map |
| 3j38A | 1 | 0.7656 | 100 | 0.353 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)