| 3HAP |
| ID: | 1448274225 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 249 (229) | ||
| Sequences: | 729 (531.4) | ||
| Seq/Len: | 3.183 | ||
| Nf(neff/√len): | 35.1 |
HHblits Results: (2015_06)
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: 3.183).
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 |
| 52_I | 88_F | 4.139 | 1.00 |
| 19_L | 213_V | 2.781 | 1.00 |
| 80_W | 84_A | 2.747 | 1.00 |
| 90_T | 115_D | 2.601 | 1.00 |
| 85_D | 216_K | 2.485 | 1.00 |
| 14_A | 61_L | 2.348 | 1.00 |
| 27_F | 220_G | 2.279 | 1.00 |
| 21_G | 54_F | 2.172 | 1.00 |
| 59_S | 137_W | 2.160 | 1.00 |
| 85_D | 89_T | 2.092 | 1.00 |
| 181_L | 214_S | 2.052 | 1.00 |
| 50_P | 220_G | 1.855 | 0.99 |
| 24_T | 50_P | 1.848 | 0.99 |
| 90_T | 216_K | 1.770 | 0.99 |
| 121_T | 141_S | 1.770 | 0.99 |
| 13_L | 205_T | 1.651 | 0.98 |
| 23_G | 27_F | 1.648 | 0.98 |
| 89_T | 216_K | 1.636 | 0.98 |
| 45_I | 92_L | 1.604 | 0.98 |
| 46_T | 96_D | 1.593 | 0.98 |
| 117_I | 144_A | 1.593 | 0.98 |
| 12_W | 16_G | 1.540 | 0.97 |
| 20_M | 53_A | 1.530 | 0.97 |
| 118_M | 122_G | 1.474 | 0.96 |
| 194_E | 204_E | 1.466 | 0.95 |
| 46_T | 220_G | 1.465 | 0.95 |
| 121_T | 215_A | 1.445 | 0.95 |
| 90_T | 118_M | 1.438 | 0.95 |
| 67_T | 127_L | 1.436 | 0.95 |
| 182_W | 216_K | 1.431 | 0.95 |
| 95_L | 112_V | 1.427 | 0.94 |
| 125_G | 189_W | 1.403 | 0.94 |
| 83_Y | 86_W | 1.400 | 0.94 |
| 53_A | 60_M | 1.397 | 0.94 |
| 162_S | 206_L | 1.387 | 0.93 |
| 51_A | 214_S | 1.382 | 0.93 |
| 51_A | 55_T | 1.369 | 0.93 |
| 138_W | 142_T | 1.355 | 0.92 |
| 70_P | 75_Q | 1.345 | 0.92 |
| 16_G | 209_M | 1.341 | 0.92 |
| 184_A | 188_V | 1.338 | 0.92 |
| 87_L | 116_G | 1.329 | 0.91 |
| 26_Y | 30_K | 1.325 | 0.91 |
| 23_G | 221_L | 1.323 | 0.91 |
| 49_V | 92_L | 1.300 | 0.90 |
| 23_G | 217_V | 1.299 | 0.90 |
| 114_A | 147_Y | 1.294 | 0.90 |
| 135_F | 190_L | 1.294 | 0.90 |
| 188_V | 207_L | 1.291 | 0.90 |
| 24_T | 51_A | 1.290 | 0.90 |
| 115_D | 118_M | 1.285 | 0.89 |
| 56_M | 60_M | 1.284 | 0.89 |
| 94_L | 115_D | 1.279 | 0.89 |
| 89_T | 92_L | 1.277 | 0.89 |
| 89_T | 115_D | 1.246 | 0.87 |
| 86_W | 186_P | 1.242 | 0.87 |
| 69_V | 129_K | 1.237 | 0.87 |
| 94_L | 103_A | 1.234 | 0.87 |
| 118_M | 148_I | 1.233 | 0.87 |
| 139_A | 143_A | 1.231 | 0.86 |
| 206_L | 210_V | 1.229 | 0.86 |
| 85_D | 90_T | 1.215 | 0.85 |
| 16_G | 55_T | 1.209 | 0.85 |
| 58_L | 128_T | 1.200 | 0.84 |
| 24_T | 54_F | 1.198 | 0.84 |
| 94_L | 122_G | 1.198 | 0.84 |
| 28_L | 47_T | 1.193 | 0.84 |
| 17_T | 54_F | 1.183 | 0.83 |
| 145_M | 149_L | 1.183 | 0.83 |
| 67_T | 125_G | 1.172 | 0.83 |
| 86_W | 91_P | 1.164 | 0.82 |
| 213_V | 225_R | 1.162 | 0.82 |
| 122_G | 219_F | 1.162 | 0.82 |
| 16_G | 20_M | 1.149 | 0.81 |
| 53_A | 118_M | 1.147 | 0.81 |
| 184_A | 207_L | 1.146 | 0.81 |
| 53_A | 85_D | 1.138 | 0.80 |
| 53_A | 216_K | 1.120 | 0.78 |
| 53_A | 96_D | 1.113 | 0.78 |
| 117_I | 140_I | 1.110 | 0.78 |
| 53_A | 93_L | 1.110 | 0.78 |
| 122_G | 216_K | 1.108 | 0.77 |
| 190_L | 196_A | 1.102 | 0.77 |
| 200_P | 203_I | 1.089 | 0.76 |
| 150_Y | 154_F | 1.077 | 0.75 |
| 127_L | 194_E | 1.075 | 0.74 |
| 22_L | 146_L | 1.071 | 0.74 |
| 27_F | 46_T | 1.070 | 0.74 |
| 177_V | 222_I | 1.070 | 0.74 |
| 86_W | 185_Y | 1.069 | 0.74 |
| 91_P | 185_Y | 1.065 | 0.73 |
| 46_T | 148_I | 1.061 | 0.73 |
| 177_V | 181_L | 1.055 | 0.72 |
| 90_T | 182_W | 1.049 | 0.72 |
| 27_F | 50_P | 1.044 | 0.71 |
| 90_T | 122_G | 1.040 | 0.71 |
| 193_S | 204_E | 1.038 | 0.71 |
| 123_L | 194_E | 1.026 | 0.69 |
| 179_V | 183_S | 1.018 | 0.68 |
| 12_W | 209_M | 1.014 | 0.68 |
| 189_W | 204_E | 1.000 | 0.66 |
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 | |
| 1m0kA | 1 | 0.8916 | 100 | 0.111 | Contact Map |
| 3wqjA | 1 | 0.9197 | 100 | 0.149 | Contact Map |
| 4qi1A | 3 | 0 | 100 | 0.17 | Contact Map |
| 4fbzA | 1 | 0.9518 | 100 | 0.171 | Contact Map |
| 4l35A | 1 | 0.9558 | 100 | 0.171 | Contact Map |
| 3qapA | 1 | 0.8795 | 100 | 0.181 | Contact Map |
| 3am6A | 4 | 0.8996 | 100 | 0.193 | Contact Map |
| 3wt9A | 1 | 0.9317 | 100 | 0.197 | Contact Map |
| 1xioA | 1 | 0.8554 | 100 | 0.21 | Contact Map |
| 3qbgA | 3 | 0.9438 | 100 | 0.213 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)