| 1hzy |
| ID: | 1464686268 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 331 (311) | ||
| Sequences: | 824 (560.9) | ||
| Seq/Len: | 2.650 | ||
| Nf(neff/√len): | 31.8 |
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: 2.650).
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 |
| 56_A | 61_V | 3.022 | 1.00 |
| 303_R | 309_Q | 2.908 | 1.00 |
| 179_A | 214_Y | 2.786 | 1.00 |
| 157_S | 187_L | 2.694 | 1.00 |
| 81_E | 85_A | 2.672 | 1.00 |
| 260_K | 314_G | 2.577 | 1.00 |
| 308_P | 311_T | 2.506 | 1.00 |
| 166_T | 178_Q | 2.443 | 1.00 |
| 131_A | 162_V | 2.396 | 1.00 |
| 80_A | 84_R | 2.345 | 1.00 |
| 155_R | 185_E | 2.272 | 1.00 |
| 118_R | 122_Y | 2.259 | 1.00 |
| 4_N | 9_P | 2.239 | 1.00 |
| 167_H | 267_D | 2.144 | 1.00 |
| 208_A | 211_A | 2.128 | 1.00 |
| 117_L | 156_A | 2.063 | 1.00 |
| 259_M | 314_G | 2.059 | 1.00 |
| 221_I | 298_V | 2.054 | 1.00 |
| 134_I | 153_A | 2.021 | 1.00 |
| 120_I | 162_V | 2.011 | 1.00 |
| 91_V | 132_G | 1.972 | 0.99 |
| 207_T | 256_Q | 1.966 | 0.99 |
| 313_A | 317_V | 1.946 | 0.99 |
| 151_K | 185_E | 1.935 | 0.99 |
| 180_A | 212_R | 1.933 | 0.99 |
| 183_E | 212_R | 1.917 | 0.99 |
| 117_L | 160_T | 1.872 | 0.99 |
| 113_T | 117_L | 1.864 | 0.99 |
| 59_A | 296_L | 1.826 | 0.99 |
| 144_P | 147_E | 1.807 | 0.99 |
| 318_T | 321_A | 1.805 | 0.99 |
| 309_Q | 313_A | 1.793 | 0.99 |
| 117_L | 159_A | 1.785 | 0.99 |
| 196_H | 267_D | 1.770 | 0.98 |
| 63_T | 89_H | 1.765 | 0.98 |
| 167_H | 196_H | 1.759 | 0.98 |
| 7_R | 89_H | 1.748 | 0.98 |
| 3_I | 10_I | 1.720 | 0.98 |
| 252_A | 256_Q | 1.657 | 0.97 |
| 157_S | 164_V | 1.648 | 0.97 |
| 151_K | 184_S | 1.645 | 0.97 |
| 313_A | 318_T | 1.630 | 0.97 |
| 299_I | 303_R | 1.621 | 0.97 |
| 180_A | 184_S | 1.620 | 0.97 |
| 259_M | 311_T | 1.619 | 0.97 |
| 193_C | 323_F | 1.602 | 0.97 |
| 112_L | 152_A | 1.581 | 0.96 |
| 46_A | 81_E | 1.579 | 0.96 |
| 138_T | 178_Q | 1.578 | 0.96 |
| 189_P | 192_V | 1.558 | 0.96 |
| 138_T | 166_T | 1.536 | 0.95 |
| 67_V | 165_T | 1.519 | 0.95 |
| 264_V | 315_I | 1.517 | 0.95 |
| 67_V | 93_A | 1.506 | 0.95 |
| 254_I | 315_I | 1.503 | 0.95 |
| 50_V | 85_A | 1.490 | 0.94 |
| 147_E | 151_K | 1.484 | 0.94 |
| 113_T | 155_R | 1.467 | 0.94 |
| 295_P | 299_I | 1.432 | 0.93 |
| 53_L | 82_V | 1.420 | 0.92 |
| 50_V | 82_V | 1.415 | 0.92 |
| 151_K | 155_R | 1.413 | 0.92 |
| 307_V | 311_T | 1.413 | 0.92 |
| 215_L | 261_Q | 1.411 | 0.92 |
| 133_I | 165_T | 1.406 | 0.92 |
| 138_T | 150_L | 1.401 | 0.91 |
| 215_L | 263_L | 1.389 | 0.91 |
| 251_K | 255_D | 1.380 | 0.91 |
| 15_A | 63_T | 1.377 | 0.91 |
| 183_E | 189_P | 1.368 | 0.90 |
| 254_I | 307_V | 1.365 | 0.90 |
| 165_T | 195_G | 1.349 | 0.89 |
| 293_F | 298_V | 1.347 | 0.89 |
| 122_Y | 131_A | 1.322 | 0.88 |
| 3_I | 63_T | 1.321 | 0.88 |
| 107_R | 111_E | 1.308 | 0.87 |
| 12_I | 325_S | 1.288 | 0.86 |
| 263_L | 323_F | 1.287 | 0.86 |
| 314_G | 318_T | 1.279 | 0.86 |
| 166_T | 194_I | 1.275 | 0.85 |
| 154_A | 182_F | 1.260 | 0.84 |
| 252_A | 255_D | 1.252 | 0.84 |
| 156_A | 162_V | 1.251 | 0.84 |
| 5_T | 8_G | 1.228 | 0.82 |
| 120_I | 131_A | 1.225 | 0.82 |
| 19_L | 265_S | 1.213 | 0.81 |
| 175_G | 209_L | 1.213 | 0.81 |
| 61_V | 295_P | 1.206 | 0.81 |
| 307_V | 315_I | 1.202 | 0.80 |
| 202_D | 205_Y | 1.197 | 0.80 |
| 302_L | 307_V | 1.195 | 0.80 |
| 20_T | 316_T | 1.194 | 0.80 |
| 135_K | 267_D | 1.190 | 0.80 |
| 251_K | 254_I | 1.172 | 0.78 |
| 287_N | 290_G | 1.169 | 0.78 |
| 135_K | 167_H | 1.162 | 0.77 |
| 80_A | 128_G | 1.162 | 0.77 |
| 254_I | 259_M | 1.161 | 0.77 |
| 178_Q | 194_I | 1.160 | 0.77 |
| 69_T | 135_K | 1.156 | 0.77 |
| 292_A | 296_L | 1.151 | 0.76 |
| 24_I | 53_L | 1.147 | 0.76 |
| 22_E | 265_S | 1.145 | 0.76 |
| 211_A | 258_Y | 1.142 | 0.75 |
| 94_T | 119_E | 1.130 | 0.74 |
| 80_A | 129_I | 1.127 | 0.74 |
| 50_V | 86_A | 1.126 | 0.74 |
| 299_I | 316_T | 1.107 | 0.72 |
| 222_P | 243_W | 1.103 | 0.72 |
| 93_A | 133_I | 1.103 | 0.72 |
| 220_H | 269_L | 1.099 | 0.71 |
| 2_R | 9_P | 1.099 | 0.71 |
| 99_D | 143_T | 1.091 | 0.71 |
| 136_V | 153_A | 1.089 | 0.70 |
| 47_E | 85_A | 1.083 | 0.70 |
| 176_E | 208_A | 1.082 | 0.70 |
| 259_M | 307_V | 1.077 | 0.69 |
| 142_A | 177_Q | 1.075 | 0.69 |
| 293_F | 297_R | 1.073 | 0.69 |
| 138_T | 142_A | 1.069 | 0.68 |
| 7_R | 84_R | 1.067 | 0.68 |
| 56_A | 88_V | 1.064 | 0.68 |
| 291_M | 300_P | 1.062 | 0.68 |
| 4_N | 130_R | 1.061 | 0.68 |
| 181_I | 185_E | 1.058 | 0.67 |
| 23_H | 167_H | 1.045 | 0.66 |
| 175_G | 205_Y | 1.045 | 0.66 |
| 23_H | 196_H | 1.043 | 0.66 |
| 24_I | 90_I | 1.038 | 0.65 |
| 63_T | 112_L | 1.035 | 0.65 |
| 307_V | 313_A | 1.034 | 0.65 |
| 222_P | 265_S | 1.034 | 0.65 |
| 91_V | 292_A | 1.030 | 0.64 |
| 19_L | 295_P | 1.029 | 0.64 |
| 221_I | 293_F | 1.024 | 0.64 |
| 168_T | 194_I | 1.021 | 0.63 |
| 183_E | 192_V | 1.019 | 0.63 |
| 10_I | 63_T | 1.018 | 0.63 |
| 3_I | 47_E | 1.015 | 0.63 |
| 19_L | 22_E | 1.011 | 0.62 |
| 61_V | 88_V | 1.008 | 0.62 |
| 209_L | 214_Y | 1.006 | 0.62 |
| 219_D | 267_D | 1.004 | 0.61 |
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 | |
| 3k2gA | 4 | 0.9547 | 100 | 0.418 | Contact Map |
| 3rhgA | 1 | 0.9486 | 100 | 0.432 | Contact Map |
| 3pnzA | 6 | 0.9033 | 100 | 0.552 | Contact Map |
| 3gtxA | 1 | 0.9335 | 100 | 0.561 | Contact Map |
| 2ob3A | 2 | 0.9698 | 100 | 0.567 | Contact Map |
| 4if2A | 1 | 0.9456 | 100 | 0.569 | Contact Map |
| 3tn4A | 2 | 0.9366 | 100 | 0.571 | Contact Map |
| 3ovgA | 6 | 0.9124 | 100 | 0.578 | Contact Map |
| 4kezA | 4 | 0.9275 | 100 | 0.601 | Contact Map |
| 1bf6A | 2 | 0.8671 | 100 | 0.625 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)