| 1hzx-1 |
| ID: | 1408384985 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 326 (285) | ||
| Sequences: | 24940 (12968) | ||
| Seq/Len: | 87.509 | ||
| Nf(neff/√len): | 768.2 |
HHblits Results: (2013_03)
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: 87.509).
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 |
| 51_G | 87_V | 4.847 | 1.00 |
| 78_N | 161_W | 4.334 | 1.00 |
| 221_F | 225_Q | 3.107 | 1.00 |
| 130_V | 160_T | 2.718 | 1.00 |
| 136_Y | 141_K | 2.638 | 1.00 |
| 78_N | 127_S | 2.456 | 1.00 |
| 108_T | 112_L | 2.454 | 1.00 |
| 141_K | 144_S | 2.438 | 1.00 |
| 151_N | 155_M | 2.436 | 1.00 |
| 110_C | 187_C | 2.371 | 1.00 |
| 68_L | 73_N | 2.299 | 1.00 |
| 130_V | 156_G | 2.218 | 1.00 |
| 115_F | 119_L | 2.142 | 1.00 |
| 107_P | 111_N | 2.137 | 1.00 |
| 62_T | 77_L | 2.124 | 1.00 |
| 136_Y | 140_C | 2.070 | 1.00 |
| 225_Q | 228_F | 2.035 | 1.00 |
| 119_L | 165_L | 2.022 | 1.00 |
| 103_F | 106_G | 2.014 | 1.00 |
| 59_L | 77_L | 1.913 | 1.00 |
| 93_T | 97_T | 1.912 | 1.00 |
| 91_F | 94_T | 1.888 | 1.00 |
| 74_Y | 157_V | 1.856 | 1.00 |
| 218_V | 222_C | 1.732 | 1.00 |
| 51_G | 300_V | 1.723 | 1.00 |
| 265_W | 295_A | 1.700 | 1.00 |
| 224_G | 228_F | 1.685 | 1.00 |
| 134_E | 138_V | 1.670 | 1.00 |
| 82_A | 123_I | 1.646 | 1.00 |
| 85_F | 120_G | 1.645 | 1.00 |
| 65_H | 316_C | 1.623 | 1.00 |
| 77_L | 81_V | 1.615 | 1.00 |
| 169_A | 173_V | 1.614 | 1.00 |
| 79_L | 83_D | 1.603 | 1.00 |
| 302_N | 306_Y | 1.596 | 1.00 |
| 83_D | 302_N | 1.587 | 1.00 |
| 155_M | 159_F | 1.583 | 1.00 |
| 111_N | 176_S | 1.582 | 1.00 |
| 82_A | 124_A | 1.568 | 1.00 |
| 123_I | 164_A | 1.563 | 1.00 |
| 149_G | 152_H | 1.555 | 1.00 |
| 154_I | 158_A | 1.530 | 1.00 |
| 136_Y | 225_Q | 1.504 | 1.00 |
| 48_I | 88_F | 1.493 | 1.00 |
| 270_G | 274_Y | 1.478 | 1.00 |
| 78_N | 157_V | 1.476 | 1.00 |
| 253_M | 309_M | 1.445 | 1.00 |
| 56_F | 60_Y | 1.435 | 1.00 |
| 223_Y | 226_L | 1.429 | 1.00 |
| 144_S | 147_R | 1.428 | 1.00 |
| 127_S | 157_V | 1.425 | 1.00 |
| 138_V | 142_P | 1.417 | 1.00 |
| 248_K | 252_R | 1.414 | 1.00 |
| 63_V | 77_L | 1.409 | 1.00 |
| 106_G | 109_G | 1.408 | 1.00 |
| 75_I | 153_A | 1.384 | 0.99 |
| 156_G | 160_T | 1.381 | 0.99 |
| 228_F | 232_E | 1.375 | 0.99 |
| 260_A | 305_I | 1.371 | 0.99 |
| 70_T | 73_N | 1.359 | 0.99 |
| 93_T | 109_G | 1.343 | 0.99 |
| 56_F | 84_L | 1.340 | 0.99 |
| 92_T | 95_L | 1.338 | 0.99 |
| 230_V | 250_V | 1.334 | 0.99 |
| 81_V | 85_F | 1.333 | 0.99 |
| 125_L | 129_V | 1.330 | 0.99 |
| 75_I | 131_L | 1.311 | 0.99 |
| 58_T | 307_I | 1.309 | 0.99 |
| 128_L | 219_I | 1.296 | 0.99 |
| 125_L | 215_P | 1.288 | 0.99 |
| 115_F | 172_L | 1.279 | 0.99 |
| 122_E | 211_H | 1.275 | 0.99 |
| 243_T | 247_E | 1.265 | 0.99 |
| 58_T | 62_T | 1.261 | 0.99 |
| 225_Q | 229_T | 1.257 | 0.99 |
| 136_Y | 222_C | 1.251 | 0.99 |
| 127_S | 161_W | 1.242 | 0.98 |
| 62_T | 69_R | 1.234 | 0.98 |
| 83_D | 298_S | 1.232 | 0.98 |
| 57_L | 61_V | 1.219 | 0.98 |
| 297_T | 301_Y | 1.206 | 0.98 |
| 262_L | 266_L | 1.196 | 0.98 |
| 89_G | 92_T | 1.196 | 0.98 |
| 50_L | 300_V | 1.191 | 0.98 |
| 52_F | 87_V | 1.191 | 0.98 |
| 125_L | 261_F | 1.190 | 0.98 |
| 255_I | 259_I | 1.188 | 0.98 |
| 90_G | 94_T | 1.184 | 0.98 |
| 315_N | 318_V | 1.178 | 0.98 |
| 52_F | 84_L | 1.173 | 0.98 |
| 129_V | 222_C | 1.167 | 0.97 |
| 247_E | 251_T | 1.166 | 0.97 |
| 171_P | 174_G | 1.164 | 0.97 |
| 58_T | 313_F | 1.164 | 0.97 |
| 115_F | 165_L | 1.161 | 0.97 |
| 129_V | 218_V | 1.148 | 0.97 |
| 216_L | 262_L | 1.144 | 0.97 |
| 54_I | 80_A | 1.143 | 0.97 |
| 161_W | 303_P | 1.143 | 0.97 |
| 129_V | 219_I | 1.143 | 0.97 |
| 126_W | 163_M | 1.143 | 0.97 |
| 220_F | 224_G | 1.138 | 0.97 |
| 94_T | 98_S | 1.130 | 0.97 |
| 245_K | 249_E | 1.129 | 0.97 |
| 274_Y | 277_T | 1.129 | 0.97 |
| 74_Y | 78_N | 1.128 | 0.97 |
| 272_A | 276_F | 1.127 | 0.97 |
| 241_A | 244_Q | 1.122 | 0.97 |
| 126_W | 160_T | 1.120 | 0.96 |
| 135_R | 138_V | 1.110 | 0.96 |
| 53_P | 56_F | 1.107 | 0.96 |
| 126_W | 215_P | 1.102 | 0.96 |
| 256_I | 305_I | 1.100 | 0.96 |
| 316_C | 319_T | 1.098 | 0.96 |
| 74_Y | 154_I | 1.089 | 0.96 |
| 87_V | 91_F | 1.087 | 0.96 |
| 233_A | 237_Q | 1.084 | 0.96 |
| 256_I | 309_M | 1.083 | 0.96 |
| 54_I | 300_V | 1.080 | 0.95 |
| 133_I | 222_C | 1.078 | 0.95 |
| 93_T | 96_Y | 1.077 | 0.95 |
| 108_T | 111_N | 1.076 | 0.95 |
| 139_V | 143_M | 1.066 | 0.95 |
| 155_M | 158_A | 1.060 | 0.95 |
| 206_Y | 210_V | 1.057 | 0.95 |
| 89_G | 120_G | 1.052 | 0.95 |
| 60_Y | 64_Q | 1.046 | 0.94 |
| 61_V | 313_F | 1.044 | 0.94 |
| 227_V | 231_K | 1.043 | 0.94 |
| 62_T | 68_L | 1.042 | 0.94 |
| 66_K | 69_R | 1.033 | 0.94 |
| 230_V | 233_A | 1.032 | 0.94 |
| 150_E | 154_I | 1.028 | 0.94 |
| 209_V | 215_P | 1.027 | 0.94 |
| 86_M | 299_A | 1.026 | 0.94 |
| 118_T | 121_G | 1.022 | 0.93 |
| 83_D | 267_P | 1.018 | 0.93 |
| 227_V | 230_V | 1.010 | 0.93 |
| 119_L | 168_A | 1.006 | 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 | |
| 1u19A | 2 | 1 | 100 | 0.175 | Contact Map |
| 4iarA | 1 | 0.862 | 100 | 0.281 | Contact Map |
| 2r4rA | 1 | 0.635 | 100 | 0.288 | Contact Map |
| 4pxzA | 1 | 0.8528 | 100 | 0.293 | Contact Map |
| 2rh1A | 1 | 0.8804 | 100 | 0.295 | Contact Map |
| 4grvA | 1 | 0.8773 | 100 | 0.302 | Contact Map |
| 4phuA | 1 | 0.8098 | 100 | 0.305 | Contact Map |
| 3vw7A | 1 | 0.8681 | 100 | 0.305 | Contact Map |
| 3uonA | 1 | 0.865 | 100 | 0.306 | Contact Map |
| 4dklA | 1 | 0.8773 | 100 | 0.311 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)