| AllY-alignment |
| ID: | 1517503575 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 377 (365) | ||
| Sequences: | 1305 (890.1) | ||
| Seq/Len: | 3.575 | ||
| Nf(neff/√len): | 46.6 |
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: 3.575).
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 |
| 162_L | 351_V | 4.799 | 1.00 |
| 116_G | 333_I | 4.434 | 1.00 |
| 218_V | 237_A | 4.331 | 1.00 |
| 152_R | 156_E | 3.450 | 1.00 |
| 206_L | 245_V | 3.188 | 1.00 |
| 184_L | 219_V | 3.139 | 1.00 |
| 204_V | 249_L | 2.690 | 1.00 |
| 93_E | 97_E | 2.643 | 1.00 |
| 116_G | 335_V | 2.595 | 1.00 |
| 321_V | 332_V | 2.562 | 1.00 |
| 206_L | 221_A | 2.534 | 1.00 |
| 159_I | 320_L | 2.502 | 1.00 |
| 186_V | 206_L | 2.399 | 1.00 |
| 165_V | 354_A | 2.281 | 1.00 |
| 14_F | 22_W | 2.279 | 1.00 |
| 166_V | 216_V | 2.217 | 1.00 |
| 115_E | 124_P | 2.212 | 1.00 |
| 118_D | 331_K | 2.211 | 1.00 |
| 221_A | 248_A | 2.203 | 1.00 |
| 65_G | 74_S | 2.184 | 1.00 |
| 206_L | 219_V | 2.154 | 1.00 |
| 64_K | 254_Q | 2.145 | 1.00 |
| 210_P | 213_V | 2.065 | 1.00 |
| 158_V | 334_E | 2.036 | 1.00 |
| 334_E | 349_V | 1.947 | 1.00 |
| 162_L | 332_V | 1.908 | 1.00 |
| 127_V | 350_R | 1.884 | 1.00 |
| 238_S | 243_M | 1.870 | 1.00 |
| 236_G | 247_R | 1.841 | 0.99 |
| 115_E | 126_Y | 1.750 | 0.99 |
| 64_K | 74_S | 1.740 | 0.99 |
| 247_R | 250_L | 1.723 | 0.99 |
| 15_L | 18_E | 1.714 | 0.99 |
| 300_E | 303_D | 1.677 | 0.99 |
| 85_A | 337_L | 1.666 | 0.99 |
| 152_R | 250_L | 1.660 | 0.99 |
| 118_D | 121_T | 1.649 | 0.99 |
| 127_V | 333_I | 1.639 | 0.98 |
| 155_E | 314_E | 1.615 | 0.98 |
| 151_G | 156_E | 1.588 | 0.98 |
| 223_T | 252_V | 1.585 | 0.98 |
| 96_P | 108_T | 1.574 | 0.98 |
| 150_A | 346_V | 1.569 | 0.98 |
| 209_L | 220_G | 1.565 | 0.98 |
| 203_R | 226_E | 1.533 | 0.97 |
| 106_Y | 109_E | 1.529 | 0.97 |
| 159_I | 163_L | 1.529 | 0.97 |
| 146_N | 165_V | 1.499 | 0.97 |
| 158_V | 349_V | 1.499 | 0.97 |
| 158_V | 161_G | 1.497 | 0.97 |
| 127_V | 335_V | 1.464 | 0.96 |
| 114_V | 129_A | 1.455 | 0.96 |
| 210_P | 217_Y | 1.450 | 0.96 |
| 67_T | 70_Q | 1.441 | 0.96 |
| 125_V | 333_I | 1.434 | 0.96 |
| 148_L | 348_R | 1.429 | 0.96 |
| 209_L | 218_V | 1.422 | 0.95 |
| 85_A | 148_L | 1.416 | 0.95 |
| 120_T | 331_K | 1.395 | 0.95 |
| 74_S | 254_Q | 1.391 | 0.95 |
| 165_V | 351_V | 1.388 | 0.95 |
| 149_S | 161_G | 1.383 | 0.94 |
| 243_M | 247_R | 1.377 | 0.94 |
| 96_P | 107_R | 1.360 | 0.94 |
| 17_K | 69_I | 1.344 | 0.93 |
| 159_I | 317_T | 1.338 | 0.93 |
| 18_E | 21_R | 1.335 | 0.93 |
| 163_L | 239_P | 1.333 | 0.93 |
| 152_R | 236_G | 1.330 | 0.93 |
| 236_G | 250_L | 1.324 | 0.93 |
| 314_E | 318_E | 1.298 | 0.92 |
| 20_L | 73_V | 1.297 | 0.92 |
| 117_V | 122_R | 1.253 | 0.90 |
| 154_R | 158_V | 1.249 | 0.89 |
| 129_A | 133_F | 1.248 | 0.89 |
| 35_V | 38_F | 1.239 | 0.89 |
| 36_E | 51_R | 1.231 | 0.89 |
| 163_L | 237_A | 1.227 | 0.88 |
| 322_E | 325_A | 1.225 | 0.88 |
| 65_G | 247_R | 1.220 | 0.88 |
| 161_G | 349_V | 1.218 | 0.88 |
| 116_G | 124_P | 1.217 | 0.88 |
| 116_G | 132_V | 1.194 | 0.86 |
| 238_S | 244_A | 1.192 | 0.86 |
| 13_A | 153_L | 1.192 | 0.86 |
| 64_K | 236_G | 1.191 | 0.86 |
| 208_L | 219_V | 1.185 | 0.86 |
| 195_R | 199_R | 1.184 | 0.86 |
| 332_V | 351_V | 1.182 | 0.86 |
| 148_L | 337_L | 1.181 | 0.86 |
| 185_E | 300_E | 1.177 | 0.85 |
| 134_H | 145_T | 1.176 | 0.85 |
| 19_T | 152_R | 1.173 | 0.85 |
| 324_V | 354_A | 1.173 | 0.85 |
| 183_E | 205_E | 1.166 | 0.85 |
| 4_I | 11_F | 1.163 | 0.84 |
| 309_T | 316_L | 1.158 | 0.84 |
| 165_V | 349_V | 1.157 | 0.84 |
| 221_A | 249_L | 1.156 | 0.84 |
| 16_P | 19_T | 1.148 | 0.83 |
| 164_E | 251_E | 1.146 | 0.83 |
| 197_L | 252_V | 1.145 | 0.83 |
| 157_A | 347_V | 1.137 | 0.83 |
| 245_V | 297_G | 1.135 | 0.82 |
| 309_T | 319_E | 1.127 | 0.82 |
| 154_R | 347_V | 1.124 | 0.82 |
| 319_E | 323_R | 1.123 | 0.82 |
| 40_D | 45_I | 1.123 | 0.82 |
| 184_L | 319_E | 1.122 | 0.81 |
| 77_M | 344_V | 1.119 | 0.81 |
| 167_E | 254_Q | 1.119 | 0.81 |
| 339_L | 345_P | 1.117 | 0.81 |
| 120_T | 321_V | 1.109 | 0.80 |
| 64_K | 167_E | 1.108 | 0.80 |
| 156_E | 236_G | 1.108 | 0.80 |
| 65_G | 254_Q | 1.105 | 0.80 |
| 236_G | 254_Q | 1.102 | 0.80 |
| 198_E | 203_R | 1.101 | 0.80 |
| 149_S | 347_V | 1.100 | 0.80 |
| 219_V | 304_L | 1.097 | 0.79 |
| 324_V | 332_V | 1.092 | 0.79 |
| 91_I | 126_Y | 1.090 | 0.79 |
| 211_S | 214_E | 1.089 | 0.79 |
| 69_I | 73_V | 1.086 | 0.78 |
| 114_V | 335_V | 1.086 | 0.78 |
| 37_K | 48_E | 1.085 | 0.78 |
| 161_G | 313_L | 1.083 | 0.78 |
| 220_G | 235_F | 1.082 | 0.78 |
| 210_P | 216_V | 1.076 | 0.78 |
| 321_V | 325_A | 1.075 | 0.77 |
| 321_V | 351_V | 1.074 | 0.77 |
| 46_P | 68_R | 1.074 | 0.77 |
| 84_A | 339_L | 1.073 | 0.77 |
| 120_T | 325_A | 1.067 | 0.77 |
| 73_V | 136_W | 1.066 | 0.77 |
| 151_G | 238_S | 1.065 | 0.77 |
| 65_G | 73_V | 1.065 | 0.77 |
| 74_S | 151_G | 1.061 | 0.76 |
| 173_I | 210_P | 1.058 | 0.76 |
| 132_V | 350_R | 1.055 | 0.76 |
| 181_P | 209_L | 1.050 | 0.75 |
| 64_K | 247_R | 1.049 | 0.75 |
| 215_G | 323_R | 1.044 | 0.74 |
| 338_T | 346_V | 1.044 | 0.74 |
| 4_I | 9_E | 1.044 | 0.74 |
| 78_E | 251_E | 1.043 | 0.74 |
| 35_V | 48_E | 1.042 | 0.74 |
| 64_K | 160_Q | 1.039 | 0.74 |
| 50_R | 86_E | 1.038 | 0.74 |
| 194_R | 204_V | 1.035 | 0.74 |
| 366_N | 369_E | 1.034 | 0.73 |
| 17_K | 30_R | 1.034 | 0.73 |
| 318_E | 322_E | 1.032 | 0.73 |
| 339_L | 343_D | 1.031 | 0.73 |
| 219_V | 241_P | 1.029 | 0.73 |
| 121_T | 331_K | 1.028 | 0.73 |
| 18_E | 22_W | 1.026 | 0.73 |
| 366_N | 370_K | 1.024 | 0.72 |
| 92_I | 112_E | 1.024 | 0.72 |
| 36_E | 45_I | 1.022 | 0.72 |
| 77_M | 148_L | 1.017 | 0.72 |
| 202_G | 256_L | 1.015 | 0.72 |
| 158_V | 347_V | 1.015 | 0.72 |
| 30_R | 37_K | 1.010 | 0.71 |
| 172_S | 355_S | 1.010 | 0.71 |
| 107_R | 110_P | 1.008 | 0.71 |
| 11_F | 16_P | 1.006 | 0.71 |
| 36_E | 265_S | 1.005 | 0.70 |
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 | |
| 4v1tA | 2 | 0.9443 | 100 | 0.241 | Contact Map |
| 4q86A | 8 | 0.931 | 100 | 0.28 | Contact Map |
| 1ekzA | 1 | 0.1857 | 18.9 | 0.965 | Contact Map |
| 1sp8A | 4 | 0.2149 | 14.1 | 0.967 | Contact Map |
| 3adlA | 1 | 0.183 | 14 | 0.967 | Contact Map |
| 3llhA | 2 | 0.1671 | 12.9 | 0.967 | Contact Map |
| 2mdrA | 1 | 0.2095 | 11.4 | 0.968 | Contact Map |
| 1o0wA | 2 | 0.2069 | 10.8 | 0.969 | Contact Map |
| 4wyqB | 2 | 0.1963 | 10.7 | 0.969 | Contact Map |
| 1di2A | 2 | 0.1645 | 10.6 | 0.969 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)