| 2ndY-based-concatenated |
| ID: | 1517517198 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 397 (365) | ||
| Sequences: | 968 (650.7) | ||
| Seq/Len: | 2.652 | ||
| Nf(neff/√len): | 34.1 |
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: 2.652).
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 | 5.172 | 1.00 |
| 218_V | 237_A | 4.184 | 1.00 |
| 116_G | 333_I | 3.563 | 1.00 |
| 204_V | 249_L | 3.077 | 1.00 |
| 152_R | 156_E | 2.880 | 1.00 |
| 206_L | 245_V | 2.841 | 1.00 |
| 206_L | 221_A | 2.700 | 1.00 |
| 321_V | 332_V | 2.692 | 1.00 |
| 159_I | 320_L | 2.684 | 1.00 |
| 14_F | 22_W | 2.519 | 1.00 |
| 166_V | 216_V | 2.342 | 1.00 |
| 64_K | 254_Q | 2.282 | 1.00 |
| 236_G | 247_R | 2.215 | 1.00 |
| 210_P | 213_V | 2.150 | 1.00 |
| 162_L | 332_V | 2.099 | 1.00 |
| 115_E | 124_P | 2.090 | 1.00 |
| 221_A | 248_A | 2.011 | 1.00 |
| 152_R | 250_L | 2.004 | 0.99 |
| 236_G | 250_L | 1.964 | 0.99 |
| 159_I | 163_L | 1.960 | 0.99 |
| 65_G | 74_S | 1.934 | 0.99 |
| 247_R | 250_L | 1.902 | 0.99 |
| 186_V | 206_L | 1.895 | 0.99 |
| 184_L | 219_V | 1.886 | 0.99 |
| 17_K | 69_I | 1.863 | 0.99 |
| 94_R | 98_G | 1.855 | 0.99 |
| 15_L | 18_E | 1.843 | 0.99 |
| 334_E | 349_V | 1.786 | 0.99 |
| 20_L | 73_V | 1.771 | 0.98 |
| 116_G | 335_V | 1.724 | 0.98 |
| 155_E | 314_E | 1.703 | 0.98 |
| 19_T | 152_R | 1.700 | 0.98 |
| 13_A | 153_L | 1.642 | 0.97 |
| 149_S | 161_G | 1.635 | 0.97 |
| 158_V | 334_E | 1.622 | 0.97 |
| 125_V | 333_I | 1.590 | 0.96 |
| 300_E | 303_D | 1.590 | 0.96 |
| 238_S | 243_M | 1.562 | 0.96 |
| 64_K | 74_S | 1.555 | 0.96 |
| 50_R | 86_E | 1.553 | 0.96 |
| 332_V | 351_V | 1.542 | 0.95 |
| 221_A | 249_L | 1.520 | 0.95 |
| 118_D | 331_K | 1.498 | 0.94 |
| 96_P | 103_P | 1.490 | 0.94 |
| 156_E | 236_G | 1.483 | 0.94 |
| 210_P | 217_Y | 1.475 | 0.94 |
| 151_G | 156_E | 1.470 | 0.94 |
| 127_V | 350_R | 1.469 | 0.94 |
| 203_R | 226_E | 1.469 | 0.94 |
| 211_S | 214_E | 1.467 | 0.94 |
| 97_E | 108_T | 1.455 | 0.93 |
| 152_R | 236_G | 1.449 | 0.93 |
| 129_A | 133_F | 1.445 | 0.93 |
| 206_L | 219_V | 1.444 | 0.93 |
| 127_V | 335_V | 1.440 | 0.93 |
| 118_D | 332_V | 1.411 | 0.92 |
| 85_A | 148_L | 1.403 | 0.92 |
| 85_A | 337_L | 1.391 | 0.91 |
| 36_E | 265_S | 1.390 | 0.91 |
| 185_E | 300_E | 1.380 | 0.91 |
| 74_S | 254_Q | 1.374 | 0.90 |
| 11_F | 243_M | 1.373 | 0.90 |
| 115_E | 126_Y | 1.366 | 0.90 |
| 195_R | 199_R | 1.365 | 0.90 |
| 243_M | 247_R | 1.365 | 0.90 |
| 208_L | 217_Y | 1.362 | 0.90 |
| 110_P | 127_V | 1.360 | 0.90 |
| 46_P | 68_R | 1.357 | 0.90 |
| 209_L | 218_V | 1.344 | 0.89 |
| 18_E | 21_R | 1.329 | 0.88 |
| 157_A | 347_V | 1.309 | 0.87 |
| 158_V | 161_G | 1.307 | 0.87 |
| 64_K | 236_G | 1.302 | 0.87 |
| 134_H | 145_T | 1.296 | 0.87 |
| 160_Q | 255_G | 1.291 | 0.86 |
| 118_D | 121_T | 1.290 | 0.86 |
| 162_L | 350_R | 1.276 | 0.85 |
| 35_V | 38_F | 1.275 | 0.85 |
| 158_V | 349_V | 1.272 | 0.85 |
| 36_E | 51_R | 1.271 | 0.85 |
| 146_N | 165_V | 1.260 | 0.84 |
| 169_D | 367_M | 1.246 | 0.84 |
| 165_V | 349_V | 1.234 | 0.83 |
| 58_E | 264_E | 1.233 | 0.83 |
| 16_P | 19_T | 1.226 | 0.82 |
| 127_V | 333_I | 1.225 | 0.82 |
| 120_T | 321_V | 1.224 | 0.82 |
| 4_I | 9_E | 1.219 | 0.82 |
| 219_V | 304_L | 1.212 | 0.81 |
| 339_L | 343_D | 1.209 | 0.81 |
| 78_E | 251_E | 1.203 | 0.81 |
| 195_R | 198_E | 1.194 | 0.80 |
| 159_I | 317_T | 1.175 | 0.78 |
| 213_V | 367_M | 1.171 | 0.78 |
| 152_R | 247_R | 1.169 | 0.78 |
| 339_L | 345_P | 1.169 | 0.78 |
| 12_R | 238_S | 1.168 | 0.78 |
| 324_V | 354_A | 1.163 | 0.77 |
| 167_E | 254_Q | 1.162 | 0.77 |
| 208_L | 219_V | 1.161 | 0.77 |
| 236_G | 254_Q | 1.160 | 0.77 |
| 163_L | 237_A | 1.159 | 0.77 |
| 338_T | 346_V | 1.155 | 0.77 |
| 64_K | 167_E | 1.147 | 0.76 |
| 154_R | 158_V | 1.147 | 0.76 |
| 40_D | 45_I | 1.146 | 0.76 |
| 84_A | 339_L | 1.141 | 0.75 |
| 210_P | 214_E | 1.139 | 0.75 |
| 355_S | 365_G | 1.138 | 0.75 |
| 12_R | 247_R | 1.132 | 0.75 |
| 210_P | 216_V | 1.128 | 0.74 |
| 221_A | 252_V | 1.128 | 0.74 |
| 87_P | 249_L | 1.122 | 0.74 |
| 215_G | 332_V | 1.119 | 0.73 |
| 223_T | 252_V | 1.116 | 0.73 |
| 135_P | 261_R | 1.115 | 0.73 |
| 149_S | 347_V | 1.111 | 0.73 |
| 194_R | 204_V | 1.110 | 0.73 |
| 234_G | 248_A | 1.105 | 0.72 |
| 40_D | 256_L | 1.105 | 0.72 |
| 132_V | 350_R | 1.104 | 0.72 |
| 123_E | 315_K | 1.103 | 0.72 |
| 62_A | 263_I | 1.099 | 0.71 |
| 12_R | 156_E | 1.096 | 0.71 |
| 64_K | 247_R | 1.096 | 0.71 |
| 154_R | 336_D | 1.095 | 0.71 |
| 4_I | 11_F | 1.092 | 0.71 |
| 164_E | 251_E | 1.087 | 0.70 |
| 157_A | 245_V | 1.087 | 0.70 |
| 209_L | 220_G | 1.086 | 0.70 |
| 184_L | 319_E | 1.084 | 0.70 |
| 309_T | 316_L | 1.080 | 0.70 |
| 321_V | 351_V | 1.073 | 0.69 |
| 165_V | 351_V | 1.068 | 0.68 |
| 12_R | 236_G | 1.064 | 0.68 |
| 11_F | 16_P | 1.064 | 0.68 |
| 309_T | 312_S | 1.063 | 0.68 |
| 74_S | 250_L | 1.056 | 0.67 |
| 78_E | 164_E | 1.047 | 0.66 |
| 6_Y | 10_G | 1.045 | 0.66 |
| 366_N | 369_E | 1.044 | 0.66 |
| 65_G | 254_Q | 1.042 | 0.66 |
| 35_V | 48_E | 1.040 | 0.65 |
| 208_L | 343_D | 1.040 | 0.65 |
| 163_L | 316_L | 1.035 | 0.65 |
| 122_R | 300_E | 1.033 | 0.65 |
| 40_D | 51_R | 1.032 | 0.64 |
| 201_V | 305_D | 1.027 | 0.64 |
| 6_Y | 9_E | 1.024 | 0.64 |
| 114_V | 129_A | 1.024 | 0.64 |
| 187_H | 299_V | 1.021 | 0.63 |
| 183_E | 205_E | 1.020 | 0.63 |
| 64_K | 150_A | 1.019 | 0.63 |
| 36_E | 45_I | 1.019 | 0.63 |
| 67_T | 70_Q | 1.016 | 0.63 |
| 173_I | 210_P | 1.015 | 0.63 |
| 65_G | 247_R | 1.013 | 0.62 |
| 247_R | 254_Q | 1.012 | 0.62 |
| 260_R | 263_I | 1.011 | 0.62 |
| 77_M | 344_V | 1.005 | 0.61 |
| 165_V | 354_A | 1.003 | 0.61 |
| 14_F | 18_E | 1.000 | 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 | |
| 4v1tA | 2 | 0.9244 | 100 | 0.353 | Contact Map |
| 4q86A | 8 | 0.9345 | 100 | 0.384 | Contact Map |
| 1hbnA | 2 | 0.6348 | 91.5 | 0.946 | Contact Map |
| 3sqgA | 3 | 0.8161 | 77.4 | 0.955 | Contact Map |
| 3adlA | 1 | 0.1738 | 18.3 | 0.97 | Contact Map |
| 1ekzA | 1 | 0.1763 | 16.1 | 0.971 | Contact Map |
| 3llhA | 2 | 0.1587 | 15.8 | 0.971 | Contact Map |
| 2mdrA | 1 | 0.2191 | 13.3 | 0.972 | Contact Map |
| 4j56E | 4 | 0.2393 | 11 | 0.973 | Contact Map |
| 4wyqB | 2 | 0.1839 | 10.4 | 0.973 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)