| Ta-based-concatenated |
| ID: | 1517517305 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 397 (363) | ||
| Sequences: | 961 (637) | ||
| Seq/Len: | 2.647 | ||
| Nf(neff/√len): | 33.4 |
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: 2.647).
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 | 5.179 | 1.00 |
| 218_V | 237_A | 4.319 | 1.00 |
| 116_G | 333_I | 3.636 | 1.00 |
| 204_V | 249_L | 3.011 | 1.00 |
| 321_V | 332_V | 2.906 | 1.00 |
| 206_L | 245_V | 2.895 | 1.00 |
| 152_R | 156_E | 2.863 | 1.00 |
| 206_L | 221_A | 2.830 | 1.00 |
| 159_I | 320_L | 2.618 | 1.00 |
| 14_F | 22_W | 2.522 | 1.00 |
| 210_P | 213_V | 2.295 | 1.00 |
| 236_G | 247_R | 2.272 | 1.00 |
| 166_V | 216_V | 2.179 | 1.00 |
| 184_L | 219_V | 2.160 | 1.00 |
| 236_G | 250_L | 2.104 | 1.00 |
| 64_K | 254_Q | 2.101 | 1.00 |
| 162_L | 332_V | 2.096 | 1.00 |
| 115_E | 124_P | 2.008 | 0.99 |
| 221_A | 248_A | 1.994 | 0.99 |
| 152_R | 250_L | 1.948 | 0.99 |
| 334_E | 349_V | 1.914 | 0.99 |
| 247_R | 250_L | 1.889 | 0.99 |
| 15_L | 18_E | 1.864 | 0.99 |
| 159_I | 163_L | 1.856 | 0.99 |
| 17_K | 69_I | 1.838 | 0.99 |
| 116_G | 335_V | 1.829 | 0.99 |
| 186_V | 206_L | 1.823 | 0.99 |
| 20_L | 73_V | 1.775 | 0.98 |
| 65_G | 74_S | 1.773 | 0.98 |
| 158_V | 334_E | 1.690 | 0.98 |
| 149_S | 161_G | 1.669 | 0.97 |
| 155_E | 314_E | 1.650 | 0.97 |
| 19_T | 152_R | 1.641 | 0.97 |
| 125_V | 333_I | 1.613 | 0.97 |
| 300_E | 303_D | 1.575 | 0.96 |
| 13_A | 153_L | 1.563 | 0.96 |
| 127_V | 335_V | 1.538 | 0.95 |
| 238_S | 243_M | 1.530 | 0.95 |
| 129_A | 133_F | 1.527 | 0.95 |
| 210_P | 217_Y | 1.524 | 0.95 |
| 152_R | 236_G | 1.513 | 0.95 |
| 206_L | 219_V | 1.500 | 0.95 |
| 118_D | 332_V | 1.484 | 0.94 |
| 64_K | 74_S | 1.476 | 0.94 |
| 46_P | 68_R | 1.463 | 0.94 |
| 158_V | 161_G | 1.461 | 0.93 |
| 156_E | 236_G | 1.451 | 0.93 |
| 151_G | 156_E | 1.435 | 0.93 |
| 118_D | 331_K | 1.427 | 0.92 |
| 195_R | 199_R | 1.422 | 0.92 |
| 203_R | 226_E | 1.420 | 0.92 |
| 36_E | 265_S | 1.402 | 0.91 |
| 158_V | 349_V | 1.402 | 0.91 |
| 127_V | 350_R | 1.394 | 0.91 |
| 332_V | 351_V | 1.394 | 0.91 |
| 134_H | 145_T | 1.389 | 0.91 |
| 115_E | 126_Y | 1.377 | 0.91 |
| 221_A | 249_L | 1.375 | 0.90 |
| 11_F | 243_M | 1.369 | 0.90 |
| 195_R | 198_E | 1.360 | 0.90 |
| 50_R | 86_E | 1.347 | 0.89 |
| 339_L | 345_P | 1.337 | 0.89 |
| 213_V | 367_M | 1.336 | 0.89 |
| 36_E | 51_R | 1.318 | 0.88 |
| 96_P | 108_T | 1.301 | 0.87 |
| 219_V | 304_L | 1.285 | 0.86 |
| 18_E | 21_R | 1.283 | 0.86 |
| 157_A | 347_V | 1.281 | 0.86 |
| 74_S | 254_Q | 1.272 | 0.85 |
| 211_S | 214_E | 1.270 | 0.85 |
| 152_R | 247_R | 1.266 | 0.85 |
| 321_V | 351_V | 1.266 | 0.85 |
| 35_V | 38_F | 1.264 | 0.85 |
| 243_M | 247_R | 1.250 | 0.84 |
| 4_I | 11_F | 1.249 | 0.84 |
| 123_E | 315_K | 1.249 | 0.84 |
| 151_G | 236_G | 1.248 | 0.84 |
| 127_V | 333_I | 1.245 | 0.83 |
| 165_V | 349_V | 1.239 | 0.83 |
| 149_S | 347_V | 1.234 | 0.83 |
| 146_N | 165_V | 1.228 | 0.82 |
| 221_A | 252_V | 1.228 | 0.82 |
| 118_D | 121_T | 1.224 | 0.82 |
| 78_E | 251_E | 1.220 | 0.82 |
| 163_L | 237_A | 1.216 | 0.81 |
| 64_K | 236_G | 1.208 | 0.81 |
| 122_R | 300_E | 1.207 | 0.81 |
| 120_T | 321_V | 1.201 | 0.80 |
| 12_R | 238_S | 1.191 | 0.80 |
| 339_L | 343_D | 1.190 | 0.79 |
| 169_D | 367_M | 1.180 | 0.79 |
| 208_L | 217_Y | 1.180 | 0.79 |
| 110_P | 127_V | 1.179 | 0.79 |
| 16_P | 19_T | 1.177 | 0.78 |
| 185_E | 300_E | 1.170 | 0.78 |
| 324_V | 354_A | 1.159 | 0.77 |
| 12_R | 247_R | 1.158 | 0.77 |
| 162_L | 350_R | 1.151 | 0.76 |
| 62_A | 263_I | 1.150 | 0.76 |
| 355_S | 365_G | 1.147 | 0.76 |
| 74_S | 250_L | 1.143 | 0.76 |
| 204_V | 303_D | 1.140 | 0.75 |
| 64_K | 247_R | 1.136 | 0.75 |
| 236_G | 254_Q | 1.134 | 0.75 |
| 309_T | 315_K | 1.131 | 0.74 |
| 12_R | 236_G | 1.127 | 0.74 |
| 132_V | 350_R | 1.124 | 0.74 |
| 160_Q | 255_G | 1.124 | 0.74 |
| 223_T | 252_V | 1.123 | 0.74 |
| 209_L | 218_V | 1.118 | 0.73 |
| 12_R | 156_E | 1.116 | 0.73 |
| 159_I | 317_T | 1.112 | 0.73 |
| 154_R | 336_D | 1.109 | 0.72 |
| 58_E | 264_E | 1.107 | 0.72 |
| 35_V | 48_E | 1.104 | 0.72 |
| 164_E | 251_E | 1.104 | 0.72 |
| 85_A | 148_L | 1.100 | 0.72 |
| 4_I | 9_E | 1.099 | 0.71 |
| 167_E | 217_Y | 1.095 | 0.71 |
| 123_E | 326_E | 1.093 | 0.71 |
| 40_D | 256_L | 1.092 | 0.71 |
| 85_A | 337_L | 1.091 | 0.71 |
| 135_P | 261_R | 1.090 | 0.71 |
| 234_G | 252_V | 1.089 | 0.70 |
| 312_S | 315_K | 1.081 | 0.70 |
| 274_F | 278_G | 1.078 | 0.69 |
| 208_L | 219_V | 1.078 | 0.69 |
| 37_K | 48_E | 1.074 | 0.69 |
| 93_E | 97_E | 1.072 | 0.69 |
| 84_A | 339_L | 1.067 | 0.68 |
| 40_D | 45_I | 1.064 | 0.68 |
| 78_E | 164_E | 1.063 | 0.68 |
| 154_R | 158_V | 1.063 | 0.68 |
| 268_R | 273_E | 1.061 | 0.68 |
| 146_N | 168_R | 1.060 | 0.67 |
| 65_G | 250_L | 1.057 | 0.67 |
| 206_L | 332_V | 1.052 | 0.67 |
| 309_T | 316_L | 1.051 | 0.66 |
| 247_R | 254_Q | 1.050 | 0.66 |
| 67_T | 70_Q | 1.048 | 0.66 |
| 163_L | 316_L | 1.045 | 0.66 |
| 220_G | 235_F | 1.044 | 0.66 |
| 197_L | 249_L | 1.043 | 0.66 |
| 48_E | 75_A | 1.038 | 0.65 |
| 157_A | 245_V | 1.036 | 0.65 |
| 210_P | 214_E | 1.036 | 0.65 |
| 234_G | 248_A | 1.031 | 0.64 |
| 23_I | 73_V | 1.029 | 0.64 |
| 36_E | 45_I | 1.029 | 0.64 |
| 151_G | 254_Q | 1.029 | 0.64 |
| 3_D | 8_V | 1.024 | 0.64 |
| 6_Y | 10_G | 1.019 | 0.63 |
| 210_P | 216_V | 1.014 | 0.62 |
| 64_K | 150_A | 1.013 | 0.62 |
| 338_T | 343_D | 1.012 | 0.62 |
| 114_V | 129_A | 1.012 | 0.62 |
| 209_L | 220_G | 1.010 | 0.62 |
| 65_G | 277_P | 1.008 | 0.62 |
| 194_R | 204_V | 1.006 | 0.62 |
| 11_F | 16_P | 1.005 | 0.61 |
| 64_K | 167_E | 1.005 | 0.61 |
| 173_I | 210_P | 1.004 | 0.61 |
| 91_I | 126_Y | 1.001 | 0.61 |
| 338_T | 346_V | 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 | 0.927 | 100 | 0.361 | Contact Map |
| 4q86A | 8 | 0.927 | 100 | 0.384 | Contact Map |
| 3sqgA | 3 | 0.6524 | 93.7 | 0.943 | Contact Map |
| 1hbnA | 2 | 0.6423 | 91.8 | 0.946 | Contact Map |
| 4j56E | 4 | 0.2393 | 17.4 | 0.971 | Contact Map |
| 1ekzA | 1 | 0.1763 | 17 | 0.971 | Contact Map |
| 3llhA | 2 | 0.1587 | 16.6 | 0.971 | Contact Map |
| 2mdrA | 1 | 0.199 | 13.5 | 0.972 | Contact Map |
| 3adlA | 1 | 0.1738 | 13.2 | 0.973 | Contact Map |
| 4wyqB | 2 | 0.1839 | 13.1 | 0.973 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)