| human syx |
| ID: | 1502376483 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 288 (256) | ||
| Sequences: | 2313 (1475.6) | ||
| Seq/Len: | 9.035 | ||
| Nf(neff/√len): | 92.2 |
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: 9.035).
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 |
| 50_N | 82_I | 2.810 | 1.00 |
| 260_K | 264_K | 2.336 | 1.00 |
| 48_A | 133_E | 2.016 | 1.00 |
| 267_M | 271_C | 1.988 | 1.00 |
| 264_K | 267_M | 1.977 | 1.00 |
| 37_V | 123_L | 1.830 | 1.00 |
| 52_E | 133_E | 1.803 | 1.00 |
| 94_K | 97_E | 1.761 | 1.00 |
| 270_I | 273_V | 1.754 | 1.00 |
| 227_G | 230_I | 1.730 | 1.00 |
| 54_V | 75_L | 1.709 | 1.00 |
| 41_R | 126_K | 1.666 | 1.00 |
| 261_A | 265_K | 1.646 | 1.00 |
| 44_I | 130_V | 1.627 | 1.00 |
| 161_T | 164_E | 1.583 | 1.00 |
| 270_I | 274_I | 1.571 | 1.00 |
| 254_A | 258_Q | 1.551 | 1.00 |
| 200_S | 203_I | 1.547 | 1.00 |
| 231_D | 235_Y | 1.535 | 1.00 |
| 275_L | 279_I | 1.525 | 1.00 |
| 263_R | 267_M | 1.519 | 1.00 |
| 97_E | 124_S | 1.517 | 1.00 |
| 32_E | 35_E | 1.513 | 1.00 |
| 54_V | 82_I | 1.488 | 1.00 |
| 274_I | 278_V | 1.466 | 1.00 |
| 33_F | 96_I | 1.457 | 1.00 |
| 246_R | 249_S | 1.456 | 1.00 |
| 227_G | 231_D | 1.442 | 0.99 |
| 214_D | 218_D | 1.442 | 0.99 |
| 43_F | 89_V | 1.432 | 0.99 |
| 232_R | 235_Y | 1.412 | 0.99 |
| 36_Q | 92_K | 1.404 | 0.99 |
| 198_R | 216_F | 1.377 | 0.99 |
| 276_G | 279_I | 1.365 | 0.99 |
| 138_Q | 208_S | 1.356 | 0.99 |
| 193_S | 197_T | 1.354 | 0.99 |
| 55_K | 59_S | 1.342 | 0.99 |
| 237_V | 240_A | 1.337 | 0.99 |
| 47_I | 50_N | 1.335 | 0.99 |
| 200_S | 207_N | 1.334 | 0.99 |
| 268_I | 272_C | 1.332 | 0.99 |
| 256_K | 260_K | 1.318 | 0.99 |
| 187_I | 191_A | 1.303 | 0.99 |
| 234_E | 238_E | 1.300 | 0.99 |
| 197_T | 200_S | 1.295 | 0.99 |
| 36_Q | 99_S | 1.284 | 0.99 |
| 86_A | 131_M | 1.282 | 0.99 |
| 261_A | 264_K | 1.281 | 0.99 |
| 100_I | 116_R | 1.279 | 0.98 |
| 225_S | 228_E | 1.277 | 0.98 |
| 30_M | 34_F | 1.270 | 0.98 |
| 246_R | 250_D | 1.270 | 0.98 |
| 249_S | 253_K | 1.267 | 0.98 |
| 229_M | 232_R | 1.262 | 0.98 |
| 258_Q | 261_A | 1.257 | 0.98 |
| 124_S | 128_V | 1.250 | 0.98 |
| 89_V | 93_L | 1.249 | 0.98 |
| 257_Y | 261_A | 1.248 | 0.98 |
| 58_H | 209_I | 1.243 | 0.98 |
| 251_T | 255_V | 1.227 | 0.98 |
| 273_V | 277_I | 1.225 | 0.98 |
| 47_I | 89_V | 1.225 | 0.98 |
| 262_R | 267_M | 1.220 | 0.98 |
| 244_V | 247_A | 1.220 | 0.98 |
| 209_I | 229_M | 1.220 | 0.98 |
| 119_Q | 123_L | 1.219 | 0.98 |
| 220_A | 224_E | 1.214 | 0.98 |
| 195_I | 251_T | 1.214 | 0.98 |
| 275_L | 278_V | 1.214 | 0.98 |
| 89_V | 138_Q | 1.209 | 0.98 |
| 264_K | 268_I | 1.209 | 0.98 |
| 209_I | 216_F | 1.208 | 0.98 |
| 240_A | 243_Y | 1.201 | 0.97 |
| 48_A | 130_V | 1.197 | 0.97 |
| 53_E | 56_R | 1.195 | 0.97 |
| 126_K | 129_E | 1.193 | 0.97 |
| 188_S | 192_L | 1.192 | 0.97 |
| 218_D | 221_M | 1.191 | 0.97 |
| 132_S | 136_A | 1.177 | 0.97 |
| 50_N | 85_T | 1.169 | 0.97 |
| 257_Y | 260_K | 1.168 | 0.97 |
| 213_H | 217_M | 1.165 | 0.97 |
| 276_G | 280_A | 1.150 | 0.96 |
| 58_H | 141_Y | 1.143 | 0.96 |
| 88_K | 91_S | 1.142 | 0.96 |
| 82_I | 85_T | 1.142 | 0.96 |
| 89_V | 127_F | 1.135 | 0.96 |
| 273_V | 279_I | 1.130 | 0.96 |
| 33_F | 230_I | 1.128 | 0.96 |
| 216_F | 222_L | 1.126 | 0.96 |
| 144_R | 147_G | 1.126 | 0.96 |
| 205_L | 233_I | 1.125 | 0.96 |
| 95_S | 98_Q | 1.122 | 0.96 |
| 236_N | 239_H | 1.120 | 0.96 |
| 202_I | 240_A | 1.115 | 0.96 |
| 253_K | 257_Y | 1.115 | 0.96 |
| 266_I | 270_I | 1.112 | 0.96 |
| 130_V | 133_E | 1.106 | 0.95 |
| 58_H | 76_E | 1.103 | 0.95 |
| 250_D | 253_K | 1.102 | 0.95 |
| 221_M | 224_E | 1.094 | 0.95 |
| 210_R | 213_H | 1.087 | 0.95 |
| 248_V | 252_K | 1.087 | 0.95 |
| 90_R | 94_K | 1.075 | 0.94 |
| 118_T | 124_S | 1.073 | 0.94 |
| 45_D | 48_A | 1.072 | 0.94 |
| 239_H | 243_Y | 1.071 | 0.94 |
| 203_I | 206_E | 1.070 | 0.94 |
| 250_D | 257_Y | 1.061 | 0.94 |
| 43_F | 85_T | 1.061 | 0.94 |
| 72_K | 76_E | 1.060 | 0.94 |
| 258_Q | 266_I | 1.060 | 0.94 |
| 174_P | 179_S | 1.058 | 0.94 |
| 146_K | 206_E | 1.058 | 0.94 |
| 204_K | 214_D | 1.054 | 0.94 |
| 245_E | 248_V | 1.050 | 0.93 |
| 90_R | 212_L | 1.047 | 0.93 |
| 193_S | 196_E | 1.044 | 0.93 |
| 268_I | 271_C | 1.042 | 0.93 |
| 187_I | 190_Q | 1.042 | 0.93 |
| 218_D | 222_L | 1.042 | 0.93 |
| 124_S | 138_Q | 1.041 | 0.93 |
| 246_R | 259_S | 1.033 | 0.93 |
| 122_T | 202_I | 1.029 | 0.92 |
| 218_D | 240_A | 1.029 | 0.92 |
| 131_M | 135_N | 1.022 | 0.92 |
| 34_F | 37_V | 1.021 | 0.92 |
| 181_I | 185_S | 1.021 | 0.92 |
| 131_M | 195_I | 1.021 | 0.92 |
| 83_K | 124_S | 1.019 | 0.92 |
| 52_E | 55_K | 1.015 | 0.92 |
| 77_E | 81_D | 1.015 | 0.92 |
| 46_K | 49_E | 1.005 | 0.91 |
| 257_Y | 264_K | 1.003 | 0.91 |
| 179_S | 183_M | 1.002 | 0.91 |
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 | |
| 3c98B | 1 | 0.7986 | 100 | 0.194 | Contact Map |
| 4jehB | 1 | 0.7674 | 100 | 0.269 | Contact Map |
| 2xheB | 1 | 0.7396 | 100 | 0.279 | Contact Map |
| 1fioA | 1 | 0.6493 | 100 | 0.488 | Contact Map |
| 2m8rA | 1 | 0.3785 | 99.9 | 0.546 | Contact Map |
| 1s94A | 2 | 0.4167 | 99.9 | 0.581 | Contact Map |
| 1jthB | 2 | 0.2326 | 99.9 | 0.619 | Contact Map |
| 1sfcB | 3 | 0.2639 | 99.8 | 0.64 | Contact Map |
| 2npsB | 1 | 0.2361 | 99.8 | 0.655 | Contact Map |
| 3b5nB | 3 | 0.2396 | 99.7 | 0.666 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)