| HiF1 notothena coriicepts full |
| ID: | 1492650028 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 695 (275) | ||
| Sequences: | 18657 (14170.6) | ||
| Seq/Len: | 67.844 | ||
| Nf(neff/√len): | 854.5 |
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: 67.844).
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 |
| 309_A | 313_G | 3.154 | 1.00 |
| 241_T | 340_F | 2.963 | 1.00 |
| 258_R | 261_E | 2.582 | 1.00 |
| 116_N | 119_K | 2.554 | 1.00 |
| 98_E | 225_D | 2.553 | 1.00 |
| 346_Q | 349_K | 2.142 | 1.00 |
| 242_F | 262_L | 2.106 | 1.00 |
| 304_Q | 346_Q | 2.097 | 1.00 |
| 115_E | 119_K | 2.057 | 1.00 |
| 173_C | 186_S | 2.055 | 1.00 |
| 305_Y | 319_T | 2.054 | 1.00 |
| 255_C | 259_I | 2.012 | 1.00 |
| 318_E | 340_F | 2.003 | 1.00 |
| 193_H | 225_D | 1.997 | 1.00 |
| 308_L | 314_F | 1.991 | 1.00 |
| 323_V | 332_P | 1.972 | 1.00 |
| 118_N | 125_Q | 1.956 | 1.00 |
| 113_L | 117_V | 1.952 | 1.00 |
| 102_M | 222_L | 1.937 | 1.00 |
| 257_E | 261_E | 1.917 | 1.00 |
| 326_N | 329_N | 1.913 | 1.00 |
| 309_A | 315_V | 1.910 | 1.00 |
| 326_N | 331_Q | 1.909 | 1.00 |
| 247_T | 251_K | 1.880 | 1.00 |
| 244_S | 337_C | 1.870 | 1.00 |
| 231_S | 234_E | 1.862 | 1.00 |
| 345_I | 349_K | 1.859 | 1.00 |
| 173_C | 188_A | 1.833 | 1.00 |
| 302_T | 318_E | 1.830 | 1.00 |
| 265_Y | 310_K | 1.798 | 1.00 |
| 201_Y | 214_E | 1.795 | 1.00 |
| 306_R | 316_W | 1.776 | 1.00 |
| 93_Y | 112_Y | 1.775 | 1.00 |
| 105_S | 109_D | 1.738 | 1.00 |
| 260_T | 267_P | 1.730 | 1.00 |
| 173_C | 190_K | 1.721 | 1.00 |
| 123_L | 185_K | 1.713 | 1.00 |
| 230_P | 234_E | 1.704 | 1.00 |
| 306_R | 314_F | 1.693 | 1.00 |
| 86_D | 90_N | 1.693 | 1.00 |
| 138_H | 141_D | 1.676 | 1.00 |
| 273_R | 277_E | 1.648 | 1.00 |
| 194_C | 224_C | 1.643 | 1.00 |
| 319_T | 339_N | 1.643 | 1.00 |
| 245_R | 334_C | 1.625 | 1.00 |
| 131_Y | 135_D | 1.621 | 1.00 |
| 280_H | 283_D | 1.621 | 1.00 |
| 113_L | 118_N | 1.618 | 1.00 |
| 318_E | 345_I | 1.608 | 1.00 |
| 124_A | 127_D | 1.577 | 1.00 |
| 242_F | 339_N | 1.574 | 1.00 |
| 260_T | 266_D | 1.573 | 1.00 |
| 325_Y | 332_P | 1.572 | 1.00 |
| 169_L | 194_C | 1.561 | 1.00 |
| 255_C | 260_T | 1.553 | 1.00 |
| 254_Y | 267_P | 1.527 | 1.00 |
| 356_Q | 359_D | 1.526 | 1.00 |
| 269_D | 310_K | 1.523 | 1.00 |
| 257_E | 260_T | 1.519 | 1.00 |
| 266_D | 269_D | 1.517 | 1.00 |
| 244_S | 252_F | 1.516 | 1.00 |
| 115_E | 118_N | 1.514 | 1.00 |
| 102_M | 110_M | 1.498 | 1.00 |
| 114_T | 117_V | 1.489 | 1.00 |
| 112_Y | 125_Q | 1.478 | 1.00 |
| 198_V | 217_V | 1.468 | 1.00 |
| 90_N | 94_L | 1.466 | 1.00 |
| 172_K | 189_W | 1.464 | 1.00 |
| 239_T | 243_L | 1.456 | 1.00 |
| 168_F | 231_S | 1.447 | 1.00 |
| 118_N | 124_A | 1.438 | 1.00 |
| 115_E | 125_Q | 1.411 | 1.00 |
| 127_D | 185_K | 1.409 | 1.00 |
| 283_D | 306_R | 1.408 | 1.00 |
| 103_V | 221_V | 1.391 | 0.99 |
| 166_S | 193_H | 1.390 | 0.99 |
| 99_G | 120_C | 1.385 | 0.99 |
| 256_D | 259_I | 1.363 | 0.99 |
| 267_P | 271_L | 1.356 | 0.99 |
| 201_Y | 216_T | 1.356 | 0.99 |
| 347_D | 351_V | 1.354 | 0.99 |
| 348_E | 351_V | 1.354 | 0.99 |
| 109_D | 132_S | 1.349 | 0.99 |
| 259_I | 263_M | 1.348 | 0.99 |
| 193_H | 230_P | 1.342 | 0.99 |
| 293_N | 297_K | 1.340 | 0.99 |
| 103_V | 219_Y | 1.332 | 0.99 |
| 102_M | 117_V | 1.316 | 0.99 |
| 117_V | 121_L | 1.312 | 0.99 |
| 356_Q | 360_V | 1.305 | 0.99 |
| 111_I | 219_Y | 1.304 | 0.99 |
| 351_V | 354_L | 1.304 | 0.99 |
| 245_R | 254_Y | 1.301 | 0.99 |
| 184_V | 188_A | 1.301 | 0.99 |
| 344_G | 347_D | 1.296 | 0.99 |
| 248_M | 332_P | 1.285 | 0.99 |
| 228_Q | 232_N | 1.283 | 0.99 |
| 321_A | 335_I | 1.282 | 0.99 |
| 125_Q | 129_T | 1.276 | 0.99 |
| 192_L | 224_C | 1.273 | 0.99 |
| 132_S | 135_D | 1.252 | 0.99 |
| 231_S | 235_V | 1.230 | 0.98 |
| 317_V | 339_N | 1.228 | 0.98 |
| 349_K | 353_S | 1.226 | 0.98 |
| 355_E | 358_E | 1.222 | 0.98 |
| 350_L | 353_S | 1.209 | 0.98 |
| 244_S | 259_I | 1.205 | 0.98 |
| 245_R | 336_V | 1.201 | 0.98 |
| 170_R | 189_W | 1.196 | 0.98 |
| 342_L | 346_Q | 1.192 | 0.98 |
| 304_Q | 318_E | 1.190 | 0.98 |
| 343_S | 347_D | 1.188 | 0.98 |
| 251_K | 274_S | 1.183 | 0.98 |
| 200_V | 217_V | 1.169 | 0.97 |
| 351_V | 355_E | 1.152 | 0.97 |
| 280_H | 306_R | 1.146 | 0.97 |
| 123_L | 127_D | 1.144 | 0.97 |
| 257_E | 267_P | 1.143 | 0.97 |
| 247_T | 253_T | 1.142 | 0.97 |
| 345_I | 348_E | 1.134 | 0.97 |
| 168_F | 193_H | 1.132 | 0.97 |
| 141_D | 170_R | 1.130 | 0.97 |
| 138_H | 189_W | 1.126 | 0.97 |
| 94_L | 115_E | 1.123 | 0.97 |
| 110_M | 113_L | 1.117 | 0.96 |
| 348_E | 352_L | 1.109 | 0.96 |
| 106_E | 217_V | 1.103 | 0.96 |
| 280_H | 314_F | 1.102 | 0.96 |
| 105_S | 111_I | 1.091 | 0.96 |
| 265_Y | 269_D | 1.086 | 0.96 |
| 146_R | 150_V | 1.083 | 0.96 |
| 196_G | 220_L | 1.083 | 0.96 |
| 113_L | 128_L | 1.078 | 0.95 |
| 354_L | 358_E | 1.070 | 0.95 |
| 227_I | 231_S | 1.068 | 0.95 |
| 263_M | 307_M | 1.063 | 0.95 |
| 117_V | 128_L | 1.054 | 0.95 |
| 191_V | 231_S | 1.051 | 0.94 |
| 302_T | 320_Q | 1.050 | 0.94 |
| 253_T | 334_C | 1.049 | 0.94 |
| 96_A | 101_L | 1.044 | 0.94 |
| 229_H | 232_N | 1.042 | 0.94 |
| 355_E | 359_D | 1.041 | 0.94 |
| 89_L | 93_Y | 1.031 | 0.94 |
| 324_I | 336_V | 1.030 | 0.94 |
| 232_N | 236_P | 1.027 | 0.94 |
| 147_E | 151_H | 1.026 | 0.94 |
| 292_H | 296_A | 1.026 | 0.94 |
| 170_R | 191_V | 1.022 | 0.93 |
| 131_Y | 136_F | 1.022 | 0.93 |
| 307_M | 315_V | 1.016 | 0.93 |
| 289_K | 293_N | 1.013 | 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 | |
| 4f3lA | 1 | 0.4388 | 100 | 0.714 | Contact Map |
| 4f3lB | 1 | 0.4245 | 100 | 0.714 | Contact Map |
| 3rtyA | 8 | 0.4058 | 100 | 0.812 | Contact Map |
| 3gdiA | 2 | 0.3655 | 100 | 0.816 | Contact Map |
| 4dj3A | 2 | 0.3813 | 100 | 0.829 | Contact Map |
| 4dj2A | 4 | 0.3683 | 100 | 0.834 | Contact Map |
| 3ewkA | 1 | 0.3065 | 99.9 | 0.838 | Contact Map |
| 4hh3A | 2 | 0.3252 | 99.9 | 0.857 | Contact Map |
| 4hh2A | 4 | 0.4331 | 99.9 | 0.859 | Contact Map |
| 2ykfA | 1 | 0.3237 | 99.9 | 0.867 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)