| Hif1 notothenia coriiceps |
| ID: | 1492649420 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 658 (272) | ||
| Sequences: | 19444 (14733.6) | ||
| Seq/Len: | 71.485 | ||
| Nf(neff/√len): | 893.4 |
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: 71.485).
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 |
| 308_A | 312_G | 3.076 | 1.00 |
| 240_T | 339_F | 2.942 | 1.00 |
| 97_E | 224_D | 2.586 | 1.00 |
| 115_N | 118_K | 2.491 | 1.00 |
| 257_R | 260_E | 2.482 | 1.00 |
| 172_C | 185_S | 2.238 | 1.00 |
| 345_Q | 348_K | 2.142 | 1.00 |
| 254_C | 258_I | 2.093 | 1.00 |
| 241_F | 261_L | 2.092 | 1.00 |
| 325_N | 330_Q | 2.033 | 1.00 |
| 192_H | 224_D | 2.031 | 1.00 |
| 344_I | 348_K | 2.011 | 1.00 |
| 304_Y | 318_T | 2.005 | 1.00 |
| 307_L | 313_F | 2.002 | 1.00 |
| 317_E | 339_F | 1.986 | 1.00 |
| 303_Q | 345_Q | 1.983 | 1.00 |
| 112_L | 116_V | 1.966 | 1.00 |
| 322_V | 331_P | 1.965 | 1.00 |
| 114_E | 118_K | 1.953 | 1.00 |
| 308_A | 314_V | 1.949 | 1.00 |
| 101_M | 221_L | 1.879 | 1.00 |
| 172_C | 187_A | 1.866 | 1.00 |
| 117_N | 124_Q | 1.861 | 1.00 |
| 325_N | 328_N | 1.839 | 1.00 |
| 246_T | 250_K | 1.835 | 1.00 |
| 301_T | 317_E | 1.824 | 1.00 |
| 256_E | 260_E | 1.792 | 1.00 |
| 264_Y | 309_K | 1.791 | 1.00 |
| 279_H | 282_D | 1.785 | 1.00 |
| 243_S | 336_C | 1.775 | 1.00 |
| 172_C | 189_K | 1.774 | 1.00 |
| 230_S | 233_E | 1.761 | 1.00 |
| 122_L | 184_K | 1.741 | 1.00 |
| 259_T | 266_P | 1.730 | 1.00 |
| 137_H | 140_D | 1.720 | 1.00 |
| 104_S | 108_D | 1.718 | 1.00 |
| 229_P | 233_E | 1.704 | 1.00 |
| 305_R | 315_W | 1.701 | 1.00 |
| 305_R | 313_F | 1.699 | 1.00 |
| 112_L | 117_N | 1.685 | 1.00 |
| 244_R | 333_C | 1.677 | 1.00 |
| 200_Y | 213_E | 1.656 | 1.00 |
| 272_R | 276_E | 1.636 | 1.00 |
| 130_Y | 134_D | 1.618 | 1.00 |
| 92_Y | 111_Y | 1.616 | 1.00 |
| 318_T | 338_N | 1.602 | 1.00 |
| 355_Q | 358_D | 1.599 | 1.00 |
| 123_A | 126_D | 1.570 | 1.00 |
| 268_D | 309_K | 1.566 | 1.00 |
| 238_T | 242_L | 1.560 | 1.00 |
| 85_D | 89_N | 1.557 | 1.00 |
| 254_C | 259_T | 1.547 | 1.00 |
| 265_D | 268_D | 1.532 | 1.00 |
| 317_E | 344_I | 1.525 | 1.00 |
| 101_M | 109_M | 1.514 | 1.00 |
| 241_F | 338_N | 1.511 | 1.00 |
| 168_L | 193_C | 1.496 | 1.00 |
| 259_T | 265_D | 1.494 | 1.00 |
| 243_S | 251_F | 1.493 | 1.00 |
| 324_Y | 331_P | 1.491 | 1.00 |
| 113_T | 116_V | 1.488 | 1.00 |
| 282_D | 305_R | 1.487 | 1.00 |
| 102_V | 218_Y | 1.466 | 1.00 |
| 253_Y | 266_P | 1.458 | 1.00 |
| 197_V | 216_V | 1.456 | 1.00 |
| 167_F | 230_S | 1.453 | 1.00 |
| 171_K | 188_W | 1.453 | 1.00 |
| 111_Y | 124_Q | 1.451 | 1.00 |
| 193_C | 223_C | 1.447 | 1.00 |
| 256_E | 259_T | 1.445 | 1.00 |
| 98_G | 119_C | 1.433 | 1.00 |
| 114_E | 117_N | 1.427 | 1.00 |
| 89_N | 93_L | 1.426 | 1.00 |
| 247_M | 331_P | 1.419 | 1.00 |
| 102_V | 220_V | 1.416 | 1.00 |
| 126_D | 184_K | 1.410 | 1.00 |
| 117_N | 123_A | 1.404 | 0.99 |
| 114_E | 124_Q | 1.401 | 0.99 |
| 258_I | 262_M | 1.374 | 0.99 |
| 350_V | 354_E | 1.359 | 0.99 |
| 165_S | 192_H | 1.351 | 0.99 |
| 116_V | 120_L | 1.350 | 0.99 |
| 227_Q | 231_N | 1.347 | 0.99 |
| 342_S | 346_D | 1.344 | 0.99 |
| 108_D | 131_S | 1.343 | 0.99 |
| 244_R | 253_Y | 1.342 | 0.99 |
| 110_I | 218_Y | 1.336 | 0.99 |
| 316_V | 338_N | 1.313 | 0.99 |
| 347_E | 350_V | 1.308 | 0.99 |
| 346_D | 350_V | 1.306 | 0.99 |
| 255_D | 258_I | 1.304 | 0.99 |
| 266_P | 270_L | 1.299 | 0.99 |
| 350_V | 353_L | 1.298 | 0.99 |
| 101_M | 116_V | 1.294 | 0.99 |
| 348_K | 352_S | 1.288 | 0.99 |
| 349_L | 352_S | 1.280 | 0.99 |
| 191_L | 223_C | 1.279 | 0.99 |
| 343_G | 346_D | 1.267 | 0.99 |
| 200_Y | 215_T | 1.260 | 0.99 |
| 243_S | 258_I | 1.258 | 0.99 |
| 353_L | 357_E | 1.247 | 0.99 |
| 355_Q | 359_V | 1.242 | 0.98 |
| 292_N | 296_K | 1.240 | 0.98 |
| 320_A | 334_I | 1.237 | 0.98 |
| 192_H | 229_P | 1.234 | 0.98 |
| 347_E | 351_L | 1.215 | 0.98 |
| 169_R | 188_W | 1.215 | 0.98 |
| 131_S | 134_D | 1.209 | 0.98 |
| 122_L | 126_D | 1.184 | 0.98 |
| 183_V | 187_A | 1.176 | 0.98 |
| 124_Q | 128_T | 1.174 | 0.98 |
| 354_E | 357_E | 1.162 | 0.97 |
| 303_Q | 317_E | 1.162 | 0.97 |
| 145_R | 149_V | 1.150 | 0.97 |
| 344_I | 347_E | 1.150 | 0.97 |
| 341_L | 345_Q | 1.142 | 0.97 |
| 306_M | 314_V | 1.142 | 0.97 |
| 104_S | 110_I | 1.137 | 0.97 |
| 199_V | 216_V | 1.137 | 0.97 |
| 279_H | 313_F | 1.135 | 0.97 |
| 246_T | 252_T | 1.129 | 0.97 |
| 264_Y | 268_D | 1.118 | 0.96 |
| 109_M | 112_L | 1.113 | 0.96 |
| 279_H | 305_R | 1.113 | 0.96 |
| 301_T | 319_Q | 1.112 | 0.96 |
| 250_K | 273_S | 1.111 | 0.96 |
| 88_L | 92_Y | 1.109 | 0.96 |
| 167_F | 192_H | 1.102 | 0.96 |
| 244_R | 335_V | 1.089 | 0.96 |
| 195_G | 219_L | 1.086 | 0.96 |
| 323_I | 335_V | 1.079 | 0.95 |
| 105_E | 216_V | 1.078 | 0.95 |
| 256_E | 266_P | 1.071 | 0.95 |
| 230_S | 234_V | 1.070 | 0.95 |
| 285_H | 289_T | 1.067 | 0.95 |
| 140_D | 169_R | 1.066 | 0.95 |
| 262_M | 306_M | 1.066 | 0.95 |
| 252_T | 333_C | 1.064 | 0.95 |
| 116_V | 127_L | 1.056 | 0.95 |
| 137_H | 188_W | 1.054 | 0.95 |
| 226_I | 230_S | 1.052 | 0.95 |
| 112_L | 127_L | 1.050 | 0.94 |
| 354_E | 358_D | 1.048 | 0.94 |
| 228_H | 231_N | 1.044 | 0.94 |
| 95_A | 100_L | 1.031 | 0.94 |
| 288_K | 292_N | 1.030 | 0.94 |
| 190_V | 230_S | 1.027 | 0.94 |
| 287_T | 291_H | 1.027 | 0.94 |
| 90_G | 94_K | 1.019 | 0.93 |
| 102_V | 111_Y | 1.002 | 0.92 |
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 | |
| 4f3lB | 1 | 0.4483 | 100 | 0.694 | Contact Map |
| 4f3lA | 1 | 0.4635 | 100 | 0.696 | Contact Map |
| 3rtyA | 8 | 0.4255 | 100 | 0.796 | Contact Map |
| 3gdiA | 2 | 0.386 | 100 | 0.804 | Contact Map |
| 4dj3A | 2 | 0.4043 | 100 | 0.818 | Contact Map |
| 4dj2A | 4 | 0.3891 | 99.9 | 0.822 | Contact Map |
| 3ewkA | 1 | 0.3237 | 99.9 | 0.827 | Contact Map |
| 4hh3A | 2 | 0.3435 | 99.9 | 0.848 | Contact Map |
| 4hh2A | 4 | 0.4559 | 99.9 | 0.852 | Contact Map |
| 2ykfA | 1 | 0.3419 | 99.8 | 0.858 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)