| ccr6 |
| ID: | 1515681596 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 374 (309) | ||
| Sequences: | 2634 (1647.9) | ||
| Seq/Len: | 8.524 | ||
| Nf(neff/√len): | 93.7 |
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: 8.524).
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 |
| 60_G | 96_V | 5.702 | 1.00 |
| 87_N | 172_W | 3.583 | 1.00 |
| 232_F | 236_F | 2.707 | 1.00 |
| 229_F | 233_C | 2.654 | 1.00 |
| 180_S | 184_V | 2.400 | 1.00 |
| 111_W | 114_S | 2.395 | 1.00 |
| 144_Y | 149_Q | 2.326 | 1.00 |
| 77_A | 82_D | 2.324 | 1.00 |
| 138_C | 171_V | 2.256 | 1.00 |
| 116_A | 120_L | 2.233 | 1.00 |
| 135_L | 168_C | 2.109 | 1.00 |
| 188_K | 195_D | 1.999 | 1.00 |
| 123_G | 127_I | 1.903 | 1.00 |
| 123_G | 183_F | 1.858 | 1.00 |
| 267_Q | 305_A | 1.806 | 1.00 |
| 127_I | 176_V | 1.801 | 1.00 |
| 67_V | 312_N | 1.747 | 1.00 |
| 115_N | 187_Q | 1.739 | 1.00 |
| 166_I | 170_V | 1.717 | 1.00 |
| 144_Y | 148_V | 1.716 | 1.00 |
| 172_W | 313_P | 1.699 | 1.00 |
| 68_V | 86_L | 1.695 | 1.00 |
| 118_C | 197_C | 1.653 | 1.00 |
| 36_C | 288_C | 1.614 | 1.00 |
| 273_V | 297_T | 1.610 | 1.00 |
| 91_A | 172_W | 1.606 | 1.00 |
| 255_V | 319_I | 1.588 | 1.00 |
| 142_D | 157_R | 1.557 | 1.00 |
| 67_V | 71_F | 1.547 | 1.00 |
| 71_F | 86_L | 1.542 | 1.00 |
| 234_Y | 313_P | 1.539 | 1.00 |
| 101_F | 121_L | 1.510 | 1.00 |
| 235_T | 239_K | 1.467 | 0.99 |
| 267_Q | 312_N | 1.455 | 0.99 |
| 130_N | 222_G | 1.450 | 0.99 |
| 133_M | 137_T | 1.441 | 0.99 |
| 44_F | 48_F | 1.438 | 0.99 |
| 272_M | 276_V | 1.426 | 0.99 |
| 293_L | 297_T | 1.422 | 0.99 |
| 87_N | 135_L | 1.421 | 0.99 |
| 231_I | 235_T | 1.419 | 0.99 |
| 104_V | 113_F | 1.417 | 0.99 |
| 47_L | 51_I | 1.413 | 0.99 |
| 68_V | 93_I | 1.407 | 0.99 |
| 87_N | 313_P | 1.397 | 0.99 |
| 219_L | 275_L | 1.393 | 0.99 |
| 238_V | 253_I | 1.389 | 0.99 |
| 227_L | 264_L | 1.364 | 0.99 |
| 144_Y | 232_F | 1.357 | 0.99 |
| 49_V | 53_Y | 1.348 | 0.99 |
| 230_M | 260_V | 1.345 | 0.99 |
| 266_C | 304_L | 1.337 | 0.99 |
| 140_S | 260_V | 1.315 | 0.99 |
| 92_D | 132_G | 1.313 | 0.99 |
| 118_C | 313_P | 1.303 | 0.99 |
| 87_N | 168_C | 1.294 | 0.98 |
| 98_T | 102_W | 1.289 | 0.98 |
| 67_V | 313_P | 1.277 | 0.98 |
| 63_G | 310_C | 1.277 | 0.98 |
| 67_V | 317_A | 1.275 | 0.98 |
| 267_Q | 313_P | 1.271 | 0.98 |
| 142_D | 237_I | 1.266 | 0.98 |
| 70_T | 323_F | 1.266 | 0.98 |
| 219_L | 224_F | 1.257 | 0.98 |
| 165_K | 169_L | 1.256 | 0.98 |
| 62_L | 65_I | 1.248 | 0.98 |
| 323_F | 327_F | 1.245 | 0.98 |
| 91_A | 316_Y | 1.231 | 0.98 |
| 83_V | 164_S | 1.224 | 0.98 |
| 65_I | 93_I | 1.220 | 0.97 |
| 92_D | 312_N | 1.211 | 0.97 |
| 133_M | 263_F | 1.210 | 0.97 |
| 141_M | 229_F | 1.202 | 0.97 |
| 128_N | 168_C | 1.201 | 0.97 |
| 223_F | 264_L | 1.194 | 0.97 |
| 67_V | 267_Q | 1.190 | 0.97 |
| 132_G | 308_H | 1.190 | 0.97 |
| 115_N | 119_K | 1.187 | 0.97 |
| 96_V | 320_G | 1.183 | 0.97 |
| 136_L | 230_M | 1.180 | 0.97 |
| 134_L | 137_T | 1.173 | 0.97 |
| 91_A | 131_C | 1.153 | 0.96 |
| 87_N | 91_A | 1.147 | 0.96 |
| 60_G | 310_C | 1.147 | 0.96 |
| 257_I | 315_L | 1.139 | 0.96 |
| 92_D | 308_H | 1.132 | 0.96 |
| 63_G | 306_F | 1.120 | 0.95 |
| 84_Y | 164_S | 1.115 | 0.95 |
| 99_L | 136_L | 1.111 | 0.95 |
| 100_P | 313_P | 1.110 | 0.95 |
| 190_N | 261_L | 1.107 | 0.95 |
| 34_L | 38_L | 1.104 | 0.95 |
| 50_P | 103_A | 1.103 | 0.95 |
| 225_I | 279_A | 1.096 | 0.94 |
| 98_T | 121_L | 1.095 | 0.94 |
| 153_S | 157_R | 1.093 | 0.94 |
| 264_L | 268_I | 1.092 | 0.94 |
| 86_L | 90_I | 1.092 | 0.94 |
| 234_Y | 260_V | 1.089 | 0.94 |
| 146_A | 150_A | 1.088 | 0.94 |
| 236_F | 239_K | 1.082 | 0.94 |
| 187_Q | 200_K | 1.071 | 0.94 |
| 234_Y | 254_R | 1.071 | 0.94 |
| 118_C | 172_W | 1.068 | 0.93 |
| 141_M | 233_C | 1.065 | 0.93 |
| 118_C | 269_P | 1.064 | 0.93 |
| 84_Y | 167_I | 1.062 | 0.93 |
| 34_L | 37_S | 1.061 | 0.93 |
| 223_F | 227_L | 1.057 | 0.93 |
| 307_L | 311_L | 1.055 | 0.93 |
| 67_V | 91_A | 1.046 | 0.92 |
| 111_W | 313_P | 1.042 | 0.92 |
| 83_V | 168_C | 1.041 | 0.92 |
| 241_L | 252_A | 1.041 | 0.92 |
| 135_L | 171_V | 1.040 | 0.92 |
| 58_V | 62_L | 1.037 | 0.92 |
| 137_T | 230_M | 1.035 | 0.92 |
| 142_D | 256_I | 1.035 | 0.92 |
| 61_L | 93_I | 1.033 | 0.92 |
| 223_F | 313_P | 1.032 | 0.92 |
| 33_M | 38_L | 1.030 | 0.92 |
| 91_A | 140_S | 1.030 | 0.92 |
| 100_P | 223_F | 1.026 | 0.92 |
| 234_Y | 317_A | 1.024 | 0.91 |
| 115_N | 301_T | 1.021 | 0.91 |
| 33_M | 37_S | 1.020 | 0.91 |
| 335_W | 340_K | 1.020 | 0.91 |
| 274_L | 277_T | 1.015 | 0.91 |
| 142_D | 252_A | 1.013 | 0.91 |
| 162_P | 166_I | 1.013 | 0.91 |
| 85_L | 139_I | 1.011 | 0.91 |
| 139_I | 230_M | 1.011 | 0.91 |
| 113_F | 117_T | 1.007 | 0.90 |
| 134_L | 222_G | 1.007 | 0.90 |
| 146_A | 157_R | 1.005 | 0.90 |
| 80_M | 306_F | 1.005 | 0.90 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 3oduA | 2 | 0.8048 | 100 | 0.372 | Contact Map |
| 4pxzA | 1 | 0.7406 | 100 | 0.378 | Contact Map |
| 4mbsA | 2 | 0.7861 | 100 | 0.386 | Contact Map |
| 3vw7A | 1 | 0.7406 | 100 | 0.397 | Contact Map |
| 2rh1A | 1 | 0.7433 | 100 | 0.401 | Contact Map |
| 4iarA | 1 | 0.7273 | 100 | 0.402 | Contact Map |
| 3uonA | 1 | 0.7273 | 100 | 0.406 | Contact Map |
| 4grvA | 1 | 0.7567 | 100 | 0.409 | Contact Map |
| 3pblA | 2 | 0.7032 | 100 | 0.412 | Contact Map |
| 4dklA | 1 | 0.746 | 100 | 0.414 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)