| ccr6 40-340 |
| ID: | 1515684879 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 301 (285) | ||
| Sequences: | 27381 (14332.5) | ||
| Seq/Len: | 96.074 | ||
| Nf(neff/√len): | 849.0 |
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: 96.074).
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 |
| 21_G | 57_V | 4.636 | 1.00 |
| 48_N | 133_W | 3.965 | 1.00 |
| 193_F | 197_F | 3.457 | 1.00 |
| 48_N | 96_L | 2.842 | 1.00 |
| 99_C | 132_V | 2.429 | 1.00 |
| 123_P | 127_I | 2.423 | 1.00 |
| 196_T | 200_K | 2.386 | 1.00 |
| 52_A | 92_C | 2.322 | 1.00 |
| 77_A | 81_L | 2.276 | 1.00 |
| 88_I | 137_V | 2.253 | 1.00 |
| 105_Y | 110_Q | 2.185 | 1.00 |
| 190_F | 194_C | 2.161 | 1.00 |
| 29_V | 47_L | 2.154 | 1.00 |
| 105_Y | 197_F | 2.132 | 1.00 |
| 99_C | 128_I | 2.104 | 1.00 |
| 76_N | 80_K | 2.078 | 1.00 |
| 79_C | 158_C | 2.060 | 1.00 |
| 55_L | 89_N | 2.034 | 1.00 |
| 110_Q | 113_K | 2.024 | 1.00 |
| 216_V | 280_I | 2.015 | 1.00 |
| 32_F | 47_L | 1.963 | 1.00 |
| 92_C | 136_S | 1.954 | 1.00 |
| 105_Y | 109_V | 1.950 | 1.00 |
| 44_V | 129_C | 1.932 | 1.00 |
| 96_L | 129_C | 1.914 | 1.00 |
| 197_F | 200_K | 1.838 | 1.00 |
| 26_I | 30_I | 1.819 | 1.00 |
| 197_F | 201_T | 1.819 | 1.00 |
| 127_I | 131_V | 1.782 | 1.00 |
| 21_G | 271_C | 1.782 | 1.00 |
| 48_N | 129_C | 1.779 | 1.00 |
| 109_V | 201_T | 1.766 | 1.00 |
| 84_G | 88_I | 1.744 | 1.00 |
| 72_W | 75_S | 1.741 | 1.00 |
| 233_M | 237_V | 1.736 | 1.00 |
| 200_K | 204_Q | 1.716 | 1.00 |
| 98_T | 194_C | 1.679 | 1.00 |
| 35_Y | 287_Y | 1.640 | 1.00 |
| 105_Y | 194_C | 1.615 | 1.00 |
| 53_D | 273_N | 1.590 | 1.00 |
| 45_Y | 125_S | 1.582 | 1.00 |
| 8_L | 12_I | 1.556 | 1.00 |
| 47_L | 51_I | 1.540 | 1.00 |
| 287_Y | 290_K | 1.539 | 1.00 |
| 22_L | 54_I | 1.525 | 1.00 |
| 223_V | 276_L | 1.498 | 1.00 |
| 26_I | 54_I | 1.483 | 1.00 |
| 126_K | 130_L | 1.471 | 1.00 |
| 106_I | 117_L | 1.464 | 1.00 |
| 38_A | 43_D | 1.462 | 1.00 |
| 228_Q | 266_A | 1.445 | 1.00 |
| 44_V | 126_K | 1.440 | 1.00 |
| 128_I | 132_V | 1.439 | 1.00 |
| 123_P | 126_K | 1.436 | 1.00 |
| 98_T | 190_F | 1.418 | 1.00 |
| 33_A | 47_L | 1.414 | 1.00 |
| 199_V | 203_V | 1.405 | 0.99 |
| 103_D | 107_A | 1.385 | 0.99 |
| 201_T | 204_Q | 1.380 | 0.99 |
| 62_F | 66_S | 1.373 | 0.99 |
| 92_C | 133_W | 1.368 | 0.99 |
| 52_A | 93_G | 1.359 | 0.99 |
| 178_L | 182_F | 1.339 | 0.99 |
| 75_S | 78_T | 1.336 | 0.99 |
| 258_T | 262_T | 1.333 | 0.99 |
| 24_G | 271_C | 1.329 | 0.99 |
| 53_D | 93_G | 1.327 | 0.99 |
| 18_C | 64_A | 1.326 | 0.99 |
| 102_M | 194_C | 1.320 | 0.99 |
| 119_S | 124_R | 1.308 | 0.99 |
| 192_I | 196_T | 1.307 | 0.99 |
| 50_A | 53_D | 1.306 | 0.99 |
| 254_L | 258_T | 1.304 | 0.99 |
| 188_L | 225_L | 1.303 | 0.99 |
| 23_L | 26_I | 1.299 | 0.99 |
| 107_A | 111_A | 1.298 | 0.99 |
| 45_Y | 100_I | 1.282 | 0.99 |
| 141_S | 145_V | 1.267 | 0.99 |
| 22_L | 57_V | 1.264 | 0.99 |
| 92_C | 96_L | 1.262 | 0.99 |
| 113_K | 117_L | 1.259 | 0.99 |
| 268_L | 272_L | 1.254 | 0.99 |
| 113_K | 116_R | 1.252 | 0.99 |
| 257_Y | 261_V | 1.251 | 0.99 |
| 273_N | 277_Y | 1.236 | 0.98 |
| 41_M | 125_S | 1.234 | 0.98 |
| 95_L | 187_P | 1.232 | 0.98 |
| 122_L | 126_K | 1.228 | 0.98 |
| 136_S | 140_S | 1.224 | 0.98 |
| 29_V | 51_I | 1.218 | 0.98 |
| 229_I | 233_M | 1.203 | 0.98 |
| 210_R | 214_I | 1.199 | 0.98 |
| 52_A | 89_N | 1.198 | 0.98 |
| 30_I | 291_I | 1.186 | 0.98 |
| 101_S | 195_Y | 1.181 | 0.98 |
| 65_V | 74_F | 1.178 | 0.98 |
| 29_V | 50_A | 1.174 | 0.98 |
| 91_N | 183_G | 1.171 | 0.98 |
| 97_L | 191_M | 1.170 | 0.97 |
| 56_F | 270_C | 1.169 | 0.97 |
| 96_L | 133_W | 1.161 | 0.97 |
| 195_Y | 198_I | 1.157 | 0.97 |
| 29_V | 54_I | 1.157 | 0.97 |
| 84_G | 144_F | 1.157 | 0.97 |
| 24_G | 275_V | 1.154 | 0.97 |
| 49_M | 96_L | 1.146 | 0.97 |
| 119_S | 123_P | 1.142 | 0.97 |
| 76_N | 148_Q | 1.142 | 0.97 |
| 106_I | 110_Q | 1.137 | 0.97 |
| 211_H | 215_R | 1.131 | 0.97 |
| 199_V | 214_I | 1.131 | 0.97 |
| 11_P | 15_S | 1.128 | 0.97 |
| 91_N | 136_S | 1.121 | 0.97 |
| 32_F | 38_A | 1.121 | 0.97 |
| 223_V | 272_L | 1.120 | 0.96 |
| 94_M | 187_P | 1.118 | 0.96 |
| 20_F | 23_L | 1.116 | 0.96 |
| 88_I | 140_S | 1.114 | 0.96 |
| 61_P | 64_A | 1.113 | 0.96 |
| 127_I | 130_L | 1.112 | 0.96 |
| 234_V | 262_T | 1.109 | 0.96 |
| 30_I | 34_F | 1.102 | 0.96 |
| 49_M | 53_D | 1.101 | 0.96 |
| 103_D | 118_R | 1.099 | 0.96 |
| 95_L | 132_V | 1.096 | 0.96 |
| 77_A | 80_K | 1.093 | 0.96 |
| 28_V | 32_F | 1.090 | 0.96 |
| 20_F | 271_C | 1.086 | 0.96 |
| 284_F | 288_F | 1.080 | 0.95 |
| 105_Y | 193_F | 1.075 | 0.95 |
| 98_T | 191_M | 1.071 | 0.95 |
| 11_P | 64_A | 1.066 | 0.95 |
| 62_F | 78_T | 1.055 | 0.95 |
| 102_M | 106_I | 1.054 | 0.95 |
| 109_V | 197_F | 1.048 | 0.94 |
| 225_L | 229_I | 1.047 | 0.94 |
| 95_L | 135_L | 1.046 | 0.94 |
| 132_V | 136_S | 1.040 | 0.94 |
| 45_Y | 99_C | 1.038 | 0.94 |
| 114_S | 118_R | 1.034 | 0.94 |
| 44_V | 48_N | 1.032 | 0.94 |
| 107_A | 112_T | 1.029 | 0.94 |
| 40_S | 43_D | 1.027 | 0.94 |
| 18_C | 57_V | 1.024 | 0.93 |
| 35_Y | 38_A | 1.020 | 0.93 |
| 213_A | 216_V | 1.016 | 0.93 |
| 218_I | 222_L | 1.010 | 0.93 |
| 92_C | 132_V | 1.009 | 0.93 |
| 87_A | 140_S | 1.007 | 0.93 |
| 237_V | 241_N | 1.005 | 0.93 |
| 199_V | 202_L | 1.004 | 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
- 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 | |
| 4pxzA | 1 | 0.907 | 100 | 0.042 | Contact Map |
| 3oduA | 2 | 0.9767 | 100 | 0.048 | Contact Map |
| 3vw7A | 1 | 0.9037 | 100 | 0.061 | Contact Map |
| 2rh1A | 1 | 0.9236 | 100 | 0.068 | Contact Map |
| 4iarA | 1 | 0.887 | 100 | 0.069 | Contact Map |
| 3uonA | 1 | 0.9037 | 100 | 0.071 | Contact Map |
| 4mbsA | 2 | 0.9601 | 100 | 0.072 | Contact Map |
| 4grvA | 1 | 0.9203 | 100 | 0.083 | Contact Map |
| 4dklA | 1 | 0.9269 | 100 | 0.088 | Contact Map |
| 4xnvA | 1 | 0.9369 | 100 | 0.089 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)