| ABCA4-1913-2183 |
| ID: | 1490921603 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 271 (236) | ||
| Sequences: | 188371 (104659) | ||
| Seq/Len: | 798.182 | ||
| Nf(neff/√len): | 6812.7 |
Jackhmmer Results: (2016_04)
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: 798.182).
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 |
| 54_E | 227_R | 3.256 | 1.00 |
| 56_F | 229_A | 2.949 | 1.00 |
| 27_R | 49_G | 2.944 | 1.00 |
| 41_P | 44_D | 2.927 | 1.00 |
| 57_G | 225_C | 2.909 | 1.00 |
| 83_D | 90_S | 2.887 | 1.00 |
| 30_E | 45_R | 2.715 | 1.00 |
| 29_H | 83_D | 2.712 | 1.00 |
| 227_R | 239_M | 2.639 | 1.00 |
| 101_N | 178_P | 2.607 | 1.00 |
| 151_Y | 154_C | 2.523 | 1.00 |
| 27_R | 85_T | 2.472 | 1.00 |
| 51_R | 54_E | 2.470 | 1.00 |
| 34_I | 41_P | 2.375 | 1.00 |
| 29_H | 85_T | 2.307 | 1.00 |
| 32_T | 41_P | 2.301 | 1.00 |
| 32_T | 81_S | 2.234 | 1.00 |
| 44_D | 235_A | 2.210 | 1.00 |
| 229_A | 239_M | 2.151 | 1.00 |
| 240_G | 244_H | 2.143 | 1.00 |
| 241_T | 244_H | 2.109 | 1.00 |
| 32_T | 45_R | 2.052 | 1.00 |
| 87_A | 178_P | 1.980 | 1.00 |
| 28_L | 31_L | 1.935 | 1.00 |
| 131_P | 134_E | 1.913 | 1.00 |
| 140_N | 152_A | 1.848 | 1.00 |
| 33_K | 72_M | 1.826 | 1.00 |
| 202_V | 223_A | 1.807 | 1.00 |
| 229_A | 236_F | 1.787 | 1.00 |
| 70_F | 181_L | 1.742 | 1.00 |
| 70_F | 214_T | 1.717 | 1.00 |
| 140_N | 144_K | 1.709 | 1.00 |
| 118_R | 122_Y | 1.687 | 1.00 |
| 141_W | 145_S | 1.674 | 1.00 |
| 140_N | 148_L | 1.603 | 1.00 |
| 143_I | 152_A | 1.601 | 1.00 |
| 176_C | 209_R | 1.595 | 1.00 |
| 138_V | 176_C | 1.584 | 1.00 |
| 71_K | 77_T | 1.567 | 1.00 |
| 203_S | 207_E | 1.558 | 1.00 |
| 52_P | 178_P | 1.556 | 1.00 |
| 33_K | 77_T | 1.550 | 1.00 |
| 251_D | 254_I | 1.496 | 1.00 |
| 34_I | 80_T | 1.485 | 1.00 |
| 144_K | 149_T | 1.484 | 1.00 |
| 94_N | 97_E | 1.483 | 1.00 |
| 25_I | 49_G | 1.482 | 1.00 |
| 30_E | 47_C | 1.476 | 1.00 |
| 154_C | 158_T | 1.470 | 1.00 |
| 118_R | 153_D | 1.461 | 1.00 |
| 24_D | 27_R | 1.454 | 1.00 |
| 222_E | 243_Q | 1.443 | 1.00 |
| 138_V | 141_W | 1.438 | 1.00 |
| 32_T | 44_D | 1.435 | 1.00 |
| 33_K | 80_T | 1.427 | 1.00 |
| 48_V | 229_A | 1.418 | 1.00 |
| 249_F | 253_Y | 1.412 | 1.00 |
| 136_E | 140_N | 1.399 | 0.99 |
| 85_T | 90_S | 1.387 | 0.99 |
| 25_I | 87_A | 1.360 | 0.99 |
| 118_R | 152_A | 1.351 | 0.99 |
| 50_V | 56_F | 1.351 | 0.99 |
| 24_D | 51_R | 1.351 | 0.99 |
| 232_V | 237_R | 1.341 | 0.99 |
| 116_T | 119_E | 1.317 | 0.99 |
| 237_R | 251_D | 1.311 | 0.99 |
| 204_I | 209_R | 1.283 | 0.99 |
| 54_E | 226_T | 1.280 | 0.99 |
| 23_T | 52_P | 1.280 | 0.99 |
| 75_G | 78_T | 1.272 | 0.99 |
| 31_L | 79_V | 1.263 | 0.99 |
| 122_Y | 135_I | 1.245 | 0.98 |
| 56_F | 227_R | 1.243 | 0.98 |
| 28_L | 73_L | 1.240 | 0.98 |
| 145_S | 207_E | 1.238 | 0.98 |
| 252_G | 255_V | 1.230 | 0.98 |
| 215_S | 221_C | 1.216 | 0.98 |
| 25_I | 52_P | 1.209 | 0.98 |
| 178_P | 209_R | 1.201 | 0.98 |
| 118_R | 136_E | 1.196 | 0.98 |
| 25_I | 51_R | 1.194 | 0.98 |
| 134_E | 138_V | 1.194 | 0.98 |
| 90_S | 93_T | 1.190 | 0.98 |
| 137_K | 141_W | 1.185 | 0.98 |
| 51_R | 227_R | 1.180 | 0.98 |
| 28_L | 48_V | 1.179 | 0.98 |
| 35_Y | 42_A | 1.178 | 0.98 |
| 120_H | 171_I | 1.173 | 0.98 |
| 72_M | 79_V | 1.158 | 0.97 |
| 69_T | 231_M | 1.157 | 0.97 |
| 195_R | 199_N | 1.144 | 0.97 |
| 56_F | 239_M | 1.143 | 0.97 |
| 55_C | 225_C | 1.139 | 0.97 |
| 200_V | 203_S | 1.138 | 0.97 |
| 242_I | 252_G | 1.138 | 0.97 |
| 74_T | 104_Y | 1.133 | 0.97 |
| 117_G | 159_Y | 1.133 | 0.97 |
| 205_I | 226_T | 1.130 | 0.97 |
| 132_A | 136_E | 1.124 | 0.97 |
| 238_C | 248_K | 1.122 | 0.97 |
| 134_E | 137_K | 1.115 | 0.96 |
| 46_L | 69_T | 1.103 | 0.96 |
| 244_H | 248_K | 1.092 | 0.96 |
| 24_D | 49_G | 1.089 | 0.96 |
| 29_H | 49_G | 1.089 | 0.96 |
| 145_S | 203_S | 1.087 | 0.96 |
| 141_W | 144_K | 1.086 | 0.96 |
| 142_S | 170_A | 1.085 | 0.96 |
| 48_V | 69_T | 1.083 | 0.96 |
| 55_C | 213_L | 1.080 | 0.95 |
| 29_H | 47_C | 1.070 | 0.95 |
| 182_L | 211_V | 1.070 | 0.95 |
| 57_G | 221_C | 1.063 | 0.95 |
| 52_P | 87_A | 1.063 | 0.95 |
| 202_V | 205_I | 1.062 | 0.95 |
| 43_V | 72_M | 1.057 | 0.95 |
| 142_S | 174_I | 1.054 | 0.95 |
| 55_C | 205_I | 1.044 | 0.94 |
| 35_Y | 68_T | 1.042 | 0.94 |
| 103_G | 172_A | 1.039 | 0.94 |
| 189_M | 197_L | 1.039 | 0.94 |
| 115_L | 119_E | 1.035 | 0.94 |
| 131_P | 135_I | 1.030 | 0.94 |
| 240_G | 245_L | 1.030 | 0.94 |
| 55_C | 211_V | 1.010 | 0.93 |
| 182_L | 201_I | 1.000 | 0.92 |
| 130_V | 134_E | 1.000 | 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 | |
| 3tuiC | 4 | 0.9151 | 100 | 0.109 | Contact Map |
| 4yerA | 2 | 0.8856 | 100 | 0.117 | Contact Map |
| 1oxxK | 1 | 0.9188 | 100 | 0.119 | Contact Map |
| 2yyzA | 1 | 0.9041 | 100 | 0.121 | Contact Map |
| 1g291 | 2 | 0.9114 | 100 | 0.123 | Contact Map |
| 2it1A | 2 | 0.9077 | 100 | 0.124 | Contact Map |
| 1z47A | 2 | 0.9151 | 100 | 0.125 | Contact Map |
| 1v43A | 1 | 0.8893 | 100 | 0.125 | Contact Map |
| 3rlfA | 2 | 0.9041 | 100 | 0.127 | Contact Map |
| 3fvqA | 2 | 0.9114 | 100 | 0.13 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)