| ABCA4_1936_2273 |
| ID: | 1492901016 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 338 (303) | ||
| Sequences: | 34589 (23372.7) | ||
| Seq/Len: | 114.155 | ||
| Nf(neff/√len): | 1342.7 |
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: 114.155).
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 |
| 7_E | 22_R | 3.544 | 1.00 |
| 18_P | 21_D | 3.495 | 1.00 |
| 31_E | 204_R | 3.342 | 1.00 |
| 217_G | 221_H | 3.035 | 1.00 |
| 199_E | 220_Q | 2.912 | 1.00 |
| 4_R | 26_G | 2.839 | 1.00 |
| 6_H | 60_D | 2.833 | 1.00 |
| 128_Y | 131_C | 2.829 | 1.00 |
| 5_L | 8_L | 2.702 | 1.00 |
| 94_G | 136_Y | 2.693 | 1.00 |
| 33_F | 206_A | 2.582 | 1.00 |
| 11_I | 18_P | 2.410 | 1.00 |
| 34_G | 202_C | 2.387 | 1.00 |
| 10_K | 49_M | 2.355 | 1.00 |
| 21_D | 212_A | 2.339 | 1.00 |
| 4_R | 62_T | 2.316 | 1.00 |
| 78_N | 155_P | 2.308 | 1.00 |
| 9_T | 58_S | 2.257 | 1.00 |
| 28_R | 31_E | 2.206 | 1.00 |
| 192_S | 198_C | 2.168 | 1.00 |
| 9_T | 22_R | 2.096 | 1.00 |
| 29_P | 155_P | 2.080 | 1.00 |
| 60_D | 67_S | 2.031 | 1.00 |
| 181_I | 186_R | 2.030 | 1.00 |
| 95_R | 129_A | 2.028 | 1.00 |
| 47_F | 191_T | 2.002 | 1.00 |
| 121_K | 126_T | 2.001 | 1.00 |
| 8_L | 56_V | 1.986 | 1.00 |
| 179_V | 200_A | 1.964 | 1.00 |
| 95_R | 130_D | 1.941 | 1.00 |
| 108_P | 111_E | 1.930 | 1.00 |
| 131_C | 135_T | 1.927 | 1.00 |
| 10_K | 57_T | 1.894 | 1.00 |
| 9_T | 18_P | 1.888 | 1.00 |
| 95_R | 99_Y | 1.882 | 1.00 |
| 218_T | 221_H | 1.840 | 1.00 |
| 7_E | 24_C | 1.829 | 1.00 |
| 47_F | 158_L | 1.812 | 1.00 |
| 204_R | 216_M | 1.791 | 1.00 |
| 5_L | 25_V | 1.759 | 1.00 |
| 206_A | 213_F | 1.754 | 1.00 |
| 115_V | 118_W | 1.712 | 1.00 |
| 20_V | 49_M | 1.645 | 1.00 |
| 91_L | 134_G | 1.627 | 1.00 |
| 71_N | 74_E | 1.623 | 1.00 |
| 10_K | 54_T | 1.622 | 1.00 |
| 27_V | 33_F | 1.586 | 1.00 |
| 6_H | 62_T | 1.578 | 1.00 |
| 153_C | 186_R | 1.553 | 1.00 |
| 133_A | 144_L | 1.543 | 1.00 |
| 48_K | 53_D | 1.541 | 1.00 |
| 120_I | 129_A | 1.522 | 1.00 |
| 49_M | 56_V | 1.517 | 1.00 |
| 117_N | 129_A | 1.501 | 1.00 |
| 34_G | 198_C | 1.491 | 1.00 |
| 11_I | 57_T | 1.477 | 1.00 |
| 221_H | 225_K | 1.474 | 1.00 |
| 25_V | 206_A | 1.450 | 1.00 |
| 123_L | 147_A | 1.434 | 1.00 |
| 9_T | 21_D | 1.431 | 1.00 |
| 93_T | 96_E | 1.426 | 1.00 |
| 119_S | 147_A | 1.423 | 1.00 |
| 67_S | 70_T | 1.411 | 1.00 |
| 221_H | 224_S | 1.404 | 0.99 |
| 180_S | 184_E | 1.380 | 0.99 |
| 48_K | 54_T | 1.372 | 0.99 |
| 115_V | 153_C | 1.367 | 0.99 |
| 92_L | 97_H | 1.339 | 0.99 |
| 31_E | 203_T | 1.311 | 0.99 |
| 114_K | 118_W | 1.296 | 0.99 |
| 269_N | 275_V | 1.295 | 0.99 |
| 6_H | 24_C | 1.295 | 0.99 |
| 111_E | 114_K | 1.288 | 0.99 |
| 95_R | 117_N | 1.276 | 0.99 |
| 97_H | 148_I | 1.267 | 0.99 |
| 66_K | 71_N | 1.263 | 0.99 |
| 284_F | 287_L | 1.263 | 0.99 |
| 97_H | 133_A | 1.258 | 0.99 |
| 84_Q | 138_G | 1.258 | 0.99 |
| 122_S | 180_S | 1.244 | 0.98 |
| 80_G | 149_A | 1.241 | 0.98 |
| 175_W | 200_A | 1.238 | 0.98 |
| 190_L | 202_C | 1.225 | 0.98 |
| 254_F | 258_F | 1.221 | 0.98 |
| 33_F | 189_V | 1.219 | 0.98 |
| 5_L | 50_L | 1.218 | 0.98 |
| 6_H | 26_G | 1.186 | 0.98 |
| 74_E | 77_Q | 1.182 | 0.98 |
| 132_L | 135_T | 1.172 | 0.98 |
| 51_T | 158_L | 1.168 | 0.97 |
| 118_W | 122_S | 1.163 | 0.97 |
| 273_F | 276_S | 1.157 | 0.97 |
| 64_A | 78_N | 1.153 | 0.97 |
| 202_C | 205_L | 1.150 | 0.97 |
| 82_C | 149_A | 1.148 | 0.97 |
| 5_L | 61_A | 1.139 | 0.97 |
| 99_Y | 116_A | 1.136 | 0.97 |
| 270_M | 274_Q | 1.133 | 0.97 |
| 285_Q | 288_L | 1.130 | 0.97 |
| 158_L | 189_V | 1.128 | 0.97 |
| 80_G | 154_P | 1.118 | 0.96 |
| 7_E | 58_S | 1.117 | 0.96 |
| 49_M | 61_A | 1.116 | 0.96 |
| 35_L | 189_V | 1.116 | 0.96 |
| 253_F | 257_N | 1.114 | 0.96 |
| 99_Y | 113_E | 1.112 | 0.96 |
| 117_N | 121_K | 1.105 | 0.96 |
| 12_Y | 19_A | 1.103 | 0.96 |
| 126_T | 129_A | 1.100 | 0.96 |
| 90_E | 134_G | 1.099 | 0.96 |
| 207_I | 222_L | 1.095 | 0.96 |
| 281_A | 284_F | 1.094 | 0.96 |
| 249_P | 252_Q | 1.093 | 0.96 |
| 265_E | 269_N | 1.091 | 0.96 |
| 89_D | 92_L | 1.090 | 0.96 |
| 96_E | 99_Y | 1.089 | 0.96 |
| 281_A | 285_Q | 1.079 | 0.95 |
| 95_R | 116_A | 1.071 | 0.95 |
| 268_Y | 271_L | 1.071 | 0.95 |
| 111_E | 115_V | 1.069 | 0.95 |
| 136_Y | 144_L | 1.068 | 0.95 |
| 268_Y | 272_Q | 1.064 | 0.95 |
| 92_L | 100_L | 1.062 | 0.95 |
| 284_F | 288_L | 1.060 | 0.95 |
| 205_L | 219_I | 1.052 | 0.95 |
| 257_N | 260_G | 1.051 | 0.94 |
| 207_I | 226_F | 1.050 | 0.94 |
| 119_S | 123_L | 1.045 | 0.94 |
| 33_F | 216_M | 1.043 | 0.94 |
| 266_R | 273_F | 1.038 | 0.94 |
| 288_L | 291_K | 1.036 | 0.94 |
| 13_P | 16_S | 1.036 | 0.94 |
| 265_E | 268_Y | 1.036 | 0.94 |
| 66_K | 74_E | 1.034 | 0.94 |
| 109_A | 112_I | 1.033 | 0.94 |
| 258_F | 261_S | 1.025 | 0.93 |
| 56_V | 69_L | 1.021 | 0.93 |
| 64_A | 155_P | 1.011 | 0.93 |
| 166_M | 174_L | 1.011 | 0.93 |
| 113_E | 117_N | 1.009 | 0.93 |
| 284_F | 291_K | 1.004 | 0.93 |
| 272_Q | 275_V | 1.001 | 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 | |
| 4yerA | 2 | 0.8284 | 100 | 0.205 | Contact Map |
| 3tuiC | 4 | 0.9822 | 100 | 0.252 | Contact Map |
| 4rvcA | 1 | 0.7071 | 100 | 0.261 | Contact Map |
| 1vplA | 1 | 0.7041 | 100 | 0.266 | Contact Map |
| 4ymuJ | 2 | 0 | 100 | 0.267 | Contact Map |
| 4u00A | 1 | 0 | 100 | 0.267 | Contact Map |
| 2oljA | 2 | 0.7012 | 100 | 0.268 | Contact Map |
| 1b0uA | 1 | 0.716 | 100 | 0.271 | Contact Map |
| 4mkiB | 2 | 0.8047 | 100 | 0.273 | Contact Map |
| 4f4cA | 1 | 0.6598 | 100 | 0.275 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)