| ABCA4_1166_1372 INT |
| ID: | 1491679541 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 207 (193) | ||
| Sequences: | 1230 (945.6) | ||
| Seq/Len: | 6.373 | ||
| Nf(neff/√len): | 68.1 |
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: 6.373).
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 |
| 15_S | 18_G | 3.734 | 1.00 |
| 44_M | 66_F | 3.270 | 1.00 |
| 88_T | 91_D | 2.986 | 1.00 |
| 13_S | 16_S | 2.756 | 1.00 |
| 86_E | 97_F | 2.625 | 1.00 |
| 20_S | 28_D | 2.336 | 1.00 |
| 20_S | 27_V | 2.203 | 1.00 |
| 20_S | 25_A | 2.186 | 1.00 |
| 182_G | 185_L | 2.122 | 1.00 |
| 25_A | 28_D | 2.111 | 1.00 |
| 47_V | 54_A | 1.961 | 1.00 |
| 24_P | 27_V | 1.886 | 1.00 |
| 21_T | 27_V | 1.877 | 1.00 |
| 21_T | 28_D | 1.875 | 1.00 |
| 20_S | 24_P | 1.784 | 1.00 |
| 21_T | 25_A | 1.717 | 1.00 |
| 13_S | 18_G | 1.681 | 1.00 |
| 21_T | 24_P | 1.641 | 1.00 |
| 19_F | 28_D | 1.631 | 1.00 |
| 50_H | 84_E | 1.579 | 0.99 |
| 24_P | 28_D | 1.500 | 0.99 |
| 19_F | 24_P | 1.477 | 0.99 |
| 19_F | 27_V | 1.465 | 0.99 |
| 89_L | 94_L | 1.458 | 0.99 |
| 43_L | 64_L | 1.447 | 0.99 |
| 19_F | 25_A | 1.429 | 0.99 |
| 102_T | 109_L | 1.413 | 0.99 |
| 17_K | 21_T | 1.299 | 0.97 |
| 111_V | 196_K | 1.279 | 0.97 |
| 144_K | 147_Q | 1.271 | 0.97 |
| 133_N | 136_H | 1.255 | 0.96 |
| 103_P | 107_I | 1.243 | 0.96 |
| 58_E | 101_D | 1.240 | 0.96 |
| 19_F | 22_T | 1.208 | 0.95 |
| 166_G | 170_P | 1.194 | 0.95 |
| 82_F | 102_T | 1.188 | 0.95 |
| 31_T | 34_Q | 1.185 | 0.94 |
| 151_D | 155_C | 1.171 | 0.94 |
| 13_S | 17_K | 1.166 | 0.94 |
| 32_P | 104_L | 1.155 | 0.93 |
| 98_G | 102_T | 1.153 | 0.93 |
| 82_F | 99_I | 1.152 | 0.93 |
| 15_S | 28_D | 1.152 | 0.93 |
| 198_F | 202_I | 1.150 | 0.93 |
| 38_G | 43_L | 1.140 | 0.93 |
| 34_Q | 59_C | 1.135 | 0.93 |
| 14_C | 28_D | 1.131 | 0.92 |
| 17_K | 104_L | 1.123 | 0.92 |
| 30_L | 34_Q | 1.120 | 0.92 |
| 86_E | 98_G | 1.111 | 0.92 |
| 57_V | 104_L | 1.103 | 0.91 |
| 15_S | 19_F | 1.103 | 0.91 |
| 63_E | 105_E | 1.086 | 0.90 |
| 143_E | 147_Q | 1.086 | 0.90 |
| 180_N | 188_Q | 1.078 | 0.90 |
| 15_S | 20_S | 1.073 | 0.90 |
| 40_V | 204_S | 1.072 | 0.90 |
| 128_K | 131_N | 1.072 | 0.90 |
| 16_S | 19_F | 1.071 | 0.90 |
| 150_Q | 153_N | 1.070 | 0.89 |
| 77_A | 80_S | 1.069 | 0.89 |
| 54_A | 68_L | 1.065 | 0.89 |
| 129_R | 135_R | 1.064 | 0.89 |
| 63_E | 98_G | 1.064 | 0.89 |
| 157_P | 160_P | 1.062 | 0.89 |
| 137_P | 140_G | 1.060 | 0.89 |
| 18_G | 21_T | 1.052 | 0.88 |
| 132_V | 137_P | 1.050 | 0.88 |
| 112_T | 197_R | 1.049 | 0.88 |
| 62_Q | 82_F | 1.046 | 0.88 |
| 196_K | 203_R | 1.045 | 0.88 |
| 138_C | 141_P | 1.040 | 0.88 |
| 172_P | 175_P | 1.034 | 0.87 |
| 101_D | 196_K | 1.033 | 0.87 |
| 141_P | 144_K | 1.030 | 0.87 |
| 193_L | 197_R | 1.025 | 0.87 |
| 136_H | 139_L | 1.024 | 0.87 |
| 14_C | 20_S | 1.012 | 0.86 |
| 142_R | 145_A | 1.011 | 0.86 |
| 16_S | 27_V | 1.009 | 0.85 |
| 161_A | 165_E | 1.007 | 0.85 |
| 139_L | 142_R | 1.006 | 0.85 |
| 78_Y | 82_F | 1.006 | 0.85 |
| 68_L | 93_G | 1.006 | 0.85 |
| 195_V | 199_Q | 1.004 | 0.85 |
| 17_K | 25_A | 1.002 | 0.85 |
| 155_C | 159_A | 1.001 | 0.85 |
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 | 0.3913 | 86.4 | 0.911 | Contact Map |
| 3kz5E | 3 | 0.2222 | 11.5 | 0.951 | Contact Map |
| 3qycA | 2 | 0.1691 | 8.6 | 0.954 | Contact Map |
| 1eyhA | 1 | 0.285 | 6.6 | 0.956 | Contact Map |
| 2jzyA | 1 | 0.1546 | 6.5 | 0.956 | Contact Map |
| 1y66A | 4 | 0.2415 | 6.2 | 0.957 | Contact Map |
| 4ixaA | 2 | 0.1546 | 5.9 | 0.957 | Contact Map |
| 2zxjA | 2 | 0.1498 | 5.8 | 0.957 | Contact Map |
| 2m1bA | 1 | 0.2029 | 5.5 | 0.958 | Contact Map |
| 3g5oA | 2 | 0.3913 | 5 | 0.959 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)