| OPSD_BOVIN |
| ID: | 1430408111 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 253 (253) | ||
| Sequences: | 11887 (8055.1) | ||
| Seq/Len: | 46.984 | ||
| Nf(neff/√len): | 506.4 |
HHblits Results: (2013_03)
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: 46.984).
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 |
| 25_N | 108_W | 3.917 | 1.00 |
| 168_F | 172_Q | 3.177 | 1.00 |
| 25_N | 74_S | 3.061 | 1.00 |
| 77_V | 107_T | 2.578 | 1.00 |
| 83_Y | 88_K | 2.460 | 1.00 |
| 54_P | 58_N | 2.448 | 1.00 |
| 55_T | 59_L | 2.428 | 1.00 |
| 77_V | 103_G | 2.345 | 1.00 |
| 15_L | 20_N | 2.179 | 1.00 |
| 98_N | 102_M | 2.097 | 1.00 |
| 38_F | 41_T | 2.050 | 1.00 |
| 50_F | 53_G | 2.047 | 1.00 |
| 207_A | 252_I | 2.009 | 1.00 |
| 171_G | 175_F | 2.004 | 1.00 |
| 57_C | 134_C | 2.003 | 1.00 |
| 212_W | 242_A | 1.956 | 1.00 |
| 3_F | 7_Y | 1.951 | 1.00 |
| 172_Q | 175_F | 1.942 | 1.00 |
| 83_Y | 87_C | 1.942 | 1.00 |
| 62_F | 66_L | 1.915 | 1.00 |
| 21_Y | 104_V | 1.905 | 1.00 |
| 83_Y | 172_Q | 1.890 | 1.00 |
| 165_V | 169_C | 1.886 | 1.00 |
| 9_T | 24_L | 1.807 | 1.00 |
| 217_G | 221_Y | 1.788 | 1.00 |
| 170_Y | 173_L | 1.733 | 1.00 |
| 74_S | 104_V | 1.730 | 1.00 |
| 103_G | 107_T | 1.684 | 1.00 |
| 6_L | 24_L | 1.665 | 1.00 |
| 96_G | 99_H | 1.650 | 1.00 |
| 75_L | 166_I | 1.646 | 1.00 |
| 225_H | 228_S | 1.629 | 1.00 |
| 81_E | 85_V | 1.627 | 1.00 |
| 101_I | 105_A | 1.609 | 1.00 |
| 29_A | 70_I | 1.584 | 1.00 |
| 102_M | 106_F | 1.580 | 1.00 |
| 24_L | 28_V | 1.576 | 1.00 |
| 70_I | 111_A | 1.571 | 1.00 |
| 32_F | 67_G | 1.564 | 1.00 |
| 37_G | 41_T | 1.520 | 1.00 |
| 167_F | 171_G | 1.519 | 1.00 |
| 76_V | 169_C | 1.503 | 1.00 |
| 25_N | 104_V | 1.498 | 1.00 |
| 27_A | 30_D | 1.495 | 1.00 |
| 3_F | 31_L | 1.491 | 1.00 |
| 5_T | 9_T | 1.488 | 1.00 |
| 91_S | 94_R | 1.480 | 1.00 |
| 1_I | 247_V | 1.468 | 1.00 |
| 17_T | 20_N | 1.467 | 1.00 |
| 66_L | 112_L | 1.463 | 1.00 |
| 83_Y | 169_C | 1.447 | 1.00 |
| 87_C | 176_T | 1.438 | 1.00 |
| 74_S | 108_W | 1.429 | 1.00 |
| 30_D | 71_A | 1.428 | 1.00 |
| 98_N | 101_I | 1.397 | 0.99 |
| 172_Q | 176_T | 1.390 | 0.99 |
| 22_I | 78_L | 1.363 | 0.99 |
| 153_Y | 157_V | 1.353 | 0.99 |
| 97_E | 101_I | 1.352 | 0.99 |
| 166_I | 170_Y | 1.335 | 0.99 |
| 30_D | 249_N | 1.325 | 0.99 |
| 29_A | 71_A | 1.310 | 0.99 |
| 213_L | 217_G | 1.287 | 0.99 |
| 244_T | 248_Y | 1.282 | 0.99 |
| 36_G | 39_T | 1.280 | 0.99 |
| 80_I | 169_C | 1.274 | 0.99 |
| 244_T | 247_V | 1.268 | 0.99 |
| 84_V | 88_K | 1.262 | 0.99 |
| 13_K | 16_R | 1.256 | 0.99 |
| 62_F | 119_L | 1.247 | 0.99 |
| 163_L | 209_L | 1.245 | 0.98 |
| 209_L | 213_L | 1.245 | 0.98 |
| 118_P | 121_G | 1.238 | 0.98 |
| 6_L | 10_V | 1.234 | 0.98 |
| 200_M | 203_I | 1.232 | 0.98 |
| 70_I | 74_S | 1.225 | 0.98 |
| 155_F | 160_I | 1.214 | 0.98 |
| 6_L | 31_L | 1.214 | 0.98 |
| 197_V | 200_M | 1.213 | 0.98 |
| 180_A | 184_Q | 1.211 | 0.98 |
| 6_L | 27_A | 1.203 | 0.98 |
| 21_Y | 101_I | 1.198 | 0.98 |
| 73_W | 111_A | 1.189 | 0.98 |
| 88_K | 91_S | 1.188 | 0.98 |
| 195_K | 199_R | 1.172 | 0.98 |
| 66_L | 115_A | 1.172 | 0.98 |
| 76_V | 165_V | 1.168 | 0.97 |
| 22_I | 100_A | 1.165 | 0.97 |
| 122_W | 125_Y | 1.161 | 0.97 |
| 9_T | 15_L | 1.160 | 0.97 |
| 29_A | 108_W | 1.158 | 0.97 |
| 159_F | 213_L | 1.157 | 0.97 |
| 85_V | 89_P | 1.154 | 0.97 |
| 62_F | 112_L | 1.153 | 0.97 |
| 202_I | 206_I | 1.150 | 0.97 |
| 20_N | 23_L | 1.150 | 0.97 |
| 6_L | 28_V | 1.147 | 0.97 |
| 249_N | 253_Y | 1.146 | 0.97 |
| 37_G | 40_T | 1.145 | 0.97 |
| 174_V | 178_K | 1.140 | 0.97 |
| 106_F | 110_M | 1.136 | 0.97 |
| 39_T | 42_L | 1.127 | 0.97 |
| 10_V | 24_L | 1.127 | 0.97 |
| 79_A | 170_Y | 1.124 | 0.97 |
| 83_Y | 168_F | 1.123 | 0.97 |
| 65_T | 115_A | 1.110 | 0.96 |
| 175_F | 179_E | 1.103 | 0.96 |
| 38_F | 42_L | 1.102 | 0.96 |
| 73_W | 110_M | 1.100 | 0.96 |
| 26_L | 74_S | 1.085 | 0.96 |
| 174_V | 177_V | 1.082 | 0.96 |
| 7_Y | 11_Q | 1.074 | 0.95 |
| 76_V | 162_P | 1.074 | 0.95 |
| 33_M | 246_A | 1.070 | 0.95 |
| 6_L | 9_T | 1.069 | 0.95 |
| 4_L | 8_V | 1.069 | 0.95 |
| 9_T | 16_R | 1.067 | 0.95 |
| 231_G | 234_F | 1.064 | 0.95 |
| 203_I | 252_I | 1.062 | 0.95 |
| 108_W | 250_P | 1.060 | 0.95 |
| 18_P | 100_A | 1.060 | 0.95 |
| 215_Y | 219_A | 1.046 | 0.94 |
| 39_T | 43_Y | 1.041 | 0.94 |
| 116_A | 120_V | 1.035 | 0.94 |
| 73_W | 76_V | 1.032 | 0.94 |
| 72_L | 208_F | 1.031 | 0.94 |
| 69_E | 216_A | 1.018 | 0.93 |
| 78_L | 81_E | 1.017 | 0.93 |
| 218_V | 238_P | 1.017 | 0.93 |
| 5_T | 250_P | 1.014 | 0.93 |
| 166_I | 205_V | 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
- 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 | |
| 2rh1A | 1 | 0.9921 | 100 | 0.101 | Contact Map |
| 2z73A | 2 | 0.9921 | 100 | 0.111 | Contact Map |
| 4pxzA | 1 | 0.9644 | 100 | 0.117 | Contact Map |
| 3uonA | 1 | 0.9723 | 100 | 0.129 | Contact Map |
| 1u19A | 2 | 1 | 100 | 0.135 | Contact Map |
| 4dklA | 1 | 0.9881 | 100 | 0.139 | Contact Map |
| 3pblA | 2 | 0.9526 | 100 | 0.14 | Contact Map |
| 4u15A | 2 | 0.9723 | 100 | 0.146 | Contact Map |
| 4phuA | 1 | 0.9447 | 100 | 0.147 | Contact Map |
| 4iarA | 1 | 0.9289 | 100 | 0.147 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)