| 3GD8 |
| ID: | 1448272551 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 223 (222) | ||
| Sequences: | 5254 (3147.3) | ||
| Seq/Len: | 23.667 | ||
| Nf(neff/√len): | 211.2 |
HHblits Results: (2015_06)
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: 23.667).
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 |
| 11_F | 97_I | 4.104 | 1.00 |
| 74_V | 81_I | 3.977 | 1.00 |
| 70_T | 84_S | 3.781 | 1.00 |
| 133_L | 212_L | 3.353 | 1.00 |
| 15_L | 101_I | 3.313 | 1.00 |
| 74_V | 84_S | 3.286 | 1.00 |
| 133_L | 208_I | 3.265 | 1.00 |
| 7_V | 90_A | 3.142 | 1.00 |
| 47_G | 167_A | 2.804 | 1.00 |
| 7_V | 86_F | 2.793 | 1.00 |
| 129_L | 205_G | 2.762 | 1.00 |
| 11_F | 93_L | 2.700 | 1.00 |
| 129_L | 133_L | 2.561 | 1.00 |
| 142_T | 165_S | 2.515 | 1.00 |
| 15_L | 98_G | 2.487 | 1.00 |
| 57_F | 65_I | 2.313 | 1.00 |
| 135_I | 173_A | 2.311 | 1.00 |
| 180_S | 186_S | 2.250 | 1.00 |
| 21_S | 46_F | 2.227 | 1.00 |
| 71_V | 207_I | 2.007 | 1.00 |
| 51_A | 163_G | 1.988 | 1.00 |
| 88_I | 207_I | 1.988 | 1.00 |
| 6_A | 83_K | 1.976 | 1.00 |
| 137_F | 213_A | 1.906 | 1.00 |
| 75_C | 211_V | 1.878 | 1.00 |
| 135_I | 181_M | 1.771 | 1.00 |
| 187_F | 191_V | 1.755 | 1.00 |
| 64_H | 87_Y | 1.747 | 1.00 |
| 199_H | 203_W | 1.743 | 1.00 |
| 131_V | 176_Y | 1.705 | 1.00 |
| 3_F | 7_V | 1.703 | 1.00 |
| 71_V | 88_I | 1.691 | 1.00 |
| 53_M | 57_F | 1.689 | 1.00 |
| 90_A | 94_G | 1.676 | 1.00 |
| 170_H | 179_A | 1.662 | 1.00 |
| 13_A | 65_I | 1.636 | 1.00 |
| 50_I | 166_V | 1.633 | 1.00 |
| 207_I | 211_V | 1.594 | 1.00 |
| 169_G | 181_M | 1.592 | 1.00 |
| 209_G | 213_A | 1.562 | 1.00 |
| 187_F | 203_W | 1.541 | 1.00 |
| 44_L | 167_A | 1.467 | 1.00 |
| 186_S | 190_A | 1.455 | 1.00 |
| 69_V | 143_I | 1.448 | 1.00 |
| 170_H | 174_I | 1.446 | 1.00 |
| 81_I | 84_S | 1.431 | 1.00 |
| 100_G | 104_L | 1.428 | 1.00 |
| 14_M | 95_A | 1.427 | 1.00 |
| 84_S | 88_I | 1.426 | 1.00 |
| 70_T | 91_Q | 1.414 | 1.00 |
| 77_R | 218_E | 1.409 | 1.00 |
| 43_S | 171_L | 1.390 | 0.99 |
| 70_T | 88_I | 1.385 | 0.99 |
| 22_L | 102_L | 1.383 | 0.99 |
| 196_W | 199_H | 1.378 | 0.99 |
| 15_L | 97_I | 1.366 | 0.99 |
| 72_A | 76_T | 1.361 | 0.99 |
| 92_C | 187_F | 1.343 | 0.99 |
| 40_V | 44_L | 1.339 | 0.99 |
| 137_F | 216_L | 1.317 | 0.99 |
| 100_G | 192_I | 1.300 | 0.99 |
| 132_E | 177_T | 1.284 | 0.99 |
| 22_L | 99_A | 1.274 | 0.99 |
| 85_V | 89_A | 1.272 | 0.99 |
| 54_V | 159_A | 1.270 | 0.99 |
| 16_I | 53_M | 1.262 | 0.99 |
| 64_H | 70_T | 1.253 | 0.99 |
| 105_V | 131_V | 1.252 | 0.99 |
| 23_G | 102_L | 1.251 | 0.99 |
| 79_I | 84_S | 1.245 | 0.98 |
| 128_G | 177_T | 1.243 | 0.98 |
| 4_W | 7_V | 1.242 | 0.98 |
| 97_I | 100_G | 1.218 | 0.98 |
| 67_P | 184_A | 1.216 | 0.98 |
| 70_T | 79_I | 1.204 | 0.98 |
| 99_A | 189_P | 1.195 | 0.98 |
| 140_V | 210_A | 1.193 | 0.98 |
| 185_R | 189_P | 1.181 | 0.98 |
| 136_T | 210_A | 1.179 | 0.98 |
| 72_A | 214_G | 1.177 | 0.98 |
| 24_S | 45_C | 1.176 | 0.98 |
| 68_A | 183_P | 1.171 | 0.98 |
| 166_V | 181_M | 1.152 | 0.97 |
| 61_S | 87_Y | 1.143 | 0.97 |
| 16_I | 138_Q | 1.135 | 0.97 |
| 13_A | 17_F | 1.133 | 0.97 |
| 187_F | 199_H | 1.132 | 0.97 |
| 96_I | 188_G | 1.126 | 0.97 |
| 81_I | 85_V | 1.126 | 0.97 |
| 74_V | 79_I | 1.118 | 0.96 |
| 49_S | 53_M | 1.117 | 0.96 |
| 57_F | 63_G | 1.111 | 0.96 |
| 96_I | 191_V | 1.096 | 0.96 |
| 51_A | 160_L | 1.090 | 0.96 |
| 139_L | 166_V | 1.085 | 0.96 |
| 95_A | 99_A | 1.070 | 0.95 |
| 19_L | 101_I | 1.064 | 0.95 |
| 205_G | 209_G | 1.061 | 0.95 |
| 105_V | 176_Y | 1.058 | 0.95 |
| 148_D | 217_Y | 1.052 | 0.95 |
| 101_I | 134_I | 1.047 | 0.94 |
| 184_A | 188_G | 1.047 | 0.94 |
| 146_S | 161_A | 1.045 | 0.94 |
| 68_A | 210_A | 1.041 | 0.94 |
| 17_F | 50_I | 1.040 | 0.94 |
| 73_M | 79_I | 1.040 | 0.94 |
| 55_Q | 159_A | 1.039 | 0.94 |
| 20_L | 49_S | 1.036 | 0.94 |
| 71_V | 211_V | 1.035 | 0.94 |
| 72_A | 140_V | 1.033 | 0.94 |
| 48_L | 167_A | 1.029 | 0.94 |
| 131_V | 135_I | 1.020 | 0.93 |
| 99_A | 188_G | 1.018 | 0.93 |
| 51_A | 55_Q | 1.003 | 0.93 |
| 15_L | 19_L | 1.003 | 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 | |
| 3iyzA | 1 | 0.991 | 100 | -0.014 | Contact Map |
| 3gd8A | 1 | 1 | 100 | -0.01 | Contact Map |
| 2zz9A | 1 | 0.991 | 100 | -0.004 | Contact Map |
| 1j4nA | 1 | 1 | 100 | 0 | Contact Map |
| 4oj2X | 1 | 0.9821 | 100 | 0.003 | Contact Map |
| 2b6oA | 1 | 0.9821 | 100 | 0.008 | Contact Map |
| 3d9sA | 4 | 0.9821 | 100 | 0.021 | Contact Map |
| 3c02A | 1 | 0.9865 | 100 | 0.024 | Contact Map |
| 4nefA | 4 | 0.9821 | 100 | 0.024 | Contact Map |
| 3cn5A | 1 | 1 | 100 | 0.024 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)