| 4nt9A |
| ID: | 1491921468 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 184 (165) | ||
| Sequences: | 1317 (1055.7) | ||
| Seq/Len: | 7.982 | ||
| Nf(neff/√len): | 82.2 |
HHblits Results: (2016_02)
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: 7.982).
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 |
| 128_H | 131_D | 5.818 | 1.00 |
| 136_V | 155_L | 3.950 | 1.00 |
| 76_Y | 89_D | 2.814 | 1.00 |
| 51_A | 132_Y | 2.665 | 1.00 |
| 69_Y | 101_Q | 2.564 | 1.00 |
| 130_A | 166_A | 2.554 | 1.00 |
| 45_L | 49_I | 2.519 | 1.00 |
| 73_T | 77_Q | 2.423 | 1.00 |
| 135_V | 165_I | 2.396 | 1.00 |
| 164_E | 168_S | 2.242 | 1.00 |
| 158_V | 165_I | 2.187 | 1.00 |
| 85_K | 89_D | 2.179 | 1.00 |
| 89_D | 94_R | 2.134 | 1.00 |
| 83_D | 91_Y | 2.043 | 1.00 |
| 163_K | 167_A | 2.001 | 1.00 |
| 142_K | 174_E | 1.954 | 1.00 |
| 108_V | 155_L | 1.949 | 1.00 |
| 87_A | 90_R | 1.798 | 1.00 |
| 79_Y | 92_S | 1.758 | 1.00 |
| 57_F | 121_A | 1.689 | 1.00 |
| 125_L | 155_L | 1.622 | 1.00 |
| 122_A | 126_L | 1.604 | 1.00 |
| 91_Y | 149_M | 1.599 | 1.00 |
| 34_N | 66_F | 1.592 | 1.00 |
| 145_E | 174_E | 1.584 | 1.00 |
| 75_L | 79_Y | 1.582 | 1.00 |
| 76_Y | 85_K | 1.492 | 0.99 |
| 51_A | 55_A | 1.490 | 0.99 |
| 62_H | 106_F | 1.480 | 0.99 |
| 42_K | 46_V | 1.467 | 0.99 |
| 65_G | 106_F | 1.420 | 0.99 |
| 160_K | 163_K | 1.406 | 0.99 |
| 158_V | 168_S | 1.402 | 0.99 |
| 136_V | 150_A | 1.370 | 0.99 |
| 151_E | 154_H | 1.361 | 0.99 |
| 100_H | 151_E | 1.356 | 0.99 |
| 45_L | 106_F | 1.343 | 0.99 |
| 80_V | 88_A | 1.340 | 0.99 |
| 137_R | 173_E | 1.338 | 0.99 |
| 139_L | 150_A | 1.337 | 0.99 |
| 79_Y | 91_Y | 1.327 | 0.99 |
| 83_D | 87_A | 1.325 | 0.99 |
| 76_Y | 80_V | 1.306 | 0.98 |
| 25_K | 148_Y | 1.283 | 0.98 |
| 124_W | 128_H | 1.283 | 0.98 |
| 107_D | 154_H | 1.271 | 0.98 |
| 47_K | 160_K | 1.262 | 0.98 |
| 110_G | 121_A | 1.258 | 0.98 |
| 64_S | 67_R | 1.248 | 0.98 |
| 67_R | 72_Q | 1.237 | 0.97 |
| 67_R | 100_H | 1.225 | 0.97 |
| 41_A | 44_E | 1.219 | 0.97 |
| 64_S | 100_H | 1.212 | 0.97 |
| 23_A | 102_T | 1.196 | 0.97 |
| 100_H | 107_D | 1.194 | 0.97 |
| 79_Y | 88_A | 1.193 | 0.97 |
| 116_V | 119_E | 1.190 | 0.97 |
| 158_V | 172_L | 1.187 | 0.96 |
| 67_R | 151_E | 1.185 | 0.96 |
| 104_L | 137_R | 1.178 | 0.96 |
| 145_E | 171_S | 1.175 | 0.96 |
| 74_K | 78_D | 1.174 | 0.96 |
| 71_T | 74_K | 1.174 | 0.96 |
| 28_P | 97_Y | 1.173 | 0.96 |
| 100_H | 154_H | 1.164 | 0.96 |
| 93_A | 148_Y | 1.139 | 0.95 |
| 22_V | 27_Y | 1.139 | 0.95 |
| 48_L | 57_F | 1.126 | 0.95 |
| 79_Y | 83_D | 1.114 | 0.94 |
| 122_A | 150_A | 1.109 | 0.94 |
| 46_V | 49_I | 1.096 | 0.94 |
| 136_V | 139_L | 1.093 | 0.94 |
| 162_A | 165_I | 1.084 | 0.93 |
| 67_R | 98_S | 1.079 | 0.93 |
| 72_Q | 98_S | 1.070 | 0.93 |
| 63_Y | 109_I | 1.066 | 0.93 |
| 48_L | 155_L | 1.064 | 0.92 |
| 142_K | 145_E | 1.037 | 0.91 |
| 123_Q | 127_D | 1.031 | 0.91 |
| 126_L | 155_L | 1.029 | 0.91 |
| 94_R | 97_Y | 1.029 | 0.91 |
| 43_A | 47_K | 1.017 | 0.90 |
| 165_I | 170_L | 1.013 | 0.90 |
| 67_R | 153_W | 1.011 | 0.90 |
| 68_S | 96_G | 1.009 | 0.90 |
| 20_I | 176_Y | 1.008 | 0.89 |
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 | |
| 4nt9B | 3 | 1 | 100 | 0.164 | Contact Map |
| 4ox3A | 1 | 0.9837 | 100 | 0.22 | Contact Map |
| 4mphA | 2 | 0.8696 | 100 | 0.229 | Contact Map |
| 4muqA | 1 | 0.962 | 100 | 0.254 | Contact Map |
| 4murA | 2 | 0.9022 | 100 | 0.256 | Contact Map |
| 1r44A | 6 | 0.8804 | 99.9 | 0.593 | Contact Map |
| 2vo9A | 3 | 0.7609 | 99.7 | 0.704 | Contact Map |
| 2mxzA | 1 | 0.663 | 99 | 0.801 | Contact Map |
| 3n1gB | 2 | 0.6467 | 95 | 0.899 | Contact Map |
| 2ibgE | 4 | 0.6087 | 92.2 | 0.91 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)