| d4kqxa1 |
| ID: | 1447473655 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 180 (180) | ||
| Sequences: | 1731 (676.3) | ||
| Seq/Len: | 9.617 | ||
| Nf(neff/√len): | 50.4 |
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: 9.617).
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 |
| 17_V | 38_V | 4.281 | 1.00 |
| 96_K | 99_N | 4.081 | 1.00 |
| 146_D | 171_G | 3.933 | 1.00 |
| 100_T | 123_I | 3.035 | 1.00 |
| 172_A | 176_I | 2.860 | 1.00 |
| 97_A | 119_D | 2.781 | 1.00 |
| 78_V | 86_V | 2.728 | 1.00 |
| 137_Q | 140_E | 2.612 | 1.00 |
| 148_A | 159_W | 2.583 | 1.00 |
| 117_P | 120_V | 2.536 | 1.00 |
| 16_K | 39_D | 2.450 | 1.00 |
| 29_H | 104_A | 2.443 | 1.00 |
| 88_Q | 92_A | 2.430 | 1.00 |
| 52_K | 55_E | 2.368 | 1.00 |
| 85_K | 89_E | 2.344 | 1.00 |
| 7_V | 172_A | 2.087 | 1.00 |
| 102_A | 123_I | 2.047 | 1.00 |
| 34_M | 59_L | 1.977 | 1.00 |
| 100_T | 121_N | 1.866 | 1.00 |
| 100_T | 161_I | 1.828 | 1.00 |
| 46_E | 63_D | 1.809 | 1.00 |
| 76_V | 91_I | 1.809 | 1.00 |
| 153_D | 160_D | 1.784 | 1.00 |
| 65_D | 90_H | 1.772 | 1.00 |
| 62_T | 70_E | 1.761 | 1.00 |
| 133_I | 136_R | 1.756 | 1.00 |
| 22_Y | 57_A | 1.750 | 1.00 |
| 167_W | 172_A | 1.738 | 1.00 |
| 129_G | 171_G | 1.733 | 1.00 |
| 51_W | 55_E | 1.686 | 1.00 |
| 12_I | 164_S | 1.673 | 1.00 |
| 10_K | 13_Q | 1.654 | 1.00 |
| 75_M | 102_A | 1.652 | 1.00 |
| 159_W | 178_K | 1.619 | 1.00 |
| 64_M | 90_H | 1.593 | 1.00 |
| 119_D | 154_A | 1.590 | 1.00 |
| 69_E | 94_H | 1.583 | 1.00 |
| 121_N | 158_A | 1.559 | 1.00 |
| 41_R | 62_T | 1.540 | 1.00 |
| 33_L | 168_G | 1.512 | 1.00 |
| 18_G | 67_A | 1.500 | 1.00 |
| 46_E | 51_W | 1.486 | 1.00 |
| 4_E | 172_A | 1.481 | 1.00 |
| 121_N | 157_N | 1.481 | 1.00 |
| 20_I | 43_G | 1.454 | 1.00 |
| 42_V | 59_L | 1.444 | 1.00 |
| 41_R | 70_E | 1.433 | 1.00 |
| 51_W | 63_D | 1.425 | 1.00 |
| 36_S | 138_F | 1.421 | 0.99 |
| 137_Q | 142_S | 1.388 | 0.99 |
| 29_H | 75_M | 1.378 | 0.99 |
| 75_M | 104_A | 1.374 | 0.99 |
| 68_A | 94_H | 1.352 | 0.99 |
| 16_K | 41_R | 1.350 | 0.99 |
| 74_I | 99_N | 1.343 | 0.99 |
| 44_L | 48_D | 1.305 | 0.99 |
| 16_K | 70_E | 1.302 | 0.99 |
| 52_K | 56_E | 1.300 | 0.99 |
| 9_P | 167_W | 1.283 | 0.99 |
| 27_H | 132_H | 1.262 | 0.99 |
| 107_F | 113_Y | 1.260 | 0.99 |
| 7_V | 176_I | 1.258 | 0.98 |
| 134_V | 144_V | 1.255 | 0.98 |
| 2_L | 159_W | 1.254 | 0.98 |
| 55_E | 60_K | 1.250 | 0.98 |
| 157_N | 160_D | 1.246 | 0.98 |
| 129_G | 144_V | 1.229 | 0.98 |
| 60_K | 70_E | 1.217 | 0.98 |
| 84_P | 88_Q | 1.209 | 0.98 |
| 123_I | 158_A | 1.207 | 0.98 |
| 20_I | 76_V | 1.202 | 0.98 |
| 68_A | 99_N | 1.189 | 0.98 |
| 20_I | 78_V | 1.168 | 0.97 |
| 45_R | 49_S | 1.163 | 0.97 |
| 63_D | 66_T | 1.159 | 0.97 |
| 63_D | 68_A | 1.156 | 0.97 |
| 83_Q | 108_N | 1.148 | 0.97 |
| 48_D | 51_W | 1.144 | 0.97 |
| 65_D | 94_H | 1.143 | 0.97 |
| 121_N | 154_A | 1.138 | 0.97 |
| 7_V | 167_W | 1.110 | 0.96 |
| 112_G | 115_V | 1.100 | 0.96 |
| 100_T | 155_T | 1.055 | 0.94 |
| 48_D | 59_L | 1.040 | 0.94 |
| 116_P | 119_D | 1.029 | 0.93 |
| 129_G | 146_D | 1.027 | 0.93 |
| 87_Y | 101_L | 1.014 | 0.93 |
| 159_W | 163_L | 1.011 | 0.92 |
| 148_A | 162_V | 1.006 | 0.92 |
| 166_C | 176_I | 1.002 | 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 | |
| 4xdyA | 2 | 0 | 100 | 0.53 | Contact Map |
| 4xdzA | 2 | 0 | 100 | 0.532 | Contact Map |
| 4tskA | 1 | 0.9944 | 100 | 0.544 | Contact Map |
| 3ulkA | 2 | 0.9833 | 100 | 0.579 | Contact Map |
| 1np3A | 4 | 1 | 100 | 0.597 | Contact Map |
| 3fr7A | 2 | 0.9833 | 100 | 0.616 | Contact Map |
| 4kqwA | 2 | 1 | 100 | 0.624 | Contact Map |
| 4yt2A | 2 | 0 | 99.6 | 0.796 | Contact Map |
| 3triA | 2 | 0.8722 | 99.2 | 0.835 | Contact Map |
| 2izzA | 5 | 0.8833 | 99.1 | 0.84 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)