| cd81 |
| ID: | 1443710476 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 165 (161) | ||
| Sequences: | 2775 (1834.9) | ||
| Seq/Len: | 17.236 | ||
| Nf(neff/√len): | 144.6 |
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: 17.236).
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 |
| 100_K | 103_L | 5.019 | 1.00 |
| 136_I | 140_V | 4.072 | 1.00 |
| 34_E | 145_M | 3.200 | 1.00 |
| 18_C | 22_T | 2.990 | 1.00 |
| 117_E | 122_K | 2.889 | 1.00 |
| 42_F | 135_G | 2.824 | 1.00 |
| 36_A | 40_W | 2.762 | 1.00 |
| 77_K | 80_H | 2.616 | 1.00 |
| 80_H | 94_L | 2.309 | 1.00 |
| 24_F | 149_M | 1.976 | 1.00 |
| 21_G | 25_T | 1.860 | 1.00 |
| 87_G | 93_A | 1.807 | 1.00 |
| 80_H | 102_N | 1.790 | 1.00 |
| 28_V | 149_M | 1.684 | 1.00 |
| 149_M | 153_M | 1.679 | 1.00 |
| 99_L | 103_L | 1.674 | 1.00 |
| 76_V | 88_S | 1.662 | 1.00 |
| 17_Q | 21_G | 1.641 | 1.00 |
| 100_K | 105_P | 1.621 | 1.00 |
| 152_S | 155_L | 1.576 | 1.00 |
| 153_M | 157_C | 1.555 | 1.00 |
| 133_L | 137_A | 1.553 | 1.00 |
| 40_W | 44_N | 1.525 | 1.00 |
| 7_L | 22_T | 1.513 | 1.00 |
| 8_G | 11_G | 1.496 | 1.00 |
| 39_I | 43_V | 1.465 | 1.00 |
| 24_F | 156_C | 1.456 | 1.00 |
| 76_V | 80_H | 1.453 | 1.00 |
| 148_E | 152_S | 1.438 | 1.00 |
| 99_L | 102_N | 1.406 | 0.99 |
| 148_E | 155_L | 1.395 | 0.99 |
| 21_G | 156_C | 1.378 | 0.99 |
| 6_F | 10_Y | 1.370 | 0.99 |
| 99_L | 105_P | 1.353 | 0.99 |
| 132_Y | 136_I | 1.341 | 0.99 |
| 88_S | 120_H | 1.337 | 0.99 |
| 17_Q | 20_L | 1.323 | 0.99 |
| 37_A | 41_G | 1.306 | 0.99 |
| 38_G | 142_A | 1.279 | 0.99 |
| 10_Y | 19_L | 1.269 | 0.99 |
| 11_G | 19_L | 1.268 | 0.99 |
| 24_F | 28_V | 1.259 | 0.99 |
| 6_F | 9_C | 1.220 | 0.98 |
| 120_H | 124_D | 1.206 | 0.98 |
| 131_L | 134_I | 1.199 | 0.98 |
| 84_D | 115_F | 1.165 | 0.97 |
| 65_V | 73_K | 1.155 | 0.97 |
| 9_C | 15_E | 1.139 | 0.97 |
| 27_L | 34_E | 1.137 | 0.97 |
| 24_F | 153_M | 1.135 | 0.97 |
| 95_T | 99_L | 1.133 | 0.97 |
| 78_T | 82_T | 1.127 | 0.97 |
| 60_L | 76_V | 1.123 | 0.97 |
| 142_A | 148_E | 1.116 | 0.96 |
| 42_F | 139_I | 1.111 | 0.96 |
| 117_E | 125_D | 1.111 | 0.96 |
| 7_L | 19_L | 1.111 | 0.96 |
| 77_K | 118_D | 1.109 | 0.96 |
| 17_Q | 156_C | 1.102 | 0.96 |
| 148_E | 151_L | 1.099 | 0.96 |
| 135_G | 139_I | 1.081 | 0.95 |
| 77_K | 100_K | 1.077 | 0.95 |
| 28_V | 31_F | 1.058 | 0.95 |
| 53_K | 89_S | 1.055 | 0.95 |
| 151_L | 159_I | 1.055 | 0.95 |
| 153_M | 156_C | 1.054 | 0.95 |
| 125_D | 129_G | 1.050 | 0.94 |
| 9_C | 12_A | 1.036 | 0.94 |
| 33_C | 37_A | 1.035 | 0.94 |
| 139_I | 143_V | 1.023 | 0.93 |
| 6_F | 18_C | 1.019 | 0.93 |
| 76_V | 120_H | 1.018 | 0.93 |
| 154_V | 158_G | 1.012 | 0.93 |
| 154_V | 157_C | 1.005 | 0.93 |
| 11_G | 20_L | 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 | |
| 3x0fA | 2 | 0 | 99.6 | 0.532 | Contact Map |
| 2m7zA | 1 | 0.4909 | 99.4 | 0.574 | Contact Map |
| 2ks1B | 1 | 0.2667 | 17.1 | 0.915 | Contact Map |
| 2jwaA | 2 | 0.2667 | 7.7 | 0.928 | Contact Map |
| 2kluA | 1 | 0.2424 | 4.9 | 0.934 | Contact Map |
| 2m20A | 2 | 0.2182 | 3.9 | 0.937 | Contact Map |
| 4mbsA | 2 | 0.2909 | 3.7 | 0.938 | Contact Map |
| 1q90G | 1 | 0.1818 | 3.5 | 0.939 | Contact Map |
| 4l6rA | 1 | 0.8606 | 3 | 0.94 | Contact Map |
| 4pxzA | 1 | 0.2848 | 2.9 | 0.941 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)