| 2y6y |
| ID: | 1453799338 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 176 (161) | ||
| Sequences: | 1118 (800.4) | ||
| Seq/Len: | 6.944 | ||
| Nf(neff/√len): | 63.1 |
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: 6.944).
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 |
| 78_Y | 99_F | 3.667 | 1.00 |
| 18_F | 150_V | 3.245 | 1.00 |
| 75_K | 90_A | 3.106 | 1.00 |
| 52_E | 144_A | 2.653 | 1.00 |
| 7_R | 157_D | 2.547 | 1.00 |
| 67_A | 133_H | 2.444 | 1.00 |
| 11_Y | 157_D | 2.371 | 1.00 |
| 7_R | 11_Y | 2.322 | 1.00 |
| 142_P | 151_R | 2.296 | 1.00 |
| 7_R | 126_Q | 2.230 | 1.00 |
| 93_I | 138_V | 2.213 | 1.00 |
| 100_M | 126_Q | 2.062 | 1.00 |
| 81_Y | 125_A | 2.062 | 1.00 |
| 19_Y | 94_A | 2.036 | 1.00 |
| 67_A | 96_E | 1.984 | 1.00 |
| 142_P | 148_N | 1.953 | 1.00 |
| 138_V | 154_V | 1.938 | 1.00 |
| 14_L | 150_V | 1.921 | 1.00 |
| 70_Y | 140_N | 1.799 | 1.00 |
| 54_R | 58_L | 1.759 | 1.00 |
| 83_F | 102_K | 1.739 | 1.00 |
| 25_E | 29_K | 1.721 | 1.00 |
| 17_I | 146_L | 1.714 | 1.00 |
| 104_V | 126_Q | 1.589 | 1.00 |
| 15_S | 98_A | 1.544 | 0.99 |
| 18_F | 146_L | 1.525 | 0.99 |
| 11_Y | 153_F | 1.521 | 0.99 |
| 99_F | 129_F | 1.510 | 0.99 |
| 11_Y | 126_Q | 1.504 | 0.99 |
| 12_A | 101_S | 1.500 | 0.99 |
| 67_A | 71_E | 1.489 | 0.99 |
| 141_L | 147_L | 1.479 | 0.99 |
| 100_M | 153_F | 1.471 | 0.99 |
| 22_F | 53_L | 1.440 | 0.99 |
| 115_K | 118_E | 1.434 | 0.99 |
| 74_M | 78_Y | 1.382 | 0.99 |
| 74_M | 96_E | 1.374 | 0.99 |
| 59_I | 89_H | 1.371 | 0.98 |
| 67_A | 136_P | 1.347 | 0.98 |
| 64_Q | 69_V | 1.313 | 0.98 |
| 68_E | 89_H | 1.287 | 0.97 |
| 139_K | 151_R | 1.286 | 0.97 |
| 22_F | 27_I | 1.274 | 0.97 |
| 128_R | 132_A | 1.271 | 0.97 |
| 58_L | 92_H | 1.256 | 0.97 |
| 18_F | 93_I | 1.245 | 0.97 |
| 16_K | 24_D | 1.243 | 0.97 |
| 17_I | 31_C | 1.239 | 0.97 |
| 22_F | 38_F | 1.238 | 0.97 |
| 53_L | 57_V | 1.233 | 0.96 |
| 18_F | 57_V | 1.207 | 0.96 |
| 65_S | 89_H | 1.201 | 0.96 |
| 11_Y | 100_M | 1.199 | 0.96 |
| 100_M | 157_D | 1.182 | 0.95 |
| 101_S | 105_E | 1.180 | 0.95 |
| 104_V | 157_D | 1.154 | 0.94 |
| 51_R | 54_R | 1.137 | 0.94 |
| 12_A | 105_E | 1.126 | 0.93 |
| 66_L | 89_H | 1.124 | 0.93 |
| 65_S | 137_L | 1.115 | 0.93 |
| 80_R | 125_A | 1.074 | 0.91 |
| 97_L | 150_V | 1.066 | 0.91 |
| 80_R | 128_R | 1.065 | 0.91 |
| 54_R | 60_K | 1.062 | 0.90 |
| 7_R | 100_M | 1.057 | 0.90 |
| 15_S | 94_A | 1.037 | 0.89 |
| 71_E | 136_P | 1.034 | 0.89 |
| 10_V | 38_F | 1.026 | 0.88 |
| 151_R | 155_R | 1.026 | 0.88 |
| 131_K | 158_A | 1.024 | 0.88 |
| 7_R | 153_F | 1.019 | 0.88 |
| 66_L | 98_A | 1.015 | 0.88 |
| 129_F | 133_H | 1.000 | 0.86 |
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 | |
| 2xolA | 2 | 0.9489 | 100 | 0.25 | Contact Map |
| 1n1cA | 2 | 0.9034 | 99.9 | 0.433 | Contact Map |
| 1s9uA | 1 | 0.875 | 99.9 | 0.448 | Contact Map |
| 2o9xA | 1 | 0.7386 | 99.9 | 0.499 | Contact Map |
| 4wmuA | 1 | 0 | 14.1 | 0.936 | Contact Map |
| 4hw4A | 2 | 0.7841 | 10.2 | 0.939 | Contact Map |
| 1i2tA | 1 | 0.2898 | 8.5 | 0.942 | Contact Map |
| 3pk1A | 2 | 0.75 | 7.8 | 0.943 | Contact Map |
| 2vofA | 2 | 0.7784 | 7.7 | 0.943 | Contact Map |
| 4cimA | 2 | 0.7557 | 7.5 | 0.943 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)