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| ID: | 1481230947 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 131 (131) | ||
| Sequences: | 379 (361.5) | ||
| Seq/Len: | 2.893 | ||
| Nf(neff/√len): | 31.6 |
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: 2.893).
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 |
| 22_H | 63_E | 3.581 | 1.00 |
| 74_P | 130_Y | 3.073 | 1.00 |
| 10_N | 13_N | 2.318 | 1.00 |
| 50_I | 108_M | 2.196 | 1.00 |
| 32_R | 52_L | 2.006 | 1.00 |
| 24_R | 28_D | 1.788 | 0.99 |
| 86_F | 90_A | 1.711 | 0.98 |
| 56_V | 120_I | 1.705 | 0.98 |
| 12_L | 121_Q | 1.640 | 0.98 |
| 115_W | 120_I | 1.619 | 0.97 |
| 67_V | 131_L | 1.510 | 0.96 |
| 69_S | 76_L | 1.505 | 0.95 |
| 14_M | 128_A | 1.492 | 0.95 |
| 86_F | 89_R | 1.483 | 0.95 |
| 86_F | 113_A | 1.464 | 0.94 |
| 96_A | 101_D | 1.460 | 0.94 |
| 8_W | 79_H | 1.427 | 0.93 |
| 21_R | 24_R | 1.416 | 0.93 |
| 23_H | 60_H | 1.341 | 0.90 |
| 66_E | 78_E | 1.334 | 0.90 |
| 13_N | 20_D | 1.319 | 0.89 |
| 56_V | 115_W | 1.276 | 0.87 |
| 14_M | 115_W | 1.274 | 0.87 |
| 69_S | 80_R | 1.239 | 0.85 |
| 37_M | 111_Y | 1.235 | 0.85 |
| 6_L | 86_F | 1.220 | 0.84 |
| 62_R | 66_E | 1.214 | 0.83 |
| 19_I | 111_Y | 1.213 | 0.83 |
| 74_P | 128_A | 1.204 | 0.83 |
| 56_V | 116_L | 1.190 | 0.82 |
| 19_I | 122_M | 1.189 | 0.82 |
| 9_D | 12_L | 1.181 | 0.81 |
| 83_H | 119_H | 1.178 | 0.81 |
| 18_N | 63_E | 1.177 | 0.81 |
| 79_H | 124_D | 1.177 | 0.81 |
| 64_E | 119_H | 1.176 | 0.81 |
| 73_Y | 130_Y | 1.165 | 0.80 |
| 50_I | 97_V | 1.158 | 0.79 |
| 68_M | 76_L | 1.147 | 0.78 |
| 27_F | 112_V | 1.143 | 0.78 |
| 29_E | 56_V | 1.126 | 0.76 |
| 57_M | 118_N | 1.124 | 0.76 |
| 19_I | 127_L | 1.113 | 0.75 |
| 119_H | 124_D | 1.110 | 0.75 |
| 83_H | 124_D | 1.107 | 0.75 |
| 8_W | 13_N | 1.106 | 0.75 |
| 64_E | 124_D | 1.102 | 0.74 |
| 53_I | 56_V | 1.086 | 0.73 |
| 114_T | 122_M | 1.083 | 0.72 |
| 82_H | 123_E | 1.077 | 0.72 |
| 17_G | 36_K | 1.076 | 0.72 |
| 1_S | 106_A | 1.075 | 0.72 |
| 69_S | 78_E | 1.073 | 0.71 |
| 30_V | 112_V | 1.067 | 0.71 |
| 77_D | 81_R | 1.064 | 0.70 |
| 54_D | 86_F | 1.053 | 0.69 |
| 51_T | 94_K | 1.052 | 0.69 |
| 12_L | 27_F | 1.036 | 0.68 |
| 8_W | 33_L | 1.027 | 0.67 |
| 8_W | 65_E | 1.020 | 0.66 |
| 20_D | 64_E | 1.019 | 0.66 |
| 4_K | 7_N | 1.015 | 0.65 |
| 60_H | 64_E | 1.004 | 0.64 |
| 84_R | 87_L | 1.000 | 0.64 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 4xpxA | 1 | 0 | 100 | 0.074 | Contact Map |
| 3agtA | 2 | 0.9695 | 100 | 0.088 | Contact Map |
| 2hmqA | 4 | 0.8473 | 100 | 0.169 | Contact Map |
| 2mhrA | 1 | 0.8855 | 100 | 0.176 | Contact Map |
| 3caxA | 1 | 0.916 | 92.2 | 0.839 | Contact Map |
| 2p0nA | 2 | 0.916 | 91 | 0.844 | Contact Map |
| 4i3hA | 2 | 0.5191 | 10.5 | 0.923 | Contact Map |
| 1x4pA | 1 | 0.4656 | 8.8 | 0.925 | Contact Map |
| 3i4hX | 1 | 0.3664 | 6.4 | 0.93 | Contact Map |
| 4l9mA | 1 | 0.6794 | 6.2 | 0.93 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)