| 1CYE |
| ID: | 1449144010 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 129 (123) | ||
| Sequences: | 108418 (80088.5) | ||
| Seq/Len: | 881.447 | ||
| Nf(neff/√len): | 7221.3 |
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: 881.447).
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 |
| 18_R | 35_E | 3.002 | 1.00 |
| 18_R | 37_E | 2.685 | 1.00 |
| 22_R | 35_E | 2.677 | 1.00 |
| 11_V | 42_A | 2.364 | 1.00 |
| 59_N | 89_E | 2.083 | 1.00 |
| 40_V | 62_N | 1.956 | 1.00 |
| 43_L | 71_T | 1.950 | 1.00 |
| 105_G | 119_K | 1.922 | 1.00 |
| 56_S | 68_L | 1.919 | 1.00 |
| 36_A | 45_K | 1.831 | 1.00 |
| 85_M | 103_A | 1.811 | 1.00 |
| 63_M | 71_T | 1.789 | 1.00 |
| 39_G | 63_M | 1.780 | 1.00 |
| 28_L | 117_E | 1.767 | 1.00 |
| 7_K | 33_V | 1.749 | 1.00 |
| 69_L | 83_V | 1.708 | 1.00 |
| 37_E | 41_D | 1.705 | 1.00 |
| 38_D | 62_N | 1.680 | 1.00 |
| 33_V | 51_Y | 1.664 | 1.00 |
| 47_Q | 75_D | 1.657 | 1.00 |
| 24_L | 113_A | 1.642 | 1.00 |
| 7_K | 31_N | 1.600 | 1.00 |
| 9_L | 36_A | 1.532 | 1.00 |
| 73_R | 104_S | 1.484 | 1.00 |
| 22_R | 26_K | 1.379 | 0.99 |
| 58_W | 66_L | 1.377 | 0.99 |
| 71_T | 75_D | 1.375 | 0.99 |
| 70_K | 101_A | 1.373 | 0.99 |
| 39_G | 68_L | 1.360 | 0.99 |
| 38_D | 41_D | 1.358 | 0.99 |
| 54_V | 81_L | 1.351 | 0.99 |
| 7_K | 52_G | 1.331 | 0.99 |
| 33_V | 45_K | 1.294 | 0.99 |
| 89_E | 94_N | 1.291 | 0.99 |
| 6_L | 124_F | 1.245 | 0.98 |
| 64_D | 67_E | 1.235 | 0.98 |
| 105_G | 122_K | 1.234 | 0.98 |
| 63_M | 67_E | 1.217 | 0.98 |
| 96_I | 100_Q | 1.212 | 0.98 |
| 43_L | 68_L | 1.192 | 0.98 |
| 119_K | 122_K | 1.188 | 0.98 |
| 45_K | 51_Y | 1.178 | 0.98 |
| 71_T | 74_A | 1.154 | 0.97 |
| 40_V | 63_M | 1.152 | 0.97 |
| 69_L | 85_M | 1.148 | 0.97 |
| 46_L | 72_I | 1.139 | 0.97 |
| 86_V | 111_F | 1.131 | 0.97 |
| 7_K | 49_G | 1.127 | 0.97 |
| 115_T | 119_K | 1.123 | 0.97 |
| 33_V | 49_G | 1.112 | 0.96 |
| 6_L | 30_F | 1.105 | 0.96 |
| 13_D | 57_D | 1.104 | 0.96 |
| 97_A | 101_A | 1.102 | 0.96 |
| 104_S | 123_I | 1.102 | 0.96 |
| 9_L | 42_A | 1.096 | 0.96 |
| 66_L | 98_A | 1.092 | 0.96 |
| 85_M | 98_A | 1.092 | 0.96 |
| 77_A | 81_L | 1.087 | 0.96 |
| 92_K | 96_I | 1.082 | 0.96 |
| 117_E | 121_N | 1.079 | 0.95 |
| 34_E | 51_Y | 1.078 | 0.95 |
| 91_K | 94_N | 1.055 | 0.95 |
| 45_K | 49_G | 1.055 | 0.95 |
| 42_A | 68_L | 1.051 | 0.94 |
| 19_R | 22_R | 1.041 | 0.94 |
| 66_L | 97_A | 1.037 | 0.94 |
| 36_A | 42_A | 1.026 | 0.94 |
| 9_L | 51_Y | 1.018 | 0.93 |
| 15_S | 37_E | 1.011 | 0.93 |
| 10_V | 21_V | 1.001 | 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 | |
| 3dzdA | 2 | 0.938 | 99.5 | -0.129 | Contact Map |
| 4l4uA | 1 | 0.9767 | 99.5 | -0.124 | Contact Map |
| 3eq2A | 2 | 0.9535 | 99.5 | -0.122 | Contact Map |
| 4g97A | 1 | 0.9612 | 99.5 | -0.121 | Contact Map |
| 1w25A | 2 | 0.9612 | 99.5 | -0.119 | Contact Map |
| 3n0rA | 1 | 0.9612 | 99.5 | -0.111 | Contact Map |
| 3r0jA | 2 | 0.9612 | 99.5 | -0.11 | Contact Map |
| 2vycA | 10 | 0.938 | 99.5 | -0.109 | Contact Map |
| 1jbeA | 1 | 0.969 | 99.5 | -0.106 | Contact Map |
| 3rqiA | 1 | 0.938 | 99.5 | -0.106 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)