| Xtln |
| ID: | 1518123914 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 173 (171) | ||
| Sequences: | 888 (456.2) | ||
| Seq/Len: | 5.193 | ||
| Nf(neff/√len): | 34.9 |
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: 5.193).
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 |
| 43_M | 56_F | 2.249 | 1.00 |
| 4_T | 17_E | 2.144 | 1.00 |
| 134_E | 141_R | 2.081 | 1.00 |
| 4_T | 38_D | 1.940 | 1.00 |
| 5_L | 18_C | 1.837 | 1.00 |
| 7_E | 11_F | 1.810 | 1.00 |
| 143_Y | 156_W | 1.702 | 1.00 |
| 129_S | 144_L | 1.610 | 0.99 |
| 2_K | 17_E | 1.580 | 0.99 |
| 25_L | 29_L | 1.580 | 0.99 |
| 111_L | 166_L | 1.553 | 0.99 |
| 131_V | 142_Q | 1.552 | 0.99 |
| 88_R | 103_E | 1.548 | 0.99 |
| 98_R | 105_T | 1.536 | 0.99 |
| 55_Y | 70_G | 1.526 | 0.99 |
| 129_S | 147_P | 1.508 | 0.99 |
| 24_N | 27_P | 1.480 | 0.98 |
| 93_E | 103_E | 1.464 | 0.98 |
| 125_V | 128_G | 1.458 | 0.98 |
| 122_S | 125_V | 1.454 | 0.98 |
| 89_I | 125_V | 1.449 | 0.98 |
| 3_I | 37_V | 1.434 | 0.98 |
| 13_G | 34_S | 1.401 | 0.98 |
| 35_A | 44_L | 1.365 | 0.97 |
| 93_E | 97_Y | 1.349 | 0.97 |
| 55_Y | 72_S | 1.349 | 0.97 |
| 53_L | 56_F | 1.332 | 0.96 |
| 3_I | 7_E | 1.326 | 0.96 |
| 96_D | 109_S | 1.312 | 0.96 |
| 84_S | 87_H | 1.308 | 0.96 |
| 165_S | 169_V | 1.290 | 0.96 |
| 143_Y | 158_A | 1.282 | 0.95 |
| 45_Y | 60_G | 1.279 | 0.95 |
| 35_A | 68_W | 1.270 | 0.95 |
| 6_Y | 11_F | 1.241 | 0.94 |
| 133_Y | 142_Q | 1.238 | 0.94 |
| 153_Y | 171_D | 1.237 | 0.94 |
| 42_W | 130_W | 1.233 | 0.94 |
| 34_S | 37_V | 1.224 | 0.94 |
| 165_S | 168_R | 1.224 | 0.94 |
| 109_S | 138_Y | 1.212 | 0.93 |
| 130_W | 165_S | 1.210 | 0.93 |
| 44_L | 79_R | 1.209 | 0.93 |
| 64_D | 76_R | 1.198 | 0.93 |
| 6_Y | 13_G | 1.186 | 0.92 |
| 142_Q | 145_L | 1.184 | 0.92 |
| 7_E | 19_S | 1.176 | 0.92 |
| 134_E | 140_G | 1.166 | 0.91 |
| 143_Y | 157_G | 1.165 | 0.91 |
| 57_L | 63_A | 1.155 | 0.91 |
| 5_L | 16_Y | 1.152 | 0.91 |
| 50_Y | 77_S | 1.140 | 0.90 |
| 118_N | 162_R | 1.136 | 0.90 |
| 44_L | 58_R | 1.134 | 0.90 |
| 39_S | 59_R | 1.130 | 0.89 |
| 123_L | 132_L | 1.128 | 0.89 |
| 90_R | 126_L | 1.127 | 0.89 |
| 151_R | 155_D | 1.122 | 0.89 |
| 62_Y | 81_I | 1.112 | 0.88 |
| 60_G | 77_S | 1.110 | 0.88 |
| 5_L | 8_D | 1.107 | 0.88 |
| 106_E | 125_V | 1.096 | 0.87 |
| 4_T | 7_E | 1.096 | 0.87 |
| 28_Y | 39_S | 1.086 | 0.87 |
| 29_L | 71_L | 1.083 | 0.87 |
| 143_Y | 150_Y | 1.078 | 0.86 |
| 62_Y | 77_S | 1.072 | 0.86 |
| 104_F | 108_C | 1.071 | 0.86 |
| 94_R | 97_Y | 1.071 | 0.86 |
| 112_Q | 117_F | 1.069 | 0.86 |
| 73_D | 76_R | 1.048 | 0.84 |
| 152_R | 156_W | 1.046 | 0.84 |
| 45_Y | 133_Y | 1.044 | 0.84 |
| 47_Q | 53_L | 1.044 | 0.84 |
| 99_G | 122_S | 1.041 | 0.84 |
| 52_G | 60_G | 1.039 | 0.83 |
| 43_M | 58_R | 1.036 | 0.83 |
| 62_Y | 70_G | 1.033 | 0.83 |
| 109_S | 115_F | 1.025 | 0.82 |
| 131_V | 144_L | 1.022 | 0.82 |
| 47_Q | 59_R | 1.016 | 0.81 |
| 54_Q | 62_Y | 1.015 | 0.81 |
| 17_E | 22_H | 1.014 | 0.81 |
| 107_D | 168_R | 1.010 | 0.81 |
| 18_C | 29_L | 1.010 | 0.81 |
| 138_Y | 141_R | 1.008 | 0.81 |
| 82_P | 147_P | 1.004 | 0.80 |
| 35_A | 57_L | 1.000 | 0.80 |
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 | |
| 1h4aX | 1 | 1 | 100 | 0.056 | Contact Map |
| 2m3cA | 1 | 0.9942 | 100 | 0.068 | Contact Map |
| 2jdgA | 1 | 0.9827 | 100 | 0.084 | Contact Map |
| 1ytqA | 1 | 1 | 100 | 0.088 | Contact Map |
| 1zwmA | 1 | 0.9884 | 100 | 0.093 | Contact Map |
| 3qk3A | 3 | 0.9884 | 100 | 0.093 | Contact Map |
| 1okiA | 2 | 0.9942 | 100 | 0.094 | Contact Map |
| 3lwkA | 1 | 0.9711 | 100 | 0.104 | Contact Map |
| 1bd7A | 2 | 0.9769 | 100 | 0.132 | Contact Map |
| 4iauA | 1 | 0.8786 | 100 | 0.204 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)