| sub2 |
| ID: | 1404136180 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 181 (161) | ||
| Sequences: | 1663 (1139.5) | ||
| Seq/Len: | 10.329 | ||
| Nf(neff/√len): | 89.8 |
HHblits Results: (2013_03)
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: 10.329).
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 | 137_N | 4.844 | 1.00 |
| 101_T | 107_G | 3.572 | 1.00 |
| 111_V | 118_S | 3.048 | 1.00 |
| 103_T | 151_E | 3.045 | 1.00 |
| 77_K | 116_L | 2.798 | 1.00 |
| 99_Y | 151_E | 2.757 | 1.00 |
| 28_M | 70_Y | 2.740 | 1.00 |
| 101_T | 119_V | 2.615 | 1.00 |
| 50_A | 60_V | 2.212 | 1.00 |
| 12_E | 52_L | 2.049 | 1.00 |
| 34_V | 49_I | 2.018 | 1.00 |
| 27_I | 55_T | 1.957 | 1.00 |
| 104_L | 112_T | 1.933 | 1.00 |
| 97_W | 108_P | 1.919 | 1.00 |
| 64_A | 72_F | 1.891 | 1.00 |
| 71_Q | 75_T | 1.856 | 1.00 |
| 96_L | 150_L | 1.807 | 1.00 |
| 103_T | 155_A | 1.748 | 1.00 |
| 116_L | 158_R | 1.715 | 1.00 |
| 46_I | 64_A | 1.639 | 1.00 |
| 98_D | 102_E | 1.634 | 1.00 |
| 134_I | 145_V | 1.630 | 1.00 |
| 80_L | 136_V | 1.613 | 1.00 |
| 49_I | 60_V | 1.606 | 1.00 |
| 106_I | 112_T | 1.583 | 1.00 |
| 79_H | 118_S | 1.573 | 1.00 |
| 41_I | 64_A | 1.545 | 1.00 |
| 76_G | 118_S | 1.536 | 1.00 |
| 76_G | 111_V | 1.506 | 1.00 |
| 106_I | 110_E | 1.498 | 1.00 |
| 12_E | 48_E | 1.493 | 1.00 |
| 82_V | 97_W | 1.475 | 1.00 |
| 24_R | 59_E | 1.463 | 1.00 |
| 99_Y | 103_T | 1.435 | 1.00 |
| 145_V | 153_L | 1.424 | 1.00 |
| 106_I | 119_V | 1.411 | 1.00 |
| 101_T | 108_P | 1.401 | 0.99 |
| 27_I | 60_V | 1.391 | 0.99 |
| 48_E | 51_R | 1.379 | 0.99 |
| 91_A | 131_A | 1.336 | 0.99 |
| 80_L | 153_L | 1.325 | 0.99 |
| 78_Y | 116_L | 1.307 | 0.99 |
| 95_E | 98_D | 1.284 | 0.99 |
| 146_T | 149_R | 1.275 | 0.99 |
| 125_L | 135_Q | 1.269 | 0.99 |
| 46_I | 60_V | 1.246 | 0.98 |
| 43_P | 47_E | 1.245 | 0.98 |
| 156_G | 161_K | 1.208 | 0.98 |
| 99_Y | 150_L | 1.204 | 0.98 |
| 23_R | 54_G | 1.199 | 0.98 |
| 42_R | 45_R | 1.189 | 0.98 |
| 27_I | 63_V | 1.174 | 0.98 |
| 141_Y | 153_L | 1.164 | 0.97 |
| 58_T | 62_G | 1.158 | 0.97 |
| 34_V | 45_R | 1.144 | 0.97 |
| 125_L | 133_V | 1.132 | 0.97 |
| 100_L | 150_L | 1.128 | 0.97 |
| 107_G | 110_E | 1.127 | 0.97 |
| 75_T | 118_S | 1.119 | 0.96 |
| 130_T | 143_E | 1.116 | 0.96 |
| 19_P | 25_A | 1.081 | 0.95 |
| 39_G | 71_Q | 1.078 | 0.95 |
| 46_I | 61_M | 1.071 | 0.95 |
| 98_D | 101_T | 1.071 | 0.95 |
| 89_K | 123_E | 1.067 | 0.95 |
| 134_I | 153_L | 1.058 | 0.95 |
| 56_T | 59_E | 1.058 | 0.95 |
| 38_E | 42_R | 1.054 | 0.95 |
| 48_E | 52_L | 1.050 | 0.94 |
| 127_S | 130_T | 1.050 | 0.94 |
| 106_I | 111_V | 1.034 | 0.94 |
| 80_L | 117_F | 1.033 | 0.94 |
| 99_Y | 147_R | 1.030 | 0.94 |
| 32_R | 69_Y | 1.027 | 0.94 |
| 82_V | 134_I | 1.025 | 0.93 |
| 99_Y | 102_E | 1.022 | 0.93 |
| 26_A | 30_L | 1.019 | 0.93 |
| 154_L | 157_L | 1.013 | 0.93 |
| 83_C | 88_C | 1.005 | 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 | |
| 3i9v2 | 2 | 0.9834 | 100 | 0.204 | Contact Map |
| 2auvA | 1 | 0.4696 | 99.9 | 0.651 | Contact Map |
| 1m2dA | 2 | 0.4972 | 99.8 | 0.707 | Contact Map |
| 3ghaA | 1 | 0.7514 | 54.6 | 0.942 | Contact Map |
| 4ihuA | 2 | 0.6575 | 51.7 | 0.943 | Contact Map |
| 1r7jA | 1 | 0.442 | 47.5 | 0.944 | Contact Map |
| 1vz0A | 8 | 0.6354 | 46 | 0.945 | Contact Map |
| 3f4sA | 1 | 0.7735 | 38.8 | 0.947 | Contact Map |
| 3or1C | 2 | 0.4475 | 37.3 | 0.947 | Contact Map |
| 1ji8A | 1 | 0.4475 | 36 | 0.948 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)