| normal prot |
| ID: | 1417293490 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 213 (164) | ||
| Sequences: | 25106 (15747.4) | ||
| Seq/Len: | 153.085 | ||
| Nf(neff/√len): | 1229.7 |
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: 153.085).
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 |
| 27_R | 157_A | 3.281 | 1.00 |
| 16_D | 99_N | 2.949 | 1.00 |
| 150_I | 166_D | 2.587 | 1.00 |
| 121_V | 163_A | 2.583 | 1.00 |
| 91_I | 122_G | 2.551 | 1.00 |
| 166_D | 169_R | 2.516 | 1.00 |
| 24_L | 88_L | 2.494 | 1.00 |
| 88_L | 123_H | 2.465 | 1.00 |
| 86_L | 121_V | 2.287 | 1.00 |
| 139_E | 143_A | 2.241 | 1.00 |
| 148_K | 166_D | 2.187 | 1.00 |
| 94_R | 137_E | 2.120 | 1.00 |
| 159_N | 162_K | 2.020 | 1.00 |
| 12_I | 82_S | 1.955 | 1.00 |
| 89_F | 149_Y | 1.943 | 1.00 |
| 91_I | 125_C | 1.897 | 1.00 |
| 122_G | 151_E | 1.885 | 1.00 |
| 123_H | 154_A | 1.879 | 1.00 |
| 125_C | 158_I | 1.819 | 1.00 |
| 23_C | 154_A | 1.819 | 1.00 |
| 13_V | 25_I | 1.809 | 1.00 |
| 166_D | 170_D | 1.800 | 1.00 |
| 125_C | 151_E | 1.757 | 1.00 |
| 119_V | 150_I | 1.754 | 1.00 |
| 135_R | 139_E | 1.751 | 1.00 |
| 84_G | 167_L | 1.735 | 1.00 |
| 152_T | 163_A | 1.687 | 1.00 |
| 138_A | 142_A | 1.630 | 1.00 |
| 13_V | 86_L | 1.628 | 1.00 |
| 24_L | 160_V | 1.601 | 1.00 |
| 24_L | 163_A | 1.598 | 1.00 |
| 140_K | 144_A | 1.592 | 1.00 |
| 119_V | 166_D | 1.572 | 1.00 |
| 9_F | 171_I | 1.567 | 1.00 |
| 90_D | 93_N | 1.553 | 1.00 |
| 93_N | 96_S | 1.526 | 1.00 |
| 121_V | 152_T | 1.488 | 1.00 |
| 141_L | 145_Y | 1.453 | 1.00 |
| 89_F | 120_L | 1.429 | 1.00 |
| 60_L | 168_T | 1.407 | 0.99 |
| 90_D | 124_K | 1.387 | 0.99 |
| 27_R | 160_V | 1.379 | 0.99 |
| 86_L | 167_L | 1.336 | 0.99 |
| 87_L | 104_L | 1.326 | 0.99 |
| 101_H | 144_A | 1.299 | 0.99 |
| 124_K | 127_L | 1.299 | 0.99 |
| 162_K | 165_T | 1.272 | 0.99 |
| 138_A | 149_Y | 1.265 | 0.99 |
| 104_L | 118_F | 1.253 | 0.99 |
| 92_T | 127_L | 1.236 | 0.98 |
| 47_S | 61_Q | 1.223 | 0.98 |
| 11_L | 84_G | 1.211 | 0.98 |
| 121_V | 150_I | 1.208 | 0.98 |
| 16_D | 19_V | 1.203 | 0.98 |
| 10_R | 61_Q | 1.194 | 0.98 |
| 161_E | 165_T | 1.189 | 0.98 |
| 170_D | 173_E | 1.188 | 0.98 |
| 131_R | 151_E | 1.186 | 0.98 |
| 24_L | 28_F | 1.158 | 0.97 |
| 165_T | 169_R | 1.145 | 0.97 |
| 40_T | 67_G | 1.134 | 0.97 |
| 89_F | 122_G | 1.130 | 0.97 |
| 137_E | 140_K | 1.123 | 0.97 |
| 105_E | 108_K | 1.122 | 0.97 |
| 86_L | 163_A | 1.119 | 0.96 |
| 139_E | 142_A | 1.117 | 0.96 |
| 104_L | 108_K | 1.102 | 0.96 |
| 95_R | 98_Q | 1.101 | 0.96 |
| 87_L | 100_V | 1.091 | 0.96 |
| 86_L | 119_V | 1.084 | 0.96 |
| 134_T | 137_E | 1.079 | 0.95 |
| 26_R | 34_A | 1.075 | 0.95 |
| 17_S | 68_Q | 1.075 | 0.95 |
| 51_E | 55_G | 1.068 | 0.95 |
| 105_E | 109_V | 1.067 | 0.95 |
| 89_F | 138_A | 1.058 | 0.95 |
| 162_K | 166_D | 1.056 | 0.95 |
| 38_D | 41_V | 1.046 | 0.94 |
| 122_G | 149_Y | 1.046 | 0.94 |
| 160_V | 164_F | 1.034 | 0.94 |
| 24_L | 154_A | 1.032 | 0.94 |
| 51_E | 57_R | 1.031 | 0.94 |
| 64_D | 67_G | 1.030 | 0.94 |
| 49_L | 59_K | 1.010 | 0.93 |
| 54_P | 168_T | 1.007 | 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 | |
| 3cpjB | 1 | 0.77 | 100 | 0.355 | Contact Map |
| 3dz8A | 1 | 0.8122 | 100 | 0.378 | Contact Map |
| 4dkxA | 2 | 0.7324 | 100 | 0.379 | Contact Map |
| 2bmeA | 4 | 0.8263 | 100 | 0.379 | Contact Map |
| 2bcgY | 1 | 0.9108 | 100 | 0.381 | Contact Map |
| 4lhwA | 5 | 0.8169 | 100 | 0.384 | Contact Map |
| 2a5jA | 1 | 0.8122 | 100 | 0.386 | Contact Map |
| 3tklA | 1 | 0.8028 | 100 | 0.389 | Contact Map |
| 2f7sA | 2 | 0.8169 | 100 | 0.39 | Contact Map |
| 2ew1A | 1 | 0.8028 | 100 | 0.394 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)