| long_an |
| ID: | 1420173405 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 225 (214) | ||
| Sequences: | 3821 (2868.3) | ||
| Seq/Len: | 17.855 | ||
| Nf(neff/√len): | 196.1 |
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: 17.855).
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 |
| 21_R | 25_I | 3.663 | 1.00 |
| 42_V | 123_L | 3.471 | 1.00 |
| 76_S | 118_I | 3.255 | 1.00 |
| 132_I | 174_V | 3.126 | 1.00 |
| 60_E | 68_L | 2.914 | 1.00 |
| 49_D | 113_T | 2.880 | 1.00 |
| 197_E | 201_K | 2.842 | 1.00 |
| 58_T | 70_K | 2.829 | 1.00 |
| 45_A | 114_V | 2.751 | 1.00 |
| 60_E | 70_K | 2.617 | 1.00 |
| 32_I | 130_F | 2.590 | 1.00 |
| 177_Y | 181_S | 2.455 | 1.00 |
| 117_F | 121_H | 2.428 | 1.00 |
| 190_K | 193_K | 2.355 | 1.00 |
| 23_L | 27_F | 2.219 | 1.00 |
| 209_S | 213_K | 2.185 | 1.00 |
| 140_V | 175_T | 2.163 | 1.00 |
| 166_I | 200_K | 2.160 | 1.00 |
| 63_G | 172_P | 1.911 | 1.00 |
| 177_Y | 197_E | 1.885 | 1.00 |
| 55_L | 72_Y | 1.857 | 1.00 |
| 29_L | 133_L | 1.851 | 1.00 |
| 80_N | 84_L | 1.840 | 1.00 |
| 47_K | 52_G | 1.826 | 1.00 |
| 43_A | 54_V | 1.826 | 1.00 |
| 53_P | 79_E | 1.820 | 1.00 |
| 140_V | 211_V | 1.814 | 1.00 |
| 47_K | 54_V | 1.775 | 1.00 |
| 42_V | 118_I | 1.768 | 1.00 |
| 28_S | 32_I | 1.765 | 1.00 |
| 42_V | 74_F | 1.751 | 1.00 |
| 58_T | 72_Y | 1.697 | 1.00 |
| 122_S | 183_R | 1.697 | 1.00 |
| 27_F | 139_L | 1.696 | 1.00 |
| 39_I | 74_F | 1.691 | 1.00 |
| 46_I | 49_D | 1.654 | 1.00 |
| 145_Y | 149_E | 1.627 | 1.00 |
| 72_Y | 131_N | 1.626 | 1.00 |
| 24_D | 138_S | 1.609 | 1.00 |
| 46_I | 50_S | 1.565 | 1.00 |
| 62_V | 68_L | 1.565 | 1.00 |
| 170_V | 199_V | 1.517 | 1.00 |
| 176_G | 179_Q | 1.502 | 1.00 |
| 20_K | 207_D | 1.500 | 1.00 |
| 68_L | 147_P | 1.497 | 1.00 |
| 182_G | 186_I | 1.458 | 1.00 |
| 129_F | 139_L | 1.456 | 1.00 |
| 57_D | 82_H | 1.449 | 1.00 |
| 21_R | 28_S | 1.445 | 1.00 |
| 28_S | 133_L | 1.431 | 1.00 |
| 31_L | 35_F | 1.431 | 1.00 |
| 149_E | 153_Q | 1.426 | 1.00 |
| 31_L | 139_L | 1.413 | 1.00 |
| 139_L | 211_V | 1.405 | 0.99 |
| 213_K | 217_A | 1.391 | 0.99 |
| 31_L | 129_F | 1.387 | 0.99 |
| 130_F | 134_K | 1.384 | 0.99 |
| 25_I | 29_L | 1.366 | 0.99 |
| 78_I | 84_L | 1.350 | 0.99 |
| 20_K | 24_D | 1.338 | 0.99 |
| 35_F | 39_I | 1.337 | 0.99 |
| 197_E | 206_Y | 1.334 | 0.99 |
| 145_Y | 150_L | 1.333 | 0.99 |
| 114_V | 118_I | 1.333 | 0.99 |
| 27_F | 31_L | 1.330 | 0.99 |
| 64_K | 171_R | 1.306 | 0.99 |
| 41_L | 45_A | 1.303 | 0.99 |
| 120_K | 221_G | 1.298 | 0.99 |
| 25_I | 28_S | 1.289 | 0.99 |
| 179_Q | 195_D | 1.273 | 0.99 |
| 216_E | 220_T | 1.261 | 0.99 |
| 32_I | 36_S | 1.257 | 0.99 |
| 204_I | 208_L | 1.239 | 0.98 |
| 33_I | 36_S | 1.238 | 0.98 |
| 177_Y | 210_I | 1.232 | 0.98 |
| 25_I | 133_L | 1.225 | 0.98 |
| 126_V | 129_F | 1.220 | 0.98 |
| 29_L | 33_I | 1.198 | 0.98 |
| 59_P | 71_M | 1.192 | 0.98 |
| 218_M | 223_G | 1.185 | 0.98 |
| 198_Y | 207_D | 1.178 | 0.98 |
| 211_V | 215_P | 1.177 | 0.98 |
| 145_Y | 188_F | 1.173 | 0.98 |
| 177_Y | 194_M | 1.141 | 0.97 |
| 166_I | 169_S | 1.140 | 0.97 |
| 176_G | 191_R | 1.135 | 0.97 |
| 146_Y | 149_E | 1.113 | 0.96 |
| 47_K | 50_S | 1.108 | 0.96 |
| 167_V | 195_D | 1.080 | 0.95 |
| 53_P | 75_R | 1.080 | 0.95 |
| 145_Y | 191_R | 1.076 | 0.95 |
| 66_G | 168_L | 1.075 | 0.95 |
| 147_P | 151_R | 1.074 | 0.95 |
| 72_Y | 134_K | 1.070 | 0.95 |
| 78_I | 81_A | 1.067 | 0.95 |
| 177_Y | 206_Y | 1.059 | 0.95 |
| 36_S | 39_I | 1.053 | 0.95 |
| 106_K | 225_L | 1.046 | 0.94 |
| 146_Y | 153_Q | 1.045 | 0.94 |
| 88_N | 92_A | 1.039 | 0.94 |
| 184_S | 191_R | 1.034 | 0.94 |
| 122_S | 191_R | 1.025 | 0.93 |
| 132_I | 139_L | 1.014 | 0.93 |
| 20_K | 138_S | 1.007 | 0.93 |
| 129_F | 174_V | 1.003 | 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 | |
| 1tteA | 1 | 0.5244 | 4.9 | 0.972 | Contact Map |
| 2kogA | 1 | 0.1867 | 4.7 | 0.972 | Contact Map |
| 3floA | 4 | 0.4889 | 3.6 | 0.974 | Contact Map |
| 3o2uA | 2 | 0.6089 | 3.3 | 0.974 | Contact Map |
| 3hd7A | 2 | 0.1867 | 3 | 0.975 | Contact Map |
| 1xqoA | 1 | 0.4 | 2.9 | 0.975 | Contact Map |
| 1fxtA | 1 | 0.52 | 2.8 | 0.975 | Contact Map |
| 3wguG | 2 | 0.1556 | 2.6 | 0.976 | Contact Map |
| 4upcA | 1 | 0.0711 | 2.5 | 0.976 | Contact Map |
| 1z2uA | 1 | 0.5289 | 2.3 | 0.976 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)