| AdKin |
| ID: | 1501847578 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 226 (211) | ||
| Sequences: | 4889 (2728.1) | ||
| Seq/Len: | 23.171 | ||
| Nf(neff/√len): | 187.8 |
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: 23.171).
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 |
| 117_F | 176_E | 4.205 | 1.00 |
| 29_H | 208_Y | 2.954 | 1.00 |
| 41_L | 70_M | 2.865 | 1.00 |
| 58_F | 66_P | 2.766 | 1.00 |
| 173_K | 177_A | 2.715 | 1.00 |
| 122_Q | 140_E | 2.615 | 1.00 |
| 71_T | 91_F | 2.507 | 1.00 |
| 124_L | 168_V | 2.492 | 1.00 |
| 43_D | 47_R | 2.456 | 1.00 |
| 44_N | 76_H | 2.288 | 1.00 |
| 25_R | 204_W | 2.287 | 1.00 |
| 131_P | 158_V | 2.268 | 1.00 |
| 102_D | 189_K | 2.226 | 1.00 |
| 130_H | 133_S | 2.209 | 1.00 |
| 128_W | 139_I | 2.197 | 1.00 |
| 126_A | 138_N | 2.097 | 1.00 |
| 119_V | 122_Q | 2.093 | 1.00 |
| 56_K | 60_D | 2.069 | 1.00 |
| 114_N | 194_T | 2.022 | 1.00 |
| 29_H | 204_W | 2.013 | 1.00 |
| 54_L | 57_T | 1.981 | 1.00 |
| 71_T | 100_A | 1.967 | 1.00 |
| 131_P | 155_E | 1.944 | 1.00 |
| 121_K | 169_V | 1.864 | 1.00 |
| 187_R | 194_T | 1.863 | 1.00 |
| 58_F | 63_K | 1.841 | 1.00 |
| 44_N | 49_T | 1.836 | 1.00 |
| 57_T | 61_Q | 1.810 | 1.00 |
| 165_P | 169_V | 1.778 | 1.00 |
| 180_E | 184_E | 1.732 | 1.00 |
| 50_E | 53_V | 1.700 | 1.00 |
| 133_S | 153_T | 1.690 | 1.00 |
| 146_T | 149_I | 1.665 | 1.00 |
| 135_R | 152_L | 1.642 | 1.00 |
| 113_L | 197_G | 1.639 | 1.00 |
| 50_E | 54_L | 1.625 | 1.00 |
| 150_D | 153_T | 1.613 | 1.00 |
| 176_E | 180_E | 1.605 | 1.00 |
| 38_G | 42_R | 1.569 | 1.00 |
| 130_H | 153_T | 1.563 | 1.00 |
| 44_N | 73_L | 1.553 | 1.00 |
| 204_W | 208_Y | 1.534 | 1.00 |
| 160_R | 163_D | 1.530 | 1.00 |
| 128_W | 159_Q | 1.528 | 1.00 |
| 22_V | 207_V | 1.514 | 1.00 |
| 33_K | 77_E | 1.510 | 1.00 |
| 196_S | 199_E | 1.499 | 1.00 |
| 130_H | 150_D | 1.476 | 1.00 |
| 170_K | 173_K | 1.476 | 1.00 |
| 117_F | 169_V | 1.459 | 1.00 |
| 102_D | 185_Y | 1.441 | 1.00 |
| 102_D | 186_Y | 1.427 | 1.00 |
| 117_F | 173_K | 1.396 | 0.99 |
| 112_N | 183_L | 1.396 | 0.99 |
| 138_N | 141_F | 1.396 | 0.99 |
| 14_A | 175_Y | 1.386 | 0.99 |
| 67_D | 97_Q | 1.382 | 0.99 |
| 175_Y | 179_T | 1.377 | 0.99 |
| 8_R | 86_W | 1.366 | 0.99 |
| 44_N | 47_R | 1.361 | 0.99 |
| 117_F | 172_L | 1.360 | 0.99 |
| 18_G | 21_T | 1.335 | 0.99 |
| 54_L | 72_R | 1.333 | 0.99 |
| 25_R | 28_K | 1.318 | 0.99 |
| 208_Y | 212_Q | 1.311 | 0.99 |
| 184_E | 188_K | 1.300 | 0.99 |
| 24_S | 28_K | 1.300 | 0.99 |
| 99_E | 102_D | 1.294 | 0.99 |
| 96_P | 99_E | 1.292 | 0.99 |
| 66_P | 69_V | 1.287 | 0.99 |
| 129_I | 136_V | 1.283 | 0.99 |
| 95_L | 99_E | 1.263 | 0.99 |
| 12_M | 183_L | 1.248 | 0.99 |
| 206_H | 209_A | 1.248 | 0.99 |
| 126_A | 139_I | 1.237 | 0.98 |
| 144_P | 151_D | 1.227 | 0.98 |
| 133_S | 150_D | 1.219 | 0.98 |
| 77_E | 80_N | 1.219 | 0.98 |
| 184_E | 187_R | 1.210 | 0.98 |
| 49_T | 52_G | 1.205 | 0.98 |
| 20_G | 89_D | 1.204 | 0.98 |
| 145_K | 151_D | 1.200 | 0.98 |
| 172_L | 176_E | 1.192 | 0.98 |
| 16_G | 124_L | 1.191 | 0.98 |
| 41_L | 45_M | 1.188 | 0.98 |
| 199_E | 206_H | 1.172 | 0.98 |
| 100_A | 103_R | 1.127 | 0.97 |
| 205_P | 209_A | 1.126 | 0.97 |
| 110_V | 192_L | 1.123 | 0.97 |
| 45_M | 59_I | 1.110 | 0.96 |
| 199_E | 203_I | 1.087 | 0.96 |
| 11_I | 23_S | 1.073 | 0.95 |
| 22_V | 204_W | 1.052 | 0.95 |
| 17_S | 115_V | 1.040 | 0.94 |
| 135_R | 142_N | 1.039 | 0.94 |
| 75_L | 104_A | 1.038 | 0.94 |
| 35_L | 40_L | 1.036 | 0.94 |
| 92_P | 97_Q | 1.030 | 0.94 |
| 199_E | 205_P | 1.029 | 0.94 |
| 72_R | 75_L | 1.028 | 0.94 |
| 45_M | 56_K | 1.022 | 0.93 |
| 26_I | 207_V | 1.021 | 0.93 |
| 40_L | 44_N | 1.020 | 0.93 |
| 48_G | 53_V | 1.016 | 0.93 |
| 125_T | 165_P | 1.009 | 0.93 |
| 77_E | 82_T | 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 | |
| 1zd8A | 1 | 0.9381 | 100 | 0.336 | Contact Map |
| 4qbgB | 1 | 0.9292 | 100 | 0.354 | Contact Map |
| 3be4A | 1 | 0.9204 | 100 | 0.359 | Contact Map |
| 3gmtA | 2 | 0.8451 | 100 | 0.364 | Contact Map |
| 4pzlA | 4 | 0.9469 | 100 | 0.367 | Contact Map |
| 2xb4A | 1 | 0.9115 | 100 | 0.37 | Contact Map |
| 3tlxA | 4 | 0.9425 | 100 | 0.374 | Contact Map |
| 4jzkA | 2 | 0.9115 | 100 | 0.378 | Contact Map |
| 1akyA | 1 | 0.9292 | 100 | 0.379 | Contact Map |
| 1ak2A | 1 | 0.9425 | 100 | 0.386 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)