| yedz |
| ID: | 1400248251 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 211 (201) | ||
| Sequences: | 584 (417.5) | ||
| Seq/Len: | 2.905 | ||
| Nf(neff/√len): | 29.4 |
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: 2.905).
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 |
| 136_T | 139_M | 2.685 | 1.00 |
| 138_A | 142_K | 2.650 | 1.00 |
| 97_L | 102_V | 2.546 | 1.00 |
| 61_I | 73_L | 2.498 | 1.00 |
| 51_A | 88_A | 2.426 | 1.00 |
| 85_F | 132_A | 2.254 | 1.00 |
| 56_L | 183_A | 2.246 | 1.00 |
| 49_R | 165_Y | 2.215 | 1.00 |
| 89_T | 125_W | 2.122 | 1.00 |
| 107_L | 111_E | 2.093 | 1.00 |
| 127_I | 157_V | 2.089 | 1.00 |
| 38_D | 41_K | 2.067 | 1.00 |
| 127_I | 130_A | 2.045 | 1.00 |
| 61_I | 80_L | 1.950 | 0.99 |
| 165_Y | 175_Q | 1.907 | 0.99 |
| 128_L | 157_V | 1.871 | 0.99 |
| 146_H | 149_Q | 1.868 | 0.99 |
| 139_M | 143_L | 1.787 | 0.99 |
| 92_L | 125_W | 1.665 | 0.98 |
| 58_T | 84_C | 1.665 | 0.98 |
| 40_V | 99_E | 1.654 | 0.98 |
| 120_L | 167_W | 1.641 | 0.98 |
| 92_L | 122_I | 1.640 | 0.98 |
| 22_P | 26_L | 1.625 | 0.97 |
| 50_T | 53_K | 1.624 | 0.97 |
| 136_T | 142_K | 1.607 | 0.97 |
| 12_K | 16_H | 1.590 | 0.97 |
| 129_L | 157_V | 1.589 | 0.97 |
| 139_M | 142_K | 1.589 | 0.97 |
| 58_T | 157_V | 1.533 | 0.96 |
| 40_V | 101_G | 1.508 | 0.96 |
| 158_A | 183_A | 1.502 | 0.95 |
| 79_L | 83_W | 1.501 | 0.95 |
| 10_W | 79_L | 1.475 | 0.95 |
| 88_A | 161_A | 1.447 | 0.94 |
| 130_A | 153_F | 1.428 | 0.94 |
| 88_A | 128_L | 1.406 | 0.93 |
| 51_A | 161_A | 1.401 | 0.93 |
| 170_K | 176_P | 1.393 | 0.92 |
| 175_Q | 179_Y | 1.388 | 0.92 |
| 53_K | 179_Y | 1.383 | 0.92 |
| 16_H | 111_E | 1.365 | 0.91 |
| 131_L | 150_L | 1.346 | 0.91 |
| 124_S | 161_A | 1.304 | 0.89 |
| 19_G | 54_F | 1.301 | 0.89 |
| 165_Y | 169_V | 1.297 | 0.88 |
| 63_P | 131_L | 1.296 | 0.88 |
| 133_F | 139_M | 1.291 | 0.88 |
| 120_L | 163_I | 1.266 | 0.87 |
| 45_H | 125_W | 1.263 | 0.87 |
| 47_T | 90_L | 1.259 | 0.86 |
| 115_R | 119_T | 1.249 | 0.86 |
| 47_T | 122_I | 1.248 | 0.86 |
| 9_T | 16_H | 1.241 | 0.85 |
| 108_L | 112_L | 1.240 | 0.85 |
| 108_L | 111_E | 1.232 | 0.85 |
| 107_L | 110_K | 1.229 | 0.84 |
| 117_Y | 171_I | 1.228 | 0.84 |
| 44_Q | 117_Y | 1.209 | 0.83 |
| 16_H | 22_P | 1.206 | 0.83 |
| 105_L | 111_E | 1.200 | 0.82 |
| 178_I | 182_L | 1.199 | 0.82 |
| 124_S | 160_L | 1.197 | 0.82 |
| 49_R | 53_K | 1.180 | 0.81 |
| 145_K | 149_Q | 1.172 | 0.80 |
| 50_T | 79_L | 1.165 | 0.80 |
| 43_I | 94_S | 1.164 | 0.80 |
| 96_A | 102_V | 1.164 | 0.80 |
| 95_Y | 100_L | 1.163 | 0.80 |
| 129_L | 133_F | 1.157 | 0.79 |
| 162_P | 183_A | 1.156 | 0.79 |
| 59_L | 63_P | 1.141 | 0.78 |
| 153_F | 156_L | 1.141 | 0.78 |
| 6_K | 10_W | 1.140 | 0.78 |
| 57_A | 158_A | 1.140 | 0.78 |
| 143_L | 146_H | 1.138 | 0.78 |
| 53_K | 95_Y | 1.101 | 0.74 |
| 83_W | 86_A | 1.079 | 0.72 |
| 82_L | 86_A | 1.077 | 0.72 |
| 51_A | 98_L | 1.077 | 0.72 |
| 154_V | 157_V | 1.068 | 0.71 |
| 122_I | 167_W | 1.067 | 0.71 |
| 16_H | 107_L | 1.061 | 0.70 |
| 66_R | 133_F | 1.059 | 0.70 |
| 8_V | 28_W | 1.056 | 0.70 |
| 184_V | 188_A | 1.056 | 0.70 |
| 22_P | 111_E | 1.050 | 0.69 |
| 16_H | 105_L | 1.048 | 0.69 |
| 72_L | 76_T | 1.038 | 0.68 |
| 47_T | 167_W | 1.032 | 0.67 |
| 13_V | 83_W | 1.019 | 0.66 |
| 34_G | 95_Y | 1.018 | 0.66 |
| 20_L | 24_L | 1.006 | 0.64 |
| 26_L | 106_A | 1.003 | 0.64 |
| 93_T | 97_L | 1.000 | 0.64 |
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 | |
| 4i0uA | 10 | 0.2844 | 2.9 | 0.971 | Contact Map |
| 4ev6A | 5 | 0.2891 | 2.2 | 0.973 | Contact Map |
| 3lbwA | 4 | 0.1043 | 2.2 | 0.973 | Contact Map |
| 2qjyA | 6 | 0.7867 | 2 | 0.974 | Contact Map |
| 3arcT | 2 | 0.1422 | 1.8 | 0.975 | Contact Map |
| 3ne5A | 1 | 0.3128 | 1.5 | 0.975 | Contact Map |
| 4cadC | 4 | 0.9147 | 1.4 | 0.976 | Contact Map |
| 4o6yA | 2 | 0.6398 | 1.4 | 0.976 | Contact Map |
| 2nrgA | 1 | 0.2607 | 1.1 | 0.978 | Contact Map |
| 3bkdA | 8 | 0.1185 | 1 | 0.978 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)