| 4158 |
| ID: | 1448018359 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 163 (162) | ||
| Sequences: | 700 (524.2) | ||
| Seq/Len: | 4.321 | ||
| Nf(neff/√len): | 41.2 |
HHblits Results: (2015_06)
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: 4.321).
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 |
| 88_Y | 98_H | 2.977 | 1.00 |
| 45_G | 88_Y | 2.795 | 1.00 |
| 26_L | 47_A | 2.474 | 1.00 |
| 136_L | 140_L | 2.342 | 1.00 |
| 123_L | 136_L | 2.325 | 1.00 |
| 33_F | 46_F | 2.299 | 1.00 |
| 46_F | 102_L | 2.182 | 1.00 |
| 153_S | 156_Q | 1.945 | 1.00 |
| 49_S | 60_L | 1.906 | 1.00 |
| 143_E | 146_Y | 1.878 | 1.00 |
| 45_G | 98_H | 1.870 | 1.00 |
| 133_G | 161_V | 1.817 | 1.00 |
| 123_L | 140_L | 1.815 | 1.00 |
| 30_D | 54_R | 1.811 | 1.00 |
| 34_I | 47_A | 1.807 | 1.00 |
| 53_M | 150_L | 1.800 | 1.00 |
| 143_E | 147_R | 1.765 | 1.00 |
| 51_C | 54_R | 1.714 | 0.99 |
| 47_A | 77_Q | 1.628 | 0.99 |
| 33_F | 105_K | 1.627 | 0.99 |
| 18_E | 34_I | 1.537 | 0.98 |
| 103_M | 150_L | 1.533 | 0.98 |
| 22_K | 38_R | 1.474 | 0.98 |
| 109_K | 115_Y | 1.462 | 0.97 |
| 91_R | 97_E | 1.456 | 0.97 |
| 80_L | 84_D | 1.454 | 0.97 |
| 7_R | 158_E | 1.436 | 0.97 |
| 30_D | 105_K | 1.374 | 0.96 |
| 44_L | 75_A | 1.342 | 0.95 |
| 155_L | 159_S | 1.331 | 0.95 |
| 151_L | 157_I | 1.329 | 0.95 |
| 130_N | 133_G | 1.279 | 0.93 |
| 151_L | 156_Q | 1.266 | 0.93 |
| 133_G | 140_L | 1.254 | 0.92 |
| 121_R | 124_T | 1.240 | 0.92 |
| 137_L | 161_V | 1.239 | 0.92 |
| 24_Y | 56_P | 1.226 | 0.91 |
| 118_E | 147_R | 1.222 | 0.91 |
| 130_N | 135_F | 1.208 | 0.91 |
| 95_R | 99_Q | 1.200 | 0.90 |
| 13_L | 52_M | 1.195 | 0.90 |
| 20_L | 70_L | 1.182 | 0.89 |
| 48_L | 71_V | 1.172 | 0.89 |
| 108_Y | 149_I | 1.171 | 0.89 |
| 30_D | 50_L | 1.165 | 0.88 |
| 133_G | 137_L | 1.156 | 0.88 |
| 111_F | 151_L | 1.152 | 0.88 |
| 66_P | 103_M | 1.149 | 0.87 |
| 24_Y | 70_L | 1.143 | 0.87 |
| 158_E | 162_S | 1.143 | 0.87 |
| 48_L | 74_I | 1.120 | 0.85 |
| 75_A | 98_H | 1.117 | 0.85 |
| 61_K | 92_A | 1.114 | 0.85 |
| 47_A | 78_L | 1.113 | 0.85 |
| 127_A | 136_L | 1.111 | 0.85 |
| 16_Q | 19_E | 1.105 | 0.84 |
| 26_L | 74_I | 1.104 | 0.84 |
| 53_M | 102_L | 1.099 | 0.84 |
| 72_E | 86_L | 1.089 | 0.83 |
| 104_Q | 107_G | 1.077 | 0.82 |
| 135_F | 139_T | 1.073 | 0.82 |
| 75_A | 88_Y | 1.051 | 0.80 |
| 59_T | 99_Q | 1.050 | 0.80 |
| 144_M | 157_I | 1.043 | 0.79 |
| 15_E | 19_E | 1.040 | 0.79 |
| 120_V | 160_M | 1.036 | 0.79 |
| 30_D | 51_C | 1.035 | 0.79 |
| 58_R | 150_L | 1.031 | 0.78 |
| 119_M | 140_L | 1.029 | 0.78 |
| 68_K | 82_Y | 1.027 | 0.78 |
| 11_E | 51_C | 1.019 | 0.77 |
| 134_I | 138_Q | 1.016 | 0.77 |
| 107_G | 148_K | 1.014 | 0.77 |
| 142_H | 146_Y | 1.005 | 0.76 |
| 3_S | 7_R | 1.004 | 0.76 |
| 92_A | 97_E | 1.000 | 0.75 |
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 | |
| 4fcyA | 2 | 0.773 | 18.6 | 0.928 | Contact Map |
| 4icgC | 2 | 0.3865 | 5.6 | 0.943 | Contact Map |
| 4gdfA | 4 | 0.6135 | 5.5 | 0.944 | Contact Map |
| 2i5uA | 1 | 0.4049 | 5.4 | 0.944 | Contact Map |
| 4n78F | 1 | 0.7975 | 4.8 | 0.945 | Contact Map |
| 3o9xA | 2 | 0.6564 | 4.8 | 0.945 | Contact Map |
| 2o4dA | 1 | 0.3926 | 4.2 | 0.947 | Contact Map |
| 4u7tA | 2 | 0.3374 | 4 | 0.947 | Contact Map |
| 3qv2A | 1 | 0.3374 | 4 | 0.947 | Contact Map |
| 2jqtA | 1 | 0.3129 | 4 | 0.947 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)