| 1CHDA |
| ID: | 1411603930 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 198 (188) | ||
| Sequences: | 2104 (1683) | ||
| Seq/Len: | 11.191 | ||
| Nf(neff/√len): | 122.7 |
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: 11.191).
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 |
| 143_M | 148_A | 3.946 | 1.00 |
| 9_A | 116_V | 3.558 | 1.00 |
| 161_F | 168_I | 3.496 | 1.00 |
| 11_G | 109_V | 3.410 | 1.00 |
| 175_E | 185_Q | 2.617 | 1.00 |
| 144_Y | 174_S | 2.593 | 1.00 |
| 140_M | 150_T | 2.524 | 1.00 |
| 141_L | 145_Q | 2.517 | 1.00 |
| 152_A | 173_V | 2.500 | 1.00 |
| 58_I | 74_A | 2.351 | 1.00 |
| 126_G | 143_M | 2.305 | 1.00 |
| 151_I | 182_V | 2.164 | 1.00 |
| 61_K | 73_H | 2.128 | 1.00 |
| 61_K | 67_E | 2.121 | 1.00 |
| 168_I | 176_V | 2.112 | 1.00 |
| 40_M | 45_T | 2.093 | 1.00 |
| 152_A | 168_I | 2.028 | 1.00 |
| 165_R | 169_N | 2.022 | 1.00 |
| 114_H | 142_A | 1.987 | 1.00 |
| 140_M | 167_A | 1.918 | 1.00 |
| 81_K | 98_D | 1.902 | 1.00 |
| 10_I | 23_V | 1.899 | 1.00 |
| 53_N | 59_S | 1.890 | 1.00 |
| 177_V | 182_V | 1.867 | 1.00 |
| 61_K | 64_E | 1.856 | 1.00 |
| 12_A | 16_G | 1.848 | 1.00 |
| 83_M | 94_I | 1.848 | 1.00 |
| 59_S | 73_H | 1.842 | 1.00 |
| 37_T | 112_L | 1.823 | 1.00 |
| 137_A | 170_M | 1.759 | 1.00 |
| 65_D | 95_K | 1.698 | 1.00 |
| 130_T | 179_L | 1.665 | 1.00 |
| 137_A | 166_E | 1.660 | 1.00 |
| 116_V | 124_A | 1.599 | 1.00 |
| 110_D | 139_G | 1.588 | 1.00 |
| 75_Y | 94_I | 1.583 | 1.00 |
| 161_F | 165_R | 1.580 | 1.00 |
| 185_Q | 188_A | 1.563 | 1.00 |
| 20_I | 36_I | 1.548 | 1.00 |
| 67_E | 75_Y | 1.536 | 1.00 |
| 24_L | 56_C | 1.528 | 1.00 |
| 86_A | 95_K | 1.524 | 1.00 |
| 12_A | 129_L | 1.506 | 1.00 |
| 23_V | 182_V | 1.492 | 1.00 |
| 23_V | 129_L | 1.491 | 1.00 |
| 28_P | 187_L | 1.482 | 1.00 |
| 166_E | 169_N | 1.468 | 1.00 |
| 22_H | 180_S | 1.465 | 1.00 |
| 32_P | 72_G | 1.446 | 1.00 |
| 153_Q | 158_C | 1.443 | 1.00 |
| 137_A | 172_G | 1.425 | 1.00 |
| 152_A | 176_V | 1.412 | 1.00 |
| 7_L | 35_I | 1.398 | 0.99 |
| 154_N | 178_D | 1.397 | 0.99 |
| 157_S | 179_L | 1.379 | 0.99 |
| 102_V | 114_H | 1.351 | 0.99 |
| 98_D | 106_R | 1.344 | 0.99 |
| 35_I | 69_V | 1.331 | 0.99 |
| 35_I | 94_I | 1.314 | 0.99 |
| 45_T | 62_E | 1.302 | 0.99 |
| 19_A | 179_L | 1.302 | 0.99 |
| 113_F | 128_I | 1.250 | 0.99 |
| 137_A | 167_A | 1.243 | 0.98 |
| 132_M | 162_G | 1.242 | 0.98 |
| 6_K | 123_N | 1.240 | 0.98 |
| 149_W | 175_E | 1.215 | 0.98 |
| 24_L | 74_A | 1.211 | 0.98 |
| 33_A | 69_V | 1.207 | 0.98 |
| 70_L | 73_H | 1.203 | 0.98 |
| 150_T | 172_G | 1.164 | 0.97 |
| 46_R | 50_E | 1.163 | 0.97 |
| 9_A | 112_L | 1.158 | 0.97 |
| 63_A | 83_M | 1.154 | 0.97 |
| 154_N | 158_C | 1.146 | 0.97 |
| 24_L | 36_I | 1.145 | 0.97 |
| 128_I | 140_M | 1.139 | 0.97 |
| 140_M | 170_M | 1.137 | 0.97 |
| 126_G | 140_M | 1.129 | 0.97 |
| 92_Y | 120_A | 1.128 | 0.97 |
| 124_A | 143_M | 1.114 | 0.96 |
| 150_T | 167_A | 1.112 | 0.96 |
| 158_C | 161_F | 1.107 | 0.96 |
| 167_A | 173_V | 1.099 | 0.96 |
| 7_L | 124_A | 1.087 | 0.96 |
| 20_I | 25_Q | 1.062 | 0.95 |
| 27_L | 34_V | 1.057 | 0.95 |
| 82_H | 106_R | 1.055 | 0.95 |
| 18_E | 159_V | 1.038 | 0.94 |
| 167_A | 172_G | 1.037 | 0.94 |
| 69_V | 85_L | 1.032 | 0.94 |
| 27_L | 186_M | 1.011 | 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 | |
| 1chdA | 1 | 1 | 100 | 0.002 | Contact Map |
| 3sftA | 1 | 0.9495 | 100 | 0.025 | Contact Map |
| 1a2oA | 2 | 0.9899 | 100 | 0.094 | Contact Map |
| 4fx9A | 2 | 0.9343 | 38.1 | 0.943 | Contact Map |
| 1zkpA | 4 | 0.3434 | 32.6 | 0.945 | Contact Map |
| 4nwzA | 4 | 0.9848 | 32.5 | 0.945 | Contact Map |
| 3ic9A | 4 | 0.9343 | 32 | 0.945 | Contact Map |
| 2xr1A | 2 | 0.3535 | 29.7 | 0.946 | Contact Map |
| 2ycbA | 2 | 0.3586 | 27.9 | 0.947 | Contact Map |
| 3af5A | 1 | 0.3586 | 20.1 | 0.95 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)