| 1h4d |
| ID: | 1453736876 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 194 (188) | ||
| Sequences: | 12535 (7859.4) | ||
| Seq/Len: | 66.676 | ||
| Nf(neff/√len): | 573.2 |
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: 66.676).
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 |
| 33_K | 41_D | 4.394 | 1.00 |
| 87_M | 147_L | 3.226 | 1.00 |
| 34_P | 37_Q | 2.953 | 1.00 |
| 77_P | 81_A | 2.431 | 1.00 |
| 145_L | 163_L | 2.347 | 1.00 |
| 9_G | 47_L | 2.344 | 1.00 |
| 49_H | 67_K | 2.314 | 1.00 |
| 10_V | 86_V | 2.310 | 1.00 |
| 94_W | 139_N | 2.308 | 1.00 |
| 20_M | 28_L | 2.273 | 1.00 |
| 26_G | 100_C | 2.176 | 1.00 |
| 43_L | 98_C | 2.153 | 1.00 |
| 187_L | 191_Q | 1.972 | 1.00 |
| 8_T | 92_G | 1.932 | 1.00 |
| 37_Q | 41_D | 1.918 | 1.00 |
| 9_G | 43_L | 1.912 | 1.00 |
| 183_T | 186_E | 1.890 | 1.00 |
| 51_V | 69_I | 1.879 | 1.00 |
| 28_L | 187_L | 1.841 | 1.00 |
| 104_Y | 190_W | 1.825 | 1.00 |
| 94_W | 137_L | 1.809 | 1.00 |
| 69_I | 85_S | 1.799 | 1.00 |
| 81_A | 85_S | 1.736 | 1.00 |
| 33_K | 37_Q | 1.692 | 1.00 |
| 33_K | 38_H | 1.689 | 1.00 |
| 35_L | 181_V | 1.658 | 1.00 |
| 109_L | 177_A | 1.639 | 1.00 |
| 8_T | 49_H | 1.605 | 1.00 |
| 53_N | 86_V | 1.580 | 1.00 |
| 94_W | 117_R | 1.554 | 1.00 |
| 40_A | 50_V | 1.547 | 1.00 |
| 106_P | 177_A | 1.517 | 1.00 |
| 83_M | 97_F | 1.513 | 1.00 |
| 10_V | 95_F | 1.512 | 1.00 |
| 13_A | 52_V | 1.478 | 1.00 |
| 84_L | 87_M | 1.471 | 1.00 |
| 90_E | 95_F | 1.462 | 1.00 |
| 145_L | 160_F | 1.452 | 1.00 |
| 51_V | 89_Q | 1.451 | 1.00 |
| 84_L | 147_L | 1.445 | 1.00 |
| 58_Q | 70_E | 1.442 | 1.00 |
| 186_E | 189_R | 1.437 | 1.00 |
| 99_P | 102_T | 1.436 | 1.00 |
| 111_A | 115_H | 1.404 | 0.99 |
| 112_R | 115_H | 1.371 | 0.99 |
| 113_L | 137_L | 1.355 | 0.99 |
| 54_A | 68_V | 1.347 | 0.99 |
| 181_V | 190_W | 1.347 | 0.99 |
| 159_V | 162_R | 1.345 | 0.99 |
| 98_C | 110_A | 1.327 | 0.99 |
| 158_M | 162_R | 1.325 | 0.99 |
| 23_V | 29_E | 1.313 | 0.99 |
| 8_T | 90_E | 1.309 | 0.99 |
| 67_K | 89_Q | 1.308 | 0.99 |
| 179_V | 189_R | 1.305 | 0.99 |
| 149_Y | 160_F | 1.304 | 0.99 |
| 188_A | 191_Q | 1.282 | 0.99 |
| 95_F | 140_R | 1.263 | 0.99 |
| 62_Q | 70_E | 1.258 | 0.99 |
| 57_H | 60_I | 1.240 | 0.98 |
| 96_L | 110_A | 1.220 | 0.98 |
| 145_L | 164_A | 1.214 | 0.98 |
| 16_K | 76_Y | 1.207 | 0.98 |
| 96_L | 137_L | 1.182 | 0.98 |
| 11_V | 43_L | 1.178 | 0.98 |
| 46_Q | 111_A | 1.170 | 0.97 |
| 81_A | 84_L | 1.170 | 0.97 |
| 102_T | 178_F | 1.165 | 0.97 |
| 11_V | 40_A | 1.163 | 0.97 |
| 29_E | 34_P | 1.151 | 0.97 |
| 148_E | 163_L | 1.150 | 0.97 |
| 124_W | 130_R | 1.150 | 0.97 |
| 6_T | 93_E | 1.146 | 0.97 |
| 160_F | 164_A | 1.138 | 0.97 |
| 54_A | 58_Q | 1.129 | 0.97 |
| 87_M | 95_F | 1.127 | 0.97 |
| 109_L | 112_R | 1.117 | 0.96 |
| 106_P | 109_L | 1.116 | 0.96 |
| 107_P | 111_A | 1.110 | 0.96 |
| 71_D | 81_A | 1.094 | 0.96 |
| 117_R | 123_V | 1.093 | 0.96 |
| 84_L | 88_Q | 1.091 | 0.96 |
| 87_M | 143_E | 1.087 | 0.96 |
| 117_R | 139_N | 1.084 | 0.96 |
| 96_L | 114_N | 1.081 | 0.95 |
| 54_A | 59_E | 1.079 | 0.95 |
| 20_M | 184_P | 1.075 | 0.95 |
| 29_E | 32_G | 1.072 | 0.95 |
| 42_A | 107_P | 1.072 | 0.95 |
| 114_N | 137_L | 1.069 | 0.95 |
| 156_R | 159_V | 1.069 | 0.95 |
| 10_V | 97_F | 1.054 | 0.95 |
| 121_P | 139_N | 1.053 | 0.95 |
| 185_E | 189_R | 1.047 | 0.94 |
| 179_V | 190_W | 1.038 | 0.94 |
| 11_V | 39_V | 1.037 | 0.94 |
| 58_Q | 62_Q | 1.032 | 0.94 |
| 102_T | 135_I | 1.032 | 0.94 |
| 94_W | 140_R | 1.031 | 0.94 |
| 79_P | 99_P | 1.030 | 0.94 |
| 7_I | 94_W | 1.007 | 0.93 |
| 34_P | 38_H | 1.007 | 0.93 |
| 39_V | 42_A | 1.005 | 0.93 |
| 36_W | 52_V | 1.003 | 0.93 |
| 27_L | 60_I | 1.003 | 0.93 |
| 145_L | 148_E | 1.001 | 0.92 |
| 8_T | 51_V | 1.000 | 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 | |
| 1e5kA | 1 | 0.9691 | 100 | 0.135 | Contact Map |
| 2e8bA | 1 | 0.9175 | 100 | 0.225 | Contact Map |
| 2weeA | 2 | 0.9433 | 100 | 0.255 | Contact Map |
| 3ngwA | 1 | 0.9278 | 100 | 0.259 | Contact Map |
| 2wawA | 1 | 0.9433 | 100 | 0.261 | Contact Map |
| 3d5nA | 8 | 0.8866 | 100 | 0.304 | Contact Map |
| 4mndA | 1 | 0.9278 | 99.9 | 0.37 | Contact Map |
| 2px7A | 2 | 0.8918 | 99.9 | 0.37 | Contact Map |
| 2xmeA | 12 | 0.9072 | 99.9 | 0.373 | Contact Map |
| 4jd0A | 1 | 0.9794 | 99.9 | 0.379 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)