| NatR |
| ID: | 1490972596 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 170 (154) | ||
| Sequences: | 55045 (39758.9) | ||
| Seq/Len: | 357.435 | ||
| Nf(neff/√len): | 3203.9 |
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: 357.435).
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 |
| 10_G | 51_Y | 2.869 | 1.00 |
| 91_T | 128_F | 2.532 | 1.00 |
| 98_L | 130_F | 2.490 | 1.00 |
| 133_I | 152_Q | 2.481 | 1.00 |
| 10_G | 16_N | 2.401 | 1.00 |
| 98_L | 153_K | 2.399 | 1.00 |
| 112_L | 125_Y | 2.361 | 1.00 |
| 109_N | 152_Q | 2.133 | 1.00 |
| 60_V | 97_V | 2.130 | 1.00 |
| 122_I | 126_R | 2.112 | 1.00 |
| 132_I | 149_H | 2.078 | 1.00 |
| 96_H | 99_N | 1.947 | 1.00 |
| 91_T | 127_K | 1.943 | 1.00 |
| 26_V | 81_L | 1.879 | 1.00 |
| 132_I | 135_T | 1.854 | 1.00 |
| 62_C | 97_V | 1.789 | 1.00 |
| 95_N | 128_F | 1.734 | 1.00 |
| 126_R | 132_I | 1.731 | 1.00 |
| 100_I | 104_D | 1.729 | 1.00 |
| 122_I | 132_I | 1.721 | 1.00 |
| 57_V | 84_Y | 1.708 | 1.00 |
| 123_D | 126_R | 1.681 | 1.00 |
| 49_L | 56_A | 1.677 | 1.00 |
| 58_G | 80_C | 1.667 | 1.00 |
| 96_H | 100_I | 1.575 | 1.00 |
| 19_Q | 56_A | 1.570 | 1.00 |
| 84_Y | 87_L | 1.561 | 1.00 |
| 94_L | 128_F | 1.548 | 1.00 |
| 50_A | 89_I | 1.517 | 1.00 |
| 100_I | 103_K | 1.517 | 1.00 |
| 19_Q | 22_R | 1.513 | 1.00 |
| 12_V | 49_L | 1.502 | 1.00 |
| 91_T | 95_N | 1.485 | 1.00 |
| 48_K | 96_H | 1.477 | 1.00 |
| 116_I | 147_D | 1.444 | 1.00 |
| 6_R | 92_K | 1.413 | 1.00 |
| 81_L | 84_Y | 1.409 | 1.00 |
| 98_L | 110_I | 1.399 | 0.99 |
| 60_V | 93_M | 1.384 | 0.99 |
| 52_F | 57_V | 1.377 | 0.99 |
| 51_Y | 56_A | 1.375 | 0.99 |
| 114_V | 122_I | 1.371 | 0.99 |
| 121_A | 125_Y | 1.354 | 0.99 |
| 102_E | 155_L | 1.347 | 0.99 |
| 62_C | 101_C | 1.333 | 0.99 |
| 90_G | 124_F | 1.311 | 0.99 |
| 122_I | 149_H | 1.274 | 0.99 |
| 55_I | 81_L | 1.260 | 0.99 |
| 116_I | 135_T | 1.260 | 0.99 |
| 135_T | 147_D | 1.246 | 0.98 |
| 92_K | 96_H | 1.236 | 0.98 |
| 99_N | 103_K | 1.231 | 0.98 |
| 118_N | 121_A | 1.213 | 0.98 |
| 55_I | 83_P | 1.211 | 0.98 |
| 13_T | 16_N | 1.207 | 0.98 |
| 22_R | 26_V | 1.202 | 0.98 |
| 132_I | 151_L | 1.201 | 0.98 |
| 119_E | 122_I | 1.199 | 0.98 |
| 47_A | 61_C | 1.193 | 0.98 |
| 50_A | 93_M | 1.192 | 0.98 |
| 48_K | 100_I | 1.190 | 0.98 |
| 101_C | 110_I | 1.185 | 0.98 |
| 55_I | 84_Y | 1.183 | 0.98 |
| 122_I | 151_L | 1.169 | 0.97 |
| 19_Q | 55_I | 1.150 | 0.97 |
| 114_V | 125_Y | 1.128 | 0.97 |
| 73_L | 107_F | 1.117 | 0.96 |
| 124_F | 128_F | 1.111 | 0.96 |
| 8_E | 51_Y | 1.106 | 0.96 |
| 109_N | 154_N | 1.105 | 0.96 |
| 52_F | 84_Y | 1.103 | 0.96 |
| 135_T | 149_H | 1.091 | 0.96 |
| 23_L | 79_G | 1.087 | 0.96 |
| 18_K | 34_D | 1.080 | 0.95 |
| 119_E | 123_D | 1.071 | 0.95 |
| 12_V | 20_L | 1.046 | 0.94 |
| 78_L | 125_Y | 1.035 | 0.94 |
| 88_G | 91_T | 1.032 | 0.94 |
| 21_K | 25_Q | 1.026 | 0.94 |
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 | |
| 2ob0A | 3 | 0.9882 | 99.9 | 0.096 | Contact Map |
| 3kkwA | 1 | 0.8824 | 99.9 | 0.227 | Contact Map |
| 2cntA | 4 | 0.8824 | 99.8 | 0.23 | Contact Map |
| 4l8aA | 1 | 0.8824 | 99.8 | 0.245 | Contact Map |
| 4kvxA | 2 | 0.8588 | 99.8 | 0.256 | Contact Map |
| 2j8mA | 2 | 0.9176 | 99.8 | 0.258 | Contact Map |
| 3dr6A | 3 | 0.9294 | 99.8 | 0.264 | Contact Map |
| 4pv6C | 16 | 0.9 | 99.8 | 0.27 | Contact Map |
| 4r3lA | 1 | 0.8647 | 99.8 | 0.274 | Contact Map |
| 4h89A | 1 | 0.8882 | 99.8 | 0.285 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)