| yym |
| ID: | 1491814420 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 119 (119) | ||
| Sequences: | 597 (366.5) | ||
| Seq/Len: | 5.017 | ||
| Nf(neff/√len): | 33.6 |
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: 5.017).
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 |
| 40_H | 74_T | 4.123 | 1.00 |
| 57_C | 64_C | 2.893 | 1.00 |
| 63_N | 100_A | 2.461 | 1.00 |
| 67_S | 97_F | 1.964 | 1.00 |
| 5_W | 9_Q | 1.794 | 1.00 |
| 21_A | 25_I | 1.745 | 1.00 |
| 9_Q | 33_K | 1.666 | 0.99 |
| 5_W | 8_I | 1.655 | 0.99 |
| 32_C | 86_C | 1.567 | 0.99 |
| 33_K | 117_H | 1.548 | 0.99 |
| 36_N | 117_H | 1.511 | 0.99 |
| 73_M | 95_K | 1.475 | 0.98 |
| 70_P | 96_F | 1.472 | 0.98 |
| 3_A | 7_E | 1.427 | 0.98 |
| 22_M | 27_N | 1.390 | 0.97 |
| 66_Q | 98_V | 1.378 | 0.97 |
| 49_T | 62_N | 1.365 | 0.97 |
| 6_F | 10_H | 1.359 | 0.97 |
| 49_T | 97_F | 1.357 | 0.97 |
| 17_Q | 27_N | 1.339 | 0.96 |
| 17_Q | 74_T | 1.336 | 0.96 |
| 12_Q | 17_Q | 1.333 | 0.96 |
| 17_Q | 46_V | 1.313 | 0.96 |
| 1_T | 5_W | 1.296 | 0.95 |
| 51_N | 94_Y | 1.265 | 0.95 |
| 70_P | 80_S | 1.256 | 0.94 |
| 9_Q | 117_H | 1.255 | 0.94 |
| 107_I | 110_P | 1.255 | 0.94 |
| 46_V | 99_V | 1.238 | 0.94 |
| 19_N | 74_T | 1.228 | 0.93 |
| 41_D | 77_R | 1.222 | 0.93 |
| 106_K | 109_P | 1.215 | 0.93 |
| 9_Q | 100_A | 1.202 | 0.92 |
| 11_I | 46_V | 1.201 | 0.92 |
| 41_D | 45_N | 1.181 | 0.91 |
| 22_M | 40_H | 1.178 | 0.91 |
| 39_L | 118_L | 1.176 | 0.91 |
| 8_I | 25_I | 1.174 | 0.91 |
| 54_N | 95_K | 1.156 | 0.90 |
| 33_K | 38_F | 1.140 | 0.89 |
| 21_A | 96_F | 1.125 | 0.89 |
| 2_K | 5_W | 1.112 | 0.88 |
| 64_C | 100_A | 1.104 | 0.87 |
| 17_Q | 21_A | 1.091 | 0.86 |
| 77_R | 91_S | 1.081 | 0.86 |
| 25_I | 28_Y | 1.079 | 0.86 |
| 107_I | 112_H | 1.075 | 0.85 |
| 26_N | 119_D | 1.065 | 0.85 |
| 3_A | 9_Q | 1.046 | 0.83 |
| 13_L | 48_A | 1.039 | 0.83 |
| 81_G | 105_Q | 1.023 | 0.81 |
| 57_C | 65_H | 1.020 | 0.81 |
| 9_Q | 36_N | 1.019 | 0.81 |
| 44_Q | 47_A | 1.002 | 0.79 |
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 | |
| 2hkyA | 1 | 1 | 100 | 0.061 | Contact Map |
| 4owzA | 2 | 1 | 100 | 0.09 | Contact Map |
| 1gqvA | 1 | 1 | 100 | 0.094 | Contact Map |
| 2apqA | 1 | 0.9244 | 100 | 0.104 | Contact Map |
| 3mwqA | 1 | 0.9412 | 100 | 0.119 | Contact Map |
| 1rraA | 1 | 0.9412 | 100 | 0.127 | Contact Map |
| 1dy5A | 2 | 0.9328 | 100 | 0.131 | Contact Map |
| 2e0jA | 2 | 0.9412 | 100 | 0.132 | Contact Map |
| 1rnfA | 2 | 0.9244 | 100 | 0.154 | Contact Map |
| 2vq9A | 1 | 0.9076 | 100 | 0.156 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)