| RNF |
| ID: | 1504827218 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 442 (167) | ||
| Sequences: | 1101 (638.3) | ||
| Seq/Len: | 6.593 | ||
| Nf(neff/√len): | 49.4 |
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: 6.593).
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 |
| 55_F | 62_L | 3.877 | 1.00 |
| 51_I | 73_V | 3.397 | 1.00 |
| 52_H | 66_K | 2.764 | 1.00 |
| 112_A | 116_E | 2.030 | 1.00 |
| 56_G | 66_K | 1.968 | 1.00 |
| 112_A | 117_F | 1.964 | 1.00 |
| 116_E | 119_D | 1.794 | 1.00 |
| 59_Q | 62_L | 1.761 | 1.00 |
| 59_Q | 63_A | 1.688 | 1.00 |
| 113_N | 117_F | 1.674 | 1.00 |
| 55_F | 66_K | 1.602 | 1.00 |
| 52_H | 70_L | 1.573 | 0.99 |
| 44_A | 73_V | 1.531 | 0.99 |
| 104_I | 127_R | 1.419 | 0.99 |
| 108_F | 120_L | 1.376 | 0.98 |
| 12_L | 80_K | 1.367 | 0.98 |
| 87_Q | 127_R | 1.356 | 0.98 |
| 87_Q | 140_P | 1.346 | 0.98 |
| 84_F | 87_Q | 1.322 | 0.98 |
| 155_A | 158_L | 1.319 | 0.98 |
| 22_L | 84_F | 1.290 | 0.97 |
| 55_F | 59_Q | 1.284 | 0.97 |
| 154_F | 158_L | 1.268 | 0.97 |
| 148_S | 151_R | 1.264 | 0.97 |
| 40_V | 47_E | 1.260 | 0.97 |
| 71_Q | 75_S | 1.245 | 0.96 |
| 154_F | 157_C | 1.243 | 0.96 |
| 106_S | 110_S | 1.240 | 0.96 |
| 65_R | 68_L | 1.239 | 0.96 |
| 104_I | 108_F | 1.231 | 0.96 |
| 6_V | 9_C | 1.224 | 0.96 |
| 104_I | 116_E | 1.222 | 0.96 |
| 5_Y | 9_C | 1.209 | 0.95 |
| 140_P | 143_S | 1.204 | 0.95 |
| 63_A | 66_K | 1.184 | 0.95 |
| 37_V | 88_L | 1.177 | 0.95 |
| 19_V | 23_Q | 1.175 | 0.95 |
| 149_D | 152_A | 1.169 | 0.94 |
| 48_E | 70_L | 1.168 | 0.94 |
| 40_V | 84_F | 1.167 | 0.94 |
| 39_E | 51_I | 1.165 | 0.94 |
| 102_L | 106_S | 1.163 | 0.94 |
| 12_L | 38_E | 1.162 | 0.94 |
| 16_V | 105_C | 1.152 | 0.94 |
| 20_K | 23_Q | 1.151 | 0.94 |
| 156_R | 162_L | 1.150 | 0.94 |
| 156_R | 159_E | 1.125 | 0.93 |
| 16_V | 109_L | 1.108 | 0.92 |
| 58_M | 62_L | 1.104 | 0.92 |
| 130_G | 133_T | 1.096 | 0.91 |
| 48_E | 74_Q | 1.094 | 0.91 |
| 146_I | 150_H | 1.092 | 0.91 |
| 149_D | 153_E | 1.089 | 0.91 |
| 153_E | 157_C | 1.088 | 0.91 |
| 20_K | 106_S | 1.085 | 0.91 |
| 55_F | 102_L | 1.085 | 0.91 |
| 138_L | 141_I | 1.083 | 0.91 |
| 33_L | 84_F | 1.081 | 0.91 |
| 19_V | 101_H | 1.080 | 0.91 |
| 140_P | 144_S | 1.066 | 0.90 |
| 21_A | 34_Q | 1.065 | 0.90 |
| 44_A | 77_Y | 1.064 | 0.90 |
| 70_L | 124_L | 1.048 | 0.89 |
| 101_H | 121_G | 1.048 | 0.89 |
| 114_K | 119_D | 1.048 | 0.89 |
| 111_L | 116_E | 1.044 | 0.88 |
| 56_G | 59_Q | 1.040 | 0.88 |
| 155_A | 159_E | 1.035 | 0.88 |
| 75_S | 78_E | 1.025 | 0.87 |
| 30_I | 124_L | 1.025 | 0.87 |
| 157_C | 160_P | 1.023 | 0.87 |
| 31_A | 53_A | 1.021 | 0.87 |
| 147_A | 150_H | 1.014 | 0.86 |
| 152_A | 155_A | 1.012 | 0.86 |
| 153_E | 156_R | 1.009 | 0.86 |
| 77_Y | 87_Q | 1.009 | 0.86 |
| 108_F | 116_E | 1.007 | 0.86 |
| 157_C | 165_G | 1.005 | 0.86 |
| 100_V | 104_I | 1.004 | 0.86 |
| 148_S | 152_A | 1.001 | 0.86 |
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 | |
| 4nqjA | 3 | 0.3801 | 98.5 | 0.923 | Contact Map |
| 4ltbA | 2 | 0.3643 | 98.3 | 0.928 | Contact Map |
| 4tn3A | 2 | 0.681 | 97.3 | 0.942 | Contact Map |
| 3okqA | 1 | 0.2805 | 96.4 | 0.948 | Contact Map |
| 4m3lA | 4 | 0.1357 | 95.9 | 0.95 | Contact Map |
| 4kblA | 2 | 0.2896 | 94.2 | 0.955 | Contact Map |
| 4cg4A | 6 | 0 | 90.9 | 0.96 | Contact Map |
| 4cfgA | 2 | 0.2964 | 88.3 | 0.962 | Contact Map |
| 1i84S | 2 | 0.1131 | 83 | 0.964 | Contact Map |
| 2dfsA | 2 | 0.276 | 47.1 | 0.972 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)