| rkm |
| ID: | 1509442165 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 154 (154) | ||
| Sequences: | 173 (102.9) | ||
| Seq/Len: | 1.123 | ||
| Nf(neff/√len): | 8.3 |
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: 1.123).
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 |
| 100_V | 133_G | 3.599 | 1.00 |
| 17_R | 68_L | 2.716 | 1.00 |
| 106_I | 109_R | 2.565 | 1.00 |
| 100_V | 134_F | 2.483 | 0.99 |
| 107_A | 125_L | 2.394 | 0.99 |
| 144_L | 150_V | 2.371 | 0.99 |
| 142_R | 148_E | 2.219 | 0.98 |
| 144_L | 149_L | 2.182 | 0.98 |
| 61_L | 82_E | 2.140 | 0.98 |
| 117_K | 122_D | 2.135 | 0.98 |
| 75_G | 83_F | 2.066 | 0.97 |
| 17_R | 53_F | 1.840 | 0.94 |
| 100_V | 132_R | 1.781 | 0.92 |
| 11_S | 80_W | 1.777 | 0.92 |
| 14_F | 57_A | 1.728 | 0.90 |
| 94_A | 121_I | 1.573 | 0.84 |
| 84_I | 87_G | 1.528 | 0.81 |
| 116_Q | 120_I | 1.498 | 0.80 |
| 103_S | 133_G | 1.475 | 0.78 |
| 13_Q | 66_D | 1.450 | 0.76 |
| 21_S | 53_F | 1.445 | 0.76 |
| 108_I | 125_L | 1.439 | 0.76 |
| 7_P | 10_E | 1.403 | 0.73 |
| 4_G | 76_D | 1.396 | 0.73 |
| 144_L | 148_E | 1.385 | 0.72 |
| 100_V | 103_S | 1.373 | 0.71 |
| 112_K | 131_F | 1.358 | 0.70 |
| 62_L | 143_E | 1.271 | 0.62 |
| 141_Y | 145_L | 1.264 | 0.61 |
| 46_I | 49_T | 1.263 | 0.61 |
| 47_E | 50_K | 1.260 | 0.61 |
| 83_F | 87_G | 1.254 | 0.61 |
| 18_E | 22_I | 1.252 | 0.60 |
| 42_I | 49_T | 1.245 | 0.60 |
| 6_T | 11_S | 1.242 | 0.59 |
| 106_I | 151_A | 1.220 | 0.57 |
| 55_N | 60_G | 1.213 | 0.57 |
| 73_V | 83_F | 1.196 | 0.55 |
| 12_K | 15_A | 1.195 | 0.55 |
| 7_P | 12_K | 1.184 | 0.54 |
| 138_I | 145_L | 1.175 | 0.53 |
| 108_I | 135_S | 1.168 | 0.52 |
| 106_I | 154_V | 1.159 | 0.52 |
| 39_A | 87_G | 1.149 | 0.51 |
| 54_D | 58_K | 1.146 | 0.50 |
| 96_W | 100_V | 1.138 | 0.50 |
| 70_H | 114_P | 1.136 | 0.49 |
| 129_L | 138_I | 1.132 | 0.49 |
| 113_K | 116_Q | 1.131 | 0.49 |
| 127_S | 131_F | 1.127 | 0.49 |
| 79_H | 82_E | 1.110 | 0.47 |
| 73_V | 91_L | 1.110 | 0.47 |
| 91_L | 117_K | 1.108 | 0.47 |
| 89_L | 141_Y | 1.081 | 0.44 |
| 96_W | 134_F | 1.081 | 0.44 |
| 55_N | 113_K | 1.078 | 0.44 |
| 139_A | 148_E | 1.078 | 0.44 |
| 47_E | 57_A | 1.064 | 0.43 |
| 109_R | 116_Q | 1.061 | 0.42 |
| 77_Q | 84_I | 1.056 | 0.42 |
| 108_I | 117_K | 1.052 | 0.41 |
| 41_A | 45_T | 1.046 | 0.41 |
| 11_S | 17_R | 1.045 | 0.41 |
| 6_T | 82_E | 1.043 | 0.41 |
| 105_L | 134_F | 1.031 | 0.39 |
| 25_L | 32_Y | 1.029 | 0.39 |
| 47_E | 105_L | 1.027 | 0.39 |
| 105_L | 139_A | 1.026 | 0.39 |
| 66_D | 115_T | 1.024 | 0.39 |
| 77_Q | 109_R | 1.023 | 0.39 |
| 94_A | 111_E | 1.022 | 0.39 |
| 42_I | 45_T | 1.006 | 0.37 |
| 55_N | 138_I | 1.001 | 0.37 |
| 3_S | 135_S | 1.001 | 0.37 |
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 | |
| 2wscF | 1 | 1 | 100 | 0.018 | Contact Map |
| 4xk8F | 2 | 0 | 100 | 0.034 | Contact Map |
| 1jb0F | 1 | 0.8701 | 100 | 0.133 | Contact Map |
| 4kt0F | 1 | 0.8701 | 100 | 0.137 | Contact Map |
| 4l6vF | 3 | 0.7597 | 100 | 0.444 | Contact Map |
| 1qzvF | 2 | 0.1948 | 100 | 0.523 | Contact Map |
| 4upkA | 3 | 0 | 15.2 | 0.963 | Contact Map |
| 1t3jA | 1 | 0.4026 | 14.7 | 0.963 | Contact Map |
| 1cf2P | 4 | 0.4091 | 12.2 | 0.964 | Contact Map |
| 2zxeA | 1 | 0.7857 | 9.6 | 0.966 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)