| babushka |
| ID: | 1399786188 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 145 (145) | ||
| Sequences: | 178 (149.4) | ||
| Seq/Len: | 1.228 | ||
| Nf(neff/√len): | 12.4 |
HHblits Results: (2013_03)
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: 1.228).
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 |
| 70_K | 116_T | 2.235 | 0.99 |
| 108_V | 127_L | 1.724 | 0.92 |
| 113_L | 117_D | 1.697 | 0.91 |
| 50_I | 72_L | 1.688 | 0.90 |
| 84_G | 113_L | 1.651 | 0.89 |
| 31_M | 91_R | 1.616 | 0.88 |
| 111_K | 135_E | 1.603 | 0.87 |
| 69_Y | 108_V | 1.550 | 0.85 |
| 134_G | 142_N | 1.537 | 0.84 |
| 72_L | 100_K | 1.514 | 0.83 |
| 2_D | 6_V | 1.474 | 0.80 |
| 109_D | 140_L | 1.450 | 0.79 |
| 130_L | 134_G | 1.439 | 0.78 |
| 70_K | 83_L | 1.433 | 0.78 |
| 104_I | 129_I | 1.431 | 0.77 |
| 93_F | 111_K | 1.427 | 0.77 |
| 17_K | 20_Q | 1.406 | 0.76 |
| 113_L | 142_N | 1.404 | 0.76 |
| 66_L | 100_K | 1.353 | 0.72 |
| 88_E | 106_K | 1.347 | 0.71 |
| 46_L | 81_V | 1.320 | 0.69 |
| 134_G | 137_K | 1.318 | 0.69 |
| 42_R | 50_I | 1.305 | 0.68 |
| 60_T | 65_E | 1.296 | 0.67 |
| 84_G | 144_Y | 1.277 | 0.65 |
| 85_L | 130_L | 1.244 | 0.62 |
| 72_L | 79_D | 1.240 | 0.62 |
| 10_G | 14_V | 1.233 | 0.61 |
| 69_Y | 137_K | 1.231 | 0.61 |
| 31_M | 142_N | 1.227 | 0.61 |
| 109_D | 134_G | 1.219 | 0.60 |
| 41_E | 112_L | 1.217 | 0.60 |
| 130_L | 135_E | 1.212 | 0.59 |
| 35_R | 59_E | 1.211 | 0.59 |
| 56_L | 140_L | 1.180 | 0.56 |
| 7_G | 14_V | 1.174 | 0.56 |
| 125_K | 128_D | 1.174 | 0.56 |
| 37_E | 41_E | 1.160 | 0.54 |
| 87_L | 92_G | 1.156 | 0.54 |
| 13_R | 20_Q | 1.152 | 0.54 |
| 7_G | 17_K | 1.128 | 0.51 |
| 89_E | 135_E | 1.128 | 0.51 |
| 7_G | 13_R | 1.123 | 0.51 |
| 49_K | 75_E | 1.119 | 0.50 |
| 78_G | 82_E | 1.116 | 0.50 |
| 116_T | 144_Y | 1.108 | 0.49 |
| 42_R | 79_D | 1.107 | 0.49 |
| 16_S | 20_Q | 1.101 | 0.49 |
| 62_T | 65_E | 1.098 | 0.48 |
| 6_V | 143_I | 1.098 | 0.48 |
| 4_Q | 16_S | 1.096 | 0.48 |
| 59_E | 143_I | 1.091 | 0.48 |
| 2_D | 56_L | 1.089 | 0.47 |
| 8_K | 15_D | 1.080 | 0.46 |
| 112_L | 135_E | 1.075 | 0.46 |
| 66_L | 70_K | 1.074 | 0.46 |
| 12_H | 20_Q | 1.074 | 0.46 |
| 5_R | 20_Q | 1.070 | 0.46 |
| 15_D | 20_Q | 1.069 | 0.45 |
| 105_V | 116_T | 1.068 | 0.45 |
| 76_F | 97_G | 1.064 | 0.45 |
| 32_G | 139_L | 1.063 | 0.45 |
| 14_V | 20_Q | 1.059 | 0.44 |
| 35_R | 43_L | 1.057 | 0.44 |
| 97_G | 102_Y | 1.053 | 0.44 |
| 11_L | 15_D | 1.052 | 0.44 |
| 63_I | 102_Y | 1.049 | 0.43 |
| 54_G | 123_E | 1.048 | 0.43 |
| 57_L | 141_I | 1.048 | 0.43 |
| 53_Q | 72_L | 1.043 | 0.43 |
| 69_Y | 140_L | 1.043 | 0.43 |
| 95_R | 98_R | 1.042 | 0.43 |
| 92_G | 95_R | 1.037 | 0.42 |
| 61_R | 70_K | 1.035 | 0.42 |
| 67_R | 110_R | 1.026 | 0.41 |
| 13_R | 19_Q | 1.023 | 0.41 |
| 53_Q | 58_S | 1.020 | 0.41 |
| 60_T | 93_F | 1.010 | 0.40 |
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 | |
| 2qupA | 1 | 0.8207 | 100 | 0.027 | Contact Map |
| 2p61A | 1 | 0.7793 | 100 | 0.059 | Contact Map |
| 2hc5A | 1 | 0.7517 | 78.5 | 0.889 | Contact Map |
| 3bghA | 2 | 0.4345 | 15.4 | 0.93 | Contact Map |
| 4l6yA | 2 | 0.7172 | 10.7 | 0.934 | Contact Map |
| 1t95A | 1 | 0.8207 | 6.2 | 0.941 | Contact Map |
| 2l60A | 1 | 0.2759 | 5.4 | 0.943 | Contact Map |
| 4lgjA | 1 | 0.4276 | 5.3 | 0.943 | Contact Map |
| 1qbfA | 1 | 0.2483 | 3.5 | 0.948 | Contact Map |
| 2bf9A | 1 | 0.2414 | 3.1 | 0.949 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)