| 1BE9_A PDZ -force run |
| ID: | 1415842115 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 119 (112) | ||
| Sequences: | 90 (44.7) | ||
| Seq/Len: | 0.804 | ||
| Nf(neff/√len): | 4.2 |
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: 0.804).
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 |
| 22_R | 59_K | 2.500 | 0.99 |
| 58_R | 63_I | 1.700 | 0.83 |
| 67_N | 79_A | 1.659 | 0.81 |
| 30_N | 43_S | 1.622 | 0.79 |
| 67_N | 83_L | 1.514 | 0.72 |
| 51_A | 57_L | 1.499 | 0.71 |
| 79_A | 83_L | 1.464 | 0.68 |
| 41_F | 63_I | 1.388 | 0.62 |
| 27_L | 55_G | 1.384 | 0.62 |
| 94_A | 99_E | 1.380 | 0.61 |
| 57_L | 61_D | 1.363 | 0.60 |
| 67_N | 76_H | 1.362 | 0.60 |
| 51_A | 61_D | 1.361 | 0.60 |
| 30_N | 60_G | 1.343 | 0.58 |
| 45_I | 57_L | 1.321 | 0.56 |
| 25_T | 41_F | 1.319 | 0.56 |
| 7_G | 10_D | 1.309 | 0.55 |
| 15_P | 96_Y | 1.294 | 0.54 |
| 36_D | 103_R | 1.292 | 0.54 |
| 45_I | 62_Q | 1.273 | 0.52 |
| 21_H | 88_Q | 1.266 | 0.51 |
| 37_G | 46_L | 1.231 | 0.48 |
| 44_F | 50_P | 1.220 | 0.47 |
| 24_S | 41_F | 1.219 | 0.47 |
| 25_T | 63_I | 1.210 | 0.47 |
| 77_E | 84_K | 1.208 | 0.46 |
| 32_I | 108_S | 1.205 | 0.46 |
| 76_H | 90_V | 1.202 | 0.46 |
| 76_H | 83_L | 1.189 | 0.45 |
| 67_N | 90_V | 1.168 | 0.43 |
| 41_F | 107_N | 1.162 | 0.42 |
| 12_P | 49_G | 1.158 | 0.42 |
| 48_G | 66_V | 1.147 | 0.41 |
| 70_D | 97_K | 1.141 | 0.41 |
| 65_S | 93_I | 1.122 | 0.39 |
| 39_G | 103_R | 1.118 | 0.39 |
| 5_F | 10_D | 1.109 | 0.38 |
| 101_Y | 108_S | 1.106 | 0.38 |
| 70_D | 75_S | 1.104 | 0.38 |
| 20_I | 54_S | 1.104 | 0.38 |
| 80_A | 104_F | 1.101 | 0.37 |
| 76_H | 79_A | 1.090 | 0.36 |
| 43_S | 60_G | 1.085 | 0.36 |
| 39_G | 63_I | 1.079 | 0.35 |
| 42_I | 66_V | 1.077 | 0.35 |
| 32_I | 46_L | 1.074 | 0.35 |
| 53_L | 107_N | 1.069 | 0.35 |
| 27_L | 90_V | 1.055 | 0.34 |
| 46_L | 104_F | 1.048 | 0.33 |
| 27_L | 82_A | 1.042 | 0.33 |
| 82_A | 87_G | 1.041 | 0.33 |
| 57_L | 62_Q | 1.040 | 0.32 |
| 79_A | 84_K | 1.036 | 0.32 |
| 54_S | 58_R | 1.035 | 0.32 |
| 65_S | 68_G | 1.034 | 0.32 |
| 79_A | 90_V | 1.029 | 0.32 |
| 89_T | 94_A | 1.028 | 0.32 |
| 104_F | 108_S | 1.026 | 0.31 |
| 8_E | 11_I | 1.022 | 0.31 |
| 38_E | 54_S | 1.013 | 0.30 |
| 17_R | 25_T | 1.007 | 0.30 |
| 65_S | 103_R | 1.002 | 0.30 |
| 81_I | 92_I | 1.000 | 0.29 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 2xkxA | 2 | 1 | 99.8 | 0.57 | Contact Map |
| 1tp5A | 1 | 0.9664 | 99.8 | 0.584 | Contact Map |
| 3i4wA | 4 | 0.8151 | 99.7 | 0.639 | Contact Map |
| 1um7A | 1 | 0.9328 | 99.7 | 0.645 | Contact Map |
| 3shwA | 1 | 0.8571 | 99.6 | 0.663 | Contact Map |
| 2enoA | 1 | 0.9328 | 99.6 | 0.669 | Contact Map |
| 3tszA | 1 | 0.8571 | 99.5 | 0.673 | Contact Map |
| 2vspA | 4 | 0.6975 | 99.5 | 0.677 | Contact Map |
| 3gslA | 2 | 0.9076 | 99.5 | 0.679 | Contact Map |
| 2jikA | 2 | 0.7983 | 99.5 | 0.679 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)