| beps_core_with 2 iterations -force run |
| ID: | 1507626336 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 123 (123) | ||
| Sequences: | 110 (67.8) | ||
| Seq/Len: | 0.894 | ||
| Nf(neff/√len): | 6.1 |
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: 0.894).
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 |
| 91_G | 95_R | 1.984 | 0.94 |
| 92_R | 95_R | 1.921 | 0.93 |
| 29_M | 123_S | 1.902 | 0.92 |
| 100_N | 103_K | 1.781 | 0.89 |
| 70_N | 117_E | 1.733 | 0.87 |
| 81_N | 119_M | 1.714 | 0.86 |
| 81_N | 91_G | 1.675 | 0.84 |
| 81_N | 94_Q | 1.507 | 0.74 |
| 66_R | 107_H | 1.500 | 0.74 |
| 63_G | 103_K | 1.435 | 0.69 |
| 100_N | 110_N | 1.431 | 0.69 |
| 46_E | 93_T | 1.429 | 0.68 |
| 63_G | 106_G | 1.428 | 0.68 |
| 3_N | 60_N | 1.425 | 0.68 |
| 42_D | 96_L | 1.415 | 0.67 |
| 38_F | 84_H | 1.344 | 0.61 |
| 44_I | 49_Q | 1.334 | 0.61 |
| 62_Q | 70_N | 1.323 | 0.60 |
| 58_K | 72_E | 1.295 | 0.57 |
| 8_A | 12_R | 1.295 | 0.57 |
| 50_R | 53_Q | 1.288 | 0.57 |
| 38_F | 92_R | 1.286 | 0.56 |
| 65_T | 77_F | 1.278 | 0.56 |
| 7_W | 18_F | 1.262 | 0.54 |
| 84_H | 92_R | 1.252 | 0.53 |
| 14_I | 79_S | 1.241 | 0.52 |
| 84_H | 87_R | 1.240 | 0.52 |
| 76_L | 98_F | 1.240 | 0.52 |
| 52_D | 109_L | 1.235 | 0.52 |
| 58_K | 68_E | 1.220 | 0.51 |
| 32_T | 51_L | 1.209 | 0.50 |
| 10_Y | 22_T | 1.205 | 0.49 |
| 57_E | 119_M | 1.205 | 0.49 |
| 51_L | 71_S | 1.195 | 0.48 |
| 20_D | 44_I | 1.178 | 0.47 |
| 39_A | 47_G | 1.175 | 0.46 |
| 23_T | 122_A | 1.163 | 0.45 |
| 60_N | 104_A | 1.157 | 0.45 |
| 11_L | 87_R | 1.156 | 0.45 |
| 35_K | 53_Q | 1.130 | 0.42 |
| 52_D | 94_Q | 1.123 | 0.42 |
| 31_R | 34_W | 1.122 | 0.42 |
| 7_W | 12_R | 1.120 | 0.42 |
| 5_F | 99_E | 1.118 | 0.41 |
| 6_E | 66_R | 1.111 | 0.41 |
| 43_E | 103_K | 1.094 | 0.39 |
| 91_G | 119_M | 1.089 | 0.39 |
| 74_I | 117_E | 1.088 | 0.39 |
| 87_R | 95_R | 1.081 | 0.38 |
| 64_L | 105_A | 1.077 | 0.38 |
| 41_G | 58_K | 1.072 | 0.37 |
| 72_E | 107_H | 1.072 | 0.37 |
| 109_L | 113_L | 1.072 | 0.37 |
| 61_L | 64_L | 1.063 | 0.37 |
| 81_N | 92_R | 1.054 | 0.36 |
| 51_L | 76_L | 1.053 | 0.36 |
| 16_F | 66_R | 1.050 | 0.36 |
| 1_F | 12_R | 1.043 | 0.35 |
| 17_T | 108_Q | 1.037 | 0.35 |
| 24_A | 84_H | 1.032 | 0.34 |
| 80_L | 101_L | 1.031 | 0.34 |
| 73_A | 107_H | 1.029 | 0.34 |
| 88_E | 109_L | 1.015 | 0.33 |
| 32_T | 37_A | 1.014 | 0.33 |
| 15_P | 73_A | 1.012 | 0.33 |
| 3_N | 96_L | 1.010 | 0.32 |
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 | |
| 4npsA | 1 | 0.9187 | 99.9 | 0.597 | Contact Map |
| 4n67A | 1 | 1 | 99.9 | 0.598 | Contact Map |
| 2jk8A | 2 | 1 | 99.9 | 0.6 | Contact Map |
| 4py3A | 10 | 0 | 99.9 | 0.603 | Contact Map |
| 4m16A | 1 | 1 | 99.9 | 0.606 | Contact Map |
| 3zc7A | 1 | 0.878 | 99.8 | 0.658 | Contact Map |
| 3shgA | 1 | 0.878 | 99.8 | 0.678 | Contact Map |
| 3se5A | 4 | 0.7886 | 99.5 | 0.749 | Contact Map |
| 2f6sA | 2 | 0.7886 | 99.5 | 0.753 | Contact Map |
| 3zlmA | 1 | 0.7886 | 99.4 | 0.764 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)